Scholars@Duke
Weitao Yang

Weitao Yang

Philip Handler Distinguished Professor of Chemistry
Chemistry
weitao.yang@duke.edu
Box 90346, Durham, NC 27708-0346
5310 French Family Science Center, Durham, NC 27708

Selected Publications

Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales.

Journal Article JACS Au · November 25, 2024 Enterobacterales, a large order of Gram-negative bacteria, including Escherichia coli and Klebsiella pneumoniae, are major causes of urinary tract and gastrointestinal infections, pneumonia, and other diseases in healthcare settings and communities. ESBL-p ... Full text Link to item Cite

Particle-Particle Random Phase Approximation for Predicting Correlated Excited States of Point Defects.

Journal Article Journal of chemical theory and computation · September 2024 The particle-particle random phase approximation (ppRPA) within the hole-hole channel was recently proposed as an efficient tool for computing excitation energies of point defects in solids [J. Phys. Chem. Lett. 2024, 15, 2757-2764]. In this work, w ... Full text Cite

BSE@GW Prediction of Charge Transfer Exciton in Molecular Complexes: Assessment of Self-Energy and Exchange-Correlation Dependence.

Journal Article The journal of physical chemistry. A · July 2024 The Bethe-Salpeter equation using the GW approximation to the self-energy (BSE@GW) is a computationally attractive method for studying electronic excitation from first principles within the many-body Green's function theory framework. We exam ... Full text Cite

Excited-State Charge Transfer Coupling from Quasiparticle Energy Density Functional Theory.

Journal Article The journal of physical chemistry letters · June 2024 The recently developed Quasiparticle Energy (QE) scheme, based on a DFT calculation with one more (or less) electron, offers a good description of excitation energies, even with charge transfer characters. In this work, QE is further extended to calculate ... Full text Cite

Chemical Potentials and the One-Electron Hamiltonian of the Second-Order Perturbation Theory from the Functional Derivative Approach.

Journal Article The journal of physical chemistry. A · June 2024 We develop a functional derivative approach to calculate the chemical potentials of second-order perturbation theory (MP2). In the functional derivative approach, the correlation part of the MP2 chemical potential, which is the derivative of the MP2 correl ... Full text Cite

Perdew Festschrift editorial.

Journal Article The Journal of chemical physics · June 2024 This Special Issue of the Journal of Chemical Physics is dedicated to the work and life of John P. Perdew. A short bio is available within the issue [J. P. Perdew, J. Chem. Phys. 160, 010402 (2024)]. Here, we briefly summarize key publications in density f ... Full text Cite

Accurate Excitation Energies of Point Defects from Fast Particle-Particle Random Phase Approximation Calculations.

Journal Article The journal of physical chemistry letters · March 2024 We present an efficient particle-particle random phase approximation (ppRPA) approach that predicts accurate excitation energies of point defects, including the nitrogen-vacancy (NV-) and silicon-vacancy (SiV0) centers in diamond and ... Full text Cite

Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery.

Journal Article Protein science : a publication of the Protein Society · February 2024 Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. Whi ... Full text Cite

Development of a machine learning finite-range nonlocal density functional.

Journal Article The Journal of chemical physics · January 2024 Kohn-Sham density functional theory has been the most popular method in electronic structure calculations. To fulfill the increasing accuracy requirements, new approximate functionals are needed to address key issues in existing approximations. It is well ... Full text Cite

Chemical Concepts from Molecular Orbital Theory

Chapter · January 1, 2024 This chapter provides an overview of the history and application of molecular orbital theory, with a focus on the localization of molecular orbitals (MOs) and its connection to chemical concepts and algorithms in computational chemistry. Two main strategie ... Full text Cite

Linear Scaling Calculations of Excitation Energies with Active-Space Particle-Particle Random-Phase Approximation.

Journal Article The journal of physical chemistry. A · September 2023 We developed an efficient active-space particle-particle random-phase approximation (ppRPA) approach to calculate accurate charge-neutral excitation energies of molecular systems. The active-space ppRPA approach constrains both indexes in particle and hole ... Full text Cite

Efficient Computation of the Electrostatic Component of Solvation Free Energy via a Two-Point Padé Approximation.

Journal Article Journal of chemical theory and computation · August 2023 We develop an efficient method to compute the electrostatic component of the solvation free energy via the two-point Padé approximation. The Padé approximant uses four parameters to describe the electrostatic free energy change of the solvation process, wh ... Full text Cite

Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.

Journal Article The Journal of chemical physics · July 2023 Molecular dynamics (MD) is an extremely powerful, highly effective, and widely used approach to understanding the nature of chemical processes in atomic details for proteins. The accuracy of results from MD simulations is highly dependent on force fields. ... Full text Cite

Robert Ghormley Parr: September 22, 1921–March 27, 2017

Journal Article Resonance · July 1, 2023 As one of the founders of quantum chemistry, Robert G. Parr (RGP) was an influential theoretical chemist of the last few decades. He made enormous scientific contributions to both wave function theory and density functional theory. He was also the founding ... Full text Cite

Fractional Charge Density Functional Theory and Its Application to the Electro-inductive Effect.

Journal Article The journal of physical chemistry letters · April 2023 We employed the chemical potential equalization principle to demonstrate that fractional electrons are involved in the electro-inductive effect as well as the vibrational Stark effect. By the chemical potential model, we were able to deduce that the fronti ... Full text Cite

DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science.

Journal Article Physical chemistry chemical physics : PCCP · December 2022 In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format ... Full text Cite

Benchmark of GW Methods for Core-Level Binding Energies.

Journal Article Journal of chemical theory and computation · December 2022 The GW approximation has recently gained increasing attention as a viable method for the computation of deep core-level binding energies as measured by X-ray photoelectron spectroscopy. We present a comprehensive benchmark study of different GW Full text Cite

Mechanical Unfolding and Refolding of NanoLuc via Single-Molecule Force Spectroscopy and Computer Simulations.

Journal Article Biomacromolecules · December 2022 A highly bioluminescent protein, NanoLuc (Nluc), has seen numerous applications in biological assays since its creation. We recently engineered a NanoLuc polyprotein that showed high bioluminescence but displayed a strong misfolding propensity after mechan ... Full text Cite

Combining Renormalized Singles GW Methods with the Bethe-Salpeter Equation for Accurate Neutral Excitation Energies.

Journal Article Journal of chemical theory and computation · November 2022 We apply the renormalized singles (RS) Green's function in the Bethe-Salpeter equation (BSE)/GW approach to predict accurate neutral excitation energies of molecular systems. The BSE calculations are performed on top of the GRSW ... Full text Cite

Renormalized Singles with Correlation in GW Green's Function Theory for Accurate Quasiparticle Energies.

Journal Article The journal of physical chemistry letters · October 2022 We apply the renormalized singles with the correlation (RSc) Green function in the GW approximation for accurate quasiparticle (QP) energies and orbitals. The RSc Green function includes singles contributions from the associated density functional a ... Full text Cite

Data and scripts from: Localized orbital scaling correction for periodic systems

Dataset · July 12, 2022 Density functional theory offers accurate structure prediction at acceptable computational cost, but commonly used approximations suffer from delocalization error; this results in inaccurate predictions of quantities such as energy band gaps of finite and ... Full text Cite

Localized orbital scaling correction for periodic systems.

Journal Article Physical review. B · July 2022 Density functional theory offers accurate structure prediction at acceptable computational cost, but commonly used approximations suffer from delocalization error; this results in inaccurate predictions of quantities such as energy band gaps of finite and ... Full text Cite

Describing Chemical Reactivity with Frontier Molecular Orbitalets.

Journal Article JACS Au · June 2022 Locality in physical space is critical in understanding chemical reactivity in the analysis of various phenomena and processes in chemistry, biology, and materials science, as exemplified in the concepts of reactive functional groups and active sites. Fron ... Full text Cite

Regularized Localized Molecular Orbitals in a Divide-and-Conquer Approach for Linear Scaling Calculations.

Journal Article Journal of chemical theory and computation · May 2022 Non-orthogonal localized molecular orbitals (NOLMOs) have been employed as building blocks for the divide-and-conquer (DC) linear scaling method. The NOLMOs are calculated from subsystems and used for constructing the density matrix (DM) of the entire syst ... Full text Cite

Reformulation of thermally assisted-occupation density functional theory in the Kohn-Sham framework.

Journal Article The Journal of chemical physics · May 2022 We reformulate the thermally assisted-occupation density functional theory (TAO-DFT) into the Kohn-Sham single-determinant framework and construct two new post-self-consistent field (post-SCF) static correlation correction schemes, named rTAO and rTAO-1. I ... Full text Cite

Combining localized orbital scaling correction and Bethe-Salpeter equation for accurate excitation energies.

Journal Article The Journal of chemical physics · April 2022 We applied localized orbital scaling correction (LOSC) in Bethe-Salpeter equation (BSE) to predict accurate excitation energies for molecules. LOSC systematically eliminates the delocalization error in the density functional approximation and is capable of ... Full text Cite

LibSC: Library for Scaling Correction Methods in Density Functional Theory.

Journal Article Journal of chemical theory and computation · February 2022 In recent years, a series of scaling correction (SC) methods have been developed in the Yang laboratory to reduce and eliminate the delocalization error, which is an intrinsic and systematic error existing in conventional density functional approximations ... Full text Cite

Multireference Density Functional Theory for Describing Ground and Excited States with Renormalized Singles.

Journal Article The journal of physical chemistry letters · January 2022 We applied renormalized singles (RS) in the multireference density functional theory (DFT) to calculate accurate energies of ground and excited states. The multireference DFT approach determines the total energy of the N-electron system as the sum o ... Full text Cite

Theoretical studies on triplet-state driven dissociation of formaldehyde by quasi-classical molecular dynamics simulation on machine-learning potential energy surface.

Journal Article The Journal of chemical physics · December 2021 The H-atom dissociation of formaldehyde on the lowest triplet state (T1) is studied by quasi-classical molecular dynamic simulations on the high-dimensional machine-learning potential energy surface (PES) model. An atomic-energy based deep-learn ... Full text Cite

Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3',8-Cyclase MoaA.

Journal Article J Am Chem Soc · September 1, 2021 The diversity of the reactions catalyzed by radical S-adenosyl-l-methionine (SAM) enzymes is achieved at least in part through the variety of mechanisms to quench their radical intermediates. In the SPASM-twitch family, the largest family of radical SAM en ... Full text Link to item Cite

Exact Second-Order Corrections and Accurate Quasiparticle Energy Calculations in Density Functional Theory.

Journal Article The journal of physical chemistry letters · August 2021 We develop a second-order correction to commonly used density functional approximations (DFAs) to eliminate the systematic delocalization error. The method, based on the previously developed global scaling correction (GSC), is an exact quadratic correction ... Full text Cite

Renormalized Singles Green's Function in the T-Matrix Approximation for Accurate Quasiparticle Energy Calculation.

Journal Article The journal of physical chemistry letters · July 2021 We combine the renormalized singles (RS) Green's function with the T-matrix approximation for the single-particle Green's function to compute quasiparticle energies for valence and core states of molecular systems. The GRST0 Full text Cite

Describing polymer polarizability with localized orbital scaling correction in density functional theory.

Journal Article The Journal of chemical physics · February 2021 Polarizability reflects the response of the molecular charge distribution to an applied external electric field and thus closely relates to the molecular electron density. For the calculation of polarizability within density functional theory (DFT), it is ... Full text Cite

Introductory lecture: when the density of the noninteracting reference system is not the density of the physical system in density functional theory.

Journal Article Faraday discussions · December 2020 Featured Publication A major challenge in density functional theory (DFT) is the development of density functional approximations (DFAs) to overcome errors in existing DFAs, leading to more complex functionals. For such functionals, we consider roles of the noninteracting refe ... Full text Cite

Piecewise All-Atom SMD Simulations Reveal Key Secondary Structures in Luciferase Unfolding Pathway.

Journal Article Biophysical journal · December 2020 Although the folding of single-domain proteins is well characterized theoretically and experimentally, the folding of large multidomain proteins is less well known. Firefly luciferase, a 550 residue three-domain protein, has been commonly used as a substra ... Full text Cite

Self-Consistent Calculation of the Localized Orbital Scaling Correction for Correct Electron Densities and Energy-Level Alignments in Density Functional Theory.

Journal Article The journal of physical chemistry letters · December 2020 The recently developed localized orbital scaling correction (LOSC) method shows the ability to systematically and size-consistently reduce the delocalization error existing in conventional density functional approximations (DFAs). However, the application ... Full text Cite

New density-functional approximations and beyond: general discussion.

Journal Article Faraday discussions · December 2020 Full text Cite

Strong correlation in density functional theory: general discussion.

Journal Article Faraday discussions · December 2020 Full text Cite

Arene Substitution Design for Controlled Conformational Changes of Dibenzocycloocta-1,5-dienes.

Journal Article Journal of the American Chemical Society · September 2020 We report that an agile eight-membered cycloalkane can be stabilized by fusing a benzene ring on each side, substituted with proper functional groups. The conformational change of dibenzocycloocta-1,5-diene (DBCOD), a rigid-flexible-rigid organic moiety, f ... Full text Cite

Mechanism of Rate Acceleration of Radical C-C Bond Formation Reaction by a Radical SAM GTP 3',8-Cyclase.

Journal Article J Am Chem Soc · May 20, 2020 Featured Publication While the number of characterized radical S-adenosyl-l-methionine (SAM) enzymes is increasing, the roles of these enzymes in radical catalysis remain largely ambiguous. In radical SAM enzymes, the slow radical initiation step kinetically masks the subseque ... Full text Link to item Cite

Cobalt(II)-Catalyzed [4+2] Annulation of Picolinamides with Alkynes via C-H Bond Activation.

Journal Article Chemistry (Weinheim an der Bergstrasse, Germany) · May 2020 A cobalt(II)-catalyzed [4+2] annulation of picolinamides with alkynes via C-H bond activation has been developed. The operationally simple annulation reaction allows for the synthesis of acyl-substituted 1H-benzoquinoline bearing multiple aromatic rings (u ... Full text Cite

Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections.

Journal Article The journal of physical chemistry. B · April 2020 Featured Publication The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delo ... Full text Cite

Engineering Substrate Interaction To Improve Hydrogen Evolution Catalysis of Monolayer MoS2 Films beyond Pt.

Journal Article ACS nano · February 2020 MoS2 holds great promise as a cost-effective alternative to Pt for catalyzing the hydrogen evolution reaction (HER) of water, but its reported catalytic efficiency is still worse than that of Pt, the best HER catalyst but too rare and expensive ... Full text Cite

Preserving Symmetry and Degeneracy in the Localized Orbital Scaling Correction Approach.

Journal Article The journal of physical chemistry letters · February 2020 Symmetry is a fundamental concept that plays a critical role in many chemical and physical phenomena and processes, which highlights the importance of theoretical methods to correctly handle symmetry. The recently developed localized orbital scaling correc ... Full text Cite

Density Functional Prediction of Quasiparticle, Excitation, and Resonance Energies of Molecules With a Global Scaling Correction Approach.

Journal Article Frontiers in chemistry · January 2020 Molecular quasiparticle and excitation energies determine essentially the spectral characteristics measured in various spectroscopic experiments. Accurate prediction of these energies has been rather challenging for ground-state density functional methods, ... Full text Cite

1,3-Dipolar cycloaddition of nitrones to oxa(aza)bicyclic alkenes

Journal Article Organic Chemistry Frontiers · October 7, 2019 A new 1,3-dipolar cycloaddition of oxa(aza)bicyclic alkenes with nitrones has been developed. The operationally simple cycloaddition allows efficient synthesis of fused bicyclic tetrahydroisoxazoles bearing exo- and anti-five member heterocyclic rings (76- ... Full text Cite

Excited-State Potential Energy Surfaces, Conical Intersections, and Analytical Gradients from Ground-State Density Functional Theory.

Journal Article The journal of physical chemistry letters · May 2019 Kohn-Sham density functional theory (KS-DFT) has been a well-established theoretical foundation for ground-state electronic structure and has achieved great success in practical calculations. Recently, utilizing the eigenvalues from KS or generalized KS (G ... Full text Cite

Radical Addition of Thiols to Oxa(aza)bicyclic Alkenes in Water

Journal Article Asian Journal of Organic Chemistry · April 1, 2019 An air-promoted radical addition reaction of various thiols to oxa(aza)bicyclic alkenes is reported, leading to the corresponding exo adducts in good to excellent yields (up to 99%) in water without the use of any metal catalyst, photoredox catalyst or rad ... Full text Cite

Excitation Energies from the Single-Particle Green's Function with the GW Approximation.

Journal Article The journal of physical chemistry. A · April 2019 Quasi-particle energies are important in predicting molecular ionization energies and bulk band structures. The state-of-the-art method for quasi-particle energy calculations, particularly for bulk systems, is the GW approximation. For excited state calcul ... Full text Cite

Charge transfer excitation energies from ground state density functional theory calculations.

Journal Article The Journal of chemical physics · April 2019 Calculating charge transfer (CT) excitation energies with high accuracy and low computational cost is a challenging task. Kohn-Sham density functional theory (KS-DFT), due to its efficiency and accuracy, has achieved great success in describing ground stat ... Full text Cite

Renormalized Singles Green's Function for Quasi-Particle Calculations beyond the G0 W0 Approximation.

Journal Article The journal of physical chemistry letters · February 2019 Quasi-particle energies and band gaps in particular are critical for investigating novel materials. Commonly used density functional approximations (DFAs) systematically underestimate band gaps, and GW approximation is the established method of choice for ... Full text Cite

Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network.

Journal Article Journal of chemical theory and computation · February 2019 Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computational c ... Full text Cite

Approximating Quasiparticle and Excitation Energies from Ground State Generalized Kohn-Sham Calculations.

Journal Article The journal of physical chemistry. A · January 2019 Quasiparticle energies and fundamental band gaps in particular are critical properties of molecules and materials. It was rigorously established that the generalized Kohn-Sham HOMO and LUMO orbital energies are the chemical potentials of electron removal a ... Full text Cite

Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.

Journal Article The journal of physical chemistry. B · January 2019 For exploration of chemical and biological systems, the combined quantum mechanics and molecular mechanics (QM/MM) and machine learning (ML) models have been developed recently to achieve high accuracy and efficiency for molecular dynamics (MD) simulations ... Full text Cite

Role of Conformational Fluctuations of Protein toward Methylation in DNA by Cytosine-5-methyltransferase.

Journal Article Journal of chemical theory and computation · December 2018 Methylation of cytosine is the common epigenetic modification in genomes ranging from bacteria to mammals, and aberrant methylation leads to human diseases including cancer. Recognition of a cognate DNA sequence by DNA methyltransferases and flipping of a ... Full text Cite

Spin-state energetics of iron(II) porphyrin from the particle-particle random phase approximation

Journal Article European Physical Journal B · November 1, 2018 The particle-particle random phase approximation (pp-RPA) has been deployed to study the spin-state energetics of transition metal (TM) complexes for the first time in this work. Namely, we designed and implemented a non-canonical reference pp-RPA protocol ... Full text Cite

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.

Journal Article Journal of chemical theory and computation · September 2018 Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fract ... Full text Cite

Describing strong correlation with fractional-spin correction in density functional theory.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 2018 An effective fractional-spin correction is developed to describe static/strong correlation in density functional theory. Combined with the fractional-charge correction from recently developed localized orbital scaling correction (LOSC), a functional, the f ... Full text Cite

Single, Double Electronic Excitations and Exciton Effective Conjugation Lengths in π-Conjugated Systems.

Journal Article The journal of physical chemistry letters · July 2018 The 21Ag and 11Bu excited states of two prototypical π-conjugated compounds, polyacetylene and polydiacetylene, are investigated with the recently developed particle-particle random phase approximation (pp-RPA) m ... Full text Cite

Accurate Treatment of Charge-Transfer Excitations and Thermally Activated Delayed Fluorescence Using the Particle-Particle Random Phase Approximation.

Journal Article Journal of chemical theory and computation · June 2018 Thermally activated delayed florescence (TADF) is a mechanism that increases the electroluminescence efficiency in organic light-emitting diodes by harnessing both singlet and triplet excitons. TADF is facilitated by a small energy difference between the f ... Full text Cite

Force Field for Water Based on Neural Network.

Journal Article The journal of physical chemistry letters · June 2018 We developed a novel neural network-based force field for water based on training with high-level ab initio theory. The force field was built based on an electrostatically embedded many-body expansion method truncated at binary interactions. The many-body ... Full text Cite

Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

Journal Article Molecular Physics · April 18, 2018 Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. H ... Full text Cite

Plasmon-Enhanced Catalysis: Distinguishing Thermal and Nonthermal Effects.

Journal Article Nano letters · March 2018 In plasmon-enhanced heterogeneous catalysis, illumination accelerates reaction rates by generating hot carriers and hot surfaces in the constituent nanostructured metals. In order to understand how photogenerated carriers enhance the nonthermal reaction ra ... Full text Cite

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

Journal Article Journal of chemical theory and computation · March 2018 Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational ... Full text Cite

Localized orbital scaling correction for systematic elimination of delocalization error in density functional approximations

Journal Article National Science Review · March 1, 2018 The delocalization error of popular density functional approximations (DFAs) leads to diversified problems in present-day density functional theory calculations. For achieving a universal elimination of delocalization error, we develop a localized orbital ... Full text Cite

Perspective: Chemical Information Encoded in Electron Density.

Journal Article Wu li hua xue xue bao = Acta physico-chimica sinica · March 2018 In this perspective, we review the chemical information encoded in electron density and other ingredients used in semilocal functionals. This information is usually looked at from the functional point of view: the exchange density or the enhancement factor ... Full text Cite

Photocatalytic activity and the radiative lifetimes of excitons via an ab initio approach

Journal Article Journal of Materials Chemistry A · January 1, 2018 This work presents the radiative lifetimes of photogenerated electron-hole (e-h) pairs in bulk anatase and rutile TiO2 calculated by solving the Bethe-Salpeter equation (BSE) at the G0W0 [F. Fuchs, J. Furthmüller, F. Bechstedt, M. Shishkin and G. Kresse, P ... Full text Cite

Field Electron Emission Images Far Away from a Semi-Infinitely Long Emitter: A Multiscale Simulation

Journal Article Journal of Physical Chemistry C · January 1, 2018 © 2018 American Chemical Society. Ab initio calculations reveal that in cold field electron emission from nanostructures, the electron state of top priority not necessarily the occupied state with largest forward kinetic energy but depends on the applied f ... Full text Cite

Activating MoS2 for pH-Universal Hydrogen Evolution Catalysis.

Journal Article Journal of the American Chemical Society · November 2017 MoS2 presents a promising catalyst for the hydrogen evolution reaction (HER) in water splitting, but its worse catalytic performance in neutral and alkaline media than in acidic environment may be problematic for practical application. This is b ... Full text Cite

Generalized Optimized Effective Potential for Orbital Functionals and Self-Consistent Calculation of Random Phase Approximations.

Journal Article The journal of physical chemistry letters · October 2017 A new self-consistent procedure for calculating the total energy with an orbital-dependent density functional approximation (DFA), the generalized optimized effective potential (GOEP), is developed in the present work. The GOEP is a nonlocal Hermitian pote ... Full text Cite

Excitation energies from particle-particle random phase approximation with accurate optimized effective potentials.

Journal Article The Journal of chemical physics · October 2017 The optimized effective potential (OEP) that gives accurate Kohn-Sham (KS) orbitals and orbital energies can be obtained from a given reference electron density. These OEP-KS orbitals and orbital energies are used here for calculating electronic excited st ... Full text Cite

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

Journal Article The Journal of chemical physics · October 2017 Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a ... Full text Cite

Time-Dependent Coupled Perturbed Hartree-Fock and Density-Functional-Theory Approach for Calculating Frequency-Dependent (Hyper)Polarizabilities with Nonorthogonal Localized Molecular Orbitals.

Journal Article Journal of chemical theory and computation · September 2017 The time-dependent coupled perturbed Hartree-Fock/density-functional-theory (TDHF/TDDFT) approach has been reformulated based on nonorthogonal localized molecular orbitals (NOLMOs). Based on the NOLMO Fock equation, we have derived the corresponding NOLMO- ... Full text Cite

Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States.

Journal Article The journal of physical chemistry letters · September 2017 To describe static correlation, we develop a new approach to density functional theory (DFT), which uses a generalized auxiliary system that is of a different symmetry, such as particle number or spin, from that of the physical system. The total energy of ... Full text Cite

Robert G. Parr (1921-2017).

Journal Article Angewandte Chemie (International ed. in English) · August 2017 Full text Cite

Accurate Quasiparticle Spectra from the T-Matrix Self-Energy and the Particle-Particle Random Phase Approximation.

Journal Article The journal of physical chemistry letters · July 2017 The GW self-energy, especially G0W0 based on the particle-hole random phase approximation (phRPA), is widely used to study quasiparticle (QP) energies. Motivated by the desirable features of the particle-particle (pp) RPA compared to ... Full text Cite

On extending Kohn-Sham density functionals to systems with fractional number of electrons.

Journal Article The Journal of chemical physics · June 2017 We analyze four ways of formulating the Kohn-Sham (KS) density functionals with a fractional number of electrons, through extending the constrained search space from the Kohn-Sham and the generalized Kohn-Sham (GKS) non-interacting v-representable density ... Full text Cite

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

Journal Article Biophysical journal · May 2017 Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events cou ... Full text Cite

Three Pyrimidine Decarboxylations in the Absence of a Catalyst.

Journal Article Biochemistry · March 2017 The epigenetic modification of DNA by 5-methylation of cytosine residues can be reversed by the action of the TET family of dioxygenases that oxidize the methyl group to produce 5-carboxycytosine (5caC), which can be converted to cytosine in a final decarb ... Full text Cite

Understanding band gaps of solids in generalized Kohn-Sham theory.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · March 2017 The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn-Sham (KS) potential substantially underest ... Full text Cite

Charge transfer excitations from particle-particle random phase approximation-Opportunities and challenges arising from two-electron deficient systems.

Journal Article The Journal of chemical physics · March 2017 The particle-particle random phase approximation (pp-RPA) is a promising method for studying charge transfer(CT) excitations. Through a detailed analysis on two-electron deficient systems, we show that the pp-RPA is always able to recover the long-distance ... Full text Cite

On the piecewise convex or concave nature of ground state energy as a function of fractional number of electrons for approximate density functionals.

Journal Article The Journal of chemical physics · February 2017 We provide a rigorous proof that the Hartree Fock energy, as a function of the fractional electron number, E(N), is piecewise concave. Moreover, for semi-local density functionals, we show that the piecewise convexity of the E(N) curve, as stated in the li ... Full text Cite

All The Catalytic Active Sites of MoS2 for Hydrogen Evolution.

Journal Article Journal of the American Chemical Society · December 2016 MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction s ... Full text Cite

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

Journal Article Journal of chemical theory and computation · October 2016 Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be ... Full text Cite

Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation.

Journal Article The Journal of chemical physics · October 2016 An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly ... Full text Cite

Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a βγ-Crystallin Protein.

Journal Article The Journal of biological chemistry · August 2016 Although multidomain proteins predominate the proteome of all organisms and are expected to display complex folding behaviors and significantly greater structural dynamics as compared with single-domain proteins, their conformational heterogeneity and its ... Full text Cite

Nature of ground and electronic excited states of higher acenes.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2016 Higher acenes have drawn much attention as promising organic semiconductors with versatile electronic properties. However, the nature of their ground state and electronic excited states is still not fully clear. Their unusual chemical reactivity and instab ... Full text Cite

Conical Intersections from Particle-Particle Random Phase and Tamm-Dancoff Approximations.

Journal Article The journal of physical chemistry letters · July 2016 The particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) are applied to the challenging conical intersection problem. Because they describe the ground and excited states on the same footing and ... Full text Cite

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

Journal Article The Journal of chemical physics · June 2016 We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting a ... Full text Cite

Accurate atomic quantum defects from particle-particle random phase approximation

Journal Article Molecular Physics · April 17, 2016 The accuracy of calculations of atomic Rydberg excitations cannot be judged by the usual measures, such as mean unsigned errors of many transitions. We show how to use quantum defect (QD) theory to (a) separate errors due to approximate ionisation potentia ... Full text Cite

Diverse Optimal Molecular Libraries for Organic Light-Emitting Diodes.

Journal Article Journal of chemical theory and computation · April 2016 Organic light-emitting diodes (OLEDs) have wide-ranging applications, from lighting to device displays. However, the repertoire of organic molecules with efficient blue emission is limited. To address this limitation, we have developed a strategy to design ... Full text Cite

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Journal Article Journal of chemical theory and computation · April 2016 We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structu ... Full text Cite

Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

Journal Article The Journal of chemical physics · December 2015 We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground stat ... Full text Cite

Scaling correction approaches for reducing delocalization error in density functional approximations

Journal Article Science China Chemistry · December 1, 2015 Delocalization error associated with the presently used density functional approximations is one of the main sources of errors which plague density functional theory calculations. In this paper, we give a comprehensive review on scaling correction (SC) app ... Full text Cite

Angular momentum dependent field emission energy distribution

Conference IVNC 2015 - Technical Digest: 28th International Vacuum Nanoelectronics Conference · August 26, 2015 We developed a multi-scale time dependent density functional method to simulate electrons in semi-infinite long nano structures emitting into vacuum via the apex of nano structures. A relation between the field emission energy distribution and the angular ... Full text Cite

Singlet-triplet energy gaps for diradicals from particle-particle random phase approximation.

Journal Article The journal of physical chemistry. A · May 2015 The particle-particle random phase approximation (pp-RPA) for calculating excitation energies has been applied to diradical systems. With pp-RPA, the two nonbonding electrons are treated in a subspace configuration interaction fashion while the remaining p ... Full text Cite

Orbital relaxation effects on Kohn-Sham frontier orbital energies in density functional theory.

Journal Article The Journal of chemical physics · April 2015 We explore effects of orbital relaxation on Kohn-Sham frontier orbital energies in density functional theory by using a nonempirical scaling correction approach developed in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)]. Relaxation of Kohn-Sham orbitals ... Full text Cite

Strategy to discover diverse optimal molecules in the small molecule universe.

Journal Article Journal of chemical information and modeling · March 2015 The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable stru ... Full text Cite

Coupled-Perturbed SCF Approach for Calculating Static Polarizabilities and Hyperpolarizabilities with Nonorthogonal Localized Molecular Orbitals.

Journal Article Journal of chemical theory and computation · March 2015 Coupled-perturbed self-consistent-field (CPSCF) approach has been broadly used for polarizabilities and hyperpolarizabilities computation. To extend this application to large systems, we have reformulated the CPSCF equations with nonorthogonal localized mo ... Full text Cite

Local scaling correction for reducing delocalization error in density functional approximations.

Journal Article Physical review letters · February 2015 Delocalization error is one of the most fundamental and dominant errors that plagues presently used density functional approximations. It is responsible for a large class of problems in the density functional theory calculations. For an effective and unive ... Full text Cite

Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization.

Journal Article ACS nano · February 2015 Understanding how protein oligomerization affects the stability of monomers in self-assembled structures is crucial to the development of new protein-based nanomaterials and protein cages for drug delivery. Here, we use single-molecule force spectroscopy ( ... Full text Cite

Analytic gradients, geometry optimization and excited state potential energy surfaces from the particle-particle random phase approximation.

Journal Article Physical chemistry chemical physics : PCCP · January 2015 The energy gradient for electronic excited states is of immense interest not only for spectroscopy but also for the theoretical study of photochemical reactions. We present the analytic excited state energy gradient of the particle-particle random phase ap ... Full text Cite

Restricted second random phase approximations and Tamm-Dancoff approximations for electronic excitation energy calculations.

Journal Article The Journal of chemical physics · December 2014 In this article, we develop systematically second random phase approximations (RPA) and Tamm-Dancoff approximations (TDA) of particle-hole and particle-particle channels for calculating molecular excitation energies. The second particle-hole RPA/TDA can ca ... Full text Cite

A tribute to Guosen Yan

Journal Article Theoretical Chemistry Accounts · December 2014 Full text Cite

Chaperones rescue luciferase folding by separating its domains.

Journal Article The Journal of biological chemistry · October 2014 Over the last 50 years, significant progress has been made toward understanding how small single-domain proteins fold. However, very little is known about folding mechanisms of medium and large multidomain proteins that predominate the proteomes of all for ... Full text Cite

Fractional charge behavior and band gap predictions with the XYG3 type of doubly hybrid density functionals.

Journal Article The journal of physical chemistry. A · October 2014 In this work, we examine the fractional charge behaviors of doubly hybrid (DH) functionals. By plotting the ground-state energies E and energy derivatives for atoms and molecules with fractional electron numbers N, we directly quantify the delocalization e ... Full text Cite

Excitation energies from particle-particle random phase approximation: Davidson algorithm and benchmark studies

Journal Article The Journal of Chemical Physics · September 28, 2014 The particle-particle random phase approximation (pp-RPA) has been used to investigate excitation problems in our recent paper [Y. Yang, H. van Aggelen, and W. Yang, J. Chem. Phys. 139, 224105 (2013)]. It has been shown to be capable of describing ... Full text Cite

Shifting Electronic Structure by Inherent Tension in Molecular Bottlebrushes with Polythiophene Backbones.

Journal Article ACS macro letters · August 2014 Bottlebrush macromolecules can be regarded as molecular tensile machines, where tension is self-generated along the backbone due to steric repulsion between densely grafted side chains. This intrinsic tension is amplified upon adsorption of bottlebrush mol ... Full text Cite

Tensor hypercontracted ppRPA: reducing the cost of the particle-particle random phase approximation from O(r(6)) to O(r(4)).

Journal Article The Journal of chemical physics · July 2014 In recent years, interest in the random-phase approximation (RPA) has grown rapidly. At the same time, tensor hypercontraction has emerged as an intriguing method to reduce the computational cost of electronic structure algorithms. In this paper, we combin ... Full text Cite

Revisiting H2O Nucleation around Au+ and Hg2+: The Peculiar "Pseudo-Soft" Character of the Gold Cation.

Journal Article Journal of chemical theory and computation · May 2014 In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical s ... Full text Cite

Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation.

Journal Article The Journal of chemical physics · May 2014 Despite their unmatched success for many applications, commonly used local, semi-local, and hybrid density functionals still face challenges when it comes to describing long-range interactions, static correlation, and electron delocalization. Density funct ... Full text Cite

Linear-response time-dependent density-functional theory with pairing fields.

Journal Article The Journal of chemical physics · May 2014 Recent development in particle-particle random phase approximation (pp-RPA) broadens the perspective on ground state correlation energies [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013), Y. Yang, H. van Aggelen, S. N. Steinmann, D. Pe ... Full text Cite

Preface: Special topic on advances in density functional theory.

Journal Article The Journal of chemical physics · May 2014 This Special Topic Issue on the Advances in Density Functional Theory, published as a celebration of the fifty years of density functional theory, contains a retrospective article, a perspective article, and a collection of original research articles that ... Full text Cite

Layer-dependent electrocatalysis of MoS2 for hydrogen evolution

Journal Article Nano Letters · February 12, 2014 The quantitative correlation of the catalytic activity with the microscopic structure of heterogeneous catalysts is a major challenge for the field of catalysis science. It requests synergistic capabilities to tailor the structure with atomic scale precisi ... Full text Cite

Characterization of a photoswitching chelator with light-modulated geometric, electronic, and metal-binding properties.

Journal Article Inorganic chemistry · February 2014 Photoswitching molecules are utilized for a variety of applications where the rapid manipulation of the molecules' chemical properties and spatial orientations allows for new spatiotemporal control over molecular-scale interactions and processes. Here, we ... Full text Cite

N-Terminal Domain of Luciferase Controls Misfolding Avoidance

Conference Biophysical Journal · January 2014 Full text Cite

Double, Rydberg and charge transfer excitations from pairing matrix fluctuation and particle-particle random phase approximation.

Journal Article The Journal of chemical physics · December 2013 Double, Rydberg, and charge transfer (CT) excitations have been great challenges for time-dependent density functional theory (TDDFT). Starting from an (N ± 2)-electron single-determinant reference, we investigate excitations for the N-electron system thro ... Full text Cite

Benchmark tests and spin adaptation for the particle-particle random phase approximation.

Journal Article The Journal of chemical physics · November 2013 The particle-particle random phase approximation (pp-RPA) provides an approximation to the correlation energy in density functional theory via the adiabatic connection [H. van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501 (2013)]. It has virtually ... Full text Cite

Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods.

Journal Article Journal of computational chemistry · October 2013 Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum-mechanical and molecular-mechanical subsystems. Instead, classical Lennard-Jones (LJ) potentials between QM and MM ... Full text Cite

Effective preconditioning for ab initio ground state energy minimization with non-orthogonal localized molecular orbitals.

Journal Article Physical chemistry chemical physics : PCCP · October 2013 The non-orthogonal localized molecular orbital (NOLMO) is the most localized representation of electronic degrees of freedom. As such, NOLMOs are thus potentially the most efficient for linear-scaling calculations of electronic structures for large systems ... Full text Cite

Dynamical second-order Bethe-Salpeter equation kernel: a method for electronic excitation beyond the adiabatic approximation.

Journal Article The Journal of chemical physics · October 2013 We present a dynamical second-order kernel for the Bethe-Salpeter equation to calculate electronic excitation energies. The derivation takes explicitly the functional derivative of the exact second-order self energy with respect to the one-particle Green's ... Full text Cite

Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random-phase approximation

Journal Article Physical Review A - Atomic, Molecular, and Optical Physics · September 24, 2013 We formulate an adiabatic connection for the exchange-correlation energy in terms of pairing matrix fluctuation. This connection opens new channels for density functional approximations based on pairing interactions. Even the simplest approximation to the ... Full text Cite

Mechanism of catalytic reactions and redox processes for solar fuel with multiscale QM/MM simulation

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · September 8, 2013 Link to item Cite

Extension of many-body theory and approximate density functionals to fractional charges and fractional spins.

Journal Article The Journal of chemical physics · September 2013 The exact conditions for density functionals and density matrix functionals in terms of fractional charges and fractional spins are known, and their violation in commonly used functionals has been shown to be the root of many major failures in practical ap ... Full text Cite

Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles.

Journal Article The Journal of chemical physics · September 2013 The recent proposal to determine the (exact) correlation energy based on pairing matrix fluctuations by van Aggelen et al. ["Exchange-correlation energy from pairing matrix fluctuation and the particle-particle random phase approximation," preprint arXiv:1 ... Full text Cite

The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r(4)) scaling.

Journal Article The Journal of chemical physics · August 2013 Tensor hypercontraction is a method that allows the representation of a high-rank tensor as a product of lower-rank tensors. In this paper, we show how tensor hypercontraction can be applied to both the electron repulsion integral tensor and the two-partic ... Full text Cite

Concerted proton transfer mechanism of Clostridium thermocellum ribose-5-phosphate isomerase.

Journal Article The journal of physical chemistry. B · August 2013 Ribose-5-phosphate isomerase (Rpi) catalyzes the interconversion of D-ribose-5-phosphate and D-ribulose-5-phosphate and plays an essential role in the pentose phosphate pathway and the Calvin cycle of photosynthesis. RpiB, one of the two isoforms of Rpi, i ... Full text Cite

Wave function methods for fractional electrons.

Journal Article The Journal of chemical physics · August 2013 Determining accurate chemical potentials is of considerable interest in various chemical and physical contexts: from small molecular charge-transfer complexes to bandgap in bulk materials such as semi-conductors. Chemical potentials are typically evaluated ... Full text Cite

Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds.

Journal Article Journal of the American Chemical Society · May 2013 The "small molecule universe" (SMU), the set of all synthetically feasible organic molecules of 500 Da molecular weight or less, is estimated to contain over 10(60) structures, making exhaustive searches for structures of interest impractical. Here, we des ... Full text Cite

Fukui function and response function for nonlocal and fractional systems.

Journal Article The Journal of chemical physics · May 2013 We present extensions to our previous work on Fukui functions and linear-response functions [W. Yang, A. J. Cohen, F. D. Proft, and P. Geerlings, J. Chem. Phys. 136, 144110 (2012)]. Viewed as energy derivatives with respect to the number of electrons and t ... Full text Cite

Noncovalent Interaction Analysis in Fluctuating Environments.

Journal Article Journal of chemical theory and computation · May 2013 Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the ... Full text Cite

A nonempirical scaling correction approach for density functional methods involving substantial amount of Hartree-Fock exchange.

Journal Article The Journal of chemical physics · May 2013 A nonempirical scaling correction (SC) approach has been developed for improving bandgap prediction in density functional theory [X. Zheng, A. J. Cohen, P. Mori-Sánchez, X. Hu, and W. Yang, Phys. Rev. Lett. 107, 026403 (2011)]. For finite systems such as a ... Full text Cite

Pushing the boundaries of intrinsically stable radicals: inverse design using the thiadiazinyl radical as a template.

Journal Article The Journal of organic chemistry · April 2013 In this study, for the first time inverse design was applied to search for the intrinsically most stable radical system in a predefined chemical space of enormous size by scanning in a rational way that entire chemical space. The focus was predominantly on ... Full text Cite

Accurate Computation of the Non-Interacting Kinetic Energy from Electron Densities

Chapter · January 1, 2013 We describe a robust and practical method for the computation of implicit density functionals from electron densities based on a regularized version of the Wu-Yang method. For any given electron density that is non-interacting v-representable, our method p ... Cite

Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs.

Journal Article The Journal of chemical physics · January 2013 In biological systems involving nucleosides, nucleotides, or their respective analogs, the ribose sugar moiety is the most common reaction site, for example, during DNA replication and repair. However, nucleic bases, which comprise a sizable portion of nuc ... Full text Cite

Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives.

Journal Article Physical chemistry chemical physics : PCCP · December 2012 The design of molecules with optimal properties is an important challenge in chemistry because of the astronomically large number of possible stable structures that is accessible in chemical space. This obstacle can be overcome through inverse molecular de ... Full text Cite

Achieving partial decoherence in surface hopping through phase correction.

Journal Article The Journal of chemical physics · December 2012 Fewest-switches surface hopping is one of the simplest and most popular methods for the computational study of nonadiabatic processes. Recently, a very simple phase correction was introduced to the traditional surface hopping algorithm, substantially impro ... Full text Cite

Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru2+-Ru3+ Self-Exchange Electron Transfer.

Journal Article Journal of chemical theory and computation · December 2012 A fragment-based fractional number of electron (FNE) approach, is developed to study entire electron transfer (ET) processes from the electron donor region to the acceptor region in condensed phase. Both regions are described by the density-fragment intera ... Full text Cite

Delocalization error of density-functional approximations: a distinct manifestation in hydrogen molecular chains.

Journal Article The Journal of chemical physics · December 2012 Delocalization error is one of the major sources of inaccuracy for mainstream density functional approximations and it is responsible for many of the most glaring failures. Quantitative identification of delocalization error in chemical species and analysi ... Full text Cite

Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions.

Journal Article Journal of chemical theory and computation · November 2012 A cross ELF-NCI analysis is tested over prototypical organic reactions. The synergetic use of ELF and NCI enables the understanding of reaction mechanisms since each method can respectively identify regions of strong and weak electron pairing. Chemically i ... Full text Cite

Theoretical study of catalytic mechanism for single-site water oxidation process.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 2012 Water oxidation is a linchpin in solar fuels formation, and catalysis by single-site ruthenium complexes has generated significant interest in this area. Combining several theoretical tools, we have studied the entire catalytic cycle of water oxidation for ... Full text Cite

Variational fractional-spin density-functional theory for diradicals.

Journal Article The Journal of chemical physics · September 2012 Accurate computation of singlet-triplet energy gaps of diradicals remains a challenging problem in density-functional theory (DFT). In this work, we propose a variational extension of our previous work [D. H. Ess, E. R. Johnson, X. Q. Hu, and W. T. Yang, J ... Full text Cite

Highly tunable spin-dependent electron transport through carbon atomic chains connecting two zigzag graphene nanoribbons.

Journal Article The Journal of chemical physics · September 2012 Motivated by recent experiments of successfully carving out stable carbon atomic chains from graphene, we investigate a device structure of a carbon chain connecting two zigzag graphene nanoribbons with highly tunable spin-dependent transport properties. O ... Full text Cite

Density-Functional Errors in Alkanes: A Real-Space Perspective.

Journal Article Journal of chemical theory and computation · August 2012 Density-functional theory (DFT) approximations are known to give systematic errors for isodesmic reaction energies of n-alkanes to form ethane. Several explanations have been proposed, involving both the exchange or correlation nature of the problem and it ... Full text Cite

Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways.

Journal Article The journal of physical chemistry. B · June 2012 4-Oxalocrotonate tautomerase (4-OT), a member of tautomerase superfamily, is an essential enzyme in the degradative metabolism pathway occurring in the Krebs cycle. The proton transfer process catalyzed by 4-OT has been explored previously using both exper ... Full text Cite

Liquid water simulations with the density fragment interaction approach.

Journal Article Physical chemistry chemical physics : PCCP · June 2012 We reformulate the density fragment interaction (DFI) approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129, 054102.] to achieve linear-scaling quantum mechanical calculations for large molecular systems. Two key approximations are developed to improve th ... Full text Cite

Optimized effective potential for calculations with orbital-free potential functionals

Journal Article Molecular Physics · May 10, 2012 Approximation of electronic kinetic energy can be naturally expressed in terms of the one-electron effective potential, namely as a potential functional. Such approximate functionals can lead to linear scaling orbital-free calculations of large systems. Fo ... Full text Cite

Design of coupled porphyrin chromophores with unusually large hyperpolarizabilities

Journal Article Journal of Physical Chemistry C · May 3, 2012 Figure Persented: A new series of push-pull porphyrin-based chromophores with unusually large static first hyperpolarizabilities are designed on the basis of coupled-perturbed Hartree-Fock and density functional calculations. The proper combination of crit ... Full text Cite

Derivative discontinuity, bandgap and lowest unoccupied molecular orbital in density functional theory.

Journal Article The Journal of chemical physics · May 2012 The conventional analysis of Perdew and Levy, and Sham and Schlüter shows that the functional derivative discontinuity of the exchange-correlation density functional plays a critical role in the correct prediction of bandgaps, or the chemical hardness. In ... Full text Cite

Failure of the random-phase-approximation correlation energy

Journal Article Physical Review A - Atomic, Molecular, and Optical Physics · April 5, 2012 The random phase approximation (RPA) is thought to be a successful method; however, basic errors have been found that have massive implications in the simplest molecular systems. The observed successes and failures are rationalized by examining its perform ... Full text Cite

Analytical evaluation of Fukui functions and real-space linear response function.

Journal Article The Journal of chemical physics · April 2012 Many useful concepts developed within density functional theory provide much insight for the understanding and prediction of chemical reactivity, one of the main aims in the field of conceptual density functional theory. While approximate evaluations of su ... Full text Cite

Mechanical anisotropy of ankyrin repeats.

Journal Article Biophys J · March 7, 2012 Red blood cells are frequently deformed and their cytoskeletal proteins such as spectrin and ankyrin-R are repeatedly subjected to mechanical forces. While the mechanics of spectrin was thoroughly investigated in vitro and in vivo, little is known about th ... Full text Link to item Cite

Higher-order split operator schemes for solving the Schrödinger equation in the time-dependent wave packet method: applications to triatomic reactive scattering calculations.

Journal Article Physical chemistry chemical physics : PCCP · February 2012 The efficiency of the numerical propagators for solving the time-dependent Schrödinger equation in the wave packet approach to reactive scattering is of vital importance. In this Perspective, we first briefly review the propagators used in quantum reactive ... Full text Cite

Challenges for density functional theory

Journal Article Chemical Reviews · 2012 Understanding current and future challenges for density functional theory (DFT) are focused. One of the main challenges for DFT is to keep as its cornerstone some element of simplicity. It also include the need to improve the description of reaction barrie ... Full text Cite

Modeling structural coordination and ligand binding in zinc proteins with a polarizable potential

Journal Article Journal of Chemical Theory and Computation · 2012 As the second most abundant cation in the human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging f ... Full text Cite

Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and simulation of growth mechanism

Journal Article Nano Research · 2012 We present a bottom-up synthesis, spectroscopic characterization, and ab initio simulations of star-shaped hexagonal zinc oxide (ZnO) nanowires. The ZnO nanostructures were synthesized by a low-temperature hydrothermal growth method. The cross-section of t ... Full text Cite

Insight and progress in density functional theory

Journal Article AIP Conference Proceedings · January 1, 2012 Density functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, there are spectacular failures for many predicted properties. The errors include underestimation of the barrie ... Full text Cite

An algebraic operator approach to electronic structure.

Journal Article The Journal of chemical physics · December 2011 In this paper, we introduce an algebraic approach to electronic structure calculations. Our approach constructs a Jordan algebra based on the second-quantized electronic Hamiltonian. From the structure factor of this algebra, we show that we can calculate ... Full text Cite

Progress in exchange-correlation energy functionals

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 28, 2011 Link to item Cite

Catalytic mechanism for single-site water oxidation process: A theoretical study

Journal Article ACS National Meeting Book of Abstracts · August 25, 2011 Water oxidation catalyzed by single-site ruthenium complexes has generated enormous interests related to solar fuels. Combining several theoretical tools, we studied the entire catalytic cycle of water oxidation for a single site catalyst starting with [Ru ... Cite

Phase-corrected surface hopping: correcting the phase evolution of the electronic wavefunction.

Journal Article The Journal of chemical physics · July 2011 In this paper, we show that a remarkably simple correction can be made to the equation of motion which governs the evolution of the electronic wavefunction over some prescribed nuclear trajectory in the fewest-switches surface hopping algorithm. This corre ... Full text Cite

Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.

Journal Article The Journal of chemical physics · May 2011 The significance of conical intersections in photophysics, photochemistry, and photodissociation of polyatomic molecules in gas phase has been demonstrated by numerous experimental and theoretical studies. Optimization of conical intersections of small- an ... Full text Cite

Simultaneous-trajectory surface hopping: a parameter-free algorithm for implementing decoherence in nonadiabatic dynamics.

Journal Article The Journal of chemical physics · April 2011 In this paper, we introduce a trajectory-based nonadiabatic dynamics algorithm which aims to correct the well-known overcoherence problem in Tully's popular fewest-switches surface hopping algorithm. Our simultaneous-trajectory surface hopping algorithm pr ... Full text Cite

Mechanics of polysaccharides

Chapter · January 1, 2011 Cite

NCIPLOT: a program for plotting non-covalent interaction regions

Journal Article J. Chem. Theory Comput. · 2011 Cite

Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation.

Journal Article Journal of the American Chemical Society · January 2011 Many gram-positive pathogens possess external pili or fimbriae with which they adhere to host cells during the infection process. Unusual dual intramolecular isopeptide bonds between Asn and Lys side chains within the N-terminal and C-terminal domains of t ... Full text Cite

Communication: An exact short-time solver for the time-dependent Schrödinger equation.

Journal Article The Journal of chemical physics · January 2011 The short-time integrator for propagating the time-dependent Schrödinger equation, which is exact to machine's round off accuracy when the Hamiltonian of the system is time-independent, was applied to solve dynamics processes. This integrator has the old C ... Full text Cite

lambda-metadynamics approach to compute absolute solvation free energy

Journal Article Journal of Physical Chemistry Letters · 2011 Cite

Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations.

Journal Article J Biol Chem · December 3, 2010 During co-translational folding, the nascent polypeptide chain is extruded sequentially from the ribosome exit tunnel and is [corrected] under severe conformational constraints [corrected] dictated by the one-dimensional geometry of the tunnel. [corrected] ... Full text Link to item Cite

Challenges with range-separated exchange-correlation functionals in time-dependent density functional theory calculations

Journal Article Molecular Physics · October 10, 2010 The conventional approximate exchange-correlation functionals and kernels can lead to a large error in time-dependent density functional theory (TDDFT) calculations in certain cases, such as in the descriptions of charge-transfer excited states, Rydberg st ... Full text Cite

Spin-state splittings, highest-occupied-molecular-orbital and lowest-unoccupied-molecular-orbital energies, and chemical hardness.

Journal Article The Journal of chemical physics · October 2010 It is known that the exact density functional must give ground-state energies that are piecewise linear as a function of electron number. In this work we prove that this is also true for the lowest-energy excited states of different spin or spatial symmetr ... Full text Open Access Cite

A gradient-directed Monte Carlo approach for protein design.

Journal Article Journal of computational chemistry · August 2010 We develop a new global optimization strategy, gradient-directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Mon ... Full text Cite

Efficient construction of nonorthogonal localized molecular orbitals in large systems.

Journal Article The journal of physical chemistry. A · August 2010 Localized molecular orbitals (LMOs) are much more compact representations of electronic degrees of freedom than canonical molecular orbitals (CMOs). The most compact representation is provided by nonorthogonal localized molecular orbitals (NOLMOs), which a ... Full text Open Access Cite

Structural manifestation of the delocalization error of density functional approximations: C(4N+2) rings and C(20) bowl, cage, and ring isomers.

Journal Article The Journal of chemical physics · June 2010 The ground state structure of C(4N+2) rings is believed to exhibit a geometric transition from angle alternation (N < or = 2) to bond alternation (N > 2). All previous density functional theory (DFT) studies on these molecules have failed to reproduce this ... Full text Open Access Cite

Revealing noncovalent interactions.

Journal Article Journal of the American Chemical Society · May 2010 Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based ... Full text Open Access Cite

Concerted O atom-proton transfer in the O-O bond forming step in water oxidation.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · April 2010 As the terminal step in photosystem II, and a potential half-reaction for artificial photosynthesis, water oxidation (2H(2)O --> O(2) + 4e(-) + 4H(+)) is key, but it imposes a significant mechanistic challenge with requirements for both 4e(-)/4H(+) loss an ... Full text Cite

Elucidating solvent contributions to solution reactions with ab initio QM/MM methods.

Journal Article The journal of physical chemistry. B · March 2010 Computer simulations of reaction processes in solution in general rely on the definition of a reaction coordinate and the determination of the thermodynamic changes of the system along the reaction coordinate. The reaction coordinate often is constituted o ... Full text Open Access Cite

Conductive junctions with parallel graphene sheets.

Journal Article The Journal of chemical physics · March 2010 The establishment of conductive graphene-molecule-graphene junction is investigated through first-principles electronic structure calculations and quantum transport calculations. The junction consists of a conjugated molecule connecting two parallel graphe ... Full text Open Access Cite

Equilibrium sampling for biomolecules under mechanical tension.

Journal Article Biophysical journal · February 2010 In the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, ... Full text Cite

Accelerating self-consistent field convergence with the augmented Roothaan-Hall energy function.

Journal Article The Journal of chemical physics · February 2010 Based on Pulay's direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented Roothaan-Hall (ARH) energy function, proposed recently by Høst and co-w ... Full text Open Access Cite

Reformulating time-dependent density functional theory with non-orthogonal localized molecular orbitals.

Journal Article Physical chemistry chemical physics : PCCP · January 2010 Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-ort ... Full text Open Access Cite

A gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding.

Journal Article The Journal of chemical physics · October 2009 We apply the gradient-directed Monte Carlo (GDMC) method to select optimal members of a discrete space, the space of chemically viable proteins described by a model Hamiltonian. In contrast to conventional Monte Carlo approaches, our GDMC method uses local ... Full text Cite

Free energies and mechanisms of chemical reactions in enzymes and in solution with QMMM minimum free energy path

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 16, 2009 Link to item Cite

Modeling allosteric regulation in GPCRs: Toward rational structure-based drug design

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 16, 2009 Link to item Cite

Coarse-grained modeling of allosteric regulation in protein receptors.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2009 Allosteric regulation provides highly specific ligand recognition and signaling by transmembrane protein receptors. Unlike functions of protein molecular machines that rely on large-scale conformational transitions, signal transduction in receptors appears ... Full text Cite

Analysis of HIF-1 inhibition by manassantin A and analogues with modified tetrahydrofuran configurations.

Journal Article Bioorg Med Chem Lett · July 15, 2009 We have shown that manassantin A downregulated the HIF-1alpha expression and inhibited the secretion of VEGF. We have also demonstrated that the 2,3-cis-3,4-trans-4,5-cis-configuration of the tetrahydrofuran is critical to the HIF-1 inhibition of manassant ... Full text Link to item Cite

Contact geometry and conductance of crossed nanotube junctions under pressure.

Journal Article Nano letters · May 2009 We explored the relative stability, structure, and conductance of crossed nanotube junctions with dispersion corrected density functional theory. We found that the most stable junction geometry, not studied before, displays the smallest conductance. While ... Full text Cite

Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations.

Journal Article The journal of physical chemistry. B · April 2009 Cdc25B is a dual-specificity phosphatase that catalyzes the dephosphorylation of the Cdk2/CycA protein complex. This enzyme is an important regulator of the human cell cycle and has been identified as a potential anticancer target. In general, protein tyro ... Full text Cite

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.

Journal Article The Journal of chemical physics · April 2009 A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describ ... Full text Cite

Second-Order Perturbation Theory with Fractional Charges and Fractional Spins.

Journal Article Journal of chemical theory and computation · April 2009 In this work the behavior of MP2 for fractional occupations is investigated. The consideration of fractional charge behavior gives a simple derivation of an expression for the chemical potential (or the derivative of energy with respect to the number of el ... Full text Cite

Thermopower of molecular junctions: an ab initio study.

Journal Article Nano letters · March 2009 Molecular nanojunctions may support efficient thermoelectric conversion through enhanced thermopower. Recently, this quantity has been measured for several conjugated molecular nanojunctions with gold electrodes. Considering the wide variety of possible me ... Full text Cite

Discontinuous nature of the exchange-correlation functional in strongly correlated systems.

Journal Article Physical review letters · February 2009 Standard approximations for the exchange-correlation functional have been found to give big errors for the linearity condition of fractional charges, leading to delocalization error, and the constancy condition of fractional spins, leading to static correl ... Full text Cite

Comparison of reaction barriers in energy and free energy for enzyme catalysis

Chapter · January 1, 2009 Reaction paths on potential energy surfaces obtained from QM/MM calculations of enzymatic or solution reactions depend on the starting structure employed for the path calculations. The free energies associated with these paths should be more reliable for s ... Full text Cite

Second-order perturbation theory with fractional charges and fractional spins

Journal Article Journal of Chemical Theory and Computation · 2009 Cite

Emergent strategies for inverse molecular design

Journal Article Science in China B: Chemistry · 2009 Cite

Discrete optimization of electronic hyperpolarizabilities in a chemical subspace

Journal Article Army Research Laboratory Publication ARL-TR-4833 · 2009 Cite

Optimized effective potentials from arbitrary basis sets.

Journal Article The Journal of chemical physics · November 2008 We investigate the use of a regularized optimized effective potential (OEP) energy functional and L-curve procedure [T. Heaton-Burgess, F. A. Bulat, and W. Yang, Phys. Rev. Lett. 98, 256401 (2007)] for determining physically meaningful OEPs from arbitrary ... Full text Cite

Optimized effective potentials from arbitrary basis sets

Journal Article Journal of Chemical Physics · November 2008 Cite

Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase.

Journal Article Journal of the American Chemical Society · November 2008 Despite extensive experimental and theoretical studies, the detailed catalytic mechanism of orotidine 5'-monophosphate decarboxylase (ODCase) remains controversial. In particular simulation studies using high level quantum mechanics have failed to reproduc ... Full text Cite

Exploring chemical space with discrete, gradient, and hybrid optimization methods.

Journal Article The Journal of chemical physics · November 2008 Discrete, gradient, and hybrid optimization methods are applied to the challenge of discovering molecules with optimized properties. The cost and performance of the approaches were studied using a tight-binding model to maximize the static first electronic ... Full text Cite

Molecular design of porphyrin-based nonlinear optical materials.

Journal Article The journal of physical chemistry. A · November 2008 Nonlinear optical chromophores containing (porphyrinato)Zn(II), proquinoid, and (terpyridyl)metal(II) building blocks were optimized in a library containing approximately 10(6) structures using the linear combination of atomic potentials (LCAP) methodology ... Full text Cite

Quantum-interference-controlled molecular electronics.

Journal Article Nano letters · October 2008 Quantum interference in coherent transport through single molecular rings may provide a mechanism to control the current in molecular electronics. We investigate its applicability, using a single-particle Green function method combined with ab initio elect ... Full text Cite

A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes.

Journal Article The Journal of chemical physics · October 2008 The pseudobond method is used in quantum mechanical/molecular mechanical (QM/MM) simulations in which a covalent bond connects the quantum mechanical and classical subsystems. In this method, the molecular mechanical boundary atom is replaced by a special ... Full text Cite

Fractional spins and static correlation error in density functional theory.

Journal Article The Journal of chemical physics · September 2008 Electronic states with fractional spins arise in systems with large static correlation (strongly correlated systems). Such fractional-spin states are shown to be ensembles of degenerate ground states with normal spins. It is proven here that the energy of ... Full text Cite

Computational design, synthesis and biological evaluation of para-quinone-based inhibitors for redox regulation of the dual-specificity phosphatase Cdc25B.

Journal Article Organic & biomolecular chemistry · September 2008 Quinoid inhibitors of Cdc25B were designed based on the Linear Combination of Atomic Potentials (LCAP) methodology. In contrast to a published hypothesis, the biological activities and hydrogen peroxide generation in reducing media of three synthetic model ... Full text Cite

A donor-nanotube paradigm for nonlinear optical materials.

Journal Article Nano letters · September 2008 Studies of the nonlinear electronic response of donor/acceptor substituted nanotubes suggest a behavior that is both surprising and qualitatively distinct from that in conventional conjugated organic species. We find that the carbon nanotubes serve as both ... Full text Cite

CINF 71-Inverse design of host-guest complexes in competitive binding problems

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 17, 2008 Link to item Cite

Insights into current limitations of density functional theory.

Journal Article Science (New York, N.Y.) · August 2008 Density functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, for many predicted properties, there are spectacular failures that can be traced to the delocalization error a ... Full text Cite

Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2+)-sensitive dye.

Journal Article The Journal of chemical physics · August 2008 A density-fragment interaction (DFI) approach for large-scale calculations is proposed. The DFI scheme describes electron density interaction between many quantum-mechanical (QM) fragments, which overcomes errors in electrostatic interactions with the fixe ... Full text Cite

Transport properties of an armchair carbon nanotube with a double vacancy under stretching

Journal Article Journal of Physics-Condensed Matter · August 2008 Cite

A gradient-directed Monte Carlo approach to molecular design.

Journal Article The Journal of chemical physics · August 2008 The recently developed linear combination of atomic potentials (LCAP) approach [M. Wang et al., J. Am. Chem. Soc. 128, 3228 (2006)] allows continuous optimization in a discrete chemical space, and thus is useful in the design of molecules for targeted prop ... Full text Cite

Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals

Journal Article Journal of Physics-Condensed Matter · July 2008 Cite

Inverse molecular design in a tight-binding framework.

Journal Article The Journal of chemical physics · July 2008 The number of chemical species of modest molecular weight that can be accessed with known synthetic methods is astronomical. An open challenge is to explore this space in a manner that will enable the discovery of molecular species and materials with optim ... Full text Cite

First-principles study for transport properties of armchair carbon nanotubes with a double vacancy under strain

Journal Article Journal of Applied Physics · June 20, 2008 Vacancies are one of the most important defects in carbon nanotubes (CNTs). Vacancies could affect the mechanical, chemical, and electronic properties of CNTs. In this study, we first use first-principles plane-wave calculation to optimize the structure of ... Full text Cite

Localization and delocalization errors in density functional theory and implications for band-gap prediction.

Journal Article Physical review letters · April 2008 The band-gap problem and other systematic failures of approximate exchange-correlation functionals are explained from an analysis of total energy for fractional charges. The deviation from the correct intrinsic linear behavior in finite systems leads to de ... Full text Cite

Lead-molecule coupling effects on the distortion-dependent conductance of carbon nanotubes

Journal Article Physical Review B - Condensed Matter and Materials Physics · April 1, 2008 The effect of the lead-molecule coupling on the zero-bias conductance of carbon nanotubes as a function of tube distortion is studied. It is shown that the coupling strength can have a dramatic effect on the electromechanical characteristics. Robust conduc ... Full text Cite

Size extensivity of the direct optimized effective potential method.

Journal Article The Journal of chemical physics · March 2008 We investigate the size extensivity of the direct optimized effective potential procedure of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)]. The choice of reference potential within the finite basis construction of the local Kohn-Sham potential can lead ... Full text Cite

Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding.

Journal Article The journal of physical chemistry. B · March 2008 The inter- and intramolecular interactions that determine the experimentally observed binding mode of the ligand (2Z)-2-(benzoylamino)-3-[4-(2-bromophenoxy)phenyl]-2-propenoate in complex with hepatitis C virus NS5B polymerase have been studied using QM/MM ... Full text Cite

Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.

Journal Article The Journal of chemical physics · March 2008 Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET pro ... Full text Cite

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Journal Article The Journal of chemical physics · January 2008 To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics ... Full text Cite

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

Journal Article Annual review of physical chemistry · January 2008 Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in ... Full text Cite

Optimized effective potentials from electron densities in finite basis sets.

Journal Article The Journal of chemical physics · November 2007 The Wu-Yang method for determining the optimized effective potential (OEP) and implicit density functionals from a given electron density is revisited to account for its ill-posed nature, as recently done for the direct minimization method for OEP's from a ... Full text Cite

Sequential quadratic programming method for determining the minimum energy path.

Journal Article The Journal of chemical physics · October 2007 A new method, referred to as the sequential quadratic programming method, is presented for determining minimum energy paths. The method is based on minimizing the points representing the path in the subspace perpendicular to the tangent of the path while u ... Full text Cite

Electron transport through single conjugated organic molecules: basis set effects in ab initio calculations.

Journal Article The Journal of chemical physics · October 2007 We investigate electron transport through single conjugated molecules--including benzenedithiol, oligophenylene ethynylenes of different lengths, and a ferrocene-containing molecule sandwiched between two gold electrodes with different contact structures-- ... Full text Cite

Contact transparency of nanotube-molecule-nanotube junctions.

Journal Article Physical review letters · October 2007 The transparency of contacts between conjugated molecules and metallic single-walled carbon nanotubes is investigated using a single-particle Green's function method which combines a Landauer approach with ab initio density functional theory. We find that ... Full text Cite

Cobaltocene as a spin filter.

Journal Article The Journal of chemical physics · October 2007 In the context of investigating organic molecules for molecular electronics, doping molecular wires with transition metal atoms provides additional means of controlling their transport behavior. The incorporation of transition metal atoms may generate spin ... Full text Cite

COMP 436-Accurate density functionals addressing the self-interaction error and potential functional formalism

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 19, 2007 Link to item Cite

PHYS 124-QM/MM calculation of electron transfer process: Fractional number of electrons approach

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 19, 2007 Link to item Cite

PHYS 301-Free energies of chemical reactions in enzyme and in solution

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 19, 2007 Link to item Cite

COMP 244-Nature of ligand binding in HCV polymerase: Characterization of specific interactions from QM/MM calculations

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · August 19, 2007 Link to item Cite

Assessment and formal properties of exchange-correlation functionals constructed from the adiabatic connection.

Journal Article The Journal of chemical physics · July 2007 We examine the development and investigate the performance of exchange-correlation functionals constructed from the adiabatic connection. Our method is based on a direct modeling of the adiabatic connection curve in the coupling-constant space and is very ... Full text Cite

Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state.

Journal Article The journal of physical chemistry. A · July 2007 The recently developed self-consistent-charge density functional tight binding (SCCDFTB) method provides an accurate and inexpensive quantum mechanical solution to many molecular systems of interests. To examine the performance of the SCCDFTB method on (li ... Full text Cite

Optimized effective potentials in finite basis sets.

Journal Article Physical review letters · June 2007 The finite basis optimized effective potential (OEP) method within density functional theory is examined as an ill-posed problem. It is shown that the generation of nonphysical potentials is a controllable manifestation of the use of unbalanced, and thus u ... Full text Cite

Role of the exchange-correlation potential in ab initio electron transport calculations.

Journal Article The Journal of chemical physics · May 2007 The effect of the exchange-correlation potential in ab initio electron transport calculations is investigated by constructing optimized effective potentials using different energy functionals or the electron density from second-order perturbation theory. T ... Full text Cite

Development of exchange-correlation functionals with minimal many-electron self-interaction error.

Journal Article The Journal of chemical physics · May 2007 New exchange-correlation functionals that address the important issue of many-electron self-interaction are developed. This is carried out by considering the performance of the functional on systems with fractional numbers of electrons at the same time as ... Full text Cite

QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.

Journal Article Journal of chemical theory and computation · March 2007 Structural and energetic changes are two important characteristic properties of a chemical reaction process. In the condensed phase, studying these two properties is very challenging because of the great computational cost associated with the quantum mecha ... Full text Cite

Spin-potential functional formalism for current-carrying noncollinear magnetic systems.

Journal Article Physical review letters · January 2007 We develop a formalism dual to spin-current-density functional theory (CDFT) where minimization with respect to the scalar and vector spin potentials is used. In this way we circumvent the issues surrounding the nonuniqueness of the mapping between spin po ... Full text Cite

Fitting molecular electrostatic potentials from quantum mechanical calculations

Journal Article Journal of Chemical Theory and Computation · 2007 Cite

Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework.

Journal Article The journal of physical chemistry. A · January 2007 The linear combination of atomic potentials (LCAP) approach is implemented in the AM1 semiempirical framework and is used to design molecular structures with optimized properties. The optimization procedure uses property derivative information to search mo ... Full text Cite

Development of ab initio calculation for electron transport and the effects of lead and contact structures in molecular electronics

Journal Article Journal of Computational and Theoretical Nanoscience · December 29, 2006 A fully self-consistent method combining density functional theory (DFT) and nonequilibrium Green function approach for calculating electron transport through molecular devices is reviewed. It uses periodic boundary conditions for DFT and treats the leads ... Full text Cite

Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods.

Journal Article The Journal of chemical physics · December 2006 The diagonally implicit Runge-Kutta framework is shown to be a general form for constructing stable, efficient steepest descent reaction path integrators, of any order. With this framework tolerance driven, adaptive step-size methods can be constructed by ... Full text Cite

Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: Role of enzyme dynamics

Journal Article International Journal of Quantum Chemistry · November 15, 2006 The enzymatic transfer of a sulfuryl group from the ubiquitous biological source of sulfate 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to estrogen is investigated by the pseudo-bond quantum mechanical/molecular mechanical method (QM/MM) method. Calculati ... Full text Cite

Density functional theory investigation of the polarizability and second hyperpolarizability of polydiacetylene and polybutatriene chains: treatment of exact exchange and role of correlation.

Journal Article The Journal of chemical physics · November 2006 The static polarizability and second hyperpolarizability of increasingly large polydiacetylene and polybutatriene (PBT) chains have been evaluated using the optimized effective potential for exact exchange (OEP-EXX) method developed by Yang and Wu [Phys. R ... Full text Cite

Many-electron self-interaction error in approximate density functionals.

Journal Article The Journal of chemical physics · November 2006 One of the most important challenges in density functional theory (DFT) is the proper description of fractional charge systems relating to the self-interaction error (SIE). Traditionally, the SIE has been formulated as a one-electron problem, which has bee ... Full text Cite

Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method.

Journal Article Biophysical journal · September 2006 Conventional steered molecular dynamics (SMD) simulations do not readily reproduce equilibrium conditions of atomic force microscopy (AFM) stretch and release measurements of polysaccharides undergoing force-induced conformational transitions because of th ... Full text Cite

Direct detection of the formation of V-amylose helix by single molecule force spectroscopy.

Journal Article Journal of the American Chemical Society · July 2006 An important polysaccharide, amylose crystallizes as a regular single left-handed helix from a propanol, butanol, or iodine solution. However, its solution structure remains elusive because amylose does not form molecular solutions in these solvents, and s ... Full text Cite

A combined explicit-implicit method for high accuracy reaction path integration.

Journal Article The Journal of chemical physics · June 2006 We present the use of an optimal combined explicit-implicit method for following the reaction path to high accuracy. This is in contrast to most purely implicit reaction path integration algorithms, which are only efficient on stiff ordinary differential e ... Full text Cite

Legendre-transform functionals for spin-density-functional theory.

Journal Article The Journal of chemical physics · June 2006 We provide a rigorous proof that the Hohenberg-Kohn theorem holds for spin densities by extending Lieb's Legendre-transform formulation to spin densities. The resulting spin-density-functional theory resolves several troublesome issues. Most importantly, t ... Full text Cite

Negative differential resistance and hysteresis through an organometallic molecule from molecular-level crossing.

Journal Article Journal of the American Chemical Society · May 2006 Analogous to a quantum double-dot system, diblock structured molecules could also show negative differential resistance (NDR). Using combined density functional theory and nonequilibrium Green function technique, we show that molecular-level crossing in a ... Full text Cite

Nanotube-metal junctions: 2- and 3-terminal electrical transport.

Journal Article The Journal of chemical physics · May 2006 We address the quality of electrical contact between carbon nanotubes and metallic electrodes by performing first-principles calculations for the electron transmission through ideal 2- and 3-terminal junctions, thus revealing the physical limit of tube-met ... Full text Cite

Designing molecules by optimizing potentials.

Journal Article Journal of the American Chemical Society · March 2006 The astronomical number of accessible discrete chemical structures makes rational molecular design extremely challenging. We formulate the design of molecules with specific tailored properties as performing a continuous optimization in the space of electro ... Full text Cite

Self-interaction-free exchange-correlation functional for thermochemistry and kinetics.

Journal Article The Journal of chemical physics · March 2006 We develop a self-interaction-free exchange-correlation functional which is very accurate for thermochemistry and kinetics. This is achieved by theoretical construction of the functional form and nonlinear fitting. We define a simple interpolation of the a ... Full text Cite

Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.

Journal Article The Journal of chemical physics · March 2006 Nuclear quantum mechanical effects have been examined for the proton transfer reaction catalyzed by triosephosphate isomerase, with the normal mode centroid path integral molecular dynamics based on the potential energy surface from the recently developed ... Full text Cite

A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution

Journal Article Chemical Physics Letters · February 15, 2006 The solvation free energies for acetic acids in the anti/syn conformations in water solution have been computed by the novel QM/MM approach combined with the theory of energy representation (QM/MM-ER). To examine the accuracy of the methodology, we have co ... Full text Cite

Quadratic string method for determining the minimum-energy path based on multiobjective optimization.

Journal Article The Journal of chemical physics · February 2006 Based on a multiobjective optimization framework, we develop a new quadratic string method for finding the minimum-energy path. In the method, each point on the minimum-energy path is minimized by integration in the descent direction perpendicular to path. ... Full text Cite

Organometallic molecular rectification.

Journal Article The Journal of chemical physics · January 2006 We study the rectification of current through a single molecule with an intrinsic spatial asymmetry. The molecule contains a cobaltocene moiety in order to take advantage of its relatively localized and high-energy d states. A rectifier with large voltage ... Full text Cite

Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase.

Journal Article The journal of physical chemistry. A · January 2006 Quantum mechanical/molecular mechanical (QM/MM) calculations and experimental kinetic studies have been performed on 4-oxalocrotonate tautomerase (4OT) for two different substrates, 2-hydroxymuconate (2HM) and 2-oxo-4-hexenedioate (2o4hex). Potential (delt ... Full text Cite

Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.

Journal Article Biochemistry · December 2005 Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack ... Full text Cite

Organometallic spintronics: dicobaltocene switch.

Journal Article Nano letters · October 2005 A single-molecule spintronic switch and spin valve using two cobaltocene moieties is proposed. Spin-dependent transport through a lead-molecule-lead junction has been calculated using first-principles density functional and nonequilibrium Green function me ... Full text Cite

Analytic energy gradients of the optimized effective potential method.

Journal Article The Journal of chemical physics · October 2005 The analytic energy gradients of the optimized effective potential (OEP) method in density-functional theory are developed. Their implementation in the direct optimization approach of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)] and Wu and Yang [J. The ... Full text Cite

Models of electrodes and contacts in molecular electronics.

Journal Article The Journal of chemical physics · September 2005 Bridging the difference in atomic structure between experiments and theoretical calculations and exploring quantum confinement effects in thin electrodes (leads) are both important issues in molecular electronics. To address these issues, we report here, b ... Full text Cite

Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure.

Journal Article The Journal of chemical physics · August 8, 2005 We have developed a second-order perturbation theory (PT) energy functional within density-functional theory (DFT). Based on PT with the Kohn-Sham (KS) determinant as a reference, this new ab initio exchange-correlation functional includes an exact exchang ... Cite

Orbital-dependent correlation energy in density-functional theory based on a second-order perturbation approach: success and failure.

Journal Article The Journal of chemical physics · August 2005 We have developed a second-order perturbation theory (PT) energy functional within density-functional theory (DFT). Based on PT with the Kohn-Sham (KS) determinant as a reference, this new ab initio exchange-correlation functional includes an exact exchang ... Full text Cite

Dual-topology/dual-coordinate free-energy simulation using QM/MM force field.

Journal Article The Journal of chemical physics · July 2005 We have developed a dual-topology/dual-coordinate free-energy simulation method for use with a QM/MM force field. By combining two parallel processes into one alchemical process, we are able to compute the double free-energy difference (delta deltaF) withi ... Full text Cite

Density-functional theory (hyper)polarizabilities of push-pull pi-conjugated systems: treatment of exact exchange and role of correlation.

Journal Article The Journal of chemical physics · July 2005 The performance of the optimized effective potential procedure for exact exchange in calculating static electric-field response properties of push-pull pi-conjugated systems has been studied, with an emphasis on NO2-(CH=CH)n-NH2 chains. Good agreement with ... Full text Cite

Near-perfect conduction through a ferrocene-based molecular wire

Journal Article Physical Review B - Condensed Matter and Materials Physics · June 15, 2005 Here we describe the design, single-molecule transport measurements, and theoretical modeling of a ferrocene-based organometallic molecular wire, whose bias-dependent conductance shows a clear Lorentzian form with magnitude exceeding 70% of the conductance ... Full text Cite

Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods.

Journal Article The Journal of chemical physics · March 2005 A two-step procedure for the determination of reaction paths in enzyme systems is presented. This procedure combines two chain-of-states methods: a quantum mechanical/molecular mechanical (QM/MM) implementation of the nudged elastic band (NEB) method and a ... Full text Cite

Contact atomic structure and electron transport through molecules.

Journal Article The Journal of chemical physics · February 2005 Using benzene sandwiched between two Au leads as a model system, we investigate from first principles the change in molecular conductance caused by different atomic structures around the metal-molecule contact. Our motivation is the variable situations tha ... Full text Cite

Intermolecular effect in molecular electronics.

Journal Article The Journal of chemical physics · January 2005 We investigate the effects of lateral interactions on the conductance of two molecules connected in parallel to semi-infinite leads. The method we use combines a Green function approach to quantum transport with density functional theory for the electronic ... Full text Cite

Molecular conductance: chemical trends of anchoring groups.

Journal Article Journal of the American Chemical Society · December 2004 Combining density functional theory calculations for molecular electronic structure with a Green function method for electron transport, we calculate from first principles the molecular conductance of benzene connected to two Au leads through different anc ... Full text Cite

Conjugate-gradient optimization method for orbital-free density functional calculations.

Journal Article The Journal of chemical physics · August 2004 Orbital-free density functional theory as an extension of traditional Thomas-Fermi theory has attracted a lot of interest in the past decade because of developments in both more accurate kinetic energy functionals and highly efficient numerical methodology ... Full text Cite

Elastic properties of single amylose chains in water: a quantum mechanical and AFM study.

Journal Article Journal of the American Chemical Society · July 2004 Recent single-molecule atomic force microscopy (AFM) experiments have revealed that some polysaccharides display large deviations from force-extension relationships of other polymers which typically behave as simple entropic springs. However, the mechanism ... Full text Cite

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method.

Journal Article The Journal of chemical physics · July 2004 A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculatio ... Full text Cite

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.

Journal Article The Journal of chemical physics · July 2004 Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connectin ... Full text Cite

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment.

Journal Article Biochemistry · June 2004 The role of polypeptide backbone interactions in 4-oxalocrotonate tautomerase (4OT) catalysis has been investigated using a combination of site-directed mutagenesis experiments with unnatural amino acids and quantum mechanical/molecular mechanical (QM/MM) ... Full text Cite

Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.

Journal Article The Journal of chemical physics · May 2004 Optimization of reaction paths for enzymatic systems is a challenging problem because such systems have a very large number of degrees of freedom and many of these degrees are flexible. To meet this challenge, an efficient, robust and general approach is p ... Full text Cite

An efficient method for constructing nonorthogonal localized molecular orbitals.

Journal Article The Journal of chemical physics · May 2004 A new method for constructing nonorthogonal localized molecular orbitals (NOLMOs) is presented. The set of highly localized NOLMOs is obtained by minimization of the spread functional starting from an initial set of canonical orthogonal molecular orbitals. ... Full text Cite

Potential functionals: dual to density functionals and solution to the v-representability problem.

Journal Article Physical review letters · April 2004 A functional of external potentials and its variational principle for the ground-state energy is constructed. This potential functional formulation is dual to the density functional approach and provides a solution to the v-representability problem in the ... Full text Cite

"Elastic Properties of Single Amylose Chains in Water"

Journal Article J. Am. Chem. Soc. · 2004 Cite

ALGEBRAIC EQUATION AND ITERATIVE OPTIMIZATION FOR THE OPTIMIZED EFFECTIVE POTENTIAL IN DENSITY FUNCTIONAL THEORY

Journal Article Journal of Theoretical and Computational Chemistry · December 2003 We further develop our recent direct method for the optimized effective potential (OEP) in density functional theory (DFT) [Yang and Wu, Phys. Rev. Lett.89, 143002 (2002)]. First, we show that the stationary condition in our optimization approach ... Full text Cite

Density Functional Theory Simulation of Large Quantum Dots

Journal Article Phys. Rev. B · October 24, 2003 Kohn-Sham spin-density functional theory provides an efficient and accurate model to study electron-electron interaction effects in quantum dots, but its application to large systems is a challenge. Here an efficient method for the simulation of quantum do ... Full text Link to item Cite

Addition energies of fullerenes and carbon nanotubes as quantum dots: the role of symmetry.

Journal Article Physical review letters · September 2003 Using density-functional theory calculations, we investigate the addition energy (AE) of quantum dots formed of fullerenes or closed single-wall carbon nanotubes. We focus on the connection between symmetry and oscillations in the AE spectrum. In the highl ... Full text Cite

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase.

Journal Article Journal of the American Chemical Society · August 2003 The mechanism for the reaction catalyzed by the 4-oxalocrotonate tautomerase (4-OT) enzyme has been studied using a quantum mechanical/molecular mechanical (QM/MM) method developed in our laboratory. Total free energy barriers were obtained for the two ste ... Full text Cite

Spin and conductance-peak-spacing distributions in large quantum dots: a density-functional theory study.

Journal Article Physical review letters · January 2003 We use spin-density-functional theory to study the spacing between conductance peaks and the ground-state spin of 2D model quantum dots with up to 200 electrons. Distributions for different ranges of electron number are obtained in both symmetric and asymm ... Full text Cite

Direct method for optimized effective potentials in density-functional theory.

Journal Article Physical review letters · September 2002 The conventional optimized effective potential method is based on a difficult-to-solve integral equation. In the new method, this potential is constructed as a sum of a fixed potential and a linear combination of basis functions. The energy derivatives wit ... Full text Cite

Structural analysis, identification, and design of calcium-binding sites in proteins.

Journal Article Proteins · May 15, 2002 Assigning proteins with functions based on the 3-D structure requires high-speed techniques to make a systematic survey of protein structures. Calcium regulates many biological systems by binding numerous proteins in different biological environments. Desp ... Full text Link to item Cite

Developments and applications of a DFT QM/MM free energy method for simulation of chemical reactions in enzymes.

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · April 7, 2002 Link to item Cite

QM/MM study of the reaction mechanism of 4-oxalocrotonate tautomerase.

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · April 7, 2002 Link to item Cite

A QM/MM study on the structure and catalysis mechanism of PDE4B.

Journal Article ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · April 7, 2002 Link to item Cite

Empirical correction to density functional theory for van der Waals interactions

Journal Article Journal of Chemical Physics · January 8, 2002 Accounting of the van der Waals interactions in pratical molecular calculations with density functional theory was analyzed by an empirical method. The coefficients of C6 for pair interactions between carbon, nitrogen, and oxygen atoms were developed by th ... Full text Cite

Quantum mechanics simulation of protein dynamics on long timescale.

Journal Article Proteins · September 2001 Protein structure and dynamics are the keys to a wide range of problems in biology. In principle, both can be fully understood by using quantum mechanics as the ultimate tool to unveil the molecular interactions involved. Indeed, quantum mechanics of atoms ... Full text Cite

Density functional study of a weakly hydrogen-bonded benzene-ammonia complex: The importance of the exchange functional

Journal Article International Journal of Quantum Chemistry · September 1, 2000 Density functional theory calculations on the benzene-ammonia complex have been performed. The benzene-ammonia complex is weakly hydrogen bonded, and crucial for obtaining good agreement with experimental results is the choice of the exchange functional us ... Full text Cite

How is the active site of enolase organized to catalyze two different reaction steps?

Journal Article Journal of the American Chemical Society · July 19, 2000 Using a combined ab initio quantum mechanical/molecular mechanical approach developed in our laboratory, we obtained the reaction paths and free energy barriers for the two steps of the reaction catalyzed by enolase. In the first step, the α-proton of the ... Full text Cite

Degenerate ground states and a fractional number of electrons in density and reduced density matrix functional theory

Journal Article Physical review letters · May 2000 For a linear combination of electron densities of degenerate ground states, it is shown that the value of any energy functional is the ground state energy, if the energy functional is exact for ground state densities, size consistent, and translational inv ... Full text Cite

Density Functional Study of A Weakly Hydrogen Bonded System: the Benzene-Ammonia Complex

Journal Article The International Journal of Quantum Chemistry · 2000 Cite

Perspective on "Density-functional theory for fractional particle number: Derivative discontinuities of the energy"

Journal Article Theoretical Chemistry Accounts · January 1, 2000 This paper provides an overview of the title paper by Perdew, Parr, Levy and Balduz [Phys Rev Lett 49:1691 (1982)]. The title paper extended density functional theory to fractional electron number by an ensemble approach and proved that the energy is a ser ... Full text Cite

A pseudobond approach to combining quantum mechanical and molecular mechanical methods

Journal Article Journal of Chemical Physics · December 1, 1999 A major challenge for combined quantum mechanical and molecular mechanical methods (QM/MM) to study large molecules is how to treat the QM/MM boundary that bisects some covalent bonds. Here a pseudobond approach has been developed to solve this problem for ... Full text Cite

Special issue: Symposium on density functional and applications (Part I of II) - Introduction

Journal Article INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY · August 15, 1998 Link to item Cite

Serial in vivo observations of cerebral vasculature after treatment with a large single fraction of radiation.

Journal Article Radiat Res · April 1998 To test whether single high doses of radiation, similar to those used with radiosurgery, given to normal cerebral vasculature can cause changes in leukocyte-vessel wall interactions and tissue perfusion, a rat pial window model was used to view the cerebra ... Link to item Cite

Comment on “generalized gradient approximation made simple”

Journal Article Physical Review Letters · January 1, 1998 Full text Cite

A chemical equalization method for molecular simulations

Journal Article J. Chem. Phys. · 1996 Cite

Density-functional theory of the electronic structure of molecules

Journal Article Ann. Rev. Phys. Chem. · 1995 Cite

Structure of the ammonia dimer studied by density functional theory

Journal Article International Journal of Quantum Chemistry · January 1, 1994 Self‐consistent Kohn–Sham density functional calculations have been carried out to study the structure of the ammonia dimer. The local‐density approximation yields unusually large binding energy and short internitrogen distance compared with the experiment ... Full text Cite

The Ar-C2H2 intermolecular potential from high resolution spectroscopy and ab initio theory: A case for multicenter interactions

Journal Article The Journal of Chemical Physics · 1993 Infrared spectra have been obtained for the Ar-C2H2 complex, which include a combination band associated with the low frequency bending mode. These data are used, together with ab initio calculations and the results of previous studies of this system, to c ... Cite

The Ar-C2H2 intermolecular potential from high resolution spectroscopy and ab initio theory: A case for multicenter interactions

Journal Article The Journal of Chemical Physics · January 1, 1993 Infrared spectra have been obtained for the Ar-C2H2 complex, which include a combination band associated with the low frequency bending mode. These data are used, together with ab initio calculations and the results of previous studies of this system, to c ... Full text Cite

The Hartley basis functions and transform: alternatives to plane waves and the Fourier transform

Journal Article Chemical Physics Letters · April 24, 1992 The Hartley "cas" basis functions are presented as alternatives to the well-known plane waves in electronic structure and molecular dynamics calculations. The cas functions are real, amenable to a fast transform, and thus offer the advantage of improved co ... Full text Cite

The divide‐and‐conquer density‐functional approach: Molecular internal rotation and density of states

Journal Article Journal of Chemical Physics · February 1, 1992 The divide‐and‐conquer density‐functional method recently developed by Yang is applied to the calculations of internal rotation energies and density of electronic states of a tetrapeptide. The method, on comparison with the conventional Kohn–Sham m ... Full text Cite

Integral Formulation of Density-Functional Theory

Journal Article Advances in Quantum Chemistry · January 1, 1990 The Hohenberg-Kohn-Sham density-functional theory is reformulated in terms of explicit relations between the electron density and the effective potential through the use of Feynman path integrals. In this formulation electron density is the only basic vari ... Full text Cite

The collocation method for calculating vibrational bound states of molecular systems - with application to Ar-HCl

Journal Article The Journal of Chemical Physics · January 1, 1989 The ability of the collocation method to calculate vibrational bound states of molecules is investigated. The technique is simpler to implement than conventional variational methods; no integration over the basis functions is involved. We apply the method ... Full text Cite

The collocation method for bound solutions of the Schrödinger equation

Journal Article Chemical Physics Letters · December 2, 1988 The collocation method for obtaining the bound solutions of the Schrödinger equation is investigated. The technique does not require the evaluation of integrals and is very simple to implement. It is closely connected with other pointwise representations u ... Full text Cite

Local softness and chemical reactivity in the molecules CO, SCN- and H2CO

Journal Article Journal of Molecular Structure: THEOCHEM · January 1, 1988 Fukui functions (softnesses) are calculated for three species - formaldehyde, the thiocyanate ion and carbon monoxide. The fukui function for a molecule has been defined as the derivative of electron density with respect to the change of number of electron ... Full text Cite

New relation between hardness and compressibility of minerals

Journal Article Physics and Chemistry of Minerals · December 1, 1987 A relation between hardness (H) for minerals and compressibility (β) is proposed: {Mathematical expression}, where M is the molecular weight, ρ the density and q the number of atoms in a formula unit. The relation is derived from thermodynamics and is base ... Full text Cite

Gradient correction in Thomas-Fermi theory.

Journal Article Physical review. A, General physics · December 1986 Full text Cite

Various functionals for the kinetic energy density of an atom or molecule.

Journal Article Physical review. A, General physics · December 1986 Full text Cite

The use of global and local molecular parameters for the analysis of the gas-phase basicity of amines.

Journal Article Journal of the American Chemical Society · September 1986 Full text Cite

Analysis of the kinetic energy functional in density functional theory

Journal Article The Journal of Chemical Physics · January 1, 1986 The density matrix that leads to a minimum kinetic energy for a given density is considered as a convex superposition of pure states. It is shown that the conditions of stationarity of the kinetic energy and collapse to the given density require that each ... Full text Cite

Hardness, softness, and the fukui function in the electronic theory of metals and catalysis.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 1985 The concepts of hardness eta = (2E/N2)nu and fukui function f(r) = [rho (r)/N]nu, which have recently been associated with the theory of chemical reactivity in molecules, are extended to the theory of metals. It is shown that at T = 0, 1/eta = g(epsilon F) ... Full text Cite

A new functional with homogeneous coordinate scaling in density functional theory: F[ρ, λ]

Journal Article The Journal of Chemical Physics · January 1, 1985 As previously shown [M. Levy and J. P. Perdew, Phys. Rev. A (in press)], the customary Hohenberg-Kohn density functional, based on the universal functional F[ρ], does not exhibit naively expected scaling properties. Namely, if ρλ = λ3ρ(λr) is the scaled de ... Full text Cite

Molecular softness as the average of atomic softnesses: Companion principle to the geometric mean principle for electronegativity equalization

Journal Article Journal of Physical Chemistry · January 1, 1985 It is demonstrated that, for a molecule consisting of M atoms, the relation, 1/(I - A) = (1/M)ΣiM[1/(Ii - Ai)], is valid to a reasonable approximation, where I and A are the ionization potential and electron affinity of the molecule and Ii, Ai denote the s ... Full text Cite

Density Functional Approach to the Frontier-Electron Theory of Chemical Reactivity

Journal Article Journal of the American Chemical Society · January 1, 1984 Full text Cite

Electron density, Kohn-Sham frontier orbitals, and Fukui functions

Journal Article The Journal of Chemical Physics · January 1, 1984 Full text Cite