Scholars@Duke
Tomasz Janowski

Tomasz Janowski

Analyst, IT, Sr
Chemistry
t.j@duke.edu
124 Science Dr, 5306A French Sci Center, Durham, NC 27708
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Selected Publications

Prostaglandin-mediated effects in early canine corpus luteum: In vivo effects on vascular and immune factors.

Journal Article Reproductive biology · March 2019 Prostaglandins (PGs) are important regulators of the early corpus luteum (CL) in the dog. Whereas, initially, CL is gonadotropin independent, in the second half of its lifespan, hypophyseal support is required. The transition period is marked by decreased ... Full text Cite

Efficient calculation of the density response function from generalized polarizabilities

Journal Article Theoretical Chemistry Accounts · January 1, 2016 We present a method to calculate the density response function (DRF), also known as the density response kernel or the polarization propagator in the static limit. Our method uses generalized polarizabilities (GPs) which are second derivatives of the molec ... Full text Cite

Selection of active spaces for multiconfigurational wavefunctions

Journal Article Journal of Chemical Physics · June 28, 2015 The efficient and accurate description of the electronic structure of strongly correlated systems is still a largely unsolved problem. The usual procedures start with a multiconfigurational (usually a Complete Active Space, CAS) wavefunction which accounts ... Full text Cite

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.

Journal Article Acta crystallographica. Section D, Biological crystallography · March 2015 Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca(2+)-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable num ... Full text Cite

Near equivalence of intrinsic atomic orbitals and quasiatomic orbitals

Journal Article Journal of Chemical Theory and Computation · August 12, 2014 A direct relationship between the Intrinsic Atomic Orbitals (IAO) method (Knizia, G. J. Chem. Theory Comp. 2013, 9, 4834-4843) and earlier work on the same topic, quasiatomic minimal basis set orbitals (QUAMBO) (Lu, W. C.; Wang, C. Z.; Schmidt, M. W.; Byta ... Full text Cite

Accuracy of quantum chemical methods for large noncovalent complexes

Journal Article Journal of Chemical Theory and Computation · August 13, 2013 We evaluate the performance of the most widely used wave function, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set) ... Full text Cite

A benchmark comparison of σ/σ and π/π dispersion: the dimers of naphthalene and decalin, and coronene and perhydrocoronene.

Journal Article Journal of the American Chemical Society · October 2012 The stacking interaction between π systems is a well-recognized structural motif, but stacking between σ systems was long considered of secondary importance. A recent paper points out that σ stacking can reach the energy of chemical bonds and concludes tha ... Full text Cite

Ultrafast Quantum Mechanics/Molecular Mechanics Monte Carlo simulations using generalized multipole polarizabilities

Journal Article Chemical Physics Letters · March 19, 2012 A fast and accurate Quantum Mechanics/Molecular Mechanics method is described for thermodynamic simulation of solutes (or active sites in flexible molecules) in polar environments. The solute is described quantum mechanically and is held fixed during avera ... Full text Cite

Recent developments in the PQS program

Journal Article Wiley Interdisciplinary Reviews: Computational Molecular Science · January 1, 2012 An overview of the PQS quantum chemistry suite is presented, with emphasis on recent developments and features that are unique to the program. The capabilities of the program, in particular the parallel implementation, are briefly described. Topics discuss ... Full text Cite

A benchmark quantum chemical study of the stacking interaction between larger polycondensed aromatic hydrocarbons

Journal Article Theoretical Chemistry Accounts · October 1, 2011 Large-scale electronic structure calculations were performed for the interaction energy between coronene, C24H12 with circumcoronene, C54H18, and between two circumcoronene molecules, in order to get a picture of the interaction between larger graphene she ... Full text Cite

Convex-concave stacking of curved conjugated networks: Benchmark calculations on the corannulene dimer

Journal Article Chemical Physics Letters · August 25, 2011 High level ab initio calculations on the eclipsed concave-convex corannulene dimer yielded a binding energy of 15.5 kcal/mol with a monomer-monomer distance of 3.69 at the (extrapolated) counterpoise corrected QCISD(T)/aug-cc-pVTZ level. Single point calcu ... Full text Cite

The ethidium-UA/AU intercalation site: Effect of model fragmentation and backbone charge state

Journal Article Journal of Chemical Theory and Computation · August 9, 2011 We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned in ... Full text Cite

Development of a 3-body:many-body integrated fragmentation method for weakly bound clusters and application to water clusters (H2O)(n = 3-10, 16, 17).

Journal Article The Journal of chemical physics · July 2011 A 3-body:many-body integrated quantum mechanical (QM) fragmentation method for non-covalent clusters is introduced within the ONIOM formalism. The technique captures all 1-, 2-, and 3-body interactions with a high-level electronic structure method, while a ... Full text Cite

A one-foetus pregnancy monitored by ultrasonography and progesterone blood levels in a German Shepherd bitch: A case report

Journal Article Veterinarni Medicina · January 1, 2011 This case study describes the pregnancy of a German Shepherd bitch with a singleton (one puppy) litter as a result of early embryo resorption. Resorption was confirmed by ultrasonography and the pregnancy was regularly monitored by USG and measurements of ... Full text Cite

Accurate correlated calculation of the intermolecular potential surface in the coronene dimer

Journal Article Molecular Physics · April 26, 2010 The binding energy of the coronene dimer was determined by high level ab initio calculations. In the first step a potential energy surface was determined for the stacked dimer at the SCS-MP2/aTZ level. The energy of the stacked parallel dimer was scanned w ... Full text Cite

Convergence of the CCSD(T) correction term for the stacked complex methyl adenine-methyl thymine: Comparison with lower-cost alternatives

Journal Article Journal of Chemical Theory and Computation · July 14, 2009 We have performed large-scale calculations for the interaction energy of the stacked methyl adenine-methyl thymine complex at the CCSD(T)/aug-ccpVXZ (X ) D,T) levels. The results can serve as benchmarks for the evaluation of two methods, MP2.5, introduced ... Full text Cite

Efficient calculation of the energy of a molecule in an arbitrary electric field

Journal Article International Journal of Quantum Chemistry · July 9, 2009 In thermodynamic (e.g., Monte Carlo) simulations with electronic embedding, the energy of the active site or solute must be calculated for millions of configurations of the environment (solvent or protein matrix) to obtain reliable statistics. This preclud ... Full text Cite

Quantum chemistry in parallel with PQS

Journal Article Journal of Computational Chemistry · January 30, 2009 This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pu ... Full text Cite

Efficient parallel implementation of the CCSD external exchange operator and the perturbative triples (T) Energy calculation

Journal Article Journal of Chemical Theory and Computation · October 14, 2008 A new, efficient parallel algorithm is presented for the most expensive step in coupled cluster singles and doubles (CCSD) energy calculations, the external exchange operator (EEO). The new implementation requires much less input/output than our previous a ... Full text Cite

Prostaglandin-mediated effects in early canine corpus luteum: In vivo effects on vascular and immune factors.

Journal Article Reproductive biology · March 2019 Prostaglandins (PGs) are important regulators of the early corpus luteum (CL) in the dog. Whereas, initially, CL is gonadotropin independent, in the second half of its lifespan, hypophyseal support is required. The transition period is marked by decreased ... Full text Cite

Efficient calculation of the density response function from generalized polarizabilities

Journal Article Theoretical Chemistry Accounts · January 1, 2016 We present a method to calculate the density response function (DRF), also known as the density response kernel or the polarization propagator in the static limit. Our method uses generalized polarizabilities (GPs) which are second derivatives of the molec ... Full text Cite

Selection of active spaces for multiconfigurational wavefunctions

Journal Article Journal of Chemical Physics · June 28, 2015 The efficient and accurate description of the electronic structure of strongly correlated systems is still a largely unsolved problem. The usual procedures start with a multiconfigurational (usually a Complete Active Space, CAS) wavefunction which accounts ... Full text Cite

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH.

Journal Article Acta crystallographica. Section D, Biological crystallography · March 2015 Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca(2+)-triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable num ... Full text Cite

Near equivalence of intrinsic atomic orbitals and quasiatomic orbitals

Journal Article Journal of Chemical Theory and Computation · August 12, 2014 A direct relationship between the Intrinsic Atomic Orbitals (IAO) method (Knizia, G. J. Chem. Theory Comp. 2013, 9, 4834-4843) and earlier work on the same topic, quasiatomic minimal basis set orbitals (QUAMBO) (Lu, W. C.; Wang, C. Z.; Schmidt, M. W.; Byta ... Full text Cite

Accuracy of quantum chemical methods for large noncovalent complexes

Journal Article Journal of Chemical Theory and Computation · August 13, 2013 We evaluate the performance of the most widely used wave function, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set) ... Full text Cite

A benchmark comparison of σ/σ and π/π dispersion: the dimers of naphthalene and decalin, and coronene and perhydrocoronene.

Journal Article Journal of the American Chemical Society · October 2012 The stacking interaction between π systems is a well-recognized structural motif, but stacking between σ systems was long considered of secondary importance. A recent paper points out that σ stacking can reach the energy of chemical bonds and concludes tha ... Full text Cite

Ultrafast Quantum Mechanics/Molecular Mechanics Monte Carlo simulations using generalized multipole polarizabilities

Journal Article Chemical Physics Letters · March 19, 2012 A fast and accurate Quantum Mechanics/Molecular Mechanics method is described for thermodynamic simulation of solutes (or active sites in flexible molecules) in polar environments. The solute is described quantum mechanically and is held fixed during avera ... Full text Cite

Recent developments in the PQS program

Journal Article Wiley Interdisciplinary Reviews: Computational Molecular Science · January 1, 2012 An overview of the PQS quantum chemistry suite is presented, with emphasis on recent developments and features that are unique to the program. The capabilities of the program, in particular the parallel implementation, are briefly described. Topics discuss ... Full text Cite

A benchmark quantum chemical study of the stacking interaction between larger polycondensed aromatic hydrocarbons

Journal Article Theoretical Chemistry Accounts · October 1, 2011 Large-scale electronic structure calculations were performed for the interaction energy between coronene, C24H12 with circumcoronene, C54H18, and between two circumcoronene molecules, in order to get a picture of the interaction between larger graphene she ... Full text Cite

Convex-concave stacking of curved conjugated networks: Benchmark calculations on the corannulene dimer

Journal Article Chemical Physics Letters · August 25, 2011 High level ab initio calculations on the eclipsed concave-convex corannulene dimer yielded a binding energy of 15.5 kcal/mol with a monomer-monomer distance of 3.69 at the (extrapolated) counterpoise corrected QCISD(T)/aug-cc-pVTZ level. Single point calcu ... Full text Cite

The ethidium-UA/AU intercalation site: Effect of model fragmentation and backbone charge state

Journal Article Journal of Chemical Theory and Computation · August 9, 2011 We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned in ... Full text Cite

Development of a 3-body:many-body integrated fragmentation method for weakly bound clusters and application to water clusters (H2O)(n = 3-10, 16, 17).

Journal Article The Journal of chemical physics · July 2011 A 3-body:many-body integrated quantum mechanical (QM) fragmentation method for non-covalent clusters is introduced within the ONIOM formalism. The technique captures all 1-, 2-, and 3-body interactions with a high-level electronic structure method, while a ... Full text Cite

A one-foetus pregnancy monitored by ultrasonography and progesterone blood levels in a German Shepherd bitch: A case report

Journal Article Veterinarni Medicina · January 1, 2011 This case study describes the pregnancy of a German Shepherd bitch with a singleton (one puppy) litter as a result of early embryo resorption. Resorption was confirmed by ultrasonography and the pregnancy was regularly monitored by USG and measurements of ... Full text Cite

Accurate correlated calculation of the intermolecular potential surface in the coronene dimer

Journal Article Molecular Physics · April 26, 2010 The binding energy of the coronene dimer was determined by high level ab initio calculations. In the first step a potential energy surface was determined for the stacked dimer at the SCS-MP2/aTZ level. The energy of the stacked parallel dimer was scanned w ... Full text Cite

Convergence of the CCSD(T) correction term for the stacked complex methyl adenine-methyl thymine: Comparison with lower-cost alternatives

Journal Article Journal of Chemical Theory and Computation · July 14, 2009 We have performed large-scale calculations for the interaction energy of the stacked methyl adenine-methyl thymine complex at the CCSD(T)/aug-ccpVXZ (X ) D,T) levels. The results can serve as benchmarks for the evaluation of two methods, MP2.5, introduced ... Full text Cite

Efficient calculation of the energy of a molecule in an arbitrary electric field

Journal Article International Journal of Quantum Chemistry · July 9, 2009 In thermodynamic (e.g., Monte Carlo) simulations with electronic embedding, the energy of the active site or solute must be calculated for millions of configurations of the environment (solvent or protein matrix) to obtain reliable statistics. This preclud ... Full text Cite

Quantum chemistry in parallel with PQS

Journal Article Journal of Computational Chemistry · January 30, 2009 This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pu ... Full text Cite

Efficient parallel implementation of the CCSD external exchange operator and the perturbative triples (T) Energy calculation

Journal Article Journal of Chemical Theory and Computation · October 14, 2008 A new, efficient parallel algorithm is presented for the most expensive step in coupled cluster singles and doubles (CCSD) energy calculations, the external exchange operator (EEO). The new implementation requires much less input/output than our previous a ... Full text Cite

High accuracy benchmark calculations on the benzene dimer potential energy surface

Journal Article Chemical Physics Letters · October 15, 2007 Using our new parallel CCSD(T)/QCISD(T) program, we have optimized the geometries of the main conformations and performed potential scans on the benzene dimer at the QCISD(T)/aug-cc-pVTZ level. For each optimized geometry, single point energies were evalua ... Full text Cite

Parallel calculation of coupled cluster singles and doubles wave functions using array files

Journal Article Journal of Chemical Theory and Computation · July 1, 2007 A new parallel implementation of the Coupled Cluster Singles and Doubles (CCSD) and related wave functions (e.g Quadratic Configuration Interaction, QCI, and Coupled Electron Pair, CEPA) is described, based on the Array Files middleware. The program can ha ... Full text Cite

Array files for computational chemistry: MP2 energies

Journal Article Journal of Computational Chemistry · May 1, 2007 A simple message-passing implementation for distributed disk storage, called array files (AF), is described. It is designed primarily for parallelizing computational chemistry applications but it should be useful for any application that handles large amou ... Full text Cite

Quantum cluster equilibrium theory treatment of hydrogen-bonded liquids: Water, methanol and ethanol

Journal Article Molecular Physics · January 1, 2003 The quantum cluster equilibrium (QCE) theory was used in order to predict the composition of the hydrogen bonded liquids: water, methanol and ethanol. The calculations were based on high accuracy theoretical data obtained at the DFT/B3LYP/6-311 G(d, p) lev ... Full text Cite

Ab initio calculations of the NMR properties of the NH3 ⋯ H2O complex

Journal Article International Journal of Quantum Chemistry · November 5, 2002 The shielding constants, nuclear quadmpole coupling constants, and spin-spin coupling constants are computed for the ammonia-water complex. Four structures of the complex are considered. A series of multiconfiguration self-consistent field (MCSCF) wavefunc ... Full text Cite

Relationship between magnetic shielding and magnetizability

Journal Article Journal of Chemical Physics · August 1, 2002 A relation between IMS and magnetizability based on a simple physical interpretation was proposed. As such, the relationship was examined and clarified by numerical calculations. Moreover, the analytical derivation of the relation between magnetic shieldin ... Full text Cite