Scholars@Duke
Julio Cesar Facelli

Julio Cesar Facelli

Adjunct Professor in the Department of Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Translational Biomedical

Selected Publications

Air pollution mixtures and stillbirth: k-means cluster analysis

Journal Article Hygiene and Environmental Health Advances · December 1, 2025 Background: Preventing stillbirths starts with identifying modifiable risk factors, such as air pollution (AP). Most research has focused on individual components of AP (e.g. PM2.5) to assess the linear relationship between air pollutant concent ... Full text Cite

Documentation of social determinants of health for patients with type 2 diabetes in Epic Cosmos

Journal Article JAMIA Open · October 1, 2025 Objectives Type 2 diabetes (T2D) is a growing public health burden with persistent racial and ethnic disparities.. This study assessed the completeness of social determinants of health (SdoH) data for patients with T2D in Epic Cosmos, a nationwide, cross-i ... Full text Cite

Conceptual framework for prediction models of patient deterioration based on nursing documentation patterns: reproducibility and generalizability with a large number of hospitals across the United States.

Journal Article J Biomed Inform · September 2025 OBJECTIVE: The Health Process Model (HPM)-ExpertSignals Conceptual Framework posits that healthcare professionals' patient care behaviors can be used to predict in-hospital deterioration. Prediction models based on this framework have been validated using ... Full text Link to item Cite

Molecular Mimicry Impact of the COVID-19 Pandemic: Sequence Homology Between SARS-CoV-2 and Autoimmune Diseases Epitopes.

Journal Article Immunoinformatics (Amst) · June 2025 Molecular mimicry is one mechanism by which an infectious agent may trigger an autoimmune disease in a human subject and occurs when foreign- and self-peptides contain similar epitopes that activate an autoimmune response in a susceptible individual. Here, ... Full text Link to item Cite

Identifying Molecular Properties of Ataxin-2 Inhibitors for Spinocerebellar Ataxia Type 2 Utilizing High-Throughput Screening and Machine Learning.

Journal Article Biology (Basel) · May 8, 2025 Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder marked by cerebellar dysfunction, ataxic gait, and progressive motor impairments. SCA2 is caused by the pathologic expansion of CAG repeats in the ataxin-2 (ATXN2) gen ... Full text Link to item Cite

Predicting the onset of Alzheimer's disease and related dementia using electronic health records: findings from the cache county study on memory in aging (1995-2008).

Journal Article BMC Med Inform Decis Mak · October 28, 2024 INTRODUCTION: Clinical notes, biomarkers, and neuroimaging have proven valuable in dementia prediction models. Whether commonly available structured clinical data can predict dementia is an emerging area of research. We aimed to predict gold-standard, rese ... Full text Link to item Cite

An open science grid implementation of the steady state genetic algorithm for crystal structure prediction

Journal Article Journal of Computational Science · October 1, 2024 In this paper we report the implementation and testing of algorithmic changes that have been implemented in MGAC, a crystal structure prediction system, to make it scalable and amenable to take advantage of such significant distributed resources as the Ope ... Full text Cite

Recommendations to promote fairness and inclusion in biomedical AI research and clinical use.

Journal Article J Biomed Inform · September 2024 OBJECTIVE: Understanding and quantifying biases when designing and implementing actionable approaches to increase fairness and inclusion is critical for artificial intelligence (AI) in biomedical applications. METHODS: In this Special Communication, we dis ... Full text Link to item Cite

Predicting the onset of Alzheimer's disease and related dementia using Electronic Health Records: Findings from the Cache County Study on Memory in Aging (1995-2008).

Journal Article Res Sq · June 7, 2024 INTRODUCTION: Clinical notes, biomarkers, and neuroimaging have been proven valuable in dementia prediction models. Whether commonly available structured clinical data can predict dementia is an emerging area of research. We aimed to predict Alzheimer's di ... Full text Link to item Cite

A Scalable and Extensible Logical Data Model of Electronic Health Record Audit Logs for Temporal Data Mining (RNteract): Model Conceptualization and Formulation.

Journal Article JMIR nursing · June 2024 BackgroundIncreased workload, including workload related to electronic health record (EHR) documentation, is reported as a main contributor to nurse burnout and adversely affects patient safety and nurse satisfaction. Traditional methods for workl ... Full text Cite

Uncertainty in Breast Cancer Risk Prediction: A Conformal Prediction Study of Race Stratification.

Chapter · January 25, 2024 The use of Artificial Intelligence (AI) in medicine has attracted a great deal of attention in the medical literature, but less is known about how to assess the uncertainty of individual predictions in clinical applications. This paper demonstrates the use ... Full text Link to item Cite

Developing 60-Day Readmission Risk Score among Home Healthcare Patients with Heart Failure.

Journal Article Home Healthc Now · January 2024 Heart failure (HF) readmissions are common, costly, and often preventable. Despite the implementation of HF programs across clinical settings, rehospitalization is still common. Efforts to identify risk factors for 60-day rehospitalization among HF patient ... Full text Link to item Cite

A Rare Variant in <i>MDH2</i> (rs111879470) Is Associated with Predisposition to Recurrent Breast Cancer in an Extended High-Risk Pedigree.

Journal Article Cancers · December 2023 A significant fraction of breast cancer recurs, with lethal outcome, but specific genetic variants responsible have yet to be identified. Five cousin pairs with recurrent breast cancer from pedigrees with a statistical excess of recurrent breast cancer wer ... Full text Cite

Molecular dynamics study of the mechanical properties of drug loaded model systems: A comparison of a polymersome with a bilayer.

Journal Article J Chem Phys · November 7, 2023 In this work we implement a new methodology to study structural and mechanical properties of systems having spherical and planar symmetries throughout Molecular Dynamics simulations. This methodology is applied here to a drug delivery system based in polym ... Full text Link to item Cite

Prioritization of infectious epitopes for translational investigation in type 1 diabetes etiology.

Journal Article J Autoimmun · November 2023 Molecular mimicry is one mechanism by which infectious agents are thought to trigger islet autoimmunity in type 1 diabetes. With a growing number of reported infectious agents and islet antigens, strategies to prioritize the study of infectious agents are ... Full text Link to item Cite

A rare FGF5 candidate variant (rs112475347) for predisposition to nonsquamous, nonsmall-cell lung cancer.

Journal Article Int J Cancer · July 15, 2023 A unique approach with rare resources was used to identify candidate variants predisposing to familial nonsquamous nonsmall-cell lung cancers (NSNSCLC). We analyzed sequence data from NSNSCLC-affected cousin pairs belonging to high-risk lung cancer pedigre ... Full text Link to item Cite

A likely HOXC4 predisposition variant for Chiari malformations.

Journal Article J Neurosurg · July 1, 2023 OBJECTIVE: Inherited variants predisposing patients to type 1 or 1.5 Chiari malformation (CM) have been hypothesized but have proven difficult to confirm. The authors used a unique high-risk pedigree population resource and approach to identify rare candid ... Full text Link to item Cite

Sequential data mining of infection patterns as predictors for onset of type 1 diabetes in genetically at-risk individuals.

Journal Article J Biomed Inform · June 2023 Infections are implicated in the etiology of type 1 diabetes mellitus (T1DM); however, conflicting epidemiologic evidence makes designing effective strategies for presymptomatic screening and disease prevention difficult. Considering the temporality and co ... Full text Link to item Cite

The IHI Rochester Report 2022 on Healthcare Informatics Research: Resuming After the CoViD-19

Journal Article Journal of Healthcare Informatics Research · June 1, 2023 In 2020, the CoViD-19 pandemic spread worldwide in an unexpected way and suddenly modified many life issues, including social habits, social relationships, teaching modalities, and more. Such changes were also observable in many different healthcare and me ... Full text Cite

Stratifying risk for onset of type 1 diabetes using islet autoantibody trajectory clustering.

Journal Article Diabetologia · March 2023 AIMS/HYPOTHESIS: Islet autoantibodies can be detected prior to the onset of type 1 diabetes and are important tools for aetiologic studies, prevention trials and disease screening. Current risk stratification models rely on the positivity status of islet a ... Full text Link to item Cite

High-Risk Pedigree Study Identifies LRBA (rs62346982) as a Likely Predisposition Variant for Prostate Cancer.

Journal Article Cancers · March 2023 There is evidence for contribution of inherited factors to prostate cancer, and more specifically to lethal prostate cancer, but few responsible genes/variants have been identified. We examined genetic sequence data for 51 affected cousin pairs who each di ... Full text Cite

Healthcare Provider Reports on Social Determinants of Health in Opioid Treatment

Journal Article Psych · January 30, 2023 Opioid overdose and death from overdose continue to present a pressing problem in the United States. It is well-established that a range of social and economic factors, often referred to as social determinants of health (SDOH), are associated with ... Full text Cite

Hypertensive disorders of pregnancy and subsequent risk of Alzheimer's disease and other dementias.

Journal Article Alzheimers Dement (Amst) · 2023 INTRODUCTION: Women with hypertensive disorders of pregnancy (HDP) have an increased risk of cardiovascular disease. Whether HDP is also associated with later-life dementia has not been fully explored. METHODS: Using the Utah Population Database, we perfor ... Full text Link to item Cite

Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design.

Journal Article PLoS One · 2023 IMPORTANCE: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or other health effects after the acute phase of infection; termed post-acute sequelae of SARS-CoV-2 infection (PASC), or long COVID. The characteristics, prevalence, trajec ... Full text Link to item Cite

Detecting hypoglycemia-induced electrocardiogram changes in a rodent model of type 1 diabetes using shape-based clustering.

Journal Article PLoS One · 2023 Sudden death related to hypoglycemia is thought to be due to cardiac arrhythmias. A clearer understanding of the cardiac changes associated with hypoglycemia is needed to reduce mortality. The objective of this work was to identify distinct patterns of ele ... Full text Link to item Cite

Structural Homology of Epitope Binding Mimicry in the Onset of Type 1 Diabetes Mellitus

Conference Proceedings 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2023 · January 1, 2023 Molecular mimicry, where foreign and self-peptides contain similar epitopes, can induce autoimmune responses. Identifying potential molecular mimics and studying their properties is key to understanding the onset of autoimmune diseases such as type 1 diabe ... Full text Cite

Environmental exposures in machine learning and data mining approaches to diabetes etiology: A scoping review.

Journal Article Artif Intell Med · January 2023 BACKGROUND: Environmental exposures are implicated in diabetes etiology, but are poorly understood due to disease heterogeneity, complexity of exposures, and analytical challenges. Machine learning and data mining are artificial intelligence methods that c ... Full text Link to item Cite

Resuming HealthCare Informatics Research after CoViD-19: the HealthCare System Perspective

Conference Proceedings 2023 IEEE 11th International Conference on Healthcare Informatics Ichi 2023 · January 1, 2023 The CoViD-19 pandemic tested many research endeavors and revealed limitations, especially where research results had an immediate impact on the social and health habits of people. The research community is called to perform a deep analysis of steps already ... Full text Cite

Computer clinical decision support that automates personalized clinical care: a challenging but needed healthcare delivery strategy.

Journal Article J Am Med Inform Assoc · December 13, 2022 How to deliver best care in various clinical settings remains a vexing problem. All pertinent healthcare-related questions have not, cannot, and will not be addressable with costly time- and resource-consuming controlled clinical trials. At present, eviden ... Full text Link to item Cite

Conformal Prediction in Clinical Medical Sciences.

Journal Article Journal of healthcare informatics research · September 2022 The use of machine learning (ML) and artificial intelligence (AI) applications in medicine has attracted a great deal of attention in the medical literature, but little is known about how to use Conformal Predictions (CP) to assess the accuracy of individu ... Full text Cite

K-means cluster analysis of cooperative effects of CO, NO2, O3, PM2.5, PM10, and SO2 on incidence of type 2 diabetes mellitus in the US.

Journal Article Environ Res · September 2022 Air pollution (AP) has been shown to increase the risk of type 2 diabetes mellitus, as well as other cardiometabolic diseases. AP is characterized by a complex mixture of components for which the composition depends on sources and metrological factors. The ... Full text Link to item Cite

Structure analysis of the proteins associated with polyA repeat expansion disorders.

Journal Article J Biomol Struct Dyn · August 2022 Repeat regions are low-complexity regions in the human genome that largely code for intrinsic disorder in proteins. Expansions outside the normal thresholds in repeat regions are likely to be pathogenic, leading to the so-called repeat expansion diseases. ... Full text Link to item Cite

Microproteins: a 3D protein structure prediction analysis.

Journal Article J Biomol Struct Dyn · 2022 Microproteins are a novel and expanding group of small proteins encoded by less than 100-150 codons that are translated from small open reading frames (smORFs). It has been shown that smORFs and their corresponding microproteins make up a sizable fraction ... Full text Link to item Cite

Utilizing a Blockchain for Managing Sensor Metadata in Exposure Health Studies

Conference 2022 Intermountain Engineering Technology and Computing Ietc 2022 · January 1, 2022 Commercial Internet of Things (IoT) sensors enable continuous data collection that benefits exposomic studies. The Exposure Health Informatics Ecosystem (EHIE) is one such sensor-based informatics platform for performing multiple simultaneous exposomic stu ... Full text Cite

Data-driven identification of temporal glucose patterns in a large cohort of nondiabetic patients with COVID-19 using time-series clustering

Journal Article JAMIA Open · July 1, 2021 Objective: Hyperglycemia has emerged as an important clinical manifestation of coronavirus disease 2019 (COVID-19) in diabetic and nondiabetic patients. Whether these glycemic changes are specific to a subgroup of patients and persist following COVID-19 re ... Full text Cite

Erratum: Data-driven identification of temporal glucose patterns in a large cohort of nondiabetic patients with COVID-19 using time-series clustering (JAMIA Open 4:3 DOI: 10.1093/jamiaopen/ooab063)

Journal Article JAMIA Open · July 1, 2021 When this paper originally published online, Julio Facelli s name appeared twice in the author list. This has been corrected online, and the name now only appears once. ... Full text Cite

Enabling a learning healthcare system with automated computer protocols that produce replicable and personalized clinician actions.

Journal Article J Am Med Inform Assoc · June 12, 2021 Clinical decision-making is based on knowledge, expertise, and authority, with clinicians approving almost every intervention-the starting point for delivery of "All the right care, but only the right care," an unachieved healthcare quality improvement goa ... Full text Link to item Cite

An intronic variant in the CELF4 gene is associated with risk for colorectal cancer.

Journal Article Cancer Epidemiol · June 2021 BACKGROUND: Germline predisposition variants associated with colorectal cancer (CRC) have been identified but all are not yet identified. We sought to identify the responsible predisposition germline variant in an extended high-risk CRC pedigree that exhib ... Full text Link to item Cite

A Rare Variant in ERF (rs144812092) Predisposes to Prostate and Bladder Cancers in an Extended Pedigree.

Journal Article Cancers · May 2021 Pairs of related bladder cancer cases who belong to pedigrees with an excess of bladder cancer were sequenced to identify rare, shared variants as candidate predisposition variants. Candidate variants were tested for association with bladder cancer risk. A ... Full text Cite

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

Journal Article J Am Med Inform Assoc · March 1, 2021 OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine lear ... Full text Link to item Cite

A role for the MEGF6 gene in predisposition to osteoporosis.

Journal Article Ann Hum Genet · March 2021 Osteoporosis is a common skeletal disorder characterized by deterioration of bone tissue. The set of genetic factors contributing to osteoporosis is not completely specified. High-risk osteoporosis pedigrees were analyzed to identify genes that may confer ... Full text Link to item Cite

Human activity pattern implications for modeling SARS-CoV-2 transmission.

Journal Article Comput Methods Programs Biomed · February 2021 BACKGROUND AND OBJECTIVES: SARS-CoV-2 emerged in December 2019 and rapidly spread into a global pandemic. Designing optimal community responses (social distancing, vaccination) is dependent on the stage of the disease progression, discovery of asymptomatic ... Full text Link to item Cite

Understanding protein structural changes for oncogenic missense variants.

Journal Article Heliyon · January 2021 Understanding and predicting the changes of protein structure and function upon mutation and their relationship to human health is a critical element to translate the genomic revolution into actionable interventions. Therefore, it is pertinent to explore h ... Full text Cite

Using supervised machine learning classifiers to estimate likelihood of participating in clinical trials of a de-identified version of ResearchMatch

Journal Article Journal of Clinical and Translational Science · January 1, 2021 Introduction: Lack of participation in clinical trials (CTs) is a major barrier for the evaluation of new pharmaceuticals and devices. Here we report the results of the analysis of a dataset from ResearchMatch, an online clinical registry, using supervised ... Full text Cite

Preface

Journal Article Proceedings 2020 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2020 · December 16, 2020 Full text Cite

Characterization of Analytic and Experimental Uncertainty of RNA-seq Co-expression Network Determination: Application to SCA2

Conference 2020 IEEE International Conference on Healthcare Informatics Ichi 2020 · November 1, 2020 Bioinformatics sequencing pipelines produce results that contain a degree of uncertainty which stem from a variety of sources. For example, uncertainty can arise from sampling bias during sample preparation, sequencing platform bias, alignment errors and/o ... Full text Cite

Associations Between the Time in Hypoglycemia and Hypoglycemia Awareness Status in Type 1 Diabetes Patients Using Continuous Glucose Monitoring Systems.

Journal Article Diabetes Technol Ther · November 2020 Background: Continuous glucose monitoring (CGM) systems help reduce hypoglycemia in patients with type 1 diabetes (T1D). It remains unclear whether T1D patients with impaired awareness of hypoglycemia (IAH) continue to develop more hypoglycemia than those ... Full text Link to item Cite

Predicting Optimal Hypertension Treatment Pathways Using Recurrent Neural Networks.

Journal Article Int J Med Inform · July 2020 BACKGROUND: In ambulatory care settings, physicians largely rely on clinical guidelines and guideline-based clinical decision support (CDS) systems to make decisions on hypertension treatment. However, current clinical evidence, which is the knowledge base ... Full text Link to item Cite

STHAM: an agent based model for simulating human exposure across high resolution spatiotemporal domains.

Journal Article J Expo Sci Environ Epidemiol · May 2020 Human exposure to particulate matter and other environmental species is difficult to estimate in large populations. Individuals can encounter significant and acute variations in exposure over small spatiotemporal scales. Exposure is strongly tied to both t ... Full text Link to item Cite

Temporal Pattern Detection to Predict Adverse Events in Critical Care: Case Study With Acute Kidney Injury.

Journal Article JMIR medical informatics · March 2020 BackgroundMore than 20% of patients admitted to the intensive care unit (ICU) develop an adverse event (AE). No previous study has leveraged patients' data to extract the temporal features using their structural temporal patterns, that is, trends. ... Full text Cite

Alarm Settings of Continuous Glucose Monitoring Systems and Associations to Glucose Outcomes in Type 1 Diabetes.

Journal Article J Endocr Soc · January 1, 2020 CONTEXT: Little evidence exists regarding the positive and negative impacts of continuous glucose monitor system (CGM) alarm settings for diabetes control in patients with type 1 diabetes (T1D). OBJECTIVE: Evaluate the associations between CGM alarm settin ... Full text Link to item Cite

Exposure Health Informatics Ecosystem

Chapter · January 1, 2020 There is a need for understanding an individual’s total exposure, including simultaneous, cumulative, and latent exposure to multiple environmental contaminants. While exact contributions differ, multiple studies suggest that the majority of a person’s hea ... Full text Cite

The Effects of Calcium on Lipid-Protein Interactions and Ion Flux in the Cx26 Connexon Embedded into a POPC Bilayer.

Journal Article J Membr Biol · October 2019 Gap junctions provide a communication pathway between adjacent cells. They are formed by paired connexons that reside in the plasma membrane of their respective cell and their activity can be modulated by the bilayer composition. In this work, we study the ... Full text Link to item Cite

A novel CDKN2A variant (p16L117P ) in a patient with familial and multiple primary melanomas.

Journal Article Pigment Cell Melanoma Res · September 2019 Germline mutations in CDKN2A (p16) are commonly found in patients with family history of melanoma or personal history of multiple primary melanomas. The p16 tumor suppressor gene regulates cell cycle progression and senescence through binding of cyclin-dep ... Full text Link to item Cite

Study of the lamellar and micellar phases of pluronic F127: A molecular dynamics approach

Journal Article Processes · September 1, 2019 In this work, we analyzed the behavior of Pluronic F127 through molecular dynamics simulations at the coarse-grain level, focusing on the micellar and lamellar phases. To this aim, two initial polymer conformations were considered, S-shape and U-shape, for ... Full text Cite

Towards a content agnostic computable knowledge repository for data quality assessment.

Journal Article Comput Methods Programs Biomed · August 2019 BACKGROUND AND OBJECTIVE: In recent years, several data quality conceptual frameworks have been proposed across the Data Quality and Information Quality domains towards assessment of quality of data. These frameworks are diverse, varying from simple lists ... Full text Link to item Cite

Magnesium interactions with a CX26 connexon in lipid bilayers.

Journal Article J Mol Model · July 20, 2019 Following our previous work, where we described the interaction of calcium with the Cx26 hemichannel, we further explore the same system by atomistic molecular dynamics simulations considering a different di-cation, magnesium. Specifically, the interaction ... Full text Link to item Cite

An Architecture for metadata-driven integration of heterogeneous sensor and health data for translational exposomic research

Conference 2019 IEEE EMBS International Conference on Biomedical and Health Informatics Bhi 2019 Proceedings · May 1, 2019 Exposomic research requires the generation of comprehensive spatio-temporal records of exposures along with capturing associated metadata describing limitations and uncertainties associated with the data. We describe the architecture of a metadata-driven B ... Full text Cite

An Architecture to Support Real-World Studies that Investigate the Autonomic Nervous System

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2019 Diabetes is a chronic disease with complications related to the autonomic nervous system (ANS) that can affect quality of life and lead to mortality. Clinicians and researchers currently rely on subjective and/or invasive means that don’t necessarily trans ... Full text Cite

Concept Bag: A New Method for Computing Concept Similarity in Biomedical Data

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2019 Biomedical data are a rich source of information and knowledge, not only for direct patient care, but also for secondary use in population health, clinical research, and translational research. Biomedical data are typically scattered across multiple system ... Full text Cite

Calcium interactions with Cx26 hemmichannel: Spatial association between MD simulations biding sites and variant pathogenicity.

Journal Article Comput Biol Chem · December 2018 Connexinophaties are a collective of diseases related to connexin channels and hemichannels. In particular many Cx26 alterations are strongly associated to human deafness. Calcium plays an important role on this structures regulation. Here, using calcium a ... Full text Link to item Cite

A Nonsynonymous Variant in the GOLM1 Gene in Cutaneous Malignant Melanoma.

Journal Article J Natl Cancer Inst · December 1, 2018 BACKGROUND: Statistically significant linkage of melanoma to chromosome 9q21 was previously reported in a Danish pedigree resource and independently confirmed in Utah high-risk pedigrees, indicating strong evidence that this region contains a melanoma pred ... Full text Link to item Cite

Comprehensive methodology to monitor longitudinal change patterns during EHR implementations: a case study at a large health care delivery network.

Journal Article Journal of biomedical informatics · July 2018 ObjectiveTo test a systematic methodology to monitor longitudinal change patterns on quality, productivity, and safety outcomes during a large-scale commercial Electronic Health Record (EHR) implementation.Materials and methodsOur method ... Full text Cite

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study.

Journal Article J Chem Phys · June 7, 2018 In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have s ... Full text Link to item Cite

Welcome Message from the General Co-Chairs

Journal Article Proceedings 2017 IEEE International Conference on Healthcare Informatics Ichi 2017 · September 8, 2017 Full text Cite

Development and classification of a robust inventory of near real-time outcome measurements for assessing information technology interventions in health care.

Journal Article Journal of biomedical informatics · September 2017 ObjectiveTo develop and classify an inventory of near real-time outcome measures for assessing information technology (IT) interventions in health care and assess their relevance as perceived by experts in the field.Materials and methodsT ... Full text Cite

Gene co-expression network analysis for identifying modules and functionally enriched pathways in SCA2.

Journal Article Hum Mol Genet · August 15, 2017 Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the ATXN2 gene. The repeat resides in an encoded region of the gene resulting in polyglutamine (polyQ) expansion which has been assume ... Full text Link to item Cite

Diblock copolymer bilayers as model for polymersomes: A coarse grain approach.

Journal Article J Chem Phys · June 28, 2017 This paper presents a new model for polymersomes developed using a poly(ethylene oxide)-poly(butadiene) diblock copolymer bilayer. The model is based on a coarse-grained approach using the MARTINI force field. Since no MARTINI parameters exist for poly(but ... Full text Link to item Cite

Solving Interoperability in Translational Health. Perspectives of Students from the International Partnership in Health Informatics Education (IPHIE) 2016 Master Class.

Journal Article Appl Clin Inform · June 20, 2017 BACKGROUND: In the summer of 2016 an international group of biomedical and health informatics faculty and graduate students gathered for the 16th meeting of the International Partnership in Health Informatics Education (IPHIE) masterclass at the University ... Full text Link to item Cite

Effects of the enlargement of polyglutamine segments on the structure and folding of ataxin-2 and ataxin-3 proteins.

Journal Article J Biomol Struct Dyn · February 2017 Spinocerebellar ataxia type 2 (SCA2) and type 3 (SCA3) are two common autosomal-dominant inherited ataxia syndromes, both of which are related to the unstable expansion of trinucleotide CAG repeats in the coding region of the related ATXN2 and ATXN3 genes, ... Full text Link to item Cite

Metadata discovery of heterogeneous biomedical datasets using token-based features

Conference Lecture Notes in Electrical Engineering · January 1, 2017 Metadata discovery is the process of recognizing semantics and descriptors of data elements and datasets. This study uses a machine-learning approach to classify biomedical dataset characteristics for metadata discovery. Four common types of biomedical dat ... Full text Cite

Molecular dynamics analysis of the aggregation propensity of polyglutamine segments.

Journal Article PLoS One · 2017 Protein misfolding and aggregation is a pathogenic feature shared among at least ten polyglutamine (polyQ) neurodegenerative diseases. While solvent-solution interaction is a key factor driving protein folding and aggregation, the solvation properties of e ... Full text Link to item Cite

Patient reported outcomes - experiences with implementation in a University Health Care setting.

Journal Article J Patient Rep Outcomes · 2017 AIM: Patient-reported outcomes (PROs) have traditionally been implemented through a manual process of paper and pencil with little standardization throughout a Healthcare System. Each practice has asked patients specific questions to understand the patient ... Full text Link to item Cite

Health information technology adoption: Understanding research protocols and outcome measurements for IT interventions in health care.

Journal Article Journal of biomedical informatics · October 2016 ObjectiveTo classify and characterize the variables commonly used to measure the impact of Information Technology (IT) adoption in health care, as well as settings and IT interventions tested, and to guide future research.Materials and methods ... Full text Cite

Report on the sixth blind test of organic crystal structure prediction methods.

Journal Article Acta crystallographica Section B, Structural science, crystal engineering and materials · August 2016 The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. Thi ... Full text Cite

A review of the applications of data mining and machine learning for the prediction of biomedical properties of nanoparticles.

Journal Article Comput Methods Programs Biomed · August 2016 This article presents a comprehensive review of applications of data mining and machine learning for the prediction of biomedical properties of nanoparticles of medical interest. The papers reviewed here present the results of research using these techniqu ... Full text Link to item Cite

Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine.

Journal Article Chem Phys Lett · April 17, 2015 Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Esp ... Full text Link to item Cite

Predicting cytotoxicity of PAMAM dendrimers using molecular descriptors.

Journal Article Beilstein J Nanotechnol · 2015 The use of data mining techniques in the field of nanomedicine has been very limited. In this paper we demonstrate that data mining techniques can be used for the development of predictive models of the cytotoxicity of poly(amido amine) (PAMAM) dendrimers ... Full text Link to item Cite

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

Journal Article SAR QSAR Environ Res · 2015 Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that ar ... Full text Link to item Cite

A domain analysis model for eIRB systems: addressing the weak link in clinical research informatics.

Journal Article J Biomed Inform · December 2014 Institutional Review Boards (IRBs) are a critical component of clinical research and can become a significant bottleneck due to the dramatic increase, in both volume and complexity of clinical research. Despite the interest in developing clinical research ... Full text Link to item Cite

iBIOMES Lite: summarizing biomolecular simulation data in limited settings.

Journal Article J Chem Inf Model · June 23, 2014 As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweigh ... Full text Link to item Cite

VIRGO: Virtual identity resolution on the go

Conference Proceedings 2014 IEEE International Conference on Healthcare Informatics Ichi 2014 · March 2, 2014 We present here the design, development and testing of an open-source software system supporting on-the-fly identity resolution, VIRGO: Virtual Identity Resolution on the Go. The system implements the open source Choice Maker algorithms and it was develope ... Full text Cite

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing.

Journal Article J Cheminform · January 30, 2014 BACKGROUND: Few environments have been developed or deployed to widely share biomolecular simulation data or to enable collaborative networks to facilitate data exploration and reuse. As the amount and complexity of data generated by these simulations is d ... Full text Link to item Cite

Welcome message from the general chair

Conference Proceedings of the 8th ACM/IEEE International Conference on Distributed Smart Cameras, ICDSC 2014 · January 1, 2014 Cite

Development of a HIPAA-compliant environment for translational research data and analytics.

Journal Article J Am Med Inform Assoc · 2014 High-performance computing centers (HPC) traditionally have far less restrictive privacy management policies than those encountered in healthcare. We show how an HPC can be re-engineered to accommodate clinical data while retaining its utility in computati ... Full text Link to item Cite

The origin of the splitting of 13C and 15N NMR signals of 3(5)-phenyl-5(3)-methylpyrazolium chloride and bromide in the solid state: Quantum Espresso calculations

Journal Article Journal of Molecular Structure · January 1, 2014 A combination of 13C and 15N CPMAS NMR spectroscopy and theoretical methods (DFT and DFT-D) was used to discuss the observation of large splittings affecting some atoms in 3(5)-phenyl-5(3)-methylpyrazolium chloride and bromide. Conven ... Full text Cite

Structure prediction of polyglutamine disease proteins: comparison of methods.

Journal Article BMC Bioinformatics · 2014 BACKGROUND: The expansion of polyglutamine (poly-Q) repeats in several unrelated proteins is associated with at least ten neurodegenerative diseases. The length of the poly-Q regions plays an important role in the progression of the diseases. The number of ... Full text Link to item Cite

Automatic extraction of nanoparticle properties using natural language processing: NanoSifter an application to acquire PAMAM dendrimer properties.

Journal Article PLoS One · 2014 In this study, we demonstrate the use of natural language processing methods to extract, from nanomedicine literature, numeric values of biomedical property terms of poly(amidoamine) dendrimers. We have developed a method for extracting these values for pr ... Full text Link to item Cite

Implementing public health analytical services: Grid enabling of MetaMap

Conference Proceedings of CBMS 2013 26th IEEE International Symposium on Computer Based Medical Systems · December 9, 2013 Public health data could be used to assist with public health surveillance and decision support. However, in most cases data has to be transformed into a coded format to make it computable and amiable to quasi real time analytical processing. Natural langu ... Full text Cite

A service oriented framework to assess the quality of electronic health data for clinical research

Conference Proceedings 2013 IEEE International Conference on Healthcare Informatics Ichi 2013 · December 1, 2013 Retrospective/observational clinical research studies are dependent on the secondary use of electronic health record (EHR) data for obtaining important results about the effectiveness of different medical interventions. In contrast to traditional clinical ... Full text Cite

Structure and electronic properties of lithium-silicon clusters

Journal Article Computational and Theoretical Chemistry · November 15, 2013 This paper reports results of global searches of the most stable structures of silicon-lithium clusters for the series Si. nLi ( n= 2-12) using parallel Genetic Algorithms (GA). For this study we have used our MGAC software directly coupled with ... Full text Cite

From NMR spectra to structure

Journal Article Concepts in Magnetic Resonance Part A Bridging Education and Research · November 1, 2013 This article discusses the existing methods to correlate NMR parameters describing the high resolution NMR spectra of liquids and solid systems with their structural parameters. Those methods are divided into direct and indirect ones. This article includes ... Full text Cite

COMPARATIVE PHARMACOKINETICS OF PAMAM-OH DENDRIMERS AND HPMA COPOLYMERS IN OVARIAN-TUMOR-BEARING MICE.

Journal Article Drug delivery and translational research · June 2013 The purpose of this study was to model data from a head to head comparison of the in vivo fate of hyper-branched PAMAM dendrimers with linear HPMA copolymers in order to understand the influence of molecular weight (MW), hydrodynamic size (Rh) and p ... Full text Cite

Optimization of crystal structures of archetypical pharmaceutical compounds: A plane-wave DFT-D study using Quantum Espresso

Journal Article Crystal Growth and Design · May 1, 2013 Previously, it was shown that crystal structure prediction based on genetic algorithms (MGAC program) coupled with force field methods could consistently find experimental structures of crystals. However, inaccuracies in the force field potentials often re ... Full text Cite

Medical informatics and bioinformatics

Chapter · March 31, 2013 In the last 50 years, computational applications have been developed to aid clinicians and researchers alike in the broad field of Biomedicine. Adopted early in the evolution of the field, the term medical informatics has been applied to the various sub-di ... Full text Cite

iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.

Journal Article J Chem Inf Model · March 25, 2013 Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The ... Full text Link to item Cite

A Grid Based Approach to Share Public Health Surveillance Applications - The R Example

Journal Article Online Journal of Public Health Informatics · March 23, 2013 Full text Cite

Three-dimensional structure of the siskin green river oil shale kerogen model: A comparison between calculated and observed properties

Journal Article Energy and Fuels · February 21, 2013 Three-dimensional (3D) structural models of the Green River kerogen based on the two-dimensional (2D) structure proposed by Siskin were generated using a combination of ab initio and molecular mechanics calculations. Several initial monomer conformations w ... Full text Cite

Medical informatics and bioinformatics

Chapter · December 1, 2012 In the last 50 years, computational applications have been developed to aid clinicians and researchers alike in the broad field of Biomedicine. Adopted early in the evolution of the field, the term medical informatics has been applied to the various sub-di ... Full text Cite

Nanoinformatics: developing new computing applications for nanomedicine.

Journal Article Computing in science & engineering · June 2012 Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the ... Full text Cite

Identification of pneumonia and influenza deaths using the Death Certificate Pipeline.

Journal Article BMC Med Inform Decis Mak · May 8, 2012 BACKGROUND: Death records are a rich source of data, which can be used to assist with public surveillance and/or decision support. However, to use this type of data for such purposes it has to be transformed into a coded format to make it computable. Becau ... Full text Link to item Cite

Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting.

Journal Article Genome medicine · May 2012 Accurate interpretation of gene testing is a key component in customizing patient therapy. Where confirming evidence for a gene variant is lacking, computational prediction may be employed. A standardized framework, however, does not yet exist for quantita ... Full text Cite

Modeling of asphaltenes: Assessment of sensitivity of 13C solid state NMR to molecular structure

Journal Article Energy and Fuels · April 19, 2012 This paper presents calculations of 13C solid state NMR (SSNMR) spectra of model asphaltenes. The overall goal of this work is to assess how valuable 13C SSNMR studies of asphaltenes can be in guiding the development of representative ... Full text Cite

An agenda for ultra-large-scale system research for global health informatics

Journal Article ACM SIGHIT Record · March 2012 This extended abstract describes the characteristics of Ultra- Large-Scale Systems (ULSS) and the gaps in our understanding of these systems. We compare the characteristics of ULSS with the desired characteristics for national and global health inf ... Full text Cite

Federated queries for comparative effectiveness research: performance analysis.

Chapter · 2012 This paper presents a study of the performance of federated queries implemented in a system that simulates the architecture proposed for the Scalable Architecture for Federated Translational Inquiries Network (SAFTINet). Performance tests were conducted us ... Link to item Cite

Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants.

Journal Article J Am Med Inform Assoc · 2012 The rapid advance of gene sequencing technologies has produced an unprecedented rate of discovery of genome variation in humans. A growing number of authoritative clinical repositories archive gene variants and disease phenotypes, yet there are currently m ... Full text Link to item Cite

Characterization of uncertainty in the classification of multivariate assays: application to PAM50 centroid-based genomic predictors for breast cancer treatment plans.

Journal Article Journal of clinical bioinformatics · December 2011 BackgroundMultivariate assays (MVAs) for assisting clinical decisions are becoming commonly available, but due to complexity, are often considered a high-risk approach. A key concern is that uncertainty on the assay's final results is not well und ... Full text Cite

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Journal Article Acta Crystallogr B · December 2011 Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologi ... Full text Link to item Cite

Chemical shift tensors: theory and application to molecular structural problems.

Journal Article Progress in nuclear magnetic resonance spectroscopy · May 2011 Full text Cite

Formation of one dimensional linear chains by Ir-Ir bonds in cis-dicarbonyldichloroiridate (I)

Journal Article Polyhedron · February 1, 2011 The particular electronic properties of K[IrCl2(CO) 2]H2O are related to its supramolecular structure. Despite the lack of a single-crystal X-ray structure, by means of a variety of powerful experimental and theoretical tec ... Full text Cite

Enabling GeneHunter as a grid service: a case study for implementing analytical services in biomedical grids.

Journal Article Methods Inf Med · 2011 BACKGROUND: A cursory analysis of the biomedical grid literature shows that most projects emphasize data sharing and the development of new applications for the grid environment. Much less is known about the best practices for the migration of existing ana ... Full text Link to item Cite

Transition from exo- to endo- Cu absorption in CuSi(n) clusters: A Genetic Algorithms Density Functional Theory (DFT) Study.

Journal Article Molecular simulation · January 2011 The characterization and prediction of the structures of metal silicon clusters is important for nanotechnology research because these clusters can be used as building blocks for nano devices, integrated circuits and solar cells. Several authors have postu ... Full text Cite

Shielding Tensor Calculations

Journal Article Emagres · January 1, 2011 This article provides a brief overview of the progress observed in the methods to calculate shielding since the publication of its original version in the 1996 edition of the Encyclopedia of Nuclear Magnetic Resonance. The introduction is followed by the p ... Full text Cite

Predicting the start week of respiratory syncytial virus outbreaks using real time weather variables.

Journal Article BMC Med Inform Decis Mak · November 2, 2010 BACKGROUND: Respiratory Syncytial Virus (RSV), a major cause of bronchiolitis, has a large impact on the census of pediatric hospitals during outbreak seasons. Reliable prediction of the week these outbreaks will start, based on readily available data, cou ... Full text Link to item Cite

Septo-hippocampal networks in chronic epilepsy.

Journal Article Exp Neurol · March 2010 The medial septum inhibits the appearance of interictal spikes and seizures through theta rhythm generation. We have determined that medial septal neurons increase their firing rates during chronic epilepsy and that the GABAergic neurons from both medial a ... Full text Link to item Cite

SaTScan on a Cloud: On-Demand Large Scale Spatial Analysis of Epidemics.

Journal Article Online journal of public health informatics · January 2010 By using cloud computing it is possible to provide on- demand resources for epidemic analysis using computer intensive applications like SaTScan. Using 15 virtual machines (VM) on the Nimbus cloud we were able to reduce the total execution time for the sam ... Full text Cite

Computational Feature Selection and Classification of RET Phenotypic Severity

Journal Article Journal of Data Mining in Genomics & Proteomics · 2010 Full text Cite

Transition from exo to endo Cu absorption in SinCu clusters: A genetic algorithms Density Functional Theory (DFT) study

Conference Technical Proceedings of the 2009 Nsti Nanotechnology Conference and Expo Nsti Nanotech 2009 · December 1, 2009 The characterization and prediction of the structures of metal silicon clusters is important for nanotechnology research because these clusters can be used as building blocks for nano devices, integrated circuits and solar cells. Several authors [1-3] have ... Cite

Parallel genetic algorithms for crystal structure prediction: Successes and failures in predicting bicalutamide polymorphs

Chapter · November 2, 2009 This paper describes the application of our distributed computing framework for crystal structure prediction, Modified Genetic Algorithms for Crystal and Cluster Prediction (MGAC), to predict the crystal structure of the two known polymorphs of bicalutamid ... Full text Cite

Intermolecular shielding contributions studied by modeling the (13)C chemical-shift tensors of organic single crystals with plane waves.

Journal Article J Chem Phys · October 14, 2009 In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge ... Full text Link to item Cite

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

Journal Article J Comput Chem · October 2009 This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the ... Full text Link to item Cite

A case for using grid architecture for state public health informatics: the Utah perspective.

Journal Article BMC Med Inform Decis Mak · June 22, 2009 This paper presents the rationale for designing and implementing the next-generation of public health information systems using grid computing concepts and tools. Our attempt is to evaluate all grid types including data grids for sharing information and co ... Full text Link to item Cite

Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test.

Journal Article Acta Crystallogr B · April 2009 We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organi ... Full text Link to item Cite

Chemical Shifts and Solid-State Molecular-Level Structure

Journal Article Emagres · January 1, 2009 This article discusses the relationship between chemical shifts and different structural and bonding characteristics that affect molecular structure. The article starts with a discussion of the effect of changes in the bonding environment and tautomeric fo ... Full text Cite

Digital Sherpa: A set of high level tools to manage scientific applications in a computational grid

Conference ACM International Conference Proceeding Series · December 1, 2008 Currently users of high performance computers are overwhelmed with non scalable tasks such as job submission and monitoring, a problem that gets compounded when trying to run complex scientific applications requiring the coordination of several interrelate ... Full text Cite

Utah's statewide informatics platform for translational and clinical science.

Journal Article AMIA Annu Symp Proc · November 6, 2008 The University of Utah has initiated the design and implementation of an innovative data and knowledge management informatics platform for the new Center for Clinical and Translational Science. The main component of the platform is described, along with pr ... Link to item Cite

Enabling GeneHunter as a grid service: a case study for implementing analytical services for biomedical grids.

Journal Article AMIA Annu Symp Proc · November 6, 2008 Advances in grid computing show promise for easier provisioning of analytical services to biomedical researchers. In this poster we present our experiences in creating a grid analytical service based on the popular genetic linkage analysis tool GeneHunter. ... Link to item Cite

A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease.

Journal Article Comput Biol Med · July 2008 This paper describes a novel algorithm to analyze genetic linkage data using pattern recognition techniques and genetic algorithms (GA). The method allows a search for regions of the chromosome that may contain genetic variations that jointly predispose in ... Full text Link to item Cite

Magnetic Shielding and Chemical Shifts: Basics

Journal Article Emagres · January 1, 2008 This article presents a brief introduction to the physical origins of the magnetic shielding tensor and its symmetry properties. Following the introduction, the basic theory of nonrelativistic magnetic shielding is presented, followed by a qualitative desc ... Full text Cite

Solid-State Effects on NMR Chemical Shifts

Chapter · September 10, 2007 This review presents first a qualitative description of the changes observed in the measured chemical shifts in solid state when compared with those obtained in solution. This qualitative description of the intermolecular interactions that affect the chemi ... Full text Cite

Solid-state 13C NMR and quantum chemical investigation of metal diene complexes.

Journal Article Magn Reson Chem · May 2007 This paper presents novel measurements and calculations of the olefinic (13)C chemical shift tensor principal values in several metal diene complexes. The experimental values and the calculations show shifts as large as 70 ppm with respect to the values in ... Full text Link to item Cite

Shielding Calculations

Journal Article · March 15, 2007 Full text Cite

Ring current effects in crystals. Evidence from 13C chemical shift tensors for intermolecular shielding in 4,7-di-t-butylacenaphthene versus 4,7-di-t-butylacenaphthylene.

Journal Article J Phys Chem A · March 15, 2007 13C chemical shift tensor data from 2D FIREMAT spectra are reported for 4,7-di-t-butylacenaphthene and 4,7-di-t-butylacenaphthylene. In addition, calculations of the chemical shielding tensors were completed at the B3LYP/6-311G** level of theory. While the ... Full text Link to item Cite

Shielding Tensor Calculations

Journal Article · March 15, 2007 Full text Cite

Indirect Coupling: Semiempirical Calculations

Journal Article Emagres · January 1, 2007 Full text Cite

A Distributed Computing Method for Crystal Structure Prediction of Flexible Molecules:  An Application to N-(2-Dimethyl-4,5-dinitrophenyl) Acetamide.

Journal Article Journal of chemical theory and computation · January 2007 In this paper, we describe a new distributed computing framework for crystal structure prediction that is capable of performing crystal structure searches for flexible molecules within any space group and with an arbitrary number of molecules in the asymme ... Full text Cite

Shielding Calculations: Perturbation Methods

Journal Article Emagres · January 1, 2007 Full text Cite

Digital Sherpa

Conference Proceedings of the 2006 ACM IEEE Conference on Supercomputing Sc 06 · December 1, 2006 Currently users of high performance computers are overwhelmed with non-scalable tasks such as job submission and monitoring. Many users are limited by the number of jobs they can submit to one High Performance Computing (HPC) resource at a time, which resu ... Full text Cite

Global optimization of atomic cluster structures using parallel genetic algorithms

Conference Materials Research Society Symposium Proceedings · June 30, 2006 The study of the structure and physical properties of atomic clusters is an extremely active area of research due to their importance, both in fundamental science and in applied technology. For medium size atomic clusters most of the structures reported to ... Cite

Modified genetic algorithms to model cluster structures in medium-sized silicon clusters: Si18 - Si60

Journal Article Physical Review A Atomic Molecular and Optical Physics · June 2, 2006 This paper presents the results obtained using a genetic algorithm (GA) to search for stable structures of medium-size silicon clusters. This is the third report in which a GA coupled with the MSINDO semiempirical molecular orbital program is used to find ... Full text Cite

Modeling the (13)C chemical-shift tensor in organic single crystals by quantum mechanical methods: finite basis set effects.

Journal Article Magn Reson Chem · March 2006 The influence of using finite basis sets to calculate (13)C magnetic shieldings were explored using the Hartree-Fock and the B3LYP hybrid density functional methods. The shielding values were compared in a linear least-squares fashion for a test group of 1 ... Full text Link to item Cite

Intermolecular shielding from molecular magnetic susceptibility. A new view of intermolecular ring current effects.

Journal Article Magn Reson Chem · March 2006 This paper presents calculations of the NICS (nuclear independent chemical shieldings) in a rectangular grid surrounding the molecules of benzene, naphthalene and coronene. Using the relationship between calculated NICS and the induced magnetic field, the ... Full text Link to item Cite

Magnetic Resonance in Chemistry: Guest editors' foreword

Journal Article Magnetic Resonance in Chemistry · January 1, 2006 Full text Cite

Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing.

Journal Article J Chem Inf Model · 2006 With the expansion of the Internet and World Wide Web (or the Web), research environments have changed dramatically. As a result, the need to be able to efficiently and securely access information and resources from remote computer systems is becoming even ... Full text Link to item Cite

Theoretical study of the adsorption of H on Si n clusters, (n=3-10).

Journal Article J Chem Phys · December 1, 2005 A recently proposed local Fukui function is used to predict the binding site of atomic hydrogen on silicon clusters. To validate the predictions, an extensive search for the more stable SinH (n=3-10) clusters has been done using a modified genetic algorith ... Full text Link to item Cite

Ab initio global optimization of the structures of SinH, n=4-10, using parallel genetic algorithms

Journal Article Physical Review A Atomic Molecular and Optical Physics · November 1, 2005 The results of ab initio global optimizations of the structures of SinH, n=4-10, atomic clusters using a parallel genetic algorithm are presented. Driving the global search with the parallel implementation of the genetic algorithm are presented and using t ... Full text Cite

A third blind test of crystal structure prediction.

Journal Article Acta Crystallogr B · October 2005 Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project (CSP2004) was hosted by the Cambridge Crystallographic Data Centre. A range of methodologies used in sear ... Full text Link to item Cite

Modeling NMR chemical shift: A survey of density functional theory approaches for calculating tensor properties.

Journal Article The journal of physical chemistry. A · February 2005 The NMR chemical shift, a six-parameter tensor property, is highly sensitive to the position of the atoms in a molecule. To extract structural parameters from chemical shifts, one must rely on theoretical models. Therefore, a high quality group of shift te ... Full text Cite

A general framework to understand parallel performance in heterogeneous clusters: Analysis of a new adaptive parallel genetic algorithm

Journal Article Journal of Parallel and Distributed Computing · January 1, 2005 This paper presents a general model to define, measure and predict the efficiency of applications running on heterogeneous parallel computer systems. Using this framework, it is possible to understand the influence that the heterogeneity of the hardware ha ... Full text Cite

Modeling solid-state effects on NMR chemical shifts using electrostatic models.

Journal Article Magn Reson Chem · October 2004 This paper presents a comparison of the embedded ion method (EIM) and the surface charge representation of the electrostatic embedding potential (SCREEP) method, two methods which can be used to calculate solid-state effects on NMR chemical shifts. The res ... Full text Link to item Cite

Modified genetic algorithms to model atomic cluster structures: CuSi clusters

Journal Article Journal of Molecular Structure THEOCHEM · July 26, 2004 This paper presents the results obtained using a genetic algorithm (GA) to search for stable structures of Cu-silicon clusters. In this work the GA uses a semiempirical energy function to find the best cluster structures, which are further optimized using ... Full text Cite

Modified Genetic Algorithm to Model Crystal Structures: III. Determination of Crystal Structures Allowing Simultaneous Molecular Geometry Relaxation

Journal Article International Journal of Quantum Chemistry · February 5, 2004 The modified genetic algorithm (MGAC) has been extended to allow simultaneous relaxation of molecular geometry during optimization of the crystalline structure. The method was applied to L-alanine and DL-alanine for two different potential functions. The g ... Full text Cite

Calculations of chemical shieldings: Theory and applications

Journal Article Concepts in Magnetic Resonance Part A Bridging Education and Research · January 1, 2004 This article presents a discussion of the origin of the chemical shieldings, which is followed by a rigorous derivation of quantum mechanical formula for their exact calculation and a discussion of the necessary approximations that make these calculations ... Full text Cite

Modified genetic algorithms to model cluster structures in medium-size silicon clusters

Journal Article Physical Review A Atomic Molecular and Optical Physics · January 1, 2004 Genetic algorithms (GA) were used to investigate the stable isomers of silicon clusters. In order to find the cluster structures, a semiempirical energy function was used by the GA that were further optimized using density-functional theory. A different st ... Full text Cite

Indirect (J) coupling of inequivalent 75As nuclei in crystalline and glassy As2Se3 and As2S3

Journal Article Journal of Chemical Physics · October 22, 2003 For glassy and crystalline As2S3, the experimental values obtained from the modulation of the decay of the transversal nuclear magnetization are consistent with values estimated using empirical correlations obtained. Unfortunately, th ... Full text Cite

Evidence of indirect spin-spin coupling in crystalline and glassy As-chalcogen compounds

Journal Article Journal of Non Crystalline Solids · October 1, 2003 Nuclear quadrupole resonance (NQR) studies on crystalline and glassy As-S/Se compounds reveal that the spin echo intensities as a function of pulse separation in the Hahn echo sequence exhibit oscillations superimposed on an exponential decay, given by the ... Full text Cite

Advances in Theoretical and Physical Aspects of Spin-Spin Coupling Constants

Chapter · January 1, 2003 In this work a selection of papers dealing with NMR indirect spin-spin coupling constants published between 1999 and May 2003 are reviewed. Care is taken to avoid overlap between this work and several important review articles published during this period. ... Full text Cite

13C NMR investigation of solid-state polymorphism in 10-deacetyl baccatin III.

Journal Article J Am Chem Soc · September 4, 2002 To investigate the origins of solid-state NMR shift differences in polymorphs, carbon NMR chemical shift tensors are measured for two forms of solid 10-deacetyl baccatin III: a dimethyl sulfoxide (DMSO) solvate and an unsolvated form. A comparison of ab in ... Full text Link to item Cite

Carbonates, thiocarbonates, and the corresponding monoalkyl derivatives: III. The 13C chemical shift tensors in potassium carbonate, bicarbonate and related monomethyl derivatives.

Journal Article Solid State Nucl Magn Reson · August 2002 The principal values of the 13C chemical shift tensors in potassium carbonate (K2CO3), trithiocarbonate (K2CS3), bicarbonate (KHCO3), methylcarbonate (KO2COCH3), S-methyl-monothiocarbonate (KO2CSCH3), O-methyl-monothiocarbonate (KOSCOCH3), S-methyl-dithioc ... Full text Link to item Cite

Modified genetic algorithm to model crystal structures. II. Determination of a polymorphic structure of benzene using enthalpy minimization

Journal Article Journal of Chemical Physics · April 8, 2002 A previous study demonstrated that the Modified Genetic Algorithm for Crystal and Cluster (MGAC) procedure is able to predict the crystal structure of small organic aromatic compounds using the rigid molecule approximation and an empirical potential functi ... Full text Cite

Modified genetic algorithm to model crystal structures. I. Benzene, naphthalene and anthracene

Journal Article Journal of Chemical Physics · April 8, 2002 Using a new modified genetic algorithm (MGAC) and knowing the geometry of the individual molecules and an empirical intermolecular potential, it is possible to predict the crystal structures of benzene, naphthalene and anthracene. The success of the method ... Full text Cite

Modeling NMR chemical shifts: Surface charge representation of the electrostatic embedding potential modeling of crystalline intermolecular effects in 19F solid state NMR chemical shifts

Journal Article Journal of Molecular Structure · January 9, 2002 This contribution compares the results obtained using two different charge models with those of the cluster model, when they are used to take into account the crystalline intermolecular interactions in the calculation of 19F chemical shifts tens ... Full text Cite

15N chemical shifts in energetic materials: CP/MAS and abinitiostudies of aminonitropyridines, aminonitropyrimidines, and theirN-oxides

Journal Article International Journal of Molecular Sciences · January 1, 2002 Solid state 15N NMR chemical shift measurements have been performed on a series of nitro- and amino-substituted nitrogen-containing heterocycles that are of interest as potential new insensitive explosives. Due to low solubilities, many of these ... Full text Cite

Cluster analysis of 13C chemical shift tensor principal values in polycyclic aromatic hydrocarbons

Journal Article Journal of Physical Chemistry A · August 9, 2001 This paper presents a hierarchical cluster analysis of the principal values of the 13C chemical shift tensors encountered in polycyclic aromatic hydrocarbons (PAHs). Because of the limited set of experimental data presently available, the analys ... Full text Cite

13C Chemical-shift tensors in an analogous series of heterosubstituted polycyclic aromatic compounds

Journal Article Magnetic Resonance in Chemistry · January 1, 2001 The 13C principal values of the chemical-shift tensor for fluorene, carbazole, dibenzofuran and dibenzothiophene were determined with the FIREMAT and PHORMAT experiments. Theoretical calculations (DFT) of the tensors were used as an aid to spect ... Full text Cite

Improving cluster utilization through set based allocation policies

Conference Proceedings of the International Conference on Parallel Processing Workshops · January 1, 2001 While clusters have already proven themselves in the world of high performance computing, some clusters are beginning to exhibit resource inefficiencies due to increasing hardware diversity. Much of the success of clusters lies in the use of commodity comp ... Full text Cite

Nitrogen-15 chemical shift in the pyridine-methanol complex

Journal Article Chemical Physics Letters · May 12, 2000 This Letter presents density functional theory calculations of the 15N chemical shifts of pyridine in the presence of a methanol molecule. These calculations were done to study the effects of hydrogen bonding (HB) on the principal components of ... Full text Cite

Carbon-13 Shift Tensors in Polycyclic Aromatic Compounds. 8.1 A Low-Temperature NMR Study of Coronene and Corannulene

Journal Article Journal of Physical Chemistry A · January 13, 2000 The principal values of the 13C chemical shift tensors were measured for coronene and corannulene, both at room temperature and at approximately 100 K. At room temperature the molecules are moving, resulting in a motionally averaged powder patte ... Full text Cite

Modeling NMR chemical shifts: Crystal potential derived point charge (CPPCh) model to calculate solid state effects on31P chemical shifts tensors

Journal Article International Journal of Molecular Sciences · January 1, 2000 This paper presents a new method to calculate solid-state effects on NMR chemical shifts. Using full crystal potentials, this new method (CPPCh) eliminates the need to arbitrarily select the point charges that are included in the calculations of the NMR ch ... Full text Cite

Advances in theoretical and physical aspects of spin-spin coupling constants

Journal Article Annual Reports on NMR Spectroscopy · January 1, 2000 Full text Cite

Effect of intramolecular interaction between polar and polarizable bonds on 13C shielding constants in different conformations of 2-methoxy- and 2-vinyloxynaphthalene molecules: An ab initio study

Journal Article Russian Chemical Bulletin · January 1, 1999 Shielding constants of 13C nuclei calculated for different conformations of 2-methoxynaphthalene and 2-vinyloxynaphthalene molecules by the GIAO ab initio method in the D95** basis set indicate a strong shielding effect of the intramolecular int ... Full text Cite

Modeling of the 15N and 13C chemical shift tensors in purine

Journal Article ACS Symposium Series · January 1, 1999 This paper presents quantum mechanical studies of the 15N and 13C chemical shifts in both the N7-H and N9-H tautomeric forms of purine. Quantum mechanical calculations of the chemical shifts were used to assign the NMR resonances and ... Full text Cite

Nitrogen-15 chemical shifts in AT (adenine-thymine) and CG (cytosine-guanine) nucleic acid base pairs.

Journal Article J Biomol Struct Dyn · December 1998 This paper presents ab initio (DFT) calculations of the 15N chemical shifts in AT (Adenine-Thymine) and CG (Cytosine-Guanine) nucleic acid base pairs. Calculations were done on 14 AT and 18 CG base pairs using experimental (X-ray) geometries obtained from ... Full text Link to item Cite

15N chemical shift tensors in nucleic acid bases

Journal Article Journal of the American Chemical Society · September 30, 1998 This paper presents measurements of the principal values of the 15N chemical shift tensors in adenine, cytosine, guanine, and thymine. The assignment of the solid-state NMR resonances was done using the liquid values in the corresponding nuclesi ... Full text Cite

NMR at cryogenic temperatures: A 13C NMR study of ferrocene

Journal Article Journal of Physical Chemistry A · September 24, 1998 A new cryogenic apparatus is described that can be used to obtain NMR spectra at temperatures down to 8-10 K. The static solid 13C NMR spectrum of ferrocene is recorded at that temperature. Spectra recorded at higher temperatures show that ferro ... Full text Cite

Carbon-13 chemical shift tensors in polycyclic aromatic compounds. 7.1 Symmetry augmented chemical shift - Chemical shift correlation spectroscopy and single crystal study of triphenylene

Journal Article Journal of the American Chemical Society · September 16, 1998 A modification is made to the chemical shift-chemical shift, CS-CS, correlation spectroscopy method for measuring shift tensors. This new approach incorporates, in an iterative fashion, the redundancy of information available in the spectrum from congruent ... Full text Cite

Density functional theory calculations of the structure and the 15N and 13C chemical shifts of methyl bacteriopheophorbide a and bacteriochlorophyll a

Journal Article Journal of Physical Chemistry B · March 12, 1998 Ab initio (DFT) chemical shifts calculations and geometry optimizations were performed in methyl bacteriopheophorbide a (MBPheo-a) using the D95 and D95** basis sets and in bacteriochlorophyll a (BChl-a) using the LanL2DZ basis set. The results show that i ... Full text Cite

Modeling NMR chemical shifts: a comparison of charge models for solid state effects on 15N chemical shift tensors.

Journal Article Solid State Nucl Magn Reson · February 1998 This paper presents results from applying different point charge models to take into account intermolecular interactions to model the solid state effects on the 15N NMR chemical shifts tensors. The DFT approach with the BLYP gradient corrected exchange cor ... Full text Link to item Cite

Solid-state 13C NMR measurements in methoxynaphthalenes: Determination of the substituent chemical shift effects in the principal values

Journal Article Journal of Physical Chemistry A · November 27, 1997 The principal values of the 13C chemical shift tensor are measured in 1-methoxy-, 2-methoxy-, 1,4-dimethoxy-, 2,6-dimethoxy-, and 2,7-dimethoxynaphthalene using the triple echo version of the 2D magic angle turning (MAT) experiment. In the case ... Full text Cite

Solid state 15N and 13C NMR study of several metal 5,10,15,20- tetraphenylporphyrin complexes

Journal Article Journal of the American Chemical Society · July 30, 1997 The principal values of both the 13C and 15N chemical shift tensors are reported for the Zn, Ni, and Mg 5,10,15,20- tetraphenylporphyrin(TPP)complexes. The principal values of the 15N chemical shift tensors were obtained fr ... Full text Cite

15N-chemical shift principal values in nitrogen heterocycles

Journal Article Journal of the American Chemical Society · January 1, 1997 This paper presents data on the 15N chemical shift tensor principal values in a series of 15N-enriched heterocycles. Compounds that are liquids at room temperature were frozen, and the principal values of all compounds studied were me ... Full text Cite

Experimental and theoretical study of the ethoxy group conformational effect on 13c chemical shifts in ortho-substituted phenetols

Journal Article Magnetic Resonance in Chemistry · January 1, 1997 The 13C chemical shifts of nine 2-X-substituted phenetol derivatives were measured together with the 13C chemical shifts of the corresponding X-monosubstituted benzenes. Using an additivity scheme, the ethoxy cis-and trans-ortho-SCSs ... Full text Cite

Carbon-13 chemical shift tensors in polycyclic aromatic compounds. 6.1 single-crystal study of perylene

Journal Article Journal of the American Chemical Society · May 22, 1996 The 40 chemical shift tensors of single-crystal perylene in the α crystalline form have been determined with a precision of 0.30 ppm using 13C chemical shift-chemical shift correlation spectroscopy. The in-plane anisotropy of these tensors descr ... Full text Cite

Carbon-13 chemical shift tensors and molecular conformation of anisole

Journal Article Journal of Physical Chemistry · May 16, 1996 The first direct measurement of the ortho steric effect of the methoxy group on the 13C chemical shifts in anisole is reported. The ortho steric effect on the isotropic 13C chemical shifts was obtained from a low-temperature MAS spect ... Full text Cite

Quantum mechanical calculations and experimental measurement of N-terminal charge effects on 1HN and 1HC alpha chemical shifts in peptides.

Journal Article Biopolymers · May 1996 Nuclear magnetic resonance spectroscopists are increasingly utilizing chemical shifts to characterize the secondary structure of proteins. The present study addresses the effects that the positively charged amino group at the N-terminus of a peptide has on ... Full text Link to item Cite

13C dipolar NMR spectrum of matrix-isolated o-benzyne-1,2-13C2

Journal Article Journal of the American Chemical Society · January 31, 1996 The 13C dipolar NMR spectrum of o-benzyne-1,2-13C2 in an argon matrix at a temperature of about 20 K is reported. The o-benzyne was generated from matrix-isolated phthalic anhydride-1,2-13C2 by UV irra ... Full text Cite

Effects of hydrogen bonding in the calculation of 15N chemical shift tensors: Benzamide

Journal Article Journal of the American Chemical Society · January 1, 1996 Full text Cite

Relationship of 13C NMR chemical shift tensors to diffraction structures.

Journal Article Acta Crystallogr B · August 1, 1995 13C chemical shift tensor measurements on single crystals provide a powerful method to study changes in the electron environment of nuclei with changes in molecular structure. Thus, diffraction structures are critical to an understanding of chemical shift ... Full text Link to item Cite

Infrared spectrum of divinyl telluride and theoretical analysis of divinyl group VI compounds

Journal Article Journal of Molecular Structure · July 1, 1995 The infrared spectrum of divinyl telluride (DVT) has been studied for the gaseous, liquid and solid phases as well as in inert matrices at low temperatures. HF-SCF calculations (using triple-zeta quality basis sets) have been carried out on DVT and on the ... Full text Cite

Carbon-13 chemical shift tensors of carboxylic acids: GIAO calculations in acetic acid + methylamine dimer

Journal Article Molecular Physics · January 1, 1995 GIAO calculations are presented of the13C chemical shift tensors of the carboxyl group in the dimer of acetic acid with methylamine. The calculations indicate that the local geometrical parameters describing the carboxyl group are related linear ... Full text Cite

15N chemical shift tensors of uracil determined from 15N powder pattern and 15N-13C dipolar NMR spectroscopy

Journal Article Journal of Physical Chemistry · January 1, 1995 The 15N chemical shift tensors of uracil are reported using 15N powder pattern techniques. The principal values of the 15N uracil tensors are obtained from the spectra of [1-15N]uracil and [3-15N]uraci ... Full text Cite

Carbon-13 Chemical Shift Tensors in Polycyclic Aromatic Compounds. 5.1 Single-Crystal Study of Acenaphthene

Journal Article Journal of the American Chemical Society · January 1, 1995 The 36 experimentally observable 13C chemical shift tensors in the acenaphthene single crystal are determined with 2D chemical shift—chemical shift correlation spectroscopy. The chemical shift tensors of the two crystallographically unique molec ... Full text Cite

Low-Temperature 13C Magnetic Resonance. 9. Steric Effects for Methyl Chemical Shift Tensors in Methylcyclohexanes

Journal Article Journal of the American Chemical Society · January 1, 1995 The solid-state low-temperature 13C NMR spectra of 1-(methyl-13C)-1-methylcyclohexane, cis-1-(methyl-13C)-3,5-dimethylcyclohexane, and trans-1-(methyl-13C)-3,5-dimethylcyclohexane have been measured and the princ ... Full text Cite

Solid-state 13C NMR, X-ray, and quantum mechanical studies of the carbon chemical shift tensors of p-tolyl ether

Journal Article Journal of Physical Chemistry® · January 1, 1994 This paper presents a detailed study of the principal components of the 13C chemical shift tensors in p-tolyl ether. The tensor components of a relative large number of carbon atoms are measured by using the two-dimensional magic angle turning ( ... Full text Cite

Determination of molecular symmetry in crystalline naphthalene using solid-state NMR

Journal Article Nature · September 23, 1993 DIFFRACTION techniques have shown that the crystal structure of naphthalene has a unit cell with Ci symmetry1-7. These studies were unable, however, to resolve any departure of the molecular structure from the D2h symmetry ... Cite

Determination of molecular symmetry in crystalline naphthalene using solid-state NMR.

Journal Article Nature · September 23, 1993 Diffraction techniques have shown that the crystal structure of naphthalene has a unit cell with Ci symmetry. These studies were unable, however, to resolve any departure of the molecular structure from the D2h symmetry observed in the gaseous state. We fo ... Full text Link to item Cite

Proximity effects on the nuclear magnetic shielding tensor. Part 1. An ab initio study of 17O and 19F chemical shifts in the proximity of a methyl group

Journal Article Journal of Molecular Structure THEOCHEM · April 22, 1993 The deshielding effect produced by repulsive interactions between proximate groups was studied from a theoretical point of view, calculating the magnetic shielding constants for the following nuclei: 17O in di-coordinated and carbonyl oxygen ato ... Full text Cite

Advances in Theoretical and Physical Aspects of Spin-Spin Coupling Constants

Chapter · January 1, 1993 This chapter discusses advances in the theoretical and physical aspects of spin–spin coupling constants. From both theoretical and experimental points of view, the analysis of high-resolution NMR parameters is an important problem, and its significance for ... Full text Cite

Ab initio study of the internal rotation barrier of formamide and the formamide–H2O complex

Journal Article International Journal of Quantum Chemistry · January 1, 1993 The barriers to internal rotation about the NC bond of formamide and the formamide–H2O complex have been examined by ab initio quantum chemistry methods. Both self‐consistent field and correlated approaches have been utilized to determine the g ... Full text Cite

Effects of electronic resonance interaction on the methoxy group NMR parameters. Theoretical and experimental study of substituted 2-methoxypyridines

Journal Article Journal of Physical Chemistry · January 1, 1993 In order to increase the understanding of the interactions which define the planar conformation of the methoxy group with respect to the aryl ring in methyl aryl ethers and the effect these interactions have on the methoxy NMR parameters, 17O an ... Full text Cite

Nonplanarity of the methoxy groups in o-dimethoxybenzene: quantum chemical calculations of the 17O chemical shieldings

Journal Article Journal of Molecular Structure THEOCHEM · December 1, 1992 Ab initio calculations of the 17O chemical shieldings in o-dimethoxybenzene and p-dimeth-oxybenzene are presented. The total energy and 17O chemical shielding tensors in the former compound were calculated as a function of the C-C-O-C ... Full text Cite

Effects of protonation on acetone: Nuclear magnetic resonance and ab initio studies

Journal Article Journal of the Chemical Society Faraday Transactions · December 1, 1992 The electronic and geometric structural changes of acetone upon protonation are studied by 13C NMR spectroscopy and by molecular orbital (MO) calculations using the LORG (local orbital/local origin) method to calculate chemical shieldings and th ... Full text Cite

How changing high performance COMPUTING technology changes the way in which we do computational chemistry

Conference Proceedings of the International Conference on Supercomputing · December 1, 1992 Developments in Computational Quantum Chemistry have been driven by the developments in hardware and software technology. Quantum chemical applications use 30-40% of the computational resources available in National and Regional supercomputer centers, ther ... Cite

Carbon-13 Chemical Shift Tensors in Aromatic Compounds. 4. Substituted Naphthalenes

Journal Article Journal of the American Chemical Society · April 1, 1992 The principal values of the 13C chemical shift tensor were measured for the aromatic carbons of 1,4,5,8-tetramethylnaphthalene, 1,2,3,6,7,8-hexahydropyrene, and pyracene using the variable angle spinning technique. Ab initio calculations of the ... Full text Cite

Carbon-13 Chemical Shift Tensors in Aromatic Compounds. 3. Phenanthrene and Triphenylene

Journal Article Journal of the American Chemical Society · April 1, 1992 Measurements of the principal values of the 13C chemical shift tensor are presented for the three carbons in triphenylene and for three different α-carbons in phenanthrene. The measurements in triphenylene were made in natural abundance samples ... Full text Cite

Ab initio study of the nitrogen lone-pair proximity effect on a methyl C-H bond in 2-methylpyridine

Journal Article Journal of Molecular Structure THEOCHEM · February 12, 1992 Ab initio optimized geometries for three different methyl conformations of 2-methylpyridine were analyzed in order to study the nitrogen lone-pair proximity effect on a methyl C-H bond. Calculations were carried out using three different basis sets in orde ... Full text Cite

Ab initio and 17O NMR studies of the substituent effects on the tautomeric equilibrium in 6-X-1H-2-pyridones

Journal Article Journal of Physical Chemistry · January 1, 1992 17O chemical shifts are found to be highly sensitive probes in the study of keto-enol tautomeric equilibria due to the strong sensitivity of these shifts to the coordination of the oxygen atom. The large shielding effect observed, both experimen ... Full text Cite

Ab initio study of cyclobutadiene and its aza-substituted derivatives. Ground state properties and vibrational frequencies

Journal Article Journal of Molecular Structure THEOCHEM · November 1, 1991 Ab initio calculations at the doubly-excited configuration interaction (CID) level of approximation are presented for cyclobutadiene and its aza-substituted derivatives. The geometries of all the compounds were fully optimized and the vibrational frequenci ... Full text Cite

Carbon-13 Chemical Shift Tensors in Polycyclic Aromatic Compounds. 2. Single-Crystal Study of Naphthalene

Journal Article Journal of the American Chemical Society · January 1, 1991 Carbon-13 chemical shift tensors have been determined in single-crystal naphthalene. The high-field component of every tensor is oriented perpendicular to the molecular plane, as in other aromatic compounds. The bridgehead carbon tensor is nearly axially s ... Full text Cite

Ab initio and 17O NMR study of aromatic compounds with dicoordinate oxygen atoms. 2. Intramolecular hydrogen bonding in hydroxy- and methoxybenzene derivatives

Journal Article Journal of Physical Chemistry · January 1, 1991 The 17O chemical shifts of several ortho-substituted phenols and anisoles are presented along with those of the corresponding para-substituted compounds. The measurements of the various ortho-para pairs were done in the same solvent and at the s ... Full text Cite

New theoretical results on the CO...cyclobutadiene complex

Journal Article Chemical Physics Letters · September 28, 1990 Ab initio molecular-orbital calculations at the 4-31G/CID level of approximation were performed for the CO...C4H4 complex. A local minimum for a C4H4CO distance of 1.386 Å has been found in the configuration in w ... Full text Cite

A comparison of the IGLO and LORG methods for the calculations of nuclear magnetic shieldings

Journal Article Journal of Computational Chemistry · January 1, 1990 The individual gauge for localized orbitals (IGLO) and localized orbital/local origin (LORG) methods for the calculation of chemical shieldings are compared from their theoretical and computational viewpoints. A detailed analysis of the fluorine α‐substitu ... Full text Cite

Ab initio and 17O NMR study of aromatic compounds with dicoordinate oxygen atoms. 1. Methoxy- and (methylenedioxy)benzene derivatives

Journal Article Journal of Physical Chemistry · January 1, 1990 17O NMR data at natural abundance in toluene-d8 at 74°C were obtained for aromatic compounds containing methoxy and methylenedioxy groups as side-chains substituents. 17O chemical shifts of this series of compounds are sign ... Full text Cite

Experimental and theoretical study of the methoxy group conformational effect on 13C chemical shifts in ortho‐substituted anisoles

Journal Article Magnetic Resonance in Chemistry · January 1, 1989 Aromatic 13C chemical shifts are reported for a number of ortho‐substituted anisoles. Quantitative determination of the substituent chemical shift (SCS) effects of the methoxy group with a fixed coplanar conformation on aryl carbon nuclei was ac ... Full text Cite

Carbon-13 chemical-shift tensors in single-crystal methoxybenzenes

Journal Article Journal of the Chemical Society Faraday Transactions 1 Physical Chemistry in Condensed Phases · December 1, 1988 Using a two-dimensional NMR orientational correlation technique, carbon-13 chemical-shift tensors have been measured in single crystals of 1,4-dimethoxybenzene, 1,3,5-trimethoxybenzene and 1,2,3-trimethoxybenzene. The two-dimensional technique greatly exte ... Full text Cite

13C dipolar spectroscopy of nitromethane

Journal Article Molecular Physics · August 20, 1988 The13C dipolar N.M.R. spectrum of 13CH314NO2 has been recorded at 25 K. The principal values of the 13C shielding tensor, obtained by a computer fit of the experimental lineshape, are similar to those ... Full text Cite

Quantitative Determination of Different Carbon Types in Fusinite and Anthracite Coals from Carbon-13 Nuclear Magnetic Resonance Chemical Shielding Line-Shape Analysis

Journal Article Analytical Chemistry · August 1, 1988 13C NMR shielding tensors have been determined for two anthracite coals and a fusinite maceral by using powder pattern line shapes which have been analyzed as a superposition of three different bands due to benzenelike, condensed (bridgehead and ... Full text Cite

Low-temperature 13C magnetic resonance. 8. Chemical shielding anisotropy of olefinic carbons

Journal Article Journal of the American Chemical Society · January 1, 1988 The principal values of the 13C NMR shielding tensor were measured at cryogenic temperatures for a series of olefinic carbons, including methyl-substituted ethylenes, 1-methyl- and 1,2-dimethylcycloalkenes, methylenecycloalkanes, and bicyclo[n.m ... Full text Cite

Vibrational and electronic spectra of matrix-isolated N3· and N3-

Journal Article Journal of Physical Chemistry · January 1, 1988 N3· and N3- were formed upon the bombardment of a N2 matrix with kiloelectronvolt-energy fast atoms and/or ions. The vibrational frequencies of N3· in the most stable site, v2 = 472.7, v Full text Cite

The effect of transverse cross relaxation on nuclear magnetic resonance dipolar spectra

Journal Article Journal of Chemical Physics · January 1, 1988 The 13C dipolar powder spectra of 13CH331PO(OH)2 at room temperature and 13CH 319F at low temperature (T = 25 K) are reported. An intense peak is observed at the cent ... Full text Cite

Theoretical study of the in-plane components of the 13C shielding tensors in condensed aromatic hydrocarbons

Journal Article Theoretica Chimica Acta · May 1, 1987 The Pople model for chemical shielding is applied to calculate the in-plane components of the 13C shielding tensors of condensed aromatic hydrocarbons. The wave functions are evaluated using the MNDO method and the calculated results are support ... Full text Cite

Carbon-13 Chemical Shielding Tensors in Polycyclic Aromatic Compounds. 1. Single-Crystal Study of Pyrene

Journal Article Journal of the American Chemical Society · April 1, 1987 The carbon-13 chemical shielding tensors measured in single-crystal pyrene are reported. The two internal bridgehead carbons have principal values of 197, 191, and -18 ppm and the four peripheral bridgehead carbons 213, 187, and -7 ppm with respect to liqu ... Full text Cite

Carbon-13 Shielding Tensors: Experimental and Theoretical Determination

Journal Article Accounts of Chemical Research · January 1, 1987 Full text Cite

Analysis of the IGLO bond contributions to the 13C shielding tensors in the local bond frame

Journal Article International Journal of Quantum Chemistry · January 1, 1987 A new method is presented to analyze the IGLO (individual gauge for localized orbitals) bond contributions in 13C chemical shielding. The IGLO bond contributions calculated in the molecular frame are rotated to a local bond frame, in which one c ... Full text Cite

Low-Temperature 13C Magnetic Resonance in Solids. 6. Methine Carbons

Journal Article Journal of the American Chemical Society · January 1, 1986 The low-temperature static solid 13C NMR spectra of the methine carbons of bicyclo[1.1.1]pentane, bicyclo-[1.1.1]pentanone, norbornadiene, cubane, trimethoxymethane, and isobutane were measured. Calculations of the shielding tensors by the indiv ... Full text Cite

Annual reports on NMR spectroscopy

Journal Article Spectrochimica Acta Part A: Molecular Spectroscopy · January 1986 Full text Cite

Low-Temperature Carbon-13 Magnetic Resonance in Solids. 7. Methyl Carbons

Journal Article Journal of the American Chemical Society · January 1, 1986 The principal values of the 13C shielding tensors for a variety of methyl groups in small organic molecules are reported at 25 K. They were measured on neat samples of natural abundance materials. The assignment of the experimental principal val ... Full text Cite

Low temperature 13C NMR magnetic resonance in solids 4. Cyclopropane, bicyclo[1.1.0]butane and [1.1.1] propellane

Journal Article Theoretica Chimica Acta · December 1, 1985 The solid state 13C NMR spectra of bicyclo[1.1.0]butane and [1.1.1]propellane have been measured at low temperature. The orientation of the principal axes of the chemical shielding tensor have been determined with ab initio calculations based on ... Full text Cite

Low-Temperature 13C Magnetic Resonance in Solids. 5. Chemical Shielding Anisotropy of the 13CH2 Group

Journal Article Journal of the American Chemical Society · January 1, 1985 The principal values of the 13CH2 shielding tensors are reported for a series of cycloalkanes, cycloalkenes, and heterocyclic compounds. They were measured on natural abundance samples, 13C-enriched tert-butylcyclohexane-4- ... Full text Cite

Iglo calculations of the antisymmetric components of nuclear magnetic shielding tensors

Journal Article Chemical Physics Letters · November 30, 1984 Calculations of the antisymmetric components of 13C shielding tensors have been performed in several compounds using the IGLO (individual gauge for localized orbitals) method. The results indicate chemical situations in which the detection of th ... Full text Cite

Low-Temperature 13C Magnetic Resonance in Solids. 3. Linear and Pseudolinear Molecules

Journal Article Journal of the American Chemical Society · November 1, 1984 The solid-state low-temperature 13C NMR spectra of five linear (CO, CO2, OCS, C3O2, acetylene) and four pseudolinear (propyne, 2-butyne, allene, ketene) molecules have been obtained. The assignments of the shield ... Full text Cite

The importance of multicenter integrals in semiempirical calculations of nuclear spin-spin coupling constants. 2. Anisotropic coupling

Journal Article Journal of Magnetic Resonance 1969 · October 1, 1984 A molecular orbital (MO) study of anisotropic nuclear spin-spin coupling is presented in terms of a semiempirical formulation with inclusion of all multicenter integrals in the Fermi contact, orbital, and spin-dipolar contributions. This formulation extend ... Full text Cite

A theoretical study of medium effects on the transmission mechanisms of the fermi contact term of spin–spin coupling constants in the acetamide molecule

Journal Article International Journal of Quantum Chemistry · January 1, 1984 Solvent effects on different transmission mechanisms of spin–spin coupling constants are analyzed from a theoretical viewpoint. Medium effects are introduced using the solvaton model, and the decomposition of coupling constants in σ‐ and π‐electron transmi ... Full text Cite

Importance of Multicenter Integrals in Semiempirical Calculations of Nuclear Spin-Spin Coupling Constants. 1. Isotropic Coupling

Journal Article Journal of the American Chemical Society · January 1, 1984 A study of Fermi contact, orbital, and spin-dipolar contributions to isotropic nuclear spin-spin coupling constants is presented in terms of a semiempirical (INDO) molecular orbital (MO) approach that extends existing theory to include all integrals for th ... Full text Cite

Natural-abundance studies of 13C13C coupling constants. Substituent dependencies of directly bonded and vicinal 13C13C coupling constants in 1-substituted bicycloalkanes

Journal Article Journal of Magnetic Resonance 1969 · January 1, 1984 A series of 1-substituted-bicyclo[2.2.2]octanes and bicycloalkane-l-carboxylic acids were synthesized and the 13C13C coupling constants were measured in natural abundance by 13C satellite and/or double-quantum coherence met ... Full text Cite

A long‐lived molecular association between acetone and 2‐methoxy‐5‐aminopyridine

Journal Article Organic Magnetic Resonance · January 1, 1984 Studies were carried out in order to determine the nature of a peculiar solvent effect observed between acetone and 2‐methoxy‐5‐aminopyridine. It is concluded that a molecular complex is formed due to specific interactions that take place between the solut ... Full text Cite

Transmission of spin-spin coupling constants through different paths in bicyclo(2,2,1)heptane: their calculation using inner projections of the polarization propagator

Journal Article Chemical Physics Letters · April 22, 1983 Inner projections of the polarization propagator are used to calculate components of the Fermi contact interaction between protons attached to the bridgehead carbon atoms of bicyclo(2,2,1)Heptane. Four- and five-bond paths and throuh-space interaction are ... Full text Cite

The importance of the localization of the π-electron system on its ability to transmit the fermi contact term of HH coupling constants. A theoretical and experimental study

Journal Article Journal of Molecular Structure THEOCHEM · January 1, 1983 Semiquantitative relationships between the localization of a π-electron system and its capacity to contribute to the spin-spin coupling constants are found theoretically and experimentally. Theoretically, enlargements of the INDO basis set and the tautomer ... Full text Cite

The importance of the localization of the π-electron system on its ability to transmit the fermi contact term of HH coupling constants. A theoretical and experimental study

Journal Article Journal of Molecular Structure · January 1, 1983 Semiquantitative relationships between the localization of a π-electron system and its capacity to contribute to the spin-spin coupling constants are found theoretically and experimentally. Theoretically, enlargements of the IN DO basis set and the tautome ... Full text Cite

A general relation between the intrinsic convergence properties of SCF Hartree-Fock calculations and the stability conditions of their solutions

Journal Article Journal of Chemical Physics · January 1, 1983 In this paper, the convergence criteria given by Stanton [J. Chem. Phys. 75, 5416 (1981)] for the Hartree-Fock SCF calculations of closed-shell systems are generalized for an unrestricted one-determinantal Hartree-Fock SCF calculation. Finally, these crite ... Full text Cite

Nuclear magnetic resonance and PCILO study of the side-chain conformations in m-anisaldehyde and 2,5-dimethoxybenzaldehyde

Journal Article Journal of Physical Chemistry · January 1, 1983 A meta effect on the methoxy-group conformation is studied from both an experimental and a theoretical point of view. Experimental NMR data show that, while in m-anisaldehyde (I) both side-chain groups undergo a restricted rotation, in 2,5-dimethoxybenzald ... Full text Cite

A proton NMR analysis of the OCH3 group conformation in 2‐methoxypyridines

Journal Article Organic Magnetic Resonance · January 1, 1982 The absence of HH couplings between the methoxy group and the ring protons observed in 2‐methoxy‐, 2,6‐dimethoxy‐ and 2‐methoxy‐6‐chloropyridines is interpreted in terms of a cis conformation between the methyl fragment and the nitrogen ring atom. Other d ... Full text Cite

The use of partially restricted molecular orbitals to investigate transmission mechanisms of spin–spin coupling constants. III—an INDO study of long‐range FH couplings in fluorinated derivatives of toluene

Journal Article Organic Magnetic Resonance · January 1, 1982 Transmission mechanisms of long‐range FH couplings in several fluorinated derivatives of toluene are analysed carrying out partially restricted molecular orbital calculations at the INDO level of approximation. All π‐components follow the A+B sin2 Full text Cite

The NMR analysis of the methoxy-group conformation in 4-methoxy-2-nitroaniline

Journal Article Journal of Molecular Structure · January 1, 1982 Full text Cite

MNDO and INDO geometrical dependences of the hydrogen diamagnetic shielding tensor of some small molecules

Journal Article Journal of Molecular Structure THEOCHEM · January 1, 1981 The structural dependence of the hydrogen diamagnetic shielding tensor in H2, CH4, NH4+, H2O and HCl has been calculated using MNDO and INDO semiempirical methods. The influence of inner shells as well ... Full text Cite

Transmission mechanisms of inter‐proton long‐range couplings in substituted anisoles

Journal Article Organic Magnetic Resonance · January 1, 1981 Inter‐proton long‐range and ring couplings were measured in o‐anisaldehyde and in seven disubstituted anisoles. In order to investigate the transmission mechanisms of long‐range couplings with the methoxy group, partially restricted molecular orbital (PRMO ... Full text Cite

The use of partially restricted molecular orbitals to investigate transmission mechanisms of spin-spin coupling constants. I. The σ and π contributions within the FPT INDO method

Journal Article Theoretica Chimica Acta · January 1, 1981 Partially restricted INDO MO Calculations have been carried out to separate the π-electron contributions to spin-spin coupling constants in ethylene, butadiene, benzene and toluene. Results reproduce very well known trends such as the pathway invariance, t ... Full text Cite

Inclusion of hydrogen p orbitals in the semiempirical calculation of NMR parameters. III: INDO CHF calculations of orbital and dipolar contributions to spin–spin coupling constants involving protons

Journal Article International Journal of Quantum Chemistry · January 1, 1981 The self‐consistent perturbation theory is used to calculate noncontract contributions to spin–spin coupling constants involving protons. Molecular wave functions were obtained with a modified version of the INDO method which includes hydrogen 2p orbitals ... Full text Cite

Inclusion of hydrogen p orbitals in the semiempirical calculation of NMR parameters. II. Influence on the geometrical dependence of the FPT-INDO spin-spin coupling constants

Journal Article Journal of Molecular Structure THEOCHEM · January 1, 1981 In this paper the structural dependence of coupling constants when hydrogen 2p orbitals are introduced into the FPT-INDO basis set is analyzed. In general it is found that trends in these dependences change to a greater extent than they do in the coupling ... Full text Cite

Population Analysis with Hydrogen 2 p Polarization Functions Included in the INDO Basis Set

Journal Article Zeitschrift Fur Naturforschung Section A Journal of Physical Sciences · December 1, 1980 Mulliken population analysis with 2p polarization functions included in the AO basis set of the INDO method has been performed for a set of molecules containing hydrogen as well as first row atoms. It is found that this enlargement of the basis set yields ... Full text Cite

Influence of the INDO parameterization on the indirect spin–spin coupling constants as calculated by the FPT INDO method

Journal Article Organic Magnetic Resonance · January 1, 1980 Alterations have been introduced in the semi‐empirical INDO parameters in order to study their influence on the Fermi contact term of the indirect spin–spin coupling constants as calculated by the finite perturbation theory (FPT). For this purpose a set of ... Full text Cite

The contribution of molecular vibrations to calculated spin-spin coupling constants: A comparison of different commonly-used methods

Journal Article Journal of Molecular Structure · January 1, 1979 The different methods commonly used to determine vibrational corrections to the calculated coupling constants, J, are compared, with reference to the HD and HF molecules. Calculations are carried out using ab initio and semi-empirical FPT INDO methods. It ... Full text Cite