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In silico geometric and energetic data of all possible simple rotamers made of non-metal elements.

ABSTRACT: This article presents theoretical data on geometric and energetic features of halogenated rotamers of the following backbone structures, C-C, N-N, P-P, O-O, S-S, N-P, O-S, C-N, C-P, C-O, C-S, N-O, N-S, P-O and P-S. The data is considered to be comprehensive combinations of non-metal elements in the form abcx-ydef whereby a,b,c,d,e,f are halogen (fluorine to iodine), hydrogen or a lone pair and x,y are carbon, nitrogen, phosphorus, oxygen and sulfur. Data were obtained from ab initio geometry optimization and frequency calculations at HF, B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 8535 non-enantiomeric structures were produced by custom-made codes in Mathematica and Q-Chem quantum chemical package. Extracted geometric and energetic data as well as raw output files, codes and scripts associated with the data production are presented in the data repository.

SUBMITTER: Limpanuparb T

PROVIDER: S-EPMC7150501 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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<i>In silico</i> geometric and energetic data of all possible simple rotamers made of non-metal elements.

Limpanuparb Taweetham T Datta Sopanant S Chinsukserm Kridtin K Teeraniramitr Peerayar P

Data in brief 20200319

This article presents theoretical data on geometric and energetic features of halogenated rotamers of the following backbone structures, C-C, N-N, P-P, O-O, S-S, N-P, O-S, C-N, C-P, C-O, C-S, N-O, N-S, P-O and P-S. The data is considered to be comprehensive combinations of non-metal elements in the form abcx-ydef whereby a,b,c,d,e,f are halogen (fluorine to iodine), hydrogen or a lone pair and x,y are carbon, nitrogen, phosphorus, oxygen and sulfur. Data were obtained from <i>ab initio</i> geome ...[more]

PMID: 32292807

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Project description:BackgroundThe increasing use of common data elements (CDEs) in numerous research projects and clinical applications has made it imperative to create an effective classification scheme for the efficient management of these data elements. We applied high-level integrative modeling of entire clinical documents from real-world practice to create the Clinical MetaData Ontology (CMDO) for the appropriate classification and integration of CDEs that are in practical use in current clinical documents.MethodsCMDO was developed using the General Formal Ontology method with a manual iterative process comprising five steps: (1) defining the scope of CMDO by conceptualizing its first-level terms based on an analysis of clinical-practice procedures, (2) identifying CMDO concepts for representing clinical data of general CDEs by examining how and what clinical data are generated with flows of clinical care practices, (3) assigning hierarchical relationships for CMDO concepts, (4) developing CMDO properties (e.g., synonyms, preferred terms, and definitions) for each CMDO concept, and (5) evaluating the utility of CMDO.ResultsWe created CMDO comprising 189 concepts under the 4 first-level classes of Description, Event, Finding, and Procedure. CMDO has 256 definitions that cover the 189 CMDO concepts, with 459 synonyms for 139 (74.0%) of the concepts. All of the CDEs extracted from 6 HL7 templates, 25 clinical documents of 5 teaching hospitals, and 1 personal health record specification were successfully annotated by 41 (21.9%), 89 (47.6%), and 13 (7.0%) of the CMDO concepts, respectively. We created a CMDO Browser to facilitate navigation of the CMDO concept hierarchy and a CMDO-enabled CDE Browser for displaying the relationships between CMDO concepts and the CDEs extracted from the clinical documents that are used in current practice.ConclusionsCMDO is an ontology and classification scheme for CDEs used in clinical documents. Given the increasing use of CDEs in many studies and real-world clinical documentation, CMDO will be a useful tool for integrating numerous CDEs from different research projects and clinical documents. The CMDO Browser and CMDO-enabled CDE Browser make it easy to search, share, and reuse CDEs, and also effectively integrate and manage CDEs from different studies and clinical documents.

Dataset Information

In silico geometric and energetic data of all possible simple rotamers made of non-metal elements.

Publications

<i>In silico</i> geometric and energetic data of all possible simple rotamers made of non-metal elements.

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