How to understand quantum chemical computations on DNA and RNA
systems? A practical guide for non-specialists

J 2013

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Pavel BANÁŠ, Petr JURECKA et. al.

Basic information

Original name

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

Authors

ŠPONER, Jiří (203 Czech Republic, guarantor, belonging to the institution), Judit ŠPONEROVÁ (348 Hungary, belonging to the institution), Arnošt MLÁDEK (203 Czech Republic, belonging to the institution), Pavel BANÁŠ (203 Czech Republic), Petr JURECKA (203 Czech Republic) and Michal OTYEPKA (203 Czech Republic)

Edition

Methods, SAN DIEGO, ACADEMIC PRESS INC ELSEVIER SCIENCE, 2013, 1046-2023

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 3.221

RIV identification code

RIV/00216224:14740/13:00072151

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1016/j.ymeth.2013.05.025

UT WoS

000326430100002

Keywords in English

DNA structure; Quantum chemistry; Molecular mechanics; Molecular structures and energies

Abstract

V originále

In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments. (C) 2013 Elsevier Inc. All rights reserved.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Pavel BANÁŠ, Petr JURECKA and Michal OTYEPKA. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE, 2013, vol. 64, No 1, p. 3-11. ISSN 1046-2023. Available from: https://dx.doi.org/10.1016/j.ymeth.2013.05.025.

@article{1165569,
   author = {Šponer, Jiří and Šponerová, Judit and Mládek, Arnošt and Banáš, Pavel and Jurecka, Petr and Otyepka, Michal},
   article_location = {SAN DIEGO},
   article_number = {1},
   doi = {http://dx.doi.org/10.1016/j.ymeth.2013.05.025},
   keywords = {DNA structure; Quantum chemistry; Molecular mechanics; Molecular structures and energies},
   language = {eng},
   issn = {1046-2023},
   journal = {Methods},
   title = {How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists},
   volume = {64},
   year = {2013}
}

TY  - JOUR
ID  - 1165569
AU  - Šponer, Jiří - Šponerová, Judit - Mládek, Arnošt - Banáš, Pavel - Jurecka, Petr - Otyepka, Michal
PY  - 2013
TI  - How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists
JF  - Methods
VL  - 64
IS  - 1
SP  - 3-11
EP  - 3-11
PB  - ACADEMIC PRESS INC ELSEVIER SCIENCE
SN  - 10462023
KW  - DNA structure
KW  - Quantum chemistry
KW  - Molecular mechanics
KW  - Molecular structures and energies
N2  - In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments. (C) 2013 Elsevier Inc. All rights reserved.
ER  -

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Pavel BANÁŠ, Petr JURECKA and Michal OTYEPKA. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. \textit{Methods}. SAN DIEGO: ACADEMIC PRESS INC ELSEVIER SCIENCE, 2013, vol.~64, No~1, p.~3-11. ISSN~1046-2023. Available from: https://dx.doi.org/10.1016/j.ymeth.2013.05.025.

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