A Computer Program for the Simulation of the NOE Effect in NMR
Spectroscopy, and Its Implementation into the CICADA
Conformational Search Program

J 2003

A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program

KŘÍŽ, Zdeněk; Jaroslav KOČA a Per H. J. CARLSEN

Základní údaje

Originální název

A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program

Autoři

KŘÍŽ, Zdeněk (203 Česká republika, garant); Jaroslav KOČA (203 Česká republika) a Per H. J. CARLSEN (578 Norsko)

Vydání

Internet Electronic Journal of Molecular Design, BioChem Press, 2003, 1538-6414

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14310/03:00009077

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Nuclear Overhauser Enhancement; Computer simulation; molecular mechanics; dingle coordinate driving method

Štítky

computer simulation, dingle coordinate driving method, molecular mechanics, Nuclear Overhauser Enhancement

Změněno: 22. 11. 2004 16:00, prof. RNDr. Jaroslav Koča, DrSc.

Anotace

V originále

Motivation. Three dimensional structure plays increasing role in the design of molecules with predefined features. Therefore, further development of methods that give 3 D information is necessary. Many molecules of interest are conformationally flexible and difficulties with interpretation of experimental (for example, Nuclear Magnetic Resonance) data may occur. Computational methods are promising tools that can assist to eliminate the above problems. To begin with, however, computational methods and computer programs must be developed that are able to reproduce data for conformationally rigid molecules. Method. The previously developed computer program CICADA was used to describe conformational Potential Energy Surfaces (PESs) of selected molecules. The conformational flexibility of these molecules was deduced from the PESs. Equations describing the NMR technique termed Nuclear Overhauser Enhancement (NOE) were used to characterize NOE for different conformations. Results. The computer program NOESIM for NOE enhancement calculation has been developed. This program is implemented as part of the CICADA computer program package. Five different models have been implemented, tested for relaxation rate calculation of methyl groups, and their results compared. Conclusions. It is shown that NOESIM adequately predicts the experimental NOE effects for rigid molecules. The effort in the future will be improve its performance also for use with flexible systems, for example, Boltzmann distribution of conformers or flexibility of conformers.

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

KŘÍŽ, Zdeněk; Jaroslav KOČA a Per H. J. CARLSEN. A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program. Internet Electronic Journal of Molecular Design. BioChem Press, 2003, roč. 2, č. 2, s. 55-69. ISSN 1538-6414.

@article{490001,
   author = {Kříž, Zdeněk and Koča, Jaroslav and Carlsen, Per H. J.},
   article_number = {2},
   keywords = {Nuclear Overhauser Enhancement; Computer simulation; molecular mechanics; dingle coordinate driving method},
   language = {eng},
   issn = {1538-6414},
   journal = {Internet Electronic Journal of Molecular Design},
   title = {A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program},
   volume = {2},
   year = {2003}
}

TY  - JOUR
ID  - 490001
AU  - Kříž, Zdeněk - Koča, Jaroslav - Carlsen, Per H. J.
PY  - 2003
TI  - A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program
JF  - Internet Electronic Journal of Molecular Design
VL  - 2
IS  - 2
SP  - 55-69
EP  - 55-69
PB  - BioChem Press
SN  - 15386414
KW  - Nuclear Overhauser Enhancement
KW  - Computer simulation
KW  - molecular mechanics
KW  - dingle coordinate driving method
N2  - Motivation. Three dimensional structure plays increasing role in the design of molecules with predefined features. Therefore, further development of methods that give 3 D information is necessary. Many molecules of interest are conformationally flexible and difficulties with interpretation of experimental (for example, Nuclear Magnetic Resonance) data may occur. Computational methods are promising tools that can assist to eliminate the above problems. To begin with, however, computational methods and computer programs must be developed that are able to reproduce data for conformationally rigid molecules. Method. The previously developed computer program CICADA was used to describe conformational Potential Energy Surfaces (PESs) of selected molecules. The conformational flexibility of these molecules was deduced from the PESs. Equations describing the NMR technique termed Nuclear Overhauser Enhancement (NOE) were used to characterize NOE for different conformations. Results. The computer program NOESIM for NOE enhancement calculation has been developed. This program is implemented as part of the CICADA computer program package. Five different models have been implemented, tested for relaxation rate calculation of methyl groups, and their results compared. Conclusions. It is shown that NOESIM adequately predicts the experimental NOE effects for rigid molecules. The effort in the future will be improve its performance also for use with flexible systems, for example, Boltzmann distribution of conformers or flexibility of conformers.
ER  -

KŘÍŽ, Zdeněk; Jaroslav KOČA a Per H. J. CARLSEN. A Computer Program for the Simulation of the NOE Effect in NMR Spectroscopy, and Its Implementation into the CICADA Conformational Search Program. \textit{Internet Electronic Journal of Molecular Design}. BioChem Press, 2003, roč.~2, č.~2, s.~55-69. ISSN~1538-6414.

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