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Conformational sampling of macrocyclic alkenes using a Kennard Stone-based algorithm

Diederica Claeys UGent, Toon Verstraelen UGent, Ewald Pauwels UGent, Chris Stevens UGent, Michel Waroquier UGent and Veronique Van Speybroeck UGent (2010) JOURNAL OF PHYSICAL CHEMISTRY A. 114(25). p.6879-6887
abstract
The properties and functions of (bio)molecules are closely related to their molecular conformations. A variety of methods are available to sample the conformational space at a relatively low level of theory. If a higher level of theory is required, the computational cost can be reduced by selecting a uniformly distributed set of conformations from the ensemble of conformations generated at a low level of theory and by optimizing this selected set at a higher level. The generation of conformers is performed using molecular dynamics runs which are analyzed using the MD-Tracks code [J. Chem. Inf. Model. 2008, 48, 2414]. This article presents a Kennard Stone-based algorithm, with a distance measure based on the distance matrix, for the selection of the most diverse set of conformations. The method has been successfully applied to macrocyclic alkenes. The correct thermodynamic stability of the double-bond isomers of a flexible macrocyclic alkene containing two chiral centers is reproduced. The double-bond configuration has a limited effect on the conformation of the whole macrocycle. The chirality of the stereocenters has a larger effect on the molecular conformations.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
FREE-ENERGY, RUTHENIUM COMPLEXES, DYNAMICS METHOD, ORGANIC-SYNTHESIS, OLEFIN METATHESIS, MONTE-CARLO, GAUSSIAN-TYPE BASIS, MOLECULAR-ORBITAL METHODS, RING-CLOSING METATHESIS, MP2 ENERGY
journal title
JOURNAL OF PHYSICAL CHEMISTRY A
J. Phys. Chem. A
volume
114
issue
25
pages
6879 - 6887
Web of Science type
Article
Web of Science id
000278981900019
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
2.732 (2010)
JCR rank
8/31 (2010)
JCR quartile
2 (2010)
ISSN
1089-5639
DOI
10.1021/jp1022778
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1002424
handle
http://hdl.handle.net/1854/LU-1002424
date created
2010-07-05 13:47:07
date last changed
2013-09-17 10:50:08
@article{1002424,
  abstract     = {The properties and functions of (bio)molecules are closely related to their molecular conformations. A variety of methods are available to sample the conformational space at a relatively low level of theory. If a higher level of theory is required, the computational cost can be reduced by selecting a uniformly distributed set of conformations from the ensemble of conformations generated at a low level of theory and by optimizing this selected set at a higher level. The generation of conformers is performed using molecular dynamics runs which are analyzed using the MD-Tracks code [J. Chem. Inf. Model. 2008, 48, 2414]. This article presents a Kennard Stone-based algorithm, with a distance measure based on the distance matrix, for the selection of the most diverse set of conformations. The method has been successfully applied to macrocyclic alkenes. The correct thermodynamic stability of the double-bond isomers of a flexible macrocyclic alkene containing two chiral centers is reproduced. The double-bond configuration has a limited effect on the conformation of the whole macrocycle. The chirality of the stereocenters has a larger effect on the molecular conformations.},
  author       = {Claeys, Diederica and Verstraelen, Toon and Pauwels, Ewald and Stevens, Chris and Waroquier, Michel and Van Speybroeck, Veronique},
  issn         = {1089-5639},
  journal      = {JOURNAL OF PHYSICAL CHEMISTRY A},
  keyword      = {FREE-ENERGY,RUTHENIUM COMPLEXES,DYNAMICS METHOD,ORGANIC-SYNTHESIS,OLEFIN METATHESIS,MONTE-CARLO,GAUSSIAN-TYPE BASIS,MOLECULAR-ORBITAL METHODS,RING-CLOSING METATHESIS,MP2 ENERGY},
  language     = {eng},
  number       = {25},
  pages        = {6879--6887},
  title        = {Conformational sampling of macrocyclic alkenes using a Kennard Stone-based algorithm},
  url          = {http://dx.doi.org/10.1021/jp1022778},
  volume       = {114},
  year         = {2010},
}

Chicago
Claeys, Diederica, Toon Verstraelen, Ewald Pauwels, Chris Stevens, Michel Waroquier, and Veronique Van Speybroeck. 2010. “Conformational Sampling of Macrocyclic Alkenes Using a Kennard Stone-based Algorithm.” Journal of Physical Chemistry A 114 (25): 6879–6887.
APA
Claeys, Diederica, Verstraelen, T., Pauwels, E., Stevens, C., Waroquier, M., & Van Speybroeck, V. (2010). Conformational sampling of macrocyclic alkenes using a Kennard Stone-based algorithm. JOURNAL OF PHYSICAL CHEMISTRY A, 114(25), 6879–6887.
Vancouver
1.
Claeys D, Verstraelen T, Pauwels E, Stevens C, Waroquier M, Van Speybroeck V. Conformational sampling of macrocyclic alkenes using a Kennard Stone-based algorithm. JOURNAL OF PHYSICAL CHEMISTRY A. 2010;114(25):6879–87.
MLA
Claeys, Diederica, Toon Verstraelen, Ewald Pauwels, et al. “Conformational Sampling of Macrocyclic Alkenes Using a Kennard Stone-based Algorithm.” JOURNAL OF PHYSICAL CHEMISTRY A 114.25 (2010): 6879–6887. Print.