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Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

Hermida-Ramon, J M; Brdarski, S; Karlström, Gunnar LU and Berg, Ulf LU (2003) In Journal of Computational Chemistry 24(2). p.161-176
Abstract
An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF... (More)
An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 161-176, 2003 (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Computational Chemistry
volume
24
issue
2
pages
161 - 176
publisher
John Wiley & Sons
external identifiers
  • wos:000180233000004
  • pmid:12497597
  • scopus:0037472684
ISSN
1096-987X
DOI
10.1002/jcc.10159
language
English
LU publication?
yes
id
4de56144-bbd6-4493-9f89-bc84328176e0 (old id 128702)
date added to LUP
2007-07-10 10:54:27
date last changed
2018-10-03 10:59:48
@article{4de56144-bbd6-4493-9f89-bc84328176e0,
  abstract     = {An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 161-176, 2003},
  author       = {Hermida-Ramon, J M and Brdarski, S and Karlström, Gunnar and Berg, Ulf},
  issn         = {1096-987X},
  language     = {eng},
  number       = {2},
  pages        = {161--176},
  publisher    = {John Wiley & Sons},
  series       = {Journal of Computational Chemistry},
  title        = {Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields},
  url          = {http://dx.doi.org/10.1002/jcc.10159},
  volume       = {24},
  year         = {2003},
}