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Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules

An Ghysels UGent, Veronique Van Speybroeck UGent, Ewald Pauwels UGent, Dimitri Van Neck UGent, Bernard R. Brooks and Michel Waroquier UGent (2009) Journal of Chemical Theory and Computation. 5(5). p.1203-1215
abstract
In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102.]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
AQUEOUS-SOLUTION, SIMULATIONS, FERMI RESONANCES, ALANINE DIPEPTIDE, NORMAL-MODE ANALYSIS, AB-INITIO, CLUSTER CALCULATIONS, VIBRATIONAL ANALYSIS, PROTEIN DYNAMICS, METHOXY ADSORPTION
journal title
Journal of Chemical Theory and Computation
J. Chem. Theory Comput.
volume
5
issue
5
pages
1203 - 1215
Web of Science type
Article
Web of Science id
000265991000002
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
4.804 (2009)
JCR rank
2/33 (2009)
JCR quartile
1 (2009)
ISSN
1549-9618
DOI
10.1021/ct800489r
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
additional info
Fund for Scientific Research - Flanders (FWO) ; Research Board of Ghent University (BOF) ; Belgian Program on Interuniversity Attraction Poles (IAP) A.G. is Aspirant of the Fund for Scientific Research - Flanders (FWO). This work was by the Fund for Scientific Research - Flanders (FWO), the Research Board of Ghent University (BOF), and the Belgian Program on Interuniversity Attraction Poles (IAP).
id
484379
handle
http://hdl.handle.net/1854/LU-484379
date created
2009-02-12 14:44:02
date last changed
2015-06-17 11:07:55
@article{484379,
  abstract     = {In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102.]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.},
  author       = {Ghysels, An and Van Speybroeck, Veronique and Pauwels, Ewald and Van Neck, Dimitri and Brooks, Bernard R. and Waroquier, Michel},
  issn         = {1549-9618},
  journal      = {Journal of Chemical Theory and Computation},
  keyword      = {AQUEOUS-SOLUTION,SIMULATIONS,FERMI RESONANCES,ALANINE DIPEPTIDE,NORMAL-MODE ANALYSIS,AB-INITIO,CLUSTER CALCULATIONS,VIBRATIONAL ANALYSIS,PROTEIN DYNAMICS,METHOXY ADSORPTION},
  language     = {eng},
  number       = {5},
  pages        = {1203--1215},
  title        = {Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules},
  url          = {http://dx.doi.org/10.1021/ct800489r},
  volume       = {5},
  year         = {2009},
}

Chicago
Ghysels, An, Veronique Van Speybroeck, Ewald Pauwels, Dimitri Van Neck, Bernard R. Brooks, and Michel Waroquier. 2009. “Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules.” Journal of Chemical Theory and Computation 5 (5): 1203–1215.
APA
Ghysels, A., Van Speybroeck, V., Pauwels, E., Van Neck, D., Brooks, B. R., & Waroquier, M. (2009). Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules. Journal of Chemical Theory and Computation, 5(5), 1203–1215.
Vancouver
1.
Ghysels A, Van Speybroeck V, Pauwels E, Van Neck D, Brooks BR, Waroquier M. Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules. Journal of Chemical Theory and Computation. 2009;5(5):1203–15.
MLA
Ghysels, An, Veronique Van Speybroeck, Ewald Pauwels, et al. “Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules.” Journal of Chemical Theory and Computation 5.5 (2009): 1203–1215. Print.