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Atomic velocity projection method: a new analysis method for vibrational spectra in terms of internal coordinates for a better understanding of zeolite nanogrowth

Marc Van Houteghem UGent, Toon Verstraelen UGent, Dimitri Van Neck UGent, Christine Kirschhock, Johan A Martens, Michel Waroquier UGent and Veronique Van Speybroeck UGent (2011) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 7(4). p.1045-1061
abstract
An efficient protocol is presented to identify signals in vibrational spectra of silica oligomers based on theoretical molecular dynamics (MD) simulations. The method is based on the projection of the atomic velocity vectors on the tangential directions of the trajectories belonging to a predefined set of internal coordinates. In this way only contributions of atomic motions along these internal coordinates are taken into consideration. The new methodology is applied to the spectra of oligomers and rings, which play an important role in zeolite synthesis. A suitable selection of the relevant internal coordinates makes the protocol very efficient but relies on intuition and theoretical insight. The simulation data necessary to compute vibrational spectra of relevant silica species are obtained through MD using proper force fields. The new methodology the so-called velocity projection method makes a detailed analysis of vibrational spectra possible by establishing a one-to-one correspondence between a spectral signal and a proper internal coordinate. It offers valuable perspectives in understanding the elementary steps in silica organization during zeolite nanogrowth. The so-called velocity projection method is generally applicable on data obtained from all types of MD and is a highly valuable alternative to normal-mode analysis which has its limitations due to the presence of many local minima on the potential energy surface. In this work the method is exclusively applied to inelastic neutron scattering, but extension to the infrared power spectrum is apparent.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
INFRARED-SPECTRA, MFI ZEOLITE, MOLECULAR-DYNAMICS, VITREOUS SILICA, RING STRUCTURES, AB-INITIO, NUCLEATION, TPA-SILICALITE-1, CRYSTALLIZATION, IDENTIFICATION
journal title
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
J. Chem. Theory Comput.
volume
7
issue
4
pages
1045 - 1061
Web of Science type
Article
Web of Science id
000289315700027
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
5.215 (2011)
JCR rank
2/32 (2011)
JCR quartile
1 (2011)
ISSN
1549-9618
DOI
10.1021/ct100538c
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
1214482
handle
http://hdl.handle.net/1854/LU-1214482
date created
2011-04-29 08:15:23
date last changed
2013-09-17 10:46:15
@article{1214482,
  abstract     = {An efficient protocol is presented to identify signals in vibrational spectra of silica oligomers based on theoretical molecular dynamics (MD) simulations. The method is based on the projection of the atomic velocity vectors on the tangential directions of the trajectories belonging to a predefined set of internal coordinates. In this way only contributions of atomic motions along these internal coordinates are taken into consideration. The new methodology is applied to the spectra of oligomers and rings, which play an important role in zeolite synthesis. A suitable selection of the relevant internal coordinates makes the protocol very efficient but relies on intuition and theoretical insight. The simulation data necessary to compute vibrational spectra of relevant silica species are obtained through MD using proper force fields. The new methodology the so-called velocity projection method makes a detailed analysis of vibrational spectra possible by establishing a one-to-one correspondence between a spectral signal and a proper internal coordinate. It offers valuable perspectives in understanding the elementary steps in silica organization during zeolite nanogrowth. The so-called velocity projection method is generally applicable on data obtained from all types of MD and is a highly valuable alternative to normal-mode analysis which has its limitations due to the presence of many local minima on the potential energy surface. In this work the method is exclusively applied to inelastic neutron scattering, but extension to the infrared power spectrum is apparent.},
  author       = {Van Houteghem, Marc and Verstraelen, Toon and Van Neck, Dimitri and Kirschhock, Christine and Martens, Johan A and Waroquier, Michel and Van Speybroeck, Veronique},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  keyword      = {INFRARED-SPECTRA,MFI ZEOLITE,MOLECULAR-DYNAMICS,VITREOUS SILICA,RING STRUCTURES,AB-INITIO,NUCLEATION,TPA-SILICALITE-1,CRYSTALLIZATION,IDENTIFICATION},
  language     = {eng},
  number       = {4},
  pages        = {1045--1061},
  title        = {Atomic velocity projection method: a new analysis method for vibrational spectra in terms of internal coordinates for a better understanding of zeolite nanogrowth},
  url          = {http://dx.doi.org/10.1021/ct100538c},
  volume       = {7},
  year         = {2011},
}

Chicago
Van Houteghem, Marc, Toon Verstraelen, Dimitri Van Neck, Christine Kirschhock, Johan A Martens, Michel Waroquier, and Veronique Van Speybroeck. 2011. “Atomic Velocity Projection Method: a New Analysis Method for Vibrational Spectra in Terms of Internal Coordinates for a Better Understanding of Zeolite Nanogrowth.” Journal of Chemical Theory and Computation 7 (4): 1045–1061.
APA
Van Houteghem, M., Verstraelen, T., Van Neck, D., Kirschhock, C., Martens, J. A., Waroquier, M., & Van Speybroeck, V. (2011). Atomic velocity projection method: a new analysis method for vibrational spectra in terms of internal coordinates for a better understanding of zeolite nanogrowth. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7(4), 1045–1061.
Vancouver
1.
Van Houteghem M, Verstraelen T, Van Neck D, Kirschhock C, Martens JA, Waroquier M, et al. Atomic velocity projection method: a new analysis method for vibrational spectra in terms of internal coordinates for a better understanding of zeolite nanogrowth. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2011;7(4):1045–61.
MLA
Van Houteghem, Marc, Toon Verstraelen, Dimitri Van Neck, et al. “Atomic Velocity Projection Method: a New Analysis Method for Vibrational Spectra in Terms of Internal Coordinates for a Better Understanding of Zeolite Nanogrowth.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7.4 (2011): 1045–1061. Print.