Fast vibrational analysis of molecular systems.
FTIR
computational chemistry
potential energy distribution
vibrations
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
30 Oct 2024
30 Oct 2024
Historique:
revised:
04
06
2024
received:
01
02
2024
accepted:
07
06
2024
medline:
2
9
2024
pubmed:
2
9
2024
entrez:
2
9
2024
Statut:
ppublish
Résumé
The development of infrared difference spectroscopy provides unprecedented insights on structures of complex molecules like metalloproteins. However, the relevant information can be hard to find among the many bands of the vibrational spectra. The ab initio modeling is very helpful to assign the frequencies to vibrational modes but it is a challenge to process the huge quantity of data into descriptors useful for experimentalists. To this end, we developed a new tool called VIBMOL allowing to analyze vibrational modes of molecules from hessian matrices calculated with common quantum chemistry codes. VIBMOL program runs on Unix machines. Through a new graphical interface, the users can calculate the normal modes of molecules, visualize them, simulate infrared spectra, and explore the Potential Energy Distribution of normal modes among any set of vibration coordinates. It is combined with an interface program (gosdmu) formatting relevant data from the GAUSSIAN program. VIBMOL code is available upon request to the authors. A discussion is provided to help the readers to choose between a large choice of different software and it shows how VIBMOL can make the IR assignment easier in the context of collaborations with experimentalists.
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
2374-2382Informations de copyright
© 2024 Wiley Periodicals LLC.
Références
C. Berthomieu, R. Hienerwadel, Photosynth. Res. 2009, 101, 157.
V. A. Lorenz‐Fonfria, Chem. Rev. 2020, 120, 3466.
B. Xerri, J. P. Flament, H. Petitjean, C. Berthomieu, D. Berthomieu, J. Phys. Chem. B 2009, 113, 15119.
S. Wolf, E. Freier, Q. Cui, K. Gerwert, J. Chem. Phys. 2014, 141, 22D524.
S. Nakamura, T. Noguchi, Proc. Natl. Acad. Sci. 2016, 113, 12727.
J. J. Goings, P. Li, Q. Zhu, S. Hammes‐Schiffer, Proc. Natl. Acad. Sci. 2020, 117, 26626.
M. Huix‐Rotllant, K. Schwinn, N. Ferré, Phys. Chem. Chem. Phys. 2021, 23, 1666.
E. B. Wilson Jr., J. C. Decius, P. C. Cross, Molecular Vibrations, McGraw‐Hill Book Co, New York 1955, p. 388.
P. Pulay, G. Foregasi, F. Pang, J. E. Boggs, J. Am. Chem. Soc. 1979, 101, 2550.
M. Huix‐Rotllant, N. Ferré, J. Chem. Theory Comput. 2016, 12, 4768.
Y. Tao, C. Tian, N. Verma, W. Zou, C. Wang, D. Cremer, E. Kraka, J. Chem. Theory Comput. 2018, 14, 2558.
F. Teixeira, M. N. D. S. Cordeiro, J. Chem. Theory Comput. 2019, 15, 456.
M.‐P. Gaigeot, M. Martinez, R. Vuilleumier, Mol. Phys. 2008, 05, 2857.
C. Eckart, Phys. Rev. 1935, 47, 552.
R. J. Malhiot, S. M. Ferigle, J. Chem. Phys. 1954, 22, 717.
Y. Morino, K. Kuchitsu, J. Chem. Phys. 1952, 20, 1809.
P. Torkington, J. Chem. Phys. 1949, 17, 357.
Z. Konkoli, D. Cremer, Int. J. Quantum Chem. 1998, 67, 1.
Z. Konkoli, D. Cremer, Int. J. Quantum Chem. 1998, 67, 29.
Z. Konkoli, J. A. Larsson, D. Cremer, Int. J. Quantum Chem. 1998, 67, 11.
Z. Konkoli, J. A. Larsson, D. Cremer, Int. J. Quantum Chem. 1998, 67, 41.
C. R. Jacob, M. Reiher, J. Chem. Phys. 2009, 130, 084106/1.
M. H. Jamroz, Spectrochim. Acta, Part A 2013, 114, 220.
J. H. Schachtschneider, R. G. Snyder, Spectrochim. Acta 1963, 19, 117.
T. Shimanouchi, NCTB, Computer program for Normal Coordinate Treatment of Polyatomic Molecules, Tokyo University, Tokyo 1968.
W. J. Taylor, J. Chem. Phys. 1954, 22, 1780.
J. H. Schachtschneider, FPERT, Adv. Chromatogr. Technical Report 1964, 19, 231.
W. J. O. Thomas, J. Chem. Phys. 1951, 19, 1162.
R. G. Snyder, J. H. Schachtschneider, Spectrochim. Acta 1965, 21, 169.
M. Tatsumi, T. Shimanouchi, Mol. Spectrosc. 1963, 11, 422.
A. J. P. Alix, D. E. Freeman, A. Muller, Zeitschrift für Naturforschung A 1974, 29, 1454.
E. Geidel, K. Krause, H. Foerster, F. Bauer, J. Chem. Soc. Faraday Trans. 1997, 93, 1439.
L. Marboutin, H. Petitjean, B. Xerri, N. Vita, F. Dupeyrat, J.‐P. Flament, D. Berthomieu, C. Berthomieu, Angew. Chem. Int. Ed. 2011, 50, 8062.
S. J. Cyvin, Acta Chim. Scand. 1966, 120, 2616.
P. Youkharibache, Doctorat d'Etat es‐sciences physiques, Université Pierre et Marie Curie ‐PARIS VI, Paris 1986.
G. Fogarasi, X. Zhou, P. W. Taylor, P. Pulay, J. Am. Chem. Soc. 1992, 114, 8191.
Y. Morino, T. Shimanouchi, Pure Appl. Chem. 1978, 50, 1707.
C. E. Sun, R. G. Parr, B. L. Crawford Jr., J. Chem. Phys. 1949, 17, 840.
P. Vismara, Electron. J. Comb. 1997, 4.
J. M. L. Martin, C. Van Alsenoy, GAR2PED, University of Antwerp, Antwerp 1995.
M. H. Jamróz, Vibrational Energy Distribution Analysis: VEDA 4. http://www.smmg.pl/, 2004–2010
T. Sundius, J. Mol. Struct. 1990, 218, 321.
T. Sundius, molvib: A program for harmonic force field calculations, QCPE Program, No. 604 (1991) and Molvib7 (2000). https://www.mv.helsinki.fi/home/sundius/molvib.html; 1991
T. Sundius, Vib. Spectrosc. 2002, 29, 89.