Synonyms
Definition
Quantum mechanical (QM) simulations of vibrational spectra use fundamental QM methods to determine the force field (FF) and predict the frequencies and intensities of IR and Raman spectral transitions with varying degrees of approximations appropriate to biopolymer applications.
Introduction
Vibrational spectroscopic methods provide important experimental data for studies of biological molecules, peptides, proteins, nucleic acids, and lipids, which are often interpreted via empirical correlation of frequencies and intensities with molecular properties (Hering and Haris 2009; Krimm and Bandekar 1986; Mantsch and Chapman 1996; Tsuboi 1987). However, to develop a deeper understanding of the observed spectra and the changes they undergo when the structure or environment varies, theoretical simulations of the spectra are needed. Initially, empirical models for force field (FF) calculations based on parameters derived from fitting...
This is a preview of subscription content, log in via an institution to check access.
References
Bartolotti LJ, Flurchick K (1996) An introduction to density functional theory. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry, vol 7. VCH, New York
Becke AD (1995) Exchange-correlation approximations in density functional theory. In: Yarkony DR (ed) Modern electronic structure theory, vol 2. World Scientific, Singapore, pp 1022–1046
Bour P, Kubelka J, Keiderling TA (2000) Simulations of oligopeptide vibrational circular dichroism. Effects of isotopic labeling. Biopolymers 53:380–395
Choi JH, Cho M (2009) Computational linear and non-linear IR spectroscopy of amide I vibrations in proteins. In: Barth A, Haris PI (eds) Biological and biomedical infrared spectroscopy, vol 2. IOS Press, Amsterdam, pp 224–260
Colvin ME, Cramer CJ, Dykstra CE, Jensen JH, Krimm S, Rivail J-L, Thakkar AJ, Yanez M (2006) Molecular quantum mechanics to biodynamics: essential connections. J Mol Struct Theochem 764:1–8
Grahnen JA, Amunson KE, Kubelka J (2010) DFT-based simulations of IR amide I’ spectra for a small protein in solution. Comparison of explicit and empirical solvent models. J Phys Chem B 114:13011–13020
Hering JA, Haris PI (2009) FTIR spectroscopy for analysis of protein secondary structure. In: Barth A, Haris PI (eds) Biological and biomedical infrared spectroscopy, vol 2. IOS Press, Amsterdam, pp 129–167
Kessler J, Keiderling TA, Bour P (2014) Arrangement of fibril side chains studied by molecular dynamics and simulated infrared and vibrational circular dichroism spectra. J Phys Chem B 118:6937–6945
Kessler J, Kapitan J, Bour P (2015) First-principles predictions of vibrational Raman optical activity of globular proteins. J Phys Chem Lett 6:3314–3319
Krimm S (1999) Vibrational spectroscopy of polypeptides. In: Zerbi G (ed) Modern polymer spectroscopy. Wiley-VCH, Weinheim
Krimm S (2000) Interpreting infrared spectra of peptides and proteins. In: Singh BR (ed) Infrared analysis of peptides and proteins. Principles and applications, ACS Symposium Series. American Chemical Society, Washington, DC, pp 38–53
Krimm S, Bandekar J (1986) Vibrational spectroscopy and conformation of peptides, polypeptides and proteins. Adv Protein Chem 38:181–364
Krimm S, Reisdorf WC Jr (1994) Understanding normal modes of proteins. Faraday Discuss 99:181–194
Kubelka J, Keiderling TA (2001) Differentiation of β-sheet-forming structures: Ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein β-sheets. J Am Chem Soc 123:12048–12058
Kubelka J, Silva RAGD, Bour P, Decatur SM, Keiderling TA (2002) Chirality in peptide vibrations. Ab initio computational studies of length, solvation, hydrogen bond, dipole coupling and isotope effects on vibrational cd. In: Hicks JM (ed) Chirality: physical chemistry, ACS Symposium Series, vol 810. American Chemical Society, Washington, DC, pp 50–64
Kubelka J, Huang R, Keiderling TA (2005) Solvent effects on IR and VCD spectra of helical peptides: insights from ab initio spectral simulations with explicit water. J Phys Chem B 109(16):8231–8243
Kubelka J, Bour P, Keiderling TA (2009) Quantum mechanical calculations of peptide vibrational force fields and spectral intensities. In: Barth A, Haris PI (eds) Biological and biomedical infrared spectroscopy, vol 2. IOS Press, Amsterdam, pp 178–223
Mantsch HH, Chapman D (1996) Infrared spectroscopy of biomolecules. Wiley-Liss, Chichester
McGill PMW (1998) Density functional theory, Hartree-Fock and the self-consistent field. In: Schleyer PR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaeffer HF, Schreiner PR (eds) Encyclopedia of computational chemistry, vol 1. Wiley, Chichester, pp 678–689
Miyazawa T (1960) Perturbation treatment of the characteristic vibrations of polypeptide chains in various configurations. J Chem Phys 32:1647–1652
Parr RG, Yang W (1995) Density functional theory of electronic structure. Ann Rev Phys Chem 46:701–728
Pulay P (1995) Analytical derivative techniques and the calculation of vibrational spectra. In: Yarkony DR (ed) Modern electronic structure theory, vol 2. World Scientific, Singapore, pp 1191–1240
Rhee H, Choi J-H, Cho M (2010) Infrared optical activity: electric field approaches in time domain. Acc Chem Res 43:1527–1536
St-Amant A (1996) Density functional methods in biomolecular modeling. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry, vol 7. VCH, New York, pp 217–259
Stephens PJ, Devlin FJ (2007) Vibrational circular dichroism. In: Mennucci B, Cammi R (eds) Continuum solvation models in chemical physics: from theory to applications. Wiley, Chichester, pp 180–205
Tsuboi M (1987) New approaches to the analysis of vibrations of nucleic acids and their components. Stud Phys Theor Chem 45:351–368
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Section Editor information
Rights and permissions
Copyright information
© 2018 European Biophysical Societies' Association (EBSA)
About this entry
Cite this entry
Keiderling, T.A. (2018). Quantum Mechanical Simulations of Biopolymer Vibrational Spectra. In: Roberts, G., Watts, A. (eds) Encyclopedia of Biophysics. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35943-9_107-1
Download citation
DOI: https://doi.org/10.1007/978-3-642-35943-9_107-1
Received:
Accepted:
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-35943-9
Online ISBN: 978-3-642-35943-9
eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences