Rationalising the vibrational spectra of biomolecules using atomistic simulations.
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Summary
An account of the recent developments in the use of atomistic simulations to predict vibrational spectra of biomolecules, with a particular focus on the vibrational dynamics of the amide group in peptides.
- Type
- review
- Published
- 2009-01-01
- Cited by
- 11
- References
- 85
- Access
- Open access
- OpenAlex
- https://openalex.org/W36907825
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:24363997
Keywords
Biomolecule, Anharmonicity, Molecular dynamics, Force field (fiction), Spectral line
References
- The Relation Between the Energy of a Hydrogen Bond and the Frequencies of the O–H Bands
- Application of SCF-SI theory to vibrational motion in polyatomic molecules
- A new approach for determining low‐frequency normal modes in macromolecules
- Anharmonic wave functions of proteins: quantum self-consistent field calculations of BPTI.
- Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution.
- A near linear-scaling smooth local coupled cluster algorithm for electronic structure.
- Harmonic frequency scaling factors for Hartree-Fock, S-VWN, B-LYP, B3-LYP, B3-PW91 and MP2 with the Sadlej pVTZ electric property basis set
- EDF2: A density functional for predicting molecular vibrational frequencies
- Molecular recognition mechanism of FK506 binding protein: An all‐electron fragment molecular orbital study
- Degenerate perturbation theory corrections for the vibrational self-consistent field approximation: Method and applications
- Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization
- Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding.
- Vibrational spectroscopy and the development of new force fields for biological molecules
- Self‐consistent field energies and wavefunctions for coupled oscillators
- Liquid theory for band structure in a liquid
- Normal Coordinates: General Theory, Redundant Coordinates, and General Analysis Using Electronic Computers
- Normal‐mode analysis of liquid‐state dynamics
- Vibrational wave functions and spectroscopy of (H2O)n, n=2,3,4,5: Vibrational self‐consistent field with correlation corrections
- Møller–Plesset perturbation theory for vibrational wave functions
- Smart Monte Carlo simulation of a globular protein
Cited by
- Ab initio study of alanine-based polypeptide secondary-structure motifs in the gas phase
- Selected new developments in vibrational structure theory: potential construction and vibrational wave function calculations.
- Vibrational quasi-degenerate perturbation theory with optimized coordinates: applications to ethylene and trans-1,3-butadiene.
- Gas-phase spectroscopy and anharmonic vibrational analysis of the 3-residue peptide Z-Pro-Leu-Gly-NH2 by the laser desorption supersonic jet technique
- Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase.
- Assessing spin-component-scaled second-order Møller-plesset theory using anharmonic frequencies.
- MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations
- Revised conformational assignments and conformational evolution of tyrosine by laser desorption supersonic jet laser spectroscopy.
- Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field.
- Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations.
- Computational molecular spectroscopy
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