Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications

Abstract

This review describes the vibrational self-consistent field (VSCF) method and its other variants for computing anharmonic vibrational spectroscopy of biological molecules. The superiority and limitations of this algorithm are discussed with examples. The spectroscopic accuracy of the VSCF method is compared with experimental results and other available state-of-the-art algorithms for various biologically important systems. For large biological molecules with many vibrational modes, the scaling of computational effort is investigated. The accuracy of the vibrational spectra of biological molecules using the VSCF approach for different electronic structure methods is also assessed. Finally, a few open problems and challenges in this field are discussed.

First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments

“…This is a case where the VSCF algorithm fails to converge to a physical value, but frequencies of other modes, if physical can be retained. 38 The intensities, as can be seen, agree nicely in comparison with the experimental vibrational pattern.…”

“…It is already found that this pair-wise coupling approximation leads to good accuracy in many applications. 22,23,38 To bring in effect of non-separability, the vibrational levels can be further corrected by second-order perturbation theory (VSCF-PT2). 33,38 This method is typically more accurate than the basic VSCF approximation.…”

“…In the present study, we used quantum chemical full pair-wise coupling potentials considering all the vibrational modes of the three dipeptides. Until now, VSCF-PT2 calculations using quantum chemical potentials of suitable accuracy were carried out for amino acids, 22,36 their complexes with water molecules 37 and other biomolecules 38 of similar sizes. The present paper extends the state-of-the-art quantum VSCF-PT2 calculations to dipeptides.…”

Chemically-bound xenon in fibrous silica

“…38 Partial charges and bond orders were calculated using NBO 39,40 analysis. In all calculations the internal coordinates were used.…”

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

“…On the contrary, consistent procedures can be derived from QM computations of vibrational properties beyond the harmonic approximation. Recently, exact solutions for the treatment of few active modes to the vibrational problem for a generic system has been proposed 55 and effective schemes to compute vibrational frequencies within the second order vibrational perturbative (VPT2) [56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74][75] or vibrational self-consistent field (VSCF) based [76][77][78][79][80][81][82][83][84][85] approaches have been developed and implemented. In particular, a general VPT2 framework to compute thermodynamic properties, vibrational energies and transition intensities from the vibrational ground state to fundamentals, overtones and combination bands 66,67,[86][87][88] has been developed in our group.…”