The SPASIBA force field for chondroitin sulfate: vibrational analysis of D-glucuronic and N-acetyl-D-galactosamine 4-sulfate sodium salts

Normal-mode analyses were carried out on the two components of the chondroitin 4-sulfate linear glycosaminoglycan, a copolymer implying alternate D-glucuronate beta-(1-->3) and N-acetyl-D-galactosamine 4-sulfate beta-(1-->4) (hereafter named D-galactosamine 4-sulfate) residues. Scaled quantum mechanical calculations (SQM) using the density functional theory approach at different levels of theory (B3LYP/6-31G** and B3LYP/6-31++G**) were performed to obtain correct vibrational assignments. The SPASIBA empirical force field parameters were then obtained from both theoretical predictions and observed IR and Raman data. It is shown that calculations including diffuse functions at the B3LP/6-31++G** level and the introduction of the Na+ counterion are necessary to give correct assignments of the CO2- symmetric (nu(s)) and antisymmetric (nu(a)) stretching modes for the glucuronic carboxylate residue.

The SPASIBA Force Field for Studying Iron-Tannins Interactions: Application to Fe3+/Fe2+ Catechol Complexes

The SPASIBA force field parameters have been obtained for Fe³⁺/Fe²⁺-Oxygen interactions occuring between non-heminic iron and hydroxyl groups of polyphenols found in tannins. These parameters were derived from normal modes analyses based on quantum chemical calculations using the Density Functional Theory (DFT). Four models involving complexation of iron with water ([Fe(H₂O)₆]³⁺, [Fe(H₂O)₆]²⁺) and with cathechol molecules ([Fe(cat)₂(H₂O)₂]⁻¹, [Fe(cat)₂(H₂O)₂]⁻²) were studied using the Density Functional Theory and the B3LYP hybrid functional under high spin states of iron.

Density functional theory and empirical derived force fields for the delocalized polaron form of polyaniline. Application to properties determination of an isolated oligomer using molecular dynamics simulations

Normal mode analyses obtained from quantum chemical calculations at the DFT level of theory have been performed for the repetitive unit of the delocalized bipolaron form of polyaniline (PANI). Empirical molecular mechanics force field parameters were consecutively refined using the SPASIBA software and applied to the molecular dynamics properties of an isolated dodeca oligomer model of the leucoemeraldine form of PANI. It is shown that effects of protonation of the emeraldine base spread over the four rings constituting the repeating unit. Molecular dynamics simulations reveal alternative bendings of the whole chain with a time period of 18-20 ps for the model of PANI under study.

The SPASIBA force field as an essential tool for studying the structure and dynamics of saccharides

The SPASIBA force field has been applied to the determination of the structure and dynamical properties of various disaccharides. It has been shown that the experimental properties (structure, dipole moment, conformational relative energies) are satisfactorily predicted. The anomeric and exo-anomeric effects are confidently reproduced without specific terms for the alpha and beta anomers and the type of glycosidic linkages.

On the use of ultraviolet resonance Raman intensities to elaborate molecular force fields: application to nucleic acid bases and aromatic amino acid residues models

Normal modes analyses for different molecules with biological interest have been performed and checked via the calculation of resonance Raman intensities. For this purpose, molecular orbital calculations were used to determine bond order changes in the lowest-lying electronic transitions. These bond order changes were used to calculate resonance Raman intensities in order to obtain correct vibrational assignments and reliable force fields.

Normal modes of vibration of a model peptide adopting the C7 C5 structure. Application toi angiotensin II

A normal coordinate treatment was performed on the C7C5 conformation using a modified Urey-Bradley force field refined from previous studies on beta-turns. The predicted frequencies were compared with the experimental ones obtained on the peptide hormone human angiotensin II. The existence of both a beta-turn and a C7C5 conformation in solid and in aqueous solution is discussed.

Raman spectroscopy and normal vibrations of peptides. Characteristic normal modes of a type-II beta turn

Raman and infrared spectra have been recorded on the peptide Gly-LPro-Gly-Gly in its zwitterionic form and on its protected homolog Z-Gly-LPro-Gly-Gly-OMe (Z = N-benzyloxycarbonyl and OMe = methyl ester). Both peptides adopt a type-II beta-turn conformation into appropriate solvents, that is in dimethylsulfoxide and chloroform respectively. A normal coordinate treatment has been performed on Gly-LPro-Gly-Gly using a modified Urey-Bradley force field and the characteristic normal modes of vibrations. Their corresponding frequencies have been extracted from experimental investigations.

Vibrational normal modes of folded prolyl-containing peptides. Application to beta turns

Normal mode analysis of standard beta turns has been performed using the refined force field obtained from type-II beta-turn-like conformation frequencies. Effects of various potentials are discussed and theoretical predictions are compared to the experimental results of various authors.