ABSTRACT
This paper reports an analysis using molecular dynamics simulations of the effect of urea on the structure of water. Two definitions of the tetrahedral distributions are used to quantify this effect. The first one is sensitive to the mutual orientation between a reference water molecule and the water molecules forming the tetrahedron, and the second is sensitive to their radial distribution. The analysis shows that increasing urea mole fraction results in a reduction of the structured tetrahedral arrangement contribution in favor of an unstructured one. In order to understand this behavior, we used the nearest neighbor approach which allows us to get unambiguous information on the radial and orientation distributions of the water molecules around a probe one. The results indicate that the decrease of the tetrahedral arrangement of the nearest neighbors around a probe water molecule is associated with both the increase of the fluctuation in their radial distances as well as with the loss of their mutual orientations with respect to those observed in pure water. The tetrahedral distribution of water in the hydration shell of urea as well as that around its carbonyl and amine groups is also discussed.
Subject(s)
Urea/chemistry , Water/chemistry , Molecular Dynamics SimulationABSTRACT
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.
Subject(s)
Acetylgalactosamine/analogs & derivatives , Chemistry, Physical/methods , Chondroitin Sulfates/chemistry , Sodium/chemistry , Acetylgalactosamine/chemistry , Anions , Carboxylic Acids/chemistry , Glucuronic Acid/chemistry , Models, Molecular , Models, Theoretical , Molecular Conformation , Polymers/chemistry , Quantum Theory , Spectrophotometry , VibrationABSTRACT
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.
Subject(s)
Aniline Compounds/chemistry , Spectrophotometry/methods , Electrons , Hydrogen/chemistry , Models, Chemical , Models, Theoretical , Molecular Conformation , Oxygen/chemistry , Software , Time FactorsABSTRACT
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.
Subject(s)
Algorithms , Carbohydrate Conformation , Disaccharides/chemistry , Glycosides/chemistry , Software , Static Electricity , Stereoisomerism , Structure-Activity Relationship , Sulfhydryl Compounds/chemistry , Thermodynamics , Trehalose/chemistryABSTRACT
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.
Subject(s)
Amino Acids/chemistry , Electromagnetic Fields , Electrons , Hydrocarbons, Aromatic/chemistry , Nucleic Acids/chemistry , Base Pairing , Cresols/chemistry , Cytosine/analogs & derivatives , Cytosine/chemistry , Guanine/analogs & derivatives , Guanine/chemistry , Imidazoles/chemistry , Indoles/chemistry , Molecular Structure , Quantum Theory , Spectrum Analysis, Raman , Statistics as Topic , Thymine/analogs & derivatives , Thymine/chemistry , Ultraviolet Rays , Uracil/analogs & derivatives , Uracil/chemistryABSTRACT
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.
Subject(s)
Angiotensin II , Models, Biological , Motion , Protein Conformation , Spectrum Analysis, RamanABSTRACT
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.
Subject(s)
Peptides/analysis , Amides/analysis , Hydrogen Bonding , Protein Conformation , Spectrophotometry, Infrared , Spectrum Analysis, RamanABSTRACT
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.