Elucidation of the Au-S bond in a passivated gold cluster through density functional theory calculations (abstract only).

Gold clusters are of increasing interest due to a number of already established as well as new potential applications in different fields of nanotechnology. The use of gold nanoparticles can be significantly extended by surface modifications, sulfidation being the most popular. The identifications of preferred adsorption geometries, bond formation, and binding energies are helpful tools for understanding the properties of these particles. This study is focused on a 38-atom gold cluster passivated with 3-hydroxypropanthiolate linkers. Starting from the re-optimized global minimum structure of a bare 38-atom gold cluster (Doye and Wales 1998 New J. Chem. 22 733-44) and aiming at a description of the passivated particle, density functional theory calculations (within the framework of the Amsterdam density functional calculation package ADF 2006.01 (ADF2006.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, http://www.scm.com)) were performed at the level of the generalized gradient approximation of Perdew and Wang from 1991, with triple-zeta Slater basis sets plus p- and f-polarization functions (TZ2P) for the 33 outermost electrons of each gold atom, and considering scalar relativistic effects. Using this methodology, the space around the gold cluster (with the distance of the S of the thiolate from the gold cluster surface in the range 2.3-2.6 Å) was examined to identify the most favourable absorption site for the thiolate linker. As a result, a 3D map was created and low energy areas corresponding to the potentially most favourable site for one 3-hydroxypropanthiolate linker on the gold cluster localized. Structures representing these areas were further optimized and consequently analysed using Mulliken population analysis to compare charge distribution over the tested structures, Mayer bond order analysis, as well as electron localization function/indicator bond formation analysis. The results obtained will be presented in comparison to ones available from studies of other research groups.

PCILO quantum-mechanical relaxed conformational energy map of methyl 4-thio-alpha-maltoside in solution.

A theoretical study is presented of the conformational properties of methyl 4-thio-alpha-maltoside. Quantum-chemical PCILO (perturbed configuration interaction with localized orbitals) energy minimization with evaluation of the solvent effect has been used to calculate semi-rigid and relaxed (phi, psi) conformational-energy surfaces in 1,4-dioxane, methanol, dimethyl sulfoxide, and water. The inclusion of molecular flexibility in the conformational analysis of this disaccharide derivative was found to have a significant effect upon the allowed conformational space of the molecule. Calculations revealed the existence of 15 stable conformers having different internal geometries. The relative abundance of these conformers is strongly influenced by solvent. The locations of the global minima and "virtual" conformations vary with solvent and the flexibility of methyl 4-thio-alpha-maltoside significantly decreases from 1,4-dioxane to water. It was found that the conformational properties of methyl 4-thio-alpha-maltoside differ from those of the corresponding 4-oxygenated analogue, methyl alpha-maltoside. The calculated solution behaviour is supported by very good agreement between the theoretical values mean value of 3JC-4,H-1' = 2.67 and mean value of 3JC-1',H-4 = 5.24 Hz calculated as ensemble averages over all conformers on the relaxed map and the experimental values of 2.95 and 5.15 Hz in water solution.

One-bond carbon-proton coupling constants: angular dependence in alpha-linked oligosaccharides.

An investigation is presented of the angular dependence of 1JC,H in model compounds related to alpha-linked oligosaccharides. Values calculated by FPT formulation in the semi-empirical INDO method for models of (1----1)-, (1----2)-, (1----3)-, and (1----4)-linked disaccharides were compared, and the effect of the orientation of HO-2 was elucidated. The angular dependence of 1JC,H on the glycosidic dihedral angles phi H and psi H was characterised in the form 1JC,H = A cos 2 phi + B cos phi + C sin 2 phi + D sin phi + E. The 1JC,H values, measured by DEPT methods for C-1-H-1 and C-X'-H-X' in various rigid carbohydrates, were used to adjust the calculated angular dependences and to determine solvent effects. Based on the abundance of the conformers for maltose and isomaltose, the thermodynamically averaged 1JC,H values have been calculated. The results obtained (less than 1JC-1,H-1 greater than 169.9, less than 1JC-4',H-4' greater than 147.7 Hz for methyl beta-maltoside and less than 1JC-1,H-1 greater than 169.8 Hz for methyl beta-isomaltoside) agree with the experimental values of 172.4, 147.7, and 170.3 Hz, respectively.

Solution behavior of methyl beta-xylobioside: conformational flexibility revealed by n.m.r. measurements and theoretical calculations.

The conformations of methyl beta-xylobioside in solution have been determined by n.m.r. spectroscopy. Interglycosidic 3JC,H values and the chemical shifts of the 13C resonances were measured at various temperatures in the range 238-378 K for solutions in 1,4-dioxane, methanol, methyl sulfoxide, and water. The temperature and solvent dependencies of the data obtained suggest conformational flexibility. Quantum-chemical PCILO calculations, with evaluation of the solvent effects, and molecular mechanics calculations revealed the existence of 7 low-energy regions for which the geometries and energies were determined. The computed abundances of conformers and averaged J values accord with the experimental data.

The conformational analysis of methyl beta-xylobioside: effect of choice of potential functions.

In order to determine the effect of the choice of potential function used in the conformational analysis of a carbohydrate, the NMR spectrum of methyl beta-xylobioside [beta-D-Xyl-(1-->4)-beta-D-Xyl-(1-->O)-Me] was interpreted using calculated J13C-H coupling constants and nuclear Overhauser effects for protons across the anomeric linkage. Conformational flexibility was described by calculating average phi and psi angles, and estimating their standard deviations. ECEPP2, ECEPP83, and HSEA potentials were used in the first series of calculations. The calculated coupling constants and nuclear Overhauser effects were averaged over the Boltzmann distribution of conformations of the disaccharide in which the entire phi, psi space was scanned in ten-degree steps while retaining fixed bond distances and angles in the remainder of the molecule. In the second series of calculations, MM2, MM2CARB, and PCILO parameters were used to calculate conformational energies. Conformational optimization was done. The effect of temperature and solvent on the calculated coupling constants was negligible. Calculated properties from conformations whose energies were based on the ECEPP parameters gave the best agreement with experiment. Exploration of the conformational space in breadth rather than on a detailed level of full optimization appears to be a preferable course of action.

Nuclear Overhauser effects and the flexibility of saccharides: methyl beta-xylobioside.

The behavior of methyl beta-xylobioside has been analysed by 1H-n.m.r. spectroscopy for solutions in water and methanol in the range - 15 degrees to 85 degrees. Experimental n.O.e. values did not change with temperature and solvent in contrast to the inter-glycosidic 3JC,H values. Experimental n.O.e. data accorded with the values calculated from time-averaged cross-relaxation terms. The tumbling times were determined from relaxation data and were in the sub-ns range.

Hydration of alpha-maltose and amylose: molecular modelling and thermodynamics study.

Hydration of alpha-maltose and amylose were investigated using molecular modelling and thermodynamics methods. The structure and energy of hydration of three low-energy conformers of alpha-maltose were determined by the MM3 molecular mechanics method. The hydration structure was found to be sensitive to the conformation of alpha-maltose and hydration numbers 10 or 11 were estimated for the different conformers. Differential scanning calorimetry and thermogravimetric analysis were used to determine the number of water molecules specifically bonded (non-freezing water) to amylose and different samples of alpha-maltose. Due to high crystallinity of alpha-maltose samples, the observed non-freezing water content was lower than predicted by molecular modelling. In contrast, the experimental number of non-freezing molecules of water per D-glucopyranose residue for amorphous amylose (nh = 3.8) is in good accordance with the value of 3.8 extracted from our calculations.

Conformational study of digalacturonic acid and sodium digalacturonate in solution.

The solution conformation of digalacturonic acid and its sodium salt have been analyzed using nuclear magnetic resonance data and molecular mechanics calculations. The flexibility around the glycosidic linkage was characterized by calculation of the relaxed (phi, psi) potential surfaces for the isolated molecule, and also for dimethyl sulfoxide and aqueous solutions using the CHARMM and SOLVOL programs. The one-bond and three-bond proton-carbon couplings were measured and H-1'-H-4 distances were estimated from NOESY experiments. The calculated potential surfaces were used to determine theoretical ensemble averages of NMR data. The agreement between the experimental and theoretical data is very satisfactory. The calculations show a strong effect of solvent on the solution behavior of both compounds. The vacuum lowest energy conformer of digalacturonic acid is stabilized by solvation, while for sodium digalacturonate the solvent induces a conformational change. An extrapolation of the stable conformers to polysaccharide chains implies that poly(galacturonic acid) occurs in solution as a three-fold helix and sodium poly(galacturonate) as a two-fold helix.

Conformational analysis of carbohydrates inferred from NMR spectroscopy and molecular modeling. Applications to the behavior of oligo-galactomannan chains.

In both the biological functions and industrial applications of carbohydrates, their conformational behavior along with the dynamic fluctuations that their structures experience are of great significance. The elucidation of the three-dimensional characteristics of carbohydrates and carbohydrate-containing molecules is in general performed by a combination of high-resolution nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Heteronuclear couplings and nuclear Overhauser effect (NOE) data are major tools for structural determination. The angular dependence of carbon-proton coupling constants has been shown to depend also on the pathways involved. Concerning molecular modeling, the goal is to generate the ensemble of structures that are consistent with the experimental data. This approach is illustrated in the galactomannan chain. It consists of the conformational study of two model disaccharides (mannobiose and epimelibiose) of galactomannans through carbon-proton coupling constants and NOE measurements. Experimental data are then compared to results of conformational analysis that predicted the stable conformers in solution. From these results helical conformations of oligomers are generated and are discussed in terms of the influence of the position and number of galactose units on the conformation of the mannan backbone.

Conformation and dynamics of a cyclic (1-->2)-beta-D-glucan.

A molecular modelling and nuclear magnetic resonance spectroscopic study was performed in order to gain insight into the conformational preferences of cyclosophoroheptadecaose. MM3 molecular mechanics calculations predicted a non-symmetric conformer with a small cavity of 3.7 A diameter as the lowest energy form. Molecular dynamics simulations gave insight into the dynamics of the free cyclosophoroheptadecaose and also supported the results of molecular mechanics calculations. A fair agreement was found between experimental data and corresponding average values predicted by molecular modelling.

Theoretical studies on the conformation of saccharides. XIV. Structure and conformational properties of the glycosylamines.

The 2-methylaminotetrahydropyran was used as a model to study conformational properties of the N-glycosidic linkage in glycosylamines. Relaxed two-dimensional conformational (phi, psi) maps in 20 solvents were calculated by a method in which the total energy is divided into the energy of the isolated molecule and the solvation energy. Molecular geometry optimization has been carried out for each conformer using the quantum chemical method PCILO. The calculated variations of the geometry are consistent with the results obtained by the statistical analysis of available experimental data retrieved from the Cambridge Structural Database. The calculated abundances of conformers show that the polarity of the solvent has little effect on the anomeric ratio, and the form having the methylamino group equatorial is favored in all considered solvents.

Structure of bovine alpha-1,3-galactosyltransferase and its complexes with UDP and DPGal inferred from molecular modeling.

A homology model of alpha-1,3-galactosyltransferase (alpha-1,3-GalT), the retaining enzyme responsible for the formation of alpha-galactosyl epitopes, has been developed by means of molecular modeling using the SpsA glycosyltransferase structure. A protein-ligand docking approach was used to model alpha-1,3-GalT complexed with UDP and UDP-Gal. The comparison of structural features found in the alpha-1,3-GalT homology model with available structural data on this class of enzymes revealed similarities in the UDP-binding pocket. In the predicted structure of the complexes, the pyrophosphate interacts with the DVD motif (Asp-225, Val-226, and Asp-227) of alpha-1,3-GalT through the Mn(2+) cation. The uridine part of the UDP binds into the well-defined cavity that consists of Phe-134, Tyr-139, Ile-140, Val-136, Arg-194, Arg-202, Lys-209, Asp-173, His-218, and Thr-137 in a conformation that is generally observed in the crystal structures of other glycosyltransferase complexes.

Computer modeling of polysaccharide-polysaccharide interactions: an approach to the kappa-carrageenan-mannan case.

A computer program SAINT has been developed for the investigation of the structure and for the prediction of minimum-energy structure of polysaccharide-polysaccharide complexes. The energy minimization is carried out on internal geometrical parameters--namely bond angles, torsional angles, and five parameters describing the mutual orientations of polysaccharide chains. For this purpose, the nonderivative method of conjugated directions is used. This procedure was applied to computer modeling of an idealized model of the binary gelling kappa-carrageenan and galactomannan system. It is shown that the interaction between two chains influences the structure of the individual polysaccharide molecule and that in the minimum-energy structures of the complex, the conformation of the chains does not correspond to the lowest energy.

Computer modelling of kappa carrageenan-mannan interactions.

Molecular modelling has been used as a theoretical approach to investigate the kappa carrageenan structure and its interactions with mannan chains. Calculations revealed the existence of six minima for the kappa carrageenan structure in solution. Two of them were very close to the structure found in the solid state. The methodology allowed the calculation of a theoretical counterpart of the structures based on x-ray fibre diffraction studies. In the second step of this study, we have shown that there is the possibility of interactions between kappa carrageenan double helices and mannan chains. This interacting process is allowed by the flexibility of the mannan chains and structural changes of the kappa carrageenan double helices. The calculations suggest that a disaccharide mannan fragment might be required for recognition. The results of our investigation are in good agreement with a model of gel structure based on experimental data. This approach could be applied to simulate and predict other associations in molecular assemblies.

Studies on the conformational behaviour of GlcNAc-Man3-GlcNAc2 oligosaccharides using molecular dynamics simulations.

Three-dimensional structures of the natural substrate unit for the enzyme N-acetylglucosamine-transferase II, GIcNAc-Man3-GlcNAc2, were investigated by molecular modelling methods. Molecular dynamics (MD) and molecular mechanics calculations on two hexasaccharides, namely GlcNAc-Man3-GlcNAc2-Asn and GlcNAc-Man3-GlcNAc2-OMe were performed by the Biosym/MSI software using the CVFF and CFF95 force fields in vacuum. The MD simulations were calculated for 3 ns at different simulation temperatures and for two values of dielectric constant, epsilon=1 and epsilon=4. From each 3 ns trajectory, 3050 structures have been optimized. The local minima obtained have been clustered into families exhibiting similar values of glycosidic torsional angles phi, psi, and omega. The influence of the simulation conditions and force fields used on the conformational behaviour and structure of the title oligosaccharides is discussed.