Polarization functions for the modified m6‐31G basis sets for atoms Ga through Kr

The 2df polarization functions for the modified m6‐31G basis sets of the third‐row atoms Ga through Kr (Int J Quantum Chem, 2007, 107, 3028; Int J. Quantum Chem, 2009, 109, 1158) are proposed. The performances of the m6‐31G, m6‐31G(d,p), and m6‐31G(2df,p) basis sets were examined in molecular calculations carried out by the density functional theory (DFT) method with B3LYP hybrid functional, Møller‐Plesset perturbation theory of the second order (MP2), quadratic configuration interaction method with single and double substitutions and were compared with those for the known 6‐31G basis sets as well as with the other similar 641 and 6‐311G basis sets with and without polarization functions. Obtained results have shown that the performances of the m6‐31G, m6‐31G(d,p), and m6‐31G(2df,p) basis sets are better in comparison with the performances of the known 6‐31G, 6‐31G(d,p) and 6‐31G(2df,p) basis sets. These improvements are mainly reached due to better approximations of different electrons belonging to the different atomic shells in the modified basis sets. Applicability of the modified basis sets in thermochemical calculations is also discussed. © 2013 Wiley Periodicals, Inc.     

CHARMM36 all‐atom additive protein force field: Validation based on comparison to NMR data

Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side‐chain amino‐ and methyl‐containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ₁ and χ₂ dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.     

Rapid parameterization of small molecules using the force field toolkit

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide‐scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM‐compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure‐solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). © 2013 Wiley Periodicals, Inc.     

Substitution pattern and stereochemistry versus liquid crystalline behaviour [1]

Abstract

Selectively O-alkylated inositols of myo-, scyllo- and chiro-configuration allow detailed studies of the relationship between the substitution pattern in the cyclohexane ring and the liquid crystalline properties observed to be made for these mainly novel cyclic compounds containing hydroxyl functions. The types of thermotropic mesophase formed and containing hydrogen bonds are strongly influenced by the number and the stereochemical arrangement of both the hydroxyl groups and the alkyloxy chains, as well as by their positions on the cyclohexane ring.

The mesophases of the various new inositol ethers have been studied by polarizing optical microscopy and differential scanning calorimetry, and are discussed here in comparison with known systems, as a function of the above mentioned structural factors.     

On the origin of high optical director tilt in a partially fluorinated orthoconic antiferroelectric liquid crystal mixture

We have investigated the orthoconic antiferroelectric liquid crystal mixture W107 by means of optical, X-ray and calorimetry measurements in order to assess the origin of the unusally high tilt angle between the optic axis and the smectic layer normal in this material. The optical birefringence increases strongly below the transition to the tilted phases, showing that the onset of tilt is coupled with a considerable increase in orientational order. The layer spacing in the smectic A* (SmA*) phase is notably smaller than the extended length of the molecules constituting the mixture, and the shrinkage in smectic C* (SmC*) and smectic C_a* (SmC_a*) is much less than the optical tilt angle would predict. These observations indicate that the tilting transition in W107 to a large extent follows the asymmetric de Vries diffuse cone model. The molecules are on average considerably tilted with respect to the layer normal already in the SmA* phase but the tilting directions are there randomly distributed, giving the phase its uniaxial characteristics. At the transition to the SmC* phase, the distribution is biased such that the molecular tilt already present in SmA* now gives a contribution to the macroscopic tilt angle. In addition, there is a certain increase of the average tilt angle, leading to a slightly smaller layer thickness in the tilted phases. Analysis of the wide angle scattering data show that the molecular tilt in SmC_a* is about 20° larger than in SmA*. The large optical tilt (45°) in the SmC_a* phase thus results from a combination of an increased average molecule tilt and a biasing of tilt direction fluctuations.     

Etching Characteristics and Mechanisms of Mo and Al2O3 Thin Films in O2/Cl2/Ar Inductively Coupled Plasmas: Effect of Gas Mixing Ratios

An investigation of etching behaviors for Mo and Al₂O₃ thin films in O₂/Cl₂/Ar inductively coupled plasmas at constant gas pressure (6 mTorr), input power (700 W) and bias power (200 W) was carried out. It was found that an increase in Ar mixing ratio for Cl₂/Ar plasma results in non-monotonic etching rates with the maximums of 160 nm/min at 60 % Ar for Mo and 27 nm/min at 20 % Ar for Al₂O₃. The addition of O₂ in the Cl₂/Ar plasma causes the non-monotonic Mo etching rate (max. 320 nm/min at 40–45 % O₂) while the Al₂O₃ etching rate decreases monotonically. The model-based analysis of etching kinetics allows one to relate the non-monotonic etching rates in Cl₂/Ar plasma to the change in the etching regime from the ion-flux-limited mode (at low Ar mixing ratios) to the neutral-flux-limited mode (for high Ar mixing ratios). In the Cl₂/O₂/Ar plasma, the non-monotonic Mo etching rate is probably due to the change in reaction probability.     

A sensitive chromatographic determination of hydrazines by naphthalene-2,3-dialdehyde derivatization

A new high-performance liquid chromatography (HPLC) method for the sensitive simultaneous determination of hydrazine (Hy), monomethylhydrazine (MMH) and 1,1-dimethylhydrazine (UDMH) based upon the derivatization of hydrazines with naphthalene-2,3-dialdehyde and the separation of the derivatives on Zorbax Eclipse AAA column in a single chromatographic run under acidic conditions (pH 2.4) was developed. Hydrazine and monomethylhydrazine derivatives were found to be strongly fluorescent at λ_ex?=?273?nm, λ_em?=?500?nm. It was shown that UDMH derivative can be detected as non-fluorescent hydrazone at 290?nm by UV-detection. Limits of detection were 0.05?µg?·?L^?1 for Hy and MMH, and 1?µg?·?L^?1 for UDMH for the injection volume of 100?µL. The method was validated for water sample analysis. It proved to be selective, accurate and precise with the supplementary advantage of the simple and rapid sample preparation.     

Selectin Receptors 4: Synthesis of Tetrasaccharides Sialyl Lewis A and Sialyl Lewis X Containing A Spacer Group1,2

ABSTRACT

Synthesis of two isomeric tetrasaccharides, namely Neu5Acα(2→3)Galβ(1→3)[Fucα(1→4)GlcNAcβ (sLe^a) and Neu5Acα(2→3)Galβ(1→4)[Fucα(1→3)]GlcNAcβ (sLe^x) as 3-aminopropyl glycosides is described. Preparation of these compounds was performed by sialylation of selectively protected trisaccharides Le^a and Le^x which contain three unsubstituted OH groups at positions 2, 3 and 4 of Gal residue. Glycosylation of Le^x trisaccharide with ethylthio sialoside under promotion by NIS and TfOH in acetonitrile was effective and regio- and stereoselective to give sLe^x derivative in 81% yield. In contrast, sialylation of the Lc^a acceptor was accompanied by a variety of undesirable by-processes, namely. N-thioethylation of the GlcNAc residue, β-sialylation, and lactonisation. In order to improve the yield of sLc^a tetrasaccharide the glycosylation of Le^a acceptor by sialyl donors of ethyl and phenyl thioglycoside (promoted by NIS-TfOH or NBS-Bu₄NBr), xanthate (promotion by NIS-TfOH mixture or MeOTf) and phosphite (promoted by TMSOTf) types was also studied. Among the reactions investigated the glycosylation by phenyl thioglycoside sialoside promoted by NIS-TfOH gives the best yield (39%) of sLe^a tetrasaccharide product.     

Synthesis Of Isomaltose Analogues

ABSTRACT

Preparation of the α-glucosides 11, 12, 13 and 14 were accomplished through glycosylation of racemic trans-1-hydroxy-2-(hydroxymethyl)cyclohexane using 2-thiopyridyl tetra-O-benzyl-glucoside as the glycosyl donor in acceptable overall yield for α-selectivity, but with poor regioselectivity. Glycosylation under thermodynamic control using tetrabenzyl glucopyranose acetate and trimethylsilyl triflate as the promotor gave similar results. The unprotected glucosides 12 and 13 were separated and characterized by NMR spectroscopy. Similarly methyl 4-deoxy-α-isomaltoside (5a) was prepared through halide catalyzed glycosylation of methyl 2,3-di-O-benzoyl-4-deoxy-α-D-glucopyranoside (15) in acceptable yield and the unprotected compound characterized by NMR spectroscopy. Compounds 5a, 12a, 13a and the mixture 11a and 14a were all tested as substrates for the enzyme glucoamylase from Aspergillus niger and proved to be very poor substrates for the enzymic hydrolysis.