Comparative performance of MM3(92) and two TINKER MM3 versions for the modeling of carbohydrates

The 1992 version of MM3 was largely used for modeling mono-, di-, and trisaccharides. In later versions of MM3 improvements were made in some parameters that may be important for carbohydrates. This corrected MM3 force field is part of the Tinker package, freely available (as its 4.1 version), and included in the Chem 3D Ultra 8.0 package (as the 3.7 version). The latter version lacks the corrections to the standard bond lengths produced by electronegativity and anomeric effects, whereas the Tinker 4.1 version only lacks the latter correction. The present work compares the performance of the three MM3 versions (and in some cases, DFT and/or HF/ab initio procedures) on several carbohydrate model problems as the chair and rotamer equilibria in 2-hydroxy- and 2-methoxytetrahydropyran, hydrogen bonding in cis-2,3-dihydroxytetrahydropyran, and the potential energy surfaces around the glycosidic bonds of two sulfated disaccharides and two trisaccharides. Tinker MM3 can be used accurately to estimate carbohydrate energies and geometries, and-with the help of some programming-to pursue studies on the potential energy surfaces of di- and trisaccharides. In most cases results obtained using the three MM3 versions are similar, although large energy differences are obtained when comparing a rotameric distribution around a O-C-O-H dihedral, which is almost forced to the exo-anomeric position by the Tinker versions. In other systems smaller energy differences are found, but they can nevertheless lead to a different global minimum when comparing conformers of similar energy. MM3(92) establishes better the differences between the bond lengths in both anomers, as an expected expression of the anomeric correction.     

Ab initio computation of force constants: Part VI. Applications of the force relaxation method for geometry optimization

Techniques to improve the computational efficiency of the force relaxation method are discussed. Force constants for fragments in previously computed smaller molecules can be transferred to construct a guess force constant matrix. Additional force constants that may be needed can be computed by a procedure which uses only one additional force calculation per diagonal force constant required. A scaling technique to improve convergence on the optimized geometry is discussed.     

Synthesis and spectral properties of 2,3-dihydro-4-(para-substituted-phenyl)-7-[(o-, m-, and p-substituted)phenoxy]-1H-1,5-benzodi-azepine-2-thiones

A series of twelve new 2,3-dihydro-4-(para-substituted-phenyl)-7-[(o-, m-, and p-substituted)phenoxy]-1H-1,5-benzodiazepine-2-thiones, which have potentially useful pharmacological properties, has been synthesized by condensing the 3,3-dimercapto-1-(para-substituted phenyl)-2-propen-1-one with 3,4-diaminophenyl-R-phenyl ethers. The structure of all products was corroborated by ir, ¹H-nmr, ¹³C-nmr and ms.     

Theoretical strategy to provide atomistic models of comblike polymers: a generation algorithm combined with configurational bias Monte Carlo

A computational strategy to model the amorphous phase of comblike polymers is presented. The strategy, denoted SuSi/CB (CB-configurational bias), combines the strength of an algorithm recently developed to generate reliable microstructures of dense amorphous polymers, which is based on a random search of energy minima, and configurational bias Monte Carlo method. The influence of different parameters used to define the characteristics of SuSi/CB on both the reliability of the generated structures and the computational effort has been examined in detail. Finally, we have modeled and characterized the supramolecular organization of poly(octadecyl acrylate) in the amorphous state.     

Molecular dynamics simulations of the surface tension of ionic liquids

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.     

Conformational changes of the amyloid beta-peptide (1-40) adsorbed on solid surfaces

The conformational change of the 39-43 residues of the amyloid beta-peptide (Abeta) toward a beta-sheet enriched state promotes self-aggregation of the peptide molecules and constitutes the major peptide component of the amyloid plaques in Alzheimer patients. The crucial question behind the self-aggregation of Abeta is related to the different pathways the peptide may take after cleavage from the amyloid precursor proteins at cellular membranes. This work is aiming at determining the conformation of the Abeta (1-40) adsorbed on hydrophobic Teflon and hydrophilic silica particles, as model sorbent surfaces mimicking the apolar transmembrane environment and the polar, charged membrane surface, respectively. The mechanism by which the Abeta interacts with solid surfaces strongly depends on the hydrophobic/hydrophilic character of the particles. Hydrophobic and electrostatic interactions contribute differently in each case, causing a completely different conformational change of the adsorbed molecules on the two surfaces. When hydrophobic interactions between the peptide and the sorbent prevail, the adsorbed Abeta (1-40) mainly adopts an alpha-helix conformation due to H-bonding in the apolar part of the peptide that is oriented towards the surface. On the other hand, when the peptide adsorbs by electrostatic interactions beta-sheet formation is promoted due to intermolecular association between the apolar parts of the adsorbed peptide. Irrespective of the characteristics of the solid sorbent, crowding the surface results in intermolecular association between adsorbed molecules leading to a strong aggregation tendency of the Abeta (1-40). [Diagram: see text] CD spectra of Abeta (1-40) at pH 7: A) in solution ([Abeta]=0.2 mg.ml(-1)) freshly prepared (line) and after overnight incubation (symbols);B) on Teflon (Gamma=0.5 mg.m(-2)).     

Use of the tubulin bound paclitaxel conformation for structure-based rational drug design

A new computational docking protocol has been developed and used in combination with conformational information inferred from REDOR-NMR experiments on microtubule bound 2-(p-fluorobenzoyl)paclitaxel to delineate a unique tubulin binding structure of paclitaxel. A conformationally constrained macrocyclic taxoid bearing a linker between the C-14 and C-3'N positions has been designed and synthesized to enforce this "REDOR-taxol" conformation. The novel taxoid SB-T-2053 inhibits the growth of MCF-7 and LCC-6 human breast cancer cells (wild-type and drug resistant) on the same order of magnitude as paclitaxel. Moreover, SB-T-2053 induces in vitro tubulin polymerization at least as well as paclitaxel, which directly validates our drug design process. These results open a new avenue for drug design of next generation taxoids and other microtubule-stabilizing agents based on the refined structural information of drug-tubulin complexes, in accordance with typical enzyme-inhibitor medicinal chemistry precepts.     

Synthesis of 4-aryl-2,3,6,7-tetrahydro-1H-pyrimido[4,5-b][1,4]-diazepin-6-ones from 4,5-diamino-1H-pyrimidin-6-ones and 1-aryl-3-(dimethylamino)-1-propanones

The reaction of 1-aryl-3-(dimethylamino)-1-propanones 1 with one equivalent of 4,5-diamino-1H-pyrimidin-6-ones 2 , in acidic medium, leads to the formation of 4-aryl-2,3,6,7-tetrahydro-1H-pyrimido[4,5-b]-[1,4]diazepin-6-ones 3 . The structure elucidation of the products is based on detail nmr analysis of experiments such as ¹³C, ¹H and DEPT including selective ¹³C{¹H} decoupling experiments.     

Paired electrosynthesis of cyanoacetic acid

Cyanoacetic acid is formed by cathodic reduction of CO(2) and anodic oxidation of the tetraalkylammonium salt anion; the process is conduced in acetonitrile using a divided cell with a medium porosity glass-frit diaphragm. A mechanism for this paired electrochemical reaction is proposed.     

Characterization of a β-glucanase produced by Rhizopus microsporus var. microsporus, and its potential for application in the brewing industry

Background  

In the barley malting process, partial hydrolysis of β-glucans begins with seed germination. However, the endogenous 1,3-1,4-β-glucanases are heat inactivated, and the remaining high molecular weight β-glucans may cause severe problems such as increased brewer mash viscosity and turbidity. Increased viscosity impairs pumping and filtration, resulting in lower efficiency, reduced yields of extracts, and lower filtration rates, as well as the appearance of gelatinous precipitates in the finished beer. Therefore, the use of exogenous β-glucanases to reduce the β-glucans already present in the malt barley is highly desirable.