Monte Carlo Molecular Mechanics Research Articles

Design, synthesis and characterization of bitumen emulsifiers based on molecular simulation

Under the guidance of molecular simulation technology, the Monte Carlo molecular mechanics simulation was used to calculate the compatibility of different lipophilic groups with each component of bitumen, and the compatibility of different hydrophilic groups with water. Based on the calculated results of interaction parameters Chi and mixture energy Emix, the preferred structures of lipophilic and hydrophilic groups of bitumen emulsifier were determined. The target bitumen emulsifier was then synthesized by the reaction of organic acid and polyamine. The molecular simulation results showed that the compatibility of lipophilic group T11 with the bitumen was the best, and the mixing ability of the hydrophilic group H5 with water was excellent. The experimental results show that the preferred structures T11H5 had a good emulsifying performance to prepare emulsified bitumen with good storage stability, consistent with the results of the molecular simulation.

Theoretical interpretation of the role of the ionic liquid phase in the (R)-Ru-BINAP catalyzed hydrogenation of methylacetoacetate

Recently, the work focusing on the role of alkyl chain length in the N[R,222][Tf2N] ionic liquids and its reflection in the kinetic parameters of stereoselective hydrogenation of methylacetoacetate over (R)-[RuCl(binap)(p-cymene)]Cl complex was reported. Irregular trends in the principle parameter of enantioselectivity were observed. Here, a possible theoretical explanation of such irregular trends elucidated with the help of molecular simulations methods is presented. A stepwise approach is proposed for evaluating the energetically most stable conformers of a series of individual N[R,222][Tf2N] for the interpretation of selectivity-structure effects observed experimentally. Initially, Monte Carlo molecular mechanics was used followed by a semi-empirical PM3 method to elucidate also the characteristic thermodynamic functions of state and theoretical molecular spectra. The density functional theory was finally applied. The specific absolute entropy data revealed that due to the partition of the cation and anion twisted closer approach the ionic liquids N[8,222][Tf2N] and N[12,222][Tf2N] may stabilize the structures of the (R)-[RuCl(binap)(p-cymene)]Cl complex.

Effect of solvation and intermolecular interactions on the structure and optical properties of PANI oligomers

AbstractPolyaniline (PANI) has attracted lasting interest due to its unconventional electronic, optical, and electro‐optical properties. A rigid backbone polymer, PANI exhibits very strong intra‐ and intermolecular interactions governing its overall behavior. The purpose of this study is to investigate theoretically the contribution of the various inter‐ and intramolecular interactions to the process of organization of PANI macromolecules in aqueous environment. The structure and spectral conduct of oligoanilines (tetramers) in different oxidation states have been calculated at the Monte Carlo/Molecular Mechanics (MC/MM) and quantum chemical (QC) semiempirical level. The effect of protonation on the optical properties of partially and fully oxidized oligomers is discussed. The role of intermolecular interactions and the influence of water as a solvent are estimated for a number of hydrated clusters. Computed results and experimental spectra are compared. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Characterization of the selenotrisulfide formed by reaction of selenite with end-capped phytochelatin-2.

The phytochelatins are a family of peptides synthesized by plants in response to exposure to heavy metals and metalloids, including selenium in the form of selenite. The amino acid sequence of the phytochelatin (PC) peptides is (gamma-Glu-Cys)n-Gly, where n typically ranges from 2 to 5. In this paper, the products of the reaction of selenite with an end-capped analogue of PC2, Ac-(gamma-Glu-Cys)2-Gly-NH2, are characterized. Selenite reacts with Ac-(gamma-Glu-Cys)2-Gly-NH2 (Ac-PC2-NH2) to form a compound that contains an intramolecular selenotrisulfide (-SSeS-)-linkage (Se[Ac-PC2-NH2]) and oxidized Ac-PC2-NH2. Both Se[Ac-PC2-NH2] and oxidized Ac-PC2-NH2 were isolated by HPLC and were characterized by MALDI-TOF mass spectrometry, by two-dimensional 1H and 13C NMR and, in the case of Se[Ac-PC2-NH2], by 77Se NMR. Using dihedral angles determined from vicinal 1H-1H coupling constants as constraints for the conformations around the Cys(CalphaH)-Cys(CbetaH) bonds, structures were predicted for the most abundant form of both compounds by Monte Carlo molecular mechanics simulations.

Conformational Analysis of Azabicycloalkane Amino Acid Scaffolds as Reverse-Turn Inducer Dipeptide Mimics

In an effort to design structural mimics of protein and peptide reverse-turns, the conformations of 5,5-, 6,5-, and 7,5-fused 1-aza-2-oxobicycloalkane amino acids have been evaluated. The conformational preferences of these proline-derived bicyclic lactams have been studied by Monte Carlo molecular mechanics searches, and the reverse-turn inducing properties of the calculated structures have been quantitatively assessed using various geometrical parameters. All of the four possible diastereoisomers arising from two of the three stereogenic centres [C3 and bridgehead carbon atom; Pro Cα is (S) in all compounds] have been considered for each bicyclic scaffold. These studies have revealed that the (3S)-Pro Cα(S) configuration is an effective turn-inducer, although the torsion angles of the backbone do not always mimic those of classical β-turns. A dependence of the turn-inducing ability on lactam ring size and bridgehead stereochemistry has also been found. Reverse-turn mimetic bicyclic lactams have been shown to exhibit a tendency to form an inverse γ-turn or a type II′ β-turn. Experimental 1H-NMR and FT-IR spectroscopic data of model compounds in chloroform solutions have complemented our computer modelling studies and have confirmed our conclusions.

Conformational Analysis of Azabicycloalkane Amino Acid Scaffolds as Reverse-Turn Inducer Dipeptide Mimics

In an effort to design structural mimics of protein and peptide reverse-turns, the conformations of 5,5-, 6,5-, and 7,5-fused 1-aza-2-oxobicycloalkane amino acids have been evaluated. The conformational preferences of these proline-derived bicyclic lactams have been studied by Monte Carlo molecular mechanics searches, and the reverse-turn inducing properties of the calculated structures have been quantitatively assessed using various geometrical parameters. All of the four possible diastereoisomers arising from two of the three stereogenic centres [C3 and bridgehead carbon atom; Pro Cα is (S) in all compounds] have been considered for each bicyclic scaffold. These studies have revealed that the (3S)-Pro Cα(S) configuration is an effective turn-inducer, although the torsion angles of the backbone do not always mimic those of classical β-turns. A dependence of the turn-inducing ability on lactam ring size and bridgehead stereochemistry has also been found. Reverse-turn mimetic bicyclic lactams have been shown to exhibit a tendency to form an inverse γ-turn or a type II′ β-turn. Experimental 1H-NMR and FT-IR spectroscopic data of model compounds in chloroform solutions have complemented our computer modelling studies and have confirmed our conclusions.

Total Synthesis of Petrosin, Petrosin A, and Petrosin B

The petrosins are a family of marine alkaloids that includes the chiral, racemic isomer petrosin (1), the meso isomer petrosin A (2), and the chiral, scalemic isomer petrosin B (3). Monte Carlo molecular mechanics calculations indicated that petrosin (1) is the most stable isomer of the group, suggesting that it might be synthesized by a route that utilizes thermodynamic control for establishing the relative configurations of the eight stereocenters. The model synthesis summarized in Scheme 1 showed that intramolecular Mannich condensation is a viable route to the quinolizidone subunit of the petrosins and that this synthesis gives isomer 5, having the relative configuration found in petrosin and petrosin A, as the kinetic product. Equilibration studies with this isomer afforded an approximate equimolar mixture of 5 and diastereomer 6, having the relative configuration found in one of the two quinolizidone units of petrosin B. On the basis of this model study, a “stereo-uncontrolled” synthesis of petrosin was carried out, as summarized in Schemes 3−5. The key step of this synthesis is a “double-barrelled” intramolecular Mannich condensation of a diamino keto dialdehyde. This transformation provides crystalline petrosin in 23% yield, along with about 37% of a mixture of petrosin diastereomers. Although simple acid- and Lewis acid-mediated equilibrations of this mixture of diastereomers were not successful, the derived mixture of bis-butylimines undergoes equilibration upon treatment with protic acid to give a mixture that is greatly enriched in petrosin, relative to the other isomers. Crystallization of this equilibration mixture provided another 10% of petrosin, bringing the overall yield of petrosin to 33%. In the course of the equilibration studies, pure samples of petrosin A (2), petrosin B (3), and petrosin B‘ (7) were isolated and characterized.

Design, Synthesis, and Conformational Analysis of a Proposed Type I β-Turn Mimic

In an effort to design a dipeptide structural mimic of protein and peptide β-turns, we have prepared and evaluated the conformation of derivatives of the novel, highly constrained ten-membered lactam, (3S,10S)-(6E)-2-azacyclodec-6-enone (1). A synthetic route utilizing ring-closing olefin metathesis (RCM) has been used to prepare this novel ten-membered ring in high yield. X-ray crystallography and 1H NMR analysis have established that ring closure proceeds to give the trans-olefin and that 1 exists in two conformations, that of a chair−chair and chair−boat. Monte Carlo-molecular mechanics conformational searching has indicated that this ring system would be a good mimic of a type I β-turn. The synthesis of model tri- and tetrapeptide analogues based on 1 is reported. NMR studies indicate that the tetrapeptide derivatives constrain the i+1 and i+2 torsion angles to within 30° of those predicted for an ideal type I β-turn (φ1 = −82°, ψ1 = −20°, φ2 = −107°, ψ2 = −18°) and that this conformation was shown to...

Application of structure-based thermodynamic calculations to the rationalization of the enantioselectivity of subtilisin in organic solvents

The effect of organic solvents on the selectivity of lyophilized or CLEC (cross-linked enzyme crystals)-subtilisin in the resolution of sec-phenethyl alcohol and trans-sobrerol was studied. A theoretical model, that tries to predict solvent effects on enantioselectivity only as a function of the activity coefficients of the desolvated part of the substrate in the relevant transition state of the reaction (Ke, T.; Wescott, C. R.; Klibanov, A. M. J. Am. Chem. Soc., 1996, 118, 3366) was examined and shown to agree poorly with the experimental data. The tetrahedral intermediate was studied with MonteCarlo molecular mechanics, and the activity coefficients were calculated with UNIFAC.