Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high‐performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Condensed‐phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur‐containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur‐containing molecules including cysteine and methionine residues in proteins. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis

Cytochrome P450 (CYP) is deeply involved in the metabolism of chemicals including pharmaceuticals. Therefore, polymorphisms of this enzyme have been widely studied to avoid unfavorable side effects of drugs in chemotherapy. In this work, we performed computational analysis of the mechanism of the decrease in enzymatic activity for three typical polymorphisms in CYP 2C9 species: *2, *3, and *5. Based on the equilibrated structure obtained by molecular dynamics simulation, the volume of the binding pocket and the fluctuation of amino residues responsible for substrate holding were compared between the wild type and the three variants. Further docking simulation was carried out to evaluate the appropriateness of the binding pocket to accommodate substrate chemicals. Every polymorphic variant was suggested to be inferior to the wild type in enzymatic ability from the structural viewpoint. F‐G helices were obviously displaced outward in CYP2C9*2. Expansion of the binding pocket, especially the space near F′ helix, was remarkable in CYP2C9*3. Disappearance of the hydrogen bond between K helix and β4 loop was observed in CYP2C9*5. The reduction of catalytic activity of those variants can be explained from the deformation of the binding pocket and the consequent change in binding mode of substrate chemicals. The computational approach is effective for predicting the enzymatic activity of polymorphic variants of CYP. This prediction will be helpful for advanced drug design because calculations forecast unexpected change in drug efficacy for individuals. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Accurate free energy calculation along optimized paths

The path‐based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10‐ALA peptide and find that the calculated free energy changes in helix‐helix and helix‐hairpin transitions are both self‐convergent and cross‐convergent. We also calculate the free energy differences between different stable states of β‐hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Temperature dependence of structure and dynamics of the hydrated Ca2+ ion according to ab initio quantum mechanical charge field and classical molecular dynamics

Simulations using ab initio quantum mechanical charge field molecular dynamics (QMCF MD) and classical molecular dynamics using two‐body and three‐body potentials were performed to investigate the hydration of the Ca²⁺ ion at different temperatures. Results from the simulations demonstrate significant effects of temperature on solution dynamics and the corresponding composition and structure of hydrated Ca²⁺. Substantial increase in ligand exchange events was observed in going from 273.15 K to 368.15 K, resulting in a redistribution of coordination numbers to lower values. The effect of temperature is also visible in a red‐shift of the ion‐oxygen stretching frequencies, reflecting weakened ligand binding. Even the moderate increase from ambient to body temperature leads to significant changes in the properties of Ca²⁺ in aqueous environment. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Atomistic in situ investigation of the morphogenesis of grains during pressure-induced phase transitions: molecular dynamics simulations of the B1-B2 transformation of RbCl

The mechanistic details of the pressure-induced B1-B2 phase transition of rubidium chloride are investigated in a series of transition path sampling molecular dynamics simulations. The B2→B1 transformation proceeds by nucleation and growth involving several, initially separated, nucleation centers. We show how independent and partially correlated nucleation events can function within a global mechanism and explore the evolution of phase domains during the transition. From this, the mechanisms of grain boundary formation are elaborated. The atomic structure of the domain-domain interfaces fully support the concept of Bernal polyhedra. Indeed, the manifold of different grain morphologies obtained from our simulations may be rationalized on the basis of essentially only two different kinds of Bernal polyhedra. The latter also play a crucial role for the B1→B2 transformation and specific grain boundary motifs are identified as preferred nucleation centers for this transition.     

The Wacker Process: Inner‐ or Outer‐Sphere Nucleophilic Addition? New Insights from Ab Initio Molecular Dynamics

The Wacker process consists of the oxidation of ethylene catalyzed by a Pd^II complex. The reaction mechanism has been largely debated in the literature; two modes for the nucleophilic addition of water to a Pd‐coordinated alkene have been proposed: syn‐inner‐ and anti‐outer‐sphere mechanisms. These reaction steps have been theoretically evaluated by means of ab initio molecular dynamics combined with metadynamics by placing the [Pd(C₂H₄)Cl₂(H₂O)] complex in a box of water molecules, thereby resembling experimental conditions at low [Cl^?]. The nucleophilic addition has also been evaluated for the [Pd(C₂H₄)Cl₃]^? complex, thus revealing that the water by chloride ligand substitution trans to ethene is kinetically favored over the generally assumed cis species in water. Hence, the resulting trans species can only directly undertake the outer‐sphere nucleophilic addition, whereas the inner‐sphere mechanism is hindered since the attacking water is located trans to ethene. In addition, all the simulations from the [Pd(C₂H₄)Cl₂(H₂O)] species (either cis or trans) support an outer‐sphere mechanism with a free‐energy barrier compatible with that obtained experimentally, whereas that for the inner‐sphere mechanism is significantly higher. Moreover, additional processes for a global understanding of the Wacker process in solution have also been identified, such as ligand substitutions, proton transfers that involve the aquo ligand, and the importance of the trans effect of the ethylene in the nucleophilic addition attack.     

Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

Solvent- and temperature-dependent functionalisation of enantioenriched aziridines

A highly stereo‐ and regioselective functionalisation of chiral non‐racemic aziridines is reported. By starting from a parent enantioenriched aziridine and finely tuning the reaction conditions, it is possible to address the regio‐ and stereoselectivity of the lithiation/electrophile trapping sequence, thereby allowing the preparation of highly enantioenriched functionalised aziridines. From chiral N‐alkyl trans‐2,3‐diphenylaziridines (S,S)‐ 1 a , b , two differently configured chiral aziridinyllithiums could be generated (trans‐ 1 a , b‐Li in toluene and cis‐ 1 a , b‐Li in THF), thus disclosing a solvent‐dependent reactivity that is useful for the synthesis of chiral tri‐substituted aziridines with different stereochemistry. In contrast, chiral aziridine (S,S)‐ 1 c showed a temperature‐dependent reactivity to give chiral ortho‐lithiated aziridine 1 c‐ ortho ‐Li at ?78 °C and α‐lithiated aziridine 1 c‐α‐Li at 0 °C. Both lithiated intermediates react with electrophiles to give enantioenriched ortho‐ and α‐functionalised aziridines. The reaction of all the lithiated aziridines with carbonyl compounds furnished useful chiral hydroxyalkylated derivatives, the stereochemistry of which was ascertained by X‐ray and NMR spectroscopic analysis. The usefulness of chiral non‐racemic functionalised aziridines has been demonstrated by reductive ring‐opening reactions furnishing chiral amines that bear quaternary stereogenic centres and chiral 1,2‐, 1,3‐ and 1,5‐aminoalcohols. It is remarkable that the solvent‐dependent reactivity observed with (S,S)‐ 1 a , b permits the preparation of both the enantiomers of amines ( 11 and ent‐ 11 ) and 1,2‐aminoalcohols ( 13 and ent‐ 13 ) starting from the same parent aziridine. Interestingly, for the first time, a configurationally stable chiral α‐lithiated aziridine ( 1 c‐α‐Li ) has been generated at 0 °C. In addition, ortho‐hydroxyalkylated aziridines have been easily converted into chiral aminoalkyl phthalans, which are useful building blocks in medicinal chemistry.