Torsional Potential Research Articles

On the applicability of the molecular dynamics SCC-DFTB treatment on optical spectra simulations for thiophene and phenyl containing oligomers

The applicability of the semiempirical Self-Consistent Charge Density-Functional Based Tight Binding approach (SCC-DFTB) is tested and compared with the reference ab initio Møller–Plesset perturbation theory up to the second-order (MP2) and density functional theory (DFT). In this context, the calculations of 2-phenylthiophene and 2,2′-bithiophene molecules are presented with respect to the optimal geometries and torsional potentials. The vibrational broadenings of absorption spectra based on the combined on-the-fly molecular dynamics (MD) simulations were analyzed for the studied model molecules as well as for selected representative oligomeres or star-shaped molecules built from the thiophene and phenyl units. Our calculations showed that the SCC-DFTB method has the tendency to planarize the mutual distortion between the thiophene–thiophene or thiophene–phenyl units and to overestimate the energy barriers for perpendicular structures with respect to the benchmark MP2 and DFT results. The semiempirical TD-B3LYP//MD(SCC-DFTB) or ZINDO//MD(SCC-DFTB) simulations at a temperature of 300K produce narrower absorption spectroscopic bands comparing to the reference TD-B3LYP//MD(B3LYP) results. The temperature increase to 600K ensures the higher population of distorted MD(SCC-DFTB) geometries and consequently a more realistic shape of the absorption bands with respect to the internal vibrational and rotational modes.

Cis–Trans Isomerization of Chemically Activated 1-Methylallyl Radical and Fate of the Resulting 2-Buten-1-peroxy Radical

The cis-trans isomerization of chemically activated 1-methylallyl is investigated using RRKM/Master Equation methods for a range of pressures and temperatures. This system is a prototype for a large range of allylic radicals formed from highly exothermic (∼35 kcal/mol) OH + alkene reactions. Energies, vibrational frequencies, anharmonic constants, and the torsional potential of the methyl group are computed with density functional theory for both isomers and the transition state connecting them. Chemically activated radicals are found to undergo rapid cis-trans isomerization leading to stabilization of significant amounts of both isomers. In addition, the thermal rate constant for trans → cis isomerization of 1-methylallyl is computed to be high enough to dominate reaction with O(2) in 10 atm of air at 700 K, so models of the chemistry of the (more abundant and more commonly studied) trans-alkenes may need to be modified to include the cis isomers of the corresponding allylic radicals. Addition of molecular oxygen to 1-methylallyl radical can form 2-butene-1-peroxy radical (CH(3)CH═CHCH(2)OO(•)), and quantum chemistry is used to thoroughly explore the possible unimolecular reactions of the cis and trans isomers of this radical. The cis isomer of the 2-butene-1-peroxy radical has the lowest barrier (via 1,6 H-shift) to further reaction, but this barrier appears to be too high to compete with loss of O(2).

Conformations and torsional potentials of poly(3-hexylthiophene) oligomers: Density functional calculations up to the dodecamer

Fully optimized conformations of poly(3-hexylthiophene) (P3HT) oligomers up to the decamer and torsional potentials up to the dodecamer (302atoms) are investigated by large-scale density functional calculations (B3LYP/6-31+G(d,p)). Fully relaxed P3HT oligomers were investigated at a variety of conformational minima, many with skeletal structures far from planarity. The lowest energy conformations found have each hexyl group ≈74° out of plane and each backbone twist angle out of plane by ≈47°. The energies of these non-planar conformations are lower than that of the planar reference geometry by ≈30meV per monomer. Backbone torsional potentials and hexyl torsional potentials converge with oligomer length by the octamer. A wide variety of oligomer conformations are sufficiently close in energy (∼kT) that the actual conformations found in a condensed phase will be determined primarily by intermolecular interactions, and substantial conformational disorder might be expected in the heterogenous environment of practical solar devices.

Symmetry-adapted formulation of the G-particle-hole hypervirial equation method

Highly accurate 2-body reduced density matrices of atoms and molecules have been directly determined without calculation of their wave functions with the use of the G-particle-hole hypervirial (GHV) equation method (Alcoba et al. in Int. J. Quantum Chem. 109:3178, 2009). Very recently, the computational efficiency of the GHV method has been significantly enhanced through the use of sum factorization and matrix-matrix multiplication (Alcoba et al. in Int. J. Quantum Chem 111:937, 2011). In this paper, a detailed analysis of the matrix contractions involved in GHV calculations is carried out. The analysis leads to a convenient strategy for exploiting point group symmetry, by which the computational efficiency of the GHV method is further improved. Implementation of the symmetry-adapted formulation of the method is reported. Computer timings and hardware requirements are illustrated for several representative chemical systems. Finally, the method is applied to the well-known challenging calculation of the torsional potential in ethylene.

Could Diastereoselectivity in the Presence of O-2 Chiral Nonparticipating Groups Be an Indicator of Glycopyranosyl Oxacarbenium Ions in Glycosylation Reactions?

Although long postulated, the existence of glycopyranosyl oxacarbenium ions as intermediates or transition states (TS) in chemical glycosylation reactions has not been convincingly demonstrated experimentally. It is anticipated that elucidation of such reactive species will greatly assist synthetic chemists to control the α/β stereoselectivity by rational means. Previous density functional theory (DFT) calculations from our group found that the torsion potential about C-2-O-2 in protected glycopyranosyl donors changed from a conventional 3-fold rotor to a 2-fold rotor with a strong syn (CH-2-C-2-O-2-CPg) preference once the donor was ionized to its oxacarbenium ion. This suggested to us that if CPg of the protecting group was a chiral carbon, then diastereoselectivity might be observed in glycosylation reactions that proceed through oxacarbenium ions. The hypothesis to test is as follows: if a nonparticipating O-2 racemic chiral protecting group exhibits diastereoselectivity in glycosylation reactions, then the reaction probably proceeds through an oxacarbenium ion intermediate or TS. We present data for O-2 ether-protected d-glucopyranosyl donors where the racemic protecting group 1-methyl 1'-methylcyclopropylmethyl (MCPM) provides the chirality. MCPM proves to be more activating than the O-2-benzyl ether, and in cases where the donor is otherwise deactivated, several examples of moderate diastereoselectivity are found. These results can be interpreted to indicate that a continuum of reactivity exists where some glycosyl donors form oxacarbenium ions in glycosylation reactions but more reactive donors do not. The strongly activating properties of the cyclopropylmethyl ether functionality and the ability to induce diastereoselectivity with chiral derivatives strongly suggest widespread applications.

Impact of Neighboring Chains on Torsional Defects in Oligothiophenes

Conjugated organic oligomers are central to the development of efficient organic electronic devices and organic photovoltaics. However, the torsional flexibility of many of these organic materials, in particular oligothiophenes, can adversely affect charge transfer properties. Although previous studies have examined the torsional flexibility of oligothiophenes, there have been only limited studies of the effects of interchain interactions on their torsional potentials. B97-D/TZV(2d,2p) was first benchmarked against a CCSD(T)/aug-cc-pVTZ torsional potential for bithiophene as well as SCS-MP2/TZVPP interaction energies for noncovalent sexithiophene (6T) dimers. The effect of neighboring chains on three distinct torsional modes of sexithiophene was studied using B97-D. Complexation with one or more neighboring chains has a dramatic effect on each of these torsional potentials. For example, for two stacked chains, alternated twisting motions are competitive with torsion about a single terminal dihedral angle, and in both cases we predict nonplanar global energy minima and large amplitude torsional motions at room temperature. In other words, the presence of a single neighboring chain induces significant deviations from planarity in oligothiophenes. However, in the environment of crystalline 6T, the trend in predicted torsional potentials match those of isolated chains, but the force constants associated with torsional motions increase by an order of magnitude. Consequently, although individual oligothiophene chains are torsionally flexible and model stacked dimers exhibit extreme deviations from planarity, in crystalline 6T these oligomers are predicted to adopt planar configurations with a steep energetic cost associated with torsional defects.

Residue-Specific α-Helix Propensities from Molecular Simulation

Formation of α-helices is a fundamental process in protein folding and assembly. By studying helix formation in molecular simulations of a series of alanine-based peptides, we obtain the temperature-dependent α-helix propensities of all 20 naturally occurring residues with two recent additive force fields, Amber ff03w and Amber ff99SB∗. Encouragingly, we find that the overall helix propensity of many residues is captured well by both energy functions, with Amber ff99SB∗ being more accurate. Nonetheless, there are some residues that deviate considerably from experiment, which can be attributed to two aspects of the energy function: i), variations of the charge model used to determine the atomic partial charges, with residues whose backbone charges differ most from alanine tending to have the largest error; ii), side-chain torsion potentials, as illustrated by the effect of modifications to the torsion angles of I, L, D, N. We find that constrained refitting of residue charges for charged residues in Amber ff99SB∗ significantly improves their helix propensity. The resulting parameters should more faithfully reproduce helix propensities in simulations of protein folding and disordered proteins.

Effect of electronic states coupling on methyl torsion in 3-methylisoquinoline

Spectroscopic studies on jet cooled 3-methylisoquinoline using fluorescence excitation and dispersed fluorescence methods were carried out. The effect of methyl substitution on the excited state behavior of isoquinoline is focused. Methyl torsional behavior and the effect on torsional potential of methyl group due to excited states mixing are addressed. The possible explanations of the observed intensity pattern of the torsional transitions in the fluorescence excitation spectrum are also presented.

A force field for naproxen

A united-atom potential model for naproxen suitable for molecular dynamics (MD) simulation has been developed. The charge distribution is approximated by point charges obtained from ab initio calculations using the CHELPG method. Also the intramolecular interactions such as bond and angle vibration, and the torsion potential are obtained from ab initio calculations. The dispersive interaction contribution is taken from the literature. By MD simulation using a naproxen film in slap geometry, the temperature dependence of the density, surface tension and self-diffusion coefficient as well as the melting temperature for the developed potential model are obtained.

Methyl branch effects on rheological behaviours of short-chain polypropylene under steady shear studied via nonequilibrium molecular dynamics simulations

The rheological behaviours of the steady sheared short-chain polypropylene (PP) fluid are studied using isobaric isothermal nonequilibrium molecular dynamics simulations. By comparing the behaviours of PP fluid with that of the linear alkane fluid of n-hexadecane (C16) having equal backbone length, we investigated the effects of the branch structure on shear thinning, rotational relaxation time, critical shear rate and potential energies. The results showed that the degree of shear thinning of the PP fluid is lower than that of the C16 fluid. With respect to different temperatures, the degree of shear thinning of the former is less sensitive than that of the latter. At the molecular level, potential energies including van der Waals nonbonding interaction and bond stretching, bond bending, and bond torsion interactions are discussed. Significantly, the varying tendency of the bending potential of the PP fluid at very high shear rates is contrary to that of the C16 fluid. We propose, therefore, that the branch structure affects the bending angle distribution such that it causes differences in the rheological behaviours of these two fluids. Furthermore, in all the molecular potentials of the PP fluid, the torsion potential of the dihedral angle is observed to be the strongest dependent upon temperature.

Ab Initio Treatment of Bond-Breaking Reactions: Accurate Course of HO3 Dissociation and Revisit to Isomerization.

An efficient scheme is devised for accurate studies of bond-breaking/forming reactions and illustrated for HO3. It is suggested and numerically demonstrated that an accurate dissociation path for the title system can be obtained by defining the central OO bond as the reaction coordinate. The approach consists of optimizing the dissociation path at the full-valence-complete-active space level of theory followed by single-point multireference configuration interaction calculations along it. Using large diffusely augmented basis sets of the correlation consistent type, accurate dissociation curves are then obtained for both the cis- and trans-HO3 isomers by extrapolating the calculated raw energies to the complete basis set limit. The profiles show a weak van der Waals type minimum and a small barrier, both lying below the dissociation asymptote. It is shown that this barrier arises at the break-off of the central OO chemical bond and onset of the OH···O2 hydrogen bond. The calculated dissociation energies (De) are 4.5 ± 0.1 and 4.7 ± 0.1 kcal mol(-1) for the cis- and trans-HO3 isomers, respectively, with a very conservative estimate of the dissociation energy (D0) for trans-HO3 being 2.7 ± 0.2 kcal mol(-1) and a more focused one being 2.8 ± 0.1 kcal mol(-1). This result improves upon our previous estimate of this quantity while overlapping in the lower range of 2.9 ± 0.1 kcal mol(-1), the commonly accepted value from the low-temperature CRESU experiments. Since the cis-HO3 isomer is predicted to be 0.15 kcal mol(-1) less stable than trans-HO3, this may partly explain the failure to obtain a clear characterization of the former. The isomerization (torsional) potential is also revisited and a comparison presented with a curve inferred from spectroscopic measurements. Good agreement is observed, with the accuracy of the new calculated data commending its use for the reanalysis of the available vibrational-rotational spectroscopic data.

Synchronization and bundling of anchored bacterial flagella

The synchronization and bundling process of bacterial flagella is investigated by mesoscale hydrodynamic simulations. Systems with two to six flagella are considered, which are anchored at one end, and are driven by a constant torque. A flagellum is modelled as a linear helical structure composed of mass points with their elastic shape maintained by bonds, bending, and torsional potentials. The characteristic times for synchronization and bundling are analyzed in terms of motor torque, separation, and number of flagella. We find that hydrodynamic interactions determine the bundling behavior. The synchronization time is smaller than the bundling time, but their ratio depends strongly on the initial separation. The bundling time decreases with increasing number of flagella at a fixed radius in a circular arrangement due to multi-helix hydrodynamics.

Nonabelian Dualization of Plane Wave Backgrounds

We investigate plane-parallel wave metrics from the point of view of their (Poisson-Lie) T-dualizability. For that purpose we reconstruct the metrics as backgrounds of nonlinear sigma models on Lie groups. For construction of dual backgrounds we use Drinfel'd doubles obtained from the isometry groups of the metrics. We find dilaton fields that enable to satisfy the vanishing beta equations for the duals of the homogenous plane-parallel wave metric. Torsion potentials or B-fields, invariant w.r.t. the isometry group of Lobachevski plane waves are obtained by the Drinfel'd double construction. We show that a certain kind of plurality, different from the (atomic) Poisson-Lie T-plurality, may exist in case that metrics admit several isometry subgroups having the dimension of the Riemannian manifold. An example of that are two different backgrounds dual to the homogenous plane-parallel wave metric.

Effect of ring torsion on intramolecular vibrational redistribution dynamics of 1,1′-binaphthyl and 2,2′-binaphthyl

The role of ring torsion in the enhancement of intramolecular vibrational energy redistribution (IVR) in aromatic molecules was investigated by conducting excitation and dispersed fluorescence spectroscopy of 1,1'-binaphthyl (1,1'-BN) and 2,2'-BN. The dispersed fluorescence spectra of 1,1'-BN in the origin region of S(1)-S(0) were well resolved, which presented 25-27 cm(-1) gaps of torsional mode in the ground state. The overall profile of the dispersed spectra of 1,1'-BN is similar to that of naphthalene. In contrast, the spectra of 2,2'-BN were not resolved due to the multitude of the active torsional modes. In both cases, dissipative IVR was observed to take place with a relatively small excess vibrational energy: 237.5 cm(-1) for 1,1'-BN and 658 cm(-1) for 2,2'-BN, which clearly shows that ring torsion efficiently enhances the IVR rate. Ab initio and density functional theory calculations with medium-sized basis sets showed that the torsional potential of 1,1'-BN has a very flat minimum over the range of torsional angles from ca. 60° to 120°, whereas that of 2,2'-BN showed two well-defined potential minima at ca. 40° and 140°, in resemblance to the case of biphenyl. In this work, we propose that aromatic molecules be classified into "strong" and "weak" torsional hindrance cases: molecules with strong hindrance case show shorter torsional progressions and more effective IVR dynamics than do those with weak hindrance.

Why Proteins Crystallize (or not): The Role of Non Specific Protein Interactions

X-ray crystallography remains the gold standard for determining protein structures. Yet obtaining high-quality protein crystals often relies on experimental trial and error. Understanding the physical principles underlying protein crystallization would thus help inform the experimental approach to the problem.Here, we use a soft matter methodology to study the crystallization mechanism of a model family of proteins. We perform atomistic simulations to characterize the surface contribution to protein pair interactions. The results indicate that the interaction varies significantly from one crystal contact to the other both in degree of attraction and in angular width of the interaction. Comparison with homologous and mutant versions of the model protein also identifies a key force in crystal contact formation: the presence of high-entropy residues significantly destabilizes the crystal interface.In order to further study the crystallization dynamics, we represent proteins with a Kern-Frenkel patchy particle model with an additional torsion potential: the patch geometry, the range of interaction and the width of the patches are determined using the data from the molecular dynamics simulations. Using Monte Carlo techniques, we trace the phase diagram and crystallization pathway of the different proteins under study. The results suggest new strategies for protein crystallization.

J056031 分子動力学法を用いた水和ナフィオン内の水・プロトン輸送特性の解析

We have performed an atomistic analysis of the vehicular transport of hydronium ions and water molecules in the nanostructure of hydrated Nafion membrane by systematically changing the hydration level using classical molecular dynamics simulations. The models of Nafion membrane based on DREIDING force field with modification of torsion potential are proposed and validated by comparing the density, water diffusivity, and Nafion morphology with experimental data. The simulated final density agrees with experiment within 1.3 % for various water contents and the trends that density decreases with increasing hydration level are reproduced. In addition to determination of diffusion coefficients of liquid molecules as a function of hydration level for dynamical analysis, we have also implemented the cluster analysis of liquid molecules for structural insight. The cluster analysis provides insights into the network formation of water channel at water content I = 6. The diffusion coefficient of water molecules is found to be in good agreement with experimental data. The diffusion coefficient of hydronium ions has showed that general trends in the experimental data are reproduced although the classical models have the limitation of hydronium dynamics.

Theoretical Studies on the Structural, Electronic and Optical Properties of the New π-conjugated Copolymers Based on Carbazole and Thiophene

This work reports a theoretical investigation of π-conjugated oligomers constituted by n units (n = 1-4) based on carbazole and ethylenedioxythiophene. The molecular geometry, torsional potential, electronic and optical properties of the oligomers [Cbz-(Edot)n-Cbz] (n = 1-4) are investigated using DFT (B3LYP/3-21G*) calculations. The discussion is focused on the influence of chain length on the properties of these copolymers. The analyses of torsional angles for [Cbz-(Edot)4-Cbz] reveal that the structure has a anti-planar conformation. The electronic properties of the molecules, HOMO, LUMO and Eg (HOMO-LUMO), are studied using B3LYP functional. The results have been compared with those of thiophene and ethylenedioxythiophene. The lowest excitation energies (Eex) and the maximal absorption wavelength (λabs) are studied using the TD/DFT, ZINDO and CIS methods. The electronic transitions of the absorption spectrum derived by TD/DFT method give useful structural and electronic information for designing novel conducting organic polymer materials. The bridging effect by C=C(CN)2 on the optoelectronic properties of the (carbazole-thiophene-carbazole) comonomer is investigated. Keywords: Conducting polymer; Carbazole-(Ethylenedioxythiophene)n-Carbazole comonomers; DFT Optoelectronic properties; absorption coefficient; Bridging effect. © 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. doi: http://dx.doi.org/10.3329/jsr.v4i1.7450J. Sci. Res. 4 (1), 119-133 (2012)

Update of the Cholesterol Force Field Parameters in CHARMM

A modification of the CHARMM36 lipid force field (C36) for cholesterol, henceforth, called C36c, is reported. A fused ring compound, decalin, was used to model the steroid section of cholesterol. For decalin, C36 inaccurately predicts the heat of vaporization (~10 kJ/mol) and molar volume (~10 cc/mol), but C36c resulted in near perfect comparison with experiment. MD simulations of decalin and heptane at various compositions were run to estimate the enthalpy and volumes of mixing to compare to experiment for this simple model of cholesterol in a chain environment. Superior estimates for these thermodynamic properties were obtained with C36c versus C36. These new parameters were applied to cholesterol, and quantum mechanical calculations were performed to modify the torsional potential of an acyl chain torsion for cholesterol. This model was tested through simulations of DMPC/10% cholesterol, DMPC/30% cholesterol, and DOPC/10% cholesterol. The C36 and C36c results were similar for surface areas per lipid, deuterium order parameters, electron density profiles, and atomic form factors and generally agree well with experiment. However, C36 and C36c produced slightly different cholesterol angle distributions with C36c adopting a more perpendicular orientation with respect to the bilayer plane. The new parameters in the C36c modification should enable more accurate simulations of lipid bilayers with cholesterol, especially for those interested in the free energy of lipid flip/flop or transfer of phospholipids and/or cholesterol.

Environment-related properties of polyhydroxylated dibenzo-p-dioxins

Polyhydroxylated dibenzo-p-dioxins (PHODDs) are important metabolic and synthetic products of polychlorinated dibenzo-p-dioxins (PCDDs). Two types of hydrogen bonds exist in PHODD molecules: one between a hydroxyl group (HO) and an oxygen atom of the ether bond, and the other between two ortho hydroxyls of a benzene ring. By fully optimized calculation with density functional theory (DFT), their bond energies were ascertained to be approximately 9–14kJ/mol and 15–19kJ/mol respectively by the comparison of standard Gibbs energy of formation (ΔfGθ) between different molecules, which was experimentally verified. The two types of hydrogen bonds affect the hydrophilicity and stability of the molecules. The torsional potential of hydroxyls and the orientation making the congener most stable were obtained. The octanol-water partition coefficients (logKows) were calculated based on the group contribution method, and the standard state entropy (Sθ), standard enthalpy (ΔfHθ) of formation and ΔfGθ were obtained from the combination of DFT calculation and isodesmic reaction for the stable PHODD congeners. The number and position of hydroxyl substitution (NPHOS) were employed as descriptors to establish quantitative structure–property relationship (QSPR) models. Although the hydrophilicity of PHODDs increases with the number of hydroxyl groups, it is impaired by the intramolecular hydrogen bonds. The logKows of PHODDs are much smaller than those of PCDDs, and the variation trend with the number of substituents is different. In addition, the relative stability order of PHODD congeners was theoretically proposed, which is quite different from that of PCDDs. Considering the ionization in water, first-order ionization constants of PHODDs were calculated according to the results of SMD method of Self-Consistent Reaction Field Theory (SCRF), and they were influenced by the hydrogen bonds.

Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins

Retinal proteins are excellent systems for understanding essential physiological processes such as signal transduction and ion pumping. Although the conjugated polyene system of the retinal chromophore is best described with quantum mechanics, simulations of the long-timescale dynamics of a retinal protein in its physiological, flexible, lipid-membrane environment can only be performed at the classical mechanical level. Torsional energy barriers are a critical ingredient of the classical force-field parameters. Here we review briefly current retinal force fields and discuss new quantum mechanical computations to assess how the retinal Schiff base model and the approach used to derive the force-field parameters may influence the torsional potentials.