Torsional Potential Research Articles

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Including Torsional Anharmonicity in Canonical and Microcanonical Reaction Path Calculations.

We reformulate multistructural variational transition state theory by removing the approximation of calculating torsional anharmonicity only at stationary points. The multistructural method with torsional anharmonicity is applied to calculate the reaction-path free energy of the hydrogen abstraction from the carbon-1 position in isobutanol by OH radical. The torsional potential anharmonicity along the reaction path is taken into account by a coupled torsional potential. The calculations show that it can be critical to include torsional anharmonicity in searching for canonical and microcanonical variational transition states. The harmonic-oscillator approximation fails to yield reasonable free energy curves along the reaction path.

Brownian Dynamics Model of Excited-State Relaxation in Solutions of Conjugated Oligomers

The effects of torsional degrees of freedom on the excited-state relaxation of conjugated oligomers in solution are explored computationally by coupling an exciton model of the oligomer to a Brownian dynamics model of the solvent. The exciton model assigns one torsional degree of freedom to each unit cell, or site, of the oligomer. A simple molecular mechanical form is used for the ground electronic state. The excitation energy is obtained assuming coherent coupling between sites that is proportional to the cosine of the difference in torsional angles. The solvent is characterized by a single parameter, which is equivalent to setting the rotational diffusion time, trot, of a single unit cell about the oligomer axis in the absence of any internal forces. The relaxation of long oligomers exhibits a fast component, with a time constant that is about 0.025trot and a slow component that is about 0.15trot. As the oligomer length is decreased, the time constant for the slow component decreases such that the biexponential behavior smoothly diminishes below 10 unit cells, nearly disappearing by three unit cells. Comparisons of the exciton model, which includes self-trapping, with molecular mechanics and harmonic oscillator models, which do not include self-trapping, show similar behaviors. The double-exponential behavior therefore appears to be a general consequence of the participation of many torsional degrees of freedom in establishing the excitation energy. Because the time scales are relatively independent of the details of the torsional potential, experimental measurements of relaxation due to planarization report primarily on trot.

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters.

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.

MSTor version 2013: A new version of the computer code for the multi-structural torsional anharmonicity, now with a coupled torsional potential

We present an improved version of the MSTor program package, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsions; the method is based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes seven utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files for the MSTor calculation and Voronoi calculation, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. New version program summaryProgram title: MSTorCatalogue identifier: AEMF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 487256No. of bytes in distributed program, including test data, etc.: 14766898Distribution format: tar.gzProgramming language: Fortran 90, C, and perl.Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), and Mac Pro (two 2.8 GHz Quad-core intel Xeon processors).Operating system: Linux/Unix/Mac OS.Has the code been vectorized or parallelized?: NoRAM: 2 MbytesCatalogue identifier of previous version: AEMF_v1_0Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1803Classification: 16.3, 16.12, 23.Does the new version supercede the previous version?: YesNature of problem:Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperature) of complex molecules involving multiple torsional motions.Solution method:The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation.Reasons for new version:We implemented the newly developed MS-T method based on a coupled torsional potential, which is called the MS-T(C) method. It has been shown to be more accurate than the original MS-T method, i.e., the MS-T(U) method, based on an uncoupled torsional potential. We simplified the input files and improved our utility codes to make the MSTor package easier to use.Summary of revisions:1.We added the MS-T method based on a coupled torsional potential, which is called MS-T(C), where C denotes coupled. The original method that is based on an uncoupled potential is called MS-T(U).2.The capability of treating linear bending motions is added.3.Definitions of frames and frame chains are no longer needed in the input file.4.The code symmetry is added to determine the group symmetry of a structure.5.The mvinput.exe utility program is added to generate the input file for the vorm.exe and/or mcvorm.exe codes. The msinput.exe utility code had been modified to write the local periodicities taken from the mvorm.out file. Both mvinput.exe and msinput.exe use the symmetry.exe program to determine the point group of each structure.6.The ConfGen.exe has been completely rewritten in Fortran 90, and it reads new fields corresponding to the Gaussian input keywords.7.We corrected a bug in which an array was not initialized.Restrictions:There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multitorsional problems for which one can afford to calculate all the conformational structures and their frequencies.Unusual features:The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes, the symmetry program for determining point group symmetry of a molecule, and seven utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes of the torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method.Additional comments:The program package includes a manual, installation script, and input and output files for a test suite.Running time:There are 26 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 s.

Accurate treatment of two-dimensional non-separable hindered internal rotors

This work presents an accurate way for calculating partition functions of strongly coupled hindered rotors in two dimensions. The two-dimensional torsional potential is generated from electronic structure calculations and fitted to Fourier series. The kinetic energy includes off-diagonal terms which are allowed to vary with the torsional angles, and these terms were also fitted to Fourier series. The resulting Hamiltonian leads to a coupled Schrödinger equation which was solved by the variational method. Therefore, the final two-dimensional non-separable (2D-NS) partition function incorporates coupling terms in both the kinetic and the potential energy. The methodology has been tested for propane, methyl formate, and a hydrogen abstraction transition state from propanone by the OH radical. How to incorporate the 2D-NS partition function in the total vibrational-rotational partition function is also discussed.

Influence of the Retinal Methyl Groups on Retinal Structure and Dynamics

The light-induced isomerization of the retinal chromophore starts the reaction cycles of retinal proteins. We review and discuss some new computations on the role of the retinal methyl groups in determining the structure, dynamics, and protein interactions of the retinal. The torsional potential of the C11=C12 bond suggests that moderate twisting of this bond can be achieved without a significant energetic cost, allowing for twisted 11-cis geometries to be sampled within the protein environment. The 9- and 13-methyl groups contribute significantly to the geometry and the ground-state torsional properties of the retinal chromophore, but the relative importance of these two methyl groups appears to be different in the dark- vs. the batho-intermediates of visual rhodopsins.

Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

Electronically Excited States in Poly(p-phenylenevinylene): Vertical Excitations and Torsional Potentials from High-Level Ab Initio Calculations

Ab initio second-order algebraic diagrammatic construction (ADC(2)) calculations using the resolution of the identity (RI) method have been performed on poly-(p-phenylenevinylene) (PPV) oligomers with chain lengths up to eight phenyl rings. Vertical excitation energies for the four lowest π–π* excitations and geometry relaxation effects for the lowest excited state (S1) are reported. Extrapolation to infinite chain length shows good agreement with analogous data derived from experiment. Analysis of the bond length alternation (BLA) based on the optimized S1 geometry provides conclusive evidence for the localization of the defect in the center of the oligomer chain. Torsional potentials have been computed for the four excited states investigated and the transition densities divided into fragment contributions have been used to identify excitonic interactions. The present investigation provides benchmark results, which can be used (i) as reference for lower level methods and (ii) give the possibility to parametrize an effective Frenkel exciton Hamiltonian for quantum dynamical simulations of ultrafast exciton transfer dynamics in PPV type systems.

The toluene-Ar complex: S and S1 van der Waals modes, changes to methyl rotation, and torsion-van der Waals vibration coupling

The methyl rotor and van der Waals vibrational levels in the S1 and S0 states of toluene-Ar have been investigated by the technique of two-dimensional laser induced fluorescence (2D-LIF). The S0 van der Waals and methyl rotor levels are reported for the first time, while improved S1 values are presented. The correlations seen in the 2D-LIF images between the S0 and S1 states lead to a reassignment of key features in the S1 ← S0 excitation spectrum. This reassignment reveals that there are significant changes in the methyl rotor levels in the complex compared with those in bare toluene, particularly at low m. The observed rotor energies are explained by the introduction of a three-fold, V3, term in the torsion potential (this term is zero in toluene) and a reduction in the height of the six-fold, V6, barriers in S0 and S1 from their values in bare toluene. The V3 term is larger in magnitude than the V6 term in both S0 and S1. The constants determined are ∣V3(S1)∣ = 33.4 ± 1.0 cm(-1), ∣V3(S0)∣ = 20.0 ± 1.0 cm(-1), V6(S1) = -10.7 ± 1.0 cm(-1), and V6(S0) = -1.7 ± 1.0 cm(-1). The methyl rotor is also found to couple with van der Waals vibration; specifically, the m(") = 2 rotor state couples with the combination level involving one quantum of the long axis bend and m(") = 1. The coupling constant is determined to be 1.9 cm(-1), which is small compared with the values typically reported for torsion-vibration coupling involving ring modes.

Quantum Thermochemistry: Multistructural Method with Torsional Anharmonicity Based on a Coupled Torsional Potential.

We present a new approximation for calculating partition functions and thermodynamic functions by the multistructural method with torsional anharmonicity (MS-T). The new approximation is based on a reference potential with torsional barriers obtained from a calculation that includes local torsional coupling. By comparing to a fully coupled classical rotational-torsional partition function evaluated as a numerical phase space integral, the method is shown to provide improved accuracy in the classical limit. Quantum effects, which are most important at low temperatures, are included based on the harmonic approximation (which can be upgraded to a quasiharmonic approximation, that is, harmonic formulas with effective frequencies). Calculations were performed for six molecules (ethanol, 1-butanol, hexane, isohexane, heptane, and isoheptane), one radical (1-pentyl radical), and the saddle point structures of a hydrogen abstraction reaction (hydroxyl plus ethanol) to illustrate the difference between the new coupled-potential MS-T approximation and the original uncoupled-potential MS-T approximation. The new method improves the agreement with experimental results of calcuated thermodynamic functions for 1-butanol, hexane, isohexane, and heptane.

A theoretical investigation of the structure of 2-nitropyridine-N-oxide and the dependency of the NO2 torsional motion on the applied wavefunction and basis set.

HF, B3LYP, and MP2 wave functions in combination with Pople 6-31, 6-311 augmented with polarization functions on all atoms and Dunning double- and triple-zeta basis sets have been employed to investigate the structures and torsional potential function of the nitro group in 2-nitropyridine-N-oxide (2-NPO) and a variety of its fluorinated derivatives. The augmentation of the basis sets with diffuse functions showed a marked effect on the profile and barriers of the NO2 torsional potential. Depending on the applied model chemistry, the heterocyclic ring in some 2-NPOs has proved to be non-planar. The non-planarity of the ring was characterized by Cremer–Pople puckering amplitude Q. The disruption of the ring planarity in some NPOs was accounted for the distinctive reactivity and impact sensitivity of these heterocycles. Consistently, the NBO and the AIM analyses furnished clear evidence for the accentuated weakness of the C–NO2 bond and provided evidence for the electronic interplay between the NO2 group, the fluorine substituent and the heterocyclic ring. Deletion of all off-diagonal Fock-matrix elements (NOSTAR) to separate hyperconjugative stabilizing interactions from steric interactions was used. The effect of nitration and fluorination on the aromaticity of the studied 2-NPOs was investigated by using the NICS descriptors NICS(1) and NICS(1)zz. These NICS indices have shown that the fluorination in para position to the nitro group exhibits the highest degree of aromaticity within the fluorinated 2-NPOs.Electronic supplementary materialThe online version of this article (doi:10.1007/s11224-012-0198-5) contains supplementary material, which is available to authorized users.

Correlated backbone torsional potentials in poly(3-methylthiophene)

Poly(3-alkylthiophenes) (P3AT) have shown great promise as solar cell materials. Knowledge of the conformations and the conformational energies is a key step toward understanding the electronic properties in such systems that contain extended electronic conjugation. In this study, poly(3-methylthiophene) (P3MT) oligomers are selected as model systems for the torsional properties of P3AT’s. A 3-dimensional torsional energy map is computed for the P3MT tetramer by density functional methods. Single-layered and ONIOM calculations were performed at B3LYP/6-31++G(d,p) level. The intra-chain torsional potential, when expressed in terms of the inter-ring torsional angles, contains correlations attributable to extended electronic conjugation along the oligomer backbone. Cross terms in the 3-D torsional energy map were found to scale such that 11% of the total variation of the potential results from the relative orientations of second-nearest-neighbor rings, and more extended torsional interactions along the chain contribute less than 3%.

106 Deriving force field dihedral angle parameters that account for conformation-dependent solvation effects

Dihedral angle parameters in force fields are often obtained with the help of quantum chemical calculations. These are usually performed in vacuum and it is assumed that the solvent model used in the molecular dynamics simulation (explicit or implicit) satisfactorily accounts for the major part of the solvation energy. However, there are certain nonspecific solvation effects that are not properly accounted for, in this approach. They relate to conformation-dependent solute polarization and solvation of conformation-dependent charge distribution. On an example of the glycosidic torsion, we show that the contribution resulting from these effects is substantial and provides important correction to the torsion potential. A parameterization procedure is suggested that incorporates the missing conformation-dependent solvation effects into the torsion parameters, based on the difference between the quantum mechanical self-consistent reaction field and Poisson–Boltzmann continuum solvation models. The suggested approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models or with the continuum solvent models. Improvements are demonstrated for the latest AMBER RNA parameters. The suggested procedure may help to provide consistently better parameters than the conventional in vacuo parameterization approach.

Effect of varying the 1–4 intramolecular scaling factor in atomistic simulations of long-chain N-alkanes with the OPLS-AA model

A comprehensive molecular dynamics simulation study of n-alkanes using the optimized potential for liquid simulation with all-atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1-4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better understand the effects of reducing the scaling factor, its influence on the torsion potential profile, and the corresponding gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane were investigated. This relatively simple procedure enables more accurate predictions of the thermo-physical properties of longer n-alkanes.

Coarse-Grained Potentials for Local Interactions in Unfolded Proteins.

Recent studies have revealed the key role of natively unfolded proteins in many important biological processes. In order to study the conformational changes of these proteins, a one-bead-per-amino-acid coarse grained (CG) model is developed, and a method is proposed to extract the potential functions for the local interactions between CG beads. Experimentally obtained Ramachandran data for the coil regions of proteins are converted into distributions of pseudo-bond and pseudo-dihedral angles between neighboring alpha-carbons in the polypeptide chain. These are then used to derive bending and torsion potentials, which are residue and sequence specific. The validity of the developed model is testified by studying the radius of gyration as well as the hydrodynamic properties of chemically denatured proteins.

Einstein–Cartan and general relativity cosmologies with a nonminimally coupled ghost scalar field

Exact general solutions for spatially flat isotropic and homogeneous cosmologies with a nonminimally coupled ghost scalar field that has polynomial potentials of the fourth degree are obtained in the framework of the Einstein–Cartan theory (ECT) and general relativity (GR). The special values of coupling constant \(\xi \) and restrictions on \(\xi \) are found for the above solutions. Some effects of torsion and scalar field potential are elucidated. It is shown that solutions can describe the bouncing models with the late-time accelerated expansion. It is demonstrated that some models admit the unified scenario for dark matter and dark energy: (i) both singular models in ECT with a de Sitter-like asymptotic and with the power-law \((t^{4/3})\) asymptotic at late times, (ii) singular and nonsingular models in GR with a de Sitter-like asymptotic at late times.

Accurate Force Field Development for Modeling Conjugated Polymers.

The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dynamics simulations of poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) and poly 3-hexylthiophene (P3HT), two of the most widely used conjugated polymers.

Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.

Coarse-grained force fields for protein simulations are usually designed and parameterized to treat proteins composed of natural L-amino-acid residues. However, D-amino-acid residues occur in bacterial, fungal (e.g., gramicidins), as well as human-designed proteins. For this reason, we have extended the UNRES coarse-grained force field developed in our laboratory to treat systems with D-amino-acid residues. We developed the respective virtual-bond-torsional and double-torsional potentials for rotation about the C α · · · C α virtual-bond axis and two consecutive C α · · · C α virtual-bond axes, respectively, as functions of virtual-bond-dihedral angles γ. In turn, these were calculated as potentials of mean force (PMFs) from the diabatic energy surfaces of terminally-blocked model compounds for glycine, alanine, and proline. The potential-energy surfaces were calculated by using the ab initio method of molecular quantum mechanics at the Møller-Plesset (MP2) level of theory and the 6-31G(d,p) basis set, with the rotation angles of the peptide groups about [Formula: see text] and [Formula: see text] used as variables, and the energy was minimized with respect to the remaining degrees of freedom. The PMFs were calculated by numerical integration for all pairs and triplets with all possible combinations of types (glycine, alanine, and proline) and chirality (D or L); however, symmetry relations reduce the number of non-equivalent torsional potentials to 13 and the number of double-torsional potentials to 63 for a given C-terminal blocking group. Subsequently, one- (for torsional) and two-dimensional (for double-torsional potentials) Fourier series were fitted to the PMFs to obtain analytical expressions. It was found that the torsional potentials of the x-Y and X-y types, where X and Y are Ala or Pro, respectively, and a lowercase letter denotes D-chirality, have global minima for small absolute values of γ, accounting for the double-helical structure of gramicidin A, which is a dimer of two chains, each possessing an alternating D-Tyr-L-Tyr sequence, and similar peptides. The side-chain and correlation potentials for D-amino-acid residues were obtained by applying the reflection about the [Formula: see text] plane to the respective potentials for the L-amino-acid residues.

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA χOL3 parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput.2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches.