General Force Field Research Articles

Development of an all-atoms force field from ab initio calculations for alternative refrigerants

A general all-atoms force field (FF) for atomistic simulation of low molecular weight hydrofluorocarbons (HFCs) was developed using state-of-art ab initio calculations and empirical parameterization techniques. The FF is based on ab initio quantum mechanical calculations for the valence parameters and on molecular dynamics (MD) simulations for the tuning of the Lennard-Jones (LJ) parameters describing the dispersion forces. Validation of the proposed FF has been made versus intramolecular properties of isolated molecules, vibrational spectra, and intermolecular properties of liquid state molecules such as cohesive energy, enthalpy of vaporization and density for molecules of interest. The reported results show that the present force filed enables accurate and simultaneous prediction of structural, conformational, vibrational and thermophysical properties for low molecular weight HFCs in isolation and in condensed phase. Detailed results of the parameterization and validation are reported.

On the Transferability of Force Field ParametersWith an ab Initio Force Field Developed for Sulfonamides

With 25 organic molecules that represent popular functional groups, we tested the transferability of force field parameters using both parametrized force fields CHARMM, CFF, and MMFF and generic force fields DREIDING and UNIVERSAL. We found that, if transferred parameters are used in a parametrized force field, the calculation quality is no longer superior to that of a generic force field. To achieve high quality in predictions, new parameters should be created from ab initio data whenever necessary. We investigated this approach and found that a custom-built force field can be made to reproduce ab initio results if parameters are derived specifically for the molecules of interest. The parametrization procedure was applied to a group of classic antibacterial drug molecules, the sulfonamides.

A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle

A polarizable electrostatic potential model for classical molecular mechanics is presented. Based on the chemical potential equalization (CPE) principle, the model is developed starting from the original formulation of Mortier, Ghosh, and Shankar [J. Am. Chem. Soc. 108, 4315 (1986)]. Following York and Yang [J. Chem. Phys. 104, 159 (1996)] we present an SP-basis CPE parametrization to describe realistically any sort of molecular system. By fitting ab initio electronic properties, such as dipole moment, polarizability and global molecular hardness of a restricted set of organic molecules, we derive atomic parameters to be applied to a more vast target set of compounds. We show, indeed, that the atomic CPE parameters calculated for the learning set of molecules give reliable values for several electronic properties of various compounds not included in the learning set. The multipole moments obtained by using the proposed CPE parametrization are compared to the results of a fixed charge parametrization like that used by a popular classical molecular mechanics force field, such as AMBER. We show that the fixed charge parametrization can well reproduce only the multipole moments of the molecular conformation or the isomer used for the fit, while being inaccurate when different molecular conformations or isomers are considered. On the contrary, the CPE model realistically reproduces the charge reorganization due to nuclear structural changes of the molecule, such as isomerization or conformational transition. The CPE model has been also tested on various molecular complexes to investigate the polarization response in the case of realistic molecule–molecule interactions. The main result of the paper is the demonstration that the construction of a general polarizable electrostatic force field for classical molecular mechanics is now a viable way.

Influence of carbon curvature on molecular adsorptions in carbon-based materials: a force field approach.

A general force field methodology is developed for description of molecular interactions in carbon-based materials. The method makes use of existing parameters of potential functions developed for sp(2) and sp(3) carbons and allows accurate representation of molecular forces in curved carbon environment. The potential parameters are explicitly curvature and site dependent. The proposed force field approach was used in molecular dynamics (MD) simulations for hydrogen adsorption in single-walled carbon nanotubes (SWNTs). The results reveal significant nanotube deformations and the calculated energies of adsorption are comparable to the reported experimental heat of adsorption for H2 in SWNTs.

Fourier transform infrared and Raman spectral analysis of trans-1,4-polyisoprene

Polyisoprene is the most widely used polymer in industry and commerce. Fourier transform infrared (FTIR) and Raman spectra of trans-1,4-polyisoprene have been recorded in the range of 4000–400 and 4000–100 cm −1, respectively. In the present investigation, detailed assignments of the observed fundamental bands of trans-1,4-polyisoprene has been analysed in terms of peak positions and relative intensities. With the hope of providing more and effective information on the fundamental vibrations, a normal co-ordinate analysis has been performed on trans-1,4-polyisoprene, by assuming C S symmetry. The simple general valance force field (SGVFF) method has been employed in normal co-ordinate analysis and to calculate the potential energy distribution (PED) for each fundamental vibration. The PED contribution corresponding to each of the observed frequencies shows the reliability and accuracy of the spectral analysis. The validity of the SGVFF method as a practical tool for complete analysis of vibrational spectra, even for a polymer of this complexity, is confirmed in the present work.

Multipoles versus charges in the 1999 crystal structure prediction test

Developments towards a new generally applicable force field for the organic solid state are reported. The new force field combines atomic multipoles with an existing generic force field, iz. Dreiding, thus integrating an accurate description of electrostatic interactions with full molecular flexibility. This model was validated by means of crystal structure prediction for the set of molecules which was considered in the 1999 blind test on crystal structure prediction. Results are compared to the 1999 submission based on standard Dreiding with atom-centered point charges derived by fitting to the electrostatic potential. The improvements seen when using atomic multipoles are promising. For two out of five structures the charge-based predictions were already accurate enough to find the experimental structure among the three “best” structures, and these findings are reproduced by the multipole model. For two other compounds the multipole model results in significant improvements in the energy ordering of the possible crystal packings. Only one structure is still problematic. According to the rules of the test, the multipoles/Dreiding model has resulted in a correct prediction for four out of the five crystal structures involved, in comparison to two out of five for the charges/Dreiding approach.

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001

Inelastic neutron scattering spectra of zeolite frameworks – experiment and modeling

Inelastic neutron scattering spectra of silicalite, Na-ZSM-5, zeolites X, and Y are measured and compared with the spectra obtained by molecular dynamics simulations of the zeolitic frameworks. Comparison of the spectra shows a good general agreement of the experimental and modeling results, indicating that a generalized force field correctly describes the dynamics of the frameworks. Some discrepancies are observed. They are assigned to defects in the samples and to the neglect of electrostatic interactions in the force field model.

Perfluoroalkanes: Conformational Analysis and Liquid-State Properties from ab Initio and Monte Carlo Calculations

Classical OPLS-AA force-field parameters are developed for perfluoroalkanes primarily by fitting to conformational profiles from gas-phase ab initio calculations (LMP2/cc-pVTZ(-f)//HF/6-31G*) and to experimental data for pure liquids. The ab initio C−C−C−C profile of n-C4F10 (perfluorobutane) is similar to those from prior high-level calculations and indicates the presence of gauche (g) and ortho (o) minima and of anti (a) minima slightly offset from 180°. Ab initio torsional profiles for n-C5F12 (perfluoropentane) and (CF3)2CFCF2CF3 (perfluoro-2-methylbutane) also show three sets of energy minima. Special OPLS-AA torsional parameters for these three molecules closely match ab initio and experimental geometries, conformational energies (ΔEmin), and conformational energy barriers. These specialized force fields were merged to provide a generalized force field for linear, branched, and cyclic perfluoroalkanes. The resultant parameters yield key ΔEmin values within 0.6 kcal/mol of the ab initio results for the three test compounds but more poorly represent the energy barriers. The parametrization also included reproduction of experimental liquid properties of these compounds, CF4 (perfluoromethane) and c-C5F10 (perfluorocyclopentane) via Monte Carlo (MC) simulations. MC simulations of six additional molecules were also performed in order to test the transferability of the force field.

The General Harmonic Force Field of Methyl Chloride

The complete general harmonic force field of methyl chloride has been recalculated using the most recent literature frequency, Coriolis ζ, and centrifugal distortion data for 12CH335Cl, 13CH335Cl, 12CD335Cl, 12CHD235Cl, 12CH2D35Cl, 12CH337Cl, 12CD337Cl, 12CHD237Cl, 12CH2D37Cl, and 13CH337Cl. The anharmonic corrections applied to the observed frequency data are considered to be more realistic than those used hitherto. There is excellent agreement between the fitted force constants and literature high-quality ab initio force fields. The results of the least-squares refinement of the full-harmonic force field is compared with least-squares refinement of only the scale factors for an SCF calculated force field since the latter approach may be useful for larger molecules where more sophisticated calculations are impractical. The results of a refinement of only the scale factors for an MP4 calculated force field are also reported.

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State.

Accurate simulation at the atomic level of the folding process of a variety of peptides into different native folds can be achieved with a general purpose force field and Newton's equations of motion. The key to understanding this peptide folding lies in the unexpectedly small size of the denatured state and an accurate description thereof.

Molecular dynamics simulation studies of liquid acetonitrile: New six‐site model

Molecular dynamics (MD) simulations are carried out for liquid acetonitrile using a new six-site model for the solvent molecules. The recent force field of Cornell et al. ( J Am Chem Soc, 1995, 117, 5179) was used under the RESP approach to obtain the atomic charges. A new flexible all-atom solvent model was achieved whose density, heat of vaporization, and isothermal compressibility values are in good agreement with available experimental data, especially for a generic force field. Radial distribution functions are calculated and discussed to study the liquid structure in detail. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 901–908, 2000

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

In this study, we present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges. This approach uses the simple generic force field model (Parm94), and attempts to add a minimal number of extra Fourier components to the torsional energies, but doing so only when there is a physical justification. The results are quite encouraging, not only for the 34-molecule set that has been studied by both the highest level ab initio model (GVB/LMP2) and experiment, but also for the 55-molecule set for which high-quality experimental data are available. Considering the 55 molecules studied by all the force field models for which there are experimental data, the average absolute errors (AAEs) are 0.28 (this model), 0.52 (MM3), 0.57 (CHARMm (MSI)), and 0.43 kcal/mol (MMFF). For the 34-molecule set, the AAEs of this model versus experiment and ab initio are 0.28 and 0.27 kcal/mol, respectively. This is a lower error than found with MM3 and CHARMm, and is comparable to that found with MMFF (0.31 and 0.22 kcal/mol). We also present two examples of how well the torsional parameters are transferred from the training set to the test set. The absolute errors of molecules in the test set are only slightly larger than in the training set (differences of <0.1 kcal/mol). Therefore, it can be concluded that a simple generic force field with a limited number of specific torsional parameters can describe intra- and intermolecular interactions, although all comparison molecules were selected from our 82-compound training set. We also show how this effective two-body

Molecular dynamics simulation studies of liquid acetonitrile: New six-site model

Molecular dynamics (MD) simulations are carried out for liquid acetonitrile using a new six-site model for the solvent molecules. The recent force field of Cornell et al. ( J Am Chem Soc, 1995, 117, 5179) was used under the RESP approach to obtain the atomic charges. A new flexible all-atom solvent model was achieved whose density, heat of vaporization, and isothermal compressibility values are in good agreement with available experimental data, especially for a generic force field. Radial distribution functions are calculated and discussed to study the liquid structure in detail. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 901–908, 2000

Computer simulations of the adsorption process of light alkanes in high-silica zeolites

The methods of molecular mechanics (MM), molecular dynamics (MD) and Monte-Carlo (MC) were used to compute adsorption energies and to determine the preferred adsorption sites of light alkanes (methane, ethane, propane, n-butane, i-propane and neopentane) in silicalite and ZSM-5. In order to compare their performance the same simulation conditions were used in all the calculations. The effect of using specific and generic force fields to represent the zeolite was also investigated. For the molecules studied, the MC and MD methods furnished comparable adsorption energies, although the MD results are slightly better when compared to experiments. For the linear akanes, the MM results are qualitatively correct but only when a specific force field is used to describe the zeolite. For the branched alkanes the MM results are comparable to the MD and MC ones even when a generic force field is used to represent the zeolite. The linear alkanes (C1–C4) showed equal probability of being found in both the straight and sinusoidal channels while the branched alkanes prefer the channel intersections.

HFF: a force field for liquid crystal molecules

Soft material simulations require an accurate representation of the intermolecular and intramolecular potential energy surface in order to achieve realistic predictions for their properties. The conformational potential of the molecules has a profound effect on many properties of molecular aggregates. This is usually a serious weakness of most commercial empirical force fields. In this paper we describe a force field (HFF), specifically designed for liquid crystal molecules. Intramolecular parameters are obtained from ab initio quantum mechanics calculations on model molecules which are substructures of liquid crystal molecules. HFF reproduces ab initio conformational energy profiles for model molecules with errors much smaller than commercial force fields. Our focus is not on creating general purpose force fields but on strategies to develop reliable force fields on-demand for specific needs.

Calculations of the phonon dispersion curves of C2H2, OC(ND2)2, and Na2CO3 from generic force field

The phonon dispersion curves of cubic acetylene, tetragonal urea, and monoclinic sodium carbonate are calculated from the generic force field using the direct method. The force constants of the dynamical matrix are determined from the forces induced by the displacement of an atom in the simulated supercell. The obtained dispersion curves are displayed along many high-symmetry lines of the Brillouin zone. For sodium carbonate, a soft mode has been found. The dispersion curves of urea fit quite well to the measured phonons. The results show that the force field approach leads to reasonable description of the lattice dynamics of crystals.

A comparative investigation of the consistent valence and extensible systematic force fields. A case study on the conformation of erythromycin A in benzene

The performances of the extensible systematic force field (esff), a general purpose force field recently developed for the molecular modeling of inorganic and organometallic compounds, and the well established consistent valence force field (cvff), known for its efficient performances, have been compared in their ability to produce accurately the conformation of organic moieties as well as for their conformational sampling properties. Erythromycin A (Ery-A), a compound with a well established conformation, was selected. After complete assignment of all 1H and 13C resonances of Ery-A in benzene solution, restrained MD simulations based on 44 nOe distance restraints were performed for both esff and cvff force fields, either by immediate application of the restraints on the X-ray structure, or on a set of 50 free MD conformers generated independently. The conformations generated by the two force fields were found to be highly similar, both mutually and to those found previously for Ery-A in the crystalline state and in chloroform. No distance violations larger than 0.22 A were observed. The structures were also validated against 17 non-trivial 3J(1H–1H) coupling constants and 26 3J(13C–1H) coupling constants, the latter determined from gradient-enhanced 1H-{13C} J-HMBC spectra. The conclusion from the present results is that both force fields generate directly comparable conformations for Ery-A.

Development of a New Force Field for Polynorbornene

A new force field has been customized for the variation of polynorbornene that contains a bicycloheptane group in the backbone structure. The force field was developed from ab initio density functional theory (DFT), and semiempirical electronic structure calculations for both stereochemical dimers of the 2,3 exo−exo isomer of polynorbornene. The bond length and bond angle parameters were determined using the HF/6-311G** ab initio SCF method. The intrinsic torsion potential was determined using the AM1 semiempirical method and the van der Waals parameters are kept same as in the Dreiding 2.21 force field. Both the bonded and torsional energy functions compared well to DFT calculations. The equilibrium geometry and the torsional energetics of the customized force field differ significantly from generic force fields such as Dreiding. Comparisons to experimentally determined geometry and infrared and Raman spectra were used to determine the optimum ab initio and semiempirical method to use for force field par...

ChemInform Abstract: Stereoselectivities of Nucleophilic Additions to Cycloheptanones. Experimental and Theoretical Studies and General Purpose Force Field for the Prediction of Nucleophilic Addition Stereoselectivities.

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