Development and testing of a general amber force field

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.     

Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase

The recently introduced force field (FF) QMPFF3 is thoroughly validated in gas, liquid, and solid phases. For the first time, it is demonstrated that a physically well-grounded general purpose FF fitted exclusively to a comprehensive set of high level vacuum quantum mechanical data applied as it is to simulation of condensed phase provides high transferability for a wide range of chemical compounds. QMPFF3 demonstrates accuracy comparable with that of the FFs explicitly fitted to condensed phase data, but due to high transferability it is expected to be successful in simulating large molecular complexes.     

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.     

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

A fluctuating charge (FQ) force field is applied to molecular dynamics simulations for six small proteins in explicit polarizable solvent represented by the TIP4P-FQ potential. The proteins include 1FSV, 1ENH, 1PGB, 1VII, 1H8K, and 1CRN, representing both helical and beta-sheet secondary structural elements. Constant pressure and temperature (NPT) molecular dynamics simulations are performed on time scales of several nanoseconds, the longest simulations yet reported using explicitly polarizable all-atom empirical potentials (for both solvent and protein) in the condensed phase. In terms of structure, the FQ force field allows deviations from native structure up to 2.5 A (with a range of 1.0 to 2.5 A). This is commensurate to the performance of the CHARMM22 nonpolarizable model and other currently existing polarizable models. Importantly, secondary structural elements maintain native structure in general to within 1 A (both helix and beta-strands), again in good agreement with the nonpolarizable case. In qualitative agreement with QM/MM ab initio dynamics on crambin (Liu et al. Proteins 2001, 44, 484), there is a sequence dependence of average condensed phase atomic charge for all proteins, a dependence one would anticipate considering the differing chemical environments around individual atoms; this is a subtle quantum mechanical feature captured in the FQ model but absent in current state-of-the-art nonpolarizable models. Furthermore, there is a mutual polarization of solvent and protein in the condensed phase. Solvent dipole moment distributions within the first and second solvation shells around the protein display a shift towards higher dipole moments (increases on the order of 0.2-0.3 Debye) relative to the bulk; protein polarization is manifested via the enhanced condensed phase charges of typical polar atoms such as backbone carbonyl oxygens, amide nitrogens, and amide hydrogens. Finally, to enlarge the sample set of proteins, gas-phase minimizations and 1 ps constant temperature simulations are performed on various-sized proteins to compare to earlier work by Kaminsky et al. (J Comp Chem 2002, 23, 1515). The present work establishes the feasibility of applying a fully polarizable force field for protein simulations and demonstrates the approach employed in extending the CHARMM force field to include these effects.     

Development of a force field for Li(2)SiF(6)

A force field has been developed for Li(2)SiF(6) for subsequent use in Molecular Dynamics (MD) simulations involving Li(+) and SiF(2-) (6) ions in a polymer electrolyte host. Both ab initio calculations and available empirical data have been used. The force field has been verified in simulations of the crystal structure of Li(2)SiF(6) in two different space groups: P321 and P3(-)m1. The use of MD simulation to assess the correct space group for Li(2)SiF(6) shows that it is probably P321.     

Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.     

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.     

Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer

Important questions exist regarding the quality of force fields used in molecular dynamics (MD) simulations and their interoperable use with other available MD implementations. NAMD is one of the most efficient and scalable parallel molecular dynamics codes for large-scale biomolecular simulations in the open source domain. It is the aim of this article to analyze and compare the dynamics of a benchmark DNA dodecamer d(CTTTTGCAAAAG)2 system, including its binding to a specific drug molecule arising from the use of various simulation protocols in NAMD using Amber98, with the dynamics arising from simulations of the same dodecamer using Amber98 in the AMBER package, one of the most well-established simulation codes for nucleic acids. Based upon a set of validation benchmarks, the details of which are discussed, we find that nucleic acid simulations using NAMD give meaningful results and that the essential features of the resulting dynamics are similar to those arising from the AMBER package. This sets the stage for reliable large-scale simulations of nucleic acids using NAMD.     

New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen‐ligated amino acid residue

Transition metal ion complexation with proteins is ubiquitous across such diverse fields as neurodegenerative and cardiovascular diseases and cancer. In this study, the structures of divalent copper ion centers including three histidine and one oxygen‐ligated amino acid residues and the relative binding affinities of the oxygen‐ligated amino acid residues with these metal ion centers, which are debated in the literature, are presented. Furthermore, new force field parameters, which are currently lacking for the full‐length metal‐ligand moieties, are developed for metalloproteins that have these centers. These new force field parameters enable investigations of metalloproteins possessing these binding sites using molecular simulations. In addition, the impact of using the atom equivalence and inequivalence atomic partial charge calculation procedures on the simulated structures of these metallopeptides, including hydration properties, is described. © 2014 Wiley Periodicals, Inc.     

Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field

We explored the energy‐parameter space of our coarse‐grained UNRES force field for large‐scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual‐bond‐angle bending and side‐chain‐rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy‐term weights were generated randomly, and good sets were selected by carrying out replica‐exchange molecular dynamics simulations of two peptides with a minimal α‐helical and a minimal β‐hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native‐like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native‐like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with α or α + β structure and found to locate native‐like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

An ab initio force field for the cofactors of bacterial photosynthesis

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.     

Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains

To establish force-field-based (molecular) modeling capability that will accurately predict condensed-phase thermophysical properties for materials containing aliphatic azide chains, potential parameters for atom types unique to such chains have been developed and added to the COMPASS force field. The development effort identified the need to define four new atom types: one for each of the three azide nitrogen atoms and one for the carbon atom bonded to the azide. Calculations performed with the expanded force field yield (gas-phase) molecular structures and vibrational frequencies for hydrazoic acid, azidomethane, and the anti and gauche forms of azidoethane in good agreement with values determined experimentally and/or through computational quantum mechanics. Liquid densities calculated via molecular dynamics (MD) simulations were also in good agreement with published values for 13 of 15 training set compounds, the exceptions being hydrazoic acid and azidomethane. Of the 13 compounds whose densities are well simulated, nine have experimentally determined heats of vaporization reported in the open literature, and in all of these cases, MD simulated values for this property are in reasonable agreement with the published values. Simulations with the force field also yielded reasonable density estimates for a series of 2-azidoethanamines that have been synthesized and tested for use as hydrazine-alternative fuels.     

Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.     

Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB

A simple and fast method to calculate charge distributions in organic molecules is presented. The method is based on charge shifts within the saturated -system, driven by orbital electronegativities, coupled to a modified Hückel treatment of the unsaturated -systems. Experimental molecular dipole moments of a set of 119 molecules are reproduced with a root mean square deviation of 0.36 Debye units. Furthermore, the obtained charge distribution is used to describe hydration free energies in terms of hydrogen-bonding donor and acceptor strengths of polar groups. Least square fitting to experimental data of 281 compounds leads to values for these strengths with accuracy limits of ±4.3% and ±2.5%, respectively. Properly normalized values are taken to parametrize the hydrogen bonding terms in our MAB force field. The method is sufficiently fast to be used in the preparatory phase of interactive force-field calculations.     

Modification of the CHARMM force field for DMPC lipid bilayer

The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids.     

Nanocomposites of ferroelectric liquid crystals and FeCo nanoparticles: towards a magnetic response via the application of a small electric field

ABSTRACT

We study a nanocomposite consisting of a ferroelectric liquid crystal and a magnetic nanoparticle in order to explore the possibility of using it as a magnetic resonant imaging contrast agent which will measure a field of 20 V/m. To achieve this we use the ferroic properties exhibited by the nanocomposite. We used the ferroelectric liquid crystal 2-(4-((2-fluorooctyl)oxy)phenyl)-5-(octyloxy)pyrimidine mixed with FeCo nanoparticles nominally 2–3 nm in diameter in concentrations of 0.56, 4.3 and 10.8 wt%. The 10.8 wt% sample was chosen for our study because the nanoparticles acted as a lubricant for the ferroelectric liquid crystal. This concentration yields nanoparticle clusters in about 5 ? 10 μm diameter spherulites. An electric field as low as 5V/cm is enough to turn and realign the spherulites where the particles are contained. We estimate the value of the magnetic in a spehrulite and associate it to the number of spherulites aligned as a function of electric field. We find thus that we can achieve low electric fields.     

Optimization of a molecular mechanics force field for polyoxometalates based on a genetic algorithm

A stochastic technique based on genetic algorithms was implemented to develop new force fields by optimizing molecular mechanics (MM) parameters. These force fields have been optimized for inorganic compounds such as polyoxometalates (POMs) and especially for type‐I polymolybdate and polytungstate clusters. Focussing on the methodology of the development of the force fields, they were tested for the prediction of structural parameters, comparing the MM optimized structures with the geometry obtained after an optimization based on density functional theory. Results show that the genetic algorithm converges toward an optimum combination of parameters which successfully reproduces POMs structures with a high degree of accuracy. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise‐additive force field. Although AMOEBA results give mean errors close to “chemical accuracy,” GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non‐potential‐specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Global optimization of parameters in the reactive force field ReaxFF for SiOH

We have used unbiased global optimization to fit a reactive force field to a given set of reference data. Specifically, we have employed genetic algorithms (GA) to fit ReaxFF to SiOH data, using an in‐house GA code that is parallelized across reference data items via the message‐passing interface (MPI). Details of GA tuning turn‐ed out to be far less important for global optimization efficiency than using suitable ranges within which the parameters are varied. To establish these ranges, either prior knowledge can be used or successive stages of GA optimizations, each building upon the best parameter vectors and ranges found in the previous stage. We have finally arrive‐ed at optimized force fields with smaller error measures than those published previously. Hence, this optimization approach will contribute to converting force‐field fitting from a specialist task to an everyday commodity, even for the more difficult case of reactive force fields. © 2013 Wiley Periodicals, Inc.