Molecular force field investigation for Sulfur Hexafluoride: A computer simulation study

Force fields for Sulfur Hexafluoride (SF₆) from the literature, were investigated by means of their ability to reproduce experimental data in a wide range of thermodynamic conditions, including liquid, gas, vapor–liquid coexistence curve as well as supercritical states. Experimental data include numerous PVT state points, corresponding structural properties in terms of radial distribution functions, diffusion coefficient and shear viscosity. The existing force fields were extensively examined in the framework of molecular dynamics simulations and it is found that they do not accurately reproduce the macroscopic properties of the fluid, especially at high densities. To overcome this problem with the aim to obtain improved potential parameters that better reproduce experimental data, a multi-variable optimization of the force field parameters procedure has been systematically applied based on the “Simplex” method. Finally, it is found that for some common functional forms of these force fields, the new optimized parameters predict better the experimental properties of SF₆ under investigation compared to the original ones.     

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.     

Derivation of class II force fields: V. Quantum force field for amides,peptides, and related compounds

As the field of biomolecular structure advances, there is an ever-growing need for accurate modeling of molecular energy surfaces to simulate and predict the properties of these important systems. To address this need, a second generation amide force field for use in simulations of small organics as well as proteins and peptides has been derived. The critical question of what accuracy can be expected from calculations in general, and with this class II force field in particular, is addressed for structural, dynamic, and energetic properties. The force field is derived from a recent methodology we have developed that involves the systematic use of quantum mechanical observables. Systematic ab initio calculations were carried out for numerous configurations of 17 amide and related compounds. Relative energies and first and second derivatives of the energy of 638 structures of these compounds resulted in 140,970 ab initio quantum mechanical observables. The class II peptide quantum mechanical force field (QMFF), containing 732 force constants and reference values, was parameterized against these observables. A major objective of this work is to help establish the role of anharmonicity and coupling in improving the accuracy of molecular force fields, as these terms have not yet become an agreed upon standard in the ever more extensive simulations being used to probe biomolecular properties. This has been addressed by deriving a class I harmonic diagonal force field (HDFF), which was fit to the same energy surface as the QMFF, thus providing an opportunity to quantify the effects of these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess the range of applicability (transferability) of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcal/mol with the class II force field, and 2.30 kcal/mol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it approaches a (rotational) barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of ever-increasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm⁻¹ was achieved with the coupled anharmonic force field, as compared to 105 cm⁻¹ with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 430–458, 1998     

The COMPASS force field: parameterization and validation for phosphazenes

A new, condensed-phase optimised ab-initio force field, COMPASS, has been developed recently. In this paper, the validation of COMPASS for phosphazenes is presented. The functional forms of this force field are of the consistent force field (CFF) type. Charges and bonded terms were derived from HF/6–31G1 calculations, while the nonbonded parameters (L-J 9-6 vdW potential) were initially transferred from the polymer consistent force field, pcff, and optimised using MD simulations of condensed-phase properties. As a validation of COMPASS, molecular mechanics calculations and molecular dynamics simulations have been made on a number of isolated molecules, liquids, and crystals. The calculated molecular structure, vibration frequencies, conformational properties for isolated molecules, crystal cell parameters and density, liquid density, and heat of evaporation agreed favourably with most experimental data. The special conformational properties of the tetracyclophosphazenes, (NPCI₂)₄ and (NPF₂)₄, in the solid state are discussed based on molecular mechanics and CASTEP ab-initio calculations. The effect of nonbonded cutoff distance and different algorithms for pressure control in NPT simulation was also investigated. Finally, molecular dynamics using the COMPASS force field was used to predict properties of three isomers of high-molecular-weight amorphous poly(dibutoxyphosphazenes). In this case, excellent agreement was achieved between densities and glass transition temperatures obtained from dynamics and experimental data.     

Molecular dynamics simulations of heptyl phosphonic acid: a potential polymer component for fuel cell polymer membrane

Atomistic molecular dynamics simulations have been performed on heptyl phosphonic acid (HPA) to understand the dynamic hydrogen bonding network in the liquid phase. HPA is a phosphonic-acid functionalized alkane (heptane) and a model compound for one of the promising polymers for high temperature (>100 degrees C) fuel cell polymer electrolyte membranes. For the simulation, a force field for this molecule has been generated with the help of quantum chemical calculations and optimized by simplex algorithm. The force field has been validated against experimentally measured properties, for example, density and self-diffusion constant. From molecular dynamics simulations conducted at different temperatures, we have confirmed the hypothesis of dynamic hydrogen bond network formation in this material.     

GLYCAM06: a generalizable biomolecular force field. Carbohydrates

A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.     

A molecular mechanics force field for lignin

A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force field will enable full simulations of lignocellulose.     

Monte carlo simulation of carboxylic acid phase equilibria

Configurational-bias Monte Carlo simulations were carried out in the Gibbs ensemble to generate phase equilibrium data for several carboxylic acids. Pure component coexistence densities and saturated vapor pressures were determined for acetic acid, propanoic acid, 2-methylpropanoic acid, and pentanoic acid, and binary vapor-liquid equilibrium (VLE) data for the propanoic acid + pentanoic acid and 2-methylpropanoic acid + pentanoic acid systems. The TraPPE-UA force field was used, as it has recently been extended to include parameters for carboxylic acids. To simulate the branched compound 2-methylpropanoic acid, certain minor assumptions were necessary regarding angle and torsion terms involving the -CH- pseudo-atom, since parameters for these terms do not exist in the TraPPE-UA force field. The pure component data showed good agreement with the available experimental data, particularly with regard to the saturated liquid densities (mean absolute errors were less than 1.1%). On average, the predicted critical temperature and density were within 1% of the experimental values. All of the binary simulations showed good agreement with the experimental x-y data. However, the TraPPE-UA force field predicts saturated vapor pressures of pure components that are larger than the experimental values, and consequently the P-x-y and T-x-y data of the binary systems also deviate from the measured data.     

Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side‐chain analogues

A previously introduced polarizable simulations with second‐order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side‐chains. Parameters have been fitted to permit reproducing many‐body energies, gas‐phase dimerization energies, and geometries and liquid‐phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second‐order approximation of the full‐scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins. © 2012 Wiley Periodicals, Inc.     

Molecular potential functions from joint analysis of gas electron diffraction and spectroscopic data

A joint analysis of electron diffraction and spectroscopic data is carried out for BF₃, PBr₃, AsBr₃, SbCl₃, SeO₂ and ClO₂ in terms of the harmonic force fields. The scheme of analysis was extended to include the following spectroscopic observables: vibrational frequencies, rotational, Coriolis coupling and centrifugal distortion constants and, whenever available, those for the isotopic species. For ClO₂ a simplified anharmonic analysis was also performed, the anharmonic spectroscopic observables being involved in this case.

Compelling evidence has been presented that the conventional harmonic approximation for the force field in terms of rectilinear internal coordinates yields the simplest satisfactory representation of diffraction and spectroscopic observations. However, a consistently better fit to experimental data was found when natural curvilinear internal coordinates were used. It is shown here that for the systems considered the joint analysis of data from various sources ensures that reliable and accurate values for equilibrium distances and force field parameters are obtained. The optimized values of spectroscopic constants, structural and force field parameters obtained are presented and compared with those available from the literature.     

Using molecular dynamics to study liquid phase behavior: simulations of the ternary sodium laurate/sodium oleate/water system

The prediction of surfactant phase behavior has applications in a wide range of areas. An accurate modeling of liquid phase behavior can aid our understanding of colloidal process or be used to design phases that respond in a defined way to their environment. In this work, we use molecular dynamics to model the phase behavior of the ternary sodium laurate/sodium oleate/water system and compare the simulation results to experimental data. Simulations were performed with the GROMOS 53A6 united-atom force field and cover the entire ternary phase diagram, producing micellar, hexagonal, and lamellar phases. The aggregate simulation time for the 33 simulations performed during this study is 4.4 μs. We find that the simulations were able to model the experimentally observed liquid phase behavior accurately, showing that the carboxylate and lipid parameters of the 53A6 force field give very good quality results for the in silico prediction of liquid system phase behavior.     

Monitoring biological membrane-potential changes: a CI QM/MM study

In recent decades, new less-invasive, nonlinear optical methods have been proposed and optimized for monitoring fast physiological processes in biological cells. One of these methods allows the action potential (AP) in cardiomyocytes or neurons to be monitored by means of second-harmonic generation (SHG). We now present the first, to our knowledge, simulations of the dependency of the intensity of the second harmonic (I(SHG)) on variations of the transmembrane potential (TMP) in a cardiomyocyte during an action potential (AP). For this, an amphiphilic potential-sensitive styryl dye molecule with nonlinear optical properties was embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer, replacing one of the phospholipid molecules. External electrical fields with different strengths were applied across the membrane to simulate the AP of a heart-muscle cell. We used a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the embedded chromophore. Two 10 ns molecular dynamics (MD) simulations provided input geometries for semiempirical molecular orbital (QM/MM) single-point configuration interaction (CI) calculations, which were used to calculate the wavelengths and oscillator strengths of electronic transitions in the di-8-ANEPPS dye molecule. The results were then used in a sum-over-states treatment to calculate the second-order hyperpolarizability. The square of the hyperpolarizability scales with the intensity of the second harmonic, which is used to monitor the action potentials of cardiomyocytes experimentally. Thus, we computed changes in the intensity of the second harmonic (DeltaI(SHG)) as function of TMP changes. Our results agree well with experimental measurements.     

Importance of van der Waals Interactions in QM/MM Simulations

The importance of accurately treating van der Waals interactions between the quantum mechanical (QM) and molecular mechanical (MM) atoms in hybrid QM/MM simulations has been investigated systematically. First, a set of van der Waals (vdW) parameters was optimized for an approximate density functional method, the self-consistent charge-tight binding density functional (SCC-DFTB) approach, based on small hydrogen-bonding clusters. The sensitivity of condensed phase observables to the SCC-DFTB vdW parameters was then quantitatively investigated by SCC-DFTB/MM simulations of several model systems using the optimized set and two sets of extreme vdW parameters selected from the CHARMM22 forcefield. The model systems include a model FAD molecule in solution and a solvated enediolate, and the properties studied include the radial distribution functions of water molecules around the solute (model FAD and enediolate), the reduction potential of the model FAD and the potential of mean force for an intramolecular proton transfer in the enediolate. Although there are noticeable differences between parameter sets for gas-phase clusters and solvent structures around the solute, thermodynamic quantities in the condensed phase (e.g., reduction potential and potential of mean force) were found to be less sensitive to the numerical values of vdW parameters. The differences between SCC-DFTB/MM results with the three vdW parameter sets for SCC-DFTB atoms were explained in terms of the effects of the parameter set on solvation. The current study has made it clear that efforts in improving the reliability of QM/MM methods for energetical properties in the condensed phase should focus on components other than van der Waals interactions between QM and MM atoms.     

氟磺酸氯分子振动光谱的从头算研究

采用从头算HF方法以6-31G^*基组研究了对ClOSO₂F分子的几何结构、振动谐性力场和红外光谱.理论力场由Pulay的标度量子力学方法进行标度,算得的振动频率与实验值比较,平均偏差为6.0cm^-1.根据振动频率的势能分布和从头算红外光谱强度值对此分子的振动基频进行了理论归属.     

New-generation amber united-atom force field

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated with a well-known toy protein folding system, an 18 residue polyalanine in distance-dependent dielectric. The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide.