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.     

Simulation of crack propagation in alumina with ab initio based polarizable force field

We present an effective atomic interaction potential for crystalline α-Al(2)O(3) generated by the program potfit. The Wolf direct, pairwise summation method with spherical truncation is used for electrostatic interactions. The polarizability of oxygen atoms is included by use of the Tangney-Scandolo interatomic force field approach. The potential is optimized to reproduce the forces, energies, and stresses in relaxed and strained configurations as well as {0001}, {1010}, and {1120} surfaces of Al(2)O(3). Details of the force field generation are given, and its validation is demonstrated. We apply the developed potential to investigate crack propagation in α-Al(2)O(3) single crystals.     

Empirical force field and ab initio calculations on allyl cations

Allyl cation geometries optimized using an extended version of MMP2, newly parameterized for localized and delocalized classical cations, compare favorably with those obtained at the MP2(full) /6–31G^* level. Hence, the force field should provide good starting structures for ab initio calculations. The π-electron densities obtained by these two very different methods are quite similar. The relative energies of various isomers at MP4/6–31G^*//MP2(full)/6–31G^* are reproduced well by the force-field calculations. The heats of formation calculated by MMP2, as well as those predicted from the ab initio data, agree with experimentally determined values. The force-field method provides interpretive capabilities. Energy differences between isomers can be separated into electronic and steric contributions, reasonable estimates of resonance energies are given, and nonbonded resonance energies in delocalized cations can be evaluated. The stabilizing 1–3 π-interactions in allyl cations are quite significant, but are reduced by alkyl groups hyperconjugatively and sterically. © 1997 by John Wiley & Sons, Inc.     

Anisotropic nonadditive ab initio force field for noncovalent interactions of H2

A quantum mechanical polarizable force field (QMPFF) has been applied to the noncovalent interactions of molecular hydrogen as well as closed-shell monoatomic species (CSMS): rare gases, alkali cations, and halide anions. The importance of all the main energy components is demonstrated: electrostatics (including penetration effect), exchange repulsion, dispersion, and induction. As the MP2 level of quantum mechanics, which is used to parametrize QMPFF, significantly underestimates the H2-H2 dimer binding energy, the force field was refined using state-of-the-art CCSD(T) data. The approach demonstrates excellent transferability, which is confirmed by accurate reproduction of mixed H2-CSMS dimers and the second virial coefficient of hydrogen vapor.     

The ab initio limit quartic force field of BH3

The complete quartic force field of BH(3) has been converged to the ab initio limit by extrapolation of core-valence correlation-consistent basis set series (cc-pCVXZ, X = T, Q, 5) of all-electron CCSD(T) (coupled-cluster singles and doubles with perturbative triples) energy points. Additional computations including full coupled-cluster treatments through quadruple excitations (CCSDTQ), scalar relativistic effects, and diagonal Born-Oppenheimer corrections (DBOC) were concurrently executed. Within second-order vibrational perturbation theory (VPT2) our quartic force field yields the fundamental frequencies nu(1) = 2502.3 cm(-1), nu(2) = 1147.2 cm(-1), nu(3) = 2602.1 cm(-1), and nu(4) = 1196.5 cm(-1), in excellent agreement with observed gas-phase fundamentals, displaying a mean absolute error of only 0.3 cm(-1). Our converged prediction for the equilibrium bond length of BH(3) is r(e) = 1.1867 A.     

Computer simulation of trifluoromethane properties with ab initio force field

Intermolecular interaction potentials of the trifluoromethane dimer in 15 orientations have been calculated using the Hartree‐Fock (HF) self‐consistent theory and the second‐order Møller‐Plesset (MP2) perturbation theory. Single point energies at important geometries were also calibrated by the coupled cluster with single and double and perturbative triple excitation [CCSD(T)] calculations. We have employed Pople's medium size basis sets [up to 6‐311++G(3df,3pd)] and Dunning's correlation consistent basis sets (up to aug‐cc‐pVQZ). Basis set limit potential values were obtained through well‐studied extrapolation methods. The calculated MP2 potential data were employed to parameterize a 5‐site force field for molecular simulations. We performed molecular dynamics simulations using the constructed ab initio force field and compared the simulation results with experiments. Quantitative agreements for the atom‐wise radial distribution functions and the self‐diffusion coefficients over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Normal coordinate ab initio force relaxation

A procedure for optimization of molecular geometries is presented, combining ab initio calculations with vibrational molecular data from spectroscopy or empirical force fields. Theoretical cartesian forces are transformed to vibrational normal coordinate forces from which geometry increments are calculated. Test results indicate that the method saves considerable effort compared to other optimization schemes.     

Ab initio based polarizable force field parametrization

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by approximately 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.     

Prediction of adsorption of small molecules in porous materials based on ab initio force field method

Computational prediction of adsorption of small molecules in porous materials has great impact on the basic and applied research in chemical engineering and material sciences. In this work,we report an approach based on grand canonical ensemble Monte Carlo(GCMC) simulations and ab initio force fields. We calculated the adsorption curves of ammonia in ZSM-5 zeolite and hydrogen in MOF-5(a metal-organic-framework material). The predictions agree well with experimental data. Because the predictions are based on the first principle force fields,this approach can be used for the adsorption prediction of new molecules or materials without experimental data as guidance.     

原子簇量子化学从头算的自洽晶体场模型

本文提出一种收敛的点电荷和Hartree-Fock表面势构成的自洽晶体场Madelung势用于原子簇量子化学从头计算。前者的计算类似于核吸引积分的单电子积分, 后者可以通过点群对称性操作从原子簇内的积分矩阵元得到。点电荷的大小和原子簇内对应的原子电荷相等, 其数目以晶体场势收敛为标准确定。介绍加速计算的程序技巧。该模型用于高温超导体YBa2Cu3O7的全电子从头计算并得到一些新结果。     

Anharmonic force field and spectroscopic constants of silene: an ab initio study

High-level ab initio calculations with large basis sets are reported for silene, H₂C=SiH₂. Correlated harmonic force fields are obtained from coupled cluster CCSD(T) calculations with the cc-pVQZ basis (cc-pVTZ for H) while the anharmonic force fields are computed at the MP2/TZ2Pf level. There is excellent agreement with the available experimental data, in particular the equilibrium geometry and the fundamental vibrational frequencies. Many other spectroscopic constants are predicted for the C _{2 v} isotopomers of silene. Received: 27 May 1998 / Accepted: 23 July 1998 / Published online: 9 October 1998     

A general ab initio molecular multi-configuration self-consistent field algorithm

The ab initio multiconfiguration self-consistent-field (MC SCF ) techniques and computer programs of Basch [1, 2] and the ab initio configuration interaction (CI ) techniques and programs of Whitten and Hackmeyer [3] have been combined and generalized to form a general technique and program to yield optimized ab initio MC SCF wavefunctions for any set of Slater determinants. The Slater determinants are read in as input data to the program along with the spin parity that is being considered (optional) and the program successively does the CI calculation and one iteration of the SCF calculation, constructing the proper Fock–Hamiltonians by examining the set of Slater determinants and their CI coefficients. The Fock–Hamiltonian matrices are calculated and diagonalized in succession, a single two-dimensional array being used to store these matrices. The basis function integrals are read from a tape only once during each MC SCF iteration (one MC SCF iteration = a CI calculation followed by one iteration of the SCF calculation).     

Vibrational frequencies and assignments for some isotopomers of urcail using a scaled ab initio force field

Vibrational frequencies and IR band intensities for 18 isotopomers of uracil, including deuterated ¹⁵N and ¹⁸O species, have been calculated using the scaled ab initio force field of Ref. 1. The results obtained are compared with available experimental data, and a number of refinements in former assignments are proposed. The good agreement between the calculated and experimental frequencies confirms the reliability of the scaled quantum mechanical-force field.     

Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method

A recently developed force-matching method for obtaining effective force fields for condensed matter systems from ab initio molecular dynamics (MD) simulations has been applied to fit a simple nonpolarizable two-site pairwise force field for liquid hydrogen fluoride. The ab initio MD in this case was a Car-Parrinello (CP) MD simulation of 64 HF molecules at nearly ambient conditions within the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure included a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The performance of the force-match potential was examined for the gas-phase dimer and for the liquid phase at various temperatures. The model was able to reproduce correctly the bent structure and energetics of the gas-phase dimer, while the results for the structural properties, self-diffusion, vibrational spectra, density, and thermodynamic properties of liquid HF were compared to both experiment and the CP MD simulation. The force-matching model performs well in reproducing nearly all of the liquid properties as well as the aggregation behavior at different temperatures. The model is computationally cheap and compares favorably to many more computationally expensive potential energy functions for liquid HF.     

A partition function‐based weighting scheme in force field parameter development using ab initio calculation results in global configurational space

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function‐based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high‐level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function‐based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function‐based weighting method may be applied in developing any types of force field parameters. © 2013 Wiley Periodicals, Inc.     

Modeling a liquid crystal dynamics by atomistic simulation with an ab initio derived force field

Atomistic molecular dynamics (MD) simulations of 4-n-pentyl 4'-cyano-biphenyl (5CB) have been performed, adopting a specific ab initio derived force field. Two state points in the nematic phase and three in the isotropic phase, as determined in a previous work, have been considered. At each state point, at least 10 ns have been produced, allowing us to accurately calculate single-molecule properties. In the isotropic phase, the values of the translational diffusion coefficient, and even more so the activation energy for the process, agree well with experimental data. Qualitatively, also the dynamic anisotropy of the nematic phase is correctly accounted for. Rotational diffusion coefficients, which describe spinning and tumbling motions, fall well within the range of experimental values. The reorientational dynamics of our model 5CB covers diverse time regimes. The longest one is strongly temperature dependent and characterized by a relaxation time in accord with experimental dielectric relaxation data. Shear viscosity and Landau-de Gennes relaxation times, typically collective variables, reproduce the experimental results very well in the isotropic phase. In the nematic phase, despite a large statistical uncertainty due to the extremely slow relaxation of the correlation functions involved, our simulation yields the correct relative order of the three experimental Miesowicz viscosities.     

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins

The implementation of molecular dynamics with the united-residue (UNRES) force field is extended to treat multichain proteins. Constant temperature was maintained in the simulations with Berendsen or Langevin thermostats. The method was tested on three alpha-helical proteins (1G6U and GCN4-p1, each with two chains, and 1C94, with four chains). Simulations were carried out for both the isolated single chains and the multichain complexes. The proteins were folded by starting from the extended conformation with random initial velocities and with the chains parallel to each other. No symmetry constraints or structure information were included for the single chains or the multichain complexes. In the case of single-chain simulations, a high percentage of the trajectories (100% for 1G6U, 90% for GCN4-p1, and 80% for 1C94) converged to nativelike structures (assumed as the experimental structure of a monomer in the multichain complex), showing that, for the proteins studied in this work with the UNRES force field, the interactions between chains are not critical for stabilization of the individual chains. In the case of multichain simulations, the native structures of the 1G6U and GCN4-p1 complexes, but not that of 1C94, are predicted successfully. The association of the subunits does not follow a unique mechanism; the monomers were observed to fold both before and simultaneously with their association.     

Effects of hydration on scale factors for ab initio force constants

Experimentally measured vibrational frequencies from the polar groups of peptides in aqueous solutions do not agree with frequencies calculated from scaled quantum mechanical force fields (SQMFF) using differential scale factors developed for molecules in the vapor phase. Measured stretching frequencies for carbonyl groups are more than 50 wavenumbers lower than the calculated values. On the other hand, frequencies for non-polar groups calculated using these scale factors are relatively accurate. Our goal is to develop a SQMFF that yields accurate calculated frequencies for peptides in aqueous solutions. To this end, we have calculated scale factors for ab initio force constants for formic acid, acetic acid, and acetone using a least squares fit of calculated and experimental frequencies. We compare these scale factors with changes observed in the ab initio force constants calculated for these molecules at various states of hydration. These force constants are calculated using fully optimized geometries for these hydrated molecules using the 4-31G basis. We present a comparison of the experimental and calculated frequencies, along with their potential energy distributions, for both vapor and aqueous phases. The results indicate that scale factors can simulate the effects of solvation on molecular force constants to yield accurate scaled ab initio force fields.     

Urea: an ab initio and force field study of the gas and solid phases

We have studied the gaseous and solid phases of urea using both quantum mechanics calculation and force field simulation methods. Our ab initio calculations confirmed experimental observations that urea structure is planar in the crystal, but nonplanar in the gas phase. Based on electron structure analysis, we suggest that the significant difference between these two structures in different environments can be qualitatively explained by two resonance structures. The planar structure is more polarized than the nonplanar one, and the former is stabilized in the solid phases due to strong electrostatic interactions. We found classical force field method is incapable to represent such strong polarization effect. Using molecular dynamics simulations with a force field optimized for condensed phases, we calculated the crystalline structures of urea in the temperature range of 12 to 293 K. The densities as well as cell parameters are within 2% deviation from the experimental data in the temperature range.