Force-field modeling through quantum mechanical calculations: Molecular dynamics simulations of a nematogenic molecule in its condensed phases (original) (raw)
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The Journal of Physical Chemistry B, 2007
Lengthy molecular dynamics (MD) simulations were performed at constant atmospheric pressure and different temperatures for the series of the 4-n-alkyl-4′-cyanobiphenyls (nCB) with n ) 6, 7, and 8. The accurate atomistic force field (Bizzarri, M.; Cacelli, I.; Prampolini, G; Tani, A. J. Phys. Chem. A 2004, 108, 10336), successfully employed to reproduce thermodynamic and transport properties of the 5CB molecule, has here been extended to higher homologues. Nematic and isotropic phases were found for all members of the series, and also, a smectic phase was (tentatively) identified for 8CB at 1 atm and 300 K. Transition temperatures reproduce the experimental values within (10 K. Also, structural properties as second and fourth rank orientational order parameters are in good agreement with the corresponding experimental quantities. This means that the well-known odd-even effect, observed for many properties along the nCB series, is well reproduced, despite the narrow range of oscillations, e.g., in clearing temperatures. A detailed analysis of the correlation between molecular properties and odd-even effects is presented. *
Multiscale Science and Engineering
Recent progress in our group on quantum chemistry calculated intermolecular interaction potential energy functions, or ab initio force fields, for use in molecular dynamics simulations is reviewed. These ab initio force fields have been calibrated by the current state-of-the-art computational techniques with respect to the correlation-method versus basis-set combinations. The case studies of CH 4 , CCl 4 , CHF 3 , and CHCl 3 molecular dimeric systems are presented and compared. The simulation scheme can serve as a modern paradigm before a full-blown quantum mechanical molecular simulation can be achieved. It is our hope that this review can help stimulating interests among computational scientists in further exploring this important field of multiscale science and engineering.
ChemPhysChem, 2009
We have studied the important n-cyano biphenyl series of mesogens, n=4-8 using modelling and molecular dynamics simulations. We have been able to obtain spontaneously ordered nematics upon cooling isotropic samples of 250 molecules. We show that, using the united atom force field developed here, the experimental isotropic-nematic transition temperatures are reproduced within 4 K, allowing a molecular level interpretation of the odd-even effect along the series. Other properties, like densities, orientational order parameters and NMR residual dipolar couplings are also well reproduced, demonstrating the feasibility of predictive in silico modelling of nematics from the molecular structure.
Modeling a Liquid Crystal Dynamics by Atomistic Simulation with an Ab Initio Derived Force Field
The Journal of Physical Chemistry B, 2006
Atomistic molecular dynamics (MD) simulations of 4-n-pentyl 4′-cyano-biphenyl (5CB) have been performed, adopting a specific ab initio derived force field. 1 Two state points in the nematic phase and three in the isotropic phase, as determined in a previous work, 2 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.
Quantum chemistry based force fields for soft matter
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 1997
We describe the use of ab initio electronic structure calculations in the development of high-quality classical interaction potentials for liquid crystal modeling. Our focus is on methods for the rapid, on-demand creation of force fields for use in mean field theory based calculations of materials properties, employed for routine pre-synthesis evaluation of novel liquid crystalline materials. The role of quantum chemistry in the development of intermolecular interaction potentials for large-scale simulations of soft matter is also discussed, and directions for future work are outlined. The utility of quantum chemistry derived force fields for liquid crystal modeling is illustrated by two example applications: mean field theory based prediction of the spontaneous polarization density P of ferroelectric liquid crystals, and large-scale simulation studies of the nanosegregation af polymer precursors in smectic liquid crystal hosts. 0 1997 Elsevier Science B.V.
Journal of Computational Chemistry, 2018
The reliability of a molecular dynamics (MD) simulation study mainly depends on the accuracy of the applied force field. Unlike the ability of some potential models for reasonably predicting the thermodynamic properties of acetonitrile (ACN), simulated dynamical properties such as self-diffusion are generally underestimated compared to experimental values. The present work focuses on the evaluation and refinement of several available all-atom force fields for ACN and proposes a refined flexible six-site potential model. The main modification is related to the reduction of intermolecular LJ parameters (r and E) for hydrogen atoms, especially E, significantly affecting the dynamical behavior. Besides, the adjustment of r and E for nitrile carbon and nitrogen atoms helps reach optimum results. Our refined model shows an excellent agreement with the experiment for self-diffusion coefficient and thermodynamic quantities as well as providing a qualitative description of the microscopic structure of liquid ACN. V C 2018 Wiley Periodicals, Inc.
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Journal of the American Chemical Society, 1995
We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.
A molecular dynamics study of the nematic phase of 4-n-pentyl-4′-cyanobiphenyl
Liquid Crystals, 1989
Preliminary molecular dynamics simulations of the nematic phase of 4-n-pentyl-4'-cyanobiphenyl are described. The simulations include all molecular degrees of freedom. The influence of the molecular dipole moment is investigated by comparing simulations with and without a charge distribution on the molecules. Inclusion of the charge distribution is found to lead to a slight broadening of the orientational distribution function, in qualitative agreement with Raman measurements of the orientational order parameters.
Force Fields for Coarse-Grained Molecular Simulations from a Corresponding States Correlation
Industrial & Engineering Chemistry Research, 2014
We present a corresponding states correlation based on the description of fluid phase properties by means of an Mie intermolecular potential applied to tangentially bonded spheres. The macroscopic properties of this model fluid are very accurately represented by a recently proposed version of the Statistical Associating Fluid Theory (the SAFT-γ version). The Mie potential can be expressed in a conformal manner in terms of three parameters that relate to a length scale, σ, an energy scale, ε, and the range or functional form of the potential, λ, while the nonsphericity or elongation of a molecule can be appropriately described by the chain length, m. For a given chain length, correlations are given to scale the SAFT equation of state in terms of three experimental parameters: the acentric factor, the critical temperature, and the saturated liquid density at a reduced temperature of 0.7. The molecular nature of the equation of state is exploited to make a direct link between the macroscopic thermodynamic parameters used to characterize the equation of state and the parameters of the underlying Mie potential. This direct link between macroscopic properties and molecular parameters is the basis to propose a top-down method to parametrize force fields that can be used in the coarse grained molecular modeling (Monte Carlo or molecular dynamics) of fluids. The resulting correlation is of quantitative accuracy and examples of the prediction of simulations of vapor−liquid equilibria and interfacial tensions are given. In essence, we present a recipe that allows one to obtain intermolecular potentials for use in the molecular simulation of simple and chain fluids from macroscopic experimentally determined constants, namely the acentric factor, the critical temperature, and a value of the liquid density at a reduced temperature of 0.7. av 2 3 av 3 (3) where N av is Avogadro's number. Comparing eqs 2 and 3 one can immediately establish a link between the macroscopic