Calculation of intramolecular force fields from second-derivative tensors

A practical procedure (FUERZA) to obtain internal force constants from Cartesian second derivatives (Hessians) is presented and discussed. It allows a systematic analysis of pair atomic interactions in a molecular system, and it is fully invariant to the choice of internal coordinates of the molecule. Force constants for bonds or for any pair of atoms in general are defined by means of the eigenanalysis of their pair interaction matrix. Force constants for the angles are obtained from their corresponding two-pair interaction matrices of the two bonds or distances forming the angle, and the dihedral force constants are similarly obtained using their corresponding three-pair interaction matrices. © 1996 John Wiley & Sons, Inc.     

Properties of liquid crystal molecules from first principles computer simulation

We explore the valence charge distribution, equilibrium geometry and harmonic force fields of the 4-pentyl-4-cyanobiphenyl (5CB) molecule and the benzene (C6H6) molecule, which provides an important mesogenic fragment, using first principles techniques adapted from large scale electronic structure calculations of periodic solids. We present for the first time accurate structural data for the isolated 5CB molecule and observe subtle broken symmetries relative to the constituent mesogenic fragments. The dynamic properties of these molecules are determined by diagonalization of dynamical matrices, the elements of which are obtained directly from quantum mechanical Hellmann-Feynman forces. Results for both molecules are in excellent agreement with available spectroscopic data, and for benzene are comparable to the most accurate quantum chemistry calculations to date. For 5CB we also present values for the molecular dipole and quadrupole moments.     

Molecular dynamics simulations of methane hydrate using polarizable force fields

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are found between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane only.     

The ab initio calculated molecular structures,force fields and vibrational frequencies of some organic azides

Double zeta basis molecular calculations were carried out on the hydrazoic acid and azidomethane molecules. The molecular structures were optimized by the gradient method and the force fields were obtained by numerical differentiation of the gradient vector. The computed harmonic force fields and vibrational frequencies were compared with experimental values.     

Empirical force fields for biological macromolecules: overview and issues

Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate reproduction of experimental observables. Presented is an overview of the issues associated with the development and application of empirical force fields to biomolecular systems. This is followed by a summary of the force fields commonly applied to the different classes of biomolecules; proteins, nucleic acids, lipids, and carbohydrates. In addition, issues associated with computational studies on "heterogeneous" biomolecular systems and the transferability of force fields to a wide range of organic molecules of pharmacological interest are discussed.     

Formulation of the vibrational theory in terms of redundant internal coordinates

Using the generalized inverse of matrices and the method of canonical matrices, this paper develops an unambiguous formulation of the theory of small vibrations of molecules which is valid when redundant internal coordinates are used. Such treatment includes the attainment of unambiguous relationships relating the compliance matrix (the generalized inverse of the canonical force constants matrix) with experimental data (vibrational frequencies, Coriolis coupling constants, centrifugal distortion constants and mean-square amplitudes). Moreover, expressions for the elements of the Jacobian matrices of the above magnitudes with respect to the compliance constants have been also obtained as well as some sum rule relationships.     

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.     

Isotopic shifts from parametrically represented vibrational perturbation equations

Kinematically defined proper vectors in parametric representation are used to formulate the first order perturbation equation for frequencies. Properties of the resulting matrices are discussed. A method of making use of the obtained equations in force constant calculations is indicated.     

Characterization of New Titanium Oxide Polymer Hybrid Membranes for Biofilm Formation

Abstract

Presently, there is great need to create new matrices for diverse applications particularly in the fields of biotechnology and food industry. Here, we report on the synthesis of new matrices based on a mixture of polymer cellulose acetate butyrate/copolymer polyacrylonitrile acrylamide/TiO₂. The characterization of the new matrices was performed using IR spectroscopy, QCM technology, and SEM. The tests revealed that when we use our polymers as carriers, there is a limit for the concentration of titanium of 5%. Further increasing of Ti concentration leads to precipitation processes. The QCM analyses show that a low concentration of Ti(OBu)₄ does not influence the viscosity of the matrices obtained, but their elasticity changes significantly. The membranes obtained were successfully applied for biofilm formation of Yeast strain Saccharomyces cerevisiae.     

Determination of force fields for formaldehyde,acetaldehyde and acetone by the CNDO/force method

CNDO/Force calculations have been done for formaldehyde, acetaldehyde and acetone, and the theoretical force fields evaluated. Experimental force fields are obtained from vibrational frequencies using the least-squares refinement method. The initial force fields considered are based on the bending and interaction force constants obtained from the CNDO/Force calculations and the stretching force constants transferred from chemically related molecules. Vibrational frequencies of H₂CO, D₂CO, HDCO, H₂¹³CO and D₂¹³CO for formaldehyde, CH₃CHO, CH₃CDO, CD₃CHO, CD₃CDO and CH₂DCHO for acetaldehyde, and CH₃COCH₃ CD₃COCH₃ and CD₃COCD₃ for acetone are employed in the force field refinements. The final force fields obtained are found to be reasonable with respect to the diagonal and interaction force constants.     

Contraction algorithms for third-order reduced density matrices: Symmetric group approach

In this work, we present the mapping formulae for the contraction of the third-order reduced density matrices represented in the basis of the irreducible representations (IR) of the symmetric group S3 into the second-order ones which are represented in the basis of the IR of group S2. These algorithms, which can be useful in several fields, have been applied for the approximation of reduced density matrices within the spin-adapted reduced Hamiltonian theory. Some results obtained with this procedure are also presented.     

Dissipative particle dynamics simulations of polymer melts. I. Building potential of mean force for polyethylene and cis-polybutadiene

We present the derivation of coarse-grained force fields for two types of polymers, polyethylene (PE), and cis-polybutadiene (cis-PB), using the concept of potential of mean force. Coarse-grained force fields were obtained from microscopic simulations for several coarse-graining levels, i.e., different number of monomers lambda per mesoscopic unit called "bead." These force fields are then used in dissipative particle dynamics (DPD) simulations to study structural and dynamical properties of polymer melts of PE and cis-PB. The radial distribution functions g(R), the end-to-end distance R0, the end-to-end vector relaxation time tau, and the chain center of mass self-diffusion D(CM), are computed for different chain lengths at different coarse-graining factor lambda. Scaling laws typical of the Rouse regime are obtained for both polymers for chain lengths ranging from 6 to 50 beads. It is found that the end-to-end distance R0 obtained from DPD simulations agree well with values obtained from both microscopic simulations and experiments. The dependence of the friction coefficient used in DPD simulations versus the coarse-graining level is discussed in view of the overall scaling of the dynamical properties.     

Solubility of NaCl in water by molecular simulation revisited

In this paper, the solubility of NaCl in water is evaluated by using computer simulations for three different force fields. The condition of chemical equilibrium (i.e., equal chemical potential of the salt in the solid and in the solution) is obtained at room temperature and pressure to determine the solubility of the salt. We used the same methodology that was described in our previous work [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] although several modifications were introduced to improve the accuracy of the calculations. It is found that the predictions of the solubility are quite sensitive to the details of the force field used. Certain force fields underestimate the experimental solubility of NaCl in water by a factor of four, whereas the predictions of other force fields are within 20% of the experimental value. Direct coexistence molecular dynamic simulations were also performed to determine the solubility of the salt. Reasonable agreement was found between the solubility obtained from free energy calculations and that obtained from direct coexistence simulations. This work shows that the evaluation of the solubility of salts in water can now be performed in computer simulations. The solubility depends on the ion-ion, ion-water, and water-water interactions. For this reason, the prediction of the solubility can be quite useful in future work to develop force fields for ions in water.     

Force fields of halide-substituted methane derivatives

The paper describes methods for determining the force fields of large sets of molecules which share the common property that in their constituent groups of molecules the equivalent force constants always change monotonically with the properties of substituent atoms belonging to the same subgroup of the periodic table. The force fields of the CH_4−nX_n (n=0–4, X=F, Cl, Br, I) molecules of the methane series are obtained. The applications of these force fields are discussed. In particular, they can serve as a basis for a data bank of the force fields of fragments suitable for constructing the force fields of more complex molecules. Russian Scientific Center “Applied Chemistry”, St. Petersburg. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 250–256, March–April, 1996. Translated by I. Izvekova     

Scaled Quantum Mechanical Force Fields for the Peroxynitrates. II. Fluorocarbonyl Peroxynitrate and Chlorocarbonyl Peroxynitrate.

The vibrational properties of fluorocarbonyl peroxynitrate, FC(O)OONO₂ and chlorocarbonyl peroxynitrate, ClC(O)OONO₂ were studied by means of density functional theory (DFT) methods. The obtained results served to revise the reported experimental spectra and their corresponding assignments. Subsequently, the revised data were used in the definition of scaled quantum mechanics (SQM) force fields for these peroxynitrates. A set of internal force constants was also calculated from such force 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     

Determination of impurities in uranium matrices by time-of-flight ICP-MS using matrix-matched method

The analysis of impurities in uranium matrices is performed in a variety of fields, e.g., for quality control in the production stream converting uranium ores to fuels, as element signatures in nuclear forensics and safeguards, and for non-proliferation control. We have investigated the capabilities of time-of-flight ICP-MS for the analysis of impurities in uranium matrices using a matrix-matched method. The method was applied to the New Brunswick Laboratory CRM 124(1–7) series. For the seven certified reference materials, an overall precision and accuracy of approximately 5% and 14%, respectively, were obtained for 18 analyzed elements.     

Structure and vibrational spectra of dinitromethane and trinitromethane

The molecular geometries of dinitromethane and trinitromethane were optimized and their harmonic force fields were calculated by the DFT/B3LYP method. The force fields obtained made it possible to interpret reliably the vibrational spectra of dinitromethane, trinitromethane and a number of isotopomers of trinitromethane. Some general conclusions on geometry and vibrational spectra of the molecules under study are made. The hybrid density functional method used is shown to predict the reliable structural parameters and vibrational frequencies for polynitromethanes.