Improving the Q2MM method for transition state force field modeling

The Quantum‐to‐molecular mechanics method (Q2MM) for converting quantum mechanical transition states (TSs) to molecular mechanical minima has been modified to allow a fit to the “natural” reaction mode eigenvalue. The resulting force field gives an improved representation of the energy curvature at the TS, but can potentially give false responses to steric interactions. Ways to address this problem while staying close to the “natural” TS force field are discussed. © 2014 Wiley Periodicals, Inc.     

Chlorosilanes: Development and application of MM2 force field parameters

The geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3–21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.     

An empirical MM2 augmented force field for the cycloimmonium ylides

An original procedure approach taking into account the implementation of parameters determined, using calculations based on density functional theory, for the amidocyano-pyridinium methylide in the MM2 augmented harmonic potential function has been proposed. A good agreement between theoretical force field calculation and X-ray diffraction data has been observed. Thus an empirical force field for cycloimmonium ylides has been established. It provides good quality geometries for cycloimmonium ylide molecules by energy minimization. In this study we proposed a new MM2 augmented atom-type for the ylidic carbon atom. To our knowledge no attempt has been done in this way for such organic systems. Thus, we have shown that parameterization established by the DFT method is able to reproduce or to predict with good accuracy the structures of the cycloimmonium ylide compounds. This study also includes a full conformational analysis.     

A force field for allenes and for nonlinear acetylenes within the MM2 approximation

Geometries and heats of formation for allenes may now be calculated with an extended version of MM2. The torsional barriers about bonds in an acetylenic unit are much more complicated than originally thought, if the unit is nonlinear. Ab initio calculations have been used to show just what these torsional barriers are, and the MM2 force field has been adapted to this information.     

The MM3 force field for amides,polypeptides and proteins

The potential functions for simple amides, several peptides and a small protein have been worked out for the MM3 force field. Structures and energies were fit as previously with MM2, but additionally, we fit the vibrational spectra of the simple amides (average rms error over four compounds, 34 cm^?1), and examined more carefully electrostatic interactions, including charge-charge and charge-dipole interactions. The parameters were obtained and tested by examining four simple amides, five electrostatic model complexes, two dipeptides, six crystalline cyclic peptides, and the protein Crambin. The average root-mean-square deviation from the X-ray structures for the six cyclic peptide crystals was only 0.10 Å for the nonhydrogen atomic positions, and 0.011 Å, 1.0°, and 4.9° for bond lengths, bond angles, and torsional angles, respectively. The parameter set was then further tested by minimizing the high resolution crystal structure of the hydrophobic protein Crambin. The resultant root-mean-square deviations for the non-hydrogen atomic data, in the presence of the crystal lattice, are 0.22 Å, 0.023 Å, 2.0°, and 6.4° for coordinates, bond lengths, bond angles, and torsional angles, respectively.     

Molecular mechanics. The MM3 force field for alkenes

The MM3 force field has been extended to include alkenes. Forty-five compounds were examined, and structures, conformational equilibria, heats of formation, and rotational barriers, were calculated. For a smaller representative group, the vibrational spectra and entropies were also calculated. In general, these quantities, except for the vibrational spectra, agree with available data to approximately within experimental error. The vibrational frequencies for a set of eight well-assigned structures were calculated to a root-mean-square error of 47 cm^?1.     

Strain energies of some bridgehead olefins as calculated with the MM2 force field

The MM 2 force field has been used to calculate the strain energies of a representative series of bridgehead alkenes, and the results compared to similar previous calculations using the MM 1 force field. The new results roughly parallel the old ones, although the strain energy of a given compound is normally higher with MM 2 than MM 1. These differences are largely negated, however, when the OS (olefinic strain) value is considered.     

Ab initio parametrized MM3 force field for the metal-organic framework MOF-5

A new valence force field has been developed and validated for a particular class of coordination polymers known as nanoporous metal-organic frameworks (MOFs), introduced recently by the group of Yaghi. The experimental, structural, and spectroscopic data in combination with density functional theory calculations on several model systems were used to parametrize the bonded terms of the force field, which explicitly treats the metal-oxygen interactions as partially covalent as well as distinguishes different types of oxygens in the framework. Both the experimental crystal structure of MOF-5 and vibrational infrared spectrum are reproduced reasonably well. The proposed force field is believed to be useful in atomistic simulations of adsorption/diffusion of guest molecules inside the flexible pores of this important class of MOF materials.     

Directional hydrogen bonding in the MM3 force field: II

Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6-31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide–water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1001–1016, 1998     

Development of an internal searching algorithm for parameterization of the MM2/MM3 force fields

Application of Allinger's MM2/MM3 force fields to molecules of real interest is frequently hindered by the lack of parameters for various heterocyclic systems and for poly-functionalized molecules. A common approach to this problem is to manually choose missing parameters “by analogy” with those that are part of the force field's internal parameter set. Naturally, this is generally attempted only by those possessing extensive experience with force fields. In order to use the MM2/MM3 force fields to study herbicides, an algorithm has been developed to automate this process for the non MM2 specialist. Using a set of “relative cost” criteria for atom type replacement, the algorithm searches the force field parameter set and selects the most appropriate parameters for a given molecule whose MM2 output file contains “missing parameter” errors. The program selects parameter error messages from a standard MM2 output file, finds analogous parameters, asks the user to verify their appropriateness and creates a standard MM2 parameter deck for the molecule of interest.     

Development of a molecular mechanics (MM2) force field for α-chlorosilanes

Molecular mechanics (MM2) parameters for silanes which have a Si-C-Cl fragment have been developed based on available experimental data and ab initio molecular orbital (MO) calculations. Molecular properties, mainly rotational barriers and geometries, of α-chlorosilanes have been studied using our new MM2 parameter set. Changes in the Si-C bond lengths and several bond angles of α-chlorosilanes due to the additional attachment of polar atom(s) have been investigated utilizing ab initio calculations. An electronegativity correction to both bond lengths and angles helps MM2 to reproduce results from ab initio calculations. The new force field has been applied to the conformational analysis of l-(chloromethyl)-1,2-dimethylsilacyclopentane, a model used in our studies of rearrangements of α-halosilanes.     

Hybrid classical quantum force field for modeling very large molecules

A coherent computational scheme on a very large molecule in which the subsystem that undergoes the most important electronic changes is treated by a semiempirical quantum chemical method, though the rest of the molecule is described by a classical force field, has been proposed recently. The continuity between the two subsystems is obtained by a strictly localized bond orbital, which is assumed to have transferable properties determined on model molecules. The computation of the forces acting on the atoms is now operating, giving rise to a hybrid classical quantum force field (CQFF ) which allows full energy minimization and modeling chemical changes in large biomolecules. As an illustrative example, we study the short hydrogen bonds and the proton-exchange process in the histidine-aspartic acid system of the catalytic triad of human neutrophil elastase. The CQFF approach reproduces the crystallographic data quite well, in opposition to a classical force field. The method also offers the possibility of switching off the electrostatic interaction between the quantum and the classical subsystems, allowing us to analyze the various components of the perturbation exerted by the macromolecule in the reactive part. Molecular dynamics confirm a fast proton exchange between the three possible energy wells. The method appears to be quite powerful and applicable to other cases of chemical interest such as surface reactivity of nonmetallic solids. © 1996 John Wiley & Sons, Inc.     

Transferable pair potentials for CdS and ZnS crystals

A set of interatomic pair potentials is developed for CdS and ZnS crystals. We show that a simple energy function, which has been used to describe the properties of CdSe [E. Rabani, J. Chem. Phys. 116, 258 (2002)], can be parametrized to accurately describe the lattice and elastic constants, and phonon dispersion relations of bulk CdS and ZnS in the wurtzite and rocksalt crystal structures. The predicted coexistence pressure of the wurtzite and rocksalt structures as well as the equation of state are in good agreement with experimental observations. These new pair potentials enable the study of a wide range of processes in bulk and nanocrystalline II-VI semiconductor materials.     

Optimization and application of lithium parameters for the reactive force field, ReaxFF

To make a practical molecular dynamics (MD) simulation of the large-scale reactive chemical systems of Li-H and Li-C, we have optimized parameters of the reactive force field (ReaxFF) for these systems. The parameters for this force field were obtained from fitting to the results of density functional theory (DFT) calculations on the structures and energy barriers for a number of Li-H and Li-C molecules, including Li(2), LiH, Li(2)H(2), H(3)C-Li, H(3)C-H(2)C-Li, H(2)C=C-LiH, HCCLi, H(6)C(5)-Li, and Li(2)C(2), and to the equations of state and lattice parameters for condensed phases of Li. The accuracy of the developed ReaxFF was also tested by comparison to the dissociation energies of lithium-benzene sandwich compounds and the collision behavior of lithium atoms with a C(60) buckyball.     

A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field

A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I‐NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H₂O, formamide, and imidazole molecular fragments and their complexes with the Mg²⁺ cation. Reference data obtained from ab initio calculations using an auc‐cc‐pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available. © 2014 Wiley Periodicals, Inc.     

Ab initio pair potentials for the ionic lithium-formate system

The potential energy surfaces for the interatomic interaction in the Li⁺HCOO^– system have been investigated byab initio methods within the rigid-molecule approximation. Analytical potential expressions were fitted to 133 calculated SCF energies for the Li⁺-HCOO^– interaction, 42 SCF energies for the Li⁺-Li⁺ interaction, and 332 SCF energies for the HCOO^–-HCOO^– interaction. The global minimum on the Li⁺-HCOO^– surface is –170 kcal/mol and corresponds to the lithium ion lying on the C₂ axis of the formate ion at 2.2 Å from the carbon atom on the oxygen side. The cation-cation and anion-anion interactions are repulsive everywhere, although the potential surface is markedly anisotropic for the HCOO^–-HCOO^– interaction.