Molecular simulation of guanidinium-based ionic liquids

A new systematic all-atom force field was developed for cyclic guanidinium-based ionic liquids (ILs) based on the AMBER force field. Optimized molecular geometries and equilibrium bond lengths and angles were obtained by ab initio calculations, and charges were allocated to each atom center by fitting the ab initio electrostatic potential. Molecular dynamics simulations were performed for eleven kinds of ILs that are comprised of NO3(-) anions and cyclic guanidinium-based cations. Validation was carried out by comparing our simulated densities with experimental and calculated data from the literature. Transport properties such as self-diffusion coefficients, viscosities, and conductivities were calculated by molecular dynamic simulation, and their dependence on the length of the alkyl chains of cyclic guanidinium-based cations are discussed. Radial distribution functions and spatial distribution functions were investigated to depict the microscopic structures of the ILs, and the relationship between their properties and microstructures is also discussed.     

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.     

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001     

Ab initio parametrized polarizable force field for rutile-type SnO<Subscript>2</Subscript>

We report a new, polarizable classical force field for the rutile-type phase of SnO₂, casserite. This force field has been parametrized using results from ab initio (density functional theory) calculations as a basis for fitting. The force field was found to provide structural, dynamical and thermodynamic properties of tin oxide that compare well with both ab initio and experimental results at ambient and high pressures.     

Glycyl C(alpha) chemical shielding in tripeptides: measurement by solid-state NMR and correlation with X-ray structure and theory

We report here (13)C(alpha) chemical shielding parameters for central Gly residues in tripeptides adopting alpha-helix, beta-strand, polyglycine II, and fully extended 2 degrees structures. To assess experimental uncertainties in the shielding parameters and the effects of (14)N-(13)C(alpha) or (15)N-(13)C(alpha) dipolar coupling, stationary and magic angle spinning (MAS) spectra with and without (15)N decoupling were obtained from natural abundance and double-labeled samples containing [2-(13)C, (15)N]Gly. We find that accurate (<1 ppm uncertainty) shielding parameters are measured with good sensitivity and resolution in (15)N decoupled 1D or 2D MAS spectra of double-labeled samples. Compared to variations of isotropic shifts with peptide angles, those of (13)C(alpha) shielding anisotropy and asymmetry are greater. Trends relating shielding parameters to the 2 degrees structure are apparent, and the correlation of the experimental values with unscaled ab initio shielding calculations has an rms error of 3 ppm. Using the experimental data and the ab initio shielding values, the empirical trends relating the 2 degrees structure to shielding are extended to the larger range of torsion angles found in proteins.     

A force field for molecular simulation of tetrabutylphosphonium amino acid ionic liquids

An all-atom force field was set up for a new class of ionic liquids (ILs), tetrabutylphosphonium amino acid, on the basis of the AMBER force field with determining parameters related to the phosphorus atom and modifying several parameters. Ab initio quantum chemical calculations were employed to obtain molecular geometries, infrared frequencies, and torsion energy profiles. Atom partial charges were obtained by using the one-conformation, two-step restraint electrostatic potential approach. Molecular dynamics simulation was carried out in the isothermal-isobaric ensemble for 14 tetrabutylphosphonium amino acid ILs at two temperatures to validate the force field against the experimental densities and heat capacities at constant pressure. Computed thermodynamic properties are in good agreement with available experimental values. Moreover, radial distribution functions were investigated to depict the microscopic structures of these ILs.     

Force field for computation of conformational energies,structures, and vibrational frequencies of aromatic polyesters

A CFF93¹ all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.     

Force‐field parameters of the Ψ and Φ around glycosidic bonds to oxygen and sulfur atoms

The Ψ and Φ torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force‐field parameters for Ψ and Φ torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein‐sugar and protein‐inhibitor complexes. First, we extracted the Ψ or Φ torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force‐field components except for the Ψ or Φ torsion angle. The Ψ and Φ energy components extracted (hereafter called “the remaining energy components”) were calculated for simple sugar models and plotted as functions of the Ψ and Φ angles. The remaining energy component curves of Ψ and Φ were well represented by the torsion force‐field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force‐field parameters and to confirm its compatibility with other force‐fields, we calculated adiabatic potential curves as functions of Ψ and Φ for the model glycosides by adopting the Ψ and Φ force‐field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Ψ and Φ well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Ψ and Φ force‐fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force‐field. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009     

Molecular mechanics (MM4) study of fluorinated hydrocarbons

A molecular mechanics study of small saturated hydrocarbons (up to C-6) substituted by up to six fluorines has been carried out with the MM4 force field. A parameter set has been developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia, and vibrational frequencies for these compounds. The results are mostly in fair to good agreement with experiment and ab initio calculations. The high electronegativity of fluorine leads to serious geometric consequences in these compounds, but these consequences can be dealt with adequately by suitable cross-terms in the force constant matrix, and by recognizing that some of the reference bond lengths and angles (l(0), theta(0)) and the corresponding stretching and bending constant parameters (k(s), k(theta)) that are usually thought of as constants must in fact be treated as functions of the electronegativity of the substituents. Additionally, the heavy mass of the fluorine (relative to the mass of hydrogen in alkanes) leads to large values for other cross-terms that were found to be unimportant in hydrocarbons. Conformational equilibria for polyfluorinated compounds are affected by the delta-two effect well-known in carbohydrates. A few larger fluorinated and polyfluorinated alkanes, including perfluoropropane, perfluorobutane, and Teflon, have also been studied.     

New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).     

分子模拟预测含配位键不饱和Cu的有机骨架(MOFs)材料的储氢性能

本文根据RI-UMP2方法、TZVPP基组和BSSE校正计算得到的能量数据,推导了描述氢分子与含有不饱和配位键的Cu的金属羧酸配合物相互作用的分子力学力场. 用巨正则系综蒙特卡洛模拟(GCMC)计算了氢在含四方形配位Cu的MOFs材料上的吸附等温线. 通过对比CuBTC的实验吸附数据发现,虽然理论预测含有四方形配位Cu的MOFs具有比含有四面体配位Zn的MOFs与氢分子更强的相互作用,实验合成得到的材料尚未反映这一区别. 以现有的CuBTC实验数据为参照消除理论计算和实验测定的系统偏差,预测了3种含有四方形配位Cu的MOFs材料以CuBTC作为参照的储氢能力.     

Rotational isomerism in divinylether studied by gas phase electron diffraction, microwave spectroscopy, infrared band profile simulation and ab initio calculations

The conformational behaviour of divinyl ether in the gas phase was explored by infrared band profile simulations and joint analysis of electron diffraction and microwave data. At 300 K the rotameric mixture contains 80% [sp, ac] and 20% [ap, ap] forms. Geometries have been studied using constraints taken from ab initio 4-21G gradient geometry and force field calculations. Differences between some unresolved bond distances and angles were constrained to the calculated values. Scale factors for the ab initio force field were refined from the diffraction data. In addition the transferability of scale factors from methyl vinyl ether to divinyl ether was tested. The investigation demonstrates that molecular orbital constrained models are consistent with and rationalize all experimental gas phase results. Subject to the ab initio constraints, the analysis yields the following model (r_g-distances, r-angles; numbers in parentheses are 6 times the least-squares ESDs): (C---H) = 1.103(12) A, (C---C) = 1.337(2) A, (C---O) = 1.389(2) A. Torsion angles for the [sp, ac] form are −13(6)° and 145(4)°.     

On the vibrational spectra and structural parameters of methyl, silyl, and germyl azide from theoretical predictions and experimental data

The infrared and Raman spectra of methyl, silyl, and germyl azide (XN3 where X=CH3, SiH3 and GeH3) have been predicted from ab initio calculations with full electron correlation by second order perturbation theory (MP2) and hybrid density function theory (DFT) by the B3LYP method with a variety of basis sets. These predicted data are compared to previously reported experimental data and complete vibrational assignments are provided for all three molecules. It is shown that several of the assignments recently proposed [J. Mol. Struct. (Theochem.) 434 (1998) 1] for methyl azide are not correct. Structural parameters for CH3N3 and GeH3N3 have been obtained by combining the previously reported microwave rotational constants with the ab initio MP2/6-311+G(d,p) predicted values. These "adjusted r0" parameters have very small uncertainties of +/-0.003 A for the XH distances and a maximum of +/-0.005 A for the heavy atom distances and +/-0.5 degrees for the angles. The predicted distance for the terminal NN bond which is nearly a triple bond is much better predicted by the B3LYP calculations, whereas the fundamental frequencies are better predicted by the scaled ab initio calculations. The results are discussed and compared to those obtained for some similar molecules.     

Modeling the global potential energy surface of the N + N2 reaction from ab initio data

A new global potential energy surface for the N + N2 exchange reaction has been built from ab initio data. To overcome the difficulty of carrying out ab initio calculations for a large set of geometries the alternative strategy of fitting the minimum energy paths of the surface and their angular dependence using a modified LAGROBO functional form has been adopted. In this way we have been able to reproduce all the main features of the potential using a fairly small set of ab initio values.     

The structure of trimethoxymethane in the gas phase,an electron diffraction,ab initio and molecular mechanics study

The structure of trimethoxymethane in the gas phase was studied by electron diffraction, ab initio molecular orbital calculations and molecular mechanics. The molecule was found to exist almost exclusively as an asymmetric all-staggered TGG conformer. The electron diffraction structural parameters (r_g distances, r_α angles) as obtained from geometrically consistent r_α-refinements are: r(C-O) central 1.382(6) Å, r(C-O) terminal 1.418(6) Å, r(C-H) 1.112(1) Å, ∠(O-C-O) in the gauche—gauche chain 115.0(1.0)°, in the gauche-anti chains 109.2(0.6)° ∠(C-O-C) 114.3(0.6)°, ∠(O-C-H)_Me 109.9(0.3)°, methyl torsion 68(6)°. The structure is adequately reproduced by molecular mechanics calculations applying Allinger's force field. The structures of methoxymethanes can be explained in terms of the anomeric effect. This is confirmed by ab initio calculations.     

Semiexperimental equilibrium structures for the equatorial conformers of N-methylpiperidone and tropinone by the mixed estimation method

N-Methylpiperidone (MPIP) and tropinone, which contain a structural motif found in numerous alkaloids, are too large to determine an accurate equilibrium structure either by ab initio methods or by experiment. However, the ground state rotational constants of the parent species and of all isotopologues with a substituted heavy atom ((13)C, (15)N, (18)O) are known from microwave spectroscopy. These constants have been corrected for the rovibrational contribution calculated from an ab initio cubic force field. These semiexperimental equilibrium rotational constants have been supplemented by carefully chosen structural parameters from medium level ab initio calculations. The two sets of data have been used in a weighted least-squares fit to determine reliable equilibrium structures for both molecules. This work shows that it is possible to determine reliable equilibrium structures for large molecules (34 degrees of freedom in the case of tropinone) at a detailed level of accuracy, and the method could be applied without too much difficulty to still larger molecules.     

Molecular force field for ionic liquids III: imidazolium, pyridinium, and phosphonium cations; chloride, bromide, and dicyanamide anions

This is the third set of parameters of a force field for the molecular simulation of ionic liquids, developed within the spirit of the OPLS-AA model and thus oriented toward the calculation of equilibrium thermodynamic and structural properties. The parameter sets reported here concern the cations alkylimidazolium, tetra-alkylphosphonium, and N-alkylpyridinium, and the anions chloride, bromide, and dicyanamide. The force field is built in a stepwise manner that allows the construction of models for an entire family of cations, with alkyl side chains of different length, for example. Due to the transferability of the present force field, the ions studied here can be combined with those reported in our two previous publications to create a large variety of ionic liquids that can be studied by molecular simulation. The parameters reported were obtained through different series of ab initio calculations concerning the geometry, force constants, torsion energy profiles, and electrostatic charge distributions of the ions under study. Validation of the force field consisted of comparison with experimental crystal structure and liquid density data.     

Using spectroscopic data on imidazolium cation conformations to test a molecular force field for ionic liquids

A molecular force field for the computer simulation of ionic liquids is evaluated a posteriori by confrontation against Raman spectroscopic data, published after the force field had been formulated. Specifically, the terms in the force field describing the conformational aspects of dialkylimidazolium cations, which were specifically developed for these compounds using high level ab initio calculations, are those affecting the distribution of conformers in simulated ionic liquids. Those distributions are compared with analyses of the liquid-phase Raman spectra, and the features of a series of dihedral torsions along the alkyl side chains in 1-alkyl-3-methylimidazolium cations in several ionic liquids are discussed.