Effect of basic set quality and electron correlation on the scale factors of a harmonic force field

The completely optimized structure and harmonic force field of s-trans-buta-1,3-diene are reported at the MP2/6-31G and MP2/6-31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4-31G and RHF/6-31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s-trans-buta-1,3-diene using the MP2/6-31G* force field. Some characteristics of the gauche and cis forms of buta-1,3-diene are also given.     

Vibrational analysis of buta-1,3-diene and its deutero and 13C derivatives and some of their rotational isomers

The wave numbers of trans-2,3-¹³C₂-buta-1,3-diene were calculated using a scaled quantum-chemical force field found at the MP2/6-31G*//MP2/6-31G* level of theory. The obtained results and the theoretical sets of wave numbers for twelve deutero and ¹³C derivatives of the trans form and five deutero and ¹³C derivatives of the gauche form of buta-1,3-diene found previously at the MP2/6-31G*//MP2/6-31G* level are compared with the corresponding experimental vibrational spectra corrected for the Fermi resonance. Combined analysis of the vibrational spectra of the above mentioned isotopomers was performed.     

Efficiency of post-Hartree-Fock force field for the interpretation of vibrational spectra ofN,N-dimethylnitramine

Harmonic force fields for the molecule ofN,N-dimethylnitramine were calculated in the RHF/6-31G^* and MP2/6-31G^** approximations. Scaling of the force fields obtained made it possible to reliably interpret the vibrational spectra of light and perdeuterated compounds reported in the literature. The assignment is confirmed by good reproducibility of experimental isotope shifts upon¹⁵N-amino- and¹⁵N-nitrosubstitution. The frequencies of intramolecular vibrations in far IR and Raman spectra as well as in neutron inelastic scattering spectra for the light and perdeuterated samples of solidN,N-dimethylnitramine were identified using the force field calculated with the inclusion of electron correlation (MP2). Although general structures of the force fields calculated in the RHF and MP2 approximations are similar, considerable differences in the force constants of the NO and NN stretching vibrations and especially in the constants of the NO_str/NO_str and NO_str/NN_str interactions remain even after scaling the force fields.     

Infrared and Raman spectra and theoretical study of methyl trifluoromethyl sulfone, CF3SO2CH3

The infrared and Raman spectra were obtained for liquid CF3SO2CH3, as well as the infrared spectrum of the gaseous substance. The molecular geometry was optimized by means of the Hartree-Fock (HF), second order electron correlation (MP2) and density functional theory (DFT) procedures of quantum chemistry, resulting in a structure with Cs symmetry. The wavenumbers corresponding to the normal modes of vibration were calculated using the DFT (B3LYP/6-31G**) approximation and their agreement with the measured values improved after scaling of the associated force field. An assignment of bands is proposed on the basis of such calculations and the comparison with related molecules.     

Anharmonic vibrational spectroscopy and investigation of intramolecular mode couplings in adenine

Vibrational frequencies for the nucleobase adenine are calculated by the vibrational self-consistent field (VSCF) and correlation corrected vibrational self-consistent field (CC-VSCF) methods using Hartree-Fock (HF), density functional theory (DFT) and second order Møller-Plesset (MP2) theories. A large number of potential energy surface (PES) points were computed in the anharmonic calculations corresponding to each method. The quartic force field (QFF) approximation was used to generate the full grid of points for the VSCF solver. We have implemented our new procedure for computing the mode-mode coupling integrals in the 2-mode coupling representations of the quartic force field (2MR-QFF) for prediction of coupling magnitudes. Calculations were performed using the 6-31G(d,p) basis set. Comparison of the calculated ab initio anharmonic spectra with Ar matrix experimental data of adenine reported in the literature reveals that, the CC-VSCF (DFT) wavenumbers show the best agreement. The experimental geometric parameters of adenine are compared with the theoretically optimized molecular structural parameters. These are found to be in good agreement. Vibrational assignments are based on the calculated potential energy distribution (PED) values.     

The geometry of the nitroguanyl fragment in the simplest nitroguanidine derivatives in the absence of intermolecular interactions: The gas electron diffraction data on 1,1,3,3-tetramethyl-2-nitroguanidine

The structures and force fields of the equilibrium forms of 2-nitroguanidine (1), 1,1,3,3-tetramethyl-2-nitroguanidine (2), and nitroguanyl azide (3) were determined in the MP2(full)/6-311G(3df, 2p) approximation; wagging-inversion motions of the N amine atoms were studied. The internal rotation potential function of the NO₂ group was calculated for 1. Similar functions for 1 and 2 were also obtained in the MP2(full)/6-311G(d, p) approximation. Direct one-dimensional problems for a nonrigid model were solved by the variational method, and the distribution of torsional levels was obtained. In the region of potential minimum, rotation in both molecules had the character of large-amplitude motions. For the first time, electron diffractions data were obtained at 100°C for molecule 2 without noticeable traces of substance decomposition. A structural r _e analysis was performed using the model of large-amplitude motions for characteristic NO₂ group torsional vibrations. Vibrational corrections to internuclear distances and mean amplitudes were calculated taking into account nonlinear kinematic effects using the force fields obtained in this work. The geometry of molecule 2 calculated in the MP2(full)/6-311G(3df, 2p) approximation well corresponds to the gas electron diffraction data. The parameters of molecule 2 in the crystalline phase, however, differ substantially from the parameters of the free molecule. This corresponds with the suggestion of the influence of intermolecular H-bonds involving the imine nitrogen atom and nitro groups oxygen atoms.     

Vibrational anharmonicity and harmonic force fields for dichloromethane from quantum-chemical calculations

Anharmonic and related constants have been calculated for CH2Cl2, CD2Cl2, and CHDCl2 by using the program Gaussian03 and B3LYP and MP2 models. Bases used were 6-311++G** and cc-pVTZ. The size of grid used in the B3LYP/6-311++G** model had a noticeable effect on resulting data. Features of the MP2/6-311++G** calculations suggested a deleterious effect of the absence of f functions in this basis set. The need for the replacement of second-order terms in the perturbation theory formulas for the vibrational anharmonic constants x ij in the presence of Fermi resonance was explored, and minor resonances were found associated with the cubic constants varphi 122 and varphi 299 (d 0 isotopomer), phi122 and phi849 (d2), and phi278 (d1). Computed xij values for nuCH and nuCD motions agree quite well with earlier experimental data. Observed anharmonic frequencies, nu obsd, were corrected to "observed" harmonic frequencies, omega obsd, by using computed differences Delta = omegaQC-nuQC. These differences Delta are larger for the antisymmetric nuasCH2 mode than for symmetric nusCH2 motion. This fact made it necessary to use differing scale factors for the two kinds of CH stretching force constants in a subsequent scaling of the harmonic force field to nuobsd. Force field scaling was also carried out by refining to omega obsd. In both approaches, the B3LYP models required differing scale factors for symmetric and antisymmetric CCl stretching force constants, indicating a failure to compute an accurate C-Cl stretch-stretch interaction force constant. The MP2/cc-pVTZ force field was preferred. Both scaled and unscaled harmonic force fields were used to calculate centrifugal distortion constants (CDCs) and contributions to the vibrational dependence of the rotational constants (alphas). Variations in the CDCs can, in part, be explained by the magnitudes of the frequencies used in the scaling process.     

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Vibrational spectra of difluoromethanimine CF2NH calculated from an ab initio CI quartic force field

Some energy levels up to 3500 cm⁻¹ above the zero point energy have been calculated for difluoromethanimine CF₂NH and its deuterated isotopmer CF₂ND from a complete quartic force field computed at MP2/6-311G^** level of theory. The results show a very good agreement with the most reliable fundamental experimental values, the mean deviations being found to be 5 and 6 cm⁻¹ for the two molecules studied. Our complete quartic force field predicts or confirms the assignment of some overtones and combination bands in the medium IR region.     

Experimental and computational studies of the structure and vibrational spectra of aminomethyl-dimethyl-phosphine oxide and its 15N labeled isomer

Infrared (4000-100 cm(-1)) spectra of aminomethyl-dimethyl-phosphine oxide and 15N-aminomethyl-dimethyl-phosphine oxide have been measured. Geometric parameters (bond distances and angles), net electronic charges and vibrational spectroscopic data of both compounds calculated at various levels of theory (B3LYP/6-31G* and Moeller-Plesset perturbational theory (MP2)/6-31G*) are reported. The theoretical spectral results are discussed mainly in terms of comparison with infrared (4000-100 cm(-1)) spectral data. Better coincidence was achieved with the frequencies calculated at the MP2/6-31G* level: the standard deviation is 16 cm(-1). The calculated isotopic frequency shifts, induced by the 15N labeling, are in good accordance with the measured ones. Complete vibrational assignment is made with the help of MP2 force field calculations. Data obtained here are used to reassign some of the vibrational frequencies.     

FC(O)NCS 分子振动光谱的理论研究

采用DFT(B3LYP)方法,以6-3G*为基组对FC(O)NCS的顺式和反式两种构型的几何结构,振动谐性力场和红外光谱进行了研究。B3LYP/6-31G*计算水平和大多数有机分子的一套固定标度因子进行标度。根据标度后的理论力场进行简正坐标分析得到的势能分布(PED)和红外光谱强度值对FC(O)NCS分子的顺式和反式两种构型的振动基频进行了理论归属。     

A coupled-cluster study of the structure and vibrational spectra of pyrazole and imidazole

Harmonic force fields were calculated at the corresponding optimized geometries for pyrazole and imidazole at the HF, B3LYP, MP2, CCSD and CCSD(T) levels using the 6-31G* basis set and at the HF and B3LYP levels using the cc-pVTZ basis set. The agreement between the calculated and experimental geometries by the CCSD and CCSD(T) methods was generally similar to that obtained with the B3LYP and MP2 methods. The force fields were scaled using one-scale-factor (1SF), 3SF and 7SF scaling schemes. The scale factors were varied with respect to the experimental frequencies. Using 7SF scaling, the root-mean-square (RMS) deviation of the calculated frequencies from the experimental frequencies by the HF, B3LYP, MP2, CCSD and CCSD(T) methods and the 6-31G* basis set was 16, 7, 13, 11 and 11 cm(-1), respectively. This shows that the B3LYP method is preferred for force field calculations over the perturbative MP2, CCSD and CCSD(T) methods. Using 1SF scaling, the CCSD(T) scale factor was 0.931, the highest among the five methods used but close to that obtained with the B3LYP method and the cc-pVTZ basis set with lower RMS deviation.     

Conformational space of 4,4′-methoxypropylstilbene molecule

Quantum-chemical simulation of the ground state [the density function B3LYP/6-31G, B3LYP/6-31G(d), and B3LYP/6-31+G(d,p) and the perturbation theory MP2/6-31G(d) methods] and the transition states [the B3LYP/6-31G(d) method] of 4,4′-methoxypropylstilbene molecule has been performed. Using the Ellinger MM2 force field method, the potentials of internal rotation have been obtained for each rotational degree of freedom of the molecule. The B3LYP simulation has revealed the planarity of the conjugated system and the orthogonal position of the alkyl substituent, whereas the benzene rings have deviated by about 20° with respect to the double bond plane according to the MP2 data. Three transition states of the molecule corresponding to the saddle points of the first and the second orders have been revealed. The stationary points have been identified by means of vibrational analysis.     

Optimization of CHARMM force field parameters for the chalcone fragment

In this work,we developed the CHARMM all-atom force field parameters for the nonstandard biological residue chalcone,followed by the standard protocol for the CHARMM27 force field development.Target data were generated via ab initio calculations at the MP2/6-31G* and HF/6-31G* levels.The reference data included interaction energies between water and the model compound F(a fragment of chalcone).Bond,angle,and torsion parameters were derived from the ab initio calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters of standard residues.The optimized CHARMM parameters perform well in reproducing the target data.We expect that the extension of the CHARMM27 force field parameters for chalcone will facilitate the molecular simulation studies of the reaction mechanism of intramolecular cyclization of chalcone catalyzed by chalcone isomerase.     

A study of factors affecting the accurac of combined calculation methods

By the example of combined calculation methods (CCMs) corresponding to calculations in MP4/6–311+G(fd,p)//MP2/6-31G(d,p) and MP4/aug-cc-pvTZ//MP2/cc-pvDZ approximations the factors affecting their accuracy are considered. By total energy calculations made for a number of compounds it is shown that the accuracy of CCMs reduces when valence double- and triple-split basis sets are applied together, and also when different methods are used to allow for electron correlation. The use of empirical corrections taking into account the character of the electron distribution in a molecule allows an enhancement of the accuracy of CCMs. The mentioned factors taken into account enable us to obtain CCM, for which the mean absolute deviation of calculation data is 1.0 kJ/mol and the largest maximum deviation is 8.0 kJ/mol in the total energy calculation in the MP4/6-311+G(f,d,p) approximation.     

Modelling of carbohydrate–aromatic interactions: <Emphasis Type="Italic">ab initio </Emphasis>energetics and force field performance

Summary Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate–aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from −2.8 to −12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree–Fock method (interaction energies from +1.0 to −6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.     

含乙烯氧基柔链的苯并菲盘状液晶清亮点的平均场理论研究

我们前期的合成和实验发现, 对于一系列含端烯氧基醚链的苯并菲分子, 它们没有分子间氢键, 其生成的液晶的清亮点的高低与端烯氧基醚链的数目有关. 本工作采用Gay-Berne势模拟液晶分子的双体势, 用量子化学和分子力学相结合的ONIOM(MP2/6-31G*(0.25):UFF)方法优化含端烯氧基醚链的苯并菲分子的单体和双体的构型和能量, 从而获得Gay-Berne势的参数. 在此基础上, 根据平均场理论, 解一个关于序参量和温度的积分方程, 求出液晶的清亮点. 计算结果与实验趋势相同, 可以解释清亮点和分子端烯氧基醚链数目的关系.     

Comparison of ab initio and density functional methods for vibrational analysis of TeCl4

Vibrational analysis of tellurium tetrachloride, TeCl₄, was performed with Hartree–Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6–31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A₂ (ν₄) fundamental, where the results of the best methods were within 4 cm⁻¹. The best force fields were obtained with the following methods: Becke3–Lee–Yang–Parr and Becke3–Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl₄; however, it provides poor results with correlated methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 308–318, 1998     

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ//MP2/6-31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc-pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone phi, psi dihedral crossterms or a phi, psi grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the phi, psi dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of phi and psi in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general.