Conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete

The conventional strain energies of 1,2-dihydroazete, 2,3-dihydroazete, 1,2-dihydrophosphete, and 2,3-dihydrophosphete are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory, and density functional theory and employing the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single-point fourth-order perturbation theory, CCSD, and CCSD(T) calculations employing the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectfully, to ascertain the contribution of higher order correlation. Three DFT functionals, B3LYP, wB97XD, and M06-2X, are employed to determine whether they can yield results similar to those obtained at the CCSD(T) level.     

Conventional strain energies of azetidine and phosphetane: Can density functional theory yield reliable results?

The conventional strain energies for azetidine and phosphetane are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero‐point vibrational energies are computed for all pertinent molecular systems using self‐consistent field theory, second‐order perturbation theory, and density functional theory and using the correlation consistent basis sets cc‐pVDZ, cc‐pVTZ, and cc‐pVQZ. Single point fourth‐order perturbation theory, CCSD, and CCSD(T) calculations using the cc‐pVTZ and the cc‐pVQZ basis sets are computed using the MP2/cc‐pVTZ and MP2/cc‐pVQZ optimized geometries, respectively, to ascertain the contribution of higher order correlation effects and to determine if the quadruple‐zeta valence basis set is needed when higher order correlation is included. In the density functional theory study, eight different functionals are used including B3LYP, wB97XD, and M06‐2X to determine if any functional can yield results similar to those obtained at the CCSD(T) level. © 2012 Wiley Periodicals, Inc.     

Semiempirical double-hybrid density functional with improved description of long-range correlation

The recently proposed new family of "double-hybrid" density functionals [Grimme, S. J. Chem. Phys. 2006, 124, 34108] replaces a fraction of the semi-local correlation energy by a non-local correlation energy expression that employs the Kohn-Sham orbitals in second-order many-body perturbation theory. These functionals have provided results of high accuracy over a wide range of properties but fail to accurately describe long-range van der Waals interactions. In this work, a distance-dependent scaling factor for the non-local correlation energy is introduced to address this problem, and two new double-hybrid density functionals are proposed. The new functionals are optimized with the finite cc-pVTZ basis on training sets of atomization energies and intermolecular interaction energies. They are compared against (scaled) second-order M?ller-Plesset perturbation theories and popular density functionals including the hybrid-GGA functional B3-LYP and the first double-hybrid functional (B2-PLYP). Tests are performed on an extensive set including reaction energies, barrier heights, weakly interacting complexes, transition-metal systems, molecular geometries, and harmonic vibrational frequencies. Within the cc-pVTZ atomic orbital basis, we have demonstrated the ability to find a parametrization scheme which is simultaneously able to describe thermochemistry and weakly bound systems with a satisfactory degree of accuracy.     

Additive empirical force field for hexopyranose monosaccharides

We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the alpha- and beta-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides, and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute-water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Although not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids.     

Comparison of ab initio,semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems

The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C₅ ? C₈ cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H? H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.     

Computational study of noncovalent complexes between formamide and formic acid

The geometries and binding energies of 1:1, 1:2, and 1:4 formic acid-formamide complexes (FA-FMA) are calculated by quantum chemical procedures. Vibrational spectra and intermolecular distances of the most stable FA-FMA dimers as well as the influence of the basis set superposition error (BSSE) on the geometries and energies of the dimers are also discussed. All FA-FMA dimers are optimized at the B3LYP/cc-pVTZ, the MP2/cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ levels of theory to study the influence of the level of theory on the calculated geometries and energies. CCSD(T)/cc-pVTZ single-point calculations at the MP2/aug-cc-pVTZ-optimized geometries were performed as reference for estimating the quality of lower level calculations. These calculations allow us to qualitatively describe the competition between different types of hydrogen-bonding interactions in FA-FMA complexes. FA-FMA dimers are compared to other formamide complexes and to the FA-FMA crystal structure.     

Properties of aromaticity indices based on the one-electron density matrix

Proper normalization of two previously published indices yields aromaticity measures that, when computed within the Hückel molecular orbital (HMO) approximation, closely match the topological resonance energies per pi electron of aromatic annulenes and their ions. The normalized indices, which quantify aromaticity of individual rings in polycyclic systems, are equally applicable to homocyclic and heterocyclic compounds and can be readily computed from 1-matrices calculated at any level of electronic structure theory. However, only the index ING, derived from the Giambiagi formula, produces proper ordering of aromaticities of heterocyclic compounds, provided it is calculated from all-electron wavefunctions in conjunction with the atoms in molecule (AIM) partitioning. Its values are shown to be strongly affected by electron correlation effects. Because of its apparent inability to distinguish between anti- and nonaromatic systems, ING should only be employed for aromatic species.     

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Some theoretical aspects of vibrational fine structure accompanying core ionizations in N2 and CO

Ab initio calculations have been carried out on CO and N₂ and the relevant core hole states with different basis sets to investigate differences in geometries and force constants. From these calculations vibrational band profiles of the core level ESCA spectra for these molecules have been interpreted, obviating the need to rely on data pertaining to the equivalent core species. The agreement with experimental profiles is excellent. The O_1s level of CO which has not been subjected to detailed theoretical analysis previously, is predicted to show substantial vibrational structure in excellent agreement with recently acquired experimental data. The effect of temperature on the band profiles has also been considered. Theoretically derived core binding and relaxation energies of these systems have been investigated both as a function of basis set, and of internuclear distance. Density difference contours have been computed and give a straightforward pictorial representation of the substantial electron reorganizations accompanying core ionizations. Small basis sets with valence exponents appropriate to the equivalent core species when used in hole state calculations describe bond lengths, force constants, core binding energies and relaxation energies with an accuracy comparable to that appropriate to the corresponding extended basis set calculations.     

Kr和Kr2的实验和理论研究

利用超声分子束技术、同步辐射和反射式飞行时间质谱仪得到了Kr和Kr2的光电离质谱和光电离效率谱, 确定了Kr和Kr2的电离能. 利用Gaussian-03程序中的MP2(Full)/6-31G*, QCISD/cc-pVTZ以及B3LYP/6-31G方法优化了Kr2的结构, 计算了它们的振动频率和电离能, 计算结果显示: 当采用相同的理论水平和基组时, 随着Kr同位素质荷比(m/z)的增大, 它们结构和电离能保持不变, 而振动频率逐渐变小. 与此同时, 用G2方法计算了Kr (84)和Kr2 (168)的电离能, 它们的电离能的理论值与实验结果符合得比较好.     

Application of an efficient multireference approach to free-base porphin and metalloporphyrins: ground, excited, and positive ion states

The improved virtual orbital-complete active space configuration interaction (IVO-CASCI) method is applied to determine the geometries of the ground state of free-base porphin and its metal derivatives, magnesium and zinc porphyrins. The vertical excitation energies and ionization potentials are computed at these optimized geometries using an IVO-based version of multireference Mo?ller-Plesset (IVO-MRMP) perturbation theory. The geometries and excitation energies obtained from the IVO-CASCI and IVO-MRMP methods agree well with experiment and with other correlated many-body methods. We also provide the ground state vibrational frequencies for free-base porphin and Mg-porphyrin. All frequencies are real in contrast to self-consistent field treatments which yield an imaginary frequency. Ground state normal mode frequencies (scaled) of free-base porphin and magnesium porphyrin from IVO-CASCI and complete active space self-consistent field methods are quite similar and are consistent with Becke-Slater-Hartree-Fock exchange and Lee-Yang-Parr correlation density functional theory calculations and with experiment. In addition, geometries are determined for low-lying excited state triplets and for positive ion states of the molecules. To our knowledge, no prior experimental and theoretical data are available for these excited state geometries of magnesium and zinc porphyrins. Given that the IVO-CASCI and IVO-MRMP computed geometries and excitation energies agree favorably with experiment and with available theoretical data, our predicted excited state geometries should be equally accurate.     

Ab initio DFT study of Z–E isomerization pathways of <Emphasis Type="Italic">N</Emphasis>–benzylideneaniline

The ground state properties and absorption spectra of N-benzylideneaniline (NBA) have been studied at the density functional (DFT) and at the time-dependent density functional (TD-DFT) level of the theory. The equilibrium geometries of the E and Z isomers in the ground state and their vibrational frequencies have been computed. Furthermore, the excitation energies of the lowest excited singlet and triplet states and the potential energy curves along the torsion and the inversion isomerization coordinates were evaluated. The results are discussed in light of the available experimental data.     

Ab initio studies of methylenecarbene and isoelectronic species

Optimum equilibrium geometries, energetics, harmonic vibrational frequencies, and infared intensities within the double harmonic approximation are computed for methylenecarbene, CCH₂, and isoelectronic species involving silicon and germanium at both the SCF level of theory and the level of second-order perturbation theory using a 6-311G(2df, 2p) basis set or its equivalent. Optimum equilibrium geometries and energetics are also computed at both levels of theory using a smaller 6-311G(d, p) basis set or its equivalent. This investigation of these species is the first to include all of the systems with germanium. In addition, this present work is the first study to includef-type polarization functions in a systematic investigation of the molecular structure and properties of all the molecules in the series. Acetylenic structures are also computed for energy comparisons. Of all the linear isomers, only acetylene is found to be a minimum on the potential energy surface. However, all of the C_2v structures are found to be local minima. Both the C_2v and linear structures will serve as a basis for future work involving mapping the entire hyperenergy surfaces of all of the molecular systems in the series.     

Structures and molecular surface electrostatic potentials of high-density C,N, H systems

Tri-s-triazine and two ditetrazolodiazines are known to have unusually high crystal densities (for unsubstituted C, N, H compounds). We have used a nonlocal density functional procedure to compute the geometries and energies of these and three related molecules, and then calculated the ab initio SCF electrostatic potentials on their molecular surfaces. We attribute the high densities to the relatively small molecular volumes and the strong intermolecular attractions arising from highly varying surface potentials. The energy differences of the two ditetrazoles and their diazide tautomers were computed, as well as for the dinitro derivative of one of the former.     

Electron and Geometry Structure of Hydrogen-Bonded Complexes of Guanine with One Molecule Methanol. A DFT Level Study

The geometries, harmonic vibrational frequencies, and energies of eight hydrogen-bonded complexes of guanine with one molecule methanol are computed using the DFT (B3LYP) method together with the 6-31+G* basis functions. In the investigation two stable tautomers of guanine (oxo-amino N9H and oxo-amino N7H) were chosen. They were included in a variety of H-bonded complexes with one molecule methanol. In order to investigate the nature of the intermolecular bonds, the bonding energies and thermodynamic properties of the complexes were calculated.     

Electron and Geometry Structure of Hydrogen-Bonded Complexes of Guanine with One Molecule Methanol. A DFT Level Study

Summary. The geometries, harmonic vibrational frequencies, and energies of eight hydrogen-bonded complexes of guanine with one molecule methanol are computed using the DFT (B3LYP) method together with the 6-31+G* basis functions. In the investigation two stable tautomers of guanine (oxo-amino N9H and oxo-amino N7H) were chosen. They were included in a variety of H-bonded complexes with one molecule methanol. In order to investigate the nature of the intermolecular bonds, the bonding energies and thermodynamic properties of the complexes were calculated.     

Theoretical Studies of Distyrylbenzene and its Optical Properties

The electronic and geometrical properties of distyrylbenzene (DSB) are investigated by using chemistry theoretical calculation methods. Specifically, the excited state properties are studied by performing ab initio correlation interaction singlet (CIS) and time‐dependent density functional theory; the ground state and Raman activities are computed by density functional theory with the B3LYP method. Eight conformers of distyrylbenzene are found and they are derived from three isomers which are cis, cis‐, cis, trans‐, and trans, trans‐, respectively. The relative energy shows that each isomer of three types is separated with a large energy barrier, but a small energy difference of each conformer is found if they are in the same type. The transition state also shows the barrier between conformers is lower than isomers. The computed excited transition energies using ZINDO/S based on the optimized geometries at a DFT/B3LYP level with 6–31+G show an excellent agreement with experimental absorption spectra.     

Corrected small basis set Hartree‐Fock method for large systems

A quantum chemical method based on a Hartree‐Fock calculation with a small Gaussian AO basis set is presented. Its main area of application is the computation of structures, vibrational frequencies, and noncovalent interaction energies in huge molecular systems. The method is suggested as a partial replacement of semiempirical approaches or density functional theory (DFT) in particular when self‐interaction errors are acute. In order to get accurate results three physically plausible atom pair‐wise correction terms are applied for London dispersion interactions (D3 scheme), basis set superposition error (gCP scheme), and short‐ranged basis set incompleteness effects. In total nine global empirical parameters are used. This so‐called Hartee‐Fock‐3c (HF‐3c) method is tested for geometries of small organic molecules, interaction energies and geometries of noncovalently bound complexes, for supramolecular systems, and protein structures. In the majority of realistic test cases good results approaching large basis set DFT quality are obtained at a tiny fraction of computational cost. © 2013 Wiley Periodicals, Inc.     

Study of the formamide–methanol dimer with ab initio and density functional theory methods

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Interactions between cyclic carbon clusters

This work reports on the results of MINDO/3 calculations of the structures and energies of monocyclic and bicyclic carbon clusters. Interactions between the rings and between the cyclic and linear clusters are considered. For the most typical reactions (cyclization of linear clusters and insertion of chains into rings and formation of bicyclic structures), the energy barriers are estimated. The bond energies of the bicyclic structures depend on the parities of the initial rings. The most stable configurations with bond energies of the order of 5 eV result from coupling of the odd-membered rings. It is shown that typical condensation conditions correspond to the absorption of the linear clusters by the cyclic structures. Institute of Theoretical and Applied Mechanics, Siberian Branch, Russian Academy of Sciences. Institute of Computational Technologies, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 6, pp. 991–997, November–December, 1995. Translated from I. Izvekova