1, 3-二氟丙烷构象和电子结构的从头算和 密度泛函理论计算

用从头算和密度泛函数理论研究了1,3-二氟丙烷的构象和电子结构。在计算的各种理论水平下,GG构象是最稳定构象,AG构象次之。利用分子力场的非键作用定量化旁式效应,由MM2力场的非键参数计算的结果较为合理。对于GG和AG构象,在HF/6-31G^*和HF/6-31+G^*^*水平预测的构象分布与实验值接近。     

Ab initio calculations on halogen-bonded complexes and comparison with density functional methods

A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the Moller-Plesset second-order perturbation (MP2) level of theory with the Dunning's correlation-consistent basis set, aug-cc-pVDZ. Binding energies are extrapolated to the complete basis set (CBS) limit by means of two most commonly used extrapolation methods and the aug-cc-pVXZ (X = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] correction term, determined as a difference between CCSD(T) and MP2 binding energies, is estimated with the aug-cc-pVDZ basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the MP2 level. The calculations described herein have shown that the CCSD(T) CBS limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory (DFT) methods has been evaluated comparing the results with those obtained from MP2 and CCSD(T). It is shown that PBEKCIS, B97-1, and MPWLYP functionals provide accuracies close to the computationally very expensive ab initio methods.     

A density functional theory study clarifying the reactions of conjugated ketenes with formaldimine. A plethora of pericyclic and pseudopericyclic pathways

The reactions of vinylketene (1a), imidoylketene (1b), and formylketene (1c) with formaldimine (2) were studied at the B3LYP/6-31G* level. For the cycloadditions of these conjugated ketenes with 2, several possible pathways to both [4 + 2] and [2 + 2] products were examined. The lowest energy [2 + 2] pathways are, in most cases, calculated to be stepwise, forming the products via rate-determining conrotatory electrocyclization of zwitterionic intermediates. However, concerted transition structures analogous to the ketene plus ethene [2 + 2] cycloaddition reaction were also located; the existence of multiple transition states offers a resolution to a long-standing controversy regarding the mechanism of ketene plus imine cycloadditions. Both stepwise and concerted [4 + 2] pathways were calculated for 2b and for 2c; both these pathways are pseudopericyclic. The inherently low barriers associated with pseudopericyclic transition states provide an explanation of the experimental preference for [4 + 2] cycloadditions of alpha-oxoketenes and predict [4 + 2] cycloadditions should also be favored for imidoylketenes. For a vinylketene constrained to a Z-geometry, the concerted [4 + 2] cycloaddition is also predicted to be the lowest energy pathway. An explanation is offered for the unusual thermal equilibration from a six-membered ring (3d) to a four-membered ring (4d) observed by Sato et al. Transition structures for facile pseudopericyclic 1,3- and 1,5-hydrogen shifts in the zwitterions were also calculated.     

X-ray crystal structure, Raman spectroscopy, and Ab initio density functional theory calculations on 1,1,3,3-tetramethylguanidinium bromide

The salt 1,1,3,3-tetramethylguanidinium bromide, [((CH(3))(2)N)(2)C═NH(2)](+)Br(-) or [tmgH]Br, was found to melt at 135(5) °C, forming what may be referred to as a moderate temperature ionic liquid. The chemistry was studied and compared with the corresponding chloride compound. We present X-ray diffraction and Raman evidence to show that also the bromide salt contains dimeric ion pair "molecules" in the crystalline state and probably also in the liquid state. The structure of [tmgH]Br determined at 120(2) K was found to be monoclinic, space group P2(1)/n, with a = 7.2072(14), b = 13.335(3), c = 9.378(2) ?, β =104.31(3)°, Z = 2, based on 11769 reflections, measured from θ = 2.71-28.00° on a small colorless needle crystal. Raman and IR spectra are presented and assigned. When heated, both the chloride and the bromide salts form vapor phases. The Raman spectra of the vapors are surprisingly alike, showing, for example, a characteristic strong band at 2229 cm(-1). This band was interpreted by some of us to show that the [tmgH]Cl gas phase should consist of monomeric ion pair "molecules" held together by a single N-H(+)···Cl(-) hydrogen bond, the stretching vibration of which should be causing the band, based on ab initio molecular orbital density functional theory type calculations. It is not likely that both the bromide and chloride should have identical spectra. As explanation, the formation of 1,1-dimethylcyanamide gas is proposed, by decomposition of [tmgH]X leaving dimethylammonium halogenide (X = Cl, Br). The Raman spectra of all gas phases were quite identical and fitted the calculated spectrum of dimethylcyanamide. It is concluded that monomeric ion pair "molecules" held together by single N-H(+)···X(-) hydrogen bonds probably do not exist in the vapor phase over the solids at about 200-230 °C.     

Ab initio calculations on 5α-androstane

The electronic structure of 5α-androstane, the parent hydrocarbon of the hormonal steroids, has been computed by ab initio SCF methods in an STO -3G basis. The results are compared with existing MNDO computations and are used to discuss long-range electronic interactions between distant substituents that might be appended to rings A and D of 5α-androstane. It is thought that these interactions are mediated by the ribbonlike MO 'S of the parent molecule.     

Ab initio and density functional calculations of mean-square amplitudes of vibration for benzene and cubane

Mean-square amplitudes of vibration were calculated using ab initio and density functional methods for benzene and cubane. Both 6-31G^* and 6-311G^** basis sets were employed. It was found that significant improvements were achieved when electron correlation was introduced, even if only at the local density functional level. The mean-square amplitudes calculated were not effected by the basis set used for benzene and slightly improved for the highly strained cubane molecule when the larger basis set was used. An attempt was also made to improve the calculated mean-square amplitudes by making use of scale factors found in the literature, which were developed to improve the calculated frequencies. It was found that only the SCF mean-square amplitudes were significantly improved.     

Ab initio and density functional theory calculations of molecular structure and vibrational spectrum of ethyl azidoacetate

Here we report ab initio and density functional results for molecular properties of ethyl azidoacetate (N₃CH₂COOC₂H₅) and for the corresponding singly ionized structure (N₃CH₂COOC₂H₅⁺). Ab initio ionization energies based on Koopmans’ theorem are in excellent agreement with the experimental data from ultraviolet photoelectron spectroscopy. DFT adiabatic energy differences between neutral and ionized structures are very sensitive to electronic correlation effects and are not in very good agreement with experiment. The results for the structure and vibrational frequencies are compared with the experimental data of related molecular structures.     

Ab initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies

A set of benchmark results for the geometries, binding energies, and protonation affinities of 24 complexes of small organic ligands with Ca(II) is provided. The chosen level of theory is CCSD(T)/CBS obtained by means of a composite procedure. The performance of four density functionals, namely, PW91, PBE, B3LYP, and TPSS and several Pople-type basis sets, namely, 6-31G(d), 6-31+G(d), 6-31+G(2d,p) and 6-311+G(d) have been assessed. Additionally, the nature of the metal ligand bonding has been analyzed by means of the Symmetry Adapted Perturbation Theory (SAPT). We have found that the B3LYP hybrid functional, in conjunction with either the polarized double-ζ 6-31+G(2d,p) or the triple-ζ 6-311+G(d) basis sets, yields the closest results compared to the benchmark data. The SAPT analysis stresses the importance of induction effects in the binding of these complexes and suggests that consideration of classical electrostatic contributions alone may not be reliable enough for the prediction of relative binding energies for Ca(II) complexes.     

A density functional theory study on the electrocyclization of 1,2,4,6-heptatetraene analogues: converting a pericyclic to a pseudopericyclic reaction

A comprehensive B3LYP/6-31+G* study on the electrocyclization of 1,2,4,6-heptatetraene analogues was conducted. Starting from the cyclization of (2Z)-2,4,5-hexatrienal, a pericyclic disrotatory process favored by the assistance of a electron lone pair, we incorporated small modifications in its molecular structure to obtain a truly pseudopericyclic process. To this purpose electronegative atoms (fluorine and nitrogen) were added to give a more electrophilic character on the carbon atom which is attacked by the electron lone pair of the oxygen atom. The complete pathway for each reaction was determined, and changes in magnetic properties were monitored with a view to estimating the aromatization associated with each process. This information, together with the energetic and structural results, allowed us to classify the reactions as pseudopericyclic or pericyclic. Among all studied reactions only one was a truly pseudopericyclic process and another was a borderline case. The features of this unequivocally pseudopericyclic case were analyzed in depth.     

Chirality and spin density: Ab initio and density functional approaches

The spin distribution in a stable nitroxide biradical that shows ferromagnetic interactions in the solid phase has been studied at three levels of theory: First, at the UHF level; then, including correlation effects in UMP 2 calculations; and finally, the results are compared with the spin density obtained using the local density functional (LDF ) approximation. It is shown that LDF spin densities are closer to UMP 2 than to UHF predictions; the difference between the UHF and the (UMP 2, LDF ) results points to a redistribution of the spin repartition between N and O due to electronic correlation. For planar conformations of the NO group, there is symmetric distribution (D_2d) of the spin density on the adamantane skeleton. For nonplanar nitroxides, the molecule is chiral (C₂), which results in a breakdown of the spin transmission on part of the adamantane cage. © 1993 John Wiley & Sons, Inc.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

Ab initio calculations on CICN and ONCI

Ab initio calculations are presented for the molecules CICN and ONCI with optimization of all geometric parameters. Calculated equilibrium geometries for CICN are in good agreement with microwave data; however, the calculated N-Cl distance in ONCI is about 0.1 Å shorter than obtained by electron diffraction. Orbital energies are calculated by means of Koopmans' theorem and also by ΔSCF calculations. The importance of relaxation energy is shown by comparing the calculated orbital energies with experimental data from photoelectron spectra of the valence levels.     

Ab initio calculations on Pro-Ala and Pro-Gly dipeptides

The geometries of the dipeptides -Pro- -Ala, -Pro- -Ala and -Pro-Gly were investigated by a grid scan ab initio calculation. The 6-31G basis set was used to estimate the effect of the alanyl side-chain on the conformation of the peptide backbone and to provide a computational basis for the interpretation of known physical-chemical properties of larger peptides that contain these dipeptides. These calculations furnish a direct quantum mechanical assessment of the energetic consequences of a methyl side-chain in the i + 2 position of a turn. The results of the calculation support the current view that the presence of a -Ala residue in the i + 2 position favors a type II β-turn over a type I β-turn conformation, while -Ala has the opposite effect. Total and relative energies for all the optimized conformations identified by the grid search are given and geometric parameters (bond lengths, bond angles and dihedral angles) and net atomic charges have been calculated.     

Ab initio calculations on the molecular structure of fluorocyanopolyynes

The molecular structure of the first three members of the fluorocyanopolyynes was studied by ab initio Hartree-Fock calculations with a polarized double zeta basis set and at MP2 level with the same basis set. Alternating triple and single bonds were found; a theoretical estimate of rotational constants and dipole moments was performed and a comparison with the available experimental data was made. An analysis of the theoretical vibrational frequencies of the title compounds was carried out.     

DNA base amino groups and their role in molecular interactions: Ab initio and preliminary density functional theory calculations

Interactions of DNA bases frequently involve the DNA base amino groups. In contrast to the empirical force fields, the ab initio calculations predict nonplanar DNA base amino groups. The same conclusion also follows from the density functional theory (DFT ) calculations. Both local and nonlocal density approximations were used. Optimized geometries of two other molecules with nonplanar amino groups (aniline, formamidine) are presented for comparison. The influence of nonplanar DNA base amino groups on the conformational variability of DNA is discussed. © 1996 John Wiley & Sons, Inc.     

Ab initio calculations on the thermodynamic properties of azaspiropentanes

Following our recent study on the usefulness of borospiropentanes as new potential high-energy materials, we propose a new series of substituted spiropentane molecules, the azaspiropentanes. Presented here are the results of our ab initio calculations at the MP2 and B3LYP levels of theory using the 6-311++G(d,p) basis set. Results include optimized structural parameters, enthalpies of formation, specific enthalpies of combustion, and proton affinities. Our results indicate that azaspiropentane gives off the most energy of any of the nitrogen-containing spiropentanes, as indicated by its specific enthalpy of combustion of -41 kJ g(-1); however, it does not give off as much energy as spiropentane itself, which gives off about 48 kJ g(-1).     

Ab initio and density functional theory studies of peri- and regioselectivity in 1,3-dipolar cycloaddition reaction of 1,2-diazepine with nitrile oxide

The first systematic study of all dipolarophile sites of 1,2-diazepine towards nitrile oxide as dipole via 1,3-dipolar cycloaddition reactions has been carried out. To this end, the structural and energetic aspects of seventy-two isomers were determined by means of ab initio and density functional theory methods at different levels of accuracy were performed on all peri- and regio-isomeric forms. The agreement between the calculated and the experimental geometries, regio- and periselectivity of the studied reaction is good in all instances. The dipole condensation with the norcaradiene dipolarophile has been considered seemingly for the first time. The bis-cycloadduct 3a,3b,7,10a-tetrahydro-10 H-[1,2] oxazolo [4,5-d] [1,2,4] oxadiazolo [4,5-b] [1,2] diazepine is the most stable one as predicted by all methods used in this work. However, the tautomerization study of all forms of 1,2-diazepine seems to rule out the existence of the tautomeric form that provides the above mentioned cycloadduct. Consequently, the bis-cycloadduct 5,10-dioxa-1,2,4,11-tetrazatricyclo[7,3,1,0^2,6]trideca-3,7,11-triene is the favored product of this reaction.     

Ab initio calculations on low-energy conformers of alpha-cyclodextrin

In this article we carried out a comprehensive investigation of true minima on the potential energy surface (PES) for the alpha-cyclodextrin molecule using ab initio Hartree-Fock (HF) and density functional theory (DFT) quantum chemical methods, employing basis sets ranging from 6-31 G(d,p) to 6-311++G(2d,2p) triple-zeta quality. Thermodynamic quantities and the solvent effect were evaluated at the DFT level of theory. We believe that the most relevant conformers present on the multidimensional PES were sampled in our work, using an adequate treatment of electron correlation effects to describe the intramolecular hydrogen bonds that are present in cyclodextrin species. We present new structures not reported so far and discuss, in detail, the relevance of the DFT gas-phase equilibrium structures for the experimental and theoretical studies involving cyclodextrins and corresponding inclusion complexes, in the condensed phase. In addition, among the various true minimum energy structures located on the DFT PES, the preferred structures in the gas phase and aqueous media, needed to be used as representative minima on the PES in further studies involving the interaction of alpha-cyclodextrin with other species, were unambiguously identified.     

Ab initio calculations and vibrational spectroscopy on the phenylenediamine isomers

Molecular orbital calculations at HF and MP2 levels have been performed using the 6-31G⁷ basis set for full geometry optimization of the phenylenediamine isomers. Our results show that only a transoid conformer is found for o-phenylenediamine, whereas cis and trans conformers exist for m- and p-phenylenediamine. Vibrational normal modes have been also analyzed for the gas phase and in chloroform solution, and compared with experimental data we have obtained using FTIR spectroscopy.