Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3 and some 1–4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds.     

Some Aspects of the Implementation of Scaling Quantum Mechanical Molecular Force Fields

Some features of software implementation of the Pulay scaling procedure are considered. The advantages of the single value decomposition method for maintaining well-conditionality of the scale factor determination problem are demonstrated. The necessity of using a rational number of scale factors is shown. The possibility of obtaining transferable scale factors with the Pulay method and thus predict the vibrational spectra of related compounds is emphasized.     

Gas phase ionization of 1,3-propanedial tautomeric forms: A theoretical study

Two stable 1,3-propanedial tautomers and three their anions have been studied theoretically at MP2 and DFT levels of theory. The energies, structural parameters, ionization potentials, and vibration frequencies have been calculated at the two theoretical levels in order to compare the accuracy of the methods used. The ionization potential of the end form of 1,3-propanedial enol form was estimated to be 752 kJ mol^?1; the first and second potentials of the diketo form of 1,3-propanedial are 661 and 1239 kJ mol^?1, respectively.     

Molecular Conformation of 2,2'-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.     

Quantum Mechanical Studies of Intensity in Electronic Spectra of Fluorescein Dianion and Monoanion Forms

Quantum chemical ab initio investigations with full geometrical optimizations of dianion and monoanion fluorescein molecules in the ground state were performed by applying the density functional theory (DFT) B3PW91/6-311G** model to clarify the difference in the geometrical and electronic structure of the dianion molecule and that of monoanion in influencing fluorescence. The mechanism of fluorescence of dianion and monoanion is explained and the reason for intensive fluorescence of dianion compared with that of monoanion is studied     

The ring-opening of an unsymmetrical tetrahedral intermediate - 2-hydroxy-1,3-oxathiolane

Ab initio calculations were performed on 2-hydroxy-1,3-oxathiolane: and the two products of its breakdown: Complete geometry optimizations were performed at minimal (STO-3G) and split-valence (3-21G) basis set levels. In addition, a single point calculation was performed at 6-31G* level withd orbitals added on sulfur only. The conformation of the oxathiolane intermediate and its stability relative to the breakdown products was investigated. The STO-3G basis set gave an envelope form while 3-21G gave the twist form of the five-membered ring as the most stable. For all three basis sets the ester product was more stable than thioester.     

Dissociation Energies and Rotational Barriers About CC Single,Double, and Triple Bonds: A Hybrid HF-DFT Approach (Becke3LYP/6-311++G**)

Structural Chemistry -     

A Quantum Chemical Study of N14 Cluster

Ab initio molecular orbital theory and density functional theory have been employed to study N₁₄ cluster with low spin at the HF/6-31G*, B3LYP/6-31G*, B3PW91/6-31G*, BP86/6-31G*, and BHLYP/6-31G* levels of theory. Twelve isomers were studied, including one previously investigated cage molecule. The most stable isomer of N₁₄ is a C _2h -symmetric molecule that contains two separated five-membered nitrogen rings connected by a —N=N—N=N— bridge. The second, third, and fifth most stable isomers each have one five-membered nitrogen ring. The theoretical results suggest that the five-membered nitrogen ring gives rise to a particularly stable structural unit, and the more side chains that the five-membered nitrogen ring links with, the less stable the structure will become.     

Structural and vibrational studies of molecular conductors using quantum mechanical methods: 1,3-Dithiole-2-thione, 1,3-dithiole-2-one, 1,3-dioxole-2-one and 1,3-dioxole-2-thione

Computations were carried out by employing the RHF and density functional theory (DFT) methods to investigate the geometries, atomic charges, harmonic vibrational frequencies for the 1,3-dithiole-2-thione (DTT), 1,3-dithiole-2-one (DTO), 1,3-dioxole-2-thione (DOT) and 1,3-dioxole-2-one (DOO) molecules and their radical cations. The geometrical parameters and atomic charges on various atomic sites of the DTT and DOT molecules and their radical cations suggest extended conjugation in these systems. Contrary to this, for the DOO⁺ and DTO⁺ ions there is no evidence in favour of such conjugation, however, the neutral molecules exhibit some conjugation. Harmonic forced field and vibrational mode calculations provided convincing theoretical evidence for the reassignment of some fundamental vibrational modes for all the four molecules. In going from the neutral species to the charged ions for all the four cases the CC stretching frequency is found to decrease drastically. The CS stretching frequency reduces drastically for the DTT and DOT molecules as compared to their radical cations whereas the CO stretching frequency is found to increase in going from the neutral molecule to its radical cation for the DOO and DTO molecules. The ring stretching mode with a₁ symmetry and CC and CO/S stretching modes in these molecules appear to help in conversion of neutral molecule into respective radical cation and neighbouring radical cation into respective neutral molecule. Thus, there appears the feasibility of stretching vibrational mode coupling with electron transfer.     

Molecular Structure of tert-Butylazide: A Gas-Phase Electron Diffraction and Quantum Chemical Study

The molecular structure of tert-butylazide has been determined by gas-phase electron diffraction and quantum chemical calculations. The HF/6-31G* and B3LYP/6-31G** calculations yielded near C _s symmetry for the tert-butyl group, anti conformation of the (C)N—N bond with respect to one of the bonds, and an essentially free rotation around the bond with a 0.34 kcal/mol energy difference between syn and anti conformations of the CNNN moiety, the anti being the more stable form. The electron diffraction analysis was carried out by modeling a mixture of conformational isomers, generated by rotating the terminal nitrogen of the azide group, using a computed rotational potential. The data are consistent with C _s symmetry for the tert-butyl group. The bond, however, was found to be rotated out of the anti position, with respect to one of the bonds, by 12.5(12)°. The electron diffraction analysis yielded the following bond lengths (r _g), bond angles, and torsional angles: , .     

鸟嘌呤红外光谱的密度泛函理论研究──标度量子力学(SQM)力场处理

用密度泛函理论DFT(B3LYP)/6-31G^*方法对鸟嘌呤分子的酮-胺式和醇-胺式异构体的几何结构、振动谐性力场和红外光谱进行了研究.理论力场由迁移自相关分子异胞嘧啶和咪唑的力常数标度因子进行标度.算得振动频率与鸟嘌呤的实验基质隔离IR光谱比较平均偏差对酮-胺式和醇-胺式分别为6.6和6.0cm^-1.根据振动频率的势能分布和DFT计算的光谱强度值对鸟嘌呤分子的实验振动基频进行了理论归属.     

Molecular structure and conformational transitions of dichloroacetylchloride

RHF and MP2 techniques in 6–31G(d) basis set have been used to determine the structure of the isolated molecule CHCl₂COCl in two stable conformations (cis-and gosh-), as well as in transition states arising due to the rotary motion of CHCl₂ group around the C—C bond. The energy gap between the conformers and the relevant potential barriers has been calculated using the obtained potential dependence of the internal rotation. Plausible conformation of dichloroacetylchloride is discussed on the basis of ³⁵Cl NQR.     

Theoretical study of the electronic spectra ofcis-1,3,5-hexatriene andcis-1,3-butadiene

Summary The electronic spectra forcis-1,3-butadiene andcis-1,3,5-hexatriene have been studied using multiconfiguration second-order perturbation theory (CASPT2) and extended ANO basis sets. The calculations comprise all singlet valence excited states below 8.0 eV, the first 3s, 3p, 3d Rydberg states, and the second 3s state. The four lowest triplet states were also studied. The resulting excitation energies forcis-hexatriene have been used in an assignment of the experimental spectrum, leading to a maximum deviation of 0.13 eV for the vertical transition energies. The calculations place the 1¹ B ₂ state 0.04 eV below the 2¹ A ₁ state. 16 excited states were studied incis-butadiene, using a CASPT2 optimized ground state geometry. The 1¹ B ₂ state was located at 5.58 eV, 0.46 eV below the 2¹ A ₁ state and 0.09 eV above the experimental value. No experimental assignments are available for the 15 other transitions. On leave from: Departmento de Quimica Física, Universidad de Valencia, Dr. Moliner 50, Burjassot, E-46100-Valencia, Spain     

Carbon <Emphasis Type="Italic">versus</Emphasis> Sulfur Addition of Nucleophiles to Sulfines. Part I. The Case of Sulfinates

Summary. The nucleophilic substitution of chlorine in chlorosulfines with arylsulfinates leads to sulfonylsulfines with complete inversion of configuration within the starting sulfines. A mechanism for this displacement reaction is proposed. The sulfonylsulfines show good reactivity as heterodienophiles and the reaction with acyclic 1,3-dienes is surprisingly regio- and diastereoselective. The stereochemical details were established by X-ray crystallography and the competitive dienophilic properties were examined.Present address: University of Antwerp, Campus Drie Eiken, Faculty of Pharmacy, Department of Medicinal Chemistry, B-2610, Wilrijk-Antwerp, Belgium.     

Electronic structure of 1,3-dinitrobenzene radical anion: A multiconfigurational quantum chemical study

The structure of 1,3-dinitrobenzene radical anion in the doublet ground and lowest excited states was studied by ab initio multiconfiguration CASSCF methods. The results of calculations suggest the existence of one symmetrical and two asymmetrical structures of the radical anion. The energies of these structures were estimated. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2645–2647, December, 2005.     

Predictive abilities of scaled quantum-mechanical molecular force fields: application to 2-methylbuta-1,3-diene (isoprene)

The ab initio-based, scaled quantum-mechanical molecular force field (SQM-FF) analysis of the vibrational spectra of the s-trans and s-gauche conformers of 2-methylbuta-1,3-diene (isoprene), reported previously at the HF/6-31G//HF/6-31G computational level [Bock, et al. J Mol Struct 160: 337, 1987], has been updated in this article using a more complete set of experimental data on the s-gauche conformer along with revised results for the s-trans conformer obtained in the gas phase, in a low-temperature matrix, and in neat crystals. Geometrical parameters and the calculated wavenumbers derived from the SQM-FF at the MP2(FC)/aug-cc-pVDZ//MP2(FC)/aug-cc-pVDZ level are compared to experiment. The analyses performed are consistent with the presence of a twisted high-energy s-gauche conformer of isoprene.     

Production of 1,3-Butadiene From C4 Raffinate-3 Through Oxidative Dehydrogenation of n-Butene Over Bismuth Molybdate Catalysts

Recent progress on the bismuth molybdate catalysts for oxidative dehydrogenation of n-butene to 1,3-butadiene was reported in this review. A number of bismuth molybdate catalysts, including pure bismuth molybdates (α-Bi₂Mo₃O₁₂, β-Bi₂Mo₂O₉, and γ-Bi₂MoO₆) and multicomponent bismuth molybdates, were prepared by a co-precipitation method for use in the production of 1,3-butadiene from C₄ raffinate-3 through oxidative dehydrogenation of n-butene. It was observed that multicomponent bismuth molybdate catalyst was more efficient than pure bismuth molybdate catalyst in the oxidative dehydrogenation of n-butene. Various experimental measurements such as temperature-programmed reoxidation, X-ray photoelectron spectroscopy, and O₂-temperature-programmed desorption analyses were carried out to elucidate the different catalytic activity of bismuth molybdate catalysts. It was revealed that a bismuth molybdate catalyst with a higher oxygen mobility showed a better catalytic performance in terms of conversion of n-butene and yield for 1,3-butadiene. We have successfully demonstrated from experimental findings that oxygen mobility of bismuth molybdate catalyst played a key role in determining the catalytic performance in the oxidative dehydrogenation of n-butene to 1,3-butadiene.     

Predictive abilities of scaled quantum mechanical molecular force fields: application to 2,3-dimethylbuta-1,3-diene

In connection with the appearance of new experimental vibrational data on the high-energy rotational isomer of 2,3-dimethylbuta-1,3-diene (I) in a low-temperature matrix and in neat crystals, the ab initio-based vibrational analysis of this molecule has been re-evaluated. Calculated wavenumbers derived from a scaled quantum-mechanical force field analysis at the MP2(FC)/aug-cc-pVDZ//MP2(FC)/aug-cc-pVDZ computational level are compared with experimental data. Several reassignments of the fundamental wavenumbers for I have been suggested in the course of the current analysis, and the existence of a high-energy non-planar s-gauche conformer of 2,3-dimethylbuta-1,3-diene has been confirmed.