The equilibrium C-H bond length

The equilibrium C-H bond length has been determined up to now for about 40 polyatomic molecules. These data are used to demonstrate the existence of quantitative correlations betweenr _e(C-H), isolated C-H bond stretching frequency and average distancer _g. It is also shown that ab initio calculations are often reliable to calculate the absolute value ofr _e(C-H), if an empirical correction is made. Some other correlations are also discussed. Finally, accurater _e(C-H) values are predicted for simple molecules.     

Conformation dependence of pKa’s of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins

Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 proteins, are perspective fluorescent markers for use in multicolor imaging and resonance energy-transfer applications. We report the results of quantum based calculations of the solution pK_a values for selected protonation sites of the denatured asFP595 and zFP538 chromophores in the trans- and cis-conformations in order to add in the interpretation of photo-physical properties of these proteins. The pK_a values were determined from the theromodynamic cycle based on B3LYP/6-311++G(2df, 2p) calculations of the gas phase free energies of the molecules and the B3LYP/6-311++G(d, p) calculations of solvation energies. The results show that the pK_a’s of the protonation sites of the chromophore from asFP595 noticeably depend on the isomer conformation (cis- or trans-), while those of zFP538 are much less sensitive to isomerization.     

Electrosynthesis of N-Arylazoles by Electrolyzing a Mixture of Azole and 1,4-Dimethoxybenzene in a Diaphragmless Cell

An analysis is performed and data are compared on the electrosynthesis of N-arylazoles and regularities of this process in conditions of a diaphragmless galvanostatic electrolysis (Pt, MeCN, Bu₄NClO₄) of a mixture of 1,4-dimethoxybenzene (DMB) with azoles (pyrazole, triazole, their derivatives, tetrazole). Electrolysis of an azole/DMB mixture leads to the formation of products of an ortho-substitution—1,4-dimethoxy-2-(azolyl-1)benzenes—and, simultaneously, hydrolytically unstable products of an ipso-bis-attachment—1,4-dimethoxy-1,4-di-(azolyl-1)cyclohexa-2,5-dienes. The overall yield of these compounds increases upon adding a base (collidine) or an acid (AcOH) into the initial mixture, and the basicity of initial azoles substantially affects the electrosynthesis results. New notions on the nature of nucleophilic species interacting with radical cation of DMB are considered. The species in question are complexes of azoles with one another or with collidine generated at the expense of the hydrogen bond, rather than azolate ions. Furthermore, the cathodic process is largely connected not with the generation of azolate ions (as a result of the reduction of initial azoles) but with the deprotonation of onium compounds (BH⁺)—products of the interaction of azoles or collidine with protons. The mechanism of electrosynthesis of N-arylazoles is discussed. The key stages of the synthesis are the attack of a nucleophile on the ipso- and, possibly, ortho-positions of the benzene ring of radical cation of DMB, as well as the rearrangement of the intermediate cation of 1,4-dimethoxy-1-(azolyl-1)arenonium into the cation of 1-(azolyl-1)-2,5-dimethoxyarenonium, which affects both the yield and ratio of final products of the reaction mixture.     

Kinetic Monte Carlo study of binary diffusion in silicalite

We report a Kinetic Monte Carlo (KMC) study of the diffusion of linear n-hexane (nC6) and 2,2-dimethylbutane (22DMB) mixture in zeolite silicalite. We first investigated the loading dependences of single component self- and corrected diffusivities of nC6 at 300 K. Anisotropic transition rates are implemented to account for the distribution of the molecules within the zeolite framework. Repulsive guest-guest interactions are modeled using the parameter introduced by Reed and Ehrlich (Surf. Sci. 102:588–601, 1981). The results are in good agreement with recent experimental Quasi Elastic Neutron Scattering data of Jobic et al. (J. Phys. Chem. B 110:2195–2201, 2006), although the influence of the adsorption isotherm inflection is not reproduced. The binary diffusion study of nC6/22DMB mixtures was performed by implementing the nC6 transition rates used for the single component study while 22DMB molecules propagate via intersection-intersection hops. This KMC model allows for different saturation capacities and accounts for interactions between molecules by introducing f _ij parameters. Results show the large impact of guest-guest interactions between nC6 and 22DMB on both self- and corrected diffusivities of the two components. Molecule-size effects are found to be predominant near 22DMB saturation capacity. Acceleration/deceleration effects already described in the literature are confirmed.     

Theoretical study on H2 elimination pathways of silylenoid H2SiLiF with CH4, NH3, H2O, HF, SiH4, PH3, H2S, and HCl

Ab initio molecular orbital calculations have been performed to explore the reaction potential energy surfaces of silylenoid H₂SiLiF with XH _n hydrides, where XH _n = CH₄, NH₃, H₂O, HF, SiH₄, PH₃, H₂S, and HCl. We have identified a previously unreported reaction pathway on each reaction surface, H₂SiLiF + H-XH _{n − 1} → H _n XSiLiF + H₂, which involves H₂ elimination following the initial formation of an association complex via a four-membered ring transition state to form the substituted three-membered ring silylenoid H _n XSiLiF and a H₂ molecule. This theoretical calculations suggest that (i) for H₂ eliminations there is a very clear trend toward lower activation barriers and more exothermic interactions on going from left to right along a given row in periodic table, and (ii) for the second-row hydrides, the H₂ elimination reactions are less exothermic than for the first-row hydrides and the reaction barriers are lower for X–S and Cl. Compared to the insertions of H₂SiLiF into XH _n , the H₂ elimination pathways should be unfavorable with higher barrier and lower exothermic.     

Ramanspektroskopische Untersuchungen an Seleninyldibromid

TheRaman spectra of solid and molten SeOBr₂ as well as of a CCl₄ solution have been recorded for the first time. The spectra indicate associated molecules in the molten state and relatively strong intermolecular interactions in the solid. Monomeric pyramidal molecules are present in the CCl₄ solution. An assignment will be discussed in analogy to SeOCl₂.

     

Ab initio studies on several species of the formula X3YO and X3YOH

Ab initio molecular orbital calculations using both minimal and extended basis sets have been applied to two isoelectronic sets of molecules. One set corresponds to the 18 electron species H₃NO, H₃CO^– and H₃COH while the second set contains the 42 electron fluorinated molecules F₃NO, F₃CO^– and F₃COH. The geometries of these molecules have been optimized, using both the minimal STO-3G and the extended 4-31G basis sets. These comparative calculations reveal that the 4-31G basis produced structural parameters in much better agreement with experiment. The effect of includingd-orbitals in the basis set was also investigated. For the fluorinated oxides it has been found that the optimized 4-31G structures were only slightly altered by the addition ofd-orbitals. For H₃NO, on the other hand, the inclusion ofd-orbitals considerably shortens the N-O bond distance. Both H₃NO and CF₃OH, which are unknown experimentally, are theoretically predicted to be capable of existence. The electronic structures of these molecules have also been examined using electronic partitioning according to the Mulliken scheme.     

Radial dependence of exterior electron distributions of molecular orbitals

A molecular surface is introduced to divide interior electron densities from exterior electron densities (EED). The radial distribution of EED (RADEED) is defined for each molecular orbital as a function of the distance from the molecular surface. Logarithmic plots of RADEED for NH₃ using various basis sets in ab initio MO calculations revealed some important features: (i) the Hartree-Fock limit for the orbital function tail may be suggested and thus qualities of basis sets can be discussed, and (ii) the slope of the curve shows the decay rate of the orbital which can be compared with the curve derived from the theoretical behavior of the long-range asymptotic form involving either the lowest ionization potential or the orbital energy of the highest occupied orbital.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

Basis-independent potential energy curves for the neutral diatomics of Li,Na and K evaluated by means of Hartree-Fock and different density functional potentials

Summary The solution of the Schrödinger equation for diatomic molecules when the finite element method is used gives the possibility to evaluate highly accurate basis-independent potential energy curves. In this work such types of numerically accurate potential energy curves on the HF level have been evaluated for Li₂, Na₂ and K₂ and could be used as benchmarks in the optimization of basis sets. A comparison between recent LCAO HF calculations in which extended basis sets are used and the accurate values determined in this work show that there is a difference in total energy of 4×10^–5 and 10^–3 a.u. for Li, Li₂, and Na, Na₂, respectively. Evaluated dissociation energies are, however, due to the cancellation of numerical errors in much better agreement. Further, it is found that different exchange correlation potentials for the heavier molecules such as those given by von Barth-Hedin and Vosko, Wilk and Nusair reproduce experimental properties such as dissociation energies, vibrational frequencies almost as well as those achieved with advanced CI methods. TheX potential gives accurate bond lengths for Na₂ and K₂, whereas the dissociation energies are too small.     

Structures,stabilities and adiabatic ionization and electron affinity energies of small sulfur clustersS 3-S 5

Summary The vertical and adiabatic ionization and electron affinity energies are calculated for the isomers ofS ₃,S ₄ andS ₅. For the existing isomers the structures of several ionic states were optimized using an RHF analytical gradient approach with a subsequent frequency analysis. The many-body effects were taken into account by Green function (for vertical energies) and CI (for vertical and adiabatic energies) techniques. The structural relaxation upon ionization or attachment of an electron is found to be of primary importance to account for the sequence of cationic states or the existence of a positive electron affinity.Dedicated to Professor W. Kutzelnigg on the occasion of his 60th birthday.     

Conformational Stability of Propenoyl Bromide from Temperature-Dependent Infrared Spectra of Krypton Solutions,Ab Initio Calculations,and r 0 Structural Parameters of the Propenoyl Halides (F,Cl, Br)

Variable temperature (–100 to –150°C) studies of the infrared spectra (3500–400 cm^–1) of propenoyl bromide, CH₂=CHCBrO, dissolved in liquid krypton, have been carried out. Utilizing six different conformer pairs, an enthalpy difference of 204 ± 20 cm^–1 (2.44 ± 0.24 kJ/mol) was obtained, with the anti conformer (carbonyl bond trans to C=C bond) the more stable form. At ambient temperature, there is approximately 28 ± 2% of the syn conformer present. The anti conformer also remains in the infrared and Raman spectra of the polycrystalline solid. The optimal geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios, and vibrational frequencies, are reported for both conformers from MP2/6-31G(d) ab initio calculations. The potential function governing the conformational interchange has been obtained from the MP2/6-31G(d) ab initio calculations. The conformational stabilities were calculated from a variety of basis sets and at the highest level of calculations, MP2/6-311 + (2df,2pd), the anti conformer is predicted to be more stable by 178 cm^–1, which is in excellent agreement with the experimental results. The r ₀ adjusted structural parameters have been obtained for propenoyl fluoride and chloride from a combination of the previously reported microwave rotational constants and ab initio predicted parameters. Several of the parameters for the chloride are significantly different than those proposed from an electron diffraction investigation. The results of these spectroscopic, structural, and theoretical studies are discussed and compared to the corresponding results for some similar molecules.     

Vibrational spectra,conformational stability,barriers to internal rotation,r0 structural parameters and ab initio calculations of fluoromethyl methyl ether

The far-infrared spectrum of gaseous fluoromethyl methyl ether, FCH₂OCH₃, along with three of the deuterium isotopes, has been recorded at a resolution of 0.10 cm^–1 in the 350 to 50 cm^–1 region. The fundamental asymmetric torsional and methyl torsional modes are extensively mixed and have been observed at 182 and 132 cm^–1, respectively, for the stablegauche conformer with the lower frequency band having several excited states falling to lower frequency. An estimate is given for the potential function governing the asymmetric rotation. On the basis of a one-dimensional model the barrier to internal rotation of the methyl moiety is determined to be 527±9 cm^–1 (1.51±0.03 kcal/mol). A complete assignment of the vibrational fundamentals for all four isotopic species observed from the infrared (3500 to 50 cm^–1) spectra of the gas and solid and from the Raman (3200 to 10 cm^–1) spectra of the gas, liquid, and solid is proposed. No evidence could be found in any of the spectra for the high-energytrans conformer. All of these data are compared to the corresponding quantities obtained from ab initio Hartree-Fock gradient calculations employing the 3-21G and 6-31G* basis sets along with the 6-31G* basis set with electron correlation at the MP2 level. Additionally, completer ₀ geometries have been determined from the previously reported microwave data and carbon-hydrogen distances determined from infrared studies. The heavy-atom structural parameters (distances in Å, angles in degrees) arer(C₁-F) = 1.395 ± 0.005;r(C₁-O) = 1.368 ± 0.007;r(C₂-O) = 1.426 ±0.003; FC₁O = 111.33 ± 0.25; C₁OC₂ = 113.50 ± 0.18 and dih FC₁OC₂ = 69.12 ± 0.26. All of these results are discussed and compared with the corresponding quantities obtained for some similar molecules.     

Thermal dehydration and decomposition of nickel chloride hydrate (NiCl2·xH2O)

The dehydration and decomposition characteristics of an undried and a partly dried sample of NiCl₂·xH₂O have been investigated by isothermal and non-isothermal (TG and DTA) methods in static air as well as flowing nitrogen environment. While the isothermal weight loss method fails to distinguish between different steps of reaction, TG curves upto 800°C reveal as many as five steps in static air and four steps in nitrogen atmosphere. However, both methods indicate that NiCl₂ is stable upto 400°C above which dehydrochlorination takes place in presence of water vapour. The intermediate products of dehydration and decomposition at different temperatures have been characterized by chemical analysis, X-ray diffraction, infrared and diffuse reflectance spectroscopy. All these methods reveal the presence of water in samples calcined at even 400°–600°C. Thermodynamic functions for different steps of dehydration have been calculated and discussed in the light of the possible structural changes occurring in the partially dehydrated products.The authors wish to express their sincere thanks to Mr. D. N. Dey, Head, Pyrometallurgy Division for his keen interest and constant support during the course of investigation. Thanks are also due to Director, Regional Research Laboratory, Bhubaneswar for his kind permission to publish this paper. One of the authors (S. K. M.) is thankful to the Council of Scientific and Industrial Research, New Delhi for awarding a Junior Research Fellowship.     

H2分子在LaFeO3表面吸附的第一性原理研究

基于密度泛函理论的第一性原理方法,通过计算表面能确定LaFeO₃(010)表面为最稳定的吸附表面,研究了H₂分子在LaFeO₃(010)表面的吸附性质。LaFeO₃(010)表面存在LaO和FeO₂两种终止表面,但吸附主要发生在FeO₂终止表面,由于LaFeO₃(010)表面弛豫的影响,使得凹凸不平的表面层增加了表面原子与H原子的接触面积,表面晶胞的纵向体积增加约2.5%,有利于H原子向晶体内扩散。研究发现,H₂分子在LaFeO₃(010)表面主要存在3种化学吸附方式:第一种吸附发生在O-O桥位,2个H原子分别吸附在2个O原子上,形成2个-OH基,这是最佳吸附位置,此时H原子与表面O原子的作用主要是H1s与O2p轨道杂化作用的结果,H-O之间为典型的共价键。H₂分子的解离能垒为1.542 eV,说明表面需要一定的热条件,H₂分子才会发生解离吸附;第二种吸附发生在Fe-O桥位,1个H原子吸附在O原子上形成1个-OH基,另一个H原子吸附在Fe原子上形成金属键;第三种吸附发生在O顶位,2个H原子吸附在同一个O原子上,形成H₂O分子,此时H₂O分子与表面形成物理吸附,H₂O分子逃离表面后容易形成氧空位。此外,H₂分子在LaFeO₃(010)表面还可以发生物理吸附。     

The electronic structure of small lithium clusters

Ab initio molecular orbital calculations using the STO-6G and STO6-21G basis sets have been performed for the cluster series Li _n ⁺ , Li _n , and Li _n ^– (wheren=2–7). Thirty-two optimized structures are discussed and reported, many of which (especially for the anionic structures) have not yet been considered. The calculations suggest that for all three species the optimum geometries are planar. Of the two levels of theories that were investigated, STO-6G//STO-6G and STO6-21G//STO-6G, the latter hybrid theory was found to be less reliable. In particular, for the anionic structures these calculations should provide a platform from which more sophisticated, i.e., configuration interaction, geometry optimization can be performed.     

Benchmarking and validating algorithms that estimate p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of drugs based on their molecular structures

The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK _a predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK _a values of organic drug-like compounds. Outlier predicted pK _a values correspond to molecules that are poorly characterized by the pK _a prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F _exp, R ², , MEP, AIC, and s(e) in pK _a units) of the results obtained when four selected pK _a prediction algorithms were applied to three datasets were examined. The highest values of F _exp, R ², , the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK _a algorithm for pK _a prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.     

Study of influences of various excitation classes onab initio calculated isotropic hyperfine coupling constants

Summary Reliable prediction of the isotropic hyperfine coupling constantA _iso is still a difficult task forab initio calculations. Strong dependence on the method employed for its calculation has been found. Within a CI ansatzA _iso is considerably affected by the excitation classes taken into account within the CI calculation. In the present work the influence of various excitation classes onA _iso is examined. Calculations including all single, double, triple and a large part of the quadruple excitations are performed and the individual effects of the excitation classes are studied. It is found that the surprisingly good agreement found for S-CI treatments is due to large error cancellations. The importance of higher than double excitations arises from their indirect influence on the single excitations.     

A theoretical study of explosive sensitizers

Quantum chemical calculations at the HF/6-31G^* and B3LYP/6-31G^* levels have been performed on five explosive sensitizers, ethyl nitrate (EN), n-propyl nitrate (NPN), isopropyl nitrate (IPN), 2-ethylhexyl nitrate (EHN) and tetraethylene glycol dinitrate (TEGDN). Theoretical study has made a detailed molecular-level investigation of the title compounds. Based on the Mulliken populations and bond lengths, the fission of the O₂–N₃ can be acceptable reasonably. Charge distribution analysis indicates that the five nitrates produce NO₂ gas during the dissociation of the O₂–N₃ weak bond. We also order the relative thermal stability of five nitrates on the basis of frontier orbital energy (E _HOMO, E _LUMO) and energy gap (ΔE = E _HOMO − E _LUMO).     

Crystal structure and ab initio calculations of a cyano-carbamimidic acid ethyl ester

The structure of one tautomer (amine form) of cyano-carbamimidic acid ethyl ester or (amino-ethoxy-methylidene)aminoformonitrile (CAS: 13947-84-7) was determined by single crystal X-ray diffraction. Ab initio quantum chemical calculations at the B3LYP, MP2 and G3 levels were performed to investigate the stability and the formation of the different tautomers and conformers. The calculations indicate that the amine form is the more stable tautomer, showing a high degree of electron conjugation. The most stable amine conformer located by the calculations corresponds to the crystallized structure. On the contrary, in the less stable imine form, the conjugation is separated by a N2–C2 single bond.     

Mn-Mo-W-O_x脱硝催化剂活性组分的配伍优化

采用等体积浸渍法制备系列Mn-Mo-W-O_x/堇青石和Mn-Mo-W-O_x/TiO_2催化剂,用于选择性催化还原NO.通过Mn、Mo、W 3种元素不同配比对催化剂配伍进行优化,确立Mn-Mo-W-O_x最佳配比.采用XRD、N_2-BET、PyIR、SEM以及XPS等表征分析催化剂的固相结构、比表面积、酸量、表面形貌和表面元素.结果表明:当Mn/Mo/W元素摩尔比为10∶0.5∶1,载体为TiO_2时,催化剂的催化性能最优.适量Mo掺入Mn-W-O_x催化剂可以增大其比表面积,提高催化剂表面L酸酸量以及Mn~(4+)离子浓度,从而有效提高了催化剂高温活性.载体替换为TiO_2时催化剂的比表面积和酸量明显提高,从而增强了催化剂的脱硝性能.