Niobium oxochlorides in the gas phase: Quantum chemical calculations of the structure and relative stability of isomers

The gas-phase niobium oxochloride anions that result by the interaction between the finely dispersed stereoselective acetylene cyclotrimerization catalyst NbCl₂(C _n H _n ) (n = 10–12) and atmospheric oxygen and moisture have been characterized by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. From the relative intensities of mass spectrometric lines, it has been deduced that, among the various niobium oxochloride species passing into the gas phase under the action of laser radiation, the most abundant monomer ion is NbO₂Cl ₂ ^? , the most abundant dimers are Nb₂O₄Cl ₃ ^? and Nb₂O₃Cl ₅ ^? , the most abundant trimer is Nb₃O₆Cl ₅ ^? , and the most abundant tetramer is Nb₄O₈Cl ₅ ^? . The gas phase also contains low concentrations of fragments corresponding to the pentanuclear anion Nb₃O₁₁Cl ₄ ^? and the hexanuclear anion Nb₆O₁₅Cl ₂ ^? . The geometric parameters and total energy of the stable isomers of the dinuclear and polynuclear niobium oxochloride anions existing in the gas phase has been calculated by quantum chemical methods, and their relative thermodynamic stabilities have been determined for different metal core configurations and different arrangements of oxygen and chlorine ions. The stereochemistry of the niobium oxochlorides is discussed.     

Electronic structure and stability of fullerene C82 isolated-pentagon-rule isomers

All nine isolated-pentagon-rule isomers of fullerene C(82) were investigated by the DFT method with the B3LYP functional at the 6-31G, 6-31G*, and 6-31+G* levels. The distribution of single, double, and delocalized π-bonds in the molecules of these isomers is shown for the first time. The obtained results are fully supported by DFT quantum-chemical calculations of electronic and geometrical structures of these isomers. The molecules of isomers 7 (C(3v)), 8 (C(3v)), and 9 (C(2v)) contain some radical substructures (such as the phenalenyl-radical substructure), which indicates that they are unstable and cannot be obtained as empty molecules. Thus, there is a possibility of obtaining them only as endohedral metallofullerenes or exohedral derivatives. Isomers 1 (C(2)), 2 (C(s)), 4 (C(s)), 5 (C(2)), and 6 (C(s)) with closed electronic shell are supposed to be stable, resembling isomer 3 (C(2)), which has just been extracted experimentally as an empty fullerene. We assume they can be produced as empty molecules.     

MRD-CI calculations of proton affinity within the ab initio method for approximation of the frozen molecular fragment

The method of approximation of the frozen molecular fragment (FMF) we derived has been applied to calculations of proton affinities. Results are in good agreement with experimental data and extended basis set calculations.     

Electronic and geometric structure of isomers of nitric acid. DFT quantum chemical calculations

Based on the B3LYP/6-311++G(3df,3pd) density functional method, quantum chemical calculations of the electronic structure, geometry, and thermodynamic parameters of eight isomers of nitric acid (three known isomers in the form of peroxynitrous acid ONOOH and five new isomers in the form of oxo-conformation OON(H)O) are presented in the work. The molecular structure of each isomer is characterized by a local minimum on the potential energy hypersurface of the HNO₃ molecular system and corresponds to one of its stationary states. A theoretical study of the reactivity of nitric acid oxo-isomers characterized for the first time can provide adequate explanation for experiments on the autocatalytic use of nitric acid vapors in binding molecular nitrogen. The results obtained can be a direction for developing principally new methods to bind atmospheric nitrogen and activate methane, which are fundamental problems in chemical science and technology.     

Quantum-chemical study of the structure and stability of pseudohalogens: OCN-NCO and its isomers

The equilibrium geometries, stability, and isomerisation of pseudohalogen isomers, C(2)N(2)O(2), have been investigated by DFT calculations at the B3LYP level and by ab initio calculations at the CCSD(T) level of theory using the 6-311+G(2d) and cc-pVTZ basis sets, as well as at the CBS-QB3 level. Minimum energy structures and their interconnecting transition states, as well as transition states for bond dissociations have been calculated, and possible isomerisation and decomposition pathways are suggested. Calculations have predicted that four isomers, OCNNCO, ONCCNO, ONCOCN, and ONCNCO are kinetically stable toward unimolecular isomerisation or dissociation at room temperature with the lowest kinetic energy barrier of 209, 232, 159, and 95 kJ mol(-1), respectively (CCSD(T)//B3LYP), and other isomers, like NCONCO, CNONCO, and CNOCNO are unstable. Calculations have also predicted that valence formulations like NCOOCN, CNOOCN, and CNOONC do not represent existing molecules. The gas-phase generation of OCNNCO has been attempted by thermolysing Me(3)SiON(Me(3)SiO)CC(OSiMe(3))NOSiMe(3), synthesised by a novel method from oxalyl chloride and N,O-bis(trimethylsilyl)hydroxylamine; the thermolysis, however, have not produced OCNNCO, but trimethylsilylisocyanate and hexamethyldisiloxane.     

Ab-initio electrostatic molecular potential contour maps for initiation step and Ab-Initio MRD-CI calculations for propagation step of cationic polymerization of oxetanes

The initiation step in the cationic polymerization of cyclic ethers is influenced by basicity and ring strain. We carried out ab-initio MODPOT/VRDDO/MERGE calculations on a variety of substituted oxetanes and generated electrostatic molecular potential contour (EMPC) maps in three-dimensions around the molecules. The size of the negative EMPC map region around the oxygen enabled us to predict the propensity to polymerize prior to the syntheses of the actual monomers themselves. We carried out ab-initio MODPOT/VRDDO/MERGE MRD-CI calculations for the propagation step of oxetane reacting with protonated oxetanes to cause ring opening of protonated oxetane. Similar MRD-CI calculations on variously substituted oxetanes will shed insight into relative copolymerization preferences.     

Ab initio calculations of structure and stability of small boron nitride clusters

Clusters of boron nitride B_xN_x (x = 1–4, 12, 15, 30) were investigated by the Hartree-Fock and density functional methods using the 6-31G* basis. It was found that linear, cyclic, and shell structures are stable against minor deformations of the B_xN_x cluster. Inclusion of electron correlation in calculation markedly changes the electron density distribution and the structure of the clusters.     

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.     

Identification of C5Hx isomers in fuel-rich flames by photoionization mass spectrometry and electronic structure calculations

The isomeric composition of C(5)H(x) (x = 2-6, 8) flame species is analyzed for rich flames fueled by allene, propyne, cyclopentene, or benzene. Different isomers are identified by their known ionization energies and/or by comparison of the observed photoionization efficiencies with theoretical simulations based on calculated ionization energies and Franck-Condon factors. The experiments combine flame-sampling molecular-beam mass spectrometry with photoionization by tunable vacuum-UV synchrotron radiation. The theoretical simulations employ the rovibrational properties obtained with B3LYP/6-311++G(d,p) density functional theory and electronic energies obtained from QCISD(T) electronic structure calculations extrapolated to the complete basis set limit. For C(5)H(3), the comparison reveals the presence of both the H(2)CCCCCH (i-C(5)H(3)) and the HCCCHCCH (n-C(5)H(3)) isomer. The simulations also suggest a modest amount of cyclo-CCHCHCCH-, which is consistent with a minor signal for C(5)H(2) that is apparently due to cyclo-CCHCCCH-. For C(5)H(4), contributions from the CH(2)CCCCH(2) (1,2,3,4-pentatetraene), CH(2)CCHCCH, and CH(3)CCCCH (1,3-pentadiyne) isomers are evident, as is some contribution from CHCCH(2)CCH (1,4-pentadiyne) in the cyclopentene and benzene flames. Signal at m/z = 65 originates mainly from the cyclopentadienyl radical. For C(5)H(6), contributions from cyclopentadiene, CH(3)CCCHCH(2), CH(3)CHCHCCH, and CH(2)CHCH(2)CCH are observed. No signal is observed for C(5)H(7) species. Cyclopentene, CH(2)CHCHCHCH(3) (1,3-pentadiene), CH(3)CCCH(2)CH(3) (2-pentyne), and CH(2)CHCH(2)CHCH(2) (1,4-pentadiene) contribute to the signal at m/z = 68. Newly derived ionization energies for i- and n-C(5)H(3) (8.20 +/- 0.05 and 8.31 +/- 0.05 eV, respectively), CH(2)CCHCCH (9.22 +/- 0.05 eV), and CH(2)CHCH(2)CCH (9.95 +/- 0.05 eV) are within the error bars of the QCISD(T) calculations. The combustion chemistry of the observed C(5)H(x) intermediates and the impact on flame chemistry models are discussed.     

Molecular orbital calculations on the ethylene episulfide molecule and its isomers

Systematic non-empirical and semi-empirical molecular orbital studies have been performed on the sulfur atom + ethylene system and its reaction products thiirane and vinylmercaptan. The results are in general agreement with earlier qualitative and semiquantitative rationalizations of the reaction but also bring to light a number of novel features.     

Protein stability and structure in HIC: hydrogen exchange experiments and COREX calculations

Hydrogen exchange mass spectrometry (HXMS) coupled to proteolytic digestion has been used to probe the conformation of bovine β-lactoglobulin (BLG), bovine α-lactalbumin (BLA), and human serum albumin (HSA) in solution and while adsorbed to the hydrophobic interaction chromatography media Phenyl Sepharose 6FF. All three proteins show evidence of EX1 exchange kinetics, indicating a loss of stability on the surface. HX protection patterns for all three proteins also indicate that the unfolded form is only partially solvent exposed. The hydrogen-deuterium exchange patterns of BLG and BLA on the surface suggest a structure that resembles each protein's respective solution phase molten globule state. The low stability of Domain II of HSA observed on Phenyl Sepharose 6FF also suggests a link to solution stability because Domain II is frequently cited as the least stable domain in solution unfolding pathways. COREX, an algorithm used to compute protein folding stabilities, correctly predicts solution hydrogen-deuterium exchange patterns for BLG and offers insight into its adsorbed phase stabilities but is unreliable for BLA predictions. The results of this work demonstrate a link between solution-phase local stability patterns and the nature of partially unfolded states that proteins can adopt on HIC surfaces.     

Wavelets for electronic structure calculations

Molecular electronic structure calculations have a multi‐scale character through the presence of a set of singularities corresponding to atomic nuclei, and thus there exists a potential to improve the efficiency of these calculations using fast wavelet transform techniques. We report on the development of a one dimensional prototype benchmark problem of sufficient complexity to capture the features of 3‐D problems that are being solved today in quantum electronics calculations. Theoretical estimates of decay across scales and spatial distribution of wavelet coefficients for the solutions of the 1‐D and 3‐D problems are derived and verified experimentally. Equivalence in a multi‐resolution context of the solutions of the 1‐D prototype and the 3‐D problem is established. This revised version was published online in July 2006 with corrections to the Cover Date.     

Conformational analysis of the four 3-methyl-isopropylphenol isomers (thymols) by molecular orbital calculations and X-ray crystal structure determinations

PCILO calculations have been used in a conformational investigation of 3-methyl-x-isopropylphenols (thymol isomers), including a study of the barrier to internal rotation of substituents. The results of the calculations are in good agreement with those available from experimental crystal structure determinations, except for 3-methyl-6-isopropylphenol. For the latter the calculated most stable conformer cannot form a crystal with hexamers bonded by H bonds, as is determined by crystallography. The heights of the barriers to internal rotation of the substituents are compared with the available experimental data and discussed in terms of steric hindrance.     

Band structure calculations for ethylene and urea

The SCF perturbation treatment for molecular crystals proposed by Bacon and Santry has been extended to the calculation of band structures. Band structure calculations are reported for a dispersive crystal, ethylene, and for a hydrogen bonded crystal, urea. It is concluded that non-dispersive forces make a significant contribution to the binding energy and crystal spectra for the ethylene crystal.     

Semiempirical atomistic calculations of kink isomers in the isotactic polystyrene chain

Summary In this paper conformational energy calculations of ideal- and defective structures as well as activation energy calculations have been carried out on sufficiently long isotactic polystyrene chains. The accuracy of the used set of semiempirical potentials, formerly fitted to polyethylene, was shown by calculations on the benzene ideal crystal. Six stable ideal conformations have been found, with tt- and tg- sequences having lowest energies. Starting with these conformations several kink isomers with low defect energies, as well as phenyl-group rotations, have been investigated. The rotational potential of a C-C-bond in the 3/1-helix parallel to the helix axis has been calculated. Using this results, the interpretation fo ultrasonic relaxation in polystyrene solutions byHässler and Bauer could be supported.

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Zusammenfassung In dieser Arbeit wurden Ideal- und Defektstrukturen, sowie Aktivierungsenergien in hinreichend langen isotaktischen Polystyrol-Ketten berechnet. Es konnte die Anwendbarkeit eines für Polyäthylen entwickelten semiempirischen Potentialsatzes durch Berechnung der Gitterkonstanten und Kohäsionsenergie des Benzol-Idealkristalls gezeigt werden. Die Rechnungen ergeben 6 stabile Idealstrukturen. Die niedrigsten Energien haben tt- und tg- Sequenzen.Ausgehend von diesen Konformationen wurden mehrere Kinkdefekte niedriger Defektenergie, sowie Phenyl-Ring-Drehungen untersucht. Für die 3/1 Helix wurde das Rotationspotential einer achsenparallelen C-C-Bindung berechnet. Damit konnte die vonHäßler undBauer gegebene Deutung der Ultraschallrelaxation in Polystyrol-Lösungen bestätigt werden.

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With 9 figures and 4 tables     

Structure and stability of (CuNO) isomers

Quantum-mechanical calculations have been performed on various isomers of the (CuNO)⁺ system. A ²Π ground state is found for the linear CuNO⁺ and CuON⁺ isomers and a ²A′ state for the bent CuNO⁺ and CuON⁺ isomers. Energy calculations indicate that the linear CuNO⁺ structure is the most stable, the bent CuNO⁺ and CuON⁺ and the linear CuON⁺ structures are at 0.86 eV, 0.99 eV and 1.04 eV above this respectively. In the CuNO⁺ → CuON⁺ interconversion between the linear isomers, three transition states are involved, whereas the bent CuNO⁺ isomer is found to be an intermediate species. The isomerization barriers, dissociation energies, equilibrium geometries and vibration frequencies are given for all isomers in their ground and first excited states.