Conformation analysis of formic acid. Extended basis set SCF and CEPA calculations

SCF computations using extended DZP and TZP basis sets have been performed to determine the structure of syn and anti formic acid and the transition state for rotation of the OH group. Effects of electron correlation were accounted for by means of CEPA calculations which predict the anti conformer to be 5 kcal/mol and the transition state 14.7 kcal/mol higher in energy than the syn conformer, with probable error estimates of 0.7 kcal/mol and 2 kcal/mol respectively.     

Pi and sigma-phenylethynyl radicals and their isomers o-, m-, and p-ethynylphenyl: structures, energetics, and electron affinities

Molecular structures, energetics, vibrational frequencies, and electron affinities are predicted for the phenylethynyl radical and its isomers. Electron affinities are computed using density functional theory, -namely, the BHLYP, BLYP, B3LYP, BP86, BPW91, and B3PW91 functionals-, employing the double-zeta plus polarization DZP++ basis set; this level of theory is known to perform well for the computation of electron affinities. Furthermore, ab initio computations employing perturbation theory, coupled cluster with single and double excitations [CCSD], and the inclusion of perturbative triples [CCSD(T)] are performed to determine the relative energies of the isomers. These higher level computations are performed with the correlation consistent family of basis sets cc-pVXZ (X = D, T, Q, 5). Three electronic states are probed for the phenylethynyl radical. In C2v symmetry, the out-of-plane (2B1) radical is predicted to lie about 10 kcal/mol below the in-plane (2B2) radical by DFT methods, which becomes 9.4 kcal/mol with the consideration of the CCSD(T) method. The energy difference between the lowest pi and sigma electronic states of the phenylethynyl radical is also about 10 kcal/mol according to DFT; however, CCSD(T) with the cc-pVQZ basis set shows this energy separation to be just 1.8 kcal/mol. The theoretical electron affinities of the phenylethynyl radical are predicted to be 3.00 eV (B3LYP/DZP++) and 3.03 eV (CCSD(T)/DZP++//MP2/DZP++). The adiabatic electron affinities (EAad) of the three isomers of phenylethynyl, that is, the ortho-, meta-, and para-ethynylphenyl, are predicted to be 1.45, 1.40, and 1.43 eV, respectively. Hence, the phenylethynyl radical binds an electron far more effectively than the three other radicals studied. Thermochemical predictions, such as the bond dissociation energies of the aromatic and ethynyl C-H bonds and the proton affinities of the phenylethynyl and ethynylphenyl anions, are also reported.     

AB initio and Dft investigations of Al, Ga, and In tricyanides and triisocyanides

Structural parameters, standard entropies, and vibrational spectra of cyanides and isocyanides of trivalent AI, Ga, and In were obtained for the first time by ab initio and B3LYP density functional methods. The isocyanide form is found to be preferable for Al; for Ga and In, the cyanide form is more stable. The considerable discrepancy between the results obtained by the SCF and B3LYP methods shows that it is important to take electron correlation energy into account; however, a comparison between the DZP and LANL2DZP basis sets demonstrates that basis sets with the effective core potential are not adequate for describing molecular tricyanides of group IIIa elements. This situation is probably characteristic for molecular systems with a cyano group in the molecule. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 42-48, January-February, 2000.     

Perfluoroadamantane and its negative ion

As a general rule, saturated hydrocarbons are unable to bind an electron, i.e., their electron affinities are negative, but the corresponding perfluorinated molecules can have significant electron affinities, especially in the case of branched and ring systems. Four different density functional theory (DFT) methods in conjunction with double-zeta plus polarization function augmented diffuse function basis sets (DZP++) have been employed to study the equilibrium geometries, electron affinities, and vibrational frequencies of the adamantane (C10H16) and perfluoroadamantane (C10F16) molecules. Three types of neutral-anion separations reported are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The adiabatic electron affinity predicted at the DZP++ B3LYP level of theory for adamantane is, as expected, negative (-0.58 eV), while that for perfluoroadamantane is distinctly positive, namely, 1.06 eV (or 1.31 eV after correction for zero-point vibrational energies).     

Structures, electron affinities, and harmonic vibrational frequencies of C6H5X/C6H5X- (X = N, S, NH, PH, CH2, and SiH2)

The molecular structures and electron affinities of the C6H5X/C6H5X- (X = N, S, NH, PH, CH2, and SiH2) species have been determined using seven different density functional or hybrid Hartree-Fock density functional methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. These methods have been carefully calibrated (Chem. Rev. 2002, 102, 231). The geometries are fully optimized with each density functional theory (DFT) method, and discussed. Harmonic vibrational frequencies were found to be within 3.2% of available experimental values for most functionals. Three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). The most reliable adiabatic electron affinities, obtained at the DZP++ BPW91 level of theory, are 1.45 (C6H5N), 2.29 (C6H5S), 1.57 (C6H5NH), 1.51 (C6H5PH), 0.91 (C6H5CH2), and 1.48 eV (C6H5SiH2), respectively. Compared with the experimental values, the average absolute error of the BPW91 method is 0.04 eV. The B3LYP and B3PW91 functionals also gave excellent predictions, with average absolute errors of 0.06 and 0.07 eV, respectively.     

Structures, electron affinities, and harmonic vibrational frequencies of the simplest alkyl peroxyl radicals and their anions

The molecular structures and electron affinities of the R-OO/R-OO(-) (R = CH3, C2H5, n-C3H7, n-C4H9, n-C5H11, i-C3H7, t-C4H9) species have been determined using seven different density functional or hybrid Hartree-Fock density functional methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s-type and p-type functions, denoted DZP++. The geometries are fully optimized with each density functional theory method. Harmonic vibrational frequencies were found to be within 3.1% of available experimental values for most functionals. Two different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity and the vertical detachment energy. The most reliable adiabatic electron affinities obtained at the DZP++ BP86 level of theory are 1.150 (CH3OO), 1.124 (C2H5OO), 1.146 (n-C3H7OO), 1.173 (n-C4H9OO), 1.184 (n-C5H11OO), 1.145 (i-C3H7OO), and 1.114 eV (t-C4H9OO). Compared with the experimental values, the average absolute error of the BPW91 method is 0.05 eV.     

Silicon hydride clusters Si5Hn (n = 3-12) and their anions: structures, thermochemistry, and electron affinities

The molecular structures, electron affinities, and dissociation energies of the Si(5)H(n)/Si(5)H(n)(-) (n = 3-12) species have been calculated by means of three density functional theory (DFT) methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. The geometries are fully optimized with each DFT method independently. Three different types of the neutral-anion energy separations presented in this work are the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). The first Si-H dissociation energies for neutral Si(5)H(n) and its anion have also been reported.     

A scheme for the economical use of numerical basis sets in calculations with SIESTA

We demonstrate the effectiveness of an economical scheme that uses numerical basis sets in computations with SIESTA. The economical basis sets demonstrated, in which high-level double-zeta basis plus polarization orbitals (DZP) are applied only for atoms of strong electronegativity and metal atoms while a double-zeta basis is applied to the rest of the atoms of small proton-bound carboxylic acid clusters and sodium–organic compounds, predict correct geometric structures very close to those obtained using DZP for all atoms. The use of economical basis sets can save about 30–50% of the CPU time that is used for calculations with large basis sets. This study provides a general guideline for basis set selection in SIESTA computations of large systems.Acknowledgement. The work described in this paper was fully supported by a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (project no. CityU 1033/00P).     

HF and MP2 calculations on CN−, N2, AlF,SiO, PN,SC, ClB,and P2 using correlated molecular wave functions

Contracted basis sets of double zeta valence quality plus polarization functions (DZP) and augmented DZP basis sets, which were recently constructed for the first‐ and second‐row atoms, are applied to study the electronic ground states of the diatomic molecules CN^?, N₂, AlF, SiO, PN, SC, ClB, and P₂. At the Hartree–Fock (HF) and/or Møller–Plesset second‐order (MP2) levels, total and molecular orbital energies, dissociation energies, bond lengths, harmonic vibrational frequencies, and dipole moments are calculated and compared with available experimental data and with the results obtained from correlation consistent polarized valence basis sets of Dunning's group. For N₂, calculations of polarizabilities at the HF and MP2 levels with the sets presented above are also done and compared with results reported in the literature. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Ab initio SCF calculations on low-energy conformers of cyclohexaglycine

Results from ab initio self-consistent field (SCF) calculations with a 3-21G and a double-zeta-plus polarization (DZP) basis set on four low-energy conformations of cyclohexaglycine are reported. In agreement with results from semiempirical and molecular mechanics force field calculations, the lowest-energy conformation found at the DZP level is a conformation forming six C₇ turns. However, the energy difference to the β-turn conformers is significantly smaller at the ab initio DZP level than calculated by the other methods. In contrast to the results obtained with some of the other methods, the present ab initio calculations show that both the double-type-I β turn and the double-type-II β-turn conformer of cyclohexaglycine are stable low-energy structures. © 1995 by John Wiley & Sons, Inc.     

Li~3Al的几何结构和垂直激发态光谱的量子化学研究

在ab initio DZP水平上, 用能量梯度法对Li~3Al的三种几何构型进行了优化, 并对其中两个能量较低的构型用单、双激发组态相互作用(CISD)进行了垂直跃迁能和振子强度计算, 结果表明: Li~3Al(C~2~v)中存在着三个强度较大的跃迁, 分别是从基态跃迁到1^1B~1, 2^1B~1, 5^1A~1态。Li~3Al(D~3~h)中存在着四个强度较大的跃迁, 分别是从基态跃迁到1^1B~2, 2^1A~1, 3^1B~2, 3^1A~1态。这些强度较大的跃迁均为粒子穴跃迁。     

Direct and Selective Production of Propene from Bio‐Ethanol on Sc‐Loaded In2O3 Catalysts

Propene, one of key building blocks for manufacturing plastics and chemicals, could be directly and stably produced from ethanol in good yields. The conversion degree of ethanol to propene reached approximately 60 mol % by using a 3 atom % scandium‐loaded indium oxide catalyst at 823 K in the presence of water and hydrogen. The introduction of Sc prevented the reduction of In₂O₃ to In metal during the reaction, and that of water decreased the coke formation. Both additions resulted in longer lifetimes of the catalysts. The hydrogen addition increased the conversion of acetone to propene. The reaction pathways are also suggested on the basis of the product distributions and the pulse experiments, ethanol→acetaldehyde→acetone→propene, which is quite different from the shape‐selective catalysis on zeolites and the dimerization‐metathesis of ethene on nickel ion‐loaded silica catalysts.     

Theoretical investigations of molecules composed only of fluorine,oxygen and nitrogen: determination of the equilibrium structures of FOOF, (NO)2 and FNNF and the transition state structure for FNNF cis-trans isomerization

The deficiencies of common ab initio methods for the reliable prediction of the equilibrium structures of compounds composed of only the fluorine, oxygen and nitrogen atoms are investigated. Specifically, the importance of using large one-particle basis sets with multiple sets of polarization functions has been studied. Additionally, the need for a set of f basis functions was investigated. Several different single reference electron correlation methods have been tested in order to determine whether it is possible for a single reference based method to be routinely used on such chemical systems. These electron correlation methods include second order Møller-Plesset perturbation theory (MP2), singles and doubles configuration interaction (CISD), the coupled pair functional (CPF) approach and singles and doubles coupled cluster (CCSD) theory. The molecular systems studied include difluoroperoxide (FOOF), the cis form of the NO dimer, cis and trans difluorodiazene (FNNF) and the transition state to interconversion of the cis and trans isomers of FNNF. To the best of our knowledge, this is the first time that the cis-trans isomerization transition state has been reported. At the highest level of theory employed, the equilibrium structures of cis and trans FNNF agree very well with the experimental structures. However, the barrier to interconversion is predicted to be 65 kcal/mole, which is substantially higher than the experimental activation energy of 32 kcal/mole. Potential sources of error are discussed. A new diagnostic method for determining a priori the reliability of single reference based electron correlation methods is suggested and discussed.Contribution CCQC No. 36     

Validated LC–MS/MS method for quantitation of a selective JAK1 inhibitor,filgotinib in rat plasma,and its application to a pharmacokinetic study in rats

Filgotinib is a selective JAK1 (Janus kinase) inhibitor, filed in Japan for the treatment of rheumatoid arthritis. In this paper, we report a validated liquid chromatography coupled with tandem mass spectrometry for the quantification of filgotinib in rat plasma using tofacitinib as an internal standard (IS) as per the Food and Drug Administration regulatory guidelines. Filgotinib and the IS were extracted from rat plasma using ethyl acetate as an extraction solvent and chromatographed using an isocratic mobile phase (0.2% formic acid:acetonitrile; 20:80, v/v) at a flow rate of 0.9 mL/min on a Gemini C₁₈ column. Filgotinib and the IS were eluted at ~1.31 and 0.89 min, respectively. The MS/MS ion transitions monitored were m/z 426.3 → 291.3 and m/z 313.2 → 149.2 for filgotinib and the IS, respectively. The calibration range was 0.78–1924 ng/mL. No matrix effect and carryover were observed. Intra- and inter-day accuracies and precisions were within the acceptance range. Filgotinib was stable for three freeze–thaw cycles: on bench-top up to 6 h, in an autosampler up to 21 h, and at −80 ° C for 1 month. This novel method has been applied to a pharmacokinetic study in rats.     

四氰基乙烯-四甲基乙烯体系光诱导电子转移双势阱的从头算研 究

以两态模型为基础,用从头算方法,在DZP[所有原子带极化函数的Dunning(9s,5p)/(3s,2p)]基组水平上对四氰基乙烯与四甲基乙烯间的电子转移进行理论计算。通过孤立给体和受体的几何构型优化,计算了给体的电离能和受体的电子亲和能。计算表明,在光诱导电荷分离之后的返回电子转移处于高放热的Marcus反转区。通过碰撞配合物的结构优化和电荷分离处理,在线性反应坐标近似下得到四甲基乙烯-四氰基乙烯配合物电荷分离反应的双势阱,进而获得反应热,键重组能,以及跃迁能。     

THE MASS SPECTRA OF PHOSPHONYL COMPOUNDS PART 31. DIMETHYL AND DIETHYL ALKANE- AND SUBSTITUTED-METHANE PHOSPHONATES

Abstract

The electron impact mass spectra of 28 related phosphonates have been determined. Ethyl, iso-propyl and tert-butyl groups which are bound directly to phosphorus, fragment to the corresponding alkenes; similar iso-propyl and tert-butyl groups in the dimethyl esters also fragment to ethylene and propene respectively, i.e. the P-alkyl group rearranges with transfer of the elements of a methyl group to the phosphorus ion. The diethyl alkenephosphonates undergo double hydrogen rearrangements of an ethoxy group to give dihydroxyphosphonium ions. The di- and trihydroxyphosphonium ions have a characteristic fragmentation which involves loss of water. This characteristic has been used as evidence for the rearrangement of a phosphacylium ion to a dihydroxyphosphonium ion. Some other unusual rearrangements involving the combination of the groups bound to phosphorus and oxygen have been observed.     

Accurate prediction for electron affinities of the radicals derived from the halide benzene

The molecular structures and electron affinities of eight radicals derived from the halide benzene by removing a hydrogen atom have been determined using seven hybrid Hartree-Fock/density-functional methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted as DZP++. These methods have been carefully calibrated [J. C. Rienstra-Kiracofe, G. S. Tschumper, H. F. Schaefer, S. Nandi, and G. B. Ellison, Chem. Rev. (Washington, D. C.) 102, 231 (2002)]. The geometries are fully optimized with each density-functional theory method and discussed, respectively. The three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The most reliable adiabatic electron affinities (with zero-point vibrational energy correction), obtained at the DZP++ B3LYP level of theory, are 1.74 eV (o-C6H4F), 1.39 eV (m-C6H4F), 1.34 eV (p-C6H4F), 1.78 eV (o-C6H4Cl), 1.53 eV (m-C6H4Cl), 1.45 eV (p-C6H4Cl), 2.06 eV (o-C6H3F2), and 2.04 eV (p-C6H3F2), respectively. Compared with the experimental values, the average absolute error of the B3LYP method is 0.03 eV. The BLYP, BP86, and BPW91 functionals also gave excellent predictions, with average absolute errors of 0.05, 0.08, and 0.08 eV, respectively.     

Electron affinity of the guanine-cytosine base pair and structural perturbations upon anion formation

The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol).     

Geometry,basis set,and correlation energy dependence of computed protonation energies of imino bases

The nitrogen protonation energies of the imino bases HN?CHR, where R is H, CH₃, NH₂, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree–Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree–Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree–Fock nitrogen protonation energies of the imino bases HN?CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O?CHR.