Calculation and properties of non-orthogonal,strictly local molecular orbitals

A general procedure to calculate non-orthogonal, strictly local molecular orbitals (NOLMOs) expanded using only a subset of the total basis set is presented. The energy of a single determinant wave function is minimised using a Newton-Raphson approach. Total energies and barriers to internal rotation for CH₄, NH₃, H₂O, CH₃CH₃, CH₃NH₂, CH₃OH, NH₂NH₂, NH₂OH and HOOH, and certain properties of the NOLMOs present in these molecules, are investigated using the 4-31G basis set.     

Geometry optimization in ab initio SCF calculations. VII. Proton affinities and ion structures calculated with floating orbital geometry optimization (FOGO)

The FOGO method is used to calculate absolute proton affinities of the molecules H₂, HF, NH₃, H₂O, CH₃OH, C₂H₅OH, H₂O₂, CH₂O, CO, and CH₂CO. Comparison with experimental values demonstrates that the geometrical and energetical data resulting from this type of ab initio calculation are of chemical accuracy. Predictive data for higher energy isomers, such as hydroxymethylene and ethynol are given as possible aid for the identification of these species.     

Generation and High‐Resolution Photoelectron Spectroscopy of Small Organic Radicals in Cold Supersonic Expansions

A general method of generating radicals in cold supersonic expansions in the gas phase is presented. The method relies on excimer laser photolysis of suitable precursor molecules in a thin quartz capillary mounted at the orifice of a pulsed gas nozzle and can easily be combined with vacuum‐UV photoionization mass spectrometry and high‐resolution photoelectron spectroscopy to study the reactivity and the rovibronic energy level structure of neutral radicals and their ions, as well as to determine highly accurate adiabatic ionization energies. The characteristics of the radical source are described in detail, and its performance is illustrated by mass spectrometric and high‐resolution photoelectron spectroscopic investigations of NH₂, CH₂, CH₃, C₂H, C₂H₃, and C₂H₅. The radical source is not only suitable to produce cold samples (rotational temperature of ca. 30 K) of radicals of moderate reactivity, such as NH₂, CH₃, or C₂H₅, but it is also useful to prepare highly reactive radicals (e.g., C₂H) for spectroscopic investigations.     

A reassessment of some restricted Hartree–Fock limit molecular energies and an investigation of the applicability of Ermler and Kern's procedure for their estimation

New estimates of Hartree–Fock limit energies (E_RHF) for selected AH and AH_n hydrides, diatomic and linear polyatomic molecules have been made utilizing E_SCF values recently reported in the literature for HF, N₂, CO, NH₃, and CH₄ which are very close to the respective limits. These new values have been used to investigate the applicability of Ermler and Kern's procedure for estimating E_RHF: i.e., a factor f is first evaluated from data for reference molecules, where f = E_RHF/E_SCF, which is then used with E_SCF values for other molecules to obtain their E_RHF values. f has been evaluated for three groups of reference molecules? HF, H₂O, NH₃, CH₄, N₂, and CO; CH₄, C₂H₂, C₂H₄, and C₂H₆; and C₂H₂, HCN, and N₂? utilizing E_SCF data in the literature for many Gaussian-type orbital (GTO) basis sets together with some new values calculated at the (9,5,1) to (13,8,2) levels. Trends in the variation of f within each group of reference molecules from one basis set to another, and the trends in f from one group of reference molecules to another, are discussed in detail. To minimize the influence of these effects in an E_RHF estimate it is recommended that the f value should be derived from reference molecules which possess a similar combination of structural features, i.e., bonded hydrogen, single, double, or triple bonds, and the number of lone-pair electrons. Further calculations show that an f value based on data for closed-shell molecules is not applicable to open-shell species.     

Quantum-Chemical Study of the Electronic and Steric Structure of Vinyltetrazoles: II. 2-Vinyltetrazoles

The total Mulliken charges on the C and N atoms, populations of the S-trans-(N¹) conformers, and rotation barriers in the molecules of 2-vinyl-5-R-tetrazoles (R = H, CH₃, CH = CH₂, C₆H₅, CH₂Cl, CF₃) were calculated ab initio (HF/6-31G**, MP2/6-31G**). The results were compared with the ¹H and ¹³C NMR data for these compounds.     

Binding energy of gas molecule with two pyrazine molecules as organic linker in metal�Corganic framework: its theoretical evaluation and understanding of determining factors

We explored the interactions of gas molecules such as H₂, CH₄, C₂H₄, C₂H₆, CO₂, and CS₂ sandwiched by two pyrazine (Pz) molecules, which were employed as a model of organic linker in the Hofmann-type metal?Corganic framework (MOF). The MP2.5/aug-cc-pVTZ method was employed here, because this method presents almost the same binding energy as that calculated by the CCSD(T)/aug-cc-pVDZ with MP2.5-evaluated basis set extension effects to aug-cc-pVTZ basis set. The binding energy of the gas molecule increases in the order H₂?<?CH₄?<?CO₂?<?C₂H₄????C₂H₆?<?CS₂. The energy decomposition analysis of the interaction energy indicates that the electrostatic term presents the largest contribution to the interaction energy at the Hartree?CFock level. However, the dispersion interaction provides dominant contribution to the total binding energy at correlated level. We newly found a linear correlation between the z-component of polarizability of gas molecules and dispersion energy, where the z-axis was taken to be perpendicular to two Pz rings. These results are useful for understanding and predicting the binding energy of the gas molecule with the organic linkers of MOF.     

Theoretical rate constant calculations for O(3P) with saturated hydrocarbons

Theoretical rate constants have been calculated for O(³P) with five saturated hydrocarbons, CH₄, C₂H₆, C₃H₈, iso-C₄H₁₀, and neo-C₅H₁₂. The method of choice is bond energy–bond order (BEBO) with activated complex theory (ACT). Because the BEBO method is empirical, O(³P) + CH₄ is evaluated first, and the theoretical results are compared to more rigorous calculations and to the empirical transition state method. Comparisons are also made between predictions and experimental results. All of these comparisons show that the BEBO-ACT method gives results which are consistent with experiment and other theory. Because the method is successful, the other four cases are then considered. Ambiguity arises for the higher hydrocarbons from the problem of internal rotations in the activated complexes, and three cases are evaluated. Best agreement with experiment is obtained if the primary rotor(s) in the complexes are considered to be free. Predictions of rate constants are made from 500 to 2500 K. Throughout the discussion issues of theory which are common to any ACT calculation from any method of potential energy evaluation (LEP, LEPS, or ab initio quantum mechanics) are featured.     

Relative rate constants for the reactions of trichloropropenyl radical. Application of the two-parameter Taft equation

The relative rate constants for the hydrogen atom abstraction by CCl₃CH?CH· radical from CH₂Cl₂, CHCl₃, CH₃COCH₃, CH₃CN, C₆H₅CH₃, C₆H₅OCH₃, CH₃CHO, and CH₃OH in the liquid phase at 20°C have been measured. It was shown that these reaction rate constants are correlated by the two-parameter Taft equation with ρ* = 0.726 ± 0.096, r* = 1.22 ± 0.16. A relationship between r* and bond dissociation energy D(R? H) has been found for the abstraction reactions of different free radicals.     

Phenomenology and scaling of electron scattering cross sections from “almost spherical” molecules over a wide energy range

Total cross sections for electron scattering on “quasi spherical” (CH₄, SiH₄, GeH₄) molecules have been analyzed phenomenologically over a wide energy range. Regions, at low and high energies can be usefully represented by simple analytical formulae. Regularities associated with characteristic points such as the Ramsauer minima have been exposed. Comparison with other simple hydrides (NH₃, H₂O, H₂S) allows the demonstration of a possible correlation between the maximum value of the total cross section and the bond length. Some points of contact with first-principles theory are noted and in particular the energy at which the maximum cross section occurs, is related to the occurrence of a partial wave resonance. In the absence of complete data for GeH₄, prediction of characteristic points in the low energy cross section proves possible via the phenomenological analysis. Similarly, in the high energy regime, predictions of the cross section for SnH₄ is made from data on the lighter molecules of the series, using non-relativistic Thomas-Fermi self consistent field scaling.     

Calculation of harmonic force constants,vibrational frequencies and integrated intensities of some organic molecules using the MINDO—Forces method

The harmonic force constants, vibrational frequencies and integrated intensity ratios of CH₂, H₂O, CH₂O, C₂H₂, CO₂, HCN, CH₃, CH₄, and C₂H₄ have been calculated using the MINDO—FORCES program and the Pulay method for the calculation of the molecular force constants. The results obtained are in general quite satisfactory when compared with available literature values. The results are, however, not as satisfactory in case of molecules containing heteroatoms, due to the neglect of some dipolar repulsion integrals for the heteroatoms by the MINDO/3 method. Calculated integrated intensities for CH₃ and C₂H₄ agree well with experimental results. The calculated integrated intensities for other molecules are obtained for the first time and no comparison with published data is therefore possible.Part of the M.Sc. Thesis of K. H. A. 1978.     

Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

We have measured the synchrotron‐induced photofragmentation of isolated 2‐deoxy‐D ‐ribose molecules (C₅H₁₀O₄) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule′s ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH₃⁺, OH⁺, H₃O⁺, C₂H₃⁺, C₂H₄⁺, CH_xO⁺ (x=1,2,3), C₂H_xO⁺ (x=1–5), C₃H_xO⁺ (x=3–5), C₂H₄O₂⁺, C₃H_xO₂⁺ (x=1,2,4–6), C₄H₅O₂⁺, C₄H_xO₃⁺ (x=6,7), C₅H₇O₃⁺, and C₅H₈O₃⁺. The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C₃H₅O⁺), whereas a general intensity decrease is observed for all other fragments— relative to the m/q=57 fragment—with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH₃⁺, H₃O⁺, C₂H₄⁺, CH₃O⁺, and C₂H₅O⁺, involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar–phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.     

The use of transition-state theory to extrapolate rate coefficients for reactions of oh with alkanes

A method is described for extrapolating existing experimental data on the reactions of OH radicals with alkanes to higher temperatures using conventional transition-state theory. Expressions are developed for the estimation of the structural properties of the activated complex necessary for calculating ΔS^± and ΔH^±. The vibrational frequencies and internal rotations of the activated complex are given by those of the reacting alkane or the analogous alcohol and a set of additional internal modes that is the same for all OH + alkane reactions considered. Differences between primary, secondary, and tertiary hydrogen attack are discussed, and the validity of representing the activated complexes of all OH + alkane reactions by a fixed set of vibrational frequencies and other internal modes is evaluated. Calculations are presented for the reaction of OH with CH₄, C₂H₆, C₃H₈, n-C₄H₁₀, i-C₄H₁₀, c-C₄H₈, c-C₅H₁₀, c-C₆H₁₂, (CH₃)₂CHCH(CH₃)₂, (CH₃)₃CCH(CH₃)₂, (CH₃)₄C, and (CH₃)₃CC(CH₃)₃, and the results are compared with experiments.     

Proton and 13C NMR spectra of substituted methyl cyanopropionates: Effects of molecular asymmetry

The proton NMR spectra at 220 MHz of two series of substituted cyanopropionates, have been investigated. In addition the ¹³C spectra at 15 MHz of the series I were also studied. In I, where the R groups are diastereotopic, differences are observed in the proton chemical shifts of the CH₃ groups in R for R = CH₃, C₂H₅, n-C₃H₇, i-C₃H₇, n-C₄H₉, n-C₅H₁₁ and n-C₆H₁₃. In II [R′ = n-C₃H₇, CH(CH₃)₂, CH₂CH(CH₃)₂ and C(CH₃)₃] diastereoisomers are found with substantial differences in chemical shifts between corresponding protons. Coupling constants are interpreted in terms of conformational preferences for certain molecules in both series.     

On the use of localized orbitals and restricted alternant orbitals in chemical systems

An analysis of the transformation of localized orbitals into restricted alternant orbitals is proposed. This approach has the advantage of expressing the wave-function in an orbital product while some electron correlation is introduced permitting the study of dissociation reactions. All applications of the orbital technique may be made as easily as with RHF, but with the additional possibility of studying chemical radicals. Some illustrations of this fact are shown for the molecules HF, H₂O, NH₃, CH₄, C₂H₆ and for the dissociation reactions of CH₄ and C₂H₆ generating CH₃ radicals.     

Long‐range π‐type hydrogen bond in dimers CH2?HF,CH2O?H2O,and CH2O?NH3

Using four basis bets, (6‐311G(d,p), 6‐31+G(d,p), 6‐31++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for the dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. In contrast with the above three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD (T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study on the gas‐phase reaction mechanism between rhodium monoxide and methane for methanol production

The gas‐phase reaction mechanism between methane and rhodium monoxide for the formation of methanol, syngas, formaldehyde, water, and methyl radical have been studied in detail on the doublet and quartet state potential energy surfaces at the CCSD(T)/6‐311+G(2d, 2p), SDD//B3LYP/6‐311+G(2d, 2p), SDD level. Over the 300–1100 K temperature range, the branching ratio for the Rh(⁴F) + CH₃OH channel is 97.5–100%, whereas the branching ratio for the D‐CH₂ORh + H₂ channel is 0.0–2.5%, and the branching ratio for the D‐CH₂ORh + H₂ channel is so small to be ruled out. The minimum energy reaction pathway for the main product methanol formation involving two spin inversions prefers to both start and terminate on the ground quartet state, where the ground doublet intermediate CH₃RhOH is energetically preferred, and its formation rate constant over the 300–1100 K temperature range is fitted by k_CH3RhOH = 7.03 × 10⁶ exp(?69.484/RT) dm³ mol^?1 s^?1. On the other hand, the main products shall be Rh + CH₃OH in the reactions of RhO + CH₄, CH₂ORh + H₂, Rh + CO +2H₂, and RhCH₂ + H₂O, whereas the main products shall be CH₂ORh + H₂ in the reaction of Rh + CH₃OH. Meanwhile, the doublet intermediates H₂RhOCH₂ and CH₃RhOH are predicted to be energetically favored in the reactions of Rh + CH₃OH and CH₂ORh + H₂ and in the reaction of RhCH₂ + H₂O, respectively. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Synthesis of 3-alkyl-6-phenyl-4(3H)-pteridinones and their 8-oxides. Potential substrates of xanthine oxidase

Synthetic routes for the preparation of 3-alkyl-6-phenyl-4(3H)-pteridinones 6 and their corresponding 8-oxides 5 (R = CH₃, C₂H₅, (CH₂)₂CH₃, (CH₂)₃CH₃, CH(CH₃)C₂H₅, CH(CH₃)₂ and CH(C₂H₅)CH₂OCH(OC₂H₅)₂ are described and their reactivities towards xanthine oxidase from Arthrobacter M-4 are determined. Only the 3-methyl derivative of 6-phenyl-4(3H)-pteridinone and its 8-oxide i. e. 6a and 5a are found to be substrates although their reactivities are still very low. Oxidation takes place at C-2 of the pteridinone nucleus. All the 3-alkyl derivatives are less tightly bound to the enzyme than 6-phenyl-4(3H)-pteridinone. Introduction of the N-oxide at N-8 considerably lowers the binding of the substrates. Inhibition studies have revealed that 3-methyl-6-phenyl-4(3H)-pteridinone ( 6a ) is a non-competitive inhibitor with a Ki-value of 47 μM and the 3-ethyl derivative ( 6b ) an uncompetitive one with a Ki-value of 19.6 μM.     

NLO‐X (X = I–III): New Gaussian basis sets for prediction of linear and nonlinear electric properties

New adjusted Gaussian basis sets are proposed for first and second rows elements (H, B, C, N, O, F, Si, P, S, and Cl) with the purpose of calculating linear and mainly nonlinear optical (L–NLO) properties for molecules. These basis sets are new generation of Thakkar‐DZ basis sets, which were recontracted and augmented with diffuse and polarization extrabasis functions. Atomic energy and polarizability were used as reference data for fitting the basis sets, which were further applied for prediction of L–NLO properties of diatomic, H₂, N₂, F₂, Cl₂, BH, BF, BCl, HF, HCl, CO, CS, SiO, PN, and polyatomic, CH₄, SiH₄, H₂O, H₂S, NH₃, PH₃, OCS, NNO, and HCN molecules. The results are satisfactory for all electric properties tested; dipole moment (µ), polarizability (α), and first hyperpolarizability (β), with an affordable computational cost. Three new basis sets are presented and called as NLO‐I (ADZP), NLO‐II (DZP), and NLO‐III (VDZP). The NLO‐III is the best choice to predict L–NLO properties of large molecular systems, because it presents a balance between computational cost and accuracy. The average errors for β at B3LYP/NLO‐III level were of 8% for diatomic molecules and 14% for polyatomic molecules that are within the experimental uncertainty. © 2014 Wiley Periodicals, Inc.     

Theoretical influence of third molecule on reaction channels of weakly bound complex CO2… HF systems

In this investigation, reaction channels of weakly bound complexes CO₂…HF, CO₂…HF…NH₃, CO₂…HF…H₂O and CO₂…HF…CH₃OH systems were established at the B3LYP/6‐311++G(3df,2pd) level, using the Gaussian 98 program. The conformers of syn‐fluoroformic acid or syn‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH) were found to be more stable than the conformers of the related anti‐fluoroformic acid or anti‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH). However, the weakly bound complexes were found to be more stable than either the related syn‐ and anti‐type fluoroformic acid or the acid plus third molecule (NH₃, H₂O, or CH₃OH) conformers. They decomposed into CO₂ + HF, CO₂ + NH₄F, CO₂ + H₃OF or CO₂ + (CH₃)OH₂F combined molecular systems. The weakly bound complexes have four reaction channels, each of which includes weakly bound complexes and related systems. Moreover, each reaction channel includes two transition state structures. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T₁₃) is significantly larger than that of internal rotation (T₂₃) between the syn‐ and anti‐FCO₂H (or FCO₂H…NH₃, FCO₂H…H₂O, or FCO₂H…CH₃OH) structures. However, adding the third molecule NH₃, H₂O, or CH₃OH can significantly reduce the activation energy of T₁₃. The catalytic strengths of the third molecules are predicted to follow the order H₂O < NH₃ < CH₃OH. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Correlated one‐electron wave functions

Using four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. By contrast with above the three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005