An ab initio molecular fragment investigation of the electronic and conformational structure of formaldoxime

An ab initio molecular fragment study of formaldoxime is reported and compared with previous semiempirical and conventional ab initio studies.     

An ab initio calculation of the molecular structure and properties of hypofluorous acid

An ab initio LCAO MO SCF calculation has been carried out on hypofluorous acid (HOF) in order to study the electronic structure, geometry and other one-electron properties of this molecule. The minimum energy geometry was found to be R_OF = 1.450 Å, R_OH = 1.080 Å, and θ = 100.8°, which is in good agreement with experiment. In general, the bonds in HOF appear to be similar to the analogous bonds in H₂O and F₂O. The first three ionization potentials 13.97, 14.94, and 17.16 eV compare well with recent photoelectron spectroscopic data.     

Interpreting ultrafast molecular fragmentation dynamics with ab initio electronic structure calculations

High-level ab initio electronic structure calculations are used to interpret the fragmentation dynamics of CHBr(2)COCF(3), following excitation with an intense ultrafast laser pulse. The potential energy surfaces of the ground and excited cationic states along the dissociative C-CF(3) bond have been calculated using multireference second order perturbation theory methods. The calculations confirm the existence of a charge transfer resonance during the evolution of a dissociative wave packet on the ground state potential energy surface of the molecular cation and yield a detailed picture of the dissociation dynamics observed in earlier work. Comparisons of the ionic spectrum for two similar molecules support a general picture in which molecules are influenced by dynamic resonances in the cation during dissociation.     

An ab initio study of the electronic structure of diimide

Ab initio calculations on the structure and geometry of the three isomers of N₂H₂ (trans-diimide, cis-diimide, and 1,1-dihydrodiazine) were performed both on HF and CI level using gaussian basis sets with polarization functions. The trans and cis isomers have singlet ground states; the trans isomer is found to be lower in energy than the cis isomer by 6.9 kcal/mol (HF) and 5.8 kcal/mol (CI), respectively. The barrier for the trans-cis isomerization is predicted to be 56 (HF) and 55 (CI) kcal/mol. H₂ N=N has a triplet ground state with a non-planar equilibrium geometry and a rather long NN bond of 1.34 Å. Its lowest singlet state, however, is planar with an NN double bond of 1.22 Å; it is found to lie about 3 kcal/mol above the triplet and 26 kcal/mol above the singlet ground state of trans-diimide.     

An ab initio analysis of the electronic structure and harmonic frequencies of nickel porphyrin

Ab initio calculations are performed to understand the geometry, electronic structure, and vibrational frequencies of nickel porphyrin (NiP). Hartree-Fock (HF) and second-order perturbation (MP2) theories are applied with polarized basis sets. The calculated geometrical parameters are in very good agreement with the crystal structure determination. The electronic structure and bonding are analyzed in terms of complexation and correlation effects. Not unexpectedly, the HF depiction of the metal-porphyrin interaction is rather ionic while ligand σ donation is dominant at the MP2 level. Scaled HF frequencies of NiP and its isotopomers are in very good agreement with observed infrared and resonance Raman data. Received: 7 January 1997 / Accepted: 6 May 1997     

The geometric and electronic structures of oxocarbons. An ab initio molecular orbital study

Ab initio molecular orbital calculations with the STO-3G and 4-31G basis sets have been carried out for the neutral oxocarbons C_nO_n (n = 3, 4, 5, 6 and 7), the dianions C_nO_n^2- (n = 3, 4, 5, 6 and 7), the monoanions C_nO_nH^? (n = 3 and 4) and the related acids C_nO_nH₂ (n = 3 and 4). Fully optimised geometries have been obtained for all species. The geometries, stabilities and acidities are discussed.     

Conformational analysis of allylamine. An ab initio molecular orbital study

The conformational characteristics of allylamine were investigated by the ab initio STO -3G basis set. The results indicate that the molecule exists in a number of stable conformations through rotations about the CC? NH and CC? CN bonds. The TE (trans-CCNLP , LP representing lone-pair electrons, and eclipsed-CCCH) is the most stable, while TC (trans-CCNLP and cis-CCCN), GE (gauche-CCNLP and eclipsed-CCCH), G′C(gauche′-CCNLP and cis-CCCN), and G′E (gauche′-CCNLP and eclipsed-CCCH) conformations are less stable, respectively, by 0.41, 0.67, 0.92, and 1.14 kcal mol^?1. These results are in general consistent with previous experimental results. Rationale for the conformational characteristics and order of stabilities are explored.     

An ab initio reinvestigation of the geometric and electronic structure of boron trioxide

In an attempt to resolve the controversy over the structure of the boron trioxide (B₂O₃) molecule an ab initio molecular orbital study employing a minimal STO-3G basis set with complete geometry optimization is reported. Our results indicate that B₂O₃ is a planar “w” shaped molecule with a rather small inversion barrier around the central atom and a quite important coupling between BOB and OBO angles. The computed bond distances are consistent with previous electron diffraction results, whereas the apex angle is in better agreement with the most recent IR study. The results obtained by the MNDO method are in good agreement with the ab initio ones. The electronic structure of B₂O₃ is discussed by means of Walsh diagrams and Mulliken population analysis.     

An ab initio LCAO-MO-SCF study of the electronic structure of phosphirane and thiirane

Wave functions have been determined for the C₂H₄PH and C₂H₄S cyclic molecules, using (951/52/3) and (95/52/3) uncontracted Gaussian basis sets for each molecule. From Mulliken population analyses and electron-density plots, it is shown that the valence orbitals of C₂H₄PH and C₂H₄S are closely related and that these are similar to the respective orbitals of cyclopropane.

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Zusammenfassung Für die zyklischen Moleküle C₂H₄PH und C₂H₄S wurden mit den nichtkontrahierten Basissätzen ((951/52/3) und (95/52/3)) von Gaußfunktionen Wellenfunktionen bestimmt. Die Mullikenschen Populationsanalysen sowie Diagramme der Elektronendichte zeigen, daß die Valenzorbitale von C₂H₄PH und C₂H₄S in enger Beziehung stehen und daß diese den entsprechenden Orbitalen des Cyclopropans ähnlich sind.

     

Thermochemical properties of HxNO molecules and ions from ab initio electronic structure theory

Coupled-cluster calculations through noniterative triple excitations were used to compute optimized structures, atomization energies at 0 K, and heats of formation at 0 and 298 K for NH2O, HNOH, NH2O-, NH2OH+, NH3OH+, HNO-, and HON. These molecules are important in the gas-phase oxidation of NH3, as well as its solution-phase chemistry. The O-H, N-H, and N-O bond energies of these molecules are given and compared. The N-H and O-H bond energies are quite low, and, for NH2OH, the O-H bond is weaker than the N-H bond (by 7.5 kcal/mol). The energetics for a variety of ionic chemical processes in the gas phase, including the electron affinities of NH2O and HNO, the proton affinities of NH2O and NH2OH, and the acidities of NH2OH and NH2O, are given. The compounds are weak bases and weak acids in the gas phase. Solvation effects were included at the PCM and COSMO levels. The COSMO model gave better values than the PCM model. The relative values for pKa for NH2O and NH2OH are in good agreement with the experimental values, showing both compounds to be very strong bases in aqueous solution with NH2OH being the stronger base by 1.8 pK units at the COSMO level, compared to the experimental pK difference of 1.1+/-0.3 pK units. We predict that NH2OH+ will not be formed in aqueous solution, because it is a very strong acid. Based on the known acidity of NH3OH+, we predict pKa(NH2OH+)=-5.4 at the COSMO level, which is in good agreement with the experimental estimate of pKa(NH2OH+)=-7+/-2.     

Some recent applications of ab initio electronic structure methods to metal,semimetal, and molecular clusters

Recent experimental and theoretical cluster studies are reviewed. Areas of current and developing interest in theoretical and computational chemistry are identified. Some promising methods applied to metal clusters, main group clusters, molecular clusters, spectroscopy, and models of cluster-molecule reactions are indicated. Results of calculations on small hydrogenated lithium clusters and hydrated sodium clusters are discussed in some detail.     

Theoretical analysis of the electronic spectrum of GeH4 from ab initio CI calculations

Ab initio CI calculations using pseudopotentials to describe germanium inner electrons are carried out on the low-lying excited singlet states (T₂) of GeH₄. A theoretical analysis of these states in terms of Mulliken population of Rydberg orbitals for each state and oscillator strengths allow us to reinterpret its experimental Vacuum UV electronic spectrum.     

An ab initio study of the stability and electronic structure of univalent magnesium salts

Large basis and well-correlated ab initio electronic structure calculations have been performed on the simple Mg(I) salts, Mg₂F₂ and Mg₂Cl₂. The electron withdrawing power of the halogens gives rise to significant metal-metal bonding and consequently these as yet unobserved, univalent salts are calculated to be 10–12 kcal more stable than if the second magnesium atom were absent from the molecule. With this stability, these species provide an energetically more accessible Mg atom for subsequent reaction than does solid magnesium where the atomization energy is 35 kcal. Thus, formal univalency of magnesium affords a route to activated magnesium.     

An ab initio MO calculation of the electronic structure and geometry of protonated methanol

Protonated methanol, CH₃ OH₂⁺, has been studied using the LCAO—MO—SCF method with a 7, 3 and 9, 5, 1 Gaussian orbital basis set on the heavy atoms and 4s on hydrogen. It is found that the ground state is non-planar around oxygen, in contrast with previous calculations, with an inversion barrier of 3 kcal mol^?1. The changes in electron distribution in the reacting systemCH₃⁺ + H₂O → CF₃OH₂⁺is also examined.     

Electronic structure and molecular conformation of furan and pyrrole azomethines. An ab initio molecular orbital study

STO-3G minimal basis set ab initio molecular orbital calculations were employed to study the electronic structure and conformational preferences in furan-2-N-methylmethyleneimide ( 1 ) and pyrrole-2-N-methylmethyleneimide ( 2 ). The theoretical results were examined by comparison with the parent molecular systems through a population analysis and molecular orbital interactions considerations. The OCCN-trans and the NCCN-cis forms were found to be the most stable structures in 1 and 2 , respectively. Comparisons were made with available experimental data. The theoretical results indicate thatπ-electron interactions and molecular orbital interactions are not significant factors in determining the conformational preferences which most likely depend on dipole-dipole interactions.     

Molecular and electronic structure of disiloxane,an ab initio MO study

The bond lengths and angels obtained by means of a 4–31G basis agree with electron diffraction data. The calculated SiOSi bending potential, showing a minimum for the linear arrangement, is discussed with regard to available experimental information. Calculated dipole moments and ionization potentials are also in reasonable agreement with experimental data. Comparison is made with STO-3G and INDO results which both overestimate the stability of cyclic structures.     

An ab initio comparison of dichalcogen hydrides

A theoretical study of HSH, HSeH, HTeH, HSSH, HSeSH, HSeSeH, HTeSH, HTeSeH, and HTeTeH was carried out by ab initio molecular orbital methods employing minimal Gaussian basis sets MINI-1 and MINI-1* of Huzinaga and his group. Both basis sets yield accurate estimates on the equilibrium geometries of monochalcogen hydrides. In the case of dichalcogen hydrides, however, the inclusion of d-polarization functions for sulfur, selenium, and tellurium greatly improve the accuracy of the geometry prediction. The unpolarized MINI-1 basis sets yield essentially correct orbital energies and therefore suffice for the comparative study on the electronic structures in similar molecules. The results with both basis sets imply close similarities in the electronic structures of SS, SeS, and SeSe bonds with more marked differences in bonds containing tellurium as a consequence of notably smaller orbital energy of the 5s- orbital of tellurium as compared to the corresponding orbitals in sulfur and selenium. The barriers to internal rotation about the chalcogen—chalcogen bond in all dichalcogen hydrides are similar. The cis- and trans-barrier heights are ca. 23 and 14 kJ mol⁻¹, respectively. The relative stabilities of different hydrides are discussed.     

CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes

We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin‐orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree–Fock (CAHF) algorithm for the determination of 4f quasi‐atomic active orbitals common to all multi‐electron spin manifolds contributing to the ground spin‐orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi‐Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem‐specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state–of–the–art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres , represents a more time‐efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non‐perturbative spin‐orbit coupling effects. © 2017 Wiley Periodicals, Inc.     

An ab initio theoretical study of electronic structure and properties of 2'-deoxyguanosine in gas phase and aqueous media

Molecular geometries of two structural forms of 2'-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2'-endo and C3'-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2'-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2'-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water-air interface. Though the normal Watson-Crick-type base pairing would not be possible with the keto-N7R form of 2'-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti-conformation of 2'-deoxyguanosine including the dihedral angle chi(CN) agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2'-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H(+) and OH(-) fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH(-) group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2'-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems.