Ab Initio Unrestricted Hartree-Fock Research Articles

Infrared Spectrum for the New Nanomolecules ASi, CSi, TSi and Gsi

The core of the work is based on the replacement of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via ab initio Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in CNTP, for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the ab initio Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of bases used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CC-pVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).

Infrared Spectrum for the New Exobiological Nanomolecules Asi, Csi, Tsi and Gsi

The core of the work is based on the replacement of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via ab initio Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in CNTP, for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the ab initio Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of basis used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CC-pVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).

Diffuse-functions effects on theoretical calculation of disulfide dianion in water

Polysulfide anions play crucial roles in the liquid phase, but they are difficult to describe in theoretical calculations. We have investigated diffuse functions dependent total energy, bond length, and molecular orbitals for disulfide dianion (S22−) in water using conventional ab initio unrestricted Hartree-Fock method (UHF/6-311G+(d)) with a polarizable continuum model (PCM, ε = 78.39) by changing ς value of diffuse functions. S22− in water turns out to be more stable than S2 and S2−, though it is too unstable to exist in vacuum so that the excess electrons will auto-detach. The optimal ς value that gives a local minimum of total energy for S22− in water is found to be 0.12. These new findings will contribute toward using more appropriate diffuse functions for other polysulfide anions as well.

Computation of the bond dissociation enthalpies and free energies of hydroxylic antioxidants using the ab initio Hartree–Fock method

IntroductionA new method for calculating theoretical bond dissociation enthalpy (BDE) and bond dissociation free energy (BDFE) of hydroxylic antioxidants is forwarded. BDE and BDFE may be understood as activation energies accompanying the formation of transition states, which may undergo downhill homolytic dissociation. The new method does not involve the complete fission of O–H bonds.MethodTheoretical gas phase BDE values were calculated with the ab initio unrestricted Hartree–Fock (UHF) method, as changes in enthalpy between ground singlet states (GS) and triplet dissociative states (DS). Similarly, gas phase BDFEs were estimated from the corresponding changes in Gibbs free energy. The results were then compared with reliable experimental reports.ResultsThe proposed theoretical approach of BDE and BDFE determination was tested using 10 simple phenols, 5 flavonoids, and l-ascorbic acid derivatives. The agreement between our calculated gas phase results and the adopted experimental values were generally within 0.5 kcal mol−1, with a very few exceptions.DiscussionGenerally, steric interactions as well as intramolecular hydrogen bonding involving the dissociating OH group should be minimized in the GS. The DS are both electronically and vibrationally exited transition states. They have one unpaired electron on the carbon atom, which bears the homolytically dissociating OH group and are second order saddle points with a fixed <C–O–H bond angel of 180°.ConclusionIt was concluded that ab initio UHF was well suited for the estimation of gas phase BDE and BDFE. The method presented has a good potential for application across a range of hydroxylic antioxidants. Currently, work is underway to extend its application in other class of antioxidants.

Computation of the bond dissociation enthalpies and free energies of hydroxylic antioxidants using the ab initio Hartree-Fock method

Introduction A new method for calculating theoretical bond dissociation enthalpy (BDE) and bond dissociation free energy (BDFE) of hydroxylic antioxidants is forwarded. BDE and BDFE may be understood as activation energies accompanying the formation of transition states, which may undergo downhill homolytic dissociation. The new method does not involve the complete fission of O–H bonds. Method Theoretical gas phase BDE values were calculated with the ab initio unrestricted Hartree–Fock (UHF) method, as changes in enthalpy between ground singlet states (GS) and triplet dissociative states (DS). Similarly, gas phase BDFEs were estimated from the corresponding changes in Gibbs free energy. The results were then compared with reliable experimental reports. Results The proposed theoretical approach of BDE and BDFE determination was tested using 10 simple phenols, 5 flavonoids, and l-ascorbic acid derivatives. The agreement between our calculated gas phase results and the adopted experimental values were genera...

Fragmentation patterns of core-ionized thymine and 5-bromouracil

Photofragmentation of thymine and 5-bromouracil into cation and neutral fragments following the core ionization by soft x-rays using photoelectron-photoion-photoion coincidence technique has been studied. The fragment ion mass spectra were recorded in coincidence with the C 1s photoelectron spectra. In the case of thymine, deuterated samples were used to identify fragments. Deuteration or bromination allowed us to study not only the main fragmentation channels of these pyrimidine bases, but also to investigate if replacement of an exocyclic functional group affects molecular fragmentation. We found that the dominant fragmentation channels involve only one starting geometry, and the base ring and other bond cleavages, leading to the detected fragments, are essentially identical between thymine and 5-bromouracil. In addition, the relative intensities of the strongest fragmentation channels were determined and compared with calculated appearance energies using ab initio unrestricted Hartree-Fock theory.

On the existence of a spin-polarized state in the n-periacene molecules

Single Slater determinant calculations have been done for the family of n-periacene molecules having n = 1–6, by applying both, the ab initio unrestricted Hartree–Fock (UHF) method, and a set of DFT functionals. The UHF results agree with previous DFT, exhibiting all of them (those for n = 1, 2 included) an anti-ferro magnetic polarized ground state. Möller–Plesset and CISD calculations have been carried out on the wave-functions previously found in the UHF calculations. All of them lead to an inversion in the relative stability found at the single Slater determinant level, predicting as the most stable the non-polarized closed shell state.

Need for electronic correlation calculations in polymers

The presence of nonsinglet instabilities of the restricted Hartree-Fock ground-state wavefunction may be an indication of strong correlation effects. We have recently observed that such instabilities persist in some conjugated polymers even with localizable electronic structure, like strongly alternating polyene [(CH)x] or its isoelectronic analog (polymethineimine) by performing ab initio STO-3G unrestricted Hartree-Fock (UHF) calculations for these chain systems, using different geometrical arrangements. We suggest that coupled-cluster calculations might give a resolution to this problem.

Theoretical Study of the Energetics of the Reactions of Triplet Dioxygen with Hydroquinone, Semiquinone, and Their Protonated Forms: Relation to the Mechanism of Superoxide Generation in the Respiratory Chain

One-electron reduction of the dioxygen molecule by the reduced form of mitochondrial ubiquinones (Q) of the NADH dehydrogenase (complex I) and mitochondrial cytochrome bc1 (complex III) is believed to be the main source of the superoxide anion radical O2*- and the hydroperoxide radical OOH*. In this work, we modeled the energetics of four possible reactions of the triplet ((3)Sigma(g)) dioxygen-molecule reduction by fully reduced and protonated ubiquinone (QH2; reaction 1), its deprotonated form (QH-; reaction 2), the semiquinone radical (QH*; reaction 3), and the semiquinone anion radical (Q*-; reaction 4), by means of ab initio calculations with the 6-31G(d) and 6-31+G(d) basis set in the restricted open-shell Hartree-Fock (ROHF), unrestricted Hartree-Fock (UHF), and complete active space self-consistent field (CASSCF) with dynamic correlation [at the second-order Møller-Plesset (MP2) or multiple reference Møller-Plesset (MRMP), respectively] schemes and the basis set superposition error (BSSE) correction included, as well as semiempirical AM1 and PM3 calculations in the UHF and ROHF schemes. 2-Butene-1,4-dione and p-benzoquinone were selected as model compounds. For the reduced forms of both compounds, reaction 1 turned out to be energetically unfavorable at all levels of theory, this agreeing with the experimentally observed diminished reductive properties of hydroquinone derivatives at low pH. For 2-butene-1,4-dione treated at the most advanced MRMP/CASSCF/6-31+G(d) level, the energies of reactions 1-4 are 4.7, -34.3, -15.0, and -4.1 kcal/mol, respectively. This finding suggests that reactions 2 and 3 are the most likely mechanisms of electron transfer to molecular oxygen in aprotic environments and that proton transfer is involved in this process. Nearly the same energies of reactions 2 and 3 were calculated at the MRMP/CASSCF/6-31+G(d) level for reduced forms of p-benzoquinone. Inclusion of diffuse functions in the basis set and dynamic correlation at the CASSCF level appears essential. Because deprotonated ubiquinol is unlikely to exist in physiological environments, reaction 3 appears to be the most likely mechanism of one-electron reduction of oxygen; however, if oxygen can penetrate cytochrome bc1 as far as the Q(o) center where ubiquinol can be deprotonated, reaction 2 can also come into play. The energies of reactions 2 and 3 calculated at the MRMP/CASSCF/6-31+G(d) level are most closely reproduced in the ab initio and semiempirical UHF PM3 calculations. Additional semiempirical calculations on more realistic models of ubiquinone, 2,3-dimethoxy-6-methyl-p-benzoquinone and 2,3-dimethoxy-5-isoprenyl-6-methyl-p-benzoquinone, gave qualitatively the same relations between the energies of reactions 2 and 3 as those carried out for p-benzoquinone species, thereby suggesting that this method could be used in studying electron-transfer reactions from reduced quinone derivatives to molecular oxygen in more complex systems, such as a model of the Q(o) site of cytochrome bc1, where applying ab initio methods is unfeasible.

Ab initio calculations of elastic constants and thermodynamic properties of Li 2O for high temperatures and pressures

The elastic constants and thermodynamic properties of Li 2O for high temperatures and pressures are calculated by the ab initio unrestricted Hartree–Fock (HF) linear combination of atomic orbital (LCAO) periodic approach. The lattice constant, elastic constants, Debye temperature, and thermal expansion coefficient obtained are in good agreement with the available experimental data and other theoretical results. It is found that at zero pressure the elastic constants C 11 , C 12 and C 44 , bulk modulus B and Debye temperature Θ D decrease monotonically over the wide range of temperatures from 0 to 1100 K. When the temperature T > 1100 K , C 12 approaches zero, consistently with the transition temperature 1200 K. However, with increasing pressure, they all increase monotonically and the anisotropy will weaken.

Ab Initio Calculations of Elastic Constants of Li2O underPressure

We investigate the equilibrium lattice constant, bulkmodulus, elastic constants and Debye temperature of Li2O underpressure by using ab initio unrestricted Hartree–Fock (HF)linear combination of atomic orbital (LCAO) periodic approach. Theobtained results at zero pressure are well consistent with theavailable experimental data and other theoretical results. It is foundthat the elastic constants C11, C12 and C44 and bulkmodulus B increase monotonously as pressure increases. Also, theanisotropy will weaken and the Debye temperature will rise with pressureincreasing.

New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models

The heme protein, cytochrome P450, is an oxidoreductase that plays an important role in drug metabolism. To model P450s using molecular mechanics methods and classical molecular dynamics simulations, force field parameters and atomic charges are required. Because these parameters are generally obtained by quantum chemical methods, an appropriate simplified model for the iron-porphyrin system was needed. In this study, two models with a five-coordinated Fe(III) mimicking the sextet spin state of P450s are proposed, which are optimized by semiempirical and ab initio unrestricted Hartree-Fock methods. The results produced using the simpler of the two models were similar to those of the more complex model; therefore, the more simplified model of P450 can be used without a loss of accuracy. Furthermore, several quantum chemical calculations were carried out on the simpler model to investigate which method was most suitable for iron-porphyrin systems. The results calculated by hybrid density functional theory (DFT), with the MIDI basis set for iron, reproduced the three-dimensional structures determined by X-ray diffraction and extended X-ray absorption fine-structure experiments. From these results, atomic charges and force-field parameters for molecular mechanics and molecular dynamics calculations were obtained.

Static Dipole Polarizability of o-, m- and p-Benzyne isomers: Ab initio, DFT and CCSD calculations

We report a study of the static dipole polarizability (α) of the o-, m- and p-benzyne isomers in their singlet ground state. Due to the biradical character of benzynes, calculations were performed at ab initio unrestricted Hartree-Fock (UHF) level of theory. The correlation effects were accounted for with second order Moller Plesset (MP2) method, Density Functional Theory (DFT) with the BLYP and B3LYP hybrid approaches and the coupled cluster CCSD method with 6-31$+$G(d,p) standard basis set with optimized geometries. C$_2$v symmetry restriction was employed for the geometry of o- and m-benzynes (closed and open conformation) and D$_2$h for p-benzynes (open and closed conformation). Because the high quality of the basis set is a requirement for accurate α determination, MP2 and DFT calculations were performed with the 6-31+G(d,p), the extended 6-311++G(3d,3p) and the specialized Sadlej basis sets. The CCSD calculations were only carried out with the 6-31+G(d,p) and the Sadlej basis sets. The results indicate that the average α polarizability values for o- and m-benzynes are lower than the corresponding to the experimental value of benzene, while this property for p-benzyne is slightly higher than the benzene one. The anisotropy Δα values of benzyne isomers are always higher than the anisotropy of benzene molecule. Finally, was found that the conformations of p-C$_6$H$_4$are the less stable isomers, and are the most polarizables and anisotropic compounds from the benzyne series.

On the variation of magnetic susceptibility of a molecular crystal with temperature: the 2,4,6-triphenylverdazyl system.

Magnetic susceptibilities of spin-1/2 systems of orthorhombic and higher crystal symmetries have been numerically investigated while taking possible anisotropy in the coupling constants along different crystal axes into account. The work relies on the magnon-based theory of ferromagnetic (FM) and antiferromagnetic (AFM) crystal systems of types FFF, AFF, AAF, and AAA [J. Chem. Phys. 111, 9009 (1999)]. The AAF crystal, in particular, shows interesting changes in the temperature dependence of magnetic susceptibility when the ferromagnetic exchange coupling constant is varied. We especially show that the susceptibility anomalies of molecular crystals fit naturally within the framework of the extended magnon-theoretical formalism, and do not necessarily imply a FM --> AFM or a reverse phase transition. A real system, molecular crystal of 2,4,6-triphenylverdazyl (2,4,6-TPV), has been investigated here. It was previously interpreted as an AAF system from observed susceptibility data [Tomiyoshi et al., Phys. Rev. B 49, 16031 (1994)]. The trend of the temperature dependence of magnetic susceptibility studied in the present work also indicates that the crystal belongs to the AAF category with a less prominent FM exchange coupling constant. To reinforce our conclusions, we have adopted a two-pronged strategy. First, the geometry of the 2,4,6-TPV monomer has been optimized here by ab initio unrestricted Hartree-Fock (UHF) calculations using the STO-3G basis set. The optimized geometry is almost planar. A subsequent calculation has been carried out with the phenyl rings twisted out of the plane of the nitrogen atoms. The STO-3G optimized geometry, and the same geometry except for the twisted phenyl rings, have been used to perform ab initio coupled-cluster (UCCSD-T) calculations with the same basis, and UHF as well as density-functional (UB3LYP) calculations using the 6-31G basis set. The calculated data can easily rationalize the twists while the species remains in crystal. The magnetic category of the crystal has been unambiguously confirmed as AFA from ab initio UHF and UB3LYP calculations of the total energy in different spin states of dimers and trimers along the crystal axes. The computed energy values, however, fail to yield accurate estimates of the exchange coupling constants Ja, Jb, and Jc, because the latter are on the order of 1kBK corresponding to energy differences on the order of 10(-6) hartree between different spin states. In the second approach, the observed features of the susceptibility minimum and maximum have been used to determine the best values of the exchange coupling constants from the theoretical formulas for an anisotropic AFA crystal. The AFM (Ja and Jc) and FM (Jb) exchange coupling constants and the Neel temperature (TN) found from this analysis correspond to Ja + Jc = -1.05 kBK, Jb = 1.35 kBK, and TN = 1.75 K. The calculated J values significantly differ from those estimated from a linear Heisenberg chain model, but generate a susceptibility versus temperature graph that mimics the experimental plot.

Effect of charge on the interaction of two C 60 molecules from MNDO and ab initio UHF methods: stability and HOMO–LUMO gaps

We have investigated the interaction between two C 60 molecules with overall charge on the system n between +1 and −4 from infinite separation to a distance of 8.5 Å, using the MNDO and ab initio unrestricted Hartree–Fock methods. We have determined the dependence of the interaction energy, charge distribution, |HOMO–LUMO| gap and charge transfer, on distance. The system is found to be most stable at an interaction distance of ∼14 Å, for system charge between −1 and −4 a.u. Charge is shared equally between the two buckyballs for even total charge n and distributed unevenly between the molecules for odd n. The smallest values of |HOMO–LUMO| are found, in general, for the systems with net negative charge and an odd number of electrons.

Theory of trapping of muon and muonium and associated hyperfine interactions in the organic ferromagnet p-NPNN (β-phase)

The ab initio unrestricted Hartree–Fock procedure has been applied to determine the trapping sites for the positive muon and muonium in β-phase ferromagnetic para-nitrophenyl nitronyl nitroxide and to calculate the associated electronic wave functions from which the corresponding contact and dipolar terms in the spin Hamiltonians have been obtained. For muonium, trapping sites were found near the oxygens of the two NO groups, resulting in a singlet electronic state for the overall molecular system, and also near the two oxygens of the NO 2 group, resulting in a triplet state for the overall system. For the muon a total of four trapping sites was found, corresponding to the oxygen and nitrogen atoms of the two NO groups. Using the easy axis along the b-axis of the orthorhombic sublattice, as found from muon spin rotation (μSR) measurements, and the calculated magnetic hyperfine interaction parameters, the observed 2.1 MHz zero-field μSR signal is assigned to the singlet state corresponding to muonium trapping near the oxygen of one of the NO groups. The large hyperfine constant of about 400 MHz inferred from longitudinal field repolarization measurements is assigned to a positive muon trapped near the nitrogen atom of one of the NO groups.

Formation of polymer complexes of transition metals with fullerene

This paper reports on the results of ab initio unrestricted Hartree-Fock (UHF) calculations of the equilibrium geometry and binding energy for the transition-metal complexes Me(C5H5)2 and Me(C6H6)2 and the energetically stable metallofullerene complexes Me(C60)2, where Me=Ti, V, Cr, Fe, and Ni. The calculation technique is worked out using the ferrocene molecule. The calculated geometry and binding energy agree satisfactorily with the experimental data.

Analytical and ab initio studies of effective exchange interactions, polyradical character, unpaired electron density, and information entropy in radical clusters (R)N: Allyl radical cluster (N=2–10) and hydrogen radical cluster (N=50)

AbstractAnalytical expressions of total energies, effective exchange integrals, polyradical character, spin density, unpaired electron density, and information entropy are derived for allyl radical dimers and trimers on the basis of the Hubbard model in order to elucidate interrelationships among several broken‐symmetry and symmetry‐adapted approaches to molecular magnetism. Ab initio unrestricted Hartree–Fock and hybrid density functional theory (DFT) calculations of allyl radical dimers to decamers are also carried out for confirmation of characteristics revealed by the analytical investigations. A mesoscopic hydrogen radical cluster with 50 radical sites is studied by the ab initio hybrid DFT methods to elucidate functional behaviors of the above quantities with change of interatomic distance. The potential curves for the lowest and highest spin states of the cluster by these methods are depicted for the purpose. Implications of the present computational results are discussed in relation to size‐consistent spin projection and size effects on effective exchange interactions in mesoscopic radical clusters. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Embedded cluster ab initio study of the neutral oxygen vacancy in quartzand cristobalite

The oxygen vacancy in silica is characterized theoretically using an abinitio unrestricted Hartree-Fock, embedded-cluster approach. Two modelsare adopted for the host crystal, α-quartz and β-cristobalite.The defect formation energy, the transition energies from the ground to thefirst excited singlet and triplet states and the corresponding luminescenceare considered. The electronic structure of the defect in the different statesis analysed, and it is shown that the excitation corresponds to a transitionbetween a bonding and an anti-bonding combination of the dangling orbitals ofthe two silicon atoms adjacent to the vacancy. The influence of the size ofthe cluster and of the basis set adopted are discussed; the latter proves tobe more important. Difficulties in the convergence procedure were encountered,especially in the case of the vacancy in quartz, which prevented us fromobtaining a complete set of results. However, from a comparison of the twocrystal systems and an analysis of the data obtained, it is concluded that theexcitation and luminescence energies (≈5.5 and ≈3.5 eVto the triplet, and ≈8.5 and ≈7 eV to the singletexcited states) are compatible with the hypothesis that the oxygen vacancy isa model of the oxygen-deficient centre SiODC(I) in silica. The formationenergy of the vacancy is estimated at about 7 eV.

Ab initio study of organic mixed valency

A series of six radical cations of the type (DLD)+ was investigated at the ab initio unrestricted Hartree–Fock level. One localized and one delocalized conformation were systematically searched by full geometry optimization. At both nuclear arrangements, mostly found as being minima in the symmetry-restrained Hartree–Fock framework, excitation energies were calculated through the expansion of the wave function on single electronic excitations of the Hartree–Fock fundamental determinant and at the unrestricted Hartree–Fock or at the multiconfigurational self consistent field levels. Few calculations were also performed by taking into account some part of the electronic correlation. Except for N,N,N′,N′-tetramethyl p-phenylenediamine, all the studied compounds are localized stable cations, at the symmetry-restrained Hartree–Fock level. However, the reoptimization of their wave function changes this observation since only three of them seem to conserve a localized stable conformation. Most of the studied systems are characterized by one or two excited electronic states very close to the fundamental one and should thus present an unresolved broadened first absorption band in the near-infrared region. These features are in agreement with the available experimental data. Strong Hartree–Fock instabilities are found for the delocalized structure and put in relation with the existence of the large nonadiabatic coupling in this conformational region. The solvent influence is discussed in the Onsager dipolar reaction field framework. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 552–573, 2000