Ab Initio SCF MO Calculations Research Articles

Electronic and conformational features of a series of N-protonated benzomorphan molecules: N-substituent effects on relative binding at the agonist and antagonist states of the opioid receptor

The fsgo molecular fragment technique has been used to perform ab initio scf-mo calculations on a series of N-protonated benzomorphan congeners. Characteristics of high-energy occupied and low-energy unoccupied molecular orbitals (homos and lumos) are discussed in this report together with correlations between orbitals from different molecules. An investigation of the N-substituent conformation has been carried out for each molecule by means of an empirical molecular mechanics procedure. Based upon geometric and electronic comparisons, a model has been developed to rationalize the relative affinities of the drugs for the agonist and antagonist states of the morphine receptor. Two features of the N-substituents are considered to govern the antagonist/agonist ratio: (1) the availability of a suitable localized lumo to serve as an electron acceptor in charge-transfer interactions, and (2) a steric factor represented by a cis configuration in the moiety N—CH2—CC—CH3.

Aspects of oxopyridine-water interactions

The hydration schemes of the lactam and lactim tautomers of 2- and 4-hydroxypyridines have been established by appropriate electrostatic calculations. It is shown that hydration stabilizes more of the lactam than the lactim tautomers of these molecules. Ab initio SCF MO calculations performed for the complex of 4-pyridone with water show that the binding energies for water situated out of the plane of pyridone are smaller than when water is placed in the plane of the molecule. The comparison of the ab initio results with earlier CNDO/2 ones shows that the latter greatly overestimate the stability of the nonplanar complexes.

Pure organic magnetic polymer and an ab initio SCF-MO calculation

An ab initio SCF-MO calculation was performed on dibenzo [cd.lm] dicyclopenta [ghi.pqr] perylene using UHF/DFT/BP86 geometry. The modified perylene compound has two degenerate highest occupied molecular orbitals (HOMOs) with single electron each at −9.605 and −9.504 eV calculated by multi-configuration self-consistent field (MCSCF) method and it is a stable triplet ground state. A ladder polymer was designed with dibenzo [cd.lm] dicyclopenta [ghi.pqr] perylene such that two different polycyclic conjugated modules were connected alternatively to the ladder chain. The basic unit of the polymer was optimized to UHF/DFT/BP86 geometry and eigen values were calculated. Each ring in the ladder polymer chain is a 4 n cyclic pi system with peripheral electrons and has a triplet ground state. Finally, NICS, EPR and ZFS spectra were calculated for the dibenzo [cd.lm] dicyclopenta [ghi.pqr] perylene and the basic unit of polymer using DFT methods. It is observed that each polymer molecule is like a single-molecule magnet (SMM) – an object that is composed of molecules each of which behaves as an individual paramagnet.

Aromaticity on the edge of chaos: an Ab initio CCSD(T) study of the bimodal balance between aromatic and non-aromatic structures for 10-π-diheterocins and heteronins

CCSD(T) coupled cluster ab initio SCF-MO calculations for 10-π-heteroannulenes reveal a range of potential surface characteristics, ranging from single-minimum aromatic planar species to triple-minimum systems involving both planar-aromatic and the two enantiomers of a C2 symmetric non-planar non-aromatic species. For the specific case of 1,4-dioxocine, the existence of barriers separating the three minima is attributed to an anti-aromatic Möbius-like transition state connecting the two equilibrium forms.

Ab initio MO studies on the stability of intercalation compound Cu–hBN

Ab initio SCF-MO calculations are carried out for intercalation compound Cu–hBN by using molecular cluster model. Geometry optimization of hBN layer is calculated at the 6-31G ∗ basis set level, while single point calculation at the same basis set level is carried out for Cu–hBN. From the calculated interlayer distances, Mulliken populations, orbital interactions, atomic net charges and frontier orbital energy levels, the electronic structure and stability of Cu–hBN are discussed. It is confirmed by vibration analysis that this intercalation compound is merely a metastable structure. The densification mechanism of hBN ceramics by copper is also discussed.

Conformational study of α,2-dimethylstyrene: Raman and FT-IR spectra and ab initio calculations

Vibrational spectra (Raman and FT-IR) of liquid phase and ab initio SCF MO calculations at the B3LYP/6-31G* level are reported for α,2-dimethylstyrene. The calculations predict two minima with different orientations of the CC double bond relative to the 2-methyl group, but only the minimum with θ (C 2C 1C αC β)=112° (named skew) is deep enough to accommodate torsional levels. The role of intramolecular interactions on the conformational preferences is accessed through the comparison of the ab initio results for α,2-, α,3- and α,4-dimethylstyrene. The Raman spectra of the liquid sample show pairs of bands whose temperature-dependent intensities are ascribed to a conformational equilibrium. From the plot of logarithm of intensity ratio vs. inverse temperature, a Δ H value of 1.1±0.1 kJ mol −1 has been derived. The temperature-dependence of other Raman bands with no measurable conformational splitting can also be related with the conformational equilibrium by assuming different molar Raman intensities. The comparison of the experimental and calculated wavenumber shifts suggests that the gauche form is more stable than the skew form in the liquid, while ab initio results predict a single skew form for the isolated molecule. This discrepancy may arise from intermolecular interactions in the liquid.

Conformational analysis of a model of the sidechains in perfluorosulfonated membranes

The changes in energy for (CF 3) 2CFOCF 2CF 2SO 3H, a model for sidechains in perfluorosulfonated membranes, such as Nafion®, as a function of chain dihedral angles have been analyzed by ab initio SCF-MO calculations. For the highest level calculations, B3LYP/6-311+G*//HF/4-31G*, the barrier for rotation about a CC bond is ∼10 kJ mol −1 and ∼30 kJ mol −1 about a CO bond. Analytical expressions fitted to the values from the ab initio calculations for both rotations are presented. The effect of different solvents on the rotation barriers has been calculated via SCRF methods and shows the barriers to decrease for highly polar solvents. The possibility of intrachain hydrogen bonding to occur is outlined and discussed in relation to the ability of the membranes to rehydrate.

Ab initio MO studies on protonation mechanism of ethylene over catalyst HZSM-5

Four calculation models (I–IV) were proposed for studying the protonation mechanism of ethylene over catalyst HZSM-5. Ab initio SCF-MO calculations were carried out at the STO-3G basis set level. From the calculation results of geometry optimization and Mulliken population of these models, it has been shown that the cis-four-centered reaction mechanism (model I) is the most reasonable one, while the vertical complex reaction mechanism (model II) is of no effect, and models III and IV are possible for the terminal radical absorption.

A Theoretical Study of the Molecular Mechanism for the Carboxylation Chemistry in Rubisco

Stereochemical and structural aspects for the carbon dioxide fixation followed by hydration of d-ribulose 1,5-bisphosphate catalyzed by Rubisco are analyzed by using two model substrates, hydroxypropanone and 3,4-dihydroxy-2-pentanone. The molecular mechanisms for the carboxylation, C3-hydration and C2-inversion processes, are theoretically characterized and discussed with saddle points of index 1 representing transition structures (TS) and relevant (molded) intermediates mirroring the experimentally proposed mechanism. Ab initio SCF MO calculations at 3-21G and 6-31G** basis set levels of theory were used, while the correlation energy is included at the MP2/6-31G** level. The mapping starts from TS1, the carboxylation transition structure, which describes now the coupling of the carbon dioxide attack to the substrate C2-center in its dienol form with a synchronous interconversion of the C3 hydroxyl into a ketone group. Thereafter, water addition leads to a gem-diol followed by another step of intramolecular hydrogen transfer coupled with the C2−C3 bond breaking process. This TS breaks into one model of 3-d-phosphoglycerate product and an intermediate. The configuration inversion at the C2-center is found to be possible via intramolecular hydrogen transfer, as suggested by the corresponding TS relating the intermediate to the C2-inverted conformation. The complete set of steps found gives a self-contained description of the carboxylation followed by hydrolysis with proper stereochemistry. Comparisons between the transition state analogue: 2-carboxy-d-arabinitol-1,5-bisphosphate and TS1 show that both structures can be superposed with minimal root-mean-square deviation for C-atoms. All other calculated stationary TSs share the gross conformational features of TS1, and consequently, all molecular rearrangements detected in a vacuum can be accommodated without constraints into the active site of Rubisco. Transition structures invariances with respect to level of theory and molecular models are discussed.

Theoretical Study of the Molecular Mechanism for the Oxygenation Chemistry in Rubisco

A set of transition structures (TSs) related to the oxygenation reaction catalyzed by Rubisco is characterized theoretically. The TSs correspond to dioxygen fixation at the C2 center, hydrolysis, and C2−C3 bond breaking; reaction intermediates were found from TSs using the intrinsic reaction coordinate approach. Hydroxypropanone and 3,4-dihydroxy-2-pentanone are used as molecular models for the substrate d-ribulose-1,5-bisphosphate. Ab initio SCF MO calculations at a 3-21G and 6-31G** basis set level of theory were used; the correlation energy has been included at the MP2/6-31G** level. The set of TSs can be docked at the active site of the enzyme without steric hindrance. The geometries of the fully optimized reactants and intermediates differ to a large extent when compared with the saddle point structures. It is inferred that a molding work would be required in order to give them a molecular surface that is complementary in shape to that of the active site. A comparison of the theoretically determined ...

A theoretical evaluation of the ionization potentials for one-electron oxidized states of cytochrome c3

The ionization potentials of one-electron oxidized states of cytochrome c 3 were evaluated by numerical calculations. In the ionization processes from cytochrome c 3 0+ to c 3 1+, four ionization potentials were observed with respect to four hemes involved in cytochrome c 3. Ab initio SCF MO calculations were carried out for the four heme complexes to obtain their ionization potentials under vacuum (IP vacuums). The electrostatic potentials (EPs) which the apo-protein and the aqueous solvent produce at the heme irons were calculated by the particle–particle/particle–mesh (PPPM) algorithm based on the self-consistent boundary (SCB) method. Final theoretical ionization potentials of cytochrome c 3 (IP proteins) were evaluated as the sum of IP vacuums and EPs. The calculated IP proteins successfully reproduced the order of corresponding experimental values. The maximum difference among IP proteins was 130 mV which was approximately twice as large as that of experimental ones. The small differences among IP proteins were given by the delicate cancellations of IP vacuums and EPs. We also discuss the detailed electronic structures of hemes in cytochrome c 3.

Conformational equilibria for 5-fluoro-, 5-chloro- and 5-bromo-trans-penta-1,3-diene: the effect of the halogen substituent

The results of ab initio SCF MO calculations at the Hartree–Fock (3–21G and 6–31G*) and DFT levels (B3LYP/6–31G*, B3LYP/6–311+G**) for 5-fluoro- (5FP), 5-chloro- (5ClP) and 5-bromo-trans -penta-1,3-diene (5BrP) molecules and vibrational spectra (Raman and FTIR) of the corresponding liquid phases are reported and discussed. For the isolated systems, ab initio calculations at the B3LYP/6–311+G** level yield the anti -skew configuration (rotations around the C2—C3 and C4—C5 bonds, respectively) as the most stable form for all the molecules considered in this study. The Raman spectra of the liquid samples show pairs of bands whose temperature-dependent intensities are ascribed to conformational equilibria. From the plot of logarithm of intensity ratio vs. inverse temperature, ΔH values of −2±0.8, 1±0.3 and 1.5±0.2 kJ mol −1 were derived for 5FP, 5ClP and 5BrP, respectively, corresponding to anti-skew→anti -syn equilibria. Considering the Boltzmann populations at room temperature, the skew form is clearly the dominant one in all cases, except for 5FP in the liquid phase, where it shares approximately 50% of the population with the slightly more populated syn form. In addition, for 5ClP and 5BrP, the skew form is practically the only form to occur in the isolated molecule situation. In all cases, passing from the isolated molecules to the liquid phase has the effect of increasing the population of the syn form, a trend which is clearly more important for 5FP, where the latter form becomes barely dominant at room temperature. Copyright © 1999 John Wiley & Sons, Ltd.

Conformational equilibria for 5‐fluoro‐, 5‐chloro‐ and 5‐bromo‐trans ‐penta‐1,3‐diene: the effect of the halogen substituent

The results of ab initio SCF MO calculations at the Hartree–Fock (3–21G and 6–31G*) and DFT levels (B3LYP/6–31G*, B3LYP/6–311+G**) for 5-fluoro- (5FP), 5-chloro- (5ClP) and 5-bromo-trans -penta-1,3-diene (5BrP) molecules and vibrational spectra (Raman and FTIR) of the corresponding liquid phases are reported and discussed. For the isolated systems, ab initio calculations at the B3LYP/6–311+G** level yield the anti -skew configuration (rotations around the C2—C3 and C4—C5 bonds, respectively) as the most stable form for all the molecules considered in this study. The Raman spectra of the liquid samples show pairs of bands whose temperature-dependent intensities are ascribed to conformational equilibria. From the plot of logarithm of intensity ratio vs. inverse temperature, ΔH values of −2±0.8, 1±0.3 and 1.5±0.2 kJ mol −1 were derived for 5FP, 5ClP and 5BrP, respectively, corresponding to anti-skew→anti -syn equilibria. Considering the Boltzmann populations at room temperature, the skew form is clearly the dominant one in all cases, except for 5FP in the liquid phase, where it shares approximately 50% of the population with the slightly more populated syn form. In addition, for 5ClP and 5BrP, the skew form is practically the only form to occur in the isolated molecule situation. In all cases, passing from the isolated molecules to the liquid phase has the effect of increasing the population of the syn form, a trend which is clearly more important for 5FP, where the latter form becomes barely dominant at room temperature. Copyright © 1999 John Wiley & Sons, Ltd.

Molecular mechanism for oxygenation pathway in Rubisco.: Mapping transition structures and intermediates for model compounds of the substrate system

Transition structures and molecular intermediates related to the molecular mechanism of the reaction catalyzed by Rubisco have been theoretically characterized for different steps in the dioxygen fixation at the C2 center, hydrolysis and C2–C3 bond breaking. Hydroxypropanone is used as a minimal model for the substrate d-ribulose-1,5-bisphosphate, while ab initio SCF MO calculations at a 6-31G ** basis set level of theory were used. The set of transition structures map out all aspects of the reaction pathway for the real system without reliance on external acidic or basic sidechain residues, these latter may play a key role at a kinetic level not only stabilizing intramolecular transition structures. The present results represent a basic model for a simpler mechanistic alternative.

Theoretical study on the electronic structures of various F centers in MgO crystals

Ab initio SCF-MO calculations were performed on low-lying electronic states of various F centers in MgO crystals by using embedded cluster models. Because a simple cluster model embedded with point charges alone gave poor results, we generated environmental potentials (EPs) in a spectral representation scheme for Mg 2+ and O 2− ions and used them instead of point charges around the clusters under consideration. Using embedded cluster models with the EPs and point charges, we calculated the low-lying electronic states of various F centers in MgO. The calculated order in energy was found to be: the 1A 1 state of the surface F center < the 1E state of the surface F center < the 1B 3u state of the bulk M center (F aggregates) < the 1T 1u state of the bulk F center. The energy separation of the 1E , 1B 3u , and 1T 1u states from the lowest state were 1.22, 2.46 and 4.05 eV, respectively, which explains the observed bands.

Molecular structure and vibrational spectra of methyl cyanoacetate: an FT-IR, raman and ab initio molecular orbital study

The results of a combined vibrational and structural study of methyl cyanoacetate undertaken by Raman and infrared spectroscopy, and ab initio SCF-MO calculations are presented. It is shown that for the isolated molecule situation, as well as in the liquid phase, methyl cyanoacetate exists as a mixture of two main conformers of similar energies, differing by the relative orientation of the NCCCO axis (the syn and skew forms, having a NCCCO dihedral angle equal to 0° and in the ± 140° region, respectively). In the crystalline state, only the thermodynamically most stable syn conformer remains. The ab initio SCF-MO optimized geometries of the various possible conformers, their relative stabilities, dipole moments and harmonic force-fields are presented, and the conformational dependence of some relevant structural parameters is used to characterise the most important intramolecular interactions present in the various forms studied. Finally, results of a normal mode analysis based on the ab initio calculated vibrational spectra are used to help interpret the experimental vibrational data, enabling a detailed assignment of both Raman and infrared spectra.

HeI photoelectron spectroscopic studies on the electronic structure of alkyl nitrosamines

HeI photoelectron spectroscopic (PES) studies on the electronic structure of alkyl nitrosamines R 2N 2O (R = CH 3−, CH 3CH 2−, and CH 3CH 2CH 2−) are reported. The assignment of the PES bands for this series of compounds has been made with the aid of the band shapes, the band intensity and ab initio SCF MO calculations based on the 631 ∗ G basis sets. Both PES experiment and the ab initio SCF MO calculations show that the detoxification ability of nitrosamine with longer alkyl chain is stronger.

A HeI photoelectron spectrum of the [Al(CH 3) 3] 2 dimer

The HeI photoelectron spectrum (PES) of the [Al(CH 3) 3] 2 dimer is recorded for the first time. To assign the PES bands, an ab initio SCF MO calculation for the dimer has also been performed. The four splitting peaks of the first PE band are respectively designated to electron ionization of the four frontier 8b u, 13a g, 7b g, and 7b u orbitals of the dimer. They originate from the recombination of the two HOMO (5e′) of the two monomers in the forming of the dimer. That is to say, during the formation of the dimer from the two monomers, the reduction of molecular symmetry (from the C 3h symmetry of the monomer to the C 2h symmetry of the dimer) leads to the undegeneration of the degenerate orbitals.

A theoretical study of the photoinduced desorption of I — from a CF3I dimer

Ab initio SCF-MO calculations using effective core-potential basis sets are employed to evaluate ionization potentials and electron affinities for CF3I and the geometries and energies of the singlet and triplet states of the CF3I dimer. The calculated geometry of the single state of the dimer is in qualitative agreement with the experimental geometry for condensed phase CF3I. The calculated energy for vertical excitation from the singlet to the triplet state is 4.1 eV at the Hartree-Fock level and 4.5 eV after incorporation of correlation at the Moller-Plesset 2nd-order level, consistent with excitation by 193 nm (6.4 eV) light. The equilibrium geometry of the triplet consists essentially of a CF3I+, CF3I− ion pair, in which the CI bond distance in the anionic component has increased to 5.5Å, compared with 2.1Åin the neutral molecule. The calculated binding energy of the triplet ion pair is about 4 eV.

Raman scattering tensors in thymine molecule from an ab initio MO calculation

Ab initio SCF MO calculations have been made of the thymine molecule for the permanent polarizability and the polarizability derivatives with respect to the normal coordinates. The latter correspond to the components of the Raman tensors, and each of these tensors was brought into a visualized form by a transformation of the tensor axes into the principal system. For a comparison with such computational findings, a polarized Raman spectroscopic measurement has been made of a single crystal of thymine with 488.0 nm excitation. For most of the in-plane vibrations, calculated tensors were found to be well correlated with the observed Raman scattering anisotropy. On the basis of such correlations, discussions are given as for the polarizability oscillations caused by the atomic displacements in the molecule.