MO Ab Initio Research Articles

ChemInform Abstract: Geometrical and Electronic Features of the Benzene Ring in Benzocycloalkenes and Related Compounds.

The fusion of a small, strained ring on a benzene molecule causes remarkable perturbations on the geometry of the latter molecule, perturbations which reduce with increasing number of atoms in the fused ring and become negligible as fusion involves rings larger than five-membered ones. The Cambridge structural database was searched for the experimental geometrical features of compounds containing from three- to ten-membered cycloalkene rings condensed with benzene. MO ab initio calculations at the 3-21 G level were employed for studying the calculated features, i.e. geometries, total energies, enthalpies of formation, strain energies and π-electron distribution, in compounds containing cycloalkenes (from three- to five-membered rings) and related rings with further unsaturation, and in systems related to benzocyclopropene with a heteroatom (oxygen) or a positively charged carbon. The effect of the additional strain, generated in the molecule by the fusion of the two rings, on molecular geometry and π-electron distribution is discussed. Strain, which is highest when a three-membered ring is annellated to the benzene molecule, seems to be the main factor responsible for the geometrical perturbations of these molecules, whereas the π-electron distribution is mainly determined by interactions between the electrons of the atoms or groups at the functions of the annellated ring and those of the benzene π-orbitals.

Theoretical and electrochemical analysis of dissociative electron transfers proceeding through formation of loose radical anion species: reduction of symmetrical and unsymmetrical disulfides.

The dissociative reduction of a series of symmetrical (RSSR, R = H, Me, t-Bu, Ph) and unsymmetrical disulfides (RSSR', R = H, R' = Me and R = Ph, R' = Me, t-Bu) was studied theoretically, by MO ab initio calculations and, for five of them, also experimentally, by convolution voltammetry in N,N-dimethylformamide. The reduction is dissociative but proceeds by a stepwise mechanism entailing the formation of the radical anion species. The electrochemical data led to estimated large intrinsic barriers, in agreement with an unusually large structural modification undergone by the disulfide molecules upon electron transfer. The theoretical results refer to MP2/3-21G*//MP2/3-21G*, MP2/3-21*G*//MP2/3-21G*, CBS-4M, and G2(MP2), the latter approach being used only for the molecules of small molecular complexity. A loose radical-anion intermediate was localized and the dissociation pattern for the relevant bonds analyzed. For all compounds, the best fragmentation pathway in solution is cleavage of the S-S bond. In addition, S-S bond elongation is the major structural modification undergone by the disulfide molecule on its way to the radical anion and eventually to the fragmentation products. The calculated energy of activation for the initial electron transfer was estimated from the crossing of the energy profiles of the neutral molecule and its radical anion (in the form of Morse-like potentials) as a function of the S-S bond length coordinate. The inner intrinsic barrier obtained in this way is in good agreement with that determined by convolution voltammetry, once the solvent effect is taken into account.

A full dimensional ab initio direct trajectory study on the ionization dynamics of SiH4

Ab initio MO and direct ab initio trajectory calculations have been applied to the ionization processes of SiH4 in order to shed light on the reaction mechanism of SiH4+ which plays an important role in plasma dry etching processes. The calculations showed that two reaction channels, I and II, were concerned with the decomposition pathways from the vertical ionized state of SiH4. The intermediates for channels I and II were expressed schematically by SiH3+–H and H2–SiH2+, respectively. The lifetime of the intermediate complex in channel I (SiH3+–H) was negligibly short, suggesting that the reaction proceeds via a direct mechanism. On the other hand, the intermediate complex H2–SiH2+ has a longer lifetime than SiH3+–H. 35% of the total available energy was partitioned into the relative translocation energy in channel I, whereas it was 8% in channel II. Vibrational- and rotational-excitation of H2 was found in channel II. The mechanism of decomposition of SiH4+ was discussed on the basis of the theoretical results.

Effect of heteroatoms in determining the rotational barrier around carbon–carbon double bond in substituted ethylenes. An MO ab initio theoretical study

Internal rotational barriers around the exocyclic partial CC double bond were calculated for a wide group of heterocyclic derivatives as a function of the different structure of the heterocyclic ring and of the nature of heteroatoms, by means of MO abinitio theory. The rotational barriers refer to the two-fold potential energy, V 2, obtained from single-determinant Hartree–Fock (HF) wave functions and at MP2/6-31G ∗//HF/6-31G ∗ level of theory. The V 2 values seem to represent homogeneously the rotational barrier in substituted ethylenes with varying polar character of the CC bond, ranging from unpolarized ethylene to molecules having a marked push–pull character, and thus allow the effect of substituents on the height of the barrier to be compared. Sets of parameters quantifying the heteroatom effect of constantly modulating the barrier in the different heterocyclic rings were extracted, and two heteroatoms were found to have an additive effect when acting in the same ring. The difference between the V 2 values and the rotational barriers calculated from the HF energy of the perpendicular conformation is discussed in the light of a qualitative approach based on calculated contributions of singlet excited states to the electronic configuration of the perpendicular conformation.

Exocyclic push–pull conjugated compounds. Part 4: rotational barriers in poorly polarized push–pull ethylenes

The rotational barrier for substituted ethylenes was calculated with MO ab initio methods, both in the Hartree–Fock (HF) single determinant scheme and with multiconfigurational self-consistent field (MCSCF) approaches. The HF model affords reliable results only when applied to molecules substituted with strong electron donor groups, assigning a push–pull character to the molecule. The MCSCF approach was employed for calculating rotational barriers in poorly polarized ethylenes not directly amenable to the HF methods; however, this method was found hard to handle for low symmetry molecules with substituents interacting with the double bond. A method is proposed based on the interpolation of the energy of the perpendicular conformation from a Fourier truncated function constructed with HF molecular energies calculated for frozen conformations twisted up to 60°. The application of HF theory for studying internal rotation in substituted ethylenes with poorly polarized character is discussed and an upper limit of 35–40kcal/mol can be set up for having reliable barriers from the calculated energy of the rotational transition state at this level of theory.

Electronic and structural effects determining rotational barriers about the C–N bond in enamines of pyran-4-one and thiopyran-4-one—A theoretical MO ab initio approach to the interpretation of experimental results

Ab initio MO calculations were carried out in 2-chloro-6-NR 2-pyran-4-ones, 2-chloro-6-NR 2-thipyran-4-ones and in their protonated forms with the aim of discussing the electronic and structural effects modulating the rotational barriers about the C–N partial double bond measured in previous research. The barriers in these molecules depend on NR 2 substituents (pyrrolidino, dimethylamino, piperidino and morpholino groups were examined), on the O/S atoms in the pyranone/thiopyranone rings and differ in neutral and protonated forms. The results of calculations, carried out at different levels of theory (HF/6-31G ∗//HF/6-31G ∗, HF/6-31G ∗∗//HF/6-31G ∗∗, B3LYP/6-31G ∗∗, MP2/6-31G ∗∗/MP2/6-31G ∗∗) and simulating the effect of a solvent (self-consistent isodensity polarized continuum model) were employed to analyse the effect of the different molecular fragments on the barrier to internal rotation about the partial C–N double bond. Parallel trends are found for calculated and experimental results as a function of changes in molecular structure even though the calculated barriers for the ions are overestimated.

Exocyclic push–pull conjugated compounds. Part 3. An experimental NMR and theoretical MO ab initio study of the structure, the electronic properties and barriers to rotation about the exocyclic partial double bond in 2- exo-methylene- and 2-cyanoimino-quinazolines and -benzodiazepines

The structure of a number of 2- exo-methylene substituted quinazolines and benzodiazepines, respectively, 1, 3a, b, 4 ( X=–CN, –COOEt ) and their 2-cyanoimino substituted analogues 2, 3c, d ( X=–CN, –SO 2C 6H 4–Me (p) was completely assigned by the whole arsenal of 1D and 2D NMR spectroscopic methods. The E/ Z isomerism at the exo-cyclic double bond was determined by both NMR spectroscopy and confirmed by ab initio quantum chemical calculations; the Z isomer is the preferred one, its amount proved dependent on steric hindrance. Due to the push–pull effect in this part of the molecules the restricted rotation about the partial C 2,C 11 and C 2,N 11 double bonds, could also be studied and the barrier to rotation measured by dynamic NMR spectroscopy. The free energies of activation of this dynamic process proved very similar along the compounds studied but being dependent on the polarity of the solvent. Quantum chemical calculations at the ab initio level were employed to prove the stereochemistry at the exo-cyclic partial double bonds of 1– 4, to calculate the barriers to rotation but also to discuss in detail both the ground and the transition state of the latter dynamic process in order to better understand electronic, inter- and intramolecular effects on the barrier to rotation which could be determined experimentally. In the cyanoimino substituted compounds 2, 3c, d, the MO ab initio calculations evidence the isomer interconversion to be better described by the internal rotation process than by the lateral shift mechanism.

MO ab initio study of the structural and electronic properties of the 5-lipoxygenase inhibitor zileuton

The conformational space of zileuton was investigated by MO ab initio calculations at the HF/6–31G ∗∗ level. The computed energies of the three most stable conformers were found to lie in a small range (< 4.0 kcal/mol), indicating a certain degree of conformational flexibility. The preferred protonation site in vacuo and in water (simulated within the Onsager reaction field model) was characterised; the cation resulting from carbonyl oxygen protonation was predicted to be the most stable, both in vacuo and in water. The UV spectrum of zileuton was also recorded in different solvents and the experimental results were implemented by the outcome of a CI-Singles theoretical study of the excited state properties of the model compound benzothiophene, which is the chromophoric moiety of zileuton.

Excited States of 1,6-Methano[10]annulene: Site Selection Fluorescence and Fluorescence Excitation Spectroscopy on S1

Fluorescence, S1 → S0, and fluorescence excitation, S0 → S1, spectra of 1,6-methano[10]annulene have been measured in glassy matrixes at low temperature under moderate site selection conditions. The polarization ratios of both spectra have been also measured at 77 K. MO ab initio calculations including correlation effects indicate that the molecule has one energy minimum in the ground state and one in the lowest excited singlet state. They correspond to bond-equalized structures of aromatic character. The spectra are accordingly discussed in terms of transitions involving the aromatic form of 1,6-methano[10]annulene. A good correlation is found between observed and calculated Franck−Condon intensities.

A theoretical MO ab initio approach to the conformational properties and homolytic bond cleavage in aryl disulphides

The structural and conformational properties of disulphides R 1S-SR 2, with R 1 = phenil ring ( Ph) and R 2 = H, Me and Ph and, for a comparison, those of the disulphides with R 1, R 2 = H, Me were determined with MO ab initio calculations. The level of theory chosen was the 3–21G ∗ with full geometry relaxation and electron correlation corrections at a second order Møller-Plesset perturbation scheme (MP2/3-21G ∗//MP2/3-21G ∗). This choice allowed a comparison of the properties calculated for the molecules containing alkyl and phenyl groups at the same level of theory. All the disulphides examined showed patterns of the potential energy for internal rotation with a minimum conformation of skew type and two maxima, one of cis and one of trans type, with the former representing the higher transition state for internal rotation. The effect of the R group is higher on the cis barrier and the effect of Me and Ph is respectively to increase and decrease the barrier, with respect to RH. The bond energy required for homolitically breaking the bonds (BDE) in these molecules and in the radicals RSS was estimated both from calculated total molecular energies, and from heats of formation of the species involved in the dissociation processes. The BDE's from the ab initio energies were found to have been largely underestimated, which applies to a different extent to the SS, SH and CS bonds. For the SS bond, the BDE's calculated at the level of theory adopted here are proportional to values from experiments or from higher levels of theoretical approaches. For the disulphides with R 1, R 2 = H, Me, calculations were performed with the sophisticated Gaussian-2 (G2) scheme and the BDE's obtained are very close to the most accurate determinations, showing that a high level of theory is necessary to obtain these quantities at a convenient level of confidence. The origin of the barriers for internal rotation and of the different bond strengths in the molecules and radicals containing the SS bond was analyzed within the natural bond orbital (NBO) description of donor-acceptor interactions.

Theoretical MO ab initio investigation of the reductive C–Cl bond cleavage in benzyl chloride, benzotrichloride † and in the analogous 4-pyridine derivatives

Reductive electron transfer on the title compounds has been studied theoretically with MO ab initio methods, using the 6-31G* basis set and second-order Moller–Plesset perturbation theory, in order to verify the eventual stability of their radical anion and to analyze the C–Cl bond breaking process both in the neutral molecules and in the anions. The effect of the basis set has been tested at single point energies with the 6-311G** basis set. The geometries of the neutral molecules and radicals formed after bond dissociation are fully relaxed. The energy profiles of the radical anions as a function of the C–Cl bond distance have been found to be dissociative. The energy of activation and the structure of the activated complex have been studied in the forbidden crossing of the energy profiles of the neutral molecule and radical anion. The results show that the activation energy of the process is affected both by the number of chlorine atoms on the methyl group and by the different aromatic ring, yet the energy of reaction is significantly affected only by the number of chlorine atoms. When compared with reduction potentials determined experimentally in a previous work, these activation energies show an excellent linear relationship. The results are discussed in the frame of the Marcus–Hush model of electron transfer and it appears that chloromethyl derivatives of pyridine and benzene do not strictly follow the same reaction mechanism at the end of applying this model.

The Source for the Difference Between Sulfhydryl and Hydroxyl Anions in Their Nucleophilic Addition Reaction to a Carbonyl Group: A DFT Approach.

Ab initio calculations show that sulfhydryl anion has a significantly lower potential than the hydroxide anion for stabilizing the products of its attack on carbonyl moieties - the tetrahedral complexes (TC). In this paper we analyze the factors that contribute to this phenomenon. Quantum mechanical MO ab initio calculations were used for studies of two reaction series, one for the attack of hydroxyl and one for the attack of sulfhydryl anion on different carbonyl compounds and their analogs. All of the anionic TCs formed by HS- are characterized by higher charge transfer, but are significantly less stable than the relevant TC of HO-. To explain the phenomenon we used a simple qualitative model based on Density Functional Theory (DFT). The crucial role of the occupied valence MOs is demonstrated in the process of electronegativity equalization between the donor and acceptor fragments in the final TC product. The sulfhydryl anion has significantly lower potential to stabilize TC products in comparison with the hydroxide anion because of the larger extent of electron back-donation from the electrophile′s HOMOA to the nucleophile′s LUMOD. This electron back-donation thus reduces the stability of the anionic TC in the case of HS- and may account for the calculational results. Applications of this work to enzyme reactions help in understanding the differences in mechanisms of serine and cysteine proteases and may be used to guide the design of inhibitors for these enzymes. In perspective, the back-donation phenomenon discussed here may be applied to the study of electron transfer processes involving oxidation-reduction enzymes.

The dissociative nature of the radical anion of benzyl chloride. A theoretical MO ab initio approach

The potential energy profile of the benzyl chloride radical anion as a function of the CCl bond distance calculated with ab initio MO theory, 6–31G ∗ level and molecular relaxation shows a purely dissociative behavior, provided that constraints are dictated to the direction of the departing chloride anion. If the departing anion is allowed complete freedom, a minimum in the energy profile is found corresponding to a molecular complex between the benzyl radical and the chloride anion. This behavior differs from that of the chlorobenzene radical anion, which shows a change of the symmetry of the electronic ground state from 2B 1 to 2A 1 on elongating the CCl bond distance.

Ab initio studies of molecules with NCCO units. Part 2. 1-Amino-2-propanone, 2-methylaminoethanal and 2-aminopropanal

A complete conformational analysis of all the monomethylated derivatives of 2-aminoethanal (2AE) was carried out using MO ab initio with the 6-31G ∗∗ basis set, and it was inferred that methylation produces an increase in stability with respect to the initial compound 2AE. Geometric tendencies related to the existence of intramolecular hydrogen bonding and anomeric effects are discussed. Finally, the differences between the ab initio results and those produced by the current consistent MM3(92) force field are analysed.

Internal rotation in α-chlorinated toluenes: A theoretical MO ab initio study of the rotational barriers and ground-state conformations

Potential energy profiles for internal rotation in benzyl chloride 1. ( 1), benzal chloride 2. ( 2), benzotrichloride 3. ( 3), and in the corresponding derivatives ortho substituted with a chlorine atom 4. ( 4–6) were derived from total molecular energies calculated with MO ab initio methods at the 6-31G ∗//6-31G ∗ level. Energy values for critical points were recalculated at the 6-311G ∗∗//6-31G ∗ level using MP2 perturbation theory. The geometrical structure of the minima and transition states is discussed and the origin of the barriers to internal rotation analysed. From a natural bond orbital (NBO) model based on localized orbitals and within a donor-acceptor viewpoint, the electronic interactions governing the energy barriers in these molecules are rationalized in terms of effects familiar to the chemical nomenclature. Thus, in compounds 1–3 an electronic interaction between the π system and the chlorine atom is found to be operative, with prevailing donor character from the π system, but interactions involving other orbitals also contribute to the rotational barrier. These effects operate to the same extent in the o-Cl substituted derivatives 4–6 and do not justify the higher rotational barrier calculated for these compounds. An empirical approach was used to estimate non-bonded atom-atom potentials. These interactions, which can be included within the so-called “steric effects”, were found to be the most important ones contributing to the energy barriers in compounds 4–6.

The ground state of antiaromatic 1,3,5,7-tetra-tert-butyl-s-indacene

The electronic and vibrational properties of the antiaromatic molecule 1,3,5,7-tetra-tert-butyl-s-indacene (TTBI) in the ground state are investigated in this paper. MO ab initio calculations have been performed on TTBI and the parent molecule, s-indacene (I). The results show that the C-C bonds of s-indacene alternate in length and the corresponding C 2h structure is more stable than the structure without bond alternation (D 2h symmetry), regardless of the basis set used. Bond length alternation is decreased by alkyl substitution in the 1, 3, 5, and 7 positions

The behaviour of lithium electrodes in propylene and ethylene carbonate: Te major factors that influence Li cycling efficiency

The Li cycling efficiency surface chemistry and Li morphology in ethylene carbonate (EC) and propylene carbonate (PC) based electrolyte solutions were investigated and correlated. Surface sensitive ex situ FTIR spectroscopy, X-ray microanalysis and scanning electron microscopy were used in conjunction with standard electrochemical techniques. EC is more reactive than PC in electroreduction processes and is reduced on noble metals to ethylene dicarbonate. The difference in reactivity between the two solvents is discussed, based on MO ab initio calculations of their radical anions (and Li + stabilized radical anions). In spite of the high reactivity of these systems to lithium, the Li cycling efficiency is strongly dependent on the presence of additives and contaminants at the ppm level that modify the Li surface chemistry in solutions. The two alkyl carbonate solvents decompose when stored over activated Al 2O 3 and CO 2 is formed. The presence of CO 2 in solutions increases the Li cycling efficiency considerably due to the formation of Li 2CO 3 on the Li surfaces.

Geometrical and electronic features of the benzene ring in benzocycloalkenes and related compounds

The fusion of a small, strained ring on a benzene molecule causes remarkable perturbations on the geometry of the latter molecule, perturbations which reduce with increasing number of atoms in the fused ring and become negligible as fusion involves rings larger than five-membered ones. The Cambridge structural database was searched for the experimental geometrical features of compounds containing from three- to ten-membered cycloalkene rings condensed with benzene. MO ab initio calculations at the 3-21 G level were employed for studying the calculated features, i.e. geometries, total energies, enthalpies of formation, strain energies and π-electron distribution, in compounds containing cycloalkenes (from three- to five-membered rings) and related rings with further unsaturation, and in systems related to benzocyclopropene with a heteroatom (oxygen) or a positively charged carbon. The effect of the additional strain, generated in the molecule by the fusion of the two rings, on molecular geometry and π-electron distribution is discussed. Strain, which is highest when a three-membered ring is annellated to the benzene molecule, seems to be the main factor responsible for the geometrical perturbations of these molecules, whereas the π-electron distribution is mainly determined by interactions between the electrons of the atoms or groups at the functions of the annellated ring and those of the benzene π-orbitals.

Probing the Anomeric Effect in OCN Systems Theory vs. Experiment: MO‐ab initio Calculations and a Structural‐Statistical Analysis

AbstractA combined computational (MO ab initio) and structural‐statistical study of molecules containing the OCN moiety is presented. Aminomethanol, the simplest member of this series, was computed using GAUSSIAN‐82 with the 3‐21G and 6‐31G* basis sets and with complete geometry optimization, as well as with MP3//6‐31G*. A set of carefully selected molecules containing the OCN unit was retrieved from the Cambridge Structural Database (CSD), and its structural parameters were analyzed according to an established procedure. Comparison between experimental and computational data was thus made possible. Results are consistent with the co‐existence of two unequal anomeric effects in this system: a strong nN‐σ*CO anomeric interaction, and a weak nπO‐σ*CN one. The ability of the two basis sets to reproduce the energies and structural characteristics of the stereoelectronic effects is assessed, including the significance of using polarization functions and the inclusion of correlation energy.

Three-dimensional aromaticity: A topological analysis of computational methods

The deltahedral boranes Bn Hn2− (6 ≤n ≤ 12) may be regarded as three-dimensional delocalized aromatic systems in which surface bonding and core bonding correspond to σ-bonding andπ-bonding, respectively, in planar polygonal two-dimensional hydrocarbons Cn Hn(n − 6)+ (n = 5, 6, 7). The two extreme types of topologies which may be used to model core bonding in deltahedral boranes are the deltahedral (Dn) topology based on the 1-skeleton of the underlying deltahedron and the complete (Kn) topology based on the corresponding complete graph. Symmetry factoring of generalized graphs representing the core-bonding interactions in the highly symmetrical octahedral borane B6 H6 and icosahedral borane B12H122− leads to methods for separating the effects of core and surface bonding in molecular orbital energy parameters. Such analyses of the Hoffmann—Lipscomb LCAO-MO extended Mickel computations, the Armstrong—Perkins—Stewart self-consistent molecular orbital computations, and SCF MO ab initio Guassian 82 computations on B6H62− and B12H122− indicate that the approximation of atomic orbitals by a sum of Gaussians, as is typical in modem ab initio computations, leads to significantly weaker apparent core bonding approximated more closely by deltahedral (Dn) rather than complete (Kn) topology. Furthermore, theT1u core orbitals which, if pure, would be nonbonding in octahedral (D6) core topology for B6 H62− and bonding in icosahedral (D12) core topology for B12H122−, become antibonding through strong core—surface mixing. Because of this, the simpler graph-theory derived model for deltahedral boranes using complete (Kn) core bonding topology gives the correct numbers of bonding orbitals even in cases where the complete graphKn is a poor approximation for the actual core bonding topology.