DFT and TDDFT study related to electron transfer in nonbonded porphine...C60 complexes

Spectroscopic properties of a ground state nonbonded porphine-buckminsterfullerene (H2P...C60) complex are studied in several different relative orientations of C60 with respect to the porphine plane by using the density functional (DFT) and time-dependent density functional (TDDFT) theories. The geometries and electronic structures of the ground states are optimized with the B3LYP and PBE functionals and a SVP basis set. Excitation energies and oscillator strengths are obtained from the TDDFT calculations. The relative orientation of C60 is found to affect the equilibrium distance between H2P and C60 especially in the case of the PBE functional. The excitation energies of different H2P...C60 complexes are found to be practically the same for the same excitations when the B3LYP functional is used but to differ notably when PBE is used in calculations. Existence of the states related to a photoinduced electron transfer within a porphyrin-fullerene dyad is also studied. All calculations predict a formation of an excited charge-transfer complex state, a locally excited donor (porphine) state, as well as a locally excited acceptor (fullerene) state in the investigated H2P...C60 complexes.     

Quantum mechanical study of stereoselectivity in the oxazaborolidine-catalyzed reduction of acetophenone

Chiral oxazaborolidines, known as CBS catalysts after the work of Corey, Bakshi and Shibata, are used for the stereoselective reduction of prochiral ketones to secondary chiral alcohols. Due to their relative low cost, ease of use, and high selectivity, their popularity has remarkably grown in the last 15 years. Oxazaborolidine-catalyzed reductions have been much studied, both experimentally and computationally, by means of semiempirical methods. Though, a more accurate high level quantum mechanical study on the complete system, capable of elucidating reliably the origins of stereoselectivity, is still lacking. Therefore, the acetophenone (PhMK) reduction with Corey's oxazaborolidine has been modeled for the first time with ab initio and DFT-B3LYP calculations on the complete system as well as with AM1. Calculations on the complexation of BH(3) to CBS, which can occur only in a cis fashion with respect to the hydrogen on the stereogenic C-4 carbon atom, have allowed us to confirm the great rigidity of Corey's catalyst, possibly determining its excellent enantioselectivity. Acetophenone-CBS-BH(3) complexes were characterized at various levels of theory, and it was found that the picture obtained depends heavily on the method adopted. A computational strategy for identifying the hydride transfer transition states of the competing pathways was developed and tested, using a model system for which the transition state geometry was already known. The application of the TS search method to the reduction of acetophenone allowed the characterization of the TS's for the competing pathways in this reaction, making it possible to predict with good quantitative accuracy the stereochemical outcome of the reaction at all the levels of theory adopted. The characterization of the intermediate oxazadiboretane products confirmed that the highly exothermic hydride transfer provides the thermodynamical drive for the reaction.     

Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction

We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.     

Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis

We report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. The assigned role of Tyr728 differs from previous suggestions but is consistent with the established mechanism of other zinc proteases.     

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential with a recently developed semiempirical AM1/d-PhoT model for phosphoryl transfer reactions. Simulations are used to derive one- and two-dimensional potentials of mean force to examine specific reaction paths and assess the feasibility of proposed general acid and base mechanisms. Density-functional calculations of truncated active site models provide complementary insight to the simulation results. Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphorylation are presented, and the roles of A38 and G8 as general acid and base catalysts are discussed. The computational results are consistent with available experimental data, provide support for a general acid/base mechanism played by functional groups on the nucleobases, and offer important insight into the ability of RNA to act as a catalyst without explicit participation by divalent metal ions.     

Quantum mechanical study of tautomerism of methimazole and the stability of methimazole–I2 complexes

DFT and ab initio theoretical methods were used to calculate the relative stability of tautomers in the methimazole (MMI). The calculations show that the thione form of MMI 1 is more stable than the thiol tautomer in good agreement with the experimental results. The DFT and ab initio calculations were also used to determine the stability of MMI–I₂ complexes. All methods suggest that the methimazole in the MMI–I₂ complex exists almost exclusively as the thione tautomer. The Gibbs free energy difference between planar and perpendicular forms of thione tautomer of MMI–I₂ complex indicates that the planar form is the predominant complex. The counterpoise corrected Gibbs free energy also shows that the MMI–I₂(plan.) complex is more stable than the MMI–I₂(perp.) complex. These predictions are in good agreement with the experimental results. By using the natural bond orbital (NBO) approach, the effects of charge transfer interactions on the stability of MMI–I₂ complexes were investigated. The LP₃(S)→σ*(I–I) and LP₃(I)→σ*(N–H) charge transfer interactions may be very important in the stability of the planar form. The results show that the LP₃(S)→σ*(I–I) charge transfer interaction causes a greater increase in the σ*(I–I) antibond occupation number, and concomitantly, a greater increase in the corresponding I–I bond length in the planar complex with respect to the perpendicular complex. The LP₃(S)→σ*(I–I) charge transfer interaction is assisted by NHI intermolecular hydrogen bonding. The atom in molecule (AIM) analysis shows that the charge density and its Laplacian at the SI bond critical point of the planar complex is greater than the perpendicular complex.     

Quantum mechanical study of the ring-closing reaction of the hexatriene radical cation

The ring-closing reaction of hexatriene radical cation 1(*)(+) to 1,3-cyclohexadiene radical cation 2(*)(+) was studied computationally at the B3LYP/6-31G* and QCISD(T)/6-311G*//QCISD/6-31G* levels of theory. Both, concerted and stepwise mechanisms were initially considered for this reaction. Upon evaluation at the B3LYP level of theory, three of the possible pathways-a concerted C(2)-symmetric via transition structure 3(*)(+) and stepwise C(1)-symmetric pathways involving three-membered ring intermediate 5(*)(+) and four-membered ring intermediate 6(*)(+)-were rejected due to high-energy stationary points along the reaction pathway. The two remaining pathways were found to be of competing energy. The first proceeds through the asymmetric, concerted transition structure 4(*)(+) with an activation barrier E(a) = 16.2 kcal/mol and an overall exothermicity of -23.8 kcal/mol. The second pathway, beginning from the cis,cis,trans rotamer of 1(*)(+), proceeds by a stepwise pathway to the cyclohexadiene product with an overall exothermicity of -18.6 kcal/mol. The activation energy for the rate-determining step in this process, the formation of the intermediate bicyclo[3.1.0]hex-2-ene via transition structure 9(*)(+), was found to be 20.4 kcal/mol. More rigorous calculations of a smaller subsection of the potential energy hypersurface at the QCISD(T)//QCISD level confirmed these findings and emphasized the importance of conformational control of the reactant.     

Quantum mechanical study of a reaction path bifurcation model

The feasibility of close coupling techniques for bifurcation processes is investigated using a simple model. Density contours and a flux map illustrate the bifurcation process. The relevance of this study to the theory of three-dimensional chemical reactions is discussed.     

Quantum mechanical study on plasmon resonances in small ring clusters

The collectivity of the electronic motion in small sodium clusters with ring structure is studied by time‐dependent density functional theory. The formation and development of collective resonances in the absorption spectra were obtained as a function of the ring radius. In small ring clusters, besides the lower‐energy mode and the higher‐energy mode, there is another plasmon resonance mode, that is, the reverse two‐dipole mode. For the reverse two‐dipole mode, the formations of these two dipoles are due to the external field inducement and the shielding effect, although the resonant excitation is mainly due to the coupling effect of the electrons of these two dipoles. © 2012 Wiley Periodicals, Inc.     

Quantum mechanical study of sulfuric acid hydration: atmospheric implications

The role of the binary nucleation of sulfuric acid in aerosol formation and its implications for global warming is one of the fundamental unsettled questions in atmospheric chemistry. We have investigated the thermodynamics of sulfuric acid hydration using ab initio quantum mechanical methods. For H(2)SO(4)(H(2)O)(n) where n = 1-6, we used a scheme combining molecular dynamics configurational sampling with high-level ab initio calculations to locate the global and many low lying local minima for each cluster size. For each isomer, we extrapolated the M?ller-Plesset perturbation theory (MP2) energies to their complete basis set (CBS) limit and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled harmonic vibrational frequencies. We found that ionic pair (HSO(4)(-)·H(3)O(+))(H(2)O)(n-1) clusters are competitive with the neutral (H(2)SO(4))(H(2)O)(n) clusters for n ≥ 3 and are more stable than neutral clusters for n ≥ 4 depending on the temperature. The Boltzmann averaged Gibbs free energies for the formation of H(2)SO(4)(H(2)O)(n) clusters are favorable in colder regions of the troposphere (T = 216.65-273.15 K) for n = 1-6, but the formation of clusters with n ≥ 5 is not favorable at higher (T > 273.15 K) temperatures. Our results suggest the critical cluster of a binary H(2)SO(4)-H(2)O system must contain more than one H(2)SO(4) and are in concert with recent findings (1) that the role of binary nucleation is small at ambient conditions, but significant at colder regions of the troposphere. Overall, the results support the idea that binary nucleation of sulfuric acid and water cannot account for nucleation of sulfuric acid in the lower troposphere.     

Quantum mechanical models in catalysis

A wave function of electrons of a catalytic complex taken as a series of products of wave functions of the reactants and catalyst was suggested for use in modeling potential energy surfaces of catalytic reactions and for analysis of catalytic activity. Quantum mechanical criteria at which catalytic transformations become possible were formulated on the basis of this concept. The character of correlations between the activity and physical properties of catalysts was explained, and a general procedure for theoretical analysis of such correlations was described.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 3, pp. 545–550, March, 1996.     

Unstable complexes of sandwich compounds with small molecules Communication 1. Quantum mechanical study of the interaction mechanism of metallocenes with co molecules

Conclusion Using the semiempirical INDO method in the Clack parametrization it has been shown that the bicyclopentadienyl systems (⁵-C₅H₅)₅M, where M=V, Cr, Mn, Fe, Co, or Ni, are capable of forming complexes with the carbon monoxide molecule, the monodentate bonding to the C atom with an M-C-O angle close to 180° being the most favored.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2721–2724, December, 1986.     

Quantum mechanical study of electronic transitions in collinear atom—diatom collisions

Quantum mechanical calculations are reported for model, nonreactive, collinear collision systems composed of the H₂ diatom and the halogen atom X = F, Cl, Br or I. The model involves two electronic potential energy surfaces, obtained in a diatomics-in-molecules formulation, that correspond asymptotically to the two spin-orbit states of X. On each surface the calculations include as many vibrational states of H₂ as are asymptotically allowed, up to a limiting number of five. The first two collision systems, FH₂ and ClH₂, are characterized by electronic splittings much smaller than any vibrational spacing included in the diatom spectrum, and as a result they show a high degree of vibrational elasticity with essentially all transition activity testricted to spin—orbit switching in the halogen. This pattern is broken for BrH₂ collisions, where the near-equality between electronic and vibrational quanta apparently leads to a resonant exchange of energy between the two modes. The greater spinorbit splitting in iodine (～ 2 vibrational quanta) results in largely elastic behavior in IH₂ collisions for both vibrational and electronic transitions. A modified Massey criterion is exhibited for some of the FH₂ and BrH₂ transitions.     

Separations based on the mechanical forces of light

A photon as a particle has an energy and a momentum. In a matter-photon interaction, the matter and photons may exchange their momenta observing the momentum conservation law. The consequence of the momentum transfer from a photon to a matter particle is a mechanical force exerted on the particle. Several separation methods based on this force of light are reviewed. Photophoresis separations for micron-sized particles and optical force chromatography for chemical-sized molecules are discussed.     

Quantum mechanical study of the coupling of plasmon excitations to atomic-scale electron transport

The coupling of optical excitation and electron transport through a sodium atom in a plasmonic dimer junction is investigated using time-dependent density functional theory. The optical absorption and dynamic conductance is determined as a function of gap size. Surface plasmons are found to couple to atomic-scale transport through several different channels including dipolar, multipolar, and charge transfer plasmon modes. These findings provide insight into subnanoscale couplings of plasmons and atoms, a subject of general interest in plasmonics and molecular electronics.     

Quantum mechanical study of regioselectivity of radical additions to substituted olefins

Regiochemical trends in the addition of free radicals to substituted olefins are investigated by different quantum chemical approaches with special reference to oxygen centered radicals. From a methodological point of view, density functional methods provide correct general trends but they do not reach quantitative accuracy, especially for intermediate complexes. More reliable results are obtained by single point post‐Hartree–Fock computations at density functional geometries. A number of test computations show that reoptimization of the geometry and computation of vibrational frequencies by correlated methods can be safely avoided. As a consequence, the overall computational approach has very reasonable computer costs. From a more chemical point of view, a careful analysis of computational results points out the significant role of anomeric and polar effects in tuning the common filicity of carbon centered radicals. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 675–691, 2000     

Quantum mechanical study on the facial selectivity of dioxa and trioxa cage molecules

High facial selectivity (>99%) of nucleophilic addition to the carbonyl groups of the title compounds (1 and 2) has been achieved for the novel trioxa cage 2, but not for the dioxa 1. Similar experimental observations were made for the carbene addition to the double bonds of cage compounds, 3 and 4. Calculations were carried out for the cage compounds and their reaction transition structures, with LiH as a nucleophile and :CCl(2) as an attacking carbene. The calculated facial preference for nucleophilic and carbene addition agreed well with experimental results. The origins of facial selectivity are examined from the viewpoints of structure, frontier orbitals, and molecular electrostatic potential of the reactants, as well as strain, electrostatic, and hyperconjugation effects in the transition state. For dioxa cages, the structural facial difference around the reaction center is minor, but the electronic difference of syn and anti faces generated by the two remote oxygen atoms is clearly demonstrated via frontier orbital and MEP analyses. For trioxa cages, the close proximity of the third ether oxygen (O(s)) to the reaction center brings large structural and electronic changes around the reaction center. The calculated electrostatic and strain energy differences of syn and anti transition structures are significantly larger for trioxa cages than for the dioxa cages. Therefore, they both contribute to the enhanced facial selectivity of trioxa compounds. Finally, analysis of hyperconjugative stabilization in transition structures reveals the danger of relying solely on Cieplak or Anh models in rationalization of facial selectivity, especially when nonequivalent steric and electrostatic effects as those present in the trioxa systems are involved.     

Quantum chemical study of the bond orders in the ruthenium,diruthenium and dirhodium nitrosyl complexes

Density functional calculations with the B3LYP functional were carried out for the [Ru(NO)Cl₅]²⁻, [Ru(NO)(NH₃)₅]³⁺, [Ru(NO)(CN)₅]²⁻, [Ru(NO)(CN)₅]³⁻, [Ru(NO)(hedta)]^q (hedta = N-(hydroxyethyl)ethylenediaminetriacetate triple-charged anion; q = 0, −1, −2), Rh₂(O₂CR)₄, Rh₂(O₂CR)₄(NO)₂, Ru₂(O₂CR)₄, Ru₂(O₂CR)₄(NO)₂, Ru₂(dpf)₄, and Ru₂(dpf)₄(NO)₂ (dpf = N,N′-diphenylformamidinate ion; R = H, CH₃, CF₃) complexes. The electronic structure was analyzed in terms of Mayer and Wiberg bond order indices. The technique of bond order indices decomposition into σ-, π-, and δ-contributions was proposed.