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PubMed2005

Generation of orbitals that control molecular reactivity: projected reactive orbital approach.

A method that generalizes the notion of frontier orbital (FO) theory is introduced. The method is based on the projected reactive orbitals (PROs). Although PROs have been shown to describe local reactivity better than FOs in high-symmetry systems, the PRO method needs an arbitrary choice of a reference atomic orbital (AO), causing ambiguity of the method and poor applicability to low-symmetry molecules. To overcome these difficulties, we examined three different kinds of methods for uniquely determining the reference AO, one of which (Method 1) was reported by other authors (Kurita, Y.; Takayama, C. J. Phys. Chem. A 1997, 101, 5593-5595). We specifically applied the methods to the prediction of basicities of heteroaromatic amines. The study showed that the newly developed reactivity-index maximization method (Method 3) yields the most reasonable PRO.

Amines↗
PubMed2005

Photodissociation reaction of 1,2-diiodoethane in solution: a theoretical and X-ray diffraction study.

Various molecular species are known to form during the photoreaction of C2H4I2 in the gas phase and in solution. We have studied all species involved in this reaction by ab initio and density functional theory (DFT) calculations: Geometries, energies, and vibrational frequencies of C2H4I2, bridged C2H4I*, anti C2H4I*, C4H4, I2, I3-, and the isomer C2H4I-I were calculated. The absorption peaks and oscillator strengths of selected species along the potential energy surface (PES) were calculated using time-dependent DFT and were compared with available experimental results. The calculated PES satisfactorily describes the observed reactions of the photoexcited C2H4I2 molecule. In the gas phase, there is only one reaction pathway: the first C-I bond ruptures followed by a secondary C-I breakage in the haloethyl radical C2H4I*. In solution, by contrast, another reaction channel, which is energetically more favored over the secondary dissociation, is switched on due to a solvation effect: the bridged C2H4I* can bind to the free iodine atom to form a C2H4I-I isomer without any energy barrier. The isomer can then break into C2H4 and I2. The rotational barriers in the gas phase and in solution were also calculated and compared. To provide experimental data on the structure of C2H4I2 in solution, the ground state structure of C2H4I2 in methanol was determined from static X-ray diffraction data using 88 keV (lambda = 0.14 A) X-rays. The structural parameters are compared with those from the theoretical results.

Computer Simulation↗
PubMed2005

Observation of the pi...H hydrogen-bonded ternary complex, (C(2)H(4))(2)H(2)O, using matrix isolation infrared spectroscopy.

FTIR absorption spectra of water-containing ethene:Ar matrices, with compositions of ethene up to 1:10 ethene:Ar, have been recorded. Systematically increasing the concentration of ethene reveals features in the spectra consistent with the known 1:1 ethene:water complex, which subsequently disappear on further increase in ethene concentration. At high concentrations of ethene, new features are observed at 3669 and 3585 cm(-1), which are red-shifted with respect to matrix-isolated nu(3) and nu(1) O-H stretching modes of water and the 1:1 ethene:water complex. These shifts are consistent with a pi...H interaction of a 2:1 ethene:water complex of the form (C(2)H(4)...H-O-H...C(2)H(4)). The analogous (C(2)D(4))(2)H(2)O complex shows little shifting from positions associated with (C(2)H(4))(2)H(2)O, while the (C(2)H(4))(2)D(2)O isotopomer shows large shifts to 2722.3 and 2617.2 cm(-1), having identical nu(3)(H(2)O)/nu(3)(D(2)O) and nu(1)(H(2)O)/nu(1)(D(2)O) values when compared with monomeric water isotopomers. Features at 3626.1 and 2666.2 cm(-1) are also observed and are attributed to (C(2)H(4))(2)HDO. DFT calculations at the B3LYP/6-311+G(d,p) level for each isotopomer are presented, and the predicted vibrational frequencies are directly compared with experimental values. The interaction energy for the formation of the 2:1 ethene:water complex from the 1:1 ethene:water complex is also presented.

Computer Simulation↗
PubMed2006

Isoelectronic homologues and isomers: tropolone, 5-azatropolone, 1-H-azepine-4,5-dione, saddle points, and ions.

Computational studies of 12 64-electron homologues and isomers of tropolone in the S(0) electronic ground state are reported. Three minimum-energy structures, tropolone (Tp), 5-azatropolone (5Azt), and 5-H-5-azatropolonium (5AztH(+)), have an internal H-bond and planar C(s)) geometry, and three, tropolonate (TpO(-)), 5-azatropolonate (5AzO(-)), and 1-H-azepine-4,5-dione (45Di), lack the H-bond and have twisted C(2) geometry. All 6 substances have an equal double-minimum potential energy surface and a saddle point with planar C(2)(v) geometry. The energy for the gas-phase isomerization reaction 45Di --> 5Azt is near +4 kJ mol(-1) at the MP4(SDQ)/6-311++G(df,pd)//MP2/6-311++G(df,pd) (energy//geometry) theoretical level and around -20 kJ mol(-1) at lower theoretical levels. The dipole moments computed for 45Di and 5Azt are 9.6 and 2.1 D, respectively, and this large difference contributes to MO-computed free energies of solvation that strongly favor--as experimentally observed--45Di over 5Azt in chloroform solvent. The MO-computed energy for the gas-phase protonation reaction 45Di + H(+) --> 5AztH(+) is -956.4 kJ mol(-1), leading to 926.8 kJ mol(-1) as the estimated proton affinity for 45Di at 298 K and 1 atm. The intramolecular dynamical properties predicted for 5Azt and 5AztH(+) parallel those observed for tropolone. They are therefore expected to exhibit spectral tunneling doublets. Once they are synthesized, they should contribute importantly to the understanding of multidimensional intramolecular H transfer and dynamical coupling processes.

Aza Compounds↗
PubMed2006

Structure and vibrational spectra of mononitrated benzo[a]pyrenes.

The molecules benzo[a]pyrene (BaP) and 1-, 3-, and 6-nitrobenzo[a]pyrene (1-NBaP, 3-NBaP, 6-NBaP) are currently of significant interest due to their presence in respirable combustion exhaust particulates and their mutagenic and carcinogenic properties. Structure-function correlations as well as spectroscopic signatures for trace analysis are necessary for these benzo[a]pyrene derivatives. In this paper, detailed infrared and Raman spectroscopic data of BaP and its three mononitrated isomers are provided for the first time. By utilizing density functional theory (DFT, B3LYP method with 6-311+G basis set), the molecular geometries and the vibrational spectra are calculated. Good agreement is noted between the calculated and experimental geometry for BaP, and predictions of the vibrational data for all compounds are within approximately 5 cm-1 of the experimental data. Normal mode assignments are proposed with particular emphasis on the nitro group vibrations. The geometrical distortions of the BaP structure upon nitro group substitution and correlations between structural parameters and vibrational data as well as structure-function relationships related to the mutagenicity of this important class of polycyclic aromatic hydrocarbons are discussed.

Air Pollutants↗
PubMed2006

On the location of conical intersections in CH2BrCl using MS-CASPT2 methods.

Multiconfigurational second-order perturbation theory has been employed to calculate two-dimensional potential energy surfaces for the lowest low-lying singlet electronic states of CH2BrCl as a function of the two carbon-halogen bonds. The photochemistry of the system is controlled by a nonadiabatic crossing occurring between the A and B bands, attributed to the b1A' and c1A' states, which are found almost degenerate and forming a near-degeneracy line of almost equidistant C-Br and C-Cl bonds. A crossing point in the near-degeneracy line is identified as a conical intersection in this reduced two-dimensional space. The positions of the conical intersection located at CASSCF, single-state (SS)-CASPT2, and multistate (MS)-CASPT2 levels of theory are compared, also paying attention to the nonorthogonality problem of perturbative approaches. To validate the presence of the conical intersection versus an avoided crossing, the geometrical phase effect has been checked using the multiconfigurational MS-CASPT2 wave function.

Computer Simulation↗
PubMed2006

Theoretical investigation of the (hyper)polarizabilities of pyrrole homologues C4H4XH (X = N, P, As, Sb, Bi). A coupled-cluster and density functional theory study.

Geometries, inversion barriers, static and dynamic electronic and vibrational dipole polarizability (alpha), and first (beta) and second (gamma) hyperpolarizability of the pyrrole homologues C(4)H(4)XH (X = N, P, As, Sb, Bi) have been calculated by Hartree-Fock, Møller-Plesset second-order perturbation theory, coupled-cluster theory accounting for singles, doubles, and noniterative triple excitations methods, as well as density functional theory using B3LYP and PBE1PBE functionals and Sadlej's Pol and 6-311G basis sets. Relativistic effects on the heavier homologues stibole and bismole have been taken into account within effective core potential approximation. The results show that the electronic (hyper)polarizabilities monotonically increase with the atomic number of the heteroatom, consistent with the decrease in the molecular hardness. Ring planarization reduces the carbon-carbon bond length alternation of the cis-butadienic unit, enhancing the electronic polarizability values (alpha(e)) by 4-12% and the (hyper)polarizability values (and gamma(e)) by 30-90%. Pure vibrational and zero-point vibrational average contributions to the (hyper)polarizabilities have been determined within the clamped nucleus approach. In the static limit, the pure vibrational hyperpolarizabilities have a major contribution. Anharmonic corrections dominate the pure vibrational hyperpolarizabilities of pyrrole, while they are less important for the heavier homologues. Static and dynamic electronic response properties of the pyrrole homologues are comparable to or larger than the corresponding properties of the furan and cyclopentadiene homologue series.

Computer Simulation↗
PubMed2006

Interaction energy of a water molecule with a single-layer graphitic surface modeled by hydrogen- and fluorine-terminated clusters.

In ab initio calculations a finite graphitic cluster model is often used to approximate the interaction energy of a water molecule with an infinite single-layer graphitic surface (graphene). In previous studies, the graphitic cluster model is a collection of fused benzene rings terminated by hydrogen atoms. In this study, the effect of using fluorine instead of hydrogen atoms for terminating the cluster model is examined to clarify the role of the boundary. The interaction energy of a water molecule with the graphitic cluster was computed using ab initio methods at the MP2 level of theory and with the 6-31G(d = 0.25) basis set. The interaction energy of a water molecule with graphene is estimated by extrapolation of two series of increasing size graphitic cluster models (C(6n2)H(6n) and C(6n2)F(6n), n = 1-3). Two fixed orientations of water molecule are considered: (a) both hydrogen atoms of water pointing toward the cluster (mode A) and (b) both hydrogen atoms of water pointing away from the cluster (mode B). The interaction energies for water mode A are found to be -2.39 and -2.49 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively. For water mode B, the interaction energies are -2.32 and -2.44 kcal/mol for C(6n2)H(6n) and C(6n2)F(6n) cluster models, respectively.

Computer Simulation↗
PubMed2006

Structure and matrix isolation infrared spectrum of formyl fluoride dimer: blue-shift of the C-H stretching frequency.

Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the dimer with two C-H...O hydrogen bonds. This observation includes the HCOF dimer to the class of hydrogen bonded complexes showing blue shift in their vibrational energies.

Computer Simulation↗
PubMed2006

Competition between nonclassical hydrogen-bonded acceptor sites in complexes of neutral AH2 Radicals (A = B, Al, and Ga): A theoretical investigation.

An ab initio computational study of the properties of the neutral AH2 radicals (A = B, Al, Ga) as hydrogen-bond (HB) acceptors, with H-X (X = F, Cl, Br, CN, and CCH) as HB donors, is carried out at the UMP2/6-311++G(2d,2p) level. Two different minima have been found for each of the 15 possible dimers. One structure corresponds to a single-electron hydrogen-bonded complex (SEHB), with the A atom acting as an HB acceptor. The second corresponds to a dihydrogen bond complex between one of the hydrogen atoms of AH2 and the H-X molecule. Thus, all the atoms of the neutral AH2 molecule can act as HB acceptors and none as donors. The stability of the SEHB complexes decreases as BH2 > AlH2 > GaH2, while for the dihydrogen-bonded complexes the order is AlH2 > GaH2 > BH2. For the BH2 radical the SEHB complexes are stronger than the dihydrogen bonded ones, while the opposite is found for the AlH2 and GaH2 systems. Regarding the HB donors, the order found for the binding energy in the two types of complexes is H2A...HF > H2A...HCl > H2A...HBr > H2A...HCN > H2A...HCCH.

Aluminum↗
PubMed2006

Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation.

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the (001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the Gamma point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH(2) group plays only a minor role as a weak hydrogen bond donor.

Computer Simulation↗
PubMed2005

Successful application of TD-DFT in transient absorption spectra assignment.

[Reaction: see text] Despite the wide application of time-resolved spectra technology in investigating various chemical and biological processes, it is still a great challenge to give an unambiguous spectra assignment for observed transient species, e.g., the curcumin-derived radicals. Here we report that time-dependent density functional theory with the B3LYP functional and an appropriate basis set can give reliable absorption spectra for carbon- and oxygen-centered radicals derived from curcumin, which indicates the potential of theoretical methods in helping assign transient spectra.

Acetonitriles↗
PubMed2005

Ab initio cluster calculations for the absorption energies of F and F+ centers in bulk ZnO.

We present the results of a series of ab initio calculations on the ground states and the low lying excited states of the F and F+ centers in bulk ZnO. Both types of F centers are oxygen vacancies, causing rather strong distortions of the local geometries. The calculations were performed by means of wave function based methods, mostly at the CASSCF level. Dynamic correlation was included for the first two coordination shells of the F centers. The calculated absorption energy for the F+ center (3.19 eV) is in excellent agreement with the experimental value of 3.03 eV. For the emission from the 3T2 state of the F center to the 1A1 ground state we obtained a transition energy of 2.73 eV. Experimentally, a green photoluminescence is observed at 2.38-2.45 eV. We estimated that the errors in our calculation should be even smaller in the latter case than for the F+ state, where the calculated transition energy differs by less than 0.2 eV from the experimental value. Therefore, we assume that the 3T2 to 1A1 transition is not the origin of the green luminescence.

Absorption↗
PubMed2006

The photodissociation dynamics of O2 at 193 nm: an O3PJ angular momentum polarization study.

In the following paper we present translational anisotropy and angular momentum polarization data for O((3)P(1)) and O((3)P(2)) products of the photodissociation of molecular oxygen at 193 nm. The data were obtained using polarized laser photodissociation coupled with resonantly enhanced multiphoton ionization and velocity-map ion imaging. Under the jet-cooled conditions employed, absorption is believed to be dominated by excitation into the Herzberg continuum. The experimental data are compared with previous experiments and theoretical calculations at this and other wavelengths. Semi-classical calculations performed by Groenenboom and van Vroonhoven [J. Chem. Phys, 2002, 116, 1965] are used to estimate the alignment parameters arising from incoherent excitation and dissociation and these are shown to agree qualitatively well with the available experimental data. Following the work of Alexander et al. [J. Chem. Phys, 2003, 118, 10566], orientation and alignment parameters arising from coherent excitation and dissociation are modelled more approximately by estimating phase differences generated subsequent to dissociation via competing adiabatic pathways leading to the same asymptotic products. These calculations lend support to the view that large values of the coherent alignment moments, but small values of the corresponding orientation moments, could arise from coherent excitation of (and subsequent dissociation via) parallel and perpendicular components of the Herzberg I, II and III transitions.

Anisotropy↗
PubMed2005

Current and noise in a model of an alternating current scanning tunneling microscope molecule-metal junction.

The transport properties of a simple model for a finite level structure (a molecule or a dot) connected to metal electrodes in an alternating current scanning tunneling microscope (ac-STM) configuration is studied. The finite level structure is assumed to have strong binding properties with the metallic substrate, and the bias between the STM tip and the hybrid metal-molecule interface has both an ac and a dc component. The finite frequency current response and the zero-frequency photoassisted shot noise are computed using the Keldysh technique, and examples for a single-site molecule (a quantum dot) and for a two-site molecule are examined. The model may be useful for the interpretation of recent experiments using an ac-STM for the study of both conducting and insulating surfaces, where the third harmonic component of the current is measured. The zero-frequency photoassisted shot noise serves as a useful diagnosis for analyzing the energy level structure of the molecule. The present work motivates the need for further analysis of current fluctuations in electronic molecular transport.

Journal Article↗
PubMed2005

Iterative Cl general singles and doubles (ICIGSD) method for calculating the exact wave functions of the ground and excited states of molecules.

The iterative configuration-interaction general singles and doubles (ICIGSD) method was applied to various closed- and open-shell electronic states of molecules within finite basis sets and was shown to give the exact results that are identical to the full CI ones. The structure of the ICIGSD is unique among the ICI formalisms, that is, the singularity problem intrinsic to atomic and molecular Hamiltonians can be avoided. The convergence of the ICIGSD method was fairly good regardless of the characters of the electronic states and the qualities of the basis sets; only several iterations were enough for obtaining microhartree accuracy. These favorable properties are attributed to the unique GSD structure. The present method was shown to be applicable to various spin states and to quasidegenerate states appearing in bond dissociation process. We have also applied the ICIGSD-CI method to calculate the excited states simultaneously. We have confirmed that the ICIGSD-CI method is accurate for calculating the excited states the symmetries of which are not only similar to but also different from that of the ground state.

Algorithms↗
PubMed2006

The state-to-state-to-state model for direct chemical reactions: application to D+H2-->HD+H.

A simple theoretical model is developed to predict the state-to-state dynamics of direct chemical reactions. Motivated by traditional ideas from transition state theory, expressions are derived for the reactive S matrix that may be computed using the local transition state dynamics. The key approximation involves the use of quantum bottleneck states to represent the near separable dynamics taking place near the transition state. Explicit expressions for the S matrix are obtained using a Franck-Condon treatment for the inelastic coupling between internal states of the collision complex. It is demonstrated that the energetic thresholds for various initial reagent states of the D+H(2) reaction can be understood in terms of our theory. Specifically, the helicity of the reagent states are found to correlate directly to the symmetry of the quantum bottleneck states, which thus possess very different thresholds. Furthermore, the rotational product state distributions for D+H(2) are found to be associated with interfering pathways through the quantum bottleneck states.

Journal Article↗
PubMed2006

Methane-water cross second virial coefficient with quantum corrections from an ab initio potential.

We present our calculations of the cross second virial coefficient (B12) and of a related quantity, phi 12 = B12-TdB12/dT, for the methane-water system in the temperature range T = 200-1000 K. These calculations were performed using one of the ab initio potentials developed in previous work [Akin-Ojo and Szalewicz, J. Chem. Phys. 123, 134311 (2005)]. Quantum corrections of order variant Planck's over 2pi(2) were added to the computed classical values. We have estimated the uncertainties in our computed B12 and phi 12(T). This allowed evaluation of the quality of the experimental data to which we compare our results. We also provide an analytical expression for B12(T) as a function of the temperature T obtained by fitting the calculated values. This formula also predicts values of phi12(T) consistent with the directly calculated values.

Journal Article↗