Reversible wurtzite-tetragonal reconstruction in ZnO(1010) surfaces

Bistable surface: The reversible phase transition between wurtzite (WZ) and body-centered-tetragonal (BCT) lattice was activated in ZnO(1010) surfaces and directly imaged at atomic scale by using aberration-corrected electron microscopy. A nucleation-growth mechanism for the surface reconstruction is further proposed based on observations and calculations of the WZ-BCT domain boundary.     

On the determination of absolute vibrational excitation probabilities in molecule-surface scattering: Case study of NO on Au(111)

We describe a method to obtain absolute vibrational excitation probabilities of molecules scattering from a surface based on measurements of the rotational state, scattering angle, and temporal distributions of the scattered molecules and apply this method to the vibrational excitation of NO scattering from Au(111). We report the absolute excitation probabilities to the v = 1 and v = 2 vibrational states, rotational excitation distributions, and final scattering angle distributions for a wide range of incidence energies and surface temperatures. In addition to demonstrating the methodology for obtaining absolute scattering probabilities, these results provide an excellent benchmark for theoretical calculations of molecule-surface scattering.     

A theoretical ab initio study on the H(2)NO + O(3) reaction

The deviation of the NH(2) pseudo-first-order decay Arrhenius plots of the NH(2) + O(3) reaction at high ozone pressures measured by experimentalists, has been attributed to the regeneration of NH(2) radicals due to the subsequent reactions of the products of this reaction with ozone. Although these products have not yet been characterized experimentally, the radical H(2)NO has been postulated, because it can regenerate NH(2) radicals through the reactions: H(2)NO + O(3) --> NH(2) + O(2) and H(2)NO + O(3) --> HNO + OH + O(2). With the purpose of providing a reasonable explanation from a theoretical point of view to the kinetic observed behaviour of the NH(2) + O(3) system, we have carried ab initio electronic structure calculations on both H(2)NO + O(3) possible reactions. The results obtained in this article, however, predict that of both reactions proposed, only the H(2)NO + O(3) --> NH(2) + O(2) reaction would regenerate indeed NH(2) radicals, explaining thus the deviation of the NH(2) pseudo-first-order decay observed experimentally.     

Chemisorption of HSi(OH)3 on silica surfaces: an ab initio periodic study

The study of the grafting of trialkoxysilane R′Si(OR)₃ molecules on amorphous silica has been undertaken at the Hartree–Fock level using a biperiodic model for the surface. Different types of slab cut out from the model system Edingtonite (a tetragonal silica structure with five SiO₂ groups per unit cell) have been used to simulate isolated and interacting silanol sites at the amorphous silica surface, while only the simple case of HSi(OH)₃ has been considered for the interacting molecule. In a first step, for each type of surface the geometrical parameters have been optimised and the surface formation energy determined. The geometrical structure of the grafted molecule is compared with that of the isolated one. The geometrical strains of the surfaces with either isolated or interacting silanols are also compared before and after the grafting reactions. The calculated values of the chemisorption energies show that the grafting process is favored on isolated silanols only if correlation effects are included.     

Modelling of interactions between volatile anaesthetics (halothane,enflurane) and aromatic compounds,ab initio study

For many years halothane and enflurane have been used clinically as volatile anaesthetics, however, their mechanism of action is still not fully understood. Recently, it has been suggested that they can act by a direct bonding to neuroreceptors containing the aromatic groups. In this work, the halothane?benzene and enflurane?benzene complexes were studied by the ab initio MP2 and CCSD(T) methods. All possible structures of the complexes were calculated by means of the counterpoise CP-corrected gradient optimization technique. It has been found that among these species, the C–H?π hydrogen bonded complexes are the most stable. The CCSD(T)/CBS calculated stabilization energies for halothane and enflurane complexes are: −10.56 and −9.72 kcal mol⁻¹, respectively. The interaction energy is mainly dominated by the dispersion attraction. In the case of enflurane, the C–H bond shows a very small contraction (by −0.0008 Å) upon complexation. This change is accompanied by the blue-shift (20 cm⁻¹) of the C–H stretching frequency and an increase of the infrared intensity of the corresponding mode by 7 km mol⁻¹. Similar results were obtained for the halothane complex: a small contraction of the C–H bond; an increase of the C–H stretching frequency by 11 cm⁻¹ (blue-shift); and an increase of the infrared intensity by 37 km mol⁻¹. In order to explain the nature of these effects, the halothane and enflurane molecules were studied in the electric field generated by benzene atoms, and Natural Bond Orbital (NBO) analyses were performed. The molecular dipole moments of these molecules were calculated with respect to the C–H bond changes. The positive dipole moment derivative obtained for halothane is in agreement with the literature data, while, in the case of enflurane, an unusual effect is observed, the blue-shift of the C–H stretching frequency is accompanied by the positive dipole moment derivative for one C–H bond and the negative for the other C–H bond. The mechanisms responsible for contraction and strengthening of the C–H bonds are discussed.     

Defective α‐Fe2O3(0001): An ab Initio Study

By using density functional theory calculations at the PBE+U level, we investigated the properties of hematite (0001) surfaces decorated with adatoms/vacancies/substituents. For the most stable surface termination over a large range of oxygen chemical potentials (${\mu _{\rm{O}} }$ ), the vacancy formation and adsorption energies were determined as a function of ${\mu _{\rm{O}} }$ . Under oxygen‐rich conditions, all defects are metastable with respect to the ideal surface. Under oxygen‐poor conditions, O vacancies and Fe adatoms become stable. Under ambient conditions, all defects are metastable; in the bulk, O vacancies form more easily than Fe vacancies, whereas at the surface the opposite is true. All defects, that is, O and Fe vacancies, Fe and Al adatoms, and Al substituents, induce important modifications to the geometry of the surface in their vicinity. Dissociative adsorption of molecular oxygen is likely to be exothermic on surfaces with Fe/Al adatoms or O vacancies.     

New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: from ab initio to molecular dynamics

We have developed new force field and parameters for copper(I) and mercury(II) to be used in molecular dynamics simulations of metalloproteins. Parameters have been derived from fitting of ab initio interaction potentials calculated at the MP2 level of theory, and results compared to experimental data when available. Nonbonded parameters for the metals have been calculated from ab initio interaction potentials with TIP3P water. Due to high charge transfer between Cu(I) or Hg(II) and their ligands, the model is restricted to a linear coordination of the metal bonded to two sulfur atoms. The experimentally observed asymmetric distribution of metal ligand bond lengths (r) is accounted for by the addition of an anharmonic (r3) term in the potential. Finally, the new parameters and potential, introduced into the CHARMM force field, are tested in short molecular dynamics simulations of two metal thiolates fragments in water. (Brooks BR et al. J Comput Chem 1983, 4, 1987.1).     

Ab initio studies of ClO(x) reactions: prediction of the rate constants of ClO+NO2 for the forward and reverse processes.

The potential-energy surface for the reaction of ClO with NO2 has been constructed at the CCSD(T)/6-311+G(3df)//B3LYP/6-311+G(3df) level of theory. Six ClNO3 isomers are located; these are ClONO2, pc-ClOONO, pt-ClOONO, OClNO2, pt-OClONO, pc-OClONO, with predicted energies relative to the reactants of -25.6, -0.5, 1.0, 1.9, 12.2 and 13.6 kcal mol-1, and heats of formation at 0 K of 7.8, 32.9, 34.4, 35.5, 45.6 and 47.0 kcal mol-1, respectively. Isomerizations among them are also discussed. The rate constants for the low-energy pathways have been computed by statistical theory calculations. For the association reaction producing exclusively ClONO2, the predicted low- and high-pressure-limit rate constants in N2 for the temperature range of 200-600 K can be represented by: (N2)=3.19 x 10-17 T-5.54 exp(-384 K/T) cm6 molecule-2 s-1 and =3.33 x 10-7 T-1.48 exp(-18 K/T) cm3 molecule-1 s-1. The predicted low- and high-pressure-limit rate constants for the decomposition of ClONO2 in N2 at 200-600 K can be expressed, respectively, by =6.08 x 1013 T-6.54 exp(-13813 K/T) cm3 molecule-1 s-1 and =4.59 x 1023 T-2.43 exp(-13437 K/T) s-1. The predicted values compare satisfactorily with available experimental data. The reverse Cl+NO3 reaction was found to be independent of the pressure, giving exclusively ClO+NO2; the predicted rate constant can be expressed as k(Cl+NO3)=1.19 x 10-9 T-0.60 exp(58 K/T) cm3 molecule-1 s-1..     

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.     

The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems

The great importance of ultrafast phenomena in photochemistry and photobiology has made dynamics simulations an essential methodology in these areas. In this work, we present the Newton-X program package containing a new implementation of a direct dynamics approach to perform adiabatic (Born–Oppenheimer) and nonadiabatic simulations. The nonadiabatic dynamics is based on Tully's surface hopping approach. The program has been developed with the aim of (1) to create a flexible tool to be used in connection with a multitude of third-party electronic-structure program packages and (2) to provide the most common options for excited-state dynamics simulations. Benchmark calculations on the nonadiabatic dynamics are presented for the methaniminium, butatriene and pentadieniminium cations. The simulation of UV absorption spectra is presented for the methaniminium cation and pyrazine.     

Structures and vibrational spectra of the sulfur-rich oxides SnO (n = 4-9): the importance of pi*-pi* interactions

The structures of a large number of isomers of the sulfur oxides S(n)O with n = 4-9 have been calculated at the G3X(MP2) level of theory. In most cases, homocyclic molecules with exocyclic oxygen atoms in an axial position are the global minimum structures. Perfect agreement is obtained with experimentally determined structures of S(7)O and S(8)O. The most stable S(4)O isomer as well as some less stable isomers of S(5)O and S(6)O are characterized by a strong pi*-pi* interaction between S==O and S==S groups, which results in relatively long S--S bonds with internuclear distances of 244-262 pm. Heterocyclic isomers are less stable than the global minimum structures, and this energy difference approximately increases with the ring size: 17 (S(4)O), 40 (S(5)O), 32 (S(6)O), 28 (S(7)O), 45 (S(8)O), and 54 kJ mol(-1) (S(9)O). Owing to a favorable pi*-pi* interaction, preference for an axial (or endo) conformation is calculated for the global energy minima of S(7)O, S(8)O, and S(9)O. Vapor-phase decomposition of S(n)O molecules to SO(2) and S(8) is strongly exothermic, whereas the formation of S(2)O and S(8) is exothermic if n<7, but slightly endothermic for S(7)O, S(8)O, and S(9)O. The calculated vibrational spectra of the most stable isomers of S(6)O, S(7)O, and S(8)O are in excellent agreement with the observed data.     

Semi-empirical (PM3 and AM1) and ab initio molecular orbital calculations of 1,2,4-oxadiazoles, 4,5-dihydro-1,2,4-oxadiazoles and 4,4-di-n-butyl-2-phenylbenzo-1,3-oxazine

Molecular orbital calculations using semi-empirical (PM3 and AM1) and ab initio (HF/6-31G) types have been carried out on several 3,5-disubstituted 1,2,4-oxadiazoles 1a–d, 5-n-butyl-3,5-diaryl-4,5-dihydro-1,2,4-oxadiazoles 2a–d, and 4,4-di-n-butyl-2-phenylbenzo-1,3-oxazine 3. A comparison of the results by the two computational procedures has been made. Transformation of the oxadiazole ring to 4,5-dihydro-1,2,4-oxadiazole having both aryl and n-butyl groups at C-5 exhibited interesting conformational features. Also, examination of 1,3-oxazine 3 gave an idea about the structure of this compound. The rotational barrier of each phenyl group in 1a and 1d has been calculated using the ab initio method HF/6-31G(d).