Experimental evidence of dynamic trapping in the scattering of H2 from Pd(110)

We have performed H2(D2) diffraction experiments on a Pd(110) surface using two different high-sensitivity set-ups. We have found that, although the total reflectivity of Pd(110) is comparable to that observed in other reactive systems, the corresponding H2(D2) diffraction patterns are quite different: no diffraction peak, including the specular one, is observed on Pd(110). This unexpected result is the consequence of dynamic trapping. Such interpretation is supported by classical dynamics calculations based on accurate ab initio potential energy surfaces.     

Ab initio molecular dynamics of hydrogen dissociation on metal surfaces using neural networks and novelty sampling

We outline a hybrid multiscale approach for the construction of ab initio potential energy surfaces (PESs) useful for performing six-dimensional (6D) classical or quantum mechanical molecular dynamics (MD) simulations of diatomic molecules reacting at single crystal surfaces. The algorithm implements concepts from the corrugation reduction procedure, which reduces energetic variation in the PES, and uses neural networks for interpolation of smoothed ab initio data. A novelty sampling scheme is implemented and used to identify configurations that are most likely to be predicted inaccurately by the neural network. This hybrid multiscale approach, which couples PES construction at the electronic structure level to MD simulations at the atomistic scale, reduces the number of density functional theory (DFT) calculations needed to specify an accurate PES. Due to the iterative nature of the novelty sampling algorithm, it is possible to obtain a quantitative measure of the convergence of the PES with respect to the number of ab initio calculations used to train the neural network. We demonstrate the algorithm by first applying it to two analytic potentials, which model the H2/Pt(111) and H2/Cu(111) systems. These potentials are of the corrugated London-Eyring-Polanyi-Sato form, which are based on DFT calculations, but are not globally accurate. After demonstrating the convergence of the PES using these simple potentials, we use DFT calculations directly and obtain converged semiclassical trajectories for the H2/Pt(111) system at the PW91/generalized gradient approximation level. We obtain a converged PES for a 6D hydrogen-surface dissociation reaction using novelty sampling coupled directly to DFT. These results, in excellent agreement with experiments and previous theoretical work, are compared to previous simulations in order to explore the sensitivity of the PES (and therefore MD) to the choice of exchange and correlation functional. Despite having a lower energetic corrugation in our PES, we obtain a broader reaction probability curve than previous simulations, which is attributed to increased geometric corrugation in the PES and the effect of nonparallel dissociation pathways.     

Experimental and theoretical study of rotationally inelastic diffraction of D2 from NiAl(110)

We present a detailed experimental and theoretical study of elastic and rotationally inelastic diffraction of D(2) from NiAl(110) in the energy range 85-150 meV. The experiments were performed using a high-resolution, fixed angle geometry apparatus. Quantum and classical dynamical calculations were performed by using a six-dimensional potential energy surface constructed upon interpolation of a set of DFT (density functional theory) data. We show that, although elastic diffraction peak intensities are accurately described by theory in the whole range of incidence energies and angles explored, significant discrepancies are obtained for RID peaks, especially for those involving rotational initial states with j(i) > 0. Possible reasons for this discrepancy are discussed.     

PbTe(111)薄膜的分子束外延生长及其表面结构特性

采用分子束外延(MBE)方法在Ba F_2(111)衬底上直接外延生长了Pb Te薄膜。反射高能电子衍射(RHEED)实时监控的衍射图样揭示了Pb Te在Ba F_2(111)表面由三维生长向二维生长的变化过程。转动对称性的研究结合第一性原理密度泛函理论(DFT)的计算揭示了在富Pb及衬底温度(Tsub)为350°C的生长条件下,得到的Pb Te(111)薄膜具有稳定的(2×1)重构表面。Pb Te(111)-(2×1)表面覆盖Te膜后,通过300°C的退火处理,重构表面可完全复原,这为大气环境下Pb Te薄膜表面结构的保护提供了有效的方法。     

Vibrational deexcitation and rotational excitation of H(2) and D(2) scattered from Cu(111): Adiabatic versus non-adiabatic dynamics

We have studied survival and rotational excitation probabilities of H(2)(v(i) = 1, J(i) = 1) and D(2)(v(i) = 1, J(i) = 2) upon scattering from Cu(111) using six-dimensional (6D) adiabatic (quantum and quasi-classical) and non-adiabatic (quasi-classical) dynamics. Non-adiabatic dynamics, based on a friction model, has been used to analyze the role of electron-hole pair excitations. Comparison between adiabatic and non-adiabatic calculations reveals a smaller influence of non-adiabatic effects on the energy dependence of the vibrational deexcitation mechanism than previously suggested by low-dimensional dynamics calculations. Specifically, we show that 6D adiabatic dynamics can account for the increase of vibrational deexcitation as a function of the incidence energy, as well as for the isotope effect observed experimentally in the energy dependence for H(2)(D(2))/Cu(100). Furthermore, a detailed analysis, based on classical trajectories, reveals that in trajectories leading to vibrational deexcitation, the minimum classical turning point is close to the top site, reflecting the multidimensionally of this mechanism. On this site, the reaction path curvature favors vibrational inelastic scattering. Finally, we show that the probability for a molecule to get close to the top site is higher for H(2) than for D(2), which explains the isotope effect found experimentally.     

On the classical behavior, coherent and incoherent contributions to scattering of atoms from a surface

In this work we calculate the coherent and incoherent contributions to the diffraction probability of atoms scattered by a surface. We are interested in exploring the relative importance of each of these contributions, and compare them with results obtained from molecular dynamics calculations. To achieve this goal, we employed a method developed by Heller that consists of writing the incident plane wave as a sum of Gaussian wave packets, propagating them independently by using the time dependent Schrödinger equation, and constructing the scattered wave function by adding coherently the scattered packets. For the system studied, the molecular dynamics results show the largest intensity in the specular region and also display a classical rainbow structure. On the other hand, the quantum results exhibit diffraction features, with the coherent contribution accounting for most of the total intensity probability.     

Interpolating moving least-squares methods for fitting potential energy surfaces: applications to classical dynamics calculations

As a continuation of our efforts to develop efficient and accurate interpolating moving least-squares (IMLS) methods for generating potential energy surfaces, we carry out classical trajectories and compute kinetics properties on higher degree IMLS surfaces. In this study, we have investigated the choice of coordinate system, the range of points (i.e., the cutoff radius) used in fitting, and strategies for selections of data points and basis elements. We illustrate and test the method by applying it to hydrogen peroxide (HOOH). In particular, reaction rates for the O-O bond breaking in HOOH are calculated on fitted surfaces using the classical trajectory approach to test the accuracy of the IMLS method for providing potentials for dynamics calculations.     

Molecular structures of the 1,6-disubstituted triptycenes Sb2(C6F4)3 and Bi2(C6F4)3 using gas-phase electron diffraction and ab initio and DFT calculations

The structures of the D(3h)-symmetric molecules dodecafluoro-1,6-distibatriptycene and dodecafluoro-1,6-dibismatriptycene [Z2(C6F4)3 (Z = Sb, Bi)] have been determined in the gas phase by electron diffraction, using the SARACEN method, with restraints obtained from quantum chemical calculations. Several methods of ab initio and density functional theory geometry calculations have been performed and recommendations made as to their relative suitabilities for determining the structures of such species. Calculations using the MP2 method with a small-core pseudopotential (aug-cc-pVQZ-PP) on the Sb and Bi atoms and the 6-311G* basis set on the light atoms were found to give the closest correlation with the experimental results for both molecules. Differences in structure were found depending on whether a large-core or small-core pseudopotential was used on the heavy atoms.     

Interpolated potential energy surfaces and dynamics for atom exchange between H and H3(+), and D and H3(+)

Two ab initio interpolated potential energy surfaces have been constructed to study the dynamics of atomic hydrogen/deuterium exchange in collisions of H(3)(+) with H (D). One of the surfaces is based on energy calculations using quadratic configuration interaction with single and double excitations. The second includes a perturbative treatment of the triple excitations and an additive correction for basis set deficiency. Results from classical dynamics simulation of the exchange reaction on these surfaces are presented and discussed.     

The photodissociation of ozone in the Hartley band: a theoretical analysis

Three-dimensional diabatic potential energy surfaces for the lowest four electronic states of ozone with 1A' symmetry-termed X, A, B, and R-are constructed from electronic structure calculations. The diabatization is performed by reassigning corresponding energy points. Although approximate, these diabatic potential energy surfaces allow one to study the uv photodissociation of ozone on a level of theory not possible before. In the present work photoexcitation in the Hartley band and subsequent dissociation into the singlet channel, O3X+hnu-->O(1D)+O2(a 1Deltag), are investigated by means of quantum mechanical and classical trajectory calculations using the diabatic potential energy surface of the B state. The calculated low-resolution absorption spectrum as well as the vibrational and rotational state distributions of O2(a 1Deltag) are in good agreement with available experimental results.     

Synthesis of two new thioesters bearing ferrocene: Vibrational characterization and ab initio calculations. X-ray crystal structure of S-(2-methoxyphenyl)ferrocenecarbothioate

Structural and conformational properties of S-benzyl ferrocenecarbothioate (I) and S-(2-methoxyphenyl) ferrocenecarbothioate (II) are analyzed using data obtained from X-ray diffraction, vibrational data and theoretical calculations. According to chemical quantum calculations, the synperiplanar and antiperiplanar forms are found as the first and second more stable conformations, respectively, for the title compounds. The geometric parameters and normal modes of vibration were calculated using a density functional theory method (B3LYP) and the 6-31+G∗∗ basis set for all atoms except for iron. For this atom the calculations were carried out with the Lanl2dz basis set. The calculated parameters are in good agreement with the corresponding X-ray diffraction values. The combined experimental and theoretical approach allows a consistent assignment for most of the fundamental modes.     

State-to-state scattering of D2 from Cu(100) and Pd(111)

Results from state resolved experiments are presented for the interaction of D2(v=1,J=2) with Cu(100) and Pd(111). The reflected molecules were probed using quantum state specific spectroscopy. For D2 scattered from Cu(100) the vibrational survival probability and some transition inelastic probabilities were measured for incident energies from 70-200 meV. The survival probability was found to be larger then that found previously for H2(v=1) scattered from the same surface; these differences are discussed in terms of the lower zero point energy and smaller vibrational energy spacings of D2. D2 translational energy exchange was studied for several different scattering channels and interpreted using simple classical calculations. The survival probability was also measured for D2(v=1) scattered from Pd(111) at one incident energy. Pd is reactive for D2 dissociation and this survival probability was measured to be small and also to be much smaller than that for H2(v=1) under similar conditions. Vibrational relaxation channels were studied for D2 scattering from both Cu(100) and Pd(111). The vibrational relaxation probability on both surfaces was also found to be smaller than that measured for comparable channels for H2. The smaller survival probability and vibrational relaxation probability for D2 on Pd(111) cannot be easily accounted for by the difference in zero point energy and vibrational energy spacings.     

Adsorption of small molecules on silver clusters

We report investigations of adsorption of N(2) and O(2) molecules on silver cluster cations. We have first revisited structures of small silver clusters based on first-principles calculations within the framework of density functional theory with hybrid functional. The 2D to 3D transition for the neutral clusters occurs from n = 6 to 7 and for cations, in agreement with experiments, from n = 4 to 5. With the refined structures, adsorption energies of N(2) and O(2) molecules have been calculated. We have identified characteristic drops in the adsorption energies of N(2) that further link our calculations and experiments, and confirm the reported 2D-3D transition for cations. We have found that perturbations caused by physisorbed molecules are small enough that the structures of most Ag clusters remain unchanged, even though physisorption stabilizes the 3D Ag(7)(+) structure slightly more than the 2D counterpart. Results for pure O(2) adsorption indicate that charge transfer from Ag(n)(+) to O(2) occurs when n > 3. Below that size oxygen essentially physisorbes such as nitrogen to the cluster. We interpret the experimentally observed mutually cooperative co-adsorption of oxygen and nitrogen using results from density functional theory with generalized gradient approximations. The key to the enhancement is N(2)-induced increase in charge transfer from Ag(n)(+) cations to O(2).     

Molecular structures of phthalocyaninatozinc and hexadecafluorophthalocyaninatozinc studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of phthalocyaninatozinc (HPc-Zn) and hexadecafluorophthalocyaninatozinc (FPc- Zn) are determined using the gas electron diffraction (GED) method and high-level density functional theory (DFT) quantum chemical calculations. Calculations at the B3LYP/6-311++G** level indicate that the equilibrium structures of HPc-Zn and FPc-Zn have D4h symmetry and yield structural parameters in good agreement with those obtained by GED at 480 and 523 degrees C respectively. The calculated force fields indicate that both molecules are flexible. Normal coordinate calculations on HPc-Zn yield five vibrational frequencies (one degenerate) in the range 22-100 cm(-1), and ten vibrational frequencies ranging from 13 to 100 cm(-1) (three degenerate) for FPc-Zn. The high-level force field calculations confirm most of the previous vibrational assignments, and some new ones are suggested. The out-of-plane vibration of the Zn atom in HPc-Zn was studied in detail optimizing models in which the distance from the Zn atom to the two symmetry equivalent diagonally opposed N atoms (h) was fixed. The calculations indicate that the vibrationally activated vertically displacement of the Zn atom is accompanied by distortion of the ligand from D4h to C2v symmetry. The average height, h, at the temperature of the GED experiment was calculated to be 14.5 pm. Small structural changes indicate that a full F substitution on the benzo-subunits do not significantly alter the geometry, however there are indications that the benzo-subunits may shrink slightly with perfluorination.     

Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: potential-energy surface effects on dynamics

We have investigated collisions between Ar and alkanethiolate self-assembled monolayers (SAMs) using classical trajectory calculations with several potential-energy surfaces. The legitimacy of the potential-energy surfaces is established through comparison with molecular-beam data and ab initio calculations. Potential-energy surfaces used in previous work overestimate the binding of Ar to the SAM, leading to larger energy transfer than found in the experiments. New calculations, based on empirical force fields that better reproduce ab initio calculations, exhibit improved agreement with the experiments. In particular, polar-angle-dependent average energies calculated with explicit-atom potential-energy surfaces are in excellent agreement with the experiments. Polar- and azimuthal-angle-dependent product translational energies are examined to gain deeper insight into the dynamics of Ar+SAM collisions.     

Guided ion beam and theoretical study of the reactions of Hf+ with H2, D2, and HD

The kinetic energy dependences of reactions of the third-row transition metal cation Hf(+) with H(2), D(2), and HD were determined using a guided ion beam tandem mass spectrometer. A flow tube ion source produces Hf(+) in its (2)D (6s(2)5d(1)) electronic ground state level. Corresponding state-specific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of HfH(+) and HfD(+) are analyzed to give a 0 K bond dissociation energy of D(0)(Hf(+)-H)=2.11±0.08 eV. Quantum chemical calculations at several levels of theory performed here generally overestimate the experimental bond energy but results obtained using the Becke-half-and-half-LYP functional show good agreement. Theory also provides the electronic structures of these species and the reactive potential energy surfaces. Results from the reactions with HD provide insight into the reaction mechanisms and indicates that Hf(+) reacts via a statistical mechanism. We also compare this third-row transition metal system with the first-row and second-row congeners, Ti(+) and Zr(+), and find that Hf(+) has a weaker M(+)-H bond. As most third-row transition metal hydride cation bonds exceed their lighter congeners, this trend is unusual but can be understood using promotion energy arguments.     

Syntheses, crystal structures, and magnetic properties of [Ln(III)2(Succinate)3(H2O)2].0.5H2O [Ln = Pr, Nd, Sm, Eu, Gd, and Dy] polymeric networks: unusual ferromagnetic coupling in Gd derivative

Lanthanide-organic coordination polymeric networks of [Ln(III)2(suc)3(H2O)2].0.5H2O [suc = succinate dianion, Ln = Pr (1), Nd (2), Sm (3), Eu (4), Gd (5), and Dy (6)] have been synthesized and characterized by single-crystal X-ray diffraction analyses. The structural determination reveals that complexes are isomorphous, all crystallizing in monoclinic system, space group I2/a(.) The complexes possess a 3D architecture with Ln ion in a nine-coordination geometry attained by eight oxygen atoms from succinate and one oxygen atom from an aqua ligand. Low-temperature magnetic study indicates that ferromagnetic interaction is present in case of Gd(III) and Dy(III). Antiferromagnetic interaction is observed for the rest of the complexes. Density functional theory calculations are performed which support the existence of a superexchange ferromagnetic coupling in Gd(III) ions, whereas classical crystal field model has been applied to study the complexes 1, 2, 3, and 6.     

Searching the "biologically relevant"conformation of dopamine: a computational approach

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.     

Unimolecular rovibrational bound and resonance states for large angular momentum: J=20 calculations for HO2

We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-->H+O2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.