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Our density-functional-based simulations demonstrate that atomic hydrogen can be encapsulated in C 60 via collisions of either H or H 2 with a C 60 molecule whose breathing mode has been properly excited by an optimized femtosecond-scale laser pulse. The basic mechanism is a ‘breathing trap’, with the C 60 first expanding, to admit the H, and then contracting, to contain it.

A bridged azobenzene was recently found by Siewertsen et al. to exhibit highly efficient photoisomerization through nπ ∗ absorption. In the work of the present Letter, cis -to- trans photoisomerization of this molecule in the gas phase was examined in detail via density-functional-based dynamical simulations. Our results indicate that rotation around the central NN bond is the dominant mechanism when this reaction proceeds via nπ ∗ excitation, and the bridging feature was found not to hinder the rotation. Nonadiabatic de-excitation occurred at an avoided crossing between the ground state and lowest singlet excited state near the midpoint of the rotational pathway.

For nonresonant femtosecond-scale laser pulses, we showed earlier that the optimum FWHM pulse duration is 0.42 T if one wishes to achieve maximum relative excitation of a specific vibrational mode with period T . Here we show that much greater enhancement of a specific mode can be achieved with a sequence of laser pulses which have both this optimized duration and optimized delays between pulses. One can thus enhance a selected set of modes that are particularly useful in identifying or characterizing a chemical system, to lift them out of the background of less informative modes.

We predict that photocyclization of trans-stilbene to 4a,4b-dihydrophenanthrene (DHP) can be achieved with a femtosecond-scale laser pulse. Specifically, we have performed dynamical simulations in which the original trans-stilbene molecule is observed first to isomerize to cis-stilbene (as an excited-state intermediate) after more than one picosecond, and then to form a new bond to become DHP, after a few hundred additional femtoseconds. The process is initiated by excitation from the S 0 electronic state to S 1 , with subsequent de-excitation at avoided crossings.

Dynamical simulations are reported for trans-to-cis photoisomerization of stilbene induced by a femtosecond-scale laser pulse. The results imply that the basic mechanism is the simplest imaginable: Electronic excitation by the laser pulse weakens the central C–C bond, and also excites vibrations of this bond. Vibrational energy redistribution then leads to rotation about the bond, resulting in isomerization. Finally, electronic de-excitation near a conical intersection restores the molecule to the electronic ground state. On the other hand, these dynamical simulations demonstrate complexity in the details and reveal supporting roles for other degrees of freedom, such as torsional motion about the vinyl-phenyl side bonds.

A realistic dynamical simulation is reported for ultrafast laser excitation and rotational de-excitation of cis -stilbene. Upon irradiation by a laser pulse with a FWHM of 100 fs, the molecule first rotates around its vinyl bond to about 90°, where an avoided crossing leads to electronic de-excitation. The molecule then immediately twists back to about −60° within only about 80 fs, avoiding isomerization. The other principal dihedral angles, within the phenyl rings, lag behind in time, so there is significant large strain between the phenyl rings and vinyl bond.

Detailed understanding of femtosecond-scale photochemical processes requires dynamical simulations that are complementary to interpretations based on transitions between energy surfaces. For cis to trans photoisomerization of azobenzene following a 100 fs laser pulse, we find that the mechanism is rotation about the central NN bond, and the process is complete in less than 1 ps. The initial excitation and subsequent de-excitation are each achieved via multiple steps, with the molecule always in a superposition of electronic states, as the 3N nuclear degrees of freedom are excited by the laser pulse.

The effect of C–C–C bond bending on the photodissociation of cyclobutane to form two ethylene molecules was investigated by performing semiclassical electron-radiation-ion dynamics simulations and also by examining the potential energy surfaces of the electronic ground state and lowest excited states. These potential energy surfaces, calculated at the CASSCF/MRPT2 level with 6-31G* basis sets along a reaction path determined by the semiclassical dynamics simulations, show well-defined energy minima and maxima in the intermediate state region. It is found that in addition to rotation of the molecule around the central C–C bond, C–C–C bond bending plays an important role in determining the features of the potential energy surfaces for the intermediate species. # 2007 Elsevier B.V. All rights reserved.

Simulations of the photoconversion of 4a,4b-dihydrophenanthrene (DHP) to stilbene, using semiclassical electron-radiation-ion dynamics, are reported. The carbon single bond connecting the phenyl rings breaks approximately 200 fs after the laser pulse is turned off. In the results shown here, the excited cis -stilbene molecule then further isomerizes to the trans conformation after about 1 ps. Each of these two changes of molecular geometry involves a HOMO–LUMO avoided crossing, which produces a transfer of electronic population from LUMO to HOMO. These detailed dynamical simulations are consistent with the interpretation that ring-opening in stilbene is a single photon process.

If robust spectroscopic techniques are to be developed for the detection and identification of pathogens, one must understand the relevant spectroscopic properties of the target molecules. In this paper, we employ density functional theory (DFT) to study the structural, electronic, vibrational, optical, and magnetic properties of dipicolinic acid (DPA) and its dianion DPA−2. Our full geometrical optimization and Mulliken charge analysis show that DFT does not lead to the significant discrepancies between charges on symmetric carbon, hydrogen, and oxygen atoms that are found in less accurate calculations based on the complete active space MCSCF method. Our calculated vibrational frequencies, Raman spectra, and infrared spectra for ground-state DPA and DPA−2 are in good agreement with experiment, and this is also true of the four calculated 13C NMR spectral lines (for α, β, γ, and carboxyl sites). Our time-dependent DFT study of the optical excitation and absorption of both DPA and DPA−2 provides the first interpretation of the observed near ultraviolet absorption and fluorescence spectra. Finally, we discuss for the first time the effect of a solvent on the spectral properties of DPA.

The intricate dynamical processes in photochemical reactions are not fully accessible to either experiment or conventional theory. Here, we outline a technique for simulations in photochemistry, which employs classical trajectories for the nuclei moving in a mean field, with the electrons coupled to a laser pulse by the time-dependent Peierls substitution. We demonstrate that it provides an illuminating description of photoisomerization. One observes a nontrivial sequence of events which include multiple electronic excitations, conversion of double bonds to single bonds (and vice versa), nonadiabatic depopulation of excited levels at avoided crossings, vibrational energy redistribution, and an elegant interdependence of the various electronic and vibrational degrees of freedom.

The usual building blocks of molecular orbital theory are one-center atomic orbitals. If we instead use two-center orbitals derived from the exact solution for H + 2 , a simple calculation of the H 2 binding energy yields 4.5 eV, with a Hylleraas correlation factor having no adjustable parameters. Variational minimization with respect to a couple of parameters in our trial function then shifts the binding energy to 4.7 eV, very near the experimental value. The approach is also applicable to heteronuclear molecules; e.g., HeH + , whose ground state energy we calculate to be −2.96 hartree with no adjustable parameters. This is to be compared with −2.98 hartree previously calculated using a wavefunction with 83 terms.

Detailed simulations are reported for the coupled dynamics of electrons and nuclei in the isomerization reaction of cis-stilbene stimulated by laser excitation. The results demonstrate that, in addition to the traditional vinyl and vinyl– phenyl torsions, the HCCH torsional coordinate of the vinyl group also makes a significant contribution to the HOMO and LUMO couplings that yield nonradiative electronic transitions to the ground state. Moreover, variations in the CCH angles of the vinyl group in the vicinity of the HOMO–LUMO couplings indicate that pyramidalization of the vinyl-group carbon atoms is strongly involved in these molecular orbital couplings. 2003 Published by Elsevier B.V.

Using the technique of tight-binding electron–ion dynamics, we have calculated the evolution of the non-linear susceptibility χ(2)(ω) in GaAs during the first few hundred femtoseconds following an ultrafast and ultra-intense laser pulse. Above a threshold fluence, our simulations show that χ(2)(ω) drops to zero, in agreement with the experimental measurements. The results indicate a rapid non-thermal transition from the original tetrahedral structure to a disordered structure, and support the conclusion that structural changes following ultrashort pulses are a direct consequence of bond destabilization.

First-principles-based molecular dynamics simulations are reported for the (100) surface of Si. Both 2×1 and 4×2 unit cells were treated, with twelve or six layers of atoms allowed to move independently. The following results were obtained: (1) There is a strong tendency toward the formation of dimer rows. (2) Tilted dimers are preferred, and in the simulations at 200 K only tilted dimers were observed. (3) At 300 K the dimers still spend most of their time in tilted positions. However, each dimer is occasionally observed to switch among the three available geometries: tilted left, untilted, and tilted right. There are low barriers (∽0.1 eV) separating these local energy minima. (4) At 750 K there are large amplitude, very anharmonic vibrations about the untilted geometry.

There are strong reasons for believing that dimers in defect-free regions of the Si(100) surface are asymmetric (tilted), but they appear to be symmetric in STM images. It has been suggested that these symmetric images result from a strong distortion of the dimer's electronic structure (and, as a consequence, its geometry) when the STM voltage is applied. Here we report first-principles calculations for the Si(100) surface in the presence of a voltage applied by a simple model of an STM tip: a uniform sphere of charge, 1.06 A in diameter and centered 2.5 A above the surface. For voltages comparable to those used in STM experiments, there is only a very small distortion of the electronic structure, both below and above the Fermi energy EF. Even for large applied voltages, the results indicate that the STM images should be far from symmetric. On the other hand, the time-averaged charge densities for rapidly flipping asymmetric dimers are fully consistent with the STM observations.

The optical dielectric functions of the high- T c superconductors, Ba 0.6 K 0.4 BiO 3 , YBa 2 Cu 3 O 7 and Tl 2 Ba 2 Ca 2 Cu 3 O 10 , have been calculated using a tight-binding model. The results are compared to experimental data. The peak recently observed by De and Woollam at about 3.5 eV in the 2223 material is interpreted as O(2p) to Tl(6p) excitations.

Recently two types of states have been observed for Sb, Bi, and other adsorbates on GaAs(110). For ordered overlayers, photoemission and inverse photoemission show adsorbate-induced states of the kinds that one might expect for systems with good two-dimensional order. On the other hand, scanning tunneling spectroscopy measurements also show states associated with various types of imperfections. The former states are consistent with no Fermi-level pinning, whereas the latter states can provide a mechanism for Fermi-level pinning. Here we report theoretical studies of the electronic states associated with Sb and Bi clusters, around and within the GaAs band gap. Incomplete bonding leads to gap states, but the Sb clusters with the most nearly complete adatom-adatom bonding show semiconducting behavior.

Introduction La chirurgie bariatrique non seulement induit une perte drastique et durable de poids, mais permet aussi une remission durable du DT2 chez les malades obeses morbides. La remission du diabete se produit souvent dans les quelques jours qui suivent la chirurgie, bien avant toute perte significative de poids. Les mecanismes physiologiques et biochimiques qui expliquent l'impact de la chirurgie bariatrique sur l'homeostasie du glucose sont cependant mal connus. Notre objectif est d'utiliser la modelisation mathematique pour essayer de mieux comprendre les mecanismes derriere la remission du DT2 apres chirurgie bariatrique. Materiels et methodes Une methode mathematique generale a ete proposee pour estimer la reponse biochimique aux medicaments, aux chirurgies, ou les autres interventions medicales. Cette methode a ete ensuite appliquee a un modele tres simple de la reponse a la derivation gastrique Roux-en-Y (Roux-en-Y gastric bypass). Resultats Il y a manifestement des effets multiples et tres complexes de la chirurgie bariatrique. Les resultats de notre modele confirment que la remission de diabete apres la chirurgie bariatrique peut etre expliquee en partie par une augmentation de la secretion postprandiale de GLP-1, et ses effets sur la secretion d'insuline. Cependant notre modele suggere aussi que d'autres mecanismes sont susceptibles d'etre impliques, y compris eventuellement par un mecanisme de transport de glucose dans les cellules des organes peripheriques independamment de l'effet de l'insuline. Cette hypothese est supportee par l'induction d'une diminution de la glycemie dans des souris souffrant de DT1 lorsqu'elles expriment une molecule isolee des cellules intestinales et dont la production est augmentee apres la chirurgie bariatrique chez le rat. Conclusion Il est possible qu'une partie de l'effet de la chirurgie bariatrique sur le DT2 soit due a un facteur qui induit le transport du glucose dans les cellules independamment de l'insulin.

Tight-binding molecular dynamics simulations have been performed for the Si(100) surface, with parameters fitted to first-principles calculations for a variety of surface geometries. The simulations yield a value J =-15meV for the dimer-dimer coupling constant along a row, and an upper limit of |J′|=5meV for the coupling across rows. These values, which differ from those of a previous study, give a two-dimensional Ising-model phase transition below 300 K, in agreement with LEED and low-temperature STM studies.

Calculations of deep electronic energy levels have been performed for impurity-vacancy pairs at relaxed (110) surfaces of III–V semiconductors. In particular, results are reported for the native complexes (As Ga , V As ) and (Ga As , v ga ) in GaAs. The predicted levels for these two complexes are respectively close to those for the isolated vacancies, V As and V Ga . This indicates that Fermi-level pinning positions due to surface vacancies will be only quantitatively shifted when the vacancies form complexes with antisite defects.

The Schottky barriers formed by deposition of transition metals on Si surfaces are explained in terms of Fermi-level pinning by Si dangling bonds that are sheltered by vacancies at Si/transition-metal-silicide interfaces.

The intrinsic electronic surface states of (110) GaAs 1− x P x are predicted as functions of alloy composition x . For x > x c ≈ 0.05, intrinsic states are found within the fundamental gap. The minimum energy of the surface band is primarily determined by the bulk electronic structure, not by the atomic relaxation at the surface.

Surface states and bulk state wavefunctions have been calculated for the (100) surfaces of Li, Na, and Cs with the mixed-representation method.

Energy levels deep within the band gap have been calculated for sp 3 -bonded substitutional impurities, for antisite defects, and for vacancies at the (110) surface of AlAs. The predictions are compared with Schottky barrier measurements, within the context of the Spicer-Bardeen model of Fermi-level pinning. An unoccupied surface antisite-defect level is predicted to lie within the band gap for Al on the As site; this level may be responsible for the Schottky barrier observed for n-type AlAs.

The height of the Schottky barrier formed at transition-metal/Si interfaces varies over a very small range (≈0.4 eV) considering the wide range of electronic structures possible from one end of the transition-metal series to the other. Furthermore, the barriers are observed to form within a few monolayers of metal coverage, suggesting that the barrier is a property of the local bonding and that the true metallic states play only a minor role. A model has been developed to explain these facts in terms of the Fermi-level pinning mechanism of Schottky barrier formation. The physics contained in the model is that of a Si dangling bond sheltered from the transition-metal-silicide by an interfacial vacancy. Since (i) the dangling-bond is sheltered from the metallic-silicide and (ii) the atomic energy levels of the transition metal are out of resonance with Si, the dangling bond (which forms a level in the Si band gap) will be only weakly perturbed by the silicide. Thus this interfacial dangling bond can pin the Fermi level at nearly the same energy for all the transition-metal-silicides. A tight-binding calculation of the electronic structure of this defect at the NiSi2/Si(111) interface has been performed for an infinite interface using the transfer-matrix technique. The results of this calculation are described in terms of a very simple molecular model.

The microscopic aspects of interfacial growth are only crudely accessible to experiment. We have therefore developed a technique for computer-experimental studies of atoms and molecules deposited on solid surfaces, in which forces are determined from the electronic structure rather than atomic potentials. Here we report simulations of Cl, O, Se, N, As, Si, Ge, Al, Ga, Zn, Hg, Cu, and Au on the (1 1 0) surface of GaAs. The results exhibit non-trivial variety in both the dynamics and final bonding sites.

We extend the (single-particle) Green function method for treating surface problems by (1) giving a simple analytical expression for the bulk Green function G0+(ω) which is completely general, and (2) giving a new procedure for achieving self-consistency in electronic problems.

Green's function techniques and tight-binding Hamiltonians provide a very versatile approach to the electronic properties of surfaces, as demonstrated in the pioneering work of Professor Koutecký. Here we show that the same general approach is useful for studies of atomic and molecular motion at surfaces; i.e., one can reliably perform molecular dynamics simulations of the various processes that occur when atoms, atomic clusters, or molecules impinge on a solid surface.

In real time computer simulations of reactive atoms incident on solid surfaces, several interesting fundamental processes have been observed. These include (1) a cascade of inelastic collisions between incident atom and substrate atoms that eventually results in equilibration and adsorption; (2) for sufficiently reactive atoms, and sufficiently high substrate temperatures, an exchange reaction in which the adsorbed atom replaces a substrate atom; and (3) the formation of defects as a result of adsorption or exchange events.

Experimental studies indicate that an intrinsic mechanism of Schottky barrier formation dominates when the concentration of defects is very small. Here we address this intrinsic mechanism by considering a one-dimensional model with one s orbital and one p orbital per semiconductor atom and one s orbital per metal atom. Our results suggest that intrinsic Schottky barriers are usually due to dangling-bond resonances , in agreement with the recent work of Lefebvre et al . Even when the resonances are broadened so much that they are unobservable in the density of states, they are still effective in pinning the Fermi energy.

The following facts, and many others, concerning III–V (e.g., GaAs, InP) Schottly barriers can be understood in terms of Fermi-level pinning by interfacial antisite defects (sheltered by vacancies) at semiconductor/metal contacts: (i) the barrier heights are almost independent of the metal in the contact; (ii) the surface Fermi levels can be pinned at sub-monolayer coverages and the pinning energies are almost unaffected by changes of stoichiometry or crystal structure; (iii) the schottky barrier heigh for n-InP with Cu, Ag, or Au is ⋍0.5 eV, but changes to ⋍0.1 eV when reactive metal contacts (Fe, Ni, or Al) are employed because the antisite defects are dominated by P vacancies; and (iv) the dependence on alloy composition or alloys of AlAs, GaAs, GaP, InAs, and GaAs is extremely complex — owing to the dependence of the binding energy for the cation-on-anion-site deep level on alloy composition. Fermi-level pinning by Si dangling bonds at Si/transition-metal silicide interfaces accounts for the following facts: (i) the barrier heights are independent of the transition-metal, to within ⋍0.3 eV; (ii) on the 0.1 eV scale there are chemical trends in barrier heights for n-Si, with the heights decreasing in the order Pt, Pd, and Ni; (iii) barriers form at low metallic coverage, (iv) barrier heights are independent of silicide crystal structure or stoichiometry to ± 0.1 eV; and (v) the barrier heights for n-Si and p-Si add up to approximately the energy of the band gap.

We have developed a technique that permits computer simulations of atomic motion in covalently-bonded systems. Here we report initial studies of chemisorption on the (110) surface of GaAs.

The discovery that cubic Ba 0.6 K 0.4 BiO 3 is a high-temperature superconductor, with T c ≈ 34 K, poses a challenge to theories based on CuO 2 planes. On the other hand, this material, like all other currently-known high- T c superconductors, contains metallic planes adjacent to insulating metal-oxide layers. In every case, these layers can support virtual oxygen p to metal d excitations.

The dependences on alloy compositions x and y are predicted for the deep energy levels of antisite defects in the quaternary alloys Inl−yGayAsl−xPx.

The “dangling-bond” surface state dispersion curves, E ( k ), have been calculated for the (2 × 1) and (1 × 1) (111) surfaces of Ge, Si, and diamond, for (1 × 1) GaAs, anand for (2 × 1) Ge on Si. The calculations employ the sp 3 s ∗ empirical tight-binding model of Vogl et al. and the atomic relaxation of Feder et al. The surface state band gaps are in good agreement with optical-absorption and electron-energy-loss measurements for Ge and Si. For the assumed epitaxial geometry, Ge on Si is predicted to shift the dangling-bond states downward by ≈0.1 to 0.4 eV.

Fermi level pinning positions were measured for Si overlayers on cleaved, n-type GaAs and GaP substrates. The observed positions are 0.73 ± 0.1 eV and 0.98 ± 0.1 eV above the top of the substrate valence band. Theoretical calculations of the surface antisite acceptor levels predict the same chemical trend on going from GaAs to GaP. This agreement and other arguments suggest an important role for surface defects in the formation of semiconductor heterojunctions.

The intrinsic electronic surface states of (110) GaAs1−xPx> are predicted as functions of alloy composition x. For x >xc ≈ 0.05, intrinsic states are found within the fundamental gap. The minimum energy of the surface band is primarily determined by the bulk electronic structure, not by the atomic relaxation at the surface.

Deep energy levels are predicted for substitutional sp 3 -bonded defects at the (110) surface of GaSb.

We report the first calculations of surface thermal-diffuse scattering intensities for extensive regions of reciprocal space including a number of reciprocal lattice rods. The results given here are for the (111) surface of xenon, which has been the subject of recent experimental studies.

Optical surface modes of a new type have been found in calculations for the (100) surface of an NaCl crystal. The problem of obtaining rapidly convergent lattice sums in such calculations is discussed.

The surface state dispersion curves E( k ) of the dangling bond states near the fundamental band gap, C3 and A5, are computed for both the established θ⋍27° model and the recently proposed θ⋍7° model of the (110) surface relaxation of GaAs, where θ is the surface bond rotation angle. The two models produce surface state dispersion curves that are similar to one another and to the data.

The discrete GaAsoxide interface states observed by Lagowski et al . can be explained by defects in the GaAs surface: The deep levels are in agreement with our predictions for surface antisite defects, and the shallow levels (observed for thick oxides) agree with our predictions for surface oxygen impurities on anion and cation sites.

We have performed molecular dynamics simulations for O, C, and N atoms released at the GaAs(110) surface, and have observed the formation of CO, NO, and N2. In most cases these molecules formed under the surface. This formation was accompanied by a disruption of the GaAs bonds. In those cases where CO, NO, and N2 formed above the surface, the energy was found to be higher, and bond disruption was minimal.

Surface states have been calculated for the (100) surfaces of Li and Na. The surface state for Li is in agreement with that calculated by Alldredge and Kleinman using a different method.

We report calculations of deep levels associated with defect complexes at semiconductor surfaces. For the antistructure defect (As Ga , Ga As ) at the (110) surface of GaAs, the results are qualitatively the same as the sum of those for the individual antisite defects As Ga and Ga As — a donor level and two acceptor levels within the band gap.

We derive an expression for the surface contribution to an arbitrary quantity which can be written as a sum over electron, phonon, magnon, etc. states.

We consider an excitonic model in which the electron is localized in a d orbital on a metal site, and the hole is in a linear combination of p orbitals on the surrounding oxygen on a metal with both electron and hole in an insulating LaO, BaO, etc. layer adjacent to a metallic CuO 2 or BiO 2 plane. Even for rather large effective dielectric constants, some of the excitons are found to be tightly bound and consequently to have sizable transition densities α e * ( x → ) β h ( x → ) . We calculate the attractive carrier-carrier interaction V ( q → ) , and use it to estimate the superconducting T c as a function of the parameters in the model. This excitonic mechanism appears to provide a natural and consistent interpretation of high-temperature superconductivity in both the cuprates and bismuthates.

The screening of an external electric field and the distribution of excess charge near a metal surface have been determined self-consistently for the jellium model.

The high-temperature coefficients of thermal expansion have been calculated in the quasiharmonic approximation for the (111) surface of a Lennard-Jones solid. The lower bound on αsurface/αbulk is 1.6, and this ratio undergoes a substantial increase with temperature.