Dynamics of excited OCS investigated by resonance-enhanced multiphoton ionization

The predissociation decay behavior of molecule carbonyl sulfide (OCS) has been investigated by resonance-enhanced multiphoton ionization spectroscopy using the pump-probe technique of dichroic femtosecond lasers in real time. The lifetime of excited OCS around 74 720 cm(-1) by two-photon absorption of 268 nm, corresponding to upsilon(1)=1 of the Rydberg state [(2)Pi(1/2)]4ppi((1)Sigma(+)), is directly determined to be tau(D)=1071+/-11 fs. This picosecond decay process indicates that the excited state is predissociative. The temporal information of dissociation enriches the knowledge of the potential-energy surface of the associative excited state.

Ab initio study on the physical properties of CoN3 and RhN3 with skutterudite structure

The elastic and electronic properties of hypothetical CoN3 and RhN3 with cubic skutterudite structure were studied by first principles calculations based on density functional theory. By choosing different initial geometries, two local minima or modifications were located on the potential energy surface, termed as modifications I and II. Both compounds are mechanically stable. For each compound, modification I is lower in energy than II. Thermodynamically stable phases can be achieved by applying pressures. Modification II is lower in energy than I at above 50 GPa for both compounds.

Density functional/Monte Carlo study of ring-opening polymerization

Density functional calculations of the structure, potential energy surface and reactivity for organic systems closely related to bisphenol-A-polycarbonate (BPA-PC) provide the basis for a model describing the ring-opening polymerization of its cyclic oligomers by nucleophilic molecules. Monte Carlo simulations using this model show a strong tendency to polymerize that is increased by increasing density and temperature, and is greater in 3D than in 2D. Entropy in the distribution of inter-particle bonds is the driving force for chain formation. (C) 2002 Elsevier Science B.V. All rights reserved.

Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure. (C) 2001 American Institute of Physics.

Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

On the origin of the forward peak and backward oscillations in the F + H2(v = 0) to HF(v' = 2) + H reaction

We present a semiclassical complex angular momentum (CAM) analysis of the forward scattering peak which occurs at a translational collision energy around 32 meV in the quantum mechanical calculations for the F + H2(v = 0, j = 0) ? HF(v' = 2, j' = 0) + H reaction on the Stark–Werner potential energy surface. The semiclassical CAM theory is modified to cover the forward and backward scattering angles. The peak is shown to result from constructive/destructive interference of the two Regge states associated with two resonances, one in the transition state region and the other in the exit channel van der Waals well. In addition, we demonstrate that the oscillations in the energy dependence of the backward differential cross section are caused by the interference between the direct backward scattering and the decay of the two resonance complexes returning to the backward direction after one full rotation.

State-Selective Photodissociation Dynamics of Formaldehyde: Near Threshold Studies of the H+HCO Product Channel

The laser-induced photodissociation of formaldehyde in the wavelength range 309<λ<330nm 309<λ<330nm has been investigated using H (Rydberg) atom photofragment translational spectroscopy. Photolysis wavelengths corresponding to specific rovibronic transitions in the A ˜ A 2 1 ←X ˜ A 1 1 ÃA21←X̃A11 2 1 0 4 3 0 201403 , 2 2 0 4 1 0 202401 , 2 2 0 4 3 0 202403 , 2 3 0 4 1 0 203401 , and 2 1 0 5 1 0 201501 bands of H 2 CO H2CO were studied. The total kinetic energy release spectra so derived can be used to determine partial rotational state population distributions of the HCO cofragment. HCO product state distributions have been derived following the population of various different N K a NKa levels in the A ˜ A 2 1 ÃA21 2 2 4 3 2243 and 2 3 4 1 2341 states. Two distinct spectral signatures are identified, suggesting competition between dissociation pathways involving the X ˜ A 1 1 X̃A11 and the a ˜ A 2 3 ãA23 potential energy surfaces. Most rovibrational states of H 2 CO(A ˜ A 2 1 ) H2CO(ÃA21) investigated in this work produceH+HCO(X ˜ A ′ 2 ) H+HCO(X̃A′2) photofragments with a broad kinetic energy distribution and significant population in high energy rotational states of HCO. Photodissociation via the A ˜ A 2 1 ÃA21 2 2 4 3 2243 1 1,1 11,1 (and 1 1,0 11,0 ) rovibronic states yields predominantly HCO fragments with low internal energy, a signature that these rovibronic levels are perturbed by the a ˜ A 2 3 ãA23 state. The results also suggest the need for further careful measurements of the H+HCO H+HCO quantum yield from H 2 CO H2CO photolysis at energies approaching, and above, the barrier to C–H bond fission on the a ˜ A 2 3 ãA23 potential energy surface.

Insight into association reactions on metal surfaces: Density-functional theory studies of hydrogenation reactions on Rh(111)

Hydrogenation reaction, as one of the simplest association reactions on surfaces, is of great importance both scientifically and technologically. They are essential steps in many industrial processes in heterogeneous catalysis, such as ammonia synthesis (N-2+3H(2)-->2NH(3)). Many issues in hydrogenation reactions remain largely elusive. In this work, the NHx (x=0,1,2) hydrogenation reactions (N+H-->NH, NH+H-->NH2 and NH2+H-->NH3) on Rh(111) are used as a model system to study the hydrogenation reactions on metal surfaces in general using density-functional theory. In addition, C and O hydrogenation (C+H-->CH and O+H-->OH) and several oxygenation reactions, i.e., C+O, N+O, O+O reactions, are also calculated in order to provide a further understanding of the barrier of association reactions. The reaction pathways and the barriers of all these reactions are determined and reported. For the C, N, NH, and O hydrogenation reactions, it is found that there is a linear relationship between the barrier and the valency of R (R=C, N, NH, and O). Detailed analyses are carried out to rationalize the barriers of the reactions, which shows that: (i) The interaction energy between two reactants in the transition state plays an important role in determining the trend in the barriers; (ii) there are two major components in the interaction energy: The bonding competition and the direct Pauli repulsion; and (iii) the Pauli repulsion effect is responsible for the linear valency-barrier trend in the C, N, NH, and O hydrogenation reactions. For the NH2+H reaction, which is different from other hydrogenation reactions studied, the energy cost of the NH2 activation from the IS to the TS is the main part of the barrier. The potential energy surface of the NH2 on metal surfaces is thus crucial to the barrier of NH2+H reaction. Three important factors that can affect the barrier of association reactions are generalized: (i) The bonding competition effect; (ii) the local charge densities of the reactants along the reaction direction; and (iii) the potential energy surface of the reactants on the surface. The lowest energy pathway for a surface association reaction should correspond to the one with the best compromise of these three factors. (C) 2003 American Institute of Physics.

General trends in the barriers of catalytic reactions on transition metal surfaces

A catalyst preparation by design is one of the ultimate goals in chemistry. The first step towards this goal is to understand the origin of reaction barriers. In this study, we have investigated several catalytic reactions on some transition metal surfaces, using density functional theory. All the reaction barriers have been determined. By detailed analyses we obtain some insight into the reaction barrier. Each barrier is related to (i) the potential energy surface of reactants on the surface, (ii) the total chemisorption energy of reactants, and (iii) the metal d orbital occupancy and the reactant valency. (C) 2001 American Institute of Physics.

General local and rectilinear vibrational coordinates consistent with Eckart's conditions

We present a general method to construct a set of local rectilinear vibrational coordinates for a nonlinear molecule whose reference structure does not necessarily correspond to a stationary point of the potential-energy surface. We show both analytically and with a numerical example that the vibrational coordinates satisfy Eckart's conditions. In addition, we find that the Watson Hamiltonian provides a fairly robust description even of highly excited vibrational states of triatomic molecules, except for a few states of large amplitude motion sampling the singular region of the Hamiltonian. These states can be identified through slow convergence.

A density functional theory study of CO and atomic oxygen chemisorption on Pt(111)

Ab initio total energy calculations within a density functional theory framework have been performed for CO and atomic oxygen chemisorbed on the Pt(111) surface. Optimised geometries and chemisorption energies for CO and O on four high-symmetry sites, namely the top, bridge, fee hollow and hcp hollow sites, are presented, the coverage in all cases being 0.25 ML. The differences in CO adsorption energies between these sites are found to be small, suggesting that the potential energy surface for CO diffusion across Pt(111) is relatively flat. The 5 sigma and 2 pi molecular orbitals of CO are found to contribute to bonding with the metal. Some mixing of the 4 sigma and 1 pi molecular orbitals with metal states is also observed. For atomic oxygen, the most stable adsorption site is found to be the fee hollow site, followed in decreasing order of stability by the hcp hollow and bridge sites, with the top site being the least stable. The differences in chemisorption energies between sites for oxygen are larger than in the case of CO, suggesting a higher barrier to diffusion for atomic oxygen. The co-adsorption of CO and O has also been investigated. Calculated chemisorption energies for CO on an O/fcc-precovered surface show that of the available chemisorption sites, the top site at the oxygen atom's next-nearest neighbour surface metal atom is the most stable, with the other four sites calculated bring at least 0.29 eV less stable. The trend of CO site stability in the coadsorption system is explained in terms of a 'bonding competition' model. (C) 2000 Elsevier Science B.V. All rights reserved.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Theory of laser-induced ultrafast structural changes in solids

The present thesis is a contribution to the study of laser-solid interaction. Despite the numerous applications resulting from the recent use of laser technology, there is still a lack of satisfactory answers to theoretical questions regarding the mechanism leading to the structural changes induced by femtosecond lasers in materials. We provide here theoretical approaches for the description of the structural response of different solids (cerium, samarium sulfide, bismuth and germanium) to femtosecond laser excitation. Particular interest is given to the description of the effects of the laser pulse on the electronic systems and changes of the potential energy surface for the ions. Although the general approach of laser-excited solids remains the same, the potential energy surface which drives the structural changes is calculated with different theoretical models for each material. This is due to the difference of the electronic properties of the studied systems. We use the Falicov model combined with an hydrodynamic method to study photoinduced phase changes in cerium. The local density approximation (LDA) together with the Hubbard-type Hamiltonian (LDA+U) in the framework of density functional theory (DFT) is used to describe the structural properties of samarium sulfide. We parametrize the time-dependent potential energy surface (calculated using DFT+ LDA) of bismuth on which we perform quantum dynamical simulations to study the experimentally observed amplitude collapse and revival of coherent $A_{1g}$ phonons. On the basis of a time-dependent potential energy surface calculated from a non-orthogonal tight binding Hamiltonian, we perform molecular dynamics simulation to analyze the time evolution (coherent phonons, ultrafast nonthermal melting) of germanium under laser excitation. The thermodynamic equilibrium properties of germanium are also reported. With the obtained results we are able to give many clarifications and interpretations of experimental results and also make predictions.

Theoretical study of magnetism, structure and chemical order in transition-metal alloy clusters

Research on transition-metal nanoalloy clusters composed of a few atoms is fascinating by their unusual properties due to the interplay among the structure, chemical order and magnetism. Such nanoalloy clusters, can be used to construct nanometer devices for technological applications by manipulating their remarkable magnetic, chemical and optical properties. Determining the nanoscopic features exhibited by the magnetic alloy clusters signifies the need for a systematic global and local exploration of their potential-energy surface in order to identify all the relevant energetically low-lying magnetic isomers. In this thesis the sampling of the potential-energy surface has been performed by employing the state-of-the-art spin-polarized density-functional theory in combination with graph theory and the basin-hopping global optimization techniques. This combination is vital for a quantitative analysis of the quantum mechanical energetics. The first approach, i.e., spin-polarized density-functional theory together with the graph theory method, is applied to study the Fe$_m$Rh$_n$ and Co$_m$Pd$_n$ clusters having $N = m+n \leq 8$ atoms. We carried out a thorough and systematic sampling of the potential-energy surface by taking into account all possible initial cluster topologies, all different distributions of the two kinds of atoms within the cluster, the entire concentration range between the pure limits, and different initial magnetic configurations such as ferro- and anti-ferromagnetic coupling. The remarkable magnetic properties shown by FeRh and CoPd nanoclusters are attributed to the extremely reduced coordination number together with the charge transfer from 3$d$ to 4$d$ elements. The second approach, i.e., spin-polarized density-functional theory together with the basin-hopping method is applied to study the small Fe$_6$, Fe$_3$Rh$_3$ and Rh$_6$ and the larger Fe$_{13}$, Fe$_6$Rh$_7$ and Rh$_{13}$ clusters as illustrative benchmark systems. This method is able to identify the true ground-state structures of Fe$_6$ and Fe$_3$Rh$_3$ which were not obtained by using the first approach. However, both approaches predict a similar cluster for the ground-state of Rh$_6$. Moreover, the computational time taken by this approach is found to be significantly lower than the first approach. The ground-state structure of Fe$_{13}$ cluster is found to be an icosahedral structure, whereas Rh$_{13}$ and Fe$_6$Rh$_7$ isomers relax into cage-like and layered-like structures, respectively. All the clusters display a remarkable variety of structural and magnetic behaviors. It is observed that the isomers having similar shape with small distortion with respect to each other can exhibit quite different magnetic moments. This has been interpreted as a probable artifact of spin-rotational symmetry breaking introduced by the spin-polarized GGA. The possibility of combining the spin-polarized density-functional theory with some other global optimization techniques such as minima-hopping method could be the next step in this direction. This combination is expected to be an ideal sampling approach having the advantage of avoiding efficiently the search over irrelevant regions of the potential energy surface.

Squeezed thermal phonons precurse nonthermal melting of silicon as a function of fluence

A femtosecond-laser pulse can induce ultrafast nonthermal melting of various materials along pathways that are inaccessible under thermodynamic conditions, but it is not known whether there is any structural modification at fluences just below the melting threshold. Here, we show for silicon that in this regime the room-temperature phonons become thermally squeezed, which is a process that has not been reported before in this material. We find that the origin of this effect is the sudden femtosecond-laser-induced softening of interatomic bonds, which can also be described in terms of a modification of the potential energy surface. We further find in ab initio molecular-dynamics simulations on laser-excited potential energy surfaces that the atoms move in the same directions during the first stages of nonthermal melting and thermal phonon squeezing. Our results demonstrate how femtosecond-laser-induced coherent fluctuations precurse complete atomic disordering as a function of fluence. The common underlying bond-softening mechanism indicates that this relation between thermal squeezing and nonthermal melting is not material specific.