Dissipative dynamics of a system passing through a conical intersection: ultrafast pump-probe observables

The dynamics of a system incorporating a conical intersection, in the presence of a dissipative environment, is studied with the purpose of identifying observable ultrafast spectroscopic signatures. A model system consisting of two vibronically coupled electronic states with two nuclear degrees of freedom is constructed. Dissipation is treated by two different methods, Lindblad semigroup formalism and the surrogate Hamiltonian approach. Pump-probe experimental expectation values such as transient emission and transient absorption are calculated and compared to the adiabatic and diabatic population transfer. The ultrafast population transfer reflecting the conical intersection is not mirrored in transient absorption measurements such as the recovery of the bleach. Emission from the excited state can be suppressed on the ultrafast time scale, but the existence of a conical intersection is only one of the possible mechanisms that can provide ultrafast damping of emission.     

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.     

Synthesis,bulk characterization,and surface characterization of p-hydroxystyrene/styrene copolymers

Styrene/p-hydroxystyrene copolymers were prepared from copolymers of styrene and p-benzyloxystyrene by cleavage of the ether bond. Nuclear magnetic resonance spectroscopy was used to characterize the polymers before and after the ether cleavage reaction. Reactivity ratios were calculated by applying the method of least squares to data generated from the Fineman–Ross equation (r₁ = 0.37, r₂ = 0.28). The surface chemistry of centrifugally cast films of the homopolymers and the copolymers was studied by using electron spectroscopy for chemical analysis (ESCA). The Zisman contact angle method was used to determine the critical surface tension in air for each polymeric surface. Water contents of hydrated films were determined gravimetrically. The polar character of the surface was shown to increase to a small degree with an increase in the p-hydroxystyrene component. Polymers with high p-hydroxystyrene contents did not exhibit pronounced hydrogel character.     

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS"

We develop an efficient technique for computing free energies corresponding to conformational transitions in complex systems by combining a Monte Carlo ensemble of trajectories generated by the shooting algorithm with umbrella sampling. Motivated by the transition path sampling method, our scheme "BOLAS" (named after a cowboy's lasso) preserves microscopic reversibility and leads to the correct equilibrium distribution. This makes possible computation of free energy profiles along complex reaction coordinates for biomolecular systems with a lower systematic error compared to traditional, force-biased umbrella sampling protocols. We demonstrate the validity of BOLAS for a bistable potential, and illustrate the method's scope with an application to the sugar repuckering transition in a solvated deoxyadenosine molecule.     

Novel type of rearrangement of the carane system into a 2-methyl-4-isopropylbicyclo[3.1.0]hexane skeleton

Conclusions X-ray structural analysis has established that one of the oxidation products of 3-carene by trivalent thallium acetate is 2-methyl-4-(1-hydroxy-1-methylethyl)bicyclo [3.1.0]-hexan-2-ol. Its formation depends primarily on rearrangement of the carane skeleton into a bicyclohexane skeleton via 1,3-trans-annular participation of the C⁶-C⁷ bond in the cyclopropane fragment.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1777–1779, August, 1988.     

Inelastic electron tunneling spectroscopy in molecular junctions: peaks and dips

We study inelastic electron tunneling through a molecular junction using the nonequilibrium Green's function formalism. The effect of the mutual influence between the phonon and the electron subsystems on the electron tunneling process is considered within a general self-consistent scheme. Results of this calculation are compared to those obtained from the simpler Born approximation and the simplest perturbation theory approaches, and some shortcomings of the latter are pointed out. The self-consistent calculation allows also for evaluating other related quantities such as the power loss during electron conduction. Regarding the inelastic spectrum, two types of inelastic contributions are discussed. Features associated with real and virtual energy transfer to phonons are usually observed in the second derivative of the current I with respect to the voltage Phi when plotted against Phi. Signatures of resonant tunneling driven by an intermediate molecular ion appear as peaks in the first derivative dI/dPhi and may show phonon sidebands. The dependence of the observed vibrationally induced lineshapes on the junction characteristics, and the linewidth associated with these features are also discussed.     

Conformationally gated switching between superexchange and hopping within oligo-p-phenylene-based molecular wires

We observe well-defined regions of superexchange and thermally activated hopping in the temperature dependence of charge recombination (CR) in a series of donor-bridge-acceptor (D-B-A) systems, where D = phenothiazine (PTZ), B = p-phenylene (Ph(n)), n = 1-4, and A = perylene-3,4:9,10-bis(dicarboximide) (PDI). A fit to the thermally activated CR rates of the n = 3 and n = 4 compounds yields activation barriers of 1290 and 2030 cm(-1), respectively, which match closely with theoretically predicted and experimentally observed barriers for the planarization of terphenyl and quaterphenyl. Negative activation of CR in the temperature regions dominated by superexchange charge transport is the result of a fast conformational equilibrium that increasingly depopulates the reactive state for CR as temperature is increased. The temperature dependence of the effective donor-acceptor superexchange coupling, V(DA), measured using magnetic field effects on the efficiency of the charge recombination process, shows that CR occurs out of the conformation with lower V(DA) via the energetically favored triplet pathway.     

Energy band structures of the chalcopyrite lattice semiconductors CuAlS2, CuAlSe2, CuInS2, and CuInSe2

The pseudopotential method is used to calculate the energy band structures of four -type semiconductors including the effect of the displacement of anions from face-centered sites in the sublattices. It was established that CuAlSe₂, CuInS₂, and CuInSe₂ are direct gap semiconductors and that CuAlS₂ has a pseudodirect energy gap. Experimental data derived from studies of the optical properties of these crystals in the U V region are also discussed.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 6, pp. 7–12, June, 1976.     

A new program for optimizing periodic boundary models of solvated biomolecules (PBCAID)

Simulations of solvated macromolecules often use periodic lattices to account for long-range electrostatics and to approximate the surface effects of bulk solvent. The large percentage of solvent molecules in such models (compared to macromolecular atoms) makes these procedures computationally expensive. The cost can be reduced by using periodic cells containing an optimized number of solvent molecules (subject to a minimal distance between the solute and the periodic images). We introduce an easy-to-use program "PBCAID" to initialize and optimize a periodic lattice specified as one of several known space-filling polyhedra. PBCAID reduces the volume of the periodic cell by finding the solute rotation that yields the smallest periodic cell dimensions. The algorithm examines rotations by using only a subset of surface atoms to measure solute/image distances, and by optimizing the distance between the solute and the periodic cell surface. Once the cell dimension is optimized, PBCAID incorporates a procedure for solvating the domain with water by filling the cell with a water lattice derived from an ice structure scaled to the bulk density of water. Results show that PBCAID can optimize system volumes by 20 to 70% and lead to computational savings in the nonbonded computations from reduced solvent sizes. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1843-1850, 2001     

Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase.

Molecular dynamics (MD) simulations have been performed to study the rehydration of compact and unfolded cytochrome c ions in the vapor phase. Experimental studies have shown that the compact conformations adsorb many more water molecules than unfolded ones when exposed to water vapor. MD simulations performed with up to 150 water molecules reproduce the key experimental observations, including a partial refolding caused by hydration. According to the calculations it is more energetically favorable to hydrate the compact conformation in the initial stages of hydration, because it is easier for a water molecule to interact simultaneously with several polar groups (due to their proximity). The protonated side chains are not favored hydration sites in the simulations because they have "self-solvation" shells which must be disrupted for the water to penetrate. For both conformations, the adsorbed water molecules are mainly located in surface crevices.