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The light-activated photoactive yellow protein (PYP) chromophore uses a series of reactions to trigger photo-motility and biological responses, and generate a wide range of structural signals. To provide a comprehensive mechanism of the overall process at the atomic level, we apply a CASPT2//CASSCF/AMBER QM/MM protocol to investigate the relaxation pathways for a variety of possible isomerization and proton transfer reactions upon photoexcitation of the wild-type PYP. The nonadiabatic relay through an S1/S0 conical intersection [CI(S1/S0)] is found to play a decisive major role in bifurcating the excited state relaxation into a complete and short photocycle. Two major and one minor deactivation channels were found starting from the CI(S1/S0)-like intermediate IT, producing the cis isomers pR1, ICP, and ICT through “hula twist”, “bicycle pedal” and one-bond flip isomerization reactions. The overall photocycle can be achieved by competitive parallel/sequential reactions, in which the ground state recovery is controlled by a series of slow volume-conserving bicycle pedal/hula twist and one-bond flip isomerization reactions, as well as fast protonation–deprotonation processes and the hydrophobic–hydrophilic state transformation.

Electronic structure calculations are performed to characterise the structures, energies, and spectroscopic data for a series of four-coordinate tris(carbene)borate {NiNO}(10) complexes. There is excellent agreement between the computational and experimental results for known complexes, allowing for structure-function relationships to be delineated. Calculations that provide insights into the synthetic accessibility of nickel(iv) nitrides by oxygen atom abstraction from these complexes are also reported.

The improved relaxation approach of Meyer and co-workers is extended by employing the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory. Within this approach the trial wave function is expressed by a recursive, multilayered expansion that is the same as in a normal ML-MCTDH simulation. Calculation of an energy eigenstate then proceeds by iteratively diagonalizing the Boltzmann operator in the top layer representation using a Lanczos/Arnoldi method while relaxing the single particle functions of all layers using the ML-MCTDH imaginary time propagation. Numerical iteration is stopped until the relative energy and/or density of the target state meet the convergence criteria. The application of this multilayer improved relaxation method is illustrated by computing the energy splitting for the lowest pair of eigenstates as well as the spin observables and entanglement entropy of the spin-boson model. A large number of degrees of freedom, up to 10,000 bath modes, can be treated, and thus the appropriate phase transition at a critical system-bath coupling strength may be predicted via appropriate extrapolations.

The nonequilibrium dynamics of a quantum dot with electron-phonon interactions described by a generalized Holstein model is presented. A combination of methodologies including the reduced density matrix formalism, the multilayer multiconfiguration time-dependent Hartree method, and a time-dependent nonequilibrium Green function approach, is used to explore the transient behavior on multiple timescales as the system approaches steady-state. The dot population dynamics on short to intermediate times is governed by the dot-lead hybridization parameter ($\Gamma$) and by the typical phonon frequency ($\omega_{c}$) and depends on the location of the energy level of the dot relative to the bias window. At longer times, the dynamics show a distinct behavior depending on whether the system is in the adiabatic or non-adiabatic regime, with a quantum dot occupation that may depend on the initial preparation of the phonons degrees of freedom. A "phase" diagram of this localization effect as a function of the polaron shift ($\lambda$) for various phonon frequencies is derived, suggesting the existence of bistability on experimentally observable timescales., Comment: 15 pages, 9 figures

A general form of a many-body Hamiltonian is considered, which includes an interacting fermionic sub-system coupled to non-interacting extended fermionic and bosonic systems. We show that the exact dynamics of the extended bosonic system can be derived from the reduced density matrix of the sub-system alone, despite the fact that the latter contains information about the sub-system only. The advantage of the formalism is immediately clear: While the reduced density matrix of the sub-system is readily available, the formalism offers access to observables contained in the full density matrix, which is often difficult to obtain. As an example, we consider an extended Holstein model and study the nonequilibrium dynamics of the, so called, "reaction mode" for different model parameters. The effects of the phonon frequency, the strength of the electron-phonon couplings, and the source-drain bias voltage on the phonon dynamics across the bistability are discussed., Comment: 5 pages, 3 figures

The self-consistent hybrid approach [H. Wang, M. Thoss, and W. H. Miller, J. Chem. Phys. 115, 2979 (2001), preceding paper] is applied to the spin-boson problem with Debye spectral density as a model for electron-transfer reactions in a solvent exhibiting Debye dielectric relaxation. The population dynamics of the donor and acceptor states in this system is studied for a broad range of parameters, including the adiabatic (slow bath), nonadiabatic (fast bath), as well as the intermediate regime. Based on illustrative examples we discuss the transition from damped coherent dynamics to purely incoherent decay. Using the numerically exact results of the self-consistent hybrid approach as a benchmark, several approximate theories that have been widely used to describe the dynamics in the spin-boson model are tested: the noninteracting blip approximation, the Bloch–Redfield theory, the Smoluchowski-equation treatment of the reaction coordinate (Zusman equations), and the classical path approach (Ehrenfest model). The parameter range where the different methods are applicable are discussed in some detail.

An efficient method, the self-consistent hybrid method, is proposed for accurately simulating time-dependent quantum dynamics in complex systems. The method is based on an iterative convergence procedure for a dynamical hybrid approach. In this approach, the overall system is first partitioned into a “core” and a “reservoir” (an initial guess). The former is treated via an accurate quantum mechanical method, namely, the time-dependent multiconfiguration self-consistent field or multiconfiguration time-dependent Hartree approach, and the latter is treated via a more approximate method, e.g., classical mechanics, semiclassical initial value representations, quantum perturbation theories, etc. Next, the number of “core” degrees of freedom, as well as other variational parameters, is systematically increased to achieve numerical convergence for the overall quantum dynamics. The method is applied to two examples of quantum dissipative dynamics in the condensed phase: the spin-boson problem and the electronic resonance decay in the presence of a vibrational bath. It is demonstrated that the method provides a practical way of obtaining accurate quantum dynamical results for complex systems.

The capability of two different, recently proposed semiclassical (SC) forward–backward (FB) initial value representations (IVR) to describe quantum interference and coherence effects is investigated. It is shown that depending on the way the observable under consideration is represented by unitary operators one can obtain rather different results. Although the FB-IVR based on an integral representation as a rule is capable of describing quantum interference, a closer analysis reveals that it depends on the observable under consideration if all interference that can be described semiclassically is actually included in the calculation. To overcome this problem a new, generalized FB-IVR method (GFB-IVR) is proposed, which combines the capability of the SC-IVR to describe quantum interference effects independent of the observable and the better convergence properties of the FB-IVR. The performance of this new approach is studied in some detail. In particular, it is shown that the GFB-IVR can describe both the...

It is shown that the forward–backward (FB) version of the semiclassical (SC) initial value representation (IVR) is able to describe quantum interference/coherence (i.e., diffraction) of particles transmitted by a two-slit potential. (In contrast, the linearized approximation to the SC-IVR, which leads to the classical Wigner model, is unable to do so.) FB-IVR calculations are also used to describe the (partial) quenching of this interference structure (i.e., “de-coherence”) when the two-slit potential is coupled to a bath of harmonic oscillators.

The forward–backward (FB) version of the semiclassical (SC) initial value representation (IVR) is used to study quantum coherence effects in the time-dependent probability distribution of an anharmonic vibrational coordinate and its quenching when coupled to a thermal bath. It is shown that the FB-IVR accurately reproduces the detailed quantum coherent structure in the weak coupling regime, and also describes how this coherence is quenched with an increase of the system–bath coupling and/or the bath temperature. Comparisons are made with other approximations and the physical implications are discussed.

The feasibility of using a basis set approach to the study of quantum dissipative dynamics is investigated for the spin-boson model, a system of two discrete states linearly coupled to a harmonic bath. The infinite Hamiltonian is discretized to a finite number of degrees of freedom. Traditional basis set approach, in a multiconfiguration time-dependent Hartree context, is used to solve the time-dependent Schrodinger equations by explicitly including all the degrees of freedom (“system”+“bath”). Quantities such as the reduced density matrix are then evaluated via a quadrature summation/Monte Carlo procedure over a certain number of time-dependent wave functions. Numerically exact results are obtained by systematically increasing the number of bath modes used to represent the condensed phase environment, as well as other variational parameters (number of basis functions, configurations, etc.). The potential of the current method is briefly discussed.

A log-derivative formulation of the prefactor term appearing in the semiclassical Herman-Kluk propagator is presented. The resulting new expression is found in practice to avoid the branch cut problem which has hampered previous formulations. The enhanced performance of the log-derivative version of the prefactor has been confirmed by testing it on several one- and two-dimensional model problems. This log-derivative algorithm is also incorporated in the forward-backward initial value representation and applied to a model of the double-slit diffraction problem.

The semiclassical (SC) initial value representation (IVR) provides a potentially practical way for including quantum effects into classical molecular dynamics simulations. The forward–backward (FB) version of the IVR provides an especially attractive way for calculating time correlation functions, in particular the reactive flux correlation function which determines chemical reaction rates. This paper presents a further analysis and development of the FB-IVR approach. Applications show that it is feasible and accurate for a reaction coordinate coupled to up to 40 degrees of freedom.

It is shown how a particular correlation function, computed quantum mechanically or semiclassically as a function of real-time, can be analytically continued to obtain thermal rate constants (or other thermally averaged quantities) over a wide range of temperature. The correlation function is first evaluated at a reference temperature, and then analytically continued to obtain information at other desired temperatures. The method is applied to the calculation of the thermal rate constant for the Cl+H2→HCl+H (J=0) reaction using the flux correlation function formalism, and it is seen to be capable of obtaining accurate rate constants over a broad temperature range.

The linearized semiclassical initial value representation (LSC-IVR) [H. Wang, X. Sun and W. H. Miller, J. Chem. Phys. 108, 9726 (1998)] is used to study the nonadiabatic dynamics of the spin-boson problem, a system of two electronic states linearly coupled to an infinite bath of harmonic oscillators. The spectral density of the bath is chosen to be of the Debye form, which is often used to model the solution environment of a charge transfer reaction. The simulation provides a rather complete understanding of the electronically nonadiabatic dynamics in a broad parameter space, including coherent to incoherent transitions along all three axes (the T-axis, the η-axis, and the ωc-axis) in the complete phase diagram and the determination of rate constants in several physically interesting regimes. Approximate analytic theories are used to compare with the simulation results, and good agreement is found in the appropriate physical limits.

It is shown how to formulate the ubiquitous quantum chemistry problem of calculating the thermal rate constant on a quantum computer. The resulting exact algorithm scales exponentially faster with the dimensionality of the system than all known ``classical'' algorithms for this problem., 10 pages, no figures

The PES(F,Cl) analytic potential energy surface, developed previously, is used in a trajectory study of the F- + CH3Cl SN2 reaction. The trajectory SN2 rate constants, as a function of reactant relative translational energy Erel and CH3Cl temperature, are in good overall agreement with the experimental rate constants and those calculated using an ion−molecule capture/RRKM statistical model applied to PES(F,Cl). The latter agreement exists even though the reaction dynamics is decidedly nonstatistical. For high Erel the reaction is direct. At lower Erel there is evidence for formation of an ion−molecule complex; however, its lifetime is too short for complete energy randomization to occur. The velocity scattering angle is isotropic at low Erel but becomes anisotropic with forward scattering as Erel is increased. The reaction exothermicity is primarily partitioned to product vibration, in disagreement with a previous experimental study. Energy transfer from the reactants to products is very selective. Excess...

Two different semiclassical approaches are presented for extending flux correlation function methodology for computing thermal reaction rate constants, which has been extremely successful for the “direct” calculation of rate constants in small molecule (∼3–4 atoms) reactions, to complex molecular systems, i.e., those with many degrees of freedom. First is the popular mixed quantum-classical approach that has been widely used by many persons, and second is an approximate version of the semiclassical initial value representation that has recently undergone a rebirth of interest as a way for including quantum effects in molecular dynamics simulations. Both of these are applied to the widely studied system-bath model, a one-dimensional double well potential linearly coupled to an infinite bath of harmonic oscillators. The former approximation is found to be rather poor while the latter is quite good.

We present “direct” calculations of the thermal rate constant for the F + H2 reaction. The rate is obtained from the time integral of the flux−flux autocorrelation function, which is efficiently evaluated by taking advantage of the low rank of the half-Boltzmannized flux operator. Total rate constants are obtained from exact total angular momentum J ≠ 0 calculations and compared with approximate approaches for including nonzero J. The rate constants obtained for the F + H2 reaction on the new, highly accurate Stark−Werner potential energy surface are in good agreement with previous experimental results.

An efficient method was recently introduced by Thompson and Miller [J. Chem. Phys. 106, 142 (1997)] for calculating thermal rate constants using the flux–flux autocorrelation function with absorbing boundary conditions. The method uses an iterative method to exploit the low rank feature of the Boltzmannized flux operator and subsequently only propagates the eigenvectors that have significant contributions to the rate constant. In the present article, this method is used to calculate the thermal rate constants of the Cl+H2→HCl+H reaction in the temperature range of 200–1500 °K. Total angular momentum is treated by employing the body-fixed axis frame, both exactly and also via various approximations. Comparisons with previous exact and approximate theoretical results are made.

The intramolecular dynamics of Cl−---CH3Br complexes is studied at an energy approximately equal to the average thermal energy of complexes formed by Cl− + CH3Br association at 300 K. Lyapunov exponents are calculated for different mode excitations of the Cl−---CH3Br complex. Without zero-point energy added to the complex, a number of the mode excitations have zero Lyapunov exponents and, thus, regular motion. The Lyapunov exponents are positive and the motion is chaotic for all mode excitations with zero-point energy added. However, the latter Lyapunov exponents are sufficiently small that the time required to form a microcanonical ensemble of Cl−---CH3Br states is much longer than the RRKM lifetime of the complex. Thus, non-RRKM unimolecular dynamics is expected for the Cl−---CH3Br complex as found in previous trajectory simulations.

International audience; An analysis of variational transition state theory rate constants, for the association reactions Cl- + CH3Cl, Cl- + CH3Br, H + CH3, H + diamond{111}, CH3 + CH3, and Al + Al2 shows that the free energy of activation ΔG varies nearly linearly with temperature, over a broad temperature range, for each reaction. This suggests that association rate constants can be parametrized by the free energy of activation at 300 K, Δ , and the change in ΔG with temperature, ΔΔG/ΔT. The near linear dependence of ΔG with temperature is supported by a semiempirical model for association kinetics. The rate constants for Cl- + CH3Cl, Cl- + CH3Br, and CH3 + CH3 decrease with increase in temperature, while those for H + CH3, H + diamond{111}, and Al + Al2 slightly increase. For the six association reactions considered here, the linear free energy relationship gives semiquantitative rate constants over a rather broad temperature range of 200−2000 K. To calculate accurate rate constants over a broader temperature range, particularly at low temperatures, nonlinear terms must be included in the free energy expansion.

Statistical theory is used to calculate the F- + CH3Cl → FCH3 + Cl- rate constant versus relative translational energy Erel and CH3Cl temperature T. The calculations are performed on a potential energy surface derived from MP2 and QCISD(T) ab initio calculations with the 6-311++G(2df,2pd) basis set. At best, statistical theory only qualitatively reproduces the dependence of the experimental rate constant on translational energy and temperature. Using the height of the central barrier with respect to the pre-reaction complex as an adjustable parameter, the experimental rate constant at Erel = 0.9 kcal/mol and T = 296 K may be fit by statistical theory with a central barrier 3 kcal/mol higher than that determined from the QCISD(T) calculation. The calculation of the SN2 rate constant is insensitive to whether the unified statistical model or standard RRKM branching ratio expression is used. Also, including anharmonicity for the F-- - -CH3Cl complex does not affect the calculated rate constant. A comparison ...

The rate constants and products for the reactions of Cl-(D2O)n + CH3Br (n = 1−3) have been measured. The n = 1 reaction was studied from 238 to 478 K. The rate constant is well described by k = (6.0 × 10-10) exp(−1270/T) cm3 s-1. We determined the reaction mechanism to be ligand switching to produce Cl-(CH3Br) followed by thermal decomposition of the complex. Cl-(CH3Br) decomposition produces greater than 90% Br- + CH3Cl with the remainder being Cl- + CH3Br. The Cl-(CH3Br) + He rate constant is well described by k = (4.5 × 10-10) exp(−2260/T) cm3 s-1. RRKM theory was used to model the decomposition of Cl-(CH3Br). The results are consistent with our experimental results if a central barrier height of 22.5 kJ mol-1 is used. The n = 2 and 3 reactions also proceed by ligand switching followed by thermal decomposition. The n = 2 reaction was studied from 203 to 298 K. The rate constant is well-described by (4.4 × 10-9) exp(−1329/T) cm3 s-1. The main product observed was Cl-(D2O) with a smaller amount of Cl-(D2...

Reduced dimensional time-dependent and time-independent quantum dynamics calculations are performed for the Cl - +CH 3 Br S N 2 reaction. In the time-dependent study, a wavepacket is initiated at the Cl - ···CH 3 Br pre-reaction complex to study its unimolecular dynamics. A large portion of the wavepacket is trapped in the pre- and post-reaction complexes for a time substantially longer than that predicted by RRKM theory. Many resonance states are seen in the power spectrum of the wavepacket's time autocorrelation function. In the time-independent study, the cumulative reaction probability for Cl - ···CH 3 Br→ClCH 3 ···Br - isomerization is obtained. It is found to be much smaller than the statistical number of states/flux at the central barrier, suggesting that dynamics effects are important. A reduced dimensionality approach, appropriate for a complex reaction, is used to extract the full dimensional Cl - +CH 3 Br→ClCH 3 +Br - bimolecular substitution rate constant from the reduced dimensional quantum dynamics calculation. For the model Hamiltonian used here, this quantum dynamics rate constant is in much better agreement with experiment than that of statistical theory.

The existence of more than one steady state in a many-body quantum system driven out of equilibrium has been a matter of debate, both in the context of simple impurity models and in the case of inelastic tunneling channels. In this paper, we combine a reduced density matrix formalism with the multilayer multiconfiguration time-dependent Hartree method to address this problem. This allows us to obtain a converged numerical solution of the nonequilibrium dynamics. Considering a generic model for quantum transport through a quantum dot with electron-phonon interaction, we prove that a unique steady state exists regardless of the initial electronic preparation of the quantum dot, consistent with the converged numerical results. However, a bistability can be observed for different initial phonon preparations. The effects of the phonon frequency and strength of the electron-phonon couplings on the nonequilibrium dynamics and on the emergence of bistability is discussed.

The multilayer multiconfiguration time-dependent Hartree method is employed to study vibrationally coupled electron transport in models of single molecule junctions. To increase the efficiency of the simulation method, a representation of the Hamiltonian in terms of the scattering states of the underlying electronic Hamiltonian is used. It is found that with an appropriate choice of the scattering states the artificial electron correlation present in the original representation of the model is greatly reduced. This allows efficient simulation of the steady-state currents in a wide physical parameter space, which is demonstrated by several numerical examples.

Hyperfine interaction (HFI) and spin-orbit coupling are two major sources that affect electron spin dynamics. Here we present a systematic study of the HFI and its role in organic spintronic applications. For electron spin dynamics in disordered $\ensuremath{\pi}$-conjugated organics, the HFI can be characterized by an effective magnetic field whose modular square is a weighted sum of contact and dipolar contributions. We determine the effective HFI fields of some common $\ensuremath{\pi}$-conjugated organics studied in the literature via first-principles calculations. Most of them are found to be less than 2 mT. While the H atoms are the major source of the HFI in organics containing only the C and H atoms, many organics contain other nuclear spins, such as Al and N in tris-(8-hydroxyquinoline) aluminum, that contribute to the total HFI. Consequently, the deuteration effect on the HFI in the latter may be much weaker than in the former. The HFI gives rise to multiple resonance peaks in electron spin resonance. In disordered organic solids, these individual resonances are unresolved, leading to a broad peak whose width is proportional to the effective HFI field. As electrons hop among adjacent organic molecules, they experience a randomly varying local HFI field, inducing electron spin relaxation and diffusion. This is analyzed rigorously based on master equations. Electron spin relaxation undergoes a crossover along the ratio between the electron hopping rate $\overline{\ensuremath{\eta}}$ and the Larmor frequency $\ensuremath{\Omega}$ of the HFI field. The spin relaxation rate increases (decreases) with $\overline{\ensuremath{\eta}}$ when $\overline{\ensuremath{\eta}}\ensuremath{\ll}\ensuremath{\Omega}$ ($\overline{\ensuremath{\eta}}\ensuremath{\gg}\ensuremath{\Omega}$). A coherent beating of electron spin at $\ensuremath{\Omega}$ is possible when the external field is small compared to the HFI. In this regime, the magnetic field is found to enhance the spin relaxation.

The multilayer multiconfiguration time-dependent Hartree theory within second quantization representation of the Fock space is applied to study correlated electron transport in models of single-molecule junctions. Extending previous work, we consider models which include both electron-electron and electronic-vibrational interaction. The results show the influence of the interactions on the transient and the stationary electrical current. The underlying physical mechanisms are analyzed in conjunction with the nonequilibrium electronic population of the molecular bridge., Comment: arXiv admin note: substantial text overlap with arXiv:1103.4945

The quasiclassical trajectory (QCT) method was used to study the dynamics of the OH(X 2Π) and OD(X 2Π)+HBr chemical reactions on an empirical potential energy surface (PES). The main emphasis in the calculation was the vibrational energy distributions of H2O (and HDO) and the magnitude and temperature dependence of the rate constant. However, this PES also serves as a generic model for the dynamics of direct H atom abstraction by OH radicals. Since this PES has no formal potential energy barrier, variational transition‐state theory was used to obtain rate constants for comparison with the QCT calculations and experimental results. The parameters of the potential energy surface were adjusted to obtain better agreement with the experimentally measured fraction of H2O vibrational energy, 〈fV(H2O)〉=0.6, without significantly changing the entrance channel. No isotope effect for the partition of energy to H2O vs HOD was found. Analysis of the trajectories indicates that the reactant OH(OD) bond is a spectator, ...

Coupling terms in the reaction path Hamiltonian (RPH) provide a qualitative interpretation of the non-statistical effects observed in classical trajectory simulations and experiments for the Cl− + CH3Br → ClCH3 + Br− SN2 nucleophilic substitution reaction. The small couplings between the Cl− + CH3Br relative translational, which is the reaction coordinate as the reactants collide, and the CH3Br vibrational modes explain why translation to vibration (T → V) energy transfer is unimportant for Cl− ⋯CH3Br complex formation and, instead, the complex is formed by T → R energy transfer. A large coupling term between the ClCBr symmetric stretch and the reaction coordinate leads to a large reaction path curvature at regions along the reaction path separating the central barrier and the pre- and post-reaction complexes. Such sharp values for the curvature can trap trajectories in the vicinity of the central barrier, which is consistent with the central barrier recrossings observed in classical trajectory simulations. Because of singularities in the RPH it is difficult to use it in classical trajectory simulations. Numerical difficulties in evaluating the long-time flux-flux autocorrelation function for the RPH precludes using this approach for calculating the quantum mechanical rate constant for Cl− + CH3Br SN2 nucleophilic substitution. Also, since the RPH does not include overall rotation and rotational/vibrational coupling and assumes a quadratic expansion for displacements away from the reaction path, this Hamiltonian may not give an accurate quantum mechanical rate constant even if a converged flux-flux autocorrelation function could be evaluated.

Direct dynamics simulations of the dynamics of the Cl-- - -CH3Br complex are performed for 25 ps or until either Cl- + CH3Br or ClCH3 + Br- are formed. Two different potential energy surfaces, AM1-SRP1 and AM1-SRP2, are investigated in the simulations by using the AM1 semiempirical model with two different sets of specific reaction parameters (SRPs). The AM1-SRP surfaces give non-RRKM unimolecular dynamics for Cl-- - -CH3Br as found in a previous simulation based on an analytic potential energy surface, PES1(Br), derived by fitting HF/SV4PP/6-31G* ab initio calculations and experimental data. However, detailed aspects of the Cl-- - -CH3Br intramolecular and unimolecular dynamics are different for the two AM1-SRP surfaces and in some cases strikingly different from those found for the PES1(Br) surface. Global potential energy surface properties, not only those of stationary points and along the reaction path, are expected to influence the Cl-- - -CH3Br nonstatistical dynamics. Of the three surfaces, only P...

The dynamics of a two-level system coupled to a spin bath is investigated via the numerically exact multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory. Consistent with the previous work on linear response approximation [N. Makri, J. Phys. Chem. B 103, 2823 (1999)], it is demonstrated numerically that this spin-spin-bath model can be mapped onto the well-known spin-boson model if the system-bath coupling strength obeys an appropriate scaling behavior. This linear response mapping, however, may require many bath spin degrees of freedom to represent the practical continuum limit. To clarify the discrepancies resulted from different approximate treatments of this model, the population dynamics of the central two-level system has been investigated near the transition boundary between the coherent and incoherent motions via the ML-MCTDH method. It is found that increasing temperature favors quantum coherence in the nonadiabatic limit of this model, which corroborates the prediction in the previous work [J. Shao and P. Hanggi, Phys. Rev. Lett. 81, 5710 (1998)] based on the non-interacting blip approximation (NIBA). However, the coherent-incoherent boundary obtained by the exact ML-MCTDH simulation is slightly different from the approximate NIBA results. Quantum dynamics in other physical regimes are also discussed.

A previous trajectory study of the dissociation of Cl−...CH3Cl complexes formed by Cl−+CH3Cl association is further analyzed to determine (1) the relationship between classical and quantum Rice–Ramsperger–Kassel–Marcus (RRKM) rate constants for Cl−...CH3Cl→Cl−+CH3Cl dissociation; (2) the importance of anharmonicity in calculating the RRKM dissociation rate constant; (3) the role of angular momentum in interpreting the trajectory distribution N(t)/N(0) of Cl−...CH3Cl complexes versus time; and (4) the pressure‐dependent collision‐averaged rate constant k(ω,E) for Cl−...CH3Cl dissociation. It is found that only the low‐frequency intermolecular modes of Cl−...CH3Cl are initially excited by Cl−+CH3Cl association. Classical and quantum RRKM rate constants for dissociation of this intermolecular complex are in excellent agreement. Anharmonicity lowers the rate constant by a factor of 4–8 from its harmonic value. The dissociation rate for the long‐time tail of the trajectory N(t)/N(0) distribution is much smaller than predicted by a RRKM model, which accurately treats angular momentum. It is suggested that the long‐lived trajectories may arise from motion on vague tori. The trajectory collision‐averaged rate constant k(ω,E) is in agreement with an experimental study at 300 K.

Photoinduced electron transfer processes in perylene-titanium dioxide dye-semiconductor systems are studied. In particular, the influence of saturated and unsaturated aliphatic spacer groups inserted between the chromophore and the semiconductor substrate is investigated. The study is based on a recently developed method that combines first-principles electronic structure calculations to characterize the dye-semiconductor systems and accurate multilayer multiconfiguration time-dependent Hartree simulations to reveal the underlying nonadiabatic dynamics. The results show that, in agreement with previous experimental studies, the spacer groups may affect the electron transfer dynamics significantly. Furthermore, the influence of electronic-vibrational coupling on the electron transfer dynamics and absorption spectra is discussed.

Pancreatic adenocarcinoma (PaCa) being the deadliest cancer is partly due to early metastatic spread. Thus, we searched for PaCa-initiating cell (PaCIC) markers with emphasis on markers contributing to metastatic progression. PaCIC were enriched from long-term and freshly established lines by repeated selection for spheroid or holoclone growth in advance of evaluating PaCIC markers. Sphere and holoclone formation steeply increased by recloning and remained stable thereafter. Cells not forming spheres or holoclones died on recloning. PaCIC enrichment in spheres and holoclones was accompanied by increased motility, anchorage independence and upregulated CXCR4 expression. After subcutaneous injection in NOD/SCID mice tumorigenicity and, impressively, recovery of metastasizing tumor cells in peripheral blood, spleen, bone marrow, lung and pancreas was strongly increased in spheres and holoclones. PaCIC enrichment in spheres and holoclones was accompanied, besides CXCR4, by upregulated CD44v6, alpha6beta4, weakly CD133 and tetraspanin Tspan8 expression. Notably, CD44v6, alpha6beta4, CXCR4 and Tspan8 expressing PaCa cells had a growth advantage in vivo and became dominating in migrating and in distant organs settled tumor cells. This is the first report showing that CD44v6, alpha6beta4, Tspan8 and CXCR4 are biomarkers in PaCIC allowing for long-term survival, expansion and migration in immunocompromised mice. The stability of the percentage of PaCIC in long-term and freshly established lines after a roughly 8-fold enrichment by cloning indicates PaCIC, though required for long-term survival, concomitantly depending on support by non-CIC.

Photoinduced electron transfer (ET) between a magnesium-porphyrin and benzoquinone in a model molecular complex is investigated employing ab initio multi-configuration electronic-structure calculations combined with quantum dynamical methods. The microscopic parameters controlling the electron-transfer process are obtained using a first-principles diabatization procedure. A model Hamiltonian which includes both linear and quadratic vibronic couplings of all nuclear degrees of freedom of the system is constructed. Quantum dynamical simulations of the ET process are performed employing the multi-layer multi-configuration time-dependent Hartree method. A detailed analysis of the ET dynamics for models of increasing complexity reveals that the dynamics is strongly influenced by resonances associated with vibronically active nuclear modes, leading to significant deviations from the results of classical ET theory. The comparison with results obtained with the simplified spin-boson model reveals the effects rela...

We investigate the transient nonequilibrium dynamics of a molecular junction biased by a finite voltage and strongly coupled to internal vibrational degrees of freedom. Using two different, numerical exact techniques, diagrammatic Monte Carlo and the multilayer multiconfiguration time-dependent Hartree method, we show that the steady state current through the junction may depend sensitively on the initial preparation of the system, thus revealing signatures of bistability. The influence of the bias voltage and the transient dynamics on the phenomenon of bistability is analyzed. Furthermore, a possible relation to the phenomenon of stochastic switching in nanoelectromecanical devices is discussed., Comment: 5 pages, 3 figures

Hartree-Fock calculations, utilizing the SV4PP split valence contracted Gaussian basis set for Cl and Br and the 6-31G * basis set for CH 3 , are used to determine potential energy surface properties for the Cl - +CH 3 Br→ClCH 3 +Br - S N 2 nucleophilic substitution reaction. This ab initio information is used in concert with experimental data to develop a multidimensional analytic potential energy function for the Cl - +CH 3 Br reaction system, by modifying the analytic potential energy function developed previously for Cl a - +CH 3 Cl b →Cl a CH 3 +Cl b

The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method is applied to simulate the quantum dynamics and thermal rate constant of the Azzouz-Borgis model of proton transfer in a polar solvent. To this end, the original atomistic potential is mapped to a system-bath model. Employing the flux correlation function formalism and importance sampling techniques, accurate quantum mechanical rate constants are obtained, which provide a benchmark for evaluating approximate approaches to study the quantum dynamics of condensed-phase chemical reactions. Furthermore, the validity of the mapping procedure is discussed based on the comparison of the classical dynamics of the original atomistic Azzouz-Borgis model and the mapped system-bath model.

An analog of the Meir-Wingreen formula for the steady-state heat current through a model molecular junction is derived. The expression relates the heat current to correlation functions that involve operators only acting on the degrees of freedom of the molecular junction. As a result, the macroscopic heat reservoirs are not treated explicitly. This allows one to exploit methods based on a reduced description of the dynamics of a relatively small part of the overall system to evaluate the heat current through a molecular junction. The derived expression is applied to calculate the steady-state heat current in a weak coupling limit, where Redfield theory is used to describe the reduced dynamics of the molecular junction. The results are compared with those from the previously developed approximate and numerically exact methods.

Intervalence electron transfer reactions were studied computationally by means of density functional theory and constrained density functional theory (CDFT). Two ferrocene moieties, connected via various bridge structures, were used as model mixed-valence compounds in the computational investigation. Features of the frontier orbitals were analyzed to offer a qualitative account of the intervalence characteristics of the model complexes. The effective electronic coupling between the donor and acceptor sites was calculated using the CDFT method, which provided a quantitative measure of the intervalence electronic communication. The relationship between the bridge linkage and the effectiveness of intervalence transfer was discussed on the basis of the theoretical results and compared to experimental data available in the literature.

The reaction of Fischer carbene complexes with conjugated enediynes that feature a pendant alkene group has been examined. The reaction proceeds through carbene-alkyne coupling to generate an enyne-ketene intermediate. This intermediate then undergoes Moore cyclization to generate a chromium complexed arene diradical, which then undergoes cyclization with the pendant alkene group. The radical cyclization prefers the 6-endo mode unless radical-stabilizing groups are present to favor the 5-exo mode. The intermediate diradical species were evaluated computationally in both the singlet and triplet configurations. Arene triplet diradicals feature minimal spin density at oxygen and delocalization to chromium. The 6-endo cyclization product was kinetically and thermodynamically favored.

Electronic structure theory, mainly the density functional theory (DFT), is applied to calculate the pK(a) values for a variety of organic acids in several nonaqueous solvents: namely DMSO, MeCN, and THF. Following the supermolecule approach the solute molecule, together with a few solvent molecules in close proximity, is treated explicitly by the electronic structure theory, and the remaining solvent environment is approximated by using a standard dielectric continuum model. It is found that in most cases including only one explicit solvent molecule gives satisfactory results for pK(a) estimations. Next, the equilibrium position free energy difference is calculated between a reference acid-base pair whose pK(a) is known experimentally and the acid-base pair whose pK(a) is to be determined theoretically. This bypasses the step of treating the solvated proton that most of the current theories have difficulty with and, to a large extent, induces favorable error cancelations in the final theoretical results. Accurate theoretical predictions of pK(a) values are thus obtained at a moderate level of theory (MP2 single point on B3LYP/6-31+G(d) optimized geometry) for a series of organic acids spanning a wide range of acidities in DMSO, MeCN, and THF. Furthermore, the correlation between the pK(a) values of these acids in different solutions is investigated theoretically, and excellent agreement is found with the experimental results.