Search

We demonstrate how recently developed Boxed Molecular Dynamics (BXD) and kinetics [D. V. Shalashilin et al., J. Chem. Phys. 137, 165102 (2012)] can provide a kinetic description of protein pulling experiments, allowing for a connection to be made between experiment and the atomistic protein structure. BXD theory applied to atomic force microscopy unfolding is similar in spirit to the kinetic two-state model [A. Noy and R. W. Friddle, Methods 60, 142 (2013)] but with some differences. First, BXD uses a large number of boxes, and therefore, it is not a two-state model. Second, BXD rate coefficients are obtained from atomistic molecular dynamics simulations. BXD can describe the dependence of the pulling force on pulling speed. Similar to Shalashilin et al. [J. Chem. Phys. 137, 165102 (2012)], we show that BXD is able to model the experiment at a very long time scale up to seconds, which is way out of reach for standard molecular dynamics.

Photo-dissociation dynamics is simulated for vibrationally pre-excited pyrrole molecules using an ab initio multiple cloning approach. Total kinetic energy release (TKER) spectra and dissociation times are calculated. It is found that pre-excitation of N-H bond vibrations facilitates fast direct dissociation, which results in a significant increase in the high-energy wing of TKER spectra. The results are in very good agreement with the recent vibrationally mediated photo-dissociation experiment, where the TKER spectrum was measured for pyrrole molecules excited by a combination of IR and UV laser pulses. Calculations for other vibrational modes show that this effect is specific for N-H bond vibrations: Pre-excitation of other modes does not result in any significant changes in TKER spectra.

We propose a new approach to simulate four-wave-mixing signals of molecular systems at finite temperatures by combining the multiconfigurational Ehrenfest method with the thermo-field dynamics theory. In our approach, the four-time correlation functions at finite temperatures are mapped onto those at zero temperature in an enlarged Hilbert space with twice the vibrational degrees of freedom. As an illustration, we have simulated three multidimensional spectroscopic signals, time- and frequency-resolved fluorescence spectra, transient-absorption pump-probe spectra, and electronic two-dimensional (2D) spectra at finite temperatures, for a conical intersection-mediated singlet fission model of a rubrene crystal. It is shown that a detailed dynamical picture of the singlet fission process can be extracted from the three spectroscopic signals. An increasing temperature leads to lower intensities of the signals and broadened vibrational peaks, which can be attributed to faster singlet-triplet population transfer and stronger bath-induced electronic dephasing at higher temperatures. Ministry of Education (MOE) Submitted/Accepted version L.P.C. acknowledges support from the Max-Planck Gesellschaft via the MPI-PKS visitors program. D.V.S. acknowledges EPSRC (Grant No. EP/P021123/1). Y.Z. thanks the Singapore Ministry of Education Academic Research Fund Tier 1 (Grant Nos. 2018-T1-002-175 and 2020-T1-002-075) for support. M.F.G. acknowledges the support of Hangzhou Dianzi University through startup funding.

The efficiency of the intramolecular energy transfer in light harvesting dendrimers is determined by their well-defined architecture with high degree of order. After photoexcitation, through-space and through-bond energy transfer mechanisms can take place, involving vectorial exciton migration among different chromophores within dendrimer highly branched structures. Their inherent intramolecular energy gradient depends on how the multiple chromophoric units have been assembled, subject to their inter-connects, spatial distances, and orientations. Herein, we compare the photoinduced nonadiabatic molecular dynamics simulations performed on a set of different combinations of a chain of linked dendrimer building blocks composed of two-, three-, and four-ring linear polyphenylene chromophoric units. The calculations are performed with the recently developed ab initio multiple cloning-time dependent diabatic basis implementation of the Multiconfigurational Ehrenfest (MCE) approach. Despite differences in short time relaxation pathways and different initial exciton localization, at longer time scales, electronic relaxation rates and exciton final redistributions are very similar for all combinations. Unlike the systems composed of two building blocks, considered previously, for the larger 3 block systems here we observe that bifurcation of the wave function accounted by cloning is important. In all the systems considered in this work, at the time scale of few hundreds of femtoseconds, cloning enhances the electronic energy relaxation by ∼13% compared to that of the MCE method without cloning. Thus, accurate description of quantum effects is essential for understanding of the energy exchange in dendrimers both at short and long time scales. Fil: Freixas Lemus, Victor Manuel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Ondarse Alvarez, Dianelys. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina Fil: Tretiak, Sergei. Los Alamos National Laboratory; Estados Unidos Fil: Makhov, D.V.. University Of Leeds; Reino Unido Fil: D. V. Shalashilin. University Of Leeds; Reino Unido Fil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

We present a new implementation of the Ab Initio Multiple Cloning (AIMC) method, which is applied for non-adiabatic excited-state molecular dynamics simulations of photoinduced processes in conjugated molecules. Within our framework, the multidimensional wave-function is decomposed into a superposition of a number of Gaussian coherent states guided by Ehrenfest trajectories that are suited to clone and swap their electronic amplitudes throughout the simulation. New generalized cloning criteria are defined and tested. Because of sharp changes of the electronic states, which are common for conjugated polymers, the electronic parts of the Gaussian coherent states are represented in the Time Dependent Diabatic Basis (TDDB). The input to these simulations in terms of the excited-state energies, gradients and non-adiabatic couplings, is calculated on-the-fly using the Collective Electron Oscillator (CEO) approach. As a test case, we consider the photoinduced unidirectional electronic and vibrational energy transfer between two- and three-ring linear poly(phenylene ethynylene) units linked by meta-substitution. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer between dendritic branches are discussed. Fil: Freixas Lemus, Victor Manuel. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Fernández Alberti, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes; Argentina Fil: Makhov, Dmitry V.. University of Leeds; Reino Unido. University of Bristol; Reino Unido Fil: Tretiak, Sergei. Los Alamos National High Magnetic Field Laboratory; Estados Unidos Fil: Shalashilin, Dmitrii. University of Leeds; Reino Unido

International audience

The results of Boxed Dynamics (BXD) fully atomistic simulations of protein unfolding by Atomic Force Microscope (AFM), in both force clamp (FC) and velocity clamp (VC) modes are reported. In AFM experiments the unfolding occurs on time scale which is too long for standard atomistic Molecular Dynamics (MD) simulations, which are usually performed with the addition of forces which exceed those of experiment by many orders of magnitude. BXD can reach the time scale of slow unfolding and sample the very high free energy unfolding pathway, reproducing the experimental dependence of pulling force against extension and extension against time. Calculations show the presence of the pulling force ‘humps’ previously observed in the Velocity Clamp (VC) AFM experiments and allow the identification of intermediate protein conformations responsible for them. Fully atomistic BXD simulations can estimate the rate of unfolding in the Force Clamp (FC) experiments up to the time scale of seconds.

Dynamics simulations were performed to study soft landing of SiNCS + and (CH3)2SiNCS+ ions on a self-assembled monolayer of perfluorinated alkanethiols on gold (F-SAM). Using classical trajectories, the short-time collision dynamics (picosecond scale) were investigated to analyze trapping probabilities for these silyl ions. Thermal desorption of trapped ions was simulated by using "boxed molecular dynamics" (BXD). The simulations predict substantial ion trapping in the collisions of these ions with the F-SAM, especially when the projectile's incident direction is normal to the surface. Desorption of the SiNCS+ ion occurs significantly faster than desorption of the methylated ion, which may explain why soft landing was experimentally observed for the latter ion only [Miller, S. A.; Luo, H.; Pachuta, S. J.; Cooks, R. G. Science 1997, 275, 1447-1450; Luo, H.; Miller, S. A.; Cooks, R. G.; Pachuta, S. J. Int. J. Mass. Spectrom. Ion Processes 1998, 174, 193-217]. The free energy profiles for desorption of these ions show minima at 15 Å above the gold slab, indicating that the silyl ion has a preference to reside on top of the monolayer. Deep penetration of the ion into the monolayer is prevented by a large free energy barrier. However, according to DFT calculations, if this process occurred, the SiNCS+ ion could strongly bind to the Au(111) surface that supports the perfluorinated alkanethiol chains.

We present an alternate version of the coupled-coherent-state method, specifically adapted for solving the time-dependent Schr\"odinger equation for multielectron dynamics in atoms and molecules. This theory takes explicit account of the exchange symmetry of fermion particles, and it uses fermion molecular dynamics to propagate trajectories. As a demonstration, calculations in the He atom are performed using the full Hamiltonian and accurate experimental parameters. Single- and double-ionization yields by 160-fs and 780-nm laser pulses are calculated as a function of field intensity in the range 10${}^{14}$--10${}^{16}$ W/cm${}^{2}$, and good agreement with experiments by Walker et al. is obtained. Since this method is trajectory based, mechanistic analysis of the dynamics is straightforward. We also calculate semiclassical momentum distributions for double ionization following 25-fs and 795-nm pulses at 1.5\ifmmode\times\else\texttimes\fi{}10${}^{15}$ W/cm${}^{2}$, in order to compare them with the detailed experiments by Rudenko et al. For this more challenging task, full convergence is not achieved. However, major effects such as the fingerlike structures in the momentum distribution are reproduced.

A number of methods proposed in the past few years have been aimed at accelerating the sampling of rare events in molecular dynamics simulations. We recently introduced a method called Boxed Molecular Dynamics (BXD) for accelerating the calculation of thermodynamics and kinetics (J. Phys. Chem. B 2009, 113, 16603 -16611). BXD relies upon confining the system in a series of adjacent "boxes" by inverting the projection of the system velocities along the reaction coordinate. The potential of mean force along the reaction coordinate is obtained from the mean first passage times (MFPTs) for exchange between neighboring boxes, simultaneously providing both kinetics and thermodynamics. In this paper, we investigate BXD in the context of its natural relation to a kinetic master equation and show that the BXD first passage times (FPTs) include different time scales-a fast short time decay due to correlated dynamical motion and slower long time decay arising from phase space diffusion. Correcting the FPTs to remove the fast correlated motion yields accurate thermodynamics and master equation kinetics. We also discuss interrelations between BXD and a recently described Markovian milestoning technique and use a simple application to show that, despite each method producing distinct nonstatistical effects on time scales on the order of dynamical decorrelation, both yield similar long-time kinetics. © 2011 American Chemical Society.