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arXiv2018

Absorption and luminescence spectroscopy of mass-selected Flavin Adenine Dinucleotide mono-anions

We report the absorption profile of isolated Flavin Adenine Dinucleotide (FAD) mono-anions recorded using Photo-Induced Dissociation action spectroscopy. In this charge state, one of the phosphoric acid groups is deprotonated and the chromophore itself is in its neutral oxidized state. These measurements cover the first four optical transitions of FAD with excitation energies from 2.3 to 6.0~eV (210--550~nm). The $S_0\rightarrow S_2$ transition is strongly blue-shifted relative to aqueous solution, supporting the view that this transition has significant charge-transfer character. The remaining bands are close to their solution-phase positions. This confirms that the large discrepancy between quantum chemical calculations of vertical transition energies and solution-phase band maxima can not be explained by solvent effects. We also report the luminescence spectrum of FAD mono-anions \textit{in vacuo}. The gas-phase Stokes shift for $S_1$ is 3000~cm$^{-1}$, which is considerably larger than any previously reported for other molecular ions and consistent with a significant displacement of the ground and excited state potential energy surfaces. Consideration of vibronic structure is thus essential for simulating the absorption and luminescence spectra of flavins.

physics.chem-ph↗

arXiv2018

Davydov-Type Excitonic Effects on the Absorption Spectra of Parallel-Stacked and Herringbone Aggregates of Pentacene: Time-Dependent Density-Functional Theory and Time-Dependent Density-Functional Tight Binding

Exciton formation leads to J-bands in solid pentacene. Describing these exciton bands represents a challenge for both time-dependent (TD) density-functional theory (DFT) and for its semiempirical analogue, namely for TD density-functional tight binding (DFTB) for three reasons (i) solid pentacene and pentacene aggregates are bound only by van der Waals forces which are notoriously difficult to describe with DFT and DFTB, (ii) the proper description of the long-range coupling between molecules, needed to describe Davydov splitting, is not easy to include in TD-DFT with traditional functionals and in TD-DFTB, and (iii) mixing may occur between local and charge transfer excitons, which may, in turn, require special functionals. We assess how far TD-DFT and TD-DFTB have progressed towards a correct description of this type of exciton by including both a dispersion correction for the ground state and a range-separated hybrid functional for the excited state. Analytic results for parallel-stacked ethylene are derived which go beyond Kasha's exciton model in that we are able to make a clear distinction between charge transfer and energy transfer excitons. This is further confirmed when it is shown that range-separated hybrids have a markedly greater effect on charge-transfer excitons than on energy-transfer excitons in the case of parallel-stacked pentacenes. TD-DFT calculations with the CAM-B3LYP functional and TD-lc-DFT calculations lead to negligeable excitonic corrections for the herringbone crystal structure, possibly because of an overcorrection of charge-transfer effects. In this case, TD-DFT calculations with the B3LYP functional or TD-DFTB calculations parameterized to B3LYP give the best results for excitonic corrections for the herringbone crystal structure as judged from comparison with experimental spectra and with Bethe-Salpeter equation calculations from the literature.

physics.chem-ph↗

arXiv2018

Development of effective stochastic potential method using random matrix theory for efficient conformational sampling of semiconductor nanoparticles at non-zero temperatures

In this work, the development and implementation of the effective stochastic potential (ESP) method is presented to perform efficient conformational sampling of molecules. The overarching goal of this work is to alleviate the computational bottleneck associated with performing a large number of electronic structure calculations required for conformational sampling. We introduce the concept of a deformation potential and demonstrate its existence by the proof-by-construction approach. A statistical description of the fluctuations in the deformation potential due to non-zero temperature was obtained using infinite-order moment expansion of the distribution. The formal mathematical definition of the ESP was derived using functional minimization approach to match the infinite-order moment expansion for the deformation potential. Practical implementation of the ESP was obtained using the random-matrix theory method. The developed method was applied to two proof-of-concept calculations of the distribution of HOMO-LUMO gap in the water molecule and solvated CdSe clusters at 300K. The need for large sample size to obtain statistically meaningful results was demonstrated by performing $10^5 $ ESP calculations. The results from these prototype calculations demonstrated the efficacy of the ESP method for performing efficient conformational sampling. We envision that the fundamental nature of this work will not only extend our knowledge of chemical systems at non-zero temperatures but will also generate new insights for innovative technological applications.

physics.chem-ph↗

arXiv2018

Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation

Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support experimental measures at both constant redox potential and pH is very important. Such computational techniques have the potential to validate experimental observations performed under these conditions and to provide additional information unachievable experimentally such as an atomic level description of macroscopic measures. We present the implementation of discrete redox and protonation states methods for constant redox potential Molecular Dynamics (CEMD), for coupled constant pH and constant redox potential MD (C(pH,E)MD), and for Replica Exchange MD along the redox potential dimension (E-REMD) on the AMBER software package. Validation results are presented for a small system that contains a single heme group: N-acetylmicroperoxidase-8 (NAcMP8) axially connected to a histidine peptide. The methods implemented allow one to make standard redox potential (Eo) predictions with the same easiness and accuracy as pKa predictions using the constant pH molecular dynamics and pH-REMD methods currently available on AMBER. In our simulations, we can correctly describe, in agreement also with theoretical predictions, the following behaviors: when a redox-active group is reduced, the pKa of a near pH-active group increases because it becomes easier for a proton to be attached; equivalently, when a pH-active group is protonated, the Eo of an adjacent redox-active group rises. Furthermore, our results also show that E-REMD is able to achieve faster statistical convergence than CEMD or C(pH,E)MD. Moreover, computational benchmarks using our methodologies show high-performance of GPU accelerated calculations in comparison to conventional CPU calculations.

physics.chem-ph↗

arXiv2018

Coupling of state-resolved rovibrational coarse-grain model for nitrogen to stochastic particle method for simulating internal energy excitation and dissociation

We propose to couple a state-resolved rovibrational coarse-grain model to a stochastic particle method for simulating internal energy excitation and dissociation of a molecular gas. An existing coarse-grain model based on the NASA Ames ab initio database for the N2-N system is modified using variably-spaced energy bins. Thermodynamic properties of the new coarse-grained model closely match those of the full set of rovibrational levels over a wide temperature range, using a number of bins much smaller than the complete mechanism. The chemical-kinetic behavior of the original equally -- and new variably -- spaced bin formulations is compared by simulating excitation and dissociation of N2 in an adiabatic, isochoric reactor. The variably-spaced formulation is better suited for reproducing the dynamics of the full database at conditions of interest in Earth reentry. Furthermore, we discuss details of our Direct Simulation Monte Carlo (DSMC) implementation for the coarse-grain model and describe changes to the collision algorithm necessary to accommodate our state-resolved reaction mechanism. The DSMC code is then verified against equivalent master equation (ME) calculations. In these simulations, state-resolved cross sections are used in analytical form. They verify micro-reversibility for the bins and allow for faster execution of the code. In our verification, we obtain very close agreement for the N and N2 concentrations, as well as the translational and rovibrational mode temperatures obtained independently using both methods. In addition to macroscopic moments, we compare internal energy populations predicted at selected time steps via DSMC and ME. We observe good agreement between both methods within the statistical scatter limits imposed by DSMC. In future work, the rovibrational coarse-grain model coupled to the particle method will allow us to study 3D reentry flow configurations.

physics.chem-ph↗

arXiv2018

Investigating Photoinduced Proton Coupled Electron Transfer Reaction using Quasi Diabatic Dynamics Propagation

We investigate photoinduced proton-coupled electron transfer (PI-PCET) reaction through a recently devel- oped quasi-diabatic (QD) quantum dynamics propagation scheme. This scheme enables interfacing accurate diabatic-based quantum dynamics approaches with adiabatic electronic structure calculations for on-the-fly simulations. Here, we use the QD scheme to directly propagate PI-PCET quantum dynamics with the di- abatic Partial Linearized Density Matrix (PLDM) path-integral approach with the instantaneous adiabatic electron-proton vibronic states. Our numerical results demonstrate the importance of treating proton quan- tum mechanically in order to obtain accurate PI-PCET dynamics, as well as the role of solvent fluctuation and vibrational relaxation on proton tunneling in various reaction regimes that exhibit different kinetic iso- tope effects. This work opens the possibility to study the challenging PI-PCET reactions through accurate diabatic quantum dynamics approaches combined with efficient adiabatic electronic structure calculations.

physics.chem-ph↗

arXiv2018

xDH double hybrid functionals can be qualitatively incorrect for non-equilibrium geometries: Dipole moment inversion and barriers to radical-radical association using XYG3 and XYGJ-OS

Double hybrid (DH) density functionals are amongst the most accurate density functional approximations developed so far, largely due to incorporation of correlation effects from unoccupied orbitals via second order perturbation theory (PT2). The xDH family of DH functionals calculate energy directly from orbitals optimized by a lower level approach like B3LYP, without self-consistent optimization. XYG3 and XYGJ-OS are two widely used xDH functionals that are known to be quite accurate at equilibrium geometries. Here, we show that the XYG3 and XYGJ-OS functionals can be ill behaved for stretched bonds well beyond the Coulson-Fischer point, predicting unphysical dipole moments and humps in potential energy curves for some simple systems like the HF molecule. Numerical experiments and analysis show these failures are not due to PT2. Instead, a large mismatch at stretched bond-lengths between the reference B3LYP orbitals and the optimized orbitals associated with the non-PT2 part of XYG3 lead to an unphysically large non-Hellman-Feynman contribution to first order properties like forces and electron densities.

physics.chem-ph↗

arXiv2018

An efficient stochastic algorithm for the perturbative density matrix renormalization group in large active spaces

We present an efficient stochastic algorithm for the recently introduced perturbative density matrix renormalization group (p-DMRG) method for large active spaces. The stochastic implementation bypasses the computational bottleneck involved in solving the first order equation in the earlier deterministic algorithm. We demonstrate the efficiency and accuracy of the algorithm on the C$_2$ and Cr$_2$ molecular benchmark systems.

physics.chem-ph↗

arXiv2018

High-resolution collision energy control through ion position modulation in atom-ion hybrid systems

We demonstrate an ion shuttling technique for high-resolution control of atom-ion collision energy by translating an ion held within a radio-frequency trap through a magneto-optical atom trap. The technique is demonstrated both experimentally and through numerical simulations, with the experimental results indicating control of ion kinetic energies from $0.05-1$ K with a fractional resolution of $\sim10$ and the simulations demonstrating that kinetic energy control up to $120$ K with a maximum predicted resolution of $\sim100$ is possible, offering order-of-magnitude improvements over most alternative techniques. Lastly, we perform a proof-of-principle chemistry experiment using this technique and outline how the method may be refined in the future and applied to the study of molecular ion chemistry.

physics.atom-ph↗

arXiv2018

Vibronic exciton theory of singlet fission. III. How vibronic coupling and thermodynamics promote rapid triplet generation in pentacene crystals

We extend the vibronic exciton theory introduced in our previous work to study singlet fission dynamics, in particular addressing recent indications of the importance of vibronic coupling in this process. A microscopic and non-perturbative treatment of electronic and selected vibrational degrees of freedom in combination with Redfield theory allows us to dynamically consider clusters of molecules under conditions close to those in molecular crystals that exhibit fission. Using bulk pentacene as a concrete example, our results identify a number of factors that render fission rapid and effective. Strong coupling to high-frequency Holstein modes generates resonances between the photo-prepared singlet and product triplet states. We furthermore find the large number of triplet combinations associated with bulk periodic systems to be critical to the fission process under such vibronically resonant conditions. In addition, we present results including, in an approximate manner, the effects of Peierls coupling, indicating that this factor can both enhance and suppress fission depending on its interplay with vibronic resonance and thermodynamics.

cond-mat.mtrl-sci↗

arXiv2018

A Spin-1 Representation for Dual-Funnel Energy Landscapes

The interconversion between left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model - left, right, and unstructured - can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 $k_B T$ to 0.3 $k_B T$ along the left-to-right interconversion pathway.

cond-mat.soft↗

arXiv2019

Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations

Smoluchowski-type models for diffusion-influenced reactions (A+B -> C) can be formulated within two frameworks: the probabilistic-based approach for a pair A, B of reacting particles and the concentration-based approach for systems in contact with a bath that generates a concentration gradient of B particles that interact with A. Although these two approaches are mathematically similar, it is not straightforward to establish a precise mathematical relationship between them. Determining this relationship is essential to derive particle-based numerical methods that are quantitatively consistent with bulk concentration dynamics. In this work, we determine the relationship between the two approaches by introducing the grand canonical Smoluchowski master equation (GC-SME), which consists of a continuous-time Markov chain that models an arbitrary number of B particles, each one of them following Smoluchowski's probabilistic dynamics. We show that the GC-SME recovers the concentration-based approach by taking either the hydrodynamic or the large copy number limit. In addition, we show that the GC-SME provides a clear statistical mechanical interpretation of the concentration-based approach and yields an emergent chemical potential for nonequilibrium spatially inhomogeneous reaction processes. We further exploit the GC-SME robust framework to accurately derive multiscale/hybrid numerical methods that couple particle-based reaction-diffusion simulations with bulk concentration descriptions, as described in detail through two computational implementations.

physics.chem-ph↗

arXiv2018

Mean-field Matsubara dynamics: Analysis of path-integral curvature effects in rovibrational spectra

It was shown recently that smooth and continuous "Matsubara" phase-space loops follow a quantum-Boltzmann-conserving classical dynamics when decoupled from non-smooth distributions, which was suggested as the reason that many dynamical observables appear to involve a mixture of classical dynamics and quantum Boltzmann statistics. Here we derive a mean-field version of this "Matsubara dynamics" which sufficiently mitigates its serious phase problem to permit numerical tests on a two-dimensional "champagne-bottle" model of a rotating OH bond. The Matsubara-dynamics rovibrational spectra are found to converge toward close agreement with the exact quantum results at all temperatures tested (200-800 K), the only significant discrepancies being a temperature-independent 22 cm$^{-1}$ blue-shift in the position of the vibrational peak and a slight broadening in its line shape. These results are compared with centroid molecular dynamics (CMD) to assess the importance of non-centroid fluctuations. Above 250 K, only the lowest-frequency non-centroid modes are needed to correct small CMD red-shifts in the vibrational peak; below 250 K, more non-centroid modes are needed to correct large CMD red-shifts and broadening. The transition between these "shallow curvature" and "deep curvature" regimes happens when imaginary-time Feynman paths become able to lower their actions by cutting through the curved potential surface, giving rise to artificial instantons in CMD.

physics.chem-ph↗

arXiv2018

Fully anharmonic infrared cascade spectra of polycyclic aromatic hydrocarbons

The infrared (IR) emission of polycyclic aromatic hydrocarbons (PAHs) permeates our universe; astronomers have detected the IR signatures of PAHs around many interstellar objects. The IR emission of interstellar PAHs differs from their emission as seen under conditions on Earth, as they emit through a collisionless cascade down through their excited vibrational states from high internal energies. The difficulty in reproducing interstellar conditions in the laboratory results in a reliance on theoretical techniques. However, the size and complexity of PAHs requires careful consideration when producing the theoretical spectra. In this work we outline the theoretical methods necessary to lead to a fully theoretical IR cascade spectra of PAHs including: an anharmonic second order vibrational perturbation theory (VPT2) treatment; the inclusion of Fermi resonances through polyads; and the calculation of anharmonic temperature band shifts and broadenings (including resonances) through a Wang--Landau approach. We also suggest a simplified scheme to calculate vibrational emission spectra that retains the essential characteristics of the full IR cascade treatment and can directly transform low temperature absorption spectra in IR cascade spectra. Additionally we show that past astronomical models were in error in assuming a 15 cm$^{-1}$ correction was needed to account for anharmonic emission effects.

astro-ph.GA↗

arXiv2018

General theory of photoexcitation induced photoelectron circular dichroism

The photoionization of chiral molecules prepared in a coherent superposition of excited states can give access to the underlying chiral coherent dynamics in a procedure known as photoexcitation induced photoelectron circular dichroism (PXECD). This exclusive dependence on coherence can also be seen in a different part of the angular spectrum, where it is not contingent on the chirality of the molecule, thus allowing extension of PXECD's sensitivity to tracking coherence to non-chiral molecules. Here we present a general theory of PXECD based on angular momentum algebra and derive explicit expressions for all pertinent asymmetry parameters which arise for arbitrary polarisation of pump and probe pulses. The theory is developed in a way that clearly and simply separates chiral and non-chiral contributions to the photoelectron angular distribution, and also demonstrates how PXECD and PECD-type contributions, which may be distinguished by whether pump or ionizing probe enables chiral response, are mixed when arbitrary polarization is used.

physics.atm-clus↗

arXiv2018

Detailed analysis of transitions in the CO oxidation on Palladium(111) under noisy conditions

It has been shown that CO oxidation on Pd(111) under ultra-high vacuum conditions can suffer rare transitions between two stable states triggered by weak intrinsic perturbations. Here we study the effects of adding controlled noise by varying the concentrations of O2 and CO that feed the vacuum chamber, while the total flux stays constant. In addition to the regime of rare transitions between states of different CO2 reaction rate induced by intrinsic fluctuations, we found three distinct effects of external noise depending on its strength: small noise suppresses transitions and stabilizes the upper rate state; medium noise induces bursting; and large noise gives rise to reversible transitions in both directions. To explain some of the features present in the dynamics, we propose an extended stochastic model that includes a global coupling through the gas phase to account for the removal of CO gas caused by the adsorption of the Pd surface. The numerical simulations based in the model show a qualitative agreement with the noise-induced transitions found in experiments, but suggest that more complex spatial phenomena are present in the observed fluctuations.

nlin.PS↗

arXiv2018

Excitation energies from diffusion Monte Carlo using selected Configuration Interaction nodes

Quantum Monte Carlo (QMC) is a stochastic method which has been particularly successful for ground-state electronic structure calculations but mostly unexplored for the computation of excited-state energies. Here, we show that, within a Jastrow-free QMC protocol relying on a deterministic and systematic construction of nodal surfaces using selected configuration interaction (sCI) expansions, one is able to obtain accurate excitation energies at the fixed-node diffusion Monte Carlo (FN-DMC) level. This evidences that the fixed-node errors in the ground and excited states obtained with sCI wave functions cancel out to a large extent. Our procedure is tested on two small organic molecules (water and formaldehyde) for which we report all-electron FN-DMC calculations. For both the singlet and triplet manifolds, accurate vertical excitation energies are obtained with relatively compact multideterminant expansions built with small (typically double-$ζ$) basis sets.

physics.chem-ph↗

arXiv2018

Spin-selective electron transfer reactions of radical pairs: beyond the Haberkorn master equation

Radical pair recombination reactions are normally described using a quantum mechanical master equation for the electronic and nuclear spin density operator. The electron spin state selective (singlet and triplet) recombination processes are described with a Haberkorn reaction term in this master equation. Here we consider a general spin state selective electron transfer reaction of a radical pair and use Nakajima-Zwanzig theory to derive the master equation for the spin density operator, thereby elucidating the relationship between non-adiabatic reaction rate theory and the Haberkorn reaction term. A second order perturbation theory treatment of the diabatic coupling naturally results in the Haberkorn master equation with an additional reactive scalar electron spin coupling term. This term has been neglected in previous spin chemistry calculations, but we show that it will often be quite significant. We also show that beyond second order in perturbation theory, i.e., beyond the Fermi golden rule limit, an additional reactive singlet-triplet dephasing term appears in the master equation. A closed form expression for the reactive scalar electron spin coupling in terms of the Marcus theory parameters that determine the singlet and triplet recombination rates is presented. By performing simulations of radical pair reactions with the exact Hierarchical Equations of Motion (HEOM) method, we demonstrate that our master equations provide a very accurate description of radical pairs undergoing spin-selective non-adiabatic electron transfer reactions. The existence of a reactive electron spin coupling may well have implications for biologically relevant radical pair reactions such as those which have been suggested to play a role in avian magnetoreception.

physics.chem-ph↗