On the influence of nonlocal molecular vibrations and charge transfer on the spectra of aggregated push-pull chromophores

Through their fluorescence spectrum, aggregates of push-pull chromophores are good reporters of their microenvironment temperature and polarity. The understanding of the fluorescence and charge-separation dynamics in arrays composed of this type of species is consequently of considerable interest. In this article, we study the effect of charge fluctuations induced by molecular nonlocal vibrations on the electronic coupling between a pair of linear push-pull chromophores, for side-to-side or head-to-tail orientations, using a valence-bond charge-transfer (VB-CT) model and the Redfield equation. The results show that the exciton-vibrational dynamics along the bond length alternation coordinate can significantly modify the inter-molecular electronic coupling, which determines the fluorescence spectral band redshift due to aggregation. Numerical results for the electronic and exciton-vibrational contributions to the Coulombic coupling between two of these chromophores are obtained using experimentally based parameters for polyene linker species. The exciton-vibrational contribution is significant relative to the electronic contribution at room temperature in some ranges of the energy gap between the VB and CT states, and it is more important for the side-to-side than for the head-to-tail configuration. Our calculations also show that, even without including solvation effects, the spectral band associated with an S(0) → S(1) transition is redshifted with increasing temperature.     

Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems

Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.     

Quantum versus classical electron transfer energy as reaction coordinate for the aqueous Ru2+/Ru3+ redox reaction

Applying density functional theory (DFT)-based molecular dynamics simulation methods we investigate the effect of explicit treatment of electronic structure on the solvation free energy of aqueous Ru²⁺ and Ru³⁺.Our approach is based on the Marcus theory of redox half reactions, focussing on the vertical energy gap for reduction or oxidation of a single aqua ion. We compare the fluctuations of the quantum and classical energy gap along the same equilibrium ab initio molecular dynamics trajectory for each oxidation state. The classical gap is evaluated using a standard point charge model for the charge distribution of the solvent molecules (water). The quantum gap is computed from the full DFT electronic ground state energies of reduced and oxidized species, thereby accounting for the delocalization of the electron in the donor orbital and reorganization of the electron cloud after electron transfer (ET). The fluctuations of the quantum ET energy are well approximated by gaussian statistics giving rise to parabolic free energy profiles. The curvature is found to be independent of the oxidation state in agreement with the linear response assumption underlying Marcus theory. By contrast, the diabatic free energy curves evaluated using the classical gap as order parameter, while also quadratic, are asymmetric reflecting the difference in oxidation state. The response of these two order parameters is further analysed by a comparison of the spectral density of the fluctuations and the corresponding reorganization free energies.     

Hydration dynamics and time scales of coupled water-protein fluctuations

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed.     

丙酮分子n→π%*跃迁光谱的平均溶剂静电势/分子动力学方法研究

采用量子力学/分子动力学方法研究了具体溶剂分子结构对溶质光谱行为的静电影响. 通过拟合溶质所处外电场和引入溶剂分子极化率, 考虑了溶质溶剂分子之间的相互极化效应, 得到合理的溶质和溶剂分子的电荷分布. 经过严格推导发现, 在传统的显溶剂模型中, 平衡和非平衡溶剂化能表达式均未考虑溶剂分子永久偶极弹簧能的贡献. 因此, 在正确计算永久偶极弹簧能的基础上, 重新建立了溶剂化能的表达式和新的吸收/发射光谱移动公式. 采用修改后的ASEP/MD程序, 计算得到了与实验值比较吻合的丙酮在水溶液中n→π*跃迁的光谱移动值, 验证了新公式的合理性.     

Juxtaposing density matrix and classical path-based wave packet dynamics

In many physical, chemical, and biological systems energy and charge transfer processes are of utmost importance. To determine the influence of the environment on these transport processes, equilibrium molecular dynamics simulations become more and more popular. From these simulations, one usually determines the thermal fluctuations of certain energy gaps, which are then either used to perform ensemble-averaged wave packet simulations, also called Ehrenfest dynamics, or to employ a density matrix approach via spectral densities. These two approaches are analyzed through energy gap fluctuations that are generated to correspond to a predetermined spectral density. Subsequently, density matrix and wave packet simulations are compared through population dynamics and absorption spectra for different parameter regimes. Furthermore, a previously proposed approach to enforce the correct long-time behavior in the wave packet simulations is probed and an improvement is proposed.     

Freezing single molecule dynamics on interfaces and in polymers

Heterogeneous line broadening and spectral diffusion of the fluorescence emission spectra of perylene diimide molecules have been investigated by means of time dependent single molecule spectroscopy. The influence of temperature and environment has been studied and reveals strong correlation to spectral diffusion processes. We followed the freezing of the molecular mobility of quasi free molecules on the surface upon temperature lowering and by embedding into a poly(methyl methacrylate) (PMMA) polymer. Thereby changes of optical transition energies as a result of both intramolecular changes of conformation and external induced dynamics by the surrounding polymer matrix could be observed. Simulations of spectral fluctuations within a two-level system (TLS) model showed good agreement with the experimental findings.     

Semiclassical theory of group vibrations for linear polymer chains

The semiclassical spectral method (SSM), which employs molecular dynamics and spectral estimators to determine transition frequencies between quantum energy levels in molecular and atomic systems, is extended to include calculations for linear polymer chains. Average differences between harmonic and transition frequencies for the symmetric and asymmetric stretch modes of polyethylene are reported to be around 50 cm⁻¹ with smaller average frequency shifts for the other group vibration dispersion curves for a certain potential surface describing the macromolecule.     

Nuclear magnetic resonance proton dipolar order relaxation in thermotropic liquid crystals: a quantum theoretical approach

By means of the Jeener-Broekaert nuclear magnetic resonance pulse sequence, the proton spin system of a liquid crystal can be prepared in quasiequilibrium states of high dipolar order, which relax to thermal equilibrium with the molecular environment with a characteristic time (T1D). Previous studies of the Larmor frequency and temperature dependence of T1D in thermotropic liquid crystals, that included field cycling and conventional high-field experiments, showed that the slow hydrodynamic modes dominate the behavior of T1D, even at high Larmor frequencies. This noticeable predominance of the cooperative fluctuations (known as order fluctuations of the director, OFD) could not be explained by standard models based on the spin-lattice relaxation theory in the limit of high temperature (weak order). This fact points out the necessity of investigating the role of the quantum terms neglected in the usual high temperature theory of dipolar order relaxation. In this work, we present a generalization of the proton dipolar order relaxation theory for highly correlated systems, which considers all the spins belonging to correlated domains as an open quantum system interacting with quantum bath. As starting point, we deduce a formulation of the Markovian master equation of relaxation for the statistical spin operator, valid for all temperatures, which is suitable for introducing a dipolar spin temperature in the quantum regime, without further assumptions about the form of the spin-lattice Hamiltonian. In order to reflect the slow dynamics occurring in correlated systems, we lift the usual short-correlation-time assumption by including the average over the motion of the dipolar Hamiltonian together with the Zeeman Hamiltonian into the time evolution operator. In this way, we calculate the time dependence of the spin operators in the interaction picture in a closed form, valid for high magnetic fields, bringing into play the spin-spin interactions within the microscopic time scale. Then, by adopting the spin-temperature density operator to represent the collective state of the spin system, and removing the traditional hypothesis of high temperature, we deduce an expression for the first order quantum contribution to T1D (-1), in terms of spectral densities, with coefficients in form of spin traces. The properties that distinguish our result from the high-temperature T1D (-1) are as follows. (a) It is exclusively associated to cooperative fluctuations. (b) Because of its quantum character, it relies on both considering the lattice degrees of freedom quantum mechanically and including the spin-spin interactions in the microscopic time scale. With regard to the average dipolar Hamiltonian, only the nonsecular part plays a relevant role. (c) Associated with the structure of the spin operator involved in the quantum contribution, a term arises which is proportional to the number of spins in the correlated molecular domains, showing that the quantum contribution may be of macroscopic size in highly correlated systems. When applied to nematic liquid crystals, the new term exhibits the typical nu(-1/2) Larmor frequency dependence through the spectral density of the OFD, in consistence with the experimental results.     

Two-photon absorption cross sections: an investigation of solvent effects. Theoretical studies on formaldehyde and water

The effects of a solvent on the two-photon absorption of microsolvated formaldehyde and liquid water have been studied using hybrid coupled-cluster/molecular mechanics (CC/MM) response theory. Both water and formaldehyde were considered solvated in water, where the solvent water molecules were described within the framework of molecular mechanics. Prior to the CC/MM calculations, molecular dynamics simulations were performed on the water/formaldehyde and water/water aggregates and many configurations were generated. By carrying out CC/MM response calculations on the individual configurations, it was possible to obtain statistically averaged results for both the excitation energies and two-photon absorption cross sections. For liquid water, the comparison between one- and two-photon absorption spectra is in good agreement with the experimental data available in the literature. In particular, the lowest energy transition occurring in the one-photon absorption spectrum of water only occurs with a relatively small strength in the two-photon absorption spectrum. This result is important for the interpretation of two-photon absorption data as these results show that in the absence of selection rules that determine which transitions are forbidden, the spectral profile of the two-photon absorption spectrum can be significantly different from the spectral profile of the one-photon absorption spectrum.     

2D regional correlation analysis of single-molecule time trajectories

We report a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anticorrelated fluctuations under a noncorrelated noise background. Using this new method, by changing and scanning the start time and end time along a pair of fluctuation trajectories, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anticorrelated, or noncorrelated; after which, a cross-correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis. We specifically discuss an application of this approach to analyze single-molecule fluorescence resonance energy transfer (FRET) fluctuation dynamics where the fluctuations are often complex, although this approach can be useful for analyzing other types of fluctuation dynamics of various physical variables as well.     

Structural fluctuations and excitation transfer between adenine and 2-aminopurine in single-stranded deoxytrinucleotides

Steady-state fluorescence measurements on the deoxytrinucleotides (5')dTp2APpA(3') and (5')dAp2APpA(3') show a temperature-dependence and a viscosity-dependence for energy transfer that qualitatively differ from those seen in our previous study of charge transfer (CT) in these systems. Time-resolved anisotropy studies and molecular dynamics simulations are presented that provide a detailed characterization of the structural dynamics of these systems and how these fluctuations modulate the electronic interaction between 2AP and its neighbors. To gain quantitative insight into the interplay of conformational fluctuations and stacking-induced energy transfer, we present results from a new hybrid quantum-classical simulation method for computing the A --> 2AP energy transfer rate that makes use of the full three-dimensional nature of the donor and acceptor transition densities. Analysis of the results shows that the standard transition dipole-transition dipole approximation for the Coulombic coupling substantially overestimates the transfer rate and that the nearest neighbor energy transfer from adenine to 2AP occurs on a much faster time scale than that for CT. This suggests that, unlike the CT dynamics where conformational "gating" plays a critical role, the large amplitude fluctuations that modulate the process are largely "frozen" out on the energy transfer time scale.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.     

Fluctuating hydrodynamics for multiscale modeling and simulation: Energy and heat transfer in molecular fluids

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.     

Excitonic effects in two-dimensional vibrational spectra of liquid formamide

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schr?dinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.     

Role of protein dynamics in reaction rate enhancement by enzymes

An integrated view of protein structure, dynamics, and function is emerging, where proteins are considered as dynamically active assemblies and internal motions are closely linked to function such as enzyme catalysis. Further, the motion of solvent bound to external regions of protein impacts internal motions and, therefore, protein function. Recently, we discovered a network of protein vibrations in enzyme cyclophilin A, coupled to its catalytic activity of peptidyl-prolyl cis-trans isomerization. Detailed studies suggest that this network, extending from surface regions to active site, is a conserved part of enzyme structure and has a role in promoting catalysis. In this report, theoretical investigations of concerted conformational fluctuations occurring on microsecond and longer time scales within the discovered network are presented. Using a new technique, kinetic energy was added to protein vibrational modes corresponding to conformational fluctuations in the network. The results reveal that protein dynamics promotes catalysis by altering transition state barrier crossing behavior of reaction trajectories. An increase in transmission coefficient and number of productive trajectories with increasing amounts of kinetic energy in vibrational modes is observed. Variations in active site enzyme-substrate interactions near transition state are found to be correlated with barrier recrossings. Simulations also showed that energy transferred from first solvation shell to surface residues impacts catalysis through network fluctuations. The detailed characterization of network presented here indicates that protein dynamics plays a role in rate enhancement by enzymes. Therefore, coupled networks in enzymes have wide implications in understanding allostericity and cooperative effects, as well as protein engineering and drug design.     

A first principles simulation study of fluctuations of hydrogen bonds and vibrational frequencies of water at liquid-vapor interface

We present a theoretical study of the structure and dynamics of water-vapor interface by means of ab initio molecular dynamics simulations. The inhomogeneous density, hydrogen bond and orientational profiles, voids and vibrational frequency distributions are investigated. We have also studied various dynamical properties of the interface such as diffusion, orientational relaxation, hydrogen bond dynamics and vibrational frequency fluctuations. The diffusion and orientational relaxation of water molecules are found to be faster at the interface which can be correlated with the voids present in the system. The hydrogen bond dynamics, however, is found to be slightly slower at the interface than that in bulk water. The correlations of hydrogen bond relaxation with the dynamics of vibrational frequency fluctuations are also discussed.