Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex

Supramolecular Catalysis of m-Xylene Isomerization by Cucurbiturils: Transition State Stabilization, Vibrational Coupling, and Dynamic Binding Equilibrium

The ability of cucurbit[6]uril (CB6) and cucurbit[7]uril (CB7) to catalyze the thermally activated 1,2-methyl shift isomerization pathway of m-xylene in vacuum is investigated using infrequent metadynamics. CB6 is predicted to effectively and selectively catalyze the meta-to-para isomerization through stabilization of the transition state (TS) by van der Waals push (packing coefficient ≈74%), while inhibiting the meta-to-ortho pathway by molding effects of the cavity. Interestingly, despite the snug binding, a very low rate of host-guest vibrational energy transfer is revealed using a novel approach of host-guest partition of the mode-specific anharmonic relaxation rates and ab initio molecular dynamics. The weak vibrational coupling suggests that CB can act as a thermal buffer, possibly shielding encapsulated guests from outside vibrational perturbations such as solvent effects. This dynamic effect could provide an additional boost to the reaction rate by blocking the occurrence of reaction barrier recrossing caused by the friction with surrounding molecules. Finally, mean residence times of xylene into the hosts' cavity were estimated for a range of host-guest complexes, revealing a highly dynamic equilibrium allowing very high guest turnover rates that could minimize catalyst inhibition effects commonly suffered by other supramolecular catalysts.

Microscopic calculation of absorption spectra of macromolecules: An analytic approach

We develop a cross-disciplinary approach to analytically compute optical response functions of open macromolecular systems by exploiting the mathematical formalism of quantum field theory (QFT). Indeed, the entries of the density matrix for the electronic excitations interacting with their open dissipative environment are mapped into vacuum-to-vacuum Green's functions in a fictitious relativistic closed quantum system. We show that by re-summing appropriate self-energy diagrams in this dual QFT, it is possible to obtain analytic expressions for the response functions in Mukamel's theory. This yields physical insight into the structure and dynamics of vibronic resonances, since their frequency and width is related to fundamental physical constants and microscopic model parameters. For illustration, we apply this scheme to compute the linear absorption spectrum of the Fenna-Matthews-Olson light harvesting complex, comparing analytic calculations, numerical Monte Carlo simulations, and experimental data.

Coarse-Grained Protein Dynamics Studies Using Elastic Network Models

Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies.

Exciton transport in the PE545 complex: insight from atomistic QM/MM-based quantum master equations and elastic network models

In this paper, we work out a parameterization of environmental noise within the Haken-Strobl-Reinenker (HSR) model for the PE545 light-harvesting complex, based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We use this approach to investigate the role of various auto- and cross-correlations in the HSR noise tensor, confirming that site-energy autocorrelations (pure dephasing) terms dominate the noise-induced exciton mobility enhancement, followed by site energy-coupling cross-correlations for specific triplets of pigments. Interestingly, several cross-correlations of the latter kind, together with coupling-coupling cross-correlations, display clear low-frequency signatures in their spectral densities in the 30-70 [Formula: see text] region. These slow components lie at the limits of validity of the HSR approach, which requires that environmental fluctuations be faster than typical exciton transfer time scales. We show that a simple coarse-grained elastic-network-model (ENM) analysis of the PE545 protein naturally spotlights collective normal modes in this frequency range that represent specific concerted motions of the subnetwork of cysteines covalenty linked to the pigments. This analysis strongly suggests that protein scaffolds in light-harvesting complexes are able to express specific collective, low-frequency normal modes providing a fold-rooted blueprint of exciton transport pathways. We speculate that ENM-based mixed quantum classical methods, such as Ehrenfest dynamics, might be promising tools to disentangle the fundamental designing principles of these dynamical processes in natural and artificial light-harvesting structures.

Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport

Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the Fenna-Matthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple network-based investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.