Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise

System–environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system–environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system–environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (<<i>k</i>_b<i>T</i>) and provides qualitative insights into systems with wide redox potential differences (≫<i>k</i>_b<i>T</i>). Specifically, we find that the temporal correlations of site energies are critical in determining the coherent–incoherent transition, while the role of spatial correlations depends on the nature of the systems. In a system with repeated bridge units of the same chemistry, spatially correlated fluctuations enhance the charge delocalization and charge-transfer rates; however, in a system of units with different site energies, spatial correlations slow the fluctuations to bring units into degeneracy, in turn, slowing the charge-transfer rates. The spatial and temporal correlations of condensed phase medium fluctuations provide another source to control and tune the kinetics and dynamics of charge-transfer systems

Strategy To Discover Diverse Optimal Molecules in the Small Molecule Universe

The small molecule universe (SMU) is defined as a set of over 10⁶⁰ synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework (Virshup et al. J. Am. Chem. Soc. 2013, 135, 7296–7303) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10⁵ molecules

Biochemistry and Theory of Proton-Coupled Electron Transfer

Biochemistry and Theory of Proton-Coupled Electron Transfe

Two-Electron Transfer Pathways

The frontiers of electron-transfer chemistry demand that we develop theoretical frameworks to describe the delivery of multiple electrons, atoms, and ions in molecular systems. When electrons move over long distances through high barriers, where the probability for thermal population of oxidized or reduced bridge-localized states is very small, the electrons will tunnel from the donor (D) to acceptor (A), facilitated by bridge-mediated superexchange interactions. If the stable donor and acceptor redox states on D and A differ by two electrons, it is possible that the electrons will propagate coherently from D to A. While structure–function relations for single-electron superexchange in molecules are well established, strategies to manipulate the coherent flow of multiple electrons are largely unknown. In contrast to one-electron superexchange, two-electron superexchange involves both one- and two-electron virtual intermediate states, the number of virtual intermediates increases very rapidly with system size, and multiple classes of pathways interfere with one another. In the study described here, we developed simple superexchange models for two-electron transfer. We explored how the bridge structure and energetics influence multielectron superexchange, and we compared two-electron superexchange interactions to single-electron superexchange. Multielectron superexchange introduces interference between singly and doubly oxidized (or reduced) bridge virtual states, so that even simple linear donor–bridge–acceptor systems have pathway topologies that resemble those seen for one-electron superexchange through bridges with multiple parallel pathways. The simple model systems studied here exhibit a richness that is amenable to experimental exploration by manipulating the multiple pathways, pathway crosstalk, and changes in the number of donor and acceptor species. The features that emerge from these studies may assist in developing new strategies to deliver multiple electrons in condensed-phase redox systems, including multiple-electron redox species, multimetallic/multielectron redox catalysts, and multiexciton excited states

Chirality Control of Electron Transfer in Quantum Dot Assemblies

Electron spin and molecular chirality are emerging as factors that can be used effectively to direct charge flow at the molecular scale. We report order of magnitude effects of molecular chirality on electron-transfer rates between quantum dots (QDs) in chiral QD assemblies. Indeed, both the circular polarization of the light that excites the electron donor and the imprinted chirality of the acceptor QDs affect the dot-to-dot electron-transfer kinetics. We define a polarization for the electron-transfer rate constant and show that it correlates with the strength of the acceptor QD circular dichroism (CD) spectrum. These findings imply that the CD strength of the QD exciton transition(s) may be used as a predictor for the spin-dependent electron transfer, indicating that chiral imprinting of the dots may lie at the origin of this phenomenon

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

The “small molecule universe” (SMU), the set of all synthetically feasible organic molecules of 500 Da molecular weight or less, is estimated to contain over 10⁶⁰ structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a “representative universal library” spanning the SMU that samples the full extent of feasible small molecule chemistries. This library was generated using the newly developed Algorithm for Chemical Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chemical space exploration: it allows the systematic search of the unexplored regions of the small molecule universe, and it facilitates the mining of chemical libraries that do not yet exist, providing a near-infinite source of diverse novel compounds

Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra

The effectiveness of solar energy capture and conversion materials derives from their ability to absorb light and to transform the excitation energy into energy stored in free carriers or chemical bonds. The Thomas–Reiche–Kuhn (TRK) sum rule mandates that the integrated (electronic) oscillator strength of an absorber equals the total number of electrons in the structure. Typical molecular chromophores place only about 1% of their oscillator strength in the UV–vis window, so individual chromophores operate at about 1% of their theoretical limit. We explore the distribution of oscillator strength as a function of excitation energy to understand this circumstance. To this aim, we use familiar independent-electron model Hamiltonians as well as first-principles electronic structure methods. While model Hamiltonians capture the qualitative electronic spectra associated with π electron chromophores, these Hamiltonians mistakenly focus the oscillator strength in the fewest low-energy transitions. Advanced electronic structure methods, in contrast, spread the oscillator strength over a very wide excitation energy range, including transitions to Rydberg and continuum states, consistent with experiment. Our analysis rationalizes the low oscillator strength in the UV–vis spectral region in molecules, a step toward the goal of oscillator strength manipulation and focusing

Determinants of Photolyase’s DNA Repair Mechanism in Mesophiles and Extremophiles

Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine’s role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

The “small molecule universe” (SMU), the set of all synthetically feasible organic molecules of 500 Da molecular weight or less, is estimated to contain over 10⁶⁰ structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a “representative universal library” spanning the SMU that samples the full extent of feasible small molecule chemistries. This library was generated using the newly developed Algorithm for Chemical Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chemical space exploration: it allows the systematic search of the unexplored regions of the small molecule universe, and it facilitates the mining of chemical libraries that do not yet exist, providing a near-infinite source of diverse novel compounds

Determinants of Photolyase’s DNA Repair Mechanism in Mesophiles and Extremophiles

Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine’s role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated