https://zenodo.org/record/1258475/files/article.pdf

Electron transfers in chemistry and biology

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

2.2. Materials 929 2.3. Factors Influencing Charge Mobility 931 2.3.1. Molecular Packing 931 2.3.2. Disorder 932 2.3.3. Temperature 933 2.3.4. Electric Field 934 2.3.5. Impurities 934 2.3.6. Pressure 934 2.3.7. Charge-Carrier Density 934 2.3.8. Size/molecular Weight 935 3. The Charge-Transport Parameters 935 3.1. Electronic Coupling 936 3.1.1. The Energy-Splitting-in-Dimer Method 936 3.1.2. The Orthogonality Issue 937 3.1.3. Impact of the Site Energy 937 3.1.4. Electronic Coupling in Oligoacene Derivatives 938

Charge transport in organic semiconductors.

T e purpose of this review is to assess the nature and magnitudes of the dominant forces in protein folding. Since proteins are only marginally stable at room temperature,’ no type of molecular interaction is unimportant, and even small interactions can contribute significantly (positively or negatively) to stability (Alber, 1989a,b; Matthews, 1987a,b). However, the present review aims to identify only the largest forces that lead to the structural features of globular proteins: their extraordinary compactness, their core of nonpolar residues, and their considerable amounts of internal architecture. This review explores contributions to the free energy of folding arising from electrostatics (classical charge repulsions and ion pairing), hydrogen-bonding and van der Waals interactions, intrinsic propensities, and hydrophobic interactions. An earlier review by Kauzmann (1959) introduced the importance of hydrophobic interactions. His insights were particularly remarkable considering that he did not have the benefit of known protein structures, model studies, high-resolution calorimetry, mutational methods, or force-field or statistical mechanical results. The present review aims to provide a reassessment of the factors important for folding in light of current knowledge. Also considered here are the opposing forces, conformational entropy and electrostatics. The process of protein folding has been known for about 60 years. In 1902, Emil Fischer and Franz Hofmeister independently concluded that proteins were chains of covalently linked amino acids (Haschemeyer & Haschemeyer, 1973) but deeper understanding of protein structure and conformational change was hindered because of the difficulty in finding conditions for solubilization. Chick and Martin (191 1) were the first to discover the process of denaturation and to distinguish it from the process of aggregation. By 1925, the denaturation process was considered to be either hydrolysis of the peptide bond (Wu & Wu, 1925; Anson & Mirsky, 1925) or dehydration of the protein (Robertson, 1918). The view that protein denaturation was an unfolding process was

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Dominant forces in protein folding

6. Rehybridization of the Acceptor (RICT) 3908 7. Planarization of the Molecule (PICT) 3909 III. Fluorescence Spectroscopy 3909 A. Solvent Effects and the Model Compounds 3909 1. Solvent Effects on the Spectra 3909 2. Steric Effects and Model Compounds 3911 3. Bandwidths 3913 4. Isoemissive Points 3914 B. Dipole Moments 3915 C. Radiative Rates and Transition Moments 3916 1. Quantum Yields and Radiationless Deactivation Processes 3916

Structural Changes Accompanying Intramolecular Electron Transfer: Focus on Twisted Intramolecular Charge-Transfer States and Structures

In this paper we consider a theory for intramolecular radiationless transitions in an isolated molecule. The Born–Oppenheimer zero‐order excited states are not pure in view of configuration interaction between nearly degenerate zero‐order states, leading to the broadening of the excited state, the line shape being Lorentzian. The optically excited state can be described in terms of a superposition of molecular eigenstates, and the resulting wavefunction exhibits an exponential nonradiative decay. The linewidth and the radiationless lifetime are expressed in terms of a single molecular parameter, that is the square of the interaction energy between the zero‐order state and the manifold of all vibronic states located within one energy unit around that state. The validity criteria for the occurrence of an unimolecular radiationless transition and for exponential decay in an isolated molecule are derived. Provided that the density of vibrational states is large enough (i.e., exceeds the reciprocal of the interaction matrix element) radiationless transitions are expected to take place. The gross effects of molecular structure on the relevant molecular parameters are discussed.

Intramolecular Radiationless Transitions

Electron Transfer Past and Future (R Marcus) Electron Transfer Reactions in Solution: A Historical Perspective (N Sutin) Electron Transfer--From Isolated Molecules to Biomolecules (M Bixon & J Jortner) Charge Transfer in Bichromophoric Molecules in the Gas Phase (D Levy) Long--Range Charge Separation in Solvent--Free Donor--Bridge--Acceptor Systems (B Wegewijs & J Verhoeven) Electron Transfer and Charge Separation in Clusters (C Dessent, et al) Control of Electron Transfer Kinetics: Models for Medium Reorganization and Donor--Acceptor Coupling (M Newton) Theories of Structure--Function Relationships for Bridge--Mediated Electron Transfer Reactions (S Skourtis & D Beratan) Fluctuations and Coherence in Long--Range and Multicenter Electron Transfer (G Iversen, et al) Lanczos Algorithm for Electron Transfer Rates in Solvents with Complex Spectral Densities (A Okada, et al) Spectroscopic Determination of Electron Transfer Barriers and Rate Constants (K Omberg, et al) Photoinduced Electron Transfer Within Donor--Spacer--Acceptor Molecular Assemblies Studied by Time--Resolved Microwave Conductivity (J Warman, et al) From Close Contact to Long--Range Intramolecular Electron Transfer (J Verhoeven) Photoinduced Electron Transfers Through sigma Bonds in Solution (N--C Yang, et al) Indexes

Electron transfer : from isolated molecules to biomolecules

We explore charge migration in DNA, advancing two distinct mechanisms of charge separation in a donor (d)–bridge ({Bj})–acceptor (a) system, where {Bj} = B1,B2, … , BN are the N-specific adjacent bases of B-DNA: (i) two-center unistep superexchange induced charge transfer, d*{Bj}a → d∓{Bj}a±, and (ii) multistep charge transport involves charge injection from d* (or d+) to {Bj}, charge hopping within {Bj}, and charge trapping by a. For off-resonance coupling, mechanism i prevails with the charge separation rate and yield exhibiting an exponential dependence ∝ exp(−βR) on the d-a distance (R). Resonance coupling results in mechanism ii with the charge separation lifetime τ ∝ Nη and yield Y ≃ (1 + δ Nη)−1 exhibiting a weak (algebraic) N and distance dependence. The power parameter η is determined by charge hopping random walk. Energetic control of the charge migration mechanism is exerted by the energetics of the ion pair state d∓B1±B2 … BNa relative to the electronically excited donor doorway state d*B1B2 … BNa. The realization of charge separation via superexchange or hopping is determined by the base sequence within the bridge. Our energetic–dynamic relations, in conjunction with the energetic data for d*/d− and for B/B+, determine the realization of the two distinct mechanisms in different hole donor systems, establishing the conditions for “chemistry at a distance” after charge transport in DNA. The energetic control of the charge migration mechanisms attained by the sequence specificity of the bridge is universal for large molecular-scale systems, for proteins, and for DNA.

https://www.pnas.org/content/pnas/95/22/12759.full.pdf

Charge transfer and transport in DNA

The velocity correlation function of an atom in a simple liquid is calculated using a frequency-dependent version of the Stokes-Einstein formula. Stokes's law for the frictional force on a moving sphere is generalized to arbitrary frequency, compressibility, and visco-elasticity, with arbitrary slip of the fluid on the surface of the sphere. This frequency-dependent friction coefficient is then used in a generalized Stokes-Einstein formula, and the velocity correlation function is found by Fourier inversion. By using physically reasonable values for viscoelastic parameters, good agreement is obtained with the velocity correlation function determined by Rahman using computer experiments.

Hydrodynamic Theory of the Velocity Correlation Function

The theory of dynamic solvent effects on outer‐sphere electron transfer (ET) was extended to incorporate the modification of the high‐frequency quantum modes, which is manifested by the reduction of the electronic coupling by nuclear Franck–Condon factors and by the change of the energy gap Explicit expressions for the ET rates were obtained in terms of a sum over parallel vibronic channels, each involving a distinct intramolecular vibrational excitation of the final state In the solvent‐controlled adiabatic limit, the effects of intramolecular vibrational excitation are exhibited by the modification of the (partial) activation energies, while the frequency factor is dominated by the longitudinal dielectric relaxation rate of the solvent

Mordechai Bixon

Papers

Intramolecular Radiationless Transitions

Electron transfer : from isolated molecules to biomolecules

Charge transfer and transport in DNA

Hydrodynamic Theory of the Velocity Correlation Function

Intramolecular vibrational excitations accompanying solvent‐controlled electron transfer reactions