Universal free-energy landscape produces efficient and reversible electron bifurcation.

For decades, it was unknown how electron-bifurcating systems in nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron-bifurcating molecular machines could not be designed and built. The underpinning free-energy landscapes for electron bifurcation were also enigmatic. We predict that a simple and universal free-energy landscape enables electron bifurcation, and we show that it enables high-efficiency bifurcation with limited short-circuiting (the EB scheme). The landscape relies on steep free-energy slopes in the two redox branches to insulate against short-circuiting using an electron occupancy blockade effect, without relying on nuanced changes in the microscopic rate constants for the short-circuiting reactions. The EB scheme thus unifies a body of observations on biological catalysis and energy conversion, and the scheme provides a blueprint to guide future campaigns to establish synthetic electron bifurcation machines.

Vibrational control of electron-transfer reactions: a feasibility study for the fast coherent transfer regime.

Molecular vibrations and electron-vibrational interactions are central to the control of biomolecular electron and energy-transfer rates. The vibrational control of molecular electron-transfer reactions by infrared pulses may enable the precise probing of electronic-vibrational interactions and of their roles in determining electron-transfer mechanisms. This type of electron-transfer rate control is advantageous because it does not alter the electronic state of the molecular electron-transfer system or irreversibly change its molecular structure. For bridge-mediated electron-transfer reactions, infrared (vibrational) excitation of the bridge linking the electron donor to the electron acceptor was suggested as being capable of influencing the electron-transfer rate by modulating the bridge-mediated donor-to-acceptor electronic coupling. This kind of electron-transfer experiment has been realized, demonstrating that bridge-mediated electron-transfer rates can be changed by exciting vibrational modes of the bridge. Here, we use simple models and ab initio computations to explore the physical constraints on one's ability to vibrationally perturb electron-transfer rates using infrared excitation. These constraints stem from the nature of molecular vibrational spectra, the strengths of the electron-vibrational coupling, and the interaction between molecular vibrations and infrared radiation. With these constraints in mind, we suggest parameter regimes and molecular architectures that may enhance the vibrational control of electron transfer for fast coherent electron-transfer reactions.

Simulation of scanning tunneling microscope images of 1,3-cyclohexadiene bound to a silicon surface.

Scanning tunneling microscope (STM) images of 1,3-cyclohexadiene bound to silicon are interpreted using a nonequilibrium Green's function method. The resolution of the carbon-carbon double bond for positive bias voltages but not for negative bias voltages is explained using a quasiprobability density analysis. The asymmetry in the images arises from the system's voltage dependent electronic structure. A pi* orbital is found to be responsible for the empty state STM images of the carbon-carbon double bond, which is observed experimentally. The pi orbital relevant for the opposite bias does not produce an STM image sharply localized in the bond region because the molecule induces a Si-surface dipole dependent on the bias. The dipole voltage dependence arises from molecular charging. This result emphasizes the importance of simulating the molecule as an element in an open quantum system.

Determining absolute configuration in flexible molecules: a case study.

Assigning absolute configuration of molecules continues to be a major problem. Determining absolute configuration in conformationally flexible systems is challenging, even for experts. Here, we present a case study in which we use a combination of molecular modeling, solution NMR, and X-ray crystallography to illustrate why it is difficult to use solution methods alone for configuration assignment. For the case examined, a comparison of calculated and experimental optical rotatory dispersion (ORD) data provides the most straightforward way to assign the absolute configuration.

Chiral action at a distance: remote substituent effects on the optical activity of calyculins A and B.

[structure--see text] Calyculins A and B differ only by the (E)- vs (Z)-configuration at C(2). Yet, they show a large difference in optical rotations. We demonstrate a new strategy that provides a physical analysis of this long-range chiro-optical effect by Boltzmann-averaged atomic contribution mapping. The polarizability characteristics of the CN substituent rather than the perturbation of the stereogenic centers or the introduction of asymmetry into the polyene chain give rise to the remarkable difference in rotation angles.

Atomic contributions to the optical rotation angle as a quantitative probe of molecular chirality.

Chiral molecules are characterized by a specific rotation angle, the angle through which plane-polarized light is rotated on passing through an enantiomerically enriched solution. Recent developments in methodology allow computation of both the sign and the magnitude of these rotation angles. However, a general strategy for assigning the individual contributions that atoms and functional groups make to the optical rotation angle and, more generally, to the molecular chirality has remained elusive. Here, a method to determine the atomic contributions to the optical rotation angle is reported. This approach links chemical structure with optical rotation angle and provides a quantitative measure of molecular asymmetry propagation from a center, axis, or plane of chirality.

Electron transfer in the photosynthetic reaction center: mechanistic implications of mutagenesis studies.

A phenomenological analysis of the driving force effects in photosynthetic reaction centers modified by mutagenesis and also by chemical means is presented. Different parameter sets associated with different mechanisms of electron transfer are consistent with the mutagenesis experiments. However, only one parameter set--connected with a sequential mechanism of electron transfer--is consistent with all known experimental data. Arguments explaining why the sequential mechanism of electron transfer is selected by nature in the wild type reaction center are provided. Why the driving force of the wild type reaction center is about 0.25 eV is explained and new driving force effects are predicted.

Synthetic and model computational studies of molar rotation additivity for interacting chiral centers: a reinvestigation of van't Hoff's principle.

When plane-polarized light impinges on a solution of optically active molecules, the polarization of the light that emerges is rotated. This simple phenomenon arises from the interaction of light with matter and is well understood, in principle, van't Hoff's rule of optical superposition correlates the molar rotation with the individual contributions to optical activity of isolated centers of asymmetry. This straightforward empirical additivity rule is rarely used for structure elucidation nowadays because of its limitations in the assessment of conformationally restricted or interacting chiral centers. However, additivity can be used successfully to assign the configuration of complex natural products such as hennoxazole A if appropriate synthetic partial structures are available. Therefore, van't Hoff's principle is a powerful stereochemical complement to natural products' total synthesis. The quest for reliable quantitative methods to calculate the angle of rotation a priori has been underway for a long time. Both classical and quantum methods for calculating molar rotation have been developed. Of particular practical importance for determining the absolute structure of molecules by calculation is the manner in which interactions between multiple chiral centers in a single molecule are included, leading to additive or non-additive optical rotation angles. This problem is addressed here using semi-empirical electronic structure models and the Rosenfeld equation.

DNA: Insulator or wire?

DNA-based electron transfer reactions are seen in processes such as biosynthesis and radiation damage/repair, but are poorly understood. What kinds of experiments might tell us how far and how fast electrons can travel in DNA? What does modern theory predict?

Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.

The simplest views of long-range electron transfer utilize flat one-dimensional barrier tunneling models, neglecting structural details of the protein medium. The pathway model of protein electron transfer reintroduces structure by distinguishing between covalent bonds, hydrogen bonds, and van der Waals contacts. These three kinds of interactions in a tunneling pathway each have distinctive decay factors associated with them. The distribution and arrangement of these bonded and nonbonded contacts in a folded protein varies tremendously between structures, adding a richness to the tunneling problem that is absent in simpler views. We review the pathway model and the predictions that it makes for protein electron transfer rates in small proteins, docked proteins, and the photosynthetic reactions center. We also review the formulation of the protein electron transfer problem as an effective two-level system. New multi-pathway approaches and improved electronic Hamiltonians are described briefly as well.

Protein electron transfer rates set by the bridging secondary and tertiary structure.

The rate of long-distance electron transfer in proteins rapidly decreases with distance, which is indicative of an electron tunneling process. Calculations predict that the distance dependence of electron transfer in native proteins is controlled by the protein's structural motif. The helix and sheet content of a protein and the tertiary arrangement of these secondary structural units define the distance dependence of electronic coupling in that protein. The calculations use a tunneling pathway model applied previously with success to ruthenated proteins. The analysis ranks the average distance decay constant for electronic coupling in electron transfer proteins and identifies the amino acids that are coupled to the charge localization site more strongly or weakly than average for their distance.

Approaches for optimizing the first electronic hyperpolarizability of conjugated organic molecules.

A two-state, four-orbital, independent electron analysis of the first optical molecular hyperpolarizability, beta, leads to the prediction that |beta| maximizes at a combination of donor and acceptor strengths for a given conjugated bridge. Molecular design strategies that focus on the energetic manipulations of the bridge states are proposed for the optimization of beta. The limitations of molecular classes based on common bridge structures are highlighted and more promising candidates are described. Experimental results supporting the validity of this approach are presented.

Electron tunneling pathways in proteins: influences on the transfer rate.

A strategy for calculating the tunneling matrix element dependence on the medium intervening between donor and acceptor in specific proteins is described. The scheme is based on prior studies of small molecules and is general enough to allow inclusion of through bond and through space contributions to the electronic tunneling interaction. This strategy should allow the prediction of relative electron transfer rates in a number of proteins. It will therefore serve as a design tool and will be explicitly testable, in contrast with calculations on single molecules. As an example, the method is applied to ruthenated myoglobin and the tunneling matrix elements are estimated. Quantitative improvements of the model are described and effects due to motion of the bridging protein are discussed. The method should be of use for designing target proteins having tailored electron transfer rates for production with site directed mutagenesis. The relevance of the technique to understanding certain photosynthetic reaction center electron transfer rates is discussed.

A molecular shift register based on electron transfer.

An electronic shift-register memory at the molecular level is described. The memory elements are based on a chain of electron-transfer molecules and the information is shifted by photoinduced electron-transfer reactions. This device integrates designed electronic molecules onto a very large scale integrated (silicon microelectronic) substrate, providing an example of a "molecular electronic device" that could actually be made. The design requirements for such a device and possible synthetic strategies are discussed. Devices along these lines should have lower energy usage and enhanced storage density.

Long-range electron transfer in myoglobin.

The distance and driving-force dependences of electron transfer (ET) in a set of four surface-ruthenated myoglobins, in which the heme prosthetic group has been systematically replaced by a series of metalloporphyrins of differing excited-state redox potentials, have provided information on the magnitude [Hab(12.7 A) approximately 6.3 x 10(-3) cm-1] and decay [beta approximately 0.8 A-1, where kET alpha exp [-beta(d - do)]] of protein-mediated donor-acceptor electronic coupling. A reorganization energy lambda approximately 1.3 eV, due to coordination and solvation changes both at and between the ET sites, has been estimated using a rate expression that allows electron-vibration coupling to classical and quantum mechanical modes. The contribution to lambda from the porphyrin and peptide matrix is approximately 0.7 eV. Specific electron-tunneling pathways in the protein have been evaluated.