Recent advances in understanding blue copper proteins

The type 1 (T1) or blue Cu (BC) proteins are a highly studied group of electron transfer (ET) active sites in bioinorganic chemistry. In this review, we cover several more recent results which extend the understanding of the geometric and electronic structure of these interesting Cu ET sites. Spectroscopic methods in tandem with density functional theory (DFT) and time dependent-DFT (TD-DFT) calculations have been used in studies of S → Se variants as well as a series of metal-varied model complexes (M = Mn²⁺ → Zn²⁺). The ligand and metal perturbations further defined the origins of the unique spectral features of BC proteins. These unique spectral features show different temperature dependencies in different T1 sites, and contrasts drawn between their behaviors define the role of the protein in tuning the geometric and electronic structure of the BC site for function. This has been termed the ‘entatic’ or ‘rack-induced’ state in bioinorganic chemistry.     

Theoretical insight to the complexation of some transition metals with cryptand

The most practicable complexes formed between Cryptand[2.2.2] and hydrated Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) cations (denoted as [ML]⁺²) were modeled using computational chemistry methods. The energies of complexation reactions were calculated in both gas phase and solution at B3LYP/6-31+G(d) and B3LYP/6-311++G(3df,2pd) levels of theory. The accuracy of selected computational methods was confirmed with comparison between available X-ray data and computational results. The results suggested that [CuL]⁺² and [CoL]⁺² structures could be the most and the least stable systems, respectively. The nature of metal-ligand interactions based on quantum theory of atoms in molecule (QTAIM) was discussed for all the complexes. This analysis confirmed the ionic nature of metal-ligand interactions due to electron density values for M-O bonds and M-N interactions. Natural bond orbital (NBO) and natural energy decomposition analysis (NEDA) were utilized to explain more details of interaction between divalent cations and donor atoms of the ligand.

     

Kinetics of dissociative electron transfer to ascaridole and dihydroascaridole-model bicyclic endoperoxides of biological relevance

The homogeneous and heterogeneous electron transfer (ET) reduction of ascaridole (ASC) and dihydroascaridole (DASC), two bicyclic endoperoxides, chosen as convenient models of the bridged bicyclic endoperoxides found in biologically relevant systems, were studied in aprotic media by using electrochemical methods. ET is shown to follow a concerted dissociative mechanism that leads to the distonic radical anion, which is itself reduced in a second step by an overall two-electron process. The kinetics of homogeneous ET to these endoperoxides from an extensive series of radical anion electron donors were measured as a function of the driving force of electron transfer (deltaG(o)ET). The kinetics of heterogeneous ET were also studied by convolution analysis. Together, the heterogeneous and homogeneous ET kinetic data provide the best example of the parabolic nature of the activation-driving force relationship for a concerted dissociative ET described by Savéant; the data is particularly illustrative due to the low bond-dissociation enthalpy (BDE) of the O-O bond and hence small intrinsic barriers. Analysis of the data allowed the dissociative reduction potentials (E(o)diss) to be determined as -1.2 and -1.1 Vagainst SCE for ASC and DASC, respectively. Unusually low pre-exponential factors measured in temperature-dependent kinetic studies suggest that ET to these O-O bonded systems is nonadiabatic. Analysis of ET kinetics for ASC and DASC by the Savéant model with a modification for nonadiabaticity allowed the intrinsic free energy for ET to be determined. The use of this approach and estimates for the BDE provide approximations of the reorganization energies. We suggest the methodology described herein can be used to evaluate the extent of ET to other endoperoxides of biological relevance and to provide thermochemical data not otherwise available.     

Perceiving molecular themes in the structures and bonding of intermetallic phases: the role of Hückel theory in an ab initio era

Qualitative molecular orbital theory is central to our understanding of the bonding and reactivity of molecules and materials across chemistry. Advances in computational technology and methodology, however, have made ab initio or density functional theory calculations a simpler alternative, offering reliable results on increasingly large systems in a reasonable time-scale without the need for concerns about the approximations and parameterization of semi-empirical one-electron based methods. In this perspective, we illustrate how the availability of higher-level computational results can augment, rather than supplant, the insights provided by approaches such as the simple and extended Hückel methods. We begin by describing a way to parameterize Hückel-type Hamiltonians against DFT results for intermetallic systems. The potential for chemical understanding embodied by such orbital-based models is then demonstrated with two schemes of bonding analysis that originated in them (but can be extended to DFT results): the μ(3)-acid/base model and the μ(2)-Hückel chemical pressure analysis, which translate the molecular concepts of acidity and electronic/steric competition, respectively, into the context of intermetallic chemistry.     

Model dialkyl peroxides of the fenton mechanistic probe 2-methyl-1-phenyl-2-propyl hydroperoxide (MPPH): kinetic probes for dissociative electron transfer

Two dialkyl peroxides, devised as kinetic probes for the heterogeneous electron transfer (ET), are studied using heterogeneous and homogeneous electrochemical techniques. The peroxides react by concerted dissociative ET reduction of the O-O bond. Under heterogeneous conditions, the only products isolated are the corresponding alcohols from a two-electron reduction as has been observed with other dialkyl peroxides studied to date. However, under homogeneous conditions, a generated alkoxyl radical undergoes a rapid beta-scission fragmentation in competition with the second ET resulting in formation of acetone and a benzyl radical. With knowledge of the rate constant for fragmentation and accounting for the diffuse double layer at the electrode interface, the heterogeneous ET rate constant to the alkoxyl radicals is estimated to be 1500 cm s(-1). The heterogeneous and homogeneous ET kinetics of the O-O bond cleavage have also been measured and examined as a function of the driving force for ET, deltaG(ET), using dissociative electron transfer theory. From both sets of kinetics, besides the evaluation of thermochemical parameters, it is demonstrated that the heterogeneous and homogeneous reduction of the O-O bond appears to be non-adiabatic.     

Inter- or intramolecular electron transfer between triruthenium clusters: we’ll cross that bridge when we come to it

The purpose of this review is to examine the fundamental differences between intermolecular self-exchange vs. intramolecular ET in mixed-valence complexes based on similar triruthenium structural units. The role of orbital overlap between ancillary ligands of the electron donor and acceptor are considered in self-exchange reactions which are found to be strongly adiabatic and again in bridged mixed-valence systems. The method of infrared (IR) reflectance spectroelectrochemistry for the determination of extremely fast (10¹¹–10¹³ s^?1) ET rate constants is reviewed as a tool to provide quantitative information about the time scales of localization and delocalization. The role of internal vibrations of the bridging ligand in strongly delocalized mixed-valence ions is investigated by resonance Raman and IR spectroscopies. The role of solvent dipolar relaxation times in determining the rates of ultrafast intramolecular ET reactions is reviewed in the context of inorganic mixed-valence chemistry. Finally, the concept of Robin–Day Class II/III “borderline” complexes is considered, and a concise definition of the localized to delocalized transition is provided in terms of the relative contributions of external solvent and internal complex ion vibrational modes to ET.     

Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4)

The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fast (ms-μs) intramolecular ET in an electrochemical environment has recently been achieved by controlling the molecular orientation of the protein assembled on a gold electrode surface. In this work we have performed computational modeling of the intramolecular ET process by a combination of density functional theory (DFT) and quantum mechanical charge transfer theory to disclose reasons for this difference. We first address the electronic structures of the model heme core with histidine and methionine axial ligands in both low- and high-spin states by structure-optimized DFT. The computations enable estimating the intramolecular reorganization energy of the ET process for different combinations of low- and high-spin heme couples. Environmental reorganization free energies, work terms ("gating") and driving force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe-Fe separations. The reactivity of low- and high-spin heme groups was notably different. The ET rate is exceedingly low for the crystallographic equilibrium orientation but increases by several orders of magnitude for thermally accessible non-equilibrium configurations. Deprotonation of the propionate carboxyl group was also found to enhance the ET rate significantly. The results are discussed in relation to the observed surface immobilization effect and support the notion of conformationally gated ET.     

Fischer carbene complexes: beautiful playgrounds to study single electron transfer (SET) reactions

The knowledge of the reactivity of Fischer carbene complexes in electron transfer processes is still in the early stage of development, but interesting advances are foreseeable in this young branch of metal-carbene chemistry. Although these compounds have a dual reactivity (which makes them good substrates for oxidation and reduction processes), their behavior towards chemical electron transfer (ET) reagents was unknown until very recently. This article covers the progress accomplished in the reactivity of these compounds towards chemical ET reagents (C(8)K or SmI(2)), as well as the use of nonconventional sources of electrons, such as electrospray ionization (ESI) to induce ET processes. Special emphasis will be made on the effect of the structure of the starting carbene in the outcome of the reaction and in discussing the different mechanisms proposed.     

Electron Transfer in DNA at Electrified Interfaces

The ability of the DNA double helix to transport electrons underlies many life‐centered biological processes and bio‐electronic applications. However, there is little consensus on how efficiently the base pair π‐stacks of DNA mediate electron transport. This minireview scrutinizes the current state‐of‐the‐art knowledge on electron transfer (ET) properties of DNA and its long‐range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA‐mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA′s ET in living systems and to advances in molecular bioelectronics.     

Ensemble density functional theory for inhomogeneous fractional quantum hall systems

The fractional quantum Hall effect (FQHE) occurs at a certain magnetic field strengths B^*(n) in a two-dimensional electron gas of density n at strong magnetic fields perpendicular to the plane of the electron gas. At these magnetic fields strengths, the system is incompressible, i.e., there is a finite cost in energy for creating charge density fluctuations in the bulk, while the boundary of the electron gas has gapless modes of density waves. The bulk energy gap arises because of the strong electron-electron interactions. While there are very good models for infinite homogeneous systems and for the gapless excitations of the boundary of the electron gas, computational methods to accurately model finite, inhomogeneous systems with more than about 10 electrons have not been available until very recently. We will here review an ensemble density functional approach to studying the ground state of large inhomogeneous spin-polarized FQHE systems. © 1996 John Wiley & Sons, Inc.     

Electron Density Studies in Materials Research

Rational material design requires a deep understanding about the relationship between the structure and properties of materials, which are both intimately related to their chemical bonding. Through the experimentally observable electron density, chemical bonding can be understood from experimental and theoretical points of view on an equal footing, and advances in accurate X-ray diffraction measurements and computational techniques over the past decades have provided access to electron density distributions in increasingly complex functional materials. In this Review, selected electron density studies from the literature on a wide range of materials classes are presented, including studies of thermoelectric materials, high pressure electrides, coordination polymers and non-linear optical materials. These studies demonstrate how detailed analysis of chemical bonding based on the electron density provides important understanding of materials beyond arguments based on structure and simple chemical concepts. In cases such as understanding the conducting properties of Zintl semiconductors or the effect of mutual electrical polarization in host–guest systems, it is clearly imperative to go beyond structure and examine the chemical bonding in detail. In the Review, the complementarity between theory and experiment is underlined, which allows for mutual validation of new chemical bonding concepts, and indeed experiment and theory may challenge each other based on the different strengths and weaknesses of each method.     

Intramolecular dissociative electron transfer

Dissociative electron transfers (ET) are reactions in which the ET is associated with the cleavage of a sigma bond. Although a rather satisfactory amount of information is currently available on the intermolecular and heterogeneous dissociative ET reactions, less is known for the corresponding intramolecular processes, despite the relevance of these reactions in both chemistry and biochemistry. This tutorial review focuses on the most recent developments in this area, with particular emphasis on the reactions occurring in well-defined Donor-Spacer-Acceptor molecular systems. The goal is to provide the reader with the essential background to understand and possibly predict the feasibility and rates of these reactions, as well as to stimulate the application of the intramolecular dissociative ET concepts and related issues to still unexplored molecular systems.     

Advancing the Electrochemistry of the Hydrogen‐Evolution Reaction through Combining Experiment and Theory

The electrocatalytic hydrogen‐evolution reaction (HER), as the main step of water splitting and the cornerstone of exploring the mechanism of other multi‐electron transfer electrochemical processes, is the subject of extensive studies. A large number of high‐performance electrocatalysts have been developed for HER accompanied by recent significant advances in exploring its electrochemical nature. Herein we present a critical appraisal of both theoretical and experimental studies of HER electrocatalysts with special emphasis on the electronic structure, surface (electro)chemistry, and molecular design. It addresses the importance of correlating theoretical calculations and electrochemical measurements toward better understanding of HER electrocatalysis at the atomic level. Fundamental concepts in the computational quantum chemistry and its relation to experimental electrochemistry are also presented along with some featured examples.     

Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.     

Past, present, and future of applications of electroanalytical techniques in analytical and physical organic chemistry

After a brief introduction describing the main milestones in the development of DC polarography (DCP) as well as linear sweep (LSV) and cyclic voltammetry (CV), attention is paid to first applications of DCP in the reduction of organic compounds. In aqueous solutions the electron transfer (ET) is often accompanied by a proton transfer. Limiting currents in DCP enable investigation of kinetics of chemical reactions preceding ET. Dependence of the limiting current on concentration of a reagent, like H⁺ or OH^{??/sup> ions, enables determination of rate constants (k) of very fast reactions, with k values between 104 and 1010?L?mol???s??, comparable with those studied by relaxation methods. Application of CV is most advantageous for investigation of rates of chemical reactions following the ET. Comparison of analytical applications of DCP (reductions) with those of LSV (oxidations) is given. Apart from fast reactions taking place before the ET in the solution in the vicinity of the electrode surface, DCP can also be used for investigation of slower reactions, taking place in the bulk of the solution. Data obtained by DCP for determination of equilibrium (K) and rate (k) constants of reactions of organic compounds. Hence, DCP can be used in physical organic chemistry of solutions, in some cases complementing data obtained by UV–vis spectrophotometry. Some examples of determinations of K and k are given. Uncertain future of practical analytical applications of DCP and LSV is discussed as is the brighter future of applications in physical organic chemistry. As the main factor limiting successful applications is considered the limited opportunity for education of future research advisors in academia and group supervisors in industry.}     

Intermolecular electron transfer between coumarin dyes and aromatic amines in Triton-X-100 micellar solutions: evidence for Marcus inverted region

Photoinduced electron transfer (ET) between coumarin dyes and aromatic amines has been investigated in Triton-X-100 micellar solutions and the results have been compared with those observed earlier in homogeneous medium. Significant static quenching of the coumarin fluorescence due to the presence of high concentration of amines around the coumarin fluorophore in the micelles has been observed in steady-state fluorescence studies. Time-resolved studies with nanosecond resolutions mostly show the dynamic part of the quenching for the excited coumarin dyes by the amine quenchers. A correlation of the quenching rate constants, estimated from the time-resolved measurements, with the free energy changes (DeltaG0) of the ET reactions shows the typical bell shaped curve as predicted by Marcus outer-sphere ET theory. The inversion in the ET rates for the present systems occurs at an exergonicity (-DeltaG0) of approximately 0.7-0.8 eV, which is unusually low considering the polarity of the Palisade layer of the micelles where the reactants reside. Present results have been rationalized on the basis of the two dimensional ET model assuming that the solvent relaxation in micellar media is much slower than the rate of the ET process. Detailed analysis of the experimental data shows that the diffusional model of the bimolecular quenching kinetics is not applicable for the ET reactions in the micellar solutions. In the present systems, the reactions can be better visualized as equivalent to intramolecular electron transfer processes, with statistical distribution of the donors and acceptors in the micelles. A low electron coupling (Vel) parameter is estimated from the correlation of the experimentally observed and the theoretically calculated ET rates, which indicates that the average donor--acceptor separation in the micellar ET reactions is substantially larger than for the donor--acceptor contact distance. Comparison of the Vel values in the micellar solution and in the donor--acceptor close contact suggests that there is an intervention of a surfactant chain between the interacting donor and acceptor in the micellar ET reaction.     

Sampling Potential Energy Surfaces in the Condensed Phase with Many-Body Electronic Structure Methods

Sampling potential energy surfaces (PES) is pivotal for understanding chemical structure, energetics and reactivity and is of special importance for complex condensed-phase systems. Until recently such simulations based on electronic structure theory have been performed only by density functional theory and semiempirical methods. Many-body electronic structure methods, almost routinely used for molecules, have been practically unavailable for sampling PES in the condensed-phase. This has changed during the last few years, as efficient algorithms and software implementations for the evaluation of electronic energies and forces on atoms have been developed, allowing for geometry optimization, molecular dynamics and Monte-Carlo simulations, which was previously unthinkable. Herein, we introduce the theory and software developments and overview the applications in the field, the most encouraging results being obtained for aqueous chemistry. Requiring state-of-the-art computer resources PES sampling with many-body electronic structure methods in the condensed phase provides high-quality benchmarks and will gradually become more available due to fast progress in reduced scaling algorithms and computational technologies.     

Peculiar Photoinduced Electron Transfer in Porphyrin–Fullerene Akamptisomers

Porphyrin–fullerene dyads are promising candidates for organic photovoltaic devices. The electron-transfer (ET) properties of the molecular devices depend significantly on the mutual position of the donor and acceptor. Recently, a new type of molecular isomerism (akamptisomerism) has been discovered. In the present study, we explore how photoinduced ET can be modulated by passing from one akamptisomer to another. To this aim, four akamptisomers of the quinoxalinoporphyrin–[60]fullerene complex are selected for computational study. The most striking finding is that, depending on the isomer, the porphyrin unit in the dyad can act as either electron donor or electron acceptor. Thus, the stereoisomeric diversity allows one to change the direction of ET between the porphyrin and fullerene moieties. To understand the effect of akamptisomerism on the photoinduced ET processes, a detailed analysis of initial and final states involved in the ET is performed. The computed rate for charge separation is estimated to be in the region of 1–10 ns⁻¹. The formation of a long-living quinoxalinoporphyrin anion radical species is predicted.     

Electron correlation: the many-body problem at the heart of chemistry

The physical interactions among electrons and nuclei, responsible for the chemistry of atoms and molecules, is well described by quantum mechanics and chemistry is therefore fully described by the solutions of the Schr?dinger equation. In all but the simplest systems we must be content with approximate solutions, the principal difficulty being the treatment of the correlation between the motions of the many electrons, arising from their mutual repulsion. This article aims to provide a clear understanding of the physical concept of electron correlation and the modern methods used for its approximation. Using helium as a simple case study and beginning with an uncorrelated orbital picture of electronic motion, we first introduce Fermi correlation, arising from the symmetry requirements of the exact wave function, and then consider the Coulomb correlation arising from the mutual Coulomb repulsion between the electrons. Finally, we briefly discuss the general treatment of electron correlation in modern electronic-structure theory, focussing on the Hartree-Fock and coupled-cluster methods and addressing static and dynamical Coulomb correlation.