Buffer-assisted proton-coupled electron transfer in a model rhenium-tyrosine complex

The mechanism for tyrosyl radical generation in the [Re(P-Y)(phen)(CO)3]PF6 complex is investigated with a multistate continuum theory for proton-coupled electron transfer (PCET) reactions. Both water and the phosphate buffer are considered as potential proton acceptors. The calculations indicate that the model in which the proton acceptor is the phosphate buffer species HPO(4)2- can successfully reproduce the experimentally observed pH dependence of the overall rate and H/D kinetic isotope effect, whereas the model in which the proton acceptor is water is not physically reasonable for this system. The phosphate buffer species HPO4(2-) is favored over water as the proton acceptor in part because the proton donor-acceptor distance is approximately 0.2 A smaller for the phosphate acceptor due to its negative charge. The physical quantities impacting the overall rate constant, including the reorganization energies, reaction free energies, activation free energies, and vibronic couplings for the various pairs of reactant/product vibronic states, are analyzed for both hydrogen and deuterium transfer. The dominant contribution to the rate arises from nonadiabatic transitions between the ground reactant vibronic state and the third product vibronic state for hydrogen transfer and the fourth product vibronic state for deuterium transfer. These contributions dominate over contributions from lower product states because of the larger vibronic coupling, which arises from the greater overlap between the reactant and product vibrational wave functions. These calculations provide insight into the fundamental mechanism of tyrosyl radical generation, which plays an important role in a wide range of biologically important processes.     

Deuterium isotope effect of single vibronic levels in naphthalene

The isotope effect on the vibronic spectrum of naphthalene has been investigated under conditions of high resolution, enabling the resolution of individual vibronic states. Comparing the isotope effect for fixed vibronic states leads to an unexpected smoothing which is taken as evidence for a triplet communicating system, even though the singlet state is clearly not communicating.     

Nuclear Coordinate dependence of electronic transition moments in orbitally forbidden transitions: A new interpretation of deuterium isotope effects

The nuclear coordinate dependence of electronic transtion moments has been investigated for the purpose of finding new interpretations of deuterium isotope effects on spectral intensities and radiative decay rates in orbitally forbidden electronic transitions. By using “AO following nuclei” wavefunctions as the building block for the electronic wavefunction in the adiabatic BO vibronic wavefunction, the spin-free hamiltonian is diagonalized to generate eigenfunctions and eigen-energies. It is found that the electronic transtion moments based on these eigenfunctions show dependences upon the vibrational modes which are not directly involved in vibronic coupling. This leads to interpretations of the deuterium isotope effects in T₁ → S₀ radiative transitions of aromatic hydrocarbons and S₀ → S₁ absorption in pyrazine which are not based on the conventional Herzberg—Teller or non-BO coupling.     

Proton-coupled electron transfer in soybean lipoxygenase

The proton-coupled electron transfer reaction catalyzed by soybean lipoxygenase-1 is studied with a multistate continuum theory that represents the transferring hydrogen nucleus as a quantum mechanical wave function. The inner-sphere reorganization energy of the iron cofactor is calculated with density functional theory, and the outer-sphere reorganization energy of the protein is calculated with the frequency-resolved cavity model for conformations obtained with docking simulations. Both classical and quantum mechanical treatments of the proton donor-acceptor vibrational motion are presented. The temperature dependence of the calculated rates and kinetic isotope effects is in agreement with the experimental data. The weak temperature dependence of the rates is due to the relatively small free energy barrier arising from a balance between the reorganization energy and the reaction free energy. The unusually high deuterium kinetic isotope effect of 81 is due to the small overlap of the reactant and product proton vibrational wave functions and the dominance of the lowest energy reactant and product vibronic states in the tunneling process. The temperature dependence of the kinetic isotope effect is strongly influenced by the proton donor-acceptor distance with the dominant contribution to the overall rate. This dominant proton donor-acceptor distance is significantly smaller than the equilibrium donor-acceptor distance and is determined by a balance between the larger coupling and the smaller Boltzmann probability as the distance decreases. Thus, the proton donor-acceptor vibrational motion plays a vital role in decreasing the dominant donor-acceptor distance relative to its equilibrium value to facilitate the proton-coupled electron transfer reaction.     

Contrasts in the 77 K emission spectra, structures, and dynamics of metal-to-metal and metal-to-ligand charge-transfer excited states

The 77 K emission spectrum of trans-[(ms-Me6[14]aneN4)Cr(CNRu(NH3)5)2]5+ has components characteristic of ligand field (LF) and metal-to-metal charge transfer (MMCT) excited states (ms-Me6[14]aneN4=5,12-meso-5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane). The LF component of the emission is best resolved for irradiations at appreciably higher energies than the MMCT absorption band, while only the MMCT emission is observed for irradiations on the low-energy side of the MMCT absorption band. The LF emission component from this complex has vibronic structure that is very similar to that of the trans-[(ms-Me6[14]aneN4)Cr(CN)2]+ parent, but it is red-shifted by 560 cm-1 and the bandwidths are much larger. The red shift and the larger bandwidths of the ruthenated complex are attributed to configurational mixing between the LF and MMCT excited states, and the inferred mixing parameters are shown to be consistent with the known electron-transfer properties of the Ru(NH3)5 moieties. The MMCT excited-state lifetime is about 1 micros at 77 K and am(m)ine perdeuteration of this complex leads to an isotope effect of kNH/kND approximately 15-20. However, the contribution of the N-H stretching vibration to the emission sideband is too weak for a single vibrational mode model to be consistent with the observed lifetimes or the isotope effect. These features are very similar to those reported previously (J. Phys. Chem. A 2004, 108, 5041) for the MMCT emission of trans-[([14]aneN4)Cr{CNRu(NH3)5}2]5+ ([14]aneN4=1,4,8,11-tetraazacyclotetradecane), with the exception that the higher energy LF emission was not well resolved in the earlier work. The energies of the charge transfer absorption and emission maxima of both of these Cr(CN)Ru complexes are very similar to those of [Ru(NH3)4bpy]2+, but the latter has a 50-fold shorter 77 K excited-state lifetime, a 10-fold smaller NH/ND isotope effect, and a very different structure of its vibronic sidebands. Thus, the vibronic sidebands imply that the dominant excited-state distortions are in the metal-ligand vibrational modes for the Cr(CN)Ru complexes and in the bipyridine vibrational modes for the [Ru(NH3)4bpy]2+ complex. While an "equivalent" single vibrational mode model based on the frequencies and amplitudes of the dominant distortion modes is not consistent the observed lifetimes, such models do appear to be a good basis for qualitatively distinguishing different classes of excited-state dynamic behavior. A multimode, multichannel model may be necessary to adequately describe the excited-state dynamics of these simple electron-transfer systems.     

Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects

The dynamical behavior and the temperature dependence of the kinetic isotope effects (KIEs) are examined for the proton-coupled electron transfer reaction catalyzed by the enzyme soybean lipoxygenase. The calculations are based on a vibronically nonadiabatic formulation that includes the quantum mechanical effects of the active electrons and the transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. The rate constant is represented by the time integral of a probability flux correlation function that depends on the vibronic coupling and on time correlation functions of the energy gap and the proton donor-acceptor mode, which can be calculated from classical molecular dynamics simulations of the entire system. The dynamical behavior of the probability flux correlation function is dominated by the equilibrium protein and solvent motions and is not significantly influenced by the proton donor-acceptor motion. The magnitude of the overall rate is strongly influenced by the proton donor-acceptor frequency, the vibronic coupling, and the protein/solvent reorganization energy. The calculations reproduce the experimentally observed magnitude and temperature dependence of the KIE for the soybean lipoxygenase reaction without fitting any parameters directly to the experimental kinetic data. The temperature dependence of the KIE is determined predominantly by the proton donor-acceptor frequency and the distance dependence of the vibronic couplings for hydrogen and deuterium. The ratio of the overlaps of the hydrogen and deuterium vibrational wavefunctions strongly impacts the magnitude of the KIE but does not significantly influence its temperature dependence. For this enzyme reaction, the large magnitude of the KIE arises mainly from the dominance of tunneling between the ground vibronic states and the relatively large ratio of the overlaps between the corresponding hydrogen and deuterium vibrational wavefunctions. The weak temperature dependence of the KIE is due in part to the dominance of the local component of the proton donor-acceptor motion.     

Unraveling the A(1)B1 <-- X(1)A1 spectrum of CCl2: The Renner-Teller effect, barrier to linearity, and vibrational analysis using an effective polyad Hamiltonian

We report studies aimed at unraveling the complicated structure of the CCl 2 A (1)B 1 <-- X (1)A 1 system. We have remeasured the fluorescence excitation spectrum from approximately 17,500 to 24,000 cm (-1) and report the term energies and A rotational constants of many new bands for both major isotopologues (C (35)Cl 2, C (35)Cl (37)Cl). We fit the observed term energies to a polyad effective Hamiltonian model and demonstrate that a single resonance term accounts for much of the observed mixing, which begins approximately 1300 cm (-1) above the vibrationless level of the A (1)B 1 state. The derived A (1)B 1 vibrational parameters are in excellent agreement with ab initio predictions, and the mixing coefficients deduced from the polyad model fit are in close agreement with those derived from direct fits of single vibronic level (SVL) emission intensities. The approach to linearity and thus the Renner-Teller (RT) intersection is probed through the energy dependence of the A rotational constant and fluorescence lifetime measurements, which indicate a barrier height above the vibrationless level of the X (1)A 1 state of approximately 23,000-23,500 cm (-1), in excellent agreement with ab initio theory.     

Estimation of the contribution of vibronic interaction to the isotope effect on the nuclear magnetic shielding constant of a hydrogen bridge

A nonadiabatic correction to the H/D isotope effect on the constant of electronic magnetic shielding of a nucleus was estimated within the framework of the first-order perturbation theory. The procedure consists in the ab initio calculation of frequencies and relative intensities in the vibronic spectrum for H and D forms of a molecule taking into account only the transitions allowed in the magnetic-dipole approximation. With the elementary assumptions (case of Herzberg vibronic interaction), the semiquantitative estimation of adiabatic (geometrical) and nonadiabatic contributions to the H/D isotope effect on the ¹⁵N shielding constant of a complex with the HF-pyridine hydrogen bond was carried out. These two contributions to the isotope effect are comparable in the order of magnitude, at least for unsaturated molecules with low-lying excited electronic states. A correct solution to the problem requires ab initio calculation that is not based on the Born-Oppenheimer approximation.     

An ab initio study of the hyperfine structure in the X2 Pi electronic state of CCCH

The results of an ab initio study of the magnetic hyperfine structure in the X (2)Pi electronic state of CCCH are reported. The potential surfaces for two components of the X (2)Pi electronic state were computed by means of an extensive configuration interaction approach. The electronically averaged hyperfine coupling constants of H and (13)C for (12)C (12)C (12)CH, (13)C (12)C (12)CH, (12)C (13)C (12)CH, and (12)C (12)C (13)CH are obtained as functions of two bending vibrational modes by the density functional theory method. The vibronic wave functions are calculated with the help of a variational approach which takes into account the Renner-Teller effect and spin-orbit coupling. The model Hamiltonian is expressed in terms of the normal bending coordinates. It is found that, due to the generally strong geometry dependence of the hyperfine coupling constants, it is necessary to carry out the vibronic averaging of the corresponding functions in order to obtain the values which can be compared to the results of the measurements. The results of the present study help to reliably interpret the experimental data previously published. They also predict the yet unobserved hyperfine structure in excited vibronic states.     

Polarization and assignment of the two-photon excitation spectrum of benzene vapor

The two-photon excitation (TPE) of benzene fluorescence in the vapor phase at 60 torr is reported for the total-energy region from 38 086 cm^?1 to 42 441 cm^?1 using both circular and linear polarized light from a nitrogen-pumped dye-laser. The theory of the polarization dependence of the vibronic transitions in benzene is briefly reviewed, and it is seen how transitions involving vibrations of b_1u symmetry are expressly forbidden for this type of TPE experiment in which the two photons are identical. Five vibronic origins with distinctive rotational contours and polarization dependence are identified in the TPE spectrum. The υ₁₄(b_2u) vibronic origin at 1570 cm^?1 (above the electronic origin of the ^IB_2u state) stands out very prominently in the linear polarized spectrum, but nearly disappears in the circular polarized spectrum. This striking polarization dependence indicates a significant contribution of A_2u electronic states to the intermediate states of this TPE vibronic transition. The relatively great strength of the υ₁₄ band may be due to vibronic borrowing by the b_2u mode from the ground electronic state (A_1g).     

Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase

The origin of the temperature dependence of kinetic isotope effects (KIEs) in enzyme reactions is a problem of general interest and a major challenge for computational chemistry. The present work simulates the nuclear quantum mechanical (NQM) effects and the corresponding KIE in dihydrofolate reductase (DHFR) and two of its mutants by using the empirical valence bond (EVB) and the quantum classical path (QCP) centroid path integral approach. Our simulations reproduce the overall observed trend while using a fully microscopic rather than a phenomenological picture and provide an interesting insight. It appears that the KIE increases when the distance between the donor and acceptor increases, in a somewhat counter intuitive way. The temperature dependence of the KIE appears to reflect mainly the temperature dependence of the distance between the donor and acceptor. This trend is also obtained from a simplified vibronic treatment, but as demonstrated here, the vibronic treatment is not valid at short and medium distances, where it is essential to use the path integral or other approaches capable of moving seamlessly from the adiabatic to the diabatic limits. It is pointed out that although the NQM effects do not contribute to catalysis in DHFR, the observed temperature dependence can be used to refine the potential of mean force for the donor and acceptor distance and its change due to distanced mutations.     

Xanthone. II. Vibronic coupling analysis from high resolution phosphorescence spectra

High resolved phosphorescence spectra of xanthone have been recorded in four host matrices in order to study vibronic coupling between the lowest tripl origin in all hosts, and the energetically close-lying second triplet state T₂, which is of nπ* orbital origin. In three hosts, there is thermall to phosphorescence from T₁. Vibrational analyses of the two emissions are reported. The vibrational structure of both emissions depends little on t vibronic mixing between the lowest two triplet states is weak, in spite of the small energy separation in some hosts. The importance of the different i ₁ and its sublevels is discussed, and it is concluded that across energy separations smaller than about 200 cm^?1 spin—orbit mixing is more orbital mixing between the ³ππ* and ³nπ* configurations of xanthone.     

Near Resonance vibronic coupling. Isoquinoline

The interaction spectrum is considered resulting from the near-resonance coupling of a small number of vibronic levels of two different electronic states. In the simple model proposed, the interactions between the near-resonance states are first explicitly considered and then the off-resonance interactions are treated by perturbation theory. The model is applied to the isoquinoline spectrum and it is shown that for isoquinoline the latter interactions may be safely ignored. Good agreement is achieved between the theoretical and experimental spectra, and many puzzling features, such as the irregular nature of the sequence structure and the ambiguous isotope effects are readily explained. The lowest excited singlet state is the nπ*, and it is located within about 1000 cm^?1 of the first excited ¹ππ*. Two vibronic levels of the ¹nπ* state, corresponding to single quanta of the out-of-plane vibrations, are in near-resonance with the vibrationless ¹ππ* level.     

Analysis of pseudo jahn–teller distortion based on natural bond orbital theory: Case study for silicene

Ground state (GS) instability of nondegenerate molecules in high symmetric structures is understood through Pseudo Jahn–Teller mixing of the electronic states through the vibronic coupling. The general approach involves setting up of a Pseudo Jahn–Teller (PJT) problem wherein one or more symmetry allowed excited states couple to the GS to create vibrational instability along a normal mode. This faces two major complications namely (1) estimating the adiabatic potential energy surfaces for the excited states which are often difficult to describe in case the excited states have charge-transfer or multi-excitonic (ME) character and (2) finding out how many such excited states (all satisfying the symmetry requirements for vibronic coupling) of increasing energies need to be coupled with the GS for a particular PJT problem. An analogous alternative approach presented here for the well-known case of symmetry breaking of planar (D_6h) hexasilabenzene (Si₆H₆) to the buckled (D_3d) structure involves identifying the second-order donor–acceptor, hyperconjugative interactions (E²_{i → j}) that stabilize the distorted structure. Following the recent work of Nori-Shargh and Weinhold, one observes that the orbitals involved in the vibronic coupling between the S₀/S_n states and those for the donor (filled)–acceptor (empty) interactions are identical. In fact, deletion of any particular pair of E²_{i → j} interaction creates vibrational instability in the buckled structure and as a corollary, deleting it for the planar structure removes its instability. The one-to-one correlation between the natural bond orbital theory and PJT theory assists in an intuitive identification of the relevant (few) excited states from a manifold of computed ones that cause symmetry breaking by vibronic coupling. © 2019 Wiley Periodicals, Inc.     

Vibronic spectral behaviour of molecules. Theoretical analysis of the biphenyl phosphorescence

The calculated vibronic structure of the phosphorescence of biphenyl is presented and compared with the experimental spectrum. An assignment of the vibronic transitions for the main peaks is given. The comparison between theory and experiment is satisfactory.     

Charge-transfer transitions in triarylamine mixed-valence systems: a joint density functional theory and vibronic coupling study

A theoretical model is developed to describe the intramolecular transfer in organic mixed-valence systems. It is applied to rationalize the intervalence charge-transfer transitions in triarylamine mixed-valence compounds. The electronic coupling parameter is evaluated at the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels. The shapes of the charge-transfer absorption bands are analyzed in the framework of a dynamic vibronic model. The influence on the optical properties of diagonal and nondiagonal vibronic couplings is discussed. Our results are compared to recent experimental data.     

A Chemist's View of BCS Theory for Low Tc Superconductivity and Its Relationship to Charge Transfer and High Tc Superconductivity

Based on a chemist's understanding of electron transfer, attempts are made to interpret the physicists' BCS theory for low Tc superconductivity in terms of quantum chemical views. To show how to improve and apply some of the principles of the BCS theory for high Tc superconductors, especially those having to do with many-body aspects of correlation, coherence and long-range order, we (1) extend the two-partner, donor-acceptor electron transfer to large periodic systems with cyclic boundary conditions and with double-well potentials beyond Peierls distortion. (2) introduce second-order Jahn-Teller stabilization and introduce vibronic mixing as configuration interaction. To take advantage of existing bonds in high Tc superconductors we propose a linear combination of bonding (two-electron) geminals to form molecular bonding geminals which we call “Vibronic Geminals” after mixing with different running waves of bond structure vibrations. To take advantage of the valence bonds and double-well potentials due to anti-symmetric and other vibrations, we propose a ‘Covalon’ type model for the propagation and tunneling of such bonds which transform as Bosons.     

Potential energy surface, van der Waals motions, and vibronic transitions in phenol-argon complex

The structure and intermolecular vibrational energy levels of the phenol-Ar complex are calculated from its potential energy surface. This surface is constructed from a large set of the interaction energy values computed using second-order Moller-Plesset perturbation theory with the augmented correlation consistent polarized valence double-zeta basis set. The global minimum in the potential energy surface corresponds to a cluster structure with Ar located over the geometric center of the phenol ring at a distance of 3.510 A and shifted by 0.1355 A towards oxygen. The calculated dissociation energy of 371 cm(-1) is in accordance with the experiment. Additional local minima higher in energy are with Ar placed in the phenol plane. However, they are too shallow to form the bound states corresponding to planar isomers. The deformation of the potential energy surface shape, created by the interaction of Ar with the phenolic oxygen, is responsible for a pronounced intermode mixing. As a result, a set of hybrid stretching-bending states appears which cannot be described in terms of the standard models. The intermode coupling is reflected in the vibronic structure of the S1-S0 electronic transition. The intensities of the vibronic bands are calculated from the electronic transition dipole moment surfaces determined using the ab initio single-excitation configuration interaction method. They allow us to correct and complete the assignment of the spectra observed in phenol-Ar, as well as in the analogous complexes of phenol with Kr and Xe.     

Method for evaluating the probability of structural isomer-isomer transformations with large numbers of quasidegenerations of the energy levels of the interactant subsystems

It is shown how the theory developed by the author and regarding the structural transformations of molecules as the result of the resonance mixing between the vibronic wave functions of the corresponding states of subsystems can be extended to the case with an arbitrary number of the resonant and quasiresonant energy levels.     

Effect of pressure on coupled electronic ground and excited states determined from luminescence spectra of trans-dioxorhenium(V) complexes

Pressure-dependent luminescence spectra of trans-dioxo complexes of rhenium(V) with ancillary ethylenediamine ligands exhibit resolved vibronic structure in the O=Re=O symmetric stretching mode at room temperature. The intensity distribution within the vibronic progression changes with pressure, leading to band shapes that are also pressure-dependent. These spectroscopic features arise from coupled electronic states and depend on the energy differences between ground and excited states, which vary by 2500 cm(-1) for the three complexes with ethylenediamine, tetramethylethylenediamine, and tetraethylethylenediamine ancillary ligands. We describe the pressure-dependent vibronic structure and band shapes with anharmonic adiabatic potential energy surfaces for the ground states of all complexes. The calculated spectra reveal the pressure dependence of the energies of electronic origins, luminescence band maximums, offsets between ground- and emitting-state potential minimums, and vibrational frequencies. The largest pressure effects are observed where the coupled electronic states are close in energy.