Bernard Levy

Ab initio Hartree-Fock instabilities in closed-shell molecular systems

The Hartree-Fock instability of twelve polyatomic systems is studied at theab initio level. It is found that all the systems with at least one double bond, exhibit a non-singlet instability. On the other hand instabilities of singlet type as well as instabilities of non-real type appear only in a small number of cases. The existence of these instabilities is discussed with respect to the location of low-lying excited states and to the weight of ionic structure.

Bond formation between positively charged species. Non-adiabatic analysis and valence-bond model in the CO2+ case

Abstract Ab initio MCSCF calculations of the potential energy curves of the first low-lying states of the CO 2+ dication have been performed. A localization procedure of MCSCF orbitals allows us to discuss the bond formation in the framework of valence-bond theory. The non-adiabatic curves corresponding to C + + O + , C 2+ + O and C + O 2+ are described using both orthogonal and non-orthogonal quasi-atomic orbitals, allowing us to re-examine the currently proposed models of bond formation between positively charged species.

Toward a qualitative understanding of the initial electron transfer site in Dawson-type heteropolyanions

EPR, NMR, optical spectra and electrochemistry experiments on an extended series of one-electron reduced Dawson-type heteropolyanions converge to support the conclusion that the equatorial (α1) tungsten atoms are first reduced in [P2W18O62]6−. This conclusion is reinforced, for instance, by the interpretation of the electrochemical behaviours of a series of [P2W18−xMoxO62]6− derivatives. In search for a rationale, the study of the electronic structure of such Dawson-type heteropolyanions by means of extended Huckel calculations provides a qualitative understanding of this reduction process. It is found that the lowest unoccupied molecular orbital (LUMO), which is likely to be involved in the initial electron transfer, is essentially “belt”-centred in [P2W18O62]6−. Also, the change of the reduction site (α1→α2) upon substitution in the “cap” region (α2 site) by a more electronegative metal centre (Mo for instance) is consistent with the localization of the LUMO on the substituted centre(s).

Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale

We have introduced a new algorithm in the parallel processing PMEMD module of the AMBER suite that allows MD simulations with a potential involving two coupled torsions. We have used this modified module to study the green fluorescent protein. A coupled torsional potential was adjusted on high accuracy quantum chemical calculations of the anionic chromophore in the first excited state, and several 15-ns-long MD simulations were performed. We have obtained an estimate of the fluorescence lifetime (2.2 ns) to be compared to the experimental value (3 ns), which is, to the best of our knowledge, the first theoretical estimate of that lifetime.

Cyan fluorescent protein carries a constitutive mutation that prevents its dimerization.

The tendency of GFP-like fluorescent proteins to dimerize in vitro is a permanent concern as it may lead to artifacts in FRET imaging applications. However, we have found recently that CFP and YFP (the couple of GFP variants mostly used in FRET studies) show no trace of association in the cytosol of living cells up to millimolar concentrations. In this study, we investigated the oligomerization properties of purified CFP, by fluorescence anisotropy and sedimentation velocity. Surprisingly, we found that CFP has a much weaker homoaffinity than other fluorescent proteins (K(d) ≥ 3 × 10(-3) M), and that this is due to the constitutive N146I mutation, originally introduced into CFP to improve its brightness.

The single T65S mutation generates brighter cyan fluorescent proteins with increased photostability and pH insensitivity.

Cyan fluorescent proteins (CFP) derived from Aequorea victoria GFP, carrying a tryptophan-based chromophore, are widely used as FRET donors in live cell fluorescence imaging experiments. Recently, several CFP variants with near-ultimate photophysical performances were obtained through a mix of site-directed and large scale random mutagenesis. To understand the structural bases of these improvements, we have studied more specifically the consequences of the single-site T65S mutation. We find that all CFP variants carrying the T65S mutation not only display an increased fluorescence quantum yield and a simpler fluorescence emission decay, but also show an improved pH stability and strongly reduced reversible photoswitching reactions. Most prominently, the Cerulean-T65S variant reaches performances nearly equivalent to those of mTurquoise, with QY  = 0.84, an almost pure single exponential fluorescence decay and an outstanding stability in the acid pH range (pK1/2 = 3.6). From the detailed examination of crystallographic structures of different CFPs and GFPs, we conclude that these improvements stem from a shift in the thermodynamic balance between two well defined configurations of the residue 65 hydroxyl. These two configurations differ in their relative stabilization of a rigid chromophore, as well as in relaying the effects of Glu222 protonation at acid pHs. Our results suggest a simple method to greatly improve numerous FRET reporters used in cell imaging, and bring novel insights into the general structure-photophysics relationships of fluorescent proteins.

Transmission Coefficients for Chemical Reactions with Multiple States: Role of Quantum Decoherence

Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.

Double-core ionization and excitation above the sulphur K-edge in , and

Experimental and theoretical results are reported on double-core excitation and ionization processes in some sulphur containing molecules. X-ray absorption spectra have been recorded at the sulphur K-edge using synchrotron radiation delivered by the DCI ring at LURE (Orsay, France). Absolute x-ray absorption cross sections have been determined for gas phase , and molecules in the 2400 - 2800 eV region. Several narrow features are observed far from the edge and assigned to double-core excited states. Two series of states are present corresponding to the triplet and singlet configurations, due to the core 1s - 2p exchange term. The energy, width and intensity of the features are strongly molecule dependent. In the case of , a theoretical determination of all the single- and double-core vacancy ionization potentials has been performed using a new theoretical approach which makes it possible to solve the convergence problem inherent in a simple SCF calculation. Results compare favourably with available experimental values. In particular, the singlet - triplet separation is correctly predicted for all the double-core ionized states. The relation between the double-core relaxation energies and the associated single-core relaxation values is discussed. Finally, the double-core excited state energies are determined within a Z + 2 core equivalent model, allowing a full assignment of the experimental spectra of .

Electron Transfer, Decoherence, and Protein Dynamics: Insights from Atomistic Simulations

Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system to leave the crossing region. In the framework of open quantum systems, τFC is a short time approximation of the characteristic decoherence time of the electronic subsystem in interaction with its nuclear environment. The comparison of the respective values of τcoh and τFC allows us to probe the occurrence of non-Condon effects. We use ab initio MD simulations to analyze how decoherence appears in several biological cofactors. We conclude that we cannot account for its order of magnitude by considering only the atoms or bonds directly concerned with the transfer. Decoherence results from contributions from all atoms of the system appearing with a time delay that increases with the distance from the primarily concerned atoms or bonds. The delay and magnitude of the contributions depend on the chemical nature of the system. Finally, we present recent developments based on constrained DFT for efficient and accurate evaluations of the electronic coupling in ab initio MD simulations. These are promising methods to study the subtle fluctuations of the electronic coupling and the mechanisms of electronic decoherence in biological systems.

New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses

Flavohemoglobins (FlavoHb) are metalloenzymes catalyzing the reaction of nitric oxide dioxygenation. The iron cation of the heme group needs to be preliminarily reduced to the ferrous state to be catalytically competent. This reduction is triggered by a flavin adenine dinucleotide (FAD) prosthetic group which is localized in a distinct domain of the protein. In this paper we obtain new insights into the internal long range electron transfer (over ca. 12 Å) using a combination of experimental and computational approaches. Employing a time-resolved pulse radiolysis technique we report the first direct measurement of the FADH˙→ HemeFe(III) electron transfer rate. A rate constant of (6.8 ± 0.5) × 10(3) s(-1) is found. A large panel of computational approaches are used to provide the first estimation of the thermodynamic characteristics of the internal electron transfer step within flavoHb: both the driving force and the reorganization energy are estimated as a function of the protonated state of the flavin semi-quinone. We also report an analysis of the electron pathways involved in the tunnelling of the electron through the aqueous interface between the globin and the flavin domains.