The line intensity and position calculations were carried out using a newly determined piecewise dipole moment function (DMF) in conjunction with the wavefunctions calculated from an experimentally determined potential energy function from Coxon & Hajigeorgiou. A direct-fit method that simultaneously fits all the reliable experimental rovibrational matrix elements has been used to construct the dipole moment function near equilibrium internuclear distance. In order to extend the amount and quality of input experimental parameters, new Cavity Ring Down Spectroscopy experiments were carried out to enable measurements of the lines in the 4-0 band with low uncertainty as well as the first measurements of lines in the 6-0 band. A new high-level ab initio DMF, derived from a finite field approach has been calculated to cover internuclear distances far from equilibrium. Accurate partition sums have been derived for temperatures up to 9000 K. In addition to air-and self-induced broadening and shift parameters, those induced by CO 2 and H 2 are now provided for planetary applications. A complete set of broadening and shift parameters was calculated based on sophisticated extrapolation of high-quality measured data. The line lists, which follow HITRAN formalism, are provided as supplementary material.

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Computer simulations of the effect of protein dynamics on the long distance tunneling mediated by the protein matrix have been carried out for a Ru-modified (His 126) azurin molecule. We find that the tunneling matrix element is a sensitive function of the atomic configuration of the part of the protein matrix in which tunneling currents (pathways) are localized. Molecular dynamics simulations show that f luctuations of the matrix element can occur on a time scale as short as 10 fs. These short time f luctuations are an indication of a strong dynamic coupling of a tunneling electron to vibrational motions of the protein nuclear coordinates. The latter results in a modification of the conventional Marcus picture of electron transfer in proteins. The new element in the modified theory is that the tunneling electron is capable of emitting or absorbing vibrational energy (phonons) from the medium. As a result, some biological reactions may occur in an activationless fashion. An analytical theoretical model is proposed to account for thermal f luctuations of the medium in long distance electron transfer reactions. The model shows that, at long distances, the phonon-modified inelastic tunneling always dominates over the conventional elastic tunneling.Electron transfer is an integral part of many biological processes, such as photosynthesis and respiration. Much effort, therefore, has been directed toward understanding transport properties of various biological materials. In particular, recent experimental studies have provided information on the distance and structural dependence of electron transfer rates in various natural and modified proteins (1-4). In these systems, electron transfer typically occurs over distances of 10-30 Å and is due to tunneling mediated by the intervening medium between donor and acceptor.It is commonly believed that fundamental principles of long distance electron transfer are essentially the same as those of any other electron transfer reaction (5). The only difference seems to be in the nature of electronic coupling; in short distance reactions, electronic orbitals of donor and acceptor directly overlap whereas in long distance reactions this coupling is indirect because of sequential overlaps of atomic orbitals of the donor, the intervening medium (bridge), and the orbitals of the acceptor. These sequential overlaps give rise to the concept of superexchange. It is assumed that all states in the bridging medium are virtual, i.e., there are no other resonant states in the system but those of donor and acceptor. The resonance between donor and acceptor occurs in the course of thermal fluctuations of the polar environment. The absence of real intermediate states and direct coupling physically means that electron transfer occurs via tunneling. In this picture, the overall rate of electron transfer is proportional to the frequency at which donor and acceptor states come to resonance and the probability to transfer an electron between donor and acceptor states at the transition state (i...

The effect of protein dynamics on the long-distance biological electron transfer reactions is discussed. Computer simulations reported recently by our group [Daizadeh, Medvedev, and Stuchebrukhov, Proc. Natl. Acad. Sci. USA 94, 3703 (1997)] have shown that in some cases a strong dynamic coupling of a tunneling electron to vibrational motions of the protein matrix can exist. This results in a modification of the conventional picture of electron transfer in proteins. The new element in the modified theory is that the tunneling electron is capable of emitting or absorbing vibrational energy (phonons) from the medium. As a result, some biological reactions may occur in an activationless fashion. In the present paper we study analytically the probabilities of such inelastic tunneling events and show how they affect the overall dependence of the reaction rate on the driving force, temperature, and the strength of electron–phonon coupling. Harmonic and anharmonic models are proposed for vibrational dynamics of the intervening medium.

Some proton pumps, such as cytochrome c oxidase (C(c)O), translocate protons across biological membranes at a rate that considerably exceeds the rate of proton transport to the entrance of the proton-conducting channel via bulk diffusion. This effect is usually ascribed to a proton-collecting antenna surrounding the channel entrance. In this paper, we consider a realistic phenomenological model of such an antenna. In our model, a homogeneous membrane surface, which can mediate proton diffusion toward the channel entrance, is populated with protolytic groups that are in dynamic equilibrium with the solution. Equations that describe coupled surface-bulk proton diffusion are derived and analyzed. A general expression for the rate constant of proton transport via such a coupled surface-bulk diffusion mechanism is obtained. A rigorous criterion is formulated of when proton diffusion along the surface enhances the transport. The enhancement factor is found to depend on the ratio of the surface and bulk diffusional constants, pK(a) values of surface protolytic groups, and their concentration. A capture radius for a proton on the surface and an effective size of the antenna are found. The theory also predicts the effective distance that a proton can migrate on the membrane surface between a source (such as CcO) and a sink (such as ATP synthase) without fully equilibrating with the bulk. In pure aqueous solutions, protons can travel over long distances (microns). In buffered solutions, the travel distance is much shorter (nanometers); still the enhancement effect of the surface diffusion on the proton flow to a target on the surface can be tens to hundreds at physiological buffer concentrations. These results are discussed in a general context of chemiosmotic theory.