Contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic ligands with DNA

A method for calculation and analysis of the contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic compounds with DNA duplex has been developed. The results of calculations of the thermodynamic parameters (ΔG, ΔH, ΔS) indicate that changes in the translational and rotational degrees of freedom destabilize, and changes in the vibrational degree of freedom stabilize the complexes, the energy contribution from the movements under consideration being predominantly of entropic character. It is shown that the energy components of changes in translational, rotational, and vibrational degrees of freedom are in the main comparable with the experimentally determined thermodynamic parameters, which requires consideration of these components in the energy analysis of complex formation of aromatic molecules with DNA. It has been found that the total contribution of changes in translational, rotational, and vibrational degrees of freedom to the Gibbs energy of complexing of aromatic molecules with DNA can be assumed to be on the average the same for different ligands and equal to 8.2 kcal/mol.     

Pink splash of active nitrogen in the discharge afterglow

Results are presented from experimental studies of the glow dynamics of active nitrogen in the stage of its excitation by a current pulse and during the discharge afterglow. The mechanism is proposed for the generation of a light splash in a highly activated nitrogen after the end of its pulsed excitation. The key role in the generation of this splash is played by the D-V processes, by which the dissociation energy is transferred to the vibrational degrees of freedom in the course of recombination of nitrogen atoms, and the V-E processes, by which the vibrational energy of highly excited molecules N₂(X, v ≥ 25–27) is transferred to the emitting electronic states N₂(B, v) after the V-V delay. Results of simulations based on the mechanism proposed are also presented.     

Negative-polarity fast ionization wave in molecular gases: Electric field, electron density, and energy branching

The charge density per unit length, the longitudinal component of the electric field, and the electron density behind the front of a fast ionization wave initiated by a nanosecond negative voltage pulse in air, N₂, and H₂ in the 1-to 24-torr pressure range are reconstructed from the experimental data. It is shown that the electron density behind the wave front depends weakly on the sort of gas used and, at relatively high pressures (8–24 torr), is (2–3)×10¹² cm^?3. The energy deposited in the internal degrees of freedom is analyzed. It is shown that, for all gases used, most of the deposited energy (40–60%) is spent on the excitation of the electron degrees of freedom. The fraction of the energy deposited in the high-energy degrees of freedom (ionization and dissociation) monotonically decreases with increasing the pressure, whereas the fraction of the energy spent on the excitation of the low-energy degrees of freedom (rotational and vibrational) monotonically increases.     

How Far Does a Receptor Influence Vibrational Properties of an Odorant?

The biophysical mechanism of the sense of smell, or olfaction, is still highly debated. The mainstream explanation argues for a shape-based recognition of odorant molecules by olfactory receptors, while recent investigations suggest the primary olfactory event to be triggered by a vibrationally-assisted electron transfer reaction. We consider this controversy by studying the influence of a receptor on the vibrational properties of an odorant in atomistic details as the coupling between electronic degrees of freedom of the receptor and the vibrations of the odorant is the key parameter of the vibrationally-assisted electron transfer. Through molecular dynamics simulations we elucidate the binding specificity of a receptor towards acetophenone odorant. The vibrational properties of acetophenone inside the receptor are then studied by the polarizable embedding density functional theory approach, allowing to quantify protein-odorant interactions. Finally, we judge whether the effects of the protein provide any indications towards the existing theories of olfaction.     

Structure-based modeling of energy transfer in photosynthesis

We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment–protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton–vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.     

Investigation of the mechanism for rapid heating of nitrogen and air in gas discharges

A rapid heating of nitrogen-oxygen mixtures excited by gas discharges is investigated numerically with allowance for the following main processes: the reactions of predissociation of highly excited electronic states of oxygen molecules (which are populated via electron impact or via the quenching of the excited states of N₂ molecules), the reactions of quenching of the excited atoms O(¹ D) by nitrogen molecules, the VT relaxation reactions, etc. The calculated results adequately describe available experimental data on the dynamics of air heating in gas-discharge plasmas. It is shown that, over a broad range of values of the reduced electric field E/N, gas heating is maintained by a fixed fraction of the discharge power that is expended on the excitation of the electronic degrees of freedom of molecules (for discharges in air, η_E?28%). The lower the oxygen content of the mixture, the smaller the quantity η_E. The question of a rapid heating of nitrogen with a small admixture of oxygen is discussed.     

Vibrational spectrum of the lumi intermediate in the room temperature rhodopsin photo-reaction.

The vibrational spectrum (650-1750 cm(-1)) of the lumi-rhodopsin (lumi) intermediate formed in the microsecond time regime of the room-temperature rhodopsin (RhRT) photoreaction is measured for the first time using picosecond time-resolved coherent anti-Stokes Raman spectroscopy (PTR/CARS). The vibrational spectrum of lumi is recorded 2.5 micros after the 3-ps, 500-nm excitation of RhRT. Complementary to Fourier transform infrared spectra recorded at Rh sample temperatures low enough to freeze lumi, these PTR/CARS results provide the first detailed view of the vibrational degrees of freedom of room-temperature lumi (lumiRT) through the identification of 21 bands. The exceptionally low intensity (compared to those observed in bathoRT) of the hydrogen out-of-plane (HOOP) bands, the moderate intensity and absolute positions of C-C stretching bands, and the presence of high-intensity C==C stretching bands suggest that lumiRT contains an almost planar (nontwisting), all-trans retinal geometry. Independently, the 944-cm(-1) position of the most intense HOOP band implies that a resonance coupling exists between the out-of-plane retinal vibrations and at least one group among the amino acids comprising the retinal binding pocket. The formation of lumiRT, monitored via PTR/CARS spectra recorded on the nanosecond time scale, can be associated with the decay of the blue-shifted intermediate (BSI(RT)) formed in equilibrium with the bathoRT intermediate. PTR/CARS spectra measured at a 210-ns delay contain distinct vibrational features attributable to BSI(RT), which suggest that the all-trans retinal in both BSI(RT) and lumiRT is strongly coupled to part of the retinal binding pocket. With regard to the energy storage/transduction mechanism in RhRT, these results support the hypothesis that during the formation of lumiRT, the majority of the photon energy absorbed by RhRT transfers to the apoprotein opsin.     

Can giant chlorosomes be part of the light-harvesting antennae of green bacteria?

Some data on the structure and composition of chlorosomes are in conflict with their energy and kinetic characteristics. Among the latter is the very short excitation lifetime of the dominant pigment C740 in the 3D giant chlorosome (about 1000 pigment molecules per reaction center). Therewith the excitation transfer from C740 to baseplate bacteriochlorophyll B795 and further to the main membrane B860 can hardly be efficient. This result was obtained by modeling the energy migration between these pigment fractions in maximally optimized conditions. The possible reasons and mechanisms responsible for such strong nonphotochemical quenching of electronic excitations in the pigments of giant chlorosomes are substantiated and discussed.     

Means of optimizing light energy conversion in the primary stages of photosynthesis. II. Optimization of the structure of an uniform photosynthetic unit lattice

The possibility of optimization of the structure of a model photosynthetic unit lattice is analysed. The efficiency of the photosynthetic unit operation is evaluated from the time of excitation energy trapping by reaction centers. The calculations assume a F?rster inductive resonance mechanism for energy transfer within light--harvesting antenna and pairwise dipolar interactions. We use the probability matrix method which is adapted to excitation trapping time (but not to excitation jumps number) calculation. It is shown that the specific anisotropy of the distances between antenna molecules (which is in principle possible due to the diskshaped form of chlorophyll molecules) in combination with the optimal spatial arrangement of reaction centers as "well regulated clusters" allows to decrease the time of excitation energy trapping by over an order of magnitude. The requirements for optimization of the structure of a macroscopic photosynthetic unit lattice and the consequences following from them for the in vivo systems are formulated.     

An Adiabatic Molecular Dynamics Method for the Calculation of Free Energy Profiles

A new molecular dynamics method for calculating free energy profiles for rare events is presented. The new method is based on the creation of an adiabatic separation between the reaction coordinate subspace and the remaining degrees of freedom within a molecular dynamics run. This is achieved by associating with the reaction coordinate(s) a high temperature and large mass, thereby allowing the activated process to occur while permitting the remaining degrees of freedom to respond adiabatically. In this limit, by applying a formal multiple time scale Liouville operator factorization, it can be rigorously shown that the free energy profiles are obtained directly from the probability distribution of the reaction coordinate subspace and, therefore, require no postprocessing of the output data. The new method is applied to a variety of model problems and its performance tested against free energy calculations using the "bluemoon ensemble" approach. The comparison shows that free energy profiles can be calculated with greater ease and efficiency using the new method.     

Specific aspects of energy migration between chlorophyll molecules in the membranes of photosynthetic organisms

Several specific characteristics of energy migration in chlorophyll-protein complexes in vivo justify a suggestion of P.C. Knox to change two main equations of the theory on inductive resonance: to substitute a real lifetime of electronic excitations in donor molecules by the radiative lifetime. Critical distances for excitation migration of the main photosynthetic pigments become more stable constants; this results in appearance of more suitable formula for an average value of the mean time of intermolecular jumps of electronic excitations. In this context, the critical distances of homogenous energy migration within spectral fractions of purple bacterium, B800 and B850, were determined. The question on the possible application of Ferster’s theory to closely positioned molecules of chlorophyll and bacteriochlorophyll in vivo is also critically analyzed.     

A nonorthogonal tight-binding model for hydrocarbon molecules and nanostructures

In spirit of extended-Hückel approximations, we have developed a nonorthogonal tight-binding total energy model for hydrocarbons with only a few adjustable parameters. Our model reproduces the geometry structures, binding energies, on-site charge transfer and vibrational frequencies of a variety of hydrocarbon molecules reasonably well. Comparative calculations on carbon fullerenes and nanotubes using tight-binding model and density functional theory demonstrate the potential of applying this model to large scale simulations of carbon nanostructures.     

Stalk model of membrane fusion: solution of energy crisis.

Membrane fusion proceeds via formation of intermediate nonbilayer structures. The stalk model of fusion intermediate is commonly recognized to account for the major phenomenology of the fusion process. However, in its current form, the stalk model poses a challenge. On one hand, it is able to describe qualitatively the modulation of the fusion reaction by the lipid composition of the membranes. On the other, it predicts very large values of the stalk energy, so that the related energy barrier for fusion cannot be overcome by membranes within a biologically reasonable span of time. We suggest a new structure for the fusion stalk, which resolves the energy crisis of the model. Our approach is based on a combined deformation of the stalk membrane including bending of the membrane surface and tilt of the hydrocarbon chains of lipid molecules. We demonstrate that the energy of the fusion stalk is a few times smaller than those predicted previously and the stalks are feasible in real systems. We account quantitatively for the experimental results on dependence of the fusion reaction on the lipid composition of different membrane monolayers. We analyze the dependence of the stalk energy on the distance between the fusing membranes and provide the experimentally testable predictions for the structural features of the stalk intermediates.     

Intramolecular dielectric screening in proteins

This paper investigates the microscopic mechanisms of charge screening by proteins. For this purpose, we introduce the generalized susceptibility of a protein in response to a point charge, which is a scalar quantity dependent on position within the protein. The contribution to the susceptibility from atomic polarizabilities, associated with electronic degrees of freedom, is found to be highly uniform. By contrast, that from dynamic dipolar relaxation, associated with nuclear degrees of freedom, varies greatly between different regions of the protein. We investigate the possible r?le of this variation in the activity of proteins that interact functionally with charged species, and we formulate and test the hypothesis that this variation is correlated to functional activity. Model calculations give encouraging support to this hypothesis. The protein's dielectric properties are represented by a standard model in which electronic relaxation is described by a set of atomic polarizabilities, and dipolar relaxation is treated as a perturbation to normal mode dynamics. The model yields the desired susceptibility in closed form. Its obvious limitations are discussed. It is applied to several test systems, and is compared to various continuum models. Four model alpha-helices are considered, three of which play a r?le in vivo in the binding of charged ligands. We show that the intramolecular screening, and its spatial variation, can indeed play a part in this binding. The electron transfer between ferri- and ferrocytochrome c is considered. The dielectric relaxation of each molecule, associated respectively with its oxidation or its reduction, is known to be directly related to the activation free energy for the electron transfer reaction. Our analysis of the dielectric susceptibility will thus permit an estimate of this activation free energy. We show that the relaxation of the atomic positions ("dipolar relaxation") contributes 1 kcal/mol to this activation free energy, and that the molecule achieves this low value by providing a low dipolar susceptibility throughout its central part. In this case, the spatial variation of the susceptibility has a clear functional r?le.     

Fluorescence decay kinetics of chlorophyll in photosynthetic membranes

The absorption of light by the pigments of photosynthetic organisms results in electronic excitation that provides the energy to drive the energy-storing light reactions. A small fraction of this excitation gives rise to fluorescence emission, which serves as a sensitive probe of the energetics and kinetics of the excited states. The wavelength dependence of the excitation and emission spectra can be used to characterize the nature of the absorbing and fluorescing molecules and to monitor the process of sensitization of the excitation transfer from one pigment to another. This excitation transfer process can also be followed by the progressive depolarization of the emitted radiation. Using time-resolved fluorescence rise and decay kinetics, measurements of these processes can now be characterized to as short as a few picoseconds. Typically, excitation transfer among the antenna or light harvesting pigments occurs within 100 psec, whereupon the excitation has reached a photosynthetic reaction center capable of initiating electron transport. When this trap is functional and capable of charge separation, the fluorescence intensity is quenched and only rapidly decaying kinetic components resulting from the loss of excitation in transit in the antenna pigment bed are observed. When the reaction centers are blocked or saturated by high light intensities, the photochemical quenching is relieved, the fluorescence intensity rises severalfold, and an additional slower decay component appears and eventually dominates the decay kinetics. This slower (1-2 nsec) decay results from initial charge separation followed by recombination in the blocked reaction centers and repopulation of the excited electronic state, leading to a rapid delayed fluorescence component that is the origin of variable fluorescence. Recent growth in the literature in this area is reviewed here, with an emphasis on new information obtained on excitation transfer, trapping, and communication between different portions of the photosynthetic membranes.     

Femtosecond relaxation processes in <Emphasis Type="Italic">Rhodobacter sphaeroides</Emphasis> reaction centers

Energy relaxation was studied with difference femtosecond spectroscopy in reaction centers of the YM210L mutant of the purple photosynthetic bacterium Rhodobacter sphaeroides at low temperature (90 K). A dynamical long-wavelength shift of stimulated emission of the excited state of the bacteriochlorophyll dimer P was found, which starts simultaneously with P* formation and is accompanied by a change in the spectral shape of this emission. The characteristic value of this shift was about 30 nm, and the characteristic time about 200 fs. Difference kinetics ΔA measured at fixed wavelengths demonstrate the femtosecond shift of the P* stimulated emission appearing as a dependence of these kinetics on wavelength. We found that the reported long-wavelength shift can be explained in terms of electron-vibrational relaxation of the P* excited state with time constants of vibrational and electronic relaxation of 100 and 50 fs, respectively. Alternative mechanisms of the dynamical shift of the P* stimulated emission spectrum are also discussed in terms of energy redistribution between vibrational modes or coherent excitation of the modes.     

C60 binds to and deforms nucleotides

Atomistic molecular dynamics simulations are performed for up to 20 ns to monitor the formation and the stability of complexes composed of single- or double-strand DNA molecules and C60 in aqueous solution. Despite the hydrophobic nature of C60, our results show that fullerenes strongly bind to nucleotides. The binding energies are in the range -27 to -42 kcal/mol; by contrast, the binding energy of two fullerenes in aqueous solution is only -7.5 kcal/mol. We observe the displacement of water molecules from the region between the nucleotides and the fullerenes and we attribute the large favorable interaction energies to hydrophobic interactions. The features of the DNA-C60 complexes depend on the nature of the nucleotides: C60 binds to double-strand DNA, either at the hydrophobic ends or at the minor groove of the nucleotide. C60 binds to single-strand DNA and deforms the nucleotides significantly. Unexpectedly, when the double-strand DNA is in the A-form, fullerenes penetrate into the double helix from the end, form stable hybrids, and frustrate the hydrogen bonds between end-group basepairs in the nucleotide. When the DNA molecule is damaged (specifically, a gap was created by removing a piece of the nucleotide from one helix), fullerenes can stably occupy the damaged site. We speculate that this strong association may negatively impact the self-repairing process of the double-strand DNA. Our results clearly indicate that the association between C60 and DNA is stronger and more favorable than that between two C60 molecules in water. Therefore, our simulation results suggest that C60 molecules have potentially negative impact on the structure, stability, and biological functions of DNA molecules.     

Self-consistent simulation of pulsed and continuous microwave discharges in hydrogen

Results are presented from numerical simulations of pulse-periodic and continuous microwave discharges in hydrogen that are used in CVD reactors for chemical vapor deposition of diamond films. Attention is focused on the processes that should be taken into account in order to construct the simplest possible adequate numerical model. It is shown that the processes of vibrational excitation of hydrogen molecules, as well as chemical reactions, play an important role in the establishment of energy balance within the discharges. The results of numerical simulations are compared to the experimental data.