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The light-harvesting chlorophyll (Chl) molecules of photosynthetic systems form the basis for light-driven energy conversion. In biological environments, the Chl chromophores occur in two distinct diastereotopic configurations, where the alpha and beta configurations have a magnesium-ligating histidine residue and a 17-propionic acid moiety on the opposite side or on the same side of the Chl ring, respectively. Although beta-ligated Chl dimers occupy conserved positions around the reaction center of photosystem I (PSI), the functional relevance of the alpha/beta configuration of the ligation is poorly understood. We employ here correlated ab initio calculations using the algebraic-diagrammatic construction through second order (ADC(2)) and the approximate second-order coupled cluster (CC2) methods in combination with the reduced virtual space (RVS) approach in studies of the intrinsic excited-state properties of alpha-ligated and beta-ligated Chl dimers of PSI. Our ab initio calculations suggest that the absorption of the alpha-ligated reaction-center Chl dimer of PSI is redshifted by 0.13-0.14 eV in comparison to the beta-ligated dimers due to combined excitonic coupling and strain effects. We also show that time-dependent density functional theory (TDDFT) calculations using range-separated density functionals underestimate the absorption shift between the alpha- and beta-ligated dimers. Our findings may provide a molecular starting point for understanding the energy flow in natural photosynthetic systems, as well as a blueprint for developing new molecules that convert sunlight into other forms of energy.

The interrelationship between the conventional thermodynamics and energetics has been discussed in detail. A number of flavors has been considered in the field of energetics, with the conclusion that the actual difference among all of them is rather superficial. A need to reconsider the foundations of thermodynamics and statistical physics has been pointed out. Such a re-consideration ought to facilitate formulating thermodynamics at any level of matter organization: from the microscopic through nano- and mesoscopic to the macroscopic one.

The history of the Meyer-Neldel rule's development and the initial collective efforts toward its comprehension have been described here. The whole story gives a nice occasion to trigger thorough analysis of the basic thermodynamic laws and looking for the true sense of the entropy notion.

Electron–ion collisions were studied for various protonated peptide monocations with disulfide bonds, using an electrostatic storage-ring equipped with a merged-electron-beam device. Resonant neutral particle emissions at the energies of 6–7 eV were observed, as well as a rise towards zero-energy, which are typical electron-capture dissociation profiles. The presence of disulfide (S–S) bonds tends to enhance the resonant bump heights. Chemical nature of the amino-acid residues adjacent to cysteines appears to correlate with the bump strength. Molecular-dynamical simulations help clarify the role of molecular vibration modes in the electron-capture dissociation process.

Nucleic acids and proteins are not only biologically important polymers. They have recently been recognized as novel functional materials surpassing conventional materials in many aspects. Although Herculean efforts have been undertaken to unravel fine functioning mechanisms of the biopolymers in question, there is still much more to be done. Here the topic of biomolecular charge transport is presented with a particular focus on charge transfer/transport in DNA and protein molecules. The experimentally revealed details, as well as the presently available theories, of charge transfer/transport along these biopolymers are critically reviewed and analyzed. A summary of the active research in this field is also given, along with a number of practical recommendations.

To rationalize coherence and mechanochemical aspects of proteins acting as molecular machines, a plasmon concept for dealing with protein nonequilibrium dynamics is introduced and tested with respect to thermodynamic consistency. A stochastic optimum-control theory for protein conformational diffusion is developed and the corresponding stochastic Newton's second law derived for optimum-controlled conformational diffusion in proteins. The plasmon concept is shown to be consistent with this theory, in that optical plasmons can pump entropy out of (or into) the protein, decreasing (or increasing) its conformational diffusion and, at the same time, help decrease intra- and intermolecular friction, as well as (potentially) break the symmetry of the latter. Instead, acoustic plasmons may break the spatial symmetry of a protein's "potential of mean force", thus converting it into an effective Brownian ratchet potential by applying quasistatic deformational corrections to the former. These concepts seem to be of rather general applicability and might also be useful when studying, for example, intercalation of cationic dyes into DNA duplexes, positively charged oligopeptide transduction through cell membranes, or even DNA translocation through nanopores.

In various chemical systems enthalpy-entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical phenomenon or a coincidence due to trivial mathematical connections between statistical-mechanical parameters or even simpler, a phantom effect resulting from the misinterpretation of experimental data. Here, we review EEC from a new standpoint and conclude that it may be rationalized in terms of hidden but physically real factors implying a Carnot-cycle model in which a micro-phase transition (MPT) plays a crucial role. Examples of such MPTs underlying physically valid EEC should be typically cooperative processes in supramolecular aggregates, like changes of structured water at hydrophobic surfaces, conformational transitions upon ligand-biopolymer binding, and so forth. The MPT notion could help rationalize the occurrence of EEC in connection with hydration and folding of proteins, functioning of molecular motors, and similar phenomena.

We investigate the influence of molecular motion on DNA conductance and charge transfer in the ballistic transport regime. We evaluate the conductance/charge transfer properties for ensembles of conformations representative of the molecular fluctuations in an explicit all-atom representation. We generate such ensembles by classical molecular dynamics (MD) and investigate the influence of conformational change on the charge transfer properties of the system. Using this approach, we can qualitatively explain the influence of base-pair mismatches on DNA electrical properties.

Electron-biomolecular ion collisions were studied using an electrostatic storage ring with a merging electron beam device. Biomolecular ions produced by an electrospray ion source and accelerated to 20 keV/charge were injected into the ring after being mass-analyzed. The circulating ion beam was then merged with an electron beam. Neutral reaction products in collisions of electrons with ions were detected by a micro-channel plate outside of the ring. Electron-ion collisions were studied for multiply-deprotonated oligonucleotide and peptide anions as well as singly protonated oligonucleotide and peptide cations. For peptide cations, neutrals were resonantly emitted at an electron energy of around 6.5 eV, which was almost independent of the ion masses. This is deduced to come from electron-ion recombination, resulting in the cleavage of a peptide bond. For DNA oligonucleotide cations, resonant neutral particle emission was also observed. In electron and DNA anion collisions, neutrals started to increase from definite threshold energies, where the threshold energies increased in proportion to the ion charge. The same was found for peptide anions. The origin of this phenomenon is discussed.

We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity the breather mobility in the latter case is comparatively restrained inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)-poly(dC) DNA molecules acts as a semiconducting nanowire and exhibits better conductance than poly(dA)-poly(dT) ones., Comment: 11 pages, 5 figures

Photodissociation of gas-phase orange I monoanions was studied by using an electrostatic storage ring. By comparing their wavelength spectra with those in the liquid phase and with theoretical predictions, it is deduced that the spectra originate from different tautomers of orange I monoanions.

In various chemical systems enthalpy-entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical phenomenon or a coincidence due to trivial mathematical connections between statistical-mechanical parameters - or even simpler: A phantom effect resulting from the misinterpretation of experimental data. Here, we review EEC from a new standpoint using the notion of correlation which is essential for the method of factor analysis, but is not conventional in physics and chemistry. We conclude that the EEC may be rationalized in terms of hidden (not directly measurable with the help of the current experimental set-up) but physically real factors, implying a Carnot-cycle model in which a micro-phase transition (MPT) plays a crucial role. Examples of such MPTs underlying physically valid EEC should be typically cooperative processes in supramolecular aggregates, like changes of structured water at hydrophobic surfaces, conformational transitions upon ligand-biopolymer binding, and so on, so forth. The MPT notion could help rationalize the occurrence of EEC in connection with hydration and folding of proteins,enzymatic reactions, functioning of molecular motors, DNA de- and rehybridization, as well as similar phenomena., 8 pages, 2 Figures, Submitted for publication

Some 80-90 years ago, George A. Linhart, unlike A. Einstein, P. Debye, M. Planck and W. Nernst, managed to derive a very simple, but ultimately general mathematical formula for heat capacity versus temperature from fundamental thermodynamic principles, using what we would nowadays dub a "Bayesian approach to probability". Moreover, he successfully applied his result to fit the experimental data for diverse substances in their solid state over a rather broad temperature range. Nevertheless, Linhart's work was undeservedly forgotten, although it represents a valid and fresh standpoint on thermodynamics and statistical physics, which may have a significant implication for academic and applied science.

Systematical differential calorimetry experiments on DNA oligomers with different lengths, and placed in water solutions with various added salt concentrations may, in principle, unravel important information about the structure and dynamics of the DNA and their water-counterion surrounding. With this in mind, to reinterpret the most recent results of calorimetric experiments on DNA oligomers; of such a kind, the recent enthalpy-entropy compensation theory has been used. It is demonstrated that the application of the latter could enable direct estimation of thermodynamic parameters of the microphase transitions connected to the changes in DNA dynamical regimes versus the length of the biopolymers and the ionic strengths of their water solutions, and this calls for much more systematical experimental and theoretical studies in this field.

Singlet electronic excitations of DNA duplex trimers and tetramers with regular homogeneous base-pair sequences ((dA)n·(dT)n and (dG)n·(dC)n, with n = 3, 4) have been investigated in vacuo using semiempirical quantum chemistry in a Zerner’s Intermediate Neglect of Differential Overlap (ZINDO) approximation. Frequencies, oscillator strengths, and single-electron assignments of many-electron transitions have been calculated as functions of all 12 possible conformational modes of DNA duplexes. Specific DNA conformational modes responsible for significant changes in the exciton parentage (onset or arrest of the charge-transfer excitons’ involvement into observable electronic transition spectra) are revealed. These computational results are thoroughly discussed in connection with numerous data of the most recent relevant experiments.

The physical-chemical sense of nonlinear entropy-enthalpy compensation based upon the standard thermodynamical parameters of high-temperature melting for doublet units in DNA duplexes has been considered. We are able to show that there are three, with no other constraints equally plausible, principal levels of DNA melting/hybridization description. First, DNA structure assembly/disassembly can be seen from the viewpoint of the conventional equilibrium thermodynamics without taking special care of the heat capacity DeltaC(p) value (by simply setting it equal to zero). Second, it is possible to assume that the DeltaC(p) is finite, but independent of temperature. At this approximation level the high-temperature DNA melting cannot be described, but only some special transition between metastable states of DNA duplexes in water solutions in the vicinity of ice melting point. Third, both the latter transition and the high-temperature DNA melting can be reproduced by one and the same approach, if the DeltaC(p) is assumed to be temperature dependent. These three approximation levels are equally justified from the nonlinear entropy-enthalpy compensation standpoint and by a generalized theory of temperature effects on themodynamical stability as is outlined here. Applicability of each of the approximation levels involved is discussed.

The controlled fabrication of actively switchable atomic-scale devices, in particular transistors, has remained elusive to date. Here, we explain the operation of an atomic-scale three-terminal device by a novel switching mechanism of bistable, self-stabilizing reconstruction of the electrode contacts at the atomic level: While the device is manufactured by electrochemical deposition, it operates entirely on the basis of mechanical effects of the solid-liquid interface. We analyze mechanically and thermally stable metallic junctions with a predefined quantized conductance of 1-5 G0 in experiment and atomistic simulation. Atomistic modeling of structural and conductance properties elucidates bistable electrode reconstruction as the underlying mechanism of the device. Independent room temperature operation of two transistors at low voltage demonstrates intriguing perspectives for quantum electronics and logics on the atomic scale.

The controlled fabrication of well-ordered atomic-scale metallic contacts is of great interest: it is expected that the experimentally observed high percentage of point contacts with a conductance at non-integer multiples of the conductance quantum G_0 = 2e^2/h in simple metals is correlated to defects resulting from the fabrication process. Here we demonstrate a combined electrochemical deposition and annealing method which allows the controlled fabrication of point contacts with pre-selectable integer quantum conductance. The resulting conductance measurements on silver point contacts are compared with tight-binding-like conductance calculations of modeled idealized junction geometries between two silver crystals with a predefined number of contact atoms.

We report the predictive de novo folding of three two-helix proteins using the free-energy protein forcefield PFF01. Starting from random initial conformations 40-90% of the members of the simulated ensembles converge to near-native conformations. The energetically lowest conformations approach the conserved part of the native conformations to within 1.64, 1.86, and 1.84 A for 1WQC, 1WQD, and 1WQE, respectively. An analysis of the low-lying conformations predicts the correct topology of the disulfide bridges, which are formed in additional simulations with a constraining potential. The free energy landscapes of these proteins are very simple, suggesting them as candidates for all-atom molecular dynamics simulations. In five independent simulations we find the formation of the correct secondary structure and several folding events into the tertiary structure.

Recent papers have considered moving breathers (MBs) in DNA models including long range interaction due to the dipole moments of the hydrogen bonds. We have recalculated the value of the charge transfer when hydrogen bonds stretch using quantum chemical methods which takes into account the whole nucleoside pairs. We explore the consequences of this value on the properties of MBs, including the range of frequencies for which they exist and their effective masses. They are able to travel through bending points with fairly large curvatures provided that their kinetic energy is larger than a minimum energy which depends on the curvature. These energies and the corresponding velocities are also calculated in function of the curvature., 4 pages and 4 figures

application/pdf, Electron-DNA anion collisions were studied using an electrostatic storage ring with a merging electron-beam technique. The rate of neutral particles emitted in collisions started to increase from definite threshold energies, which increased regularly with ion charges in steps of about 10 eV. These threshold energies were almost independent of the length and sequence of DNA, but depended strongly on the ion charges. Neutral particles came from breaks of DNAs, rather than electron detachment. The step of the threshold energy increase approximately agreed with the plasmon excitation energy. It is deduced that plasmon excitation is closely related to the reaction mechanism.

We have developed a theoretical formulation for evaluating the nonadiabatic electron-transfer (ET) rate constant in condensed medium which takes into account both inelastic electron tunneling and nuclear quantum effects. The derived formula allows us to calculate the ET rate as a function of the free-energy gap between the ET donor and acceptor states using the information on the spectral density associated with environmental polarization fluctuation and the temporal correlation function of electronic tunneling matrix element. Model calculations have been performed illustratively.

Electron-ion collisions have been studied for protonated and sodiated single-strand dinucleotide monocations with various base compositions and sequences by using an electrostatic storage ring equipped with a merged-electron-beam device. The plots of neutral-particle production rates against collision energy show typical electron-capture-dissociation profiles, which are characterized by an increase in the production rate at energies close to zero and a bump at high energies. The height of the resonant bumps varies with the number of Na+ ions as well as the base composition and sequence; in most cases, the height increases with the number of Na+ ions. Molecular mechanics and semiempirical quantum-chemical calculations suggest that the rate is correlated with various base-base interactions.