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More than 100 years ago a Swedish schoolteacher Nils Engelbrektsson could theoretically derive the thermodynamic equation of state, which is universally valid. His colleague, a Swedish schoolteacher Karl Franzen had experimentally verified his inferences and could prove their validity. About hundred years of fierce struggle to persuade the colleagues do finally bring the desiderated victory to Nils and Karl: their trains of thoughts do deserve our careful looking at them. That is just the main idea behind the translation at hand [1. E. B. Starikov (2019) A Different Thermodynamics and Its True Heroes, Jenny Stanford Publishing, Singapore; 2. Entropy-Enthalpy Compensation: Finding a Methodological Common Denominator through Probability, Statistics, Physics, E. B. Starikov, Bengt Norden, Shigenori Tanaka, Editors; Jenny Stanford Publishing, Singapore, 2020].

Around two hundred years of thermodynamics’ history have been re-analyzed. The priority of thermodynamics by Carnot for the modern scientific research has been stressed.

Modern thermodynamics is a unique but still not a logically self-consistent field of knowledge. It has a proven universal applicability and significance but its actual potential is still latent. The development of the foundations of thermodynamics was in effect non-stop but absolutely no one has any idea about this. This book is the first of its kind that will motivate researchers to build up a logically consistent field of thermodynamics. It greatly appreciates the actual depth and potential of thermodynamics which might also be of interest to readers in history and philosophy of scientific research. The book presents the life stories of the protagonists in detail and allows readers to cast a look at the whole scene of the field by showcasing a significant number of their colleagues whose works have fittingly complemented their achievements. It also tries to trigger a detailed analysis of the reasons why the actual work in this extremely important field has in effect gone astray. It comprises five chapters and introduces three scientists in the first two chapters, which are specifically devoted to the Scandinavian achievements in macroscopic thermodynamics. These introductions are novel and call for a detailed reconsideration of the field. The third chapter acquaints the readers with their fourth colleague in Germany who was working on the proper link between the macroscopic thermodynamics, kinetics, and the atomistic representation of matter. The fourth chapter brings in their fifth colleague in the United States who could formally infer the famous formula S = k * ln(W), ingeniously guessed by Ludwig Boltzmann, and thus clarify the physical sense of the entropy notion. The last chapter summarizes the above-mentioned discourses.

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.

If the physically–chemically valid entropy–enthalpy compensation (EEC) could be revealed in experiments, what are then its actual mechanisms at the atomic/molecular level? This problem is being intensively studied by many authors recently. Here, the most recent advances and the problems emerging are analyzed.

It is presently well recognised that the concept of entropy can be formulated in many different ways-and this is definitely dependent on the problem to be solved. Does this fact really mean that the entropy-enthalpy compensation underlying physically/chemically valid iso-kinetic, iso-selective, iso-equilibrium relationships immediately loses its interpretational value? By invoking the well forgotten (and sometimes even simply unknown!) work by G.A. Linhart, we would like to demonstrate that in effect entropy's anthropomorphicity opens interesting interpretational opportunities.

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.

Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion–hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion–hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA–protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA–protein molecular machines via symmetry breaking in DNA–protein friction.

Huntington's disease patients commonly have glutamine (Q) repeats longer than 37 residues in the Huntingtin protein. This unusual protein will misfold and aggregate to form insoluble amyloid-like fibrils. Although the determination of polyQ structure is very important for elucidation of the aggregation mechanism, this has not yet been accomplished due to the experimental difficulties. In this study, we performed in silico mutation analysis to examine the stability of polyQ peptide on the basis of the beta-helix structure which is known as a possible model. From the results of molecular dynamics simulations for 10ns, some mutant models were found to be unstable, and their stabilities were largely dependent on the position of replaced residues. Besides, to examine the relationship between the aggregation mechanism of polyQ and the stability of the corresponding monomer, we constructed trimer models. Through the trimer studies, we confirmed that the stability of the monomer contributes significantly to that of the oligomer, and found that some mutant polyQs have the ability to inhibit polyQ aggregation. Furthermore, we estimated the free energies in solution and the conformational entropic contributions with normal mode analysis. The entropic contributions were not exhibiting remarkable differences between the models under study compared to the differences in the free energies in solution. Supposing that the stability of monomer is associated with aggregation process, the beta-helix structure has been found to be somewhat inconsistent with the experimental results in this study. Our results thus indicate the necessity for the revalidation of the beta-helix model.

Dependence of charge transmission through several experimentally studied DNA duplexes on their lowest-frequency acoustic modes, combined with the molecular dynamics in picosecond characteristic time range, has been studied. Based on this analysis we were able to identify the specific acoustic modes responsible for the noticeable increase in DNA charge transmission. Other factors influencing electric properties of DNA duplexes are discussed.

Electron–monocation collisions for protonated and sodiated single-stranded dinucleotides with various base compositions and sequences have been studied using an electrostatic storage ring equipped with a merging-electron-beam device. Resonant neutral-particle emissions have been observed at a collision energy of 4–5 eV. The strength of the resonant bumps changes depending on the number of sodium, as well as the DNA base composition and sequence, which mostly increases with an increase in number of sodium. The results were compared with theoretical structures generated and studied by molecular mechanics and semiempirical quantum-chemistry calculations. It is deduced that the rate correlates with various base–base interactions.

We scrutinize the available (seemingly disparate) theories of protein folding and propose a new concept which brings them under one roof. First, we single out dipole–dipole coupling within protein backbone as the main reason for intrinsic double-well nature of the protein potential. Then, protein folding as a whole ought to be (at least) a two-stage process, namely: (a) both amino-acid side chains and solvent enslave the dynamics of the backbone to reach the folding transition state with the help of stochastic resonance, and (b) the backbone funnels the whole protein into the global potential energy minimum by enslaving the dynamics of the amino-acid side chains plus solvent, and simultaneously arresting the stochastic resonance prerequisites to lock the protein in its folded state. The latter is accomplished owing to the concerted action of the protein compactization (enthalpic contribution) and thermal motion intensification (entropic contribution), which is, in fact, a physical hallmark of enthalpy–entropy compensation.

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.

It is known that Huntington's disease patients commonly have glutamine (Q) repeat sequences longer than a critical length in the coding area of Huntingtin protein in their genes. As the polyglutamine (polyQ) region becomes longer than the critical length, the disease occurs and Huntingtin protein aggregates, both in vitro and in vivo, as suggested by experimental and clinical data. The determination of polyglutamine structure is thus very important for elucidation of the aggregation and disease mechanisms. Here, we perform molecular dynamics calculations on the stability of the structure based on the beta-helix structure suggested by Perutz et al. (2002) [Perutz, M.F., Finch, J.T., Berriman, J., Lesk, A., 2002. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. USA 99, 5591]. We ensure that perfect hydrogen bonds are present between main chains of the beta-helix based on the previous studies, and perform simulations of stretches with 20, 25, 30, 37 and 40 glutamine residues (20Q, 25Q, 30Q, 37Q and 40Q) for the Perutz models with 18.5 and 20 residues per turn (one coil). Our results indicate that the structure becomes more stable with the increase of repeated number of Q, and there is a critical Q number of around 30, above which the structure of the Perutz model is kept stable. In contrast to previous studies, we started molecular dynamics simulations from conformations in which the hydrogen bonds are firmly formed between stacked main chains. This has rendered the initial beta-helix structures of polyQ much more stable for longer time, as compared to those proposed previously. Model calculations for the initial structures of polyQ dimer and tetramer have also been carried out to study a possible mechanism for aggregation.

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.

Electron-ion collisions have been studied for various protonated and alkali-metal adducted peptide monocations, using an electrostatic storage ring. Neutral particle production rates vs. collision energy show typical electron-capture-dissociation profiles for all of the protonated peptides and some of alkali-metal adducted peptides, which consist of a rise towards zero-energy and a bump at high energies. The rate is often enhanced by adducting lithium or sodium cation to peptides compared to the protonated ones. For the alkali-metal adducted cations, the rate correlates with the strength of the non-covalent π–cation interaction. Molecular mechanics and quantum-chemical computations performed here help explain these results.

In spite of the numerous experimental and theoretical studies on green fluorescent protein and its modifications, there is still no definitive answer to the central question: why such systems exhibit enhanced fluorescence. Based upon detailed quantum-chemical estimations, we advocate the following hypothesis. In the green fluorescent protein ground electronic state, the protein surrounding strains the chromophore with respect to its native intramolecular conformational preference in vacuo or in solution. Absorbing a photon of the proper wavelength not only causes a joint proton–electron transfer in and around the chromophore, but also increases the intrinsic strain of the latter. Since conformational relaxation of such a structure will not require any additional energy input, the energy gained by the chromophore cannot be dissipated into the chromophore's internal non-radiative degrees of freedom, and thus it returns as a fluorescence emission.

Electron-cation collisions have been studied for various protonated deoxyoligonucleotide monocations, using an electrostatic storage ring equipped with a merged-electron-beam device. Resonant neutral-particle emissions have been observed at a collision energy of about 4.5 eV for some of them. The resonance parameters depend on DNA base composition and sequence, and the resonances occur only in oligonucleotide monocations with base stacking. The resonance widths increase with oligonucleotide length, but saturate at trimers. Quantum-chemical estimations performed here help explain these results.

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.

The coupling of all twelve possible conformational modes of DNA duplexes and four pair-wise correlations among them to positive charge (hole) motion through these biopolymers has been systematically analysed in regular homogeneous B-DNA trimers and tetramers of adenosine–thymidine (AT) and guanosine–cytidine (GC) Watson–Crick pairs using PM3 semiempirical quantum chemistry. Of these only five modes have been found to be most strongly coupled to the electron motion in DNA, namely stretching of H-bonding both in AT and GC, correlated Buckle–Rise and Stagger–Tilt motions in GC and correlated Shear–Twist motion in AT. The parameters for the corresponding polaronic Hamiltonians have been estimated. The nature of these DNA polarons is discussed taking into account the relevant experimental results currently available.

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.

Electron spectra of DNA model compounds, adenosine-thymidine and guanosine-cytidine nucleoside base pairs, as well as the relevant homogeneous stacked base pair steps in A-DNA and B-DNA conformations, were investigated using ZINDO semiempirical quantum-chemical method. This work confirms that, in DNA with intact Watson–Crick hydrogen bonding and base stacking, the highest occupied molecular orbitals (HOMO) are residing on purine base residues, whereas the lowest unoccupied molecular orbitals (LUMO) — on pyrimidine base residues. In general, the present results are satisfactorily comparable with the available experimental data. The role of charge transfer excitations in the polymer DNA 260 nm spectral band 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

The parameters of an extended Hubbard Hamiltonian for poly(dA)–poly(dT) and poly(dG)–poly(dC) homopolynucleotide duplexes in A- and B-deoxyribonucleic acid (DNA) geometries have been estimated within the framework of the Fortunelli–Painelli dimer model using Hartree–Fock semiempirical quantum chemistry reinforced by a configuration interaction scheme to include one- and two-electron excitations. It is tentatively concluded that inclusion of electron correlations is essential in treating DNA duplexes.

Enthalpy-entropy compensation (EEC) has a definite physical sense. Here, we review EEC from a new standpoint, using the notion of correlation. The latter has two basic meanings: (a) 'A' is correlated to 'B' means 'A' results from 'B' or vice versa; (b) this same means there is some real, but hidden 'C' in connection to both 'A' and 'B'). In accordance with the interpretation (b), we try rationalizing EEC in terms of hidden, but physically real factors.

The first determination of the valence electron structure of an infinite three-dimensional DNA fiber (in the all-atom representation, together with its hydration shell and sodium counterions) is reported within the tight-binding approximation. The present results suggest that actual DNA fibers are disordered systems on the verge of their metal–insulator transition, with irregularities of DNA conformation being much more important for DNA electrical properties than aperiodicity of the DNA base sequence alone. Possible mechanisms of charge carrier self-generation in DNA are discussed on the basis of semiempirical quantum-chemical calculations.

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.

Molecular dynamics and Monte Carlo simulations of β-cyclodextrin and its per-dimethylated derivative heptakis(2,6-di- O -methyl)-β-cyclodextrin have been carried out in water solutions at two temperatures, 25°C and 70°C. The structure of the hydration shells, as well as the solute–solvent and solvent–solvent correlations have been analyzed. The negative solubility coefficient of heptakis(2,6-di- O -methyl)-β-cyclodextrin is conditioned first of all by progressive destruction of the hydration shells around its methyl groups with temperature increase, whereas for β-cyclodextrin with positive temperature coefficient, solution is comparable at 25°C and 70°C.

Ab initio crystal orbital calculations on two fullerite C60 crystals heavily doped with sodium (C60Na10 and C60Na11) are reported. The former exhibits a partial charge transfer of 5.57 electrons, whereas the charge transfer in the latter is of 6 electrons. Both the compounds are metals with relatively low densities of states at the Fermi levels, but of the two, only C60Na11 could in principle superconduct.

Folding of oligoglutamine chains of different lengths is of crucial interest for exploring the molecular mechanisms of Huntington's disease. A simple oligoglutamine model based upon the Flory-Huggins theory of polymer solutions demonstrates a random coil instability in chains containing more than 40 glutamine residues with respect to beta-sheet formation. This is in striking quantitative agreement with biochemical results on the chain length dependence of polyglutamine aggregation in vivo and in vitro, as well as with clinical data on the polyglutamine chain length dependence of the onset of Huntington's disease. Furthermore, a detailed molecular-mechanical investigation of a polypeptide chain carrying 40 glutamine residues was performed. Two possible folding modes of such an oligoglutamine chain were revealed: a) a beta-hairpin and b) a highly compact random coil entity stabilized by a wealth of H-bonds among the glutamine side chains. A possible role of these folding modes in polyglutamine aggregation, as well as in the onset of Huntington's disease, is discussed.

X-ray diffraction analysis of the crystalline inclusion complex β -cyclodextrin-but-2-yne-1,4-diol heptahydrate has shown that a number of C–H…O and C–H… π interactions occur between the cavity wall and the guest molecules. The interaction energies of these contacts are estimated by ab initio quantum chemical calculations. They are in the range 0.7 to 1.1 kcal mol −1 , which is far below values of conventional hydrogen bonding (4 to 6 kcal mol −1 for O–H…O hydrogen bonds in carbohydrates), but appreciably above energies of van der Waals contacts.