Evgeni B. Starikov

Chalmers University of Technology · Research Area of Physical Chemistry

Statistical mechanics is clearly being restricted by its fuzzy basement, namely its assumption as for the 'large number of microscopic particles'. This communication tries to show and discuss some handy and useful way of how to circumvent such a restriction.

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...

The logical structure of the conventional “equilibrium” thermodynamics has been carefully analyzed here. An imperative to attentively and thoughtfully re-read the work by N. L. S. Carnot naturally emerges from such an analysis. The implications resulting from such re-reading for the whole field of thermodynamics and statistical physics are discusse...

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.

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...

This is my life-long achievement, impossible without my international co-authorship.

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 Franzén had experimentally verified his inferences and could prove their validity. About hundred years of fierce struggle to persuade the colleagu...

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.Graphic abstract

The conformational behaviour of a set of four different natural and synthetic nucleic acids, namely DNAs from salmon sperm and from micrococcus lysodeikticus as well as poly(dA) ·poly(dT) and poly(A) ·poly(U) has been investigated by means of Fourier-transform infrared spectroscopy in terms of various states of hydration and correlated with the res...

To my dear mom, Lilia Pavlovna Starikova (1939–1973) To my dear grandpa, Yosef Yakovlevich Volisson (1913–1987) To my dear grandma, Marina Naumovna Gorer (1918–1991) To my respected teacher, Vladimir Yakovlevich Maleev (1930–2018) To my dear friend, Amarin Chateau Sallarde, the Oriental Shorthair Cat (2013–2018)

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 α and β configurations have a magnesium-ligating histidine residue and a 17-propionic acid moiety on the opposit...

This work has shown the way to put the formal statistical-mechanical basement under the hotly debated notion of enthalpy-entropy compensation. The possibility of writing down the universal equation of state based upon the statistical mechanics is discussed here.

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.

It is a PPT presentation on the electronic conference CS-DC'15 ...

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 isokinetic, iso-selective, iso-equilibrium relationships immediately loses its int...

The logical structure of the conventional “equilibrium” thermodynamics has been carefully analyzed here. An imperative to attentively and thoughtfully re-read the work by N. L. S. Carnot naturally emerges from such an analysis. The implications resulting from such re-reading for the whole field of thermodynamics and statistical physics are discusse...

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.

The notion of entropy-enthalpy compensation (EEC) is well known and hotly debated up to now. Nevertheless, any valid EEC phenomenon ought to have in sooth a definite physical-chemical sense. The roots of the latter are discussed here in detail.

The basic thermodynamics behind the well-known, up to now hotly debated, notion of entropy-enthalpy compensation (EEC) is analyzed here in detail. Namely, any valid EEC phenomenon is considered using Carnot-cycle-type model, in which micro-phase transitions (MPTs) play a crucial role. Such MPTs could typically be some cooperative processes in (supr...

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.

We review here the well-known but still hotly debated notion of entropy-enthalpy compensation (EEC) from an unconventional standpoint: in terms of correlation. Specifically, correlation could mean either that 'A' is correlated to 'B' due to that 'A' directly results from 'B', or vice versa, or that there may be some real, but hidden 'C' connected t...

The name of George Augustus Linhart is in fact “widely unknown”. In effect, he was a Viennese-born USA-American physicist-chemist, partially associated with the Gilbert Newton Lewis’ school of thermodynamics at the University of California in Berkeley. As a lone small boy, he had arrived (from Austria via Hamburg) at New York in 1896, but was offic...

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 accorda...

The photodissociation of fluorescein monoanions was studied by varying the storage times of the ions in an ion trap and an electrostatic storage ring, before laser irradiation. The photodissociation neutral spectra as a function of time vary, in a manner dependent on the storage time as well as the laser wavelength; spectra consist of components wi...

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...

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 in...

The name of George Augustus Linhart is in fact "widely unknown". In effect, he was a Viennese-born USA-American physicist-chemist, partially associated with the Gilbert Newton Lewis' school of thermodynamics at the University of California in Berkeley. As a lone small boy, he had arrived (from Austria via Hamburg) at New York in 1896, but was offic...

A detailed semiempirical quantum-chemical study is reported on homogeneous adenosine-thymidine and guanosine-cytidine base pair steps, both pure ones and their complexes with oxygen molecules. The results of this study help gain detailed insight into physico-chemical mechanisms of electrical conduction control in DNA molecules when doping them with...

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 ba...

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 repres...

Dependence of charge transmission through several conventional and extended DNA duplexes on the explicit presence of their water–counterion surrounding has been theoretically studied. We show here that: (a) the latter does not form specific charge transmission channels in addition to those available in DNA duplexes themselves; (b) chemically modify...

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

A minireview on nucleic acid quantum chemistry is presented, with the special reference to solid‐state samples of nucleic acids, their constituents, and model compounds. The proper use of quantum chemical methods facilitates formulating physically correct theories of nucleic acid molecular dynamics. The results of thorough quantum chemical calculat...

Some 80-90 years ago, George A. Linhart, unlike A. Einstein, P. Debye, M. Planck and W. Nernst, has managed to derive a very simple, but ultimately general mathematical formula for heat capacity vs. temperature from the fundamental thermodynamical principles, using what we would nowadays dub a "Bayesian approach to probability". Moreover, he has su...

Nucleic acids and proteins are not only biologically important polymers: They have recently been recognized as novel functional materials surpassing in many aspects the conventional ones. Although Herculean efforts have been undertaken to unravel fine functioning mechanisms of the biopolymers in question, there is still much more to be done. This p...

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 sta...

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-dissociati...

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. Plots of neutral-particle production rates against collision energy show typical electron-capture-dissociation p...

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...

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 sing...

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....

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 manufa...

The controlled fabrication of actively switchable atomic-scale devices, in particular transistors, has remained elusive to date. Here we explain 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 manufacture...

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...

a b s t r a c t 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 inc...

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...

With the atomistic Kubo-Verges method we calculate the ballistic conductance of various conformers of DNA (A,B,Z), as well as intermediate and composite conformations, using experimental structures and model complexes. For duplexes with 6 and 15 base pairs, we find that the valence band conductivity near the Fermi edge varies dramatically between t...

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 noninteger multiples of the conductance quantum G₀=2e²/h in simple metals is correlated to defects resulting from the fabricatio...

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 N...

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 w...

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-stag...

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...

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 ev...

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 o...

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...

We numerically investigate quantum diffusion of an electron in a model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with fluctuation of the parameters due to the impact of colored noise. The randomness is introduced by fluctuations of distance between two consecutive bases along the stacked base pairs. We demonstrate that in the model th...

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 w...

Hydroxylations of octane and lauric acid by Cytochrome P450-BM3 (CYP102A1) wild-type and three active site mutants--F87A, L188Q/A74G, and F87V/L188Q/A74G--were rationalized using a combination of substrate orientation from docking, substrate binding statistics from molecular dynamics simulations, and barrier energies for hydrogen atom abstraction f...

To summarize, we have presented a technique that allows the computation of the non-equilibrium electron transport through short sequences of DNA including a dissipative environment and the non-local coupling to single base pair vibrations. The parameters of the DNA model as well as the vibrational modes and their coupling to the electrons have been...

The structural repeat unit of Poly-(. l-glutamine) or polyQ is a naturally occurring peptide sequence that is thought to be linked to the cause of several inherited neurodegenerative diseases, including Huntington's disease (HD), spinobulbar muscular atrophy, dentatorubral pallidoluysian atrophy, and the certain types of spinocerebellar ataxia. Sec...

This chapter presents and discusses DNA conductance based upon the Kubo formula. Using this approach, the effects of base pair mismatches, different conformational changes, and base pair sequence on DNA electrical properties can be investigated. This makes possible the very fast estimation of conductance spectra for oligonucleotides with hundreds o...

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...

The charge distribution of the mononucleotides within a number of the corresponding sodium-salt crystallohydrates has been estimated using the semi-empirical quantum-chemical complete neglect of differential overlap (CNDO)/2-spd technique. The chemically conventional mononucleotide dianions cannot be theoretically ‘enucleated’ from some of the crys...

A sound result: Calculations have demonstrated a strong influence of acoustic modes on the conductance of double-stranded DNA (transmission spectrum of a duplex in its ideal B-DNA conformation is shown in red, that with deformations along DNA acoustic modes in green). The observed temperature independence of the conductivity at and above room tempe...

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 dynami...

It has recently been suggested by Perutz and Windle [1] that the formation of amyloid plaques – insoluble, fibrillar deposits which are implicated in the pathology of a wide range of neurodegenerative disorders – may be related to nucleation of protein aggre-gates. This scenario is supported by recent research in which aggregation was stimulated by...

Modern Methods for Theoretical Physical Chemistry of Biopolymers provides an interesting selection of contributions from an international team of researchers in theoretical chemistry. This book is extremely useful for tackling the complicated scientific problems connected with biopolymers' physics and chemistry. The applications of both the classic...

A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible...

We have thoroughly analyzed the electronic structure of stacked DNA Watson-Crick (WC) base pair dimers using ab initio Hartree-Fock and semiempirical Haxtree-Fock-configuration-interaction quantum chemistry. We consider all the possible base compositions and sequences at the nucleoside level in vacuo. The results show that in such systems charge ca...

A Comment on the Letter by S. Nakamae et al., Phys. Rev. Lett. 94, 248102 (2005). The authors of the Letter offer a Reply.

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 semiem...

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the...

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 p...

For more than 30 years, human leukocyte antigen B27 (HLA-B27) has been known to be closely related to the autoimmune disease ankylosing spondylitis, yet little is known about the molecular mechanisms of pathogenesis. Crystal structures of two closely related, but differently disease-associated, subtypes (B*2705 and B*2709) also did not resolve this...

Recent papers have considered moving breathers (MB) 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...

We investigate the charge transport in synthetic DNA polymers built up from single type of base pairs. In the context of a polaronlike 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. Sub...

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 l...

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...

This paper has been withdrawn due to some inconsistency of the results discovered after the submission. We apologize for it.

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 sche...

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. S...

We present theoretical work on the electronic states in a model DNA double helix of poly(dA)−poly(dT) (10 base pairs) as the molecule undergoes thermal fluctuations at room temperature. We couple state-of-the art empirical force field molecular dynamics (MD) simulations with an ab initio tight-binding formalism based on density-functional theory [L...

A critical survey of the most recent quantum-chemical studies on nucleic acids and their constituents is given. Special reference is made to physico-chemical mechanisms of charge transfer in nucleic acids and to possibilities of the quantum-chemical description of this process. The merits and demerits of high-level ab initio and semiempirical quant...

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–insu...

Using an ab initio tight-binding formalism based on density-functional theory [Lewis et al., Phys. Rev. B 64, 195103-1 (2001)], we present theoretical work on the electronic states in a model periodic DNA double helix of poly(dA)–poly(dT) (10 base-pairs). Comparison of the periodic structure is made to an aperiodic DNA structure with the same seque...

Molecular dynamics simulation of biotin-RNA aptamer in absence of its ligand, as well as semiempirical quantum-chemical calculations of its biotin-binding pocket in the presence of biotin have been performed. The global 3D architecture of the aptamer seems to be guided mainly by its primary and secondary structure, whereas a local structural adjust...

Recently, much experimental and theoretical work has been performed to understand the electronic structure and electron (hole)-transfer properties of DNA. But, due to the size of the problem, atomistic models with a quantum mechanical picture for large DNA strands containing several base pairs are difficult. We will present theoretical work on the...