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Hofman, Tadeusz. "Preface." Pure and Applied Chemistry 81, no. 10 (January 1, 2009): iv. http://dx.doi.org/10.1351/pac20098110iv.
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The 20th International Conference on Chemical Thermodynamics (ICCT 2008) was held in Warsaw, Poland, 3-8 August 2008. It was organized jointly by the Institute of Physical Chemistry of the Polish Academy of Science, both Faculties of Chemistry of the Warsaw University of Technology and the Warsaw University, the Polish Chemical Society, and under the auspices of the International Association of Chemical Thermodynamics (IACT). This conference was significant in a line of traditional meetings gathering biennially chemical thermodynamists from all over the world. Almost 300 participants from 39 countries presented 153 oral presentations and 174 posters, among the former ones 12 plenary and 27 invited lectures were given by distinguished researchers.The culminating event was the Rossini lecture given by Prof. Jürgen Gmehling from the University of Oldenburg in Germany, entitled "Present status and potential of group contribution methods for process development". Prof. Gmehling was awarded the prestigious Frederick D. Rossini Award, which has been given biennially to contemporary chemical thermodynamics for an outstanding contribution.Five 2008 IACT Junior Awards were awarded to young scientists for notable achievements presented during the conference in the form of an oral communication.The conference program was grouped into the following symposia:- Molecular simulations of fluid and statistical thermodynamics- Phase equilibria, supercritical fluids, and separation techniques- Electrolyte solutions and non-electrolyte mixtures including reactive chemical systems- Thermodynamics and properties in the biological, medical, pharmaceutical, agricultural, and food sectors- Nanosystems, nanodevices, and advanced materials- Thermochemistry, calorimetry, and molecular energetics- Ionic liquids- Surface and colloid chemistry- Industrial thermodynamics and databases- Thermodynamics frontiers and education- Modulated and oscillation temperature techniques- Environmental thermodynamicsThis issue of Pure and Applied Chemistry presents 16 papers selected from the plenary and invited lectures delivered at ICCT 2008 with an emphasis on industrial thermodynamics and thermochemistry. We hope that this selection will provide insight into the scientific program of the conference.The 21st International Conference on Chemical Thermodynamics will be held in Tsukuba, Japan, 1-6 August 2010.Tadeusz HofmanConference Editor
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Haris, P., Varughese Mary, M. Haridas, and C. Sudarsanakumar. "Energetics, Thermodynamics, and Molecular Recognition of Piperine with DNA." Journal of Chemical Information and Modeling 55, no. 12 (November 13, 2015): 2644–56. http://dx.doi.org/10.1021/acs.jcim.5b00514.
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Akaogi, Masaki, and Makoto Aratono. "Preface." Pure and Applied Chemistry 83, no. 6 (January 1, 2011): iv. http://dx.doi.org/10.1351/pac20118306iv.
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The 21st International Conference on Chemical Thermodynamics (ICCT-2010) was held in Tsukuba, Japan, on 1–6 August 2010, by the International Association of Chemical Thermodynamics (IACT) under the sponsorship of IUPAC. The organizing committee was chaired by Prof. T. Atake. The conference attracted more than 600 scientists from 37 different countries. During the conference period, the Rossini lecture and 9 plenary lectures were delivered. Forty invited papers and approximately 200 contributed papers were presented in 7 parallel sessions, together with about 300 poster presentations. The wide variety of fields in chemical thermodynamics is illustrated by the titles of a number of the symposia: “Fluids and fluid mixtures”, “Phase equilibria”, “Foods and pharmaceuticals”, “Biothermodynamics”, “Colloids and interfaces”, “Thermochemistry and molecular energetics”, “Environmental issues”, “Industrial applications, databases and software”, “Theory and simulation”, “Organic materials and polymers”, “Inorganic materials and metals”, “New techniques”, “Education in chemical thermodynamics”, and a special session in honor of Profs. S. Seki and H. Suga. As part of the scientific program, two workshops were also held, the titles of which are: “Energy in subsections on petroleum, coal and alternative sources”, and “Calorimetry with commercial relaxation instruments”.This issue of Pure and Applied Chemistry collects four selected plenary lectures delivered at the conference. The topics include challenges in teaching thermodynamics, new equations-of-state model of fluids and their mixtures, Gibbs energy minimization method in multiphase equilibria, and critical evaluation of thermophysical properties database in chemical process simulation. In these papers, we hope that the readers find the essence of the various aspects of current exciting research in chemical thermodynamics, which were exhibited in a lively manner during this successful conference. Other general papers presented in the symposia and workshops will be published in J. Chem. Thermodynamics, Thermochimica Acta, and Molecular Simulation.The 22nd ICCT is scheduled to be held August 2012 in Búzios, Brazil.Masaki AkaogiMakoto AratonoConference Editors
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Akinlade, O., and A. O. Boyo. "Thermodynamics and surface properties of Fe–V and Fe–Ti liquid alloys." International Journal of Materials Research 95, no. 5 (May 1, 2004): 387–95. http://dx.doi.org/10.1515/ijmr-2004-0081.
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Abstract A simple statistical mechanical model, based on a quasi-lattice approximation in which one assumes the formation of complexes, has been used to study bulk properties, such as free energy of mixing, the thermodynamic activity and enthalpy of mixing, in liquid Fe –Vand Fe –Ti alloys. The energetics and its effect on the alloying behavior of the liquid alloys has been investigated with the aim of correlating bulk phenomena with surface effects. The analysis shows that, assuming the formation of intermetallic complexes of the form Fe2V and FeTi in the liquid alloys, one can explain the energetics of the bulk alloys. Our results for the bulk calculations indicate that Fe –V and Fe –Ti both exhibit a significant tendency for compound formation. From a perusal of the diffusion coefficient D, we observe the same trend towards compound formation, as demonstrated by the chemical short-range order parameter (CSRO) close to the assumed stoichiometric composition. Furthermore, using the model calculations in the bulk, we study some surface properties. Our calculations indicate that Fe segregates to the surface at all bulk compositions in Fe –Vand Fe –Ti liquid, though the segregation effect is more pronounced in the former alloy. The reason for this is that Fe –Ti is a more ordered system than Fe –V and, thus, the driving force for surface segregation in these alloys is their energetics.
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Dymond, John H. "Preface." Pure and Applied Chemistry 79, no. 8 (January 1, 2007): iv. http://dx.doi.org/10.1351/pac20077908iv.
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The 19th International Conference on Chemical Thermodynamics (ICCT-19) took place as part of THERMO International 2006, together with the 16th Symposium on Thermophysical Properties and the 61st Calorimetry Conference, from 30 July to 4 August 2006 at the University of Colorado, Boulder, CO, USA. Dr. W. M. Haynes was President of the Executive Board of THERMO International 2006, and Drs. M. Frenkel, R. D. Chirico, and J. W. Magee were the organizers of ICCT. Overall, 768 speakers submitted the abstracts of their presentations, including about 30 students and 11 exhibitors, from 62 countries (235 from North America, 341 from Europe, 76 from Japan, and 33 from China). About 65 % of the participants were from academia and 15 % from industry, with 20 % from governmental and international organizations.These individual conferences have an overlap of areas of interest, but this was the first time that they have been held jointly at the same site. This provided a unique opportunity for researchers and practitioners worldwide to meet and discuss a broad range of scientific problems in the fields of thermodynamics and thermophysical properties for a wide variety of systems, with applications in chemistry and other scientific and engineering disciplines.After the official opening ceremony, there was an invited keynote presentation by Prof. W. A. Wakeham from the University of Southampton, Southampton, UK, entitled "Thermophysical property measurements: The journey from accuracy to fitness for purpose". The Rossini Award lecture was given by Prof. A. Navrotsky on "Calorimetry of nanoparticles, surfaces, interfaces, thin films, and multilayers".The ICCT program consisted of nine symposia, some of which were held jointly with the other conferences. The plenary lecturers and invited speakers in these symposia, and the titles of the plenary lectures, were as follows:Electrolyte and Non-Electrolyte Solution Thermodynamics: J. M. Prausnitz (plenary), "Some promising frontiers in the thermodynamics of protein solutions"; C. G. Panayiotou, P. R. Tremaine, and T. Kimura (invited)Ionic Liquids: K. Seddon (plenary); "The mark of an educated mind"; L. P. N. Rebelo and C. J. Peters (invited)Molecular Modelling, Including Simulation: D. Evans (plenary), "The fluctuation and non-equilibrium free energy theorems: Theory and experiment"; H. Tanaka, J. Errington, and A. Klamt (invited)Thermochemistry and Molecular Energetics: J. A. de Sousa Martinho Simões (plenary), "Energetics of free radicals: Bridges between gas-phase and solution data"; W. E. Acree, Jr. and J. S. Chickos (invited)Thermodynamics and Properties in the Biological, Medical, Pharmaceutical, Agricultural, and Food Sectors: P. L. Privalov (plenary), "Thermodynamic problems in structural molecular biology"; J. M. Sanchez-Ruiz and H. H. Klump (invited)Databases, Data Systems, Software Applications, and Correlations: M. Satyro (plenary), "Life, data and everything"; R. L. Rowley and R. Sass (invited)Phase Equilibrium, Supercritical Fluids, and Separation Technologies: S. Sandler (plenary), "Computational quantum mechanics: An under-utilized tool for applied thermodynamics"; L. F. Vega and R. P. Danner (invited)Colloid and Interface Science: L. Piculell (plenary), "Controlling structure in associating polymer-surfactant mixtures"; H. K. Yan and K. Lohner (invited)New Materials: V. K. Pecharsky (plenary), "Structure, mechanism, and thermodynamics of novel rare-earth-based inter-metallic materials"; C. Staudt-Bickel and J. Pons (invited)The plenary lectures, with the exception of the lecture by Prof. K. Seddon, are published in this issue.There were workshops on New Experimental Techniques, with Profs. C. Schick and J. P. M. Trusler as invited speakers, on Properties and Processes for a Hydrogen-Based Economy, where Prof. C. J. Peters was the invited speaker, and on Thermodynamic Frontiers and Education, with Profs. R. N. Lichtenthaler and R. Battino as invited speakers.In addition, there was a workshop on the Thermodynamic Properties of Hydration (with Prof. V. Majer as invited speaker), software demonstrations, and two afternoon poster sessions, with over 400 posters. The sessions were held in the well-appointed Stadium Club, against the beautiful backdrop of the Flatirons to the west and the plains stretching across to the east. IUPAC had donated three poster prizes, a framed certificate signed by IUPAC President Brian Henry, a copy of the IUPAC "Gold Book" and a two-year subscription to Chemistry International. These were awarded to Martinez-Herrera Melchor (Mexico), Lisa Ott (USA), and Isabel Marrucho (Spain).Doctorate awards were presented by the International Association of Chemical Thermodynamics (IACT), with sponsorship from Elsevier. The four recipients were M. Fulem (Prague, Czech Republic), Y. U. Paulechka (Minsk, Belarus), E. Asabina (Nizhni Novgorod, Russian Federation), and J. Xu (Trondheim, Norway). They each received a certificate, plus a cash prize of $500, and presented their papers at the conference.All the lectures demonstrated how chemical thermodynamics is making, and will continue to make, very significant contributions to the rapidly developing interdisciplinary fields such as the life sciences, new materials, medicine and pharmacy, new energy resources, the environment, separation technologies, agriculture, green chemistry, and so on. These are all extremely important issues for scientists worldwide, and particularly for those who are in developing or economically disadvantaged countries. The opportunity for face-to-face discussion and communication with scientists from developed countries was a great benefit, which will lead to further research and improved education.The weather was most pleasant for the conference. This, together with the attractive setting of the campus, the welcoming reception, the conference banquet at the National Center for Atmospheric Research, and the high standard of the presentations, made this a memorable conference. In addition, there was a full program of tours for accompanying persons, which included a visit to the mile-high city (Denver). Our thanks are extended to the Conference Chair and Co-chairs, and to all members of the local Organizing Committee, the members of the International Advisory Committee, and the members of the International Scientific Committee. We are most grateful to IUPAC, the International Association of Chemical Thermodynamics, the National Institute of Standards and Technology, the American Society of Mechanical Engineers, and the American Institute of Chemical Engineers, Elsevier, Honeywell, and Mettler Toledo for sponsoring THERMO International 2006.Thermodynamics will continue to be an important area of research for many years to come, with a wide range of applications from chemical engineering to the biosciences. We look forward to the presentation and discussion of the results of further advances in chemical thermodynamics at the next ICCT, which will take place in Warsaw, Poland in August 2008.John H. DymondConference Editor
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Dymond, John H. "Preface." Pure and Applied Chemistry 77, no. 8 (January 1, 2005): iv. http://dx.doi.org/10.1351/pac20057708iv.
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The 18th IUPAC International Conference on Chemical Thermodynamics (ICCT-2004), concurrent with the 12th National Conference on Chemical Thermodynamics and Thermal Analysis, was held 17-21 August 2004 at the Fragrant Hill Hotel, Beijing, China. Professor Haike Yan was Conference Chair, Prof. Zhiwu Yu was Conference Co-chair, and Prof. Xibai Qiu was Secretary. The 395 participants came from 40 countries.During the official opening ceremony, there was a presentation of the first Doctorate Awards to be given by the International Association of Chemical Thermodynamics, with sponsorship from Elsevier. The three recipients were Dr. Lin Chen, Tsinghua University, Beijing; Mr. Dirk Wandschneider, University of Rostock, Germany; and Mr. Weiguo Xu, Liaoning University, China. They each received a certificate plus a cash prize of USD 500.The conference began with the Rossini lecture, presented by Prof. Jean-Pierre E. Grolier on "Advanced experimental techniques in polymer thermodynamics". The conference program consisted of eight symposia and three workshops. In Symposium 1, Electrolyte and Nonelectrolyte Solution Thermodynamics, Prof. Emmerich Wilhelm gave the plenary lecture "The fascinating world of pure and mixed nonelectrolytes". There were invited lectures by Profs. Eckhard Vogel, Fumio Hirata, and Takayoshi Kimura. In Symposium 2, New Materials, Prof. C. Richard Catlow presented the plenary lecture "Computational approaches to the catalytic activation of carbon-hydrogen bonds", and invited lectures were given by Profs. Mary Anne White and Vladimir Durov. The plenary lecture in Symposium 3, Phase Equilibrium, Supercritical Fluids, and Separation Technologies, was given by Prof. Pablo Debenedetti on "Thermodynamics of supercooled and glassy water", with invited lectures from Profs. Cornelis Peters and Ding-Yu Peng. Symposium 4, Biological, Medical, Pharmaceutical, Agricultural, and Food Thermodynamics, had as its plenary lecturer Prof. Stephan Grzesiek, who spoke on "Biomolecular interactions in solutions". Professors Lee Hansen and Ichiro Hatta were the invited lecturers.Symposium 5 was on Colloid and Interface Science. Professor Bernard Cabane presented the plenary lecture "Solid-liquid separation", and there were invited lectures from Dr. Gerd Olofsson and Profs. Watson Loh and Xueqin An. The title of Symposium 6 was Non-equilibrium Thermodynamics, Statistical Thermodynamics, and Molecular Simulation. The plenary lecture "Non-equilibrium pattern formation" was presented by Prof. Qi Ouyang, with an invited lecture by Prof. Zhen-Gang Wang. Symposium 7 considered Thermochemistry and Molecular Energetics, with Prof. Michio Sorai, the plenary lecturer, speaking on "Entropy diagnosis for phase transitions occurring in functional materials". Professor Juliana Boerio-Goates gave the invited lecture. Symposium 8 was on Industrial Thermodynamics and Data Bases. Dr. Michael Fenkel gave the plenary lecture on "Global communications and expert systems in thermodynamics: Connecting property measurement and chemical process design". Invited lectures were given by Profs. Pertti Koukkari and Zhoulan Yin.There were three workshops. Prof. Kazuya Saito was invited lecturer for the Workshop on Thermodynamic Frontiers and Education. Professors Joan Brennecke and Andreas Heintz were invited lecturers for the Ionic Liquids Workshop. Professors Joon Won Park and Junko Morikawa gave invited lectures at the Workshop on New Experimental Techniques, including Nanotechnology.In addition, there were over 180 oral presentations, spread over the symposia and workshops, and about 280 poster presentations.The Rossini lecture and plenary lectures, with the exception of the paper by Prof. P. Debenetti where the field was recently reviewed [1,2], are published in this issue, together with the invited paper by Prof. Lee Hansen entitled "A thermodynamic law of adaptation of plants to environmental temperatures". Selected papers from individual symposia will be published in the Journal of Molecular Liquids (Symposium 1), Fluid Phase Equilibria (Symposia 3 and 6), the Journal of Chemical Thermodynamics (Symposia 1, 2, and 7), Thermochimica Acta (Symposium 4), or in the Journal of Chemical and Engineering Data (Workshop on Ionic Liquids).After the previous weeks when it had been very hot and humid, the temperature dropped and the weather was most pleasant for the conference. This change in weather, together with the attractive setting of the hotel, the excellent hospitality, which included a welcome reception, an evening of acrobatics entertainment, a conference banquet in the Summer Palace, and the high standard of the presentations, made this conference memorable. In addition, there was a full program of tours for accompanying persons. Our thanks are extended to the Conference Chair and Co-chair, and to all members of the local Organizing Committee, the International Advisory Committee, and the International Scientific Committee. We are most grateful to IUPAC, the International Association of Chemical Thermodynamics, the China Association for Science and Technology, the National Natural Science Foundation of China, and the Chinese Academy of Sciences for sponsoring the conference.Thermodynamics will continue to be an important area of research for many years to come, with a wide range of applications from chemical engineering to the biosciences. We look forward to the presentation and discussion of the results of further advances in chemical thermodynamics at the next ICCT, which will take place in Boulder, Colorado in 2006.1. P. G. Debenedetti. J. Phys.: Condens. Mater. 45, R1669-1726 (2003).2. P. G. Debenedetti and H. E. Stanley. Phys. Today 56, 40-46 (2003).J. H. DymondConference Editor
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Sun, Hui, and Di Wu. "Recent advances in experimental thermodynamics of metal–organic frameworks." Powder Diffraction 34, no. 4 (September 20, 2019): 297–301. http://dx.doi.org/10.1017/s0885715619000782.
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This mini review summarizes recent advances in experimental thermodynamics of metal–organic frameworks (MOFs). Taking advantage of the development in mechanochemistry, near-room temperature solution calorimetry, and low-temperature heat capacity measurements, the energetic landscape, entropy trends, and Gibbs free energy evolutions of MOFs with true polymorphism [Zn(MeIm)2, Zn(EtIm)2, and Zn(CF3Im)2] as framework topology varies were thoroughly explored by integrated calorimetric and computational methodologies. In addition, the formation enthalpies of MOFs with ultrahigh porosity (MOF-177 and UMCM-1) and the simplest structure (metal formates) have been determined. The studies summarized below highlight the complex interplays among interrelated compositional, chemical, and topological (structural) factors in the determination of the thermodynamic parameters of MOFs.
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Ávila, M., M. F. Juárez, and E. Santos. "Energetics of chloride adlayers on Au(100) electrodes: Grand-canonical Monte Carlo simulations and ab-intio thermodynamics." Electrochimica Acta 364 (December 2020): 137289. http://dx.doi.org/10.1016/j.electacta.2020.137289.
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Trujillo, Dennis, Ayana Ghosh, Serge M. Nakhmanson, Sanjubala Sahoo, and S. Pamir Alpay. "Surface structure and energetics of low index facets of bismuth ferrite." Physical Chemistry Chemical Physics 22, no. 28 (2020): 16400–16406. http://dx.doi.org/10.1039/d0cp01575j.
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Bierbaum, Veronica M. "Anions in Space and in the Laboratory." Proceedings of the International Astronomical Union 7, S280 (June 2011): 383–89. http://dx.doi.org/10.1017/s1743921311025130.
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AbstractThe astronomical detection of molecular anions has prompted our study of their chemical reactions with atomic species that are abundant in the interstellar medium. We have recently explored the chemistry of a variety of Cx Ny− anions with hydrogen atoms and determined their reaction rate constants and products using the flowing afterglow-selected ion flow tube technique. Computational studies allow characterization of the structures of reactants and products, as well as the energetics along the reaction pathway. For anions containing one or two nitrogen atoms, reactions with hydrogen atoms are facile, and proceed primarily by associative detachment. In contrast, anions containing three nitrogen atoms are unreactive with hydrogen atoms due to reaction barriers and unfavorable thermodynamics.
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Chimal-Eguia, J., R. Paez-Hernandez, Delfino Ladino-Luna, and Juan Velázquez-Arcos. "Performance of a simple energetic-converting reaction model using Linear Irreversible Thermodynamics." Entropy 21, no. 11 (October 24, 2019): 1030. http://dx.doi.org/10.3390/e21111030.
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In this paper, the methodology of the so-called Linear Irreversible Thermodynamics (LIT) is applied to analyze the properties of an energetic-converting biological process using simple model for an enzymatic reaction that couples one exothermic and one endothermic reaction in the same fashion as Diaz-Hernandez et al. (Physica A, 2010, 389, 3476–3483). We extend the former analysis to consider three different operating regimes; namely, Maximum Power Output (MPO), Maximum Ecological Function (MEF) and Maximum Efficient Power Function (MEPF), respectively. Based on the later, it is possible to generalize the obtained results. Additionally, results show analogies in the optimal performance between the different optimization criteria where all thermodynamic features are determined by three parameters (the chemical potential gap Δ = μ 1 − μ 4 R T , the degree of coupling q and the efficiency η ). This depends on the election that leads to more or less efficient energy exchange.
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Galteland, Olav, Dick Bedeaux, and Signe Kjelstrup. "Nanothermodynamic Description and Molecular Simulation of a Single-Phase Fluid in a Slit Pore." Nanomaterials 11, no. 1 (January 11, 2021): 165. http://dx.doi.org/10.3390/nano11010165.
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We have described for the first time the thermodynamic state of a highly confined single-phase and single-component fluid in a slit pore using Hill’s thermodynamics of small systems. Hill’s theory has been named nanothermodynamics. We started by constructing an ensemble of slit pores for controlled temperature, volume, surface area, and chemical potential. We have presented the integral and differential properties according to Hill, and used them to define the disjoining pressure on the new basis. We identified all thermodynamic pressures by their mechanical counterparts in a consistent manner, and have given evidence that the identification holds true using molecular simulations. We computed the entropy and energy densities, and found in agreement with the literature, that the structures at the wall are of an energetic, not entropic nature. We have shown that the subdivision potential is unequal to zero for small wall surface areas. We have showed how Hill’s method can be used to find new Maxwell relations of a confined fluid, in addition to a scaling relation, which applies when the walls are far enough apart. By this expansion of nanothermodynamics, we have set the stage for further developments of the thermodynamics of confined fluids, a field that is central in nanotechnology.
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Minetti, Conceição A., and David P. Remeta. "Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization." Life 12, no. 9 (September 15, 2022): 1438. http://dx.doi.org/10.3390/life12091438.
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Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Woods, Dustin C., and Jeff Wereszczynski. "Elucidating the influence of linker histone variants on chromatosome dynamics and energetics." Nucleic Acids Research 48, no. 7 (March 4, 2020): 3591–604. http://dx.doi.org/10.1093/nar/gkaa121.
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Abstract Linker histones are epigenetic regulators that bind to nucleosomes and alter chromatin structures and dynamics. Biophysical studies have revealed two binding modes in the linker histone/nucleosome complex, the chromatosome, where the linker histone is either centered on or askew from the dyad axis. Each has been posited to have distinct effects on chromatin, however the molecular and thermodynamic mechanisms that drive them and their dependence on linker histone compositions remain poorly understood. We present molecular dynamics simulations of chromatosomes with the globular domain of two linker histone variants, generic H1 (genGH1) and H1.0 (GH1.0), to determine how their differences influence chromatosome structures, energetics and dynamics. Results show that both unbound linker histones adopt a single compact conformation. Upon binding, DNA flexibility is reduced, resulting in increased chromatosome compaction. While both variants enthalpically favor on-dyad binding, energetic benefits are significantly higher for GH1.0, suggesting that GH1.0 is more capable than genGH1 of overcoming the large entropic reduction required for on-dyad binding which helps rationalize experiments that have consistently demonstrated GH1.0 in on-dyad states but that show genGH1 in both locations. These simulations highlight the thermodynamic basis for different linker histone binding motifs, and details their physical and chemical effects on chromatosomes.
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Galteland, Olav, Dick Bedeaux, and Signe Kjelstrup. "Nanothermodynamic Description and Molecular Simulation of a Single-Phase Fluid in a Slit Pore." Nanomaterials 11, no. 1 (January 11, 2021): 165. http://dx.doi.org/10.3390/nano11010165.
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We have described for the first time the thermodynamic state of a highly confined single-phase and single-component fluid in a slit pore using Hill’s thermodynamics of small systems. Hill’s theory has been named nanothermodynamics. We started by constructing an ensemble of slit pores for controlled temperature, volume, surface area, and chemical potential. We have presented the integral and differential properties according to Hill, and used them to define the disjoining pressure on the new basis. We identified all thermodynamic pressures by their mechanical counterparts in a consistent manner, and have given evidence that the identification holds true using molecular simulations. We computed the entropy and energy densities, and found in agreement with the literature, that the structures at the wall are of an energetic, not entropic nature. We have shown that the subdivision potential is unequal to zero for small wall surface areas. We have showed how Hill’s method can be used to find new Maxwell relations of a confined fluid, in addition to a scaling relation, which applies when the walls are far enough apart. By this expansion of nanothermodynamics, we have set the stage for further developments of the thermodynamics of confined fluids, a field that is central in nanotechnology.
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Torrenegra-Rico, J. D., A. Arango-Restrepo, and J. M. Rubí. "Nonequilibrium thermodynamics of Janus particle self-assembly." Journal of Chemical Physics 157, no. 10 (September 14, 2022): 104103. http://dx.doi.org/10.1063/5.0097802.
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We compute the energetic cost of formation of Janus particle structures. Using an approach that couples particle dynamics to the evolution of fuel concentration in the medium, which we consider to be initially inhomogeneous, we show the different types of emerging structures. The energy dissipated in the formation of such structures is obtained from the entropy production rate, which is a non-monotonic function of the fraction of assembled particles and, thus, different in each self-assembly regime. An analysis of the free energy of these particles allows us to establish a thermodynamic criterion of structure formation based on the behavior of chemical potential as a function of the fraction of assembled particles.
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Abdank-Kozubski, Rafal, Andrzej Biborski, Mirosław Kozłowski, Christine Goyhenex, Veronique Pierron-Bohnes, Mebarek Alouani, Marcus Rennhofer, and Savko Malinov. "Atomic-Migration-Controlled Processes in Intermetallics." Defect and Diffusion Forum 277 (April 2008): 113–18. http://dx.doi.org/10.4028/www.scientific.net/ddf.277.113.
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Chemical ordering kinetics in L10- and B2-ordered AB binary intermetallics was simulated by means of Monte Carlo (MC) technique implemented with vacancy mechanism of atomic migration. While vacancy concentration is usually much lower than the antisite defect concentration in L10-ordered systems, triple defects are generated in particular B2–ordered systems. The latter definitely affects the chemical ordering process and requires that full thermal vacancy thermodynamics is involved in B2-ordering simulations. The study on L10-ordered binaries was dedicated to FePt thin layers considered as a material for ultra-high-density magnetic storage media. Metastability of the L10 c-variant with monoatomic planes parallel to the layer surface and off-plane easy magnetization was revealed. Thermal vacancy formation in B2-ordered binaries was modelled by implementing a mean-field Hamiltonian with a specific formalism of phase equilibria in a latticegas composed of atoms and vacancies. It was demonstrated that for particular pair-interaction energetics, equilibrium concentrations of vacancies and antisites result mutually proportional in well-defined temperature ranges. The MC simulations of B2-ordering kinetics involved the modelled equilibrium vacancy concentration and reproduced the experimentally observed low rate of the process.
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Zhong, Yu, Mei Yang, and Zi-Kui Liu. "Contribution of first-principles energetics to Al–Mg thermodynamic modeling." Calphad 29, no. 4 (December 2005): 303–11. http://dx.doi.org/10.1016/j.calphad.2005.08.004.
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Akinlade, O., L. A. Hussain, and O. E. Awe. "Thermodynamics of liquid Al–In, Ag–In and In–Sb alloys from a four-atom cluster model." International Journal of Materials Research 94, no. 12 (December 1, 2003): 1276–79. http://dx.doi.org/10.1515/ijmr-2003-0231.
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Abstract A model based on a cluster of four atoms has been used to obtain higher-order conditional probabilities that describe the atomic correlations in Al–In, Ag–In and In–Sb liquid alloys. Using the value of the ordering energy obtained from the model, some thermodynamic quantities such as Gibbs energy of mixing and concentration-concentration fluctuations in the long wavelength limit were calculated for these alloys. Our study of the energetics of these liquid alloys reveals that while In–Sb and Ag–In are both chemically ordered or heterocoordinated systems, Al–In is a segregating system. Furthermore, the degree of order in liquid In–Sb alloys is higher than that in liquid Ag–In alloys.
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Reverberi, Andrea Pietro, Valery Pavlovic Meshalkin, Oleg B. Butusov, Tamara B. Chistyakova, Maurizio Ferretti, Anna Maria Cardinale, and Bruno Fabiano. "Organic and Inorganic Biocidal Energetic Materials for Agent Defeat Weapons: An Overview and Research Perspectives." Energies 16, no. 2 (January 6, 2023): 675. http://dx.doi.org/10.3390/en16020675.
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A critical survey concerning biocidal energetics is proposed according to a classification depending on their chemical structure. The need of optimizing the performances of such compounds is an important target for the inertization of biological weapons, requiring a synergy between the thermal effects of combustion/detonation with the biocidal effects of reaction products released into the environment. The main physicochemical aspects related to the synthesis technique, the thermodynamic variables and the antimicrobial activity have been discussed and compared. In particular, different kinds of biocides have been taken into account, with particular attention to the role of iodine as one of the most promising and eco-friendly chemical species to this purpose, in line with the paradigms of environmental protection and the rational utilization of chemicals. Furthermore, the protocols adopted to assess the effectiveness of biocidal agents have been thoroughly examined according to the recent studies proposed by some of the most reputable research groups in the field. Finally, some insights for future investigations are proposed.
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Karbowski, Jan. "Energetics of stochastic BCM type synaptic plasticity and storing of accurate information." Journal of Computational Neuroscience 49, no. 2 (February 2, 2021): 71–106. http://dx.doi.org/10.1007/s10827-020-00775-0.
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AbstractExcitatory synaptic signaling in cortical circuits is thought to be metabolically expensive. Two fundamental brain functions, learning and memory, are associated with long-term synaptic plasticity, but we know very little about energetics of these slow biophysical processes. This study investigates the energy requirement of information storing in plastic synapses for an extended version of BCM plasticity with a decay term, stochastic noise, and nonlinear dependence of neuron’s firing rate on synaptic current (adaptation). It is shown that synaptic weights in this model exhibit bistability. In order to analyze the system analytically, it is reduced to a simple dynamic mean-field for a population averaged plastic synaptic current. Next, using the concepts of nonequilibrium thermodynamics, we derive the energy rate (entropy production rate) for plastic synapses and a corresponding Fisher information for coding presynaptic input. That energy, which is of chemical origin, is primarily used for battling fluctuations in the synaptic weights and presynaptic firing rates, and it increases steeply with synaptic weights, and more uniformly though nonlinearly with presynaptic firing. At the onset of synaptic bistability, Fisher information and memory lifetime both increase sharply, by a few orders of magnitude, but the plasticity energy rate changes only mildly. This implies that a huge gain in the precision of stored information does not have to cost large amounts of metabolic energy, which suggests that synaptic information is not directly limited by energy consumption. Interestingly, for very weak synaptic noise, such a limit on synaptic coding accuracy is imposed instead by a derivative of the plasticity energy rate with respect to the mean presynaptic firing, and this relationship has a general character that is independent of the plasticity type. An estimate for primate neocortex reveals that a relative metabolic cost of BCM type synaptic plasticity, as a fraction of neuronal cost related to fast synaptic transmission and spiking, can vary from negligible to substantial, depending on the synaptic noise level and presynaptic firing.
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Biborski, A., Rafal Abdank-Kozubski, and V. Pierron-Bohnes. "“Order-Order” Kinetics in Triple-Defect B2-Ordered Binary Intermetallics: Kinetic Monte Carlo Simulation." Diffusion Foundations 2 (September 2014): 191–220. http://dx.doi.org/10.4028/www.scientific.net/df.2.191.
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Triple-defect formation in B2-ordered binary A-B intermetallic compounds results fromthe asymmetry between the formation energies of A- and B-antisite defects. Chemical disorderingin such systems is strictly correlated with vacancy formation, which is the reason for usually veryhigh vacancy concentration. Consequently, Kinetic Monte Carlo (KMC) simulation of processes occurringin the triple-defect systems and controlled by atomic migration via vacancy mechanism mustinvolve complete vacancy thermodynamics – i.e. the simulated system must contain the equilibriumtemperature-dependent number of vacancies. The fully consistent approach based on two differentMonte Carlo techniques has been applied in the present study. The AB intermetallic was modelled withan Ising-type Hamiltonian and KMC simulated for “order-order” kinetics with temperature-dependentequilibrium number of vacancies previously determined by means of Semi Grand Canonical MonteCarlo (SGCMC) simulations. The procedure required in addition the determination of saddle -pointenergies assigned to particular atomic jumps to nn vacancies. Their values were estimated in relationto the nn pair-interaction energies with reference to Molecular Statics simulations performed for NiAlsystem with EAM energetics. The results elucidated the role of triple-defect formation as the atomisticscaleorigin of the experimentally observed surprisingly low rate of the “order-order” kinetics in bulkNiAl.
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Martínez-Bachs, Berta, and Albert Rimola. "Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations." Life 9, no. 3 (September 16, 2019): 75. http://dx.doi.org/10.3390/life9030075.
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Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.
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Mayer, Christoph, and Thomas Wallek. "Cluster-Based Thermodynamics of Interacting Dice in a Lattice." Entropy 22, no. 10 (October 1, 2020): 1111. http://dx.doi.org/10.3390/e22101111.
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In this paper, a model for two-component systems of six-sided dice in a simple cubic lattice is developed, based on a basic cluster approach previously proposed. The model represents a simplified picture of liquid mixtures of molecules with different interaction sites on their surfaces, where each interaction site can be assigned an individual energetic property to account for cooperative effects. Based on probabilities that characterize the sequential construction of the lattice using clusters, explicit expressions for the Shannon entropy, synonymously used as thermodynamic entropy, and the internal energy of the system are derived. The latter are used to formulate the Helmholtz free energy that is minimized to determine thermodynamic bulk properties of the system in equilibrium. The model is exemplarily applied to mixtures that contain distinct isomeric configurations of molecules, and the results are compared with the Monte-Carlo simulation results as a benchmark. The comparison shows that the model can be applied to distinguish between isomeric configurations, which suggests that it can be further developed towards an excess Gibbs-energy, respectively, activity coefficient model for chemical engineering applications.
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Koirala, R. P., I. Koirala, and D. Adhikari. "Energetics of mixing and transport phenomena in Cd-X (X=Pb, Sn) melts." BIBECHANA 15 (December 19, 2017): 113–20. http://dx.doi.org/10.3126/bibechana.v15i0.18751.
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We report a quasi-chemical study of the thermodynamic and transport properties of mixing of liquid Cd-Pb and Cd-Sn alloys at 773K. The interaction energy in the alloys is found to be positive which suggests homo-coordination of atoms in the alloys. The viscosities of the alloys at 773K computed from two different approaches exhibit non-linear concentration dependence with the results for Cd-Sn alloy being in very good agreement and satisfactory agreement for Cd-Pb alloy. In lower concentrations of Cd-component, Cd-Pb alloy has larger viscosity and on the other side of concentration, Cd-Sn alloy has larger value. The calculations of inter-diffusion coefficients result in concave diffusion isotherms for the alloys. The higher values of inter-diffusion coefficients for Cd-Sn suggest that Cd and Sn metals tend to mix more readily than Cd and Pb metals do in Cd-Pb alloy. The correlation between viscosity and diffusion implies that the inter-diffusion coefficient is large for low viscous liquid alloy and vice-versa.BIBECHANA 15 (2018) 113-120
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Stolyarova, Valentina L., Viktor A. Vorozhtcov, Andrey L. Shilov, and Tamara V. Sokolova. "Thermodynamic approach for prediction of oxide materials properties at high temperatures." Pure and Applied Chemistry 92, no. 8 (September 25, 2020): 1259–64. http://dx.doi.org/10.1515/pac-2019-1217.
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AbstractModern high-temperature technologies and methods of production of advanced materials impose new requirements on the quality of information on physicochemical properties of oxide systems at high temperatures. Normally, thermodynamic approach for these purposes is the most fundamental and essential. Great attention was paid by M.M. Shultz to extensive development of this approach in the studies of oxide melts, crystals, glasses, ceramics, and coatings using calorimetric, EMF, and high temperature mass spectrometric methods. Advantages of the thermodynamic approach were illustrated by examples of application of the Knudsen effusion mass spectrometric method to studies of oxide systems and materials, which were crucial for the further development of space and aviation industry, energetics, instrument making, communication engineering, metallurgy, energy-saving, and environmental safety. In the discussion of the regularities of vaporization processes and changes of thermodynamic properties in oxide systems, a number of particular systems based on silica and hafnia was considered in detail. Modeling was carried out for these systems using the Generalized Lattice Theory of Associated Solutions. The obtained results assert a necessity for creation of the national thermodynamic data- and model bases essential for further prediction of phase equilibria in oxide systems and materials at high temperatures.
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Marcucci, Lorenzo, Hiroki Fukunaga, Toshio Yanagida, and Mitsuhiro Iwaki. "The Synergic Role of Actomyosin Architecture and Biased Detachment in Muscle Energetics: Insights in Cross Bridge Mechanism beyond the Lever-Arm Swing." International Journal of Molecular Sciences 22, no. 13 (June 29, 2021): 7037. http://dx.doi.org/10.3390/ijms22137037.
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Muscle energetics reflects the ability of myosin motors to convert chemical energy into mechanical energy. How this process takes place remains one of the most elusive questions in the field. Here, we combined experimental measurements of in vitro sliding velocity based on DNA-origami built filaments carrying myosins with different lever arm length and Monte Carlo simulations based on a model which accounts for three basic components: (i) the geometrical hindrance, (ii) the mechano-sensing mechanism, and (iii) the biased kinetics for stretched or compressed motors. The model simulations showed that the geometrical hindrance due to acto-myosin spatial mismatching and the preferential detachment of compressed motors are synergic in generating the rapid increase in the ATP-ase rate from isometric to moderate velocities of contraction, thus acting as an energy-conservation strategy in muscle contraction. The velocity measurements on a DNA-origami filament that preserves the motors’ distribution showed that geometrical hindrance and biased detachment generate a non-zero sliding velocity even without rotation of the myosin lever-arm, which is widely recognized as the basic event in muscle contraction. Because biased detachment is a mechanism for the rectification of thermal fluctuations, in the Brownian-ratchet framework, we predict that it requires a non-negligible amount of energy to preserve the second law of thermodynamics. Taken together, our theoretical and experimental results elucidate less considered components in the chemo-mechanical energy transduction in muscle.
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Shenoy, Vivek B., Hailong Wang, and Xiao Wang. "A chemo-mechanical free-energy-based approach to model durotaxis and extracellular stiffness-dependent contraction and polarization of cells." Interface Focus 6, no. 1 (February 6, 2016): 20150067. http://dx.doi.org/10.1098/rsfs.2015.0067.
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We propose a chemo-mechanical model based on stress-dependent recruitment of myosin motors to describe how the contractility, polarization and strain in cells vary with the stiffness of their surroundings and their shape. A contractility tensor, which depends on the distribution of myosin motors, is introduced to describe the chemical free energy of the cell due to myosin recruitment. We explicitly include the contributions to the free energy that arise from mechanosensitive signalling pathways (such as the SFX, Rho-Rock and MLCK pathways) through chemo-mechanical coupling parameters. Taking the variations of the total free energy, which consists of the chemical and mechanical components, in accordance with the second law of thermodynamics provides equations for the temporal evolution of the active stress and the contractility tensor. Following this approach, we are able to recover the well-known Hill relation for active stresses, based on the fundamental principles of irreversible thermodynamics rather than phenomenology. We have numerically implemented our free energy-based approach to model spatial distribution of strain and contractility in (i) cells supported by flexible microposts, (ii) cells on two-dimensional substrates, and (iii) cells in three-dimensional matrices. We demonstrate how the polarization of the cells and the orientation of stress fibres can be deduced from the eigenvalues and eigenvectors of the contractility tensor. Our calculations suggest that the chemical free energy of the cell decreases with the stiffness of the extracellular environment as the cytoskeleton polarizes in response to stress-dependent recruitment of molecular motors. The mechanical energy, which includes the strain energy and motor potential energy, however, increases with stiffness, but the overall energy is lower for cells in stiffer environments. This provides a thermodynamic basis for durotaxis, whereby cells preferentially migrate towards stiffer regions of the extracellular environment. Our models also explain, from an energetic perspective, why the shape of the cells can change in response to stiffness of the surroundings. The effect of the stiffness of the nucleus on its shape and the orientation of the stress fibres is also studied for all the above geometries. Along with making testable predictions, we have estimated the magnitudes of the chemo-mechanical coupling parameters for myofibroblasts based on data reported in the literature.
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Ananthaneni, Sahithi, Zachery Smith, and Rees B. Rankin. "Graphene Supported Tungsten Carbide as Catalyst for Electrochemical Reduction of CO2." Catalysts 9, no. 7 (July 15, 2019): 604. http://dx.doi.org/10.3390/catal9070604.
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Electrochemical reduction of CO2 to useful chemical and fuels in an energy efficient way is currently an expensive and inefficient process. Recently, low-cost transition metal-carbides (TMCs) have been proven to exhibit similar electronic structure similarities to Platinum-Group-Metal (PGM) catalysts and hence, can be good substitutes for some important reduction reactions. In this work, we test graphene-supported WC (Tungsten Carbide) nanoclusters as an electrocatalyst for the CO2 reduction reaction. Specifically, we perform density functional theory (DFT) studies to understand various possible reaction mechanisms and determine the lowest thermodynamic energy landscape of CO2 reduction to various products, such as CO, HCOOH, CH3OH, and CH4. This in-depth study of reaction energetics could lead to improvements and development of more efficient electrocatalysts for CO2 reduction.
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Marahatta, Anant Babu. "Chemical Energetics and Atomic Charges Distribution of Variably Sized Hydrated Sulfate Clusters in the light of Density Functional Theory." International Journal of Progressive Sciences and Technologies 25, no. 1 (February 28, 2021): 595. http://dx.doi.org/10.52155/ijpsat.v25.1.2690.
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Among the ions classified in the Hofmeister series, the firstly ranked divalent sulfate anion has the strongest hydrating and water-structure making propensity. This unique characteristic actually makes it kosmotropic which causes water molecules to interact each other and contributes to gain structural stability of its hydrated clusters [SO42−(H2O)n]n = 1−40. In this study, few variably sized microhydrated sulfate clusters [SO42−(H2O)n]n = 1−4, 16 are considered separately, and inquired their chemical energetics and atomic charge distributions through ab initio based theoretical model. The main objective of this insight is to specify and interpret their thermodynamic stabilities, binding energies, and specific bonding and electronic interactions quantum mechanically. An in-depth analysis of their change in relative ground state electronic energy with respect to hydration number indicates stronger affinity of the sulfate ion towards water molecules while attaining structural stability in any aqueous type solutions. The mathematically determined values of their binding energy (DE) almost holds up the same with this structural stability order: [SO42−(H2O)16] > [SO42−(H2O)4] > [SO42−(H2O)3] > [SO42−(H2O)2] > [SO42−(H2O)], as reliable as experimentally and molecular dynamics simulation predicted trend. Moreover, the Mulliken derived partial atomic charges feature qualitative charge distribution in them which not only depicts electronic interactions between the specific atoms but also exemplifies the involvement of central sulfate units in hydrogen bond formation with surrounding water molecules.
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Lee, James Weifu. "Type-B Energetic Processes and Their Associated Scientific Implications." Journal of Scientific Exploration 36, no. 3 (October 22, 2022): 484–92. http://dx.doi.org/10.31275/20222517.
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Recently, our work has identified two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth: Type-A energy processes such as the classical heat engines, ATP hydrolysis, and many of the known chemical, electrical, and mechanical processes apparently well follow the second law of thermodynamics; and Type-B energy processes, such as the newly discovered thermotrophic function that isothermally utilizes environmental heat energy to do useful work in driving ATP synthesis, which follows the first law of thermodynamics (conservation of mass and energy), but does not necessarily have to be constrained by the second law, owing to their special asymmetric functions. In mitochondria, their special asymmetric functions associated with Type-B processes comprise: 1) The transmembrane asymmetry of inner mitochondrial membrane structure with the protonic outlets of redox-driven proton-pumping protein complexes protruded away from the membrane surface by about 1-3 nm into the bulk liquid p-phase while the protonic inlet of the F0F1-ATP synthase located rightly at the transmembrane electrostatically localized proton (TELP) layer; and 2) The lateral asymmetry of mitochondrial cristae with an ellipsoidal shape that enhances the density of TELP at the cristae tips where the F0F1-ATP synthase enzymes are located in supporting the TELP-associated thermotrophic function. The identification of Type-B energy processes indicates that there is an entirely new world of physical and energy sciences yet to be fully uncovered. Innovative efforts on Type-B processes to enable isothermally utilizing endless environmental heat energy could help to liberate all peoples from their dependence of fossil fuel energy, thus helping to reduce greenhouse gas CO2 emissions and control climate change toward a sustainable future for the humanity on Earth.
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Stout, R. B., E. J. Kansa, and A. M. Wijesinghe. "Kinematics and Thermodynamics Across a Propagating Non-Stoichiometric Oxidation Phase Front in Spent Fuel Grains." Applied Mechanics Reviews 47, no. 1S (January 1, 1994): S95—S111. http://dx.doi.org/10.1115/1.3122826.
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Spent fuel from power reactors contains mixtures, alloy subsets, and compounds of elements; but the aggregate atomic densities in spent fuel are dominated by uranium and oxygen atoms. With the exception of some UO2 fuels with burnable poisons (primarily gadolinia in BWR rods), the other elements with significant atomic densities in spent fuel evolve during reactor operation from neutron reactions and fission plus fission decay events. Due to nuclear decay processes, the intrinsic chemical composition and activity of spent fuel will continue to evolve after it is removed from reactors as its radioactivity decays over time. During the time interval when the radioactivity levels are significant, which is the time interval relevant for design and for performance assessment of a geological repository, it is important to develop an understanding and to develop models that describe potential chemical responses in spent fuel and its potential degradational impacts on repository design and performance. One such potential impact is the oxidation response of spent fuel. The oxidation of spent fuel results in an initial phase change of the UO2 lattice to a U4O9 lattice, and the next phase change is probably to U3O8 although it has not been observed yet at low temperatures (<200°C). The U4O9 lattice is non-stoichiometric with a oxygen to uranium weight ratio (O/U) at ~ 2.4. Preliminary indications are that the UO2 has a O/U of ~ 2.4 at the time just before it transforms into the U4O9 phase.[1,2] Also, in the oxygen weight gain versus time response, a plateau appears as the O/U approaches ~ 2.4. Part of this plateau response is due to geometrical effects of a U4O9 phase change front propagating into UO2 grain volumes. However, the plateau time response may be indicative of a metastable phase change delay kinetics or a diffusional related delay time until the oxygen density can attain a critical value to satisfy the stoichiometry and energy conditions for phase changes. In a previous paper and as a first step, a kinematic and thermodynamic ayalysis was developed to model spatially homogeneous oxidation phase transitions.[3] However, the experimental data clearly show a front of U4O9 lattice structure propagating into grains of the UO2 lattice structure. To describe this spatially inhomogeneous oxidation phase transition, as well as the expected U3O8 phase transition from the U4O9 lattice, lattice models are developed and spatially discontinuous kinematic and energetic expressions are derived. The approach will use concepts from statistical mechanics, discontinuum mechanics, and non-equilibrium thermodynamics. In addition, analytical techniques from shock wave analysis will be used to derive the surface discontinuity energetic expressions across the propagating oxidation phase front.
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Davidy, Alon. "Thermodynamic Design of Organic Rankine Cycle (ORC) Based on Petroleum Coke Combustion." ChemEngineering 5, no. 3 (July 16, 2021): 37. http://dx.doi.org/10.3390/chemengineering5030037.
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Thermodynamic analysis of Organic Rankine Cycle (ORC) was performed in this work. The Petroleum Coke burner provided the required heat flux for the Butane Boiler. The simulation of pet-coke combustion was carried out by using Fire Dynamics Simulator software (FDS) version 5.0. Validation of the FDS calculation results was carried out by comparing the temperature of the gaseous mixture and CO2 mole fractions to the literature. It was discovered that they are similar to those reported in the literature. An Artificial Intelligence (AI) time forecasting analysis was performed on this work. The AI algorithm was applied to the temperature and soot sensor readings. Two Python libraries were applied in order to forecast the time behaviour of the thermocouple readings: Statistical model—ARIMA (Auto-Regressive Integrated Moving Average) and KERAS—deep learning library. ARIMA is a class of model that captures a suite of different standard temporal structures in time series data. Keras is a python library applied for deep learning and runs on top of Tensor-Flow. It has been developed in order to perform deep learning models as fast and easily as possible for research and development. The model accuracy and model loss plot shows comparable performance (train and test). Butane has been employed as a working fluid in the ORC. Butane is considered one of the best pure fluids in terms of exergy efficiency. It has low specific radiative forcing (RF) compared to Ethane and Propane. Moreover, it has zero ozone depletion potential and low Global Warming Potential. It is considered flammable, highly stable and non-corrosive. The thermodynamic properties of Butane needed to evaluate the heat rate and the power were calculated by applying the ASIMPTOTE online thermodynamic calculator. It was shown that the calculated net power of the ORC cycle is similar to the net power reported in the literature (relative error of 4.8%). The proposed ORC energetic system obeys the first and second laws of thermodynamics. The thermal efficiency of the cycle is 20.4%.
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Guyot, Pierre, and Christophe Sigli. "Cluster Dynamics Modelling of the Precipitation Kinetics in Al(ZrSc) Alloys." Materials Science Forum 519-521 (July 2006): 291–96. http://dx.doi.org/10.4028/www.scientific.net/msf.519-521.291.
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The precipitation kinetics path in multi-component alloys may involve a competition between atomic mobilities and precipitates thermodynamic stability. Cluster dynamics modelling (CDM) is a simulation method that allows to describe this competition without introducing any heuristic assumptions as, for example, in the classical theory of nucleation. CDM consists in solving numerically, for each time increment, the master equations expressing the balance of solute exchanges (absorption and emission) between clusters/precipitates. A key issue is the energetics of the nano-clusters in the nucleation range. The computation of the precipitate size distribution function allows the complete description of the precipitates kinetic evolution, in chemical composition and in size. The method is applied to the precipitation of the Al3(Zr,Sc) L12 phase in Al solid solutions. The model predicts fairly well in the precipitation path some observed coupling effects between the two solutes, particularly during the nucleation stage.
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Song, Huan, Bing Li, Xuezhi Gao, Fenglin Shan, Xiaoxia Ma, Xiaoyan Tian, and Xiaoyan Chen. "Thermodynamics and Catalytic Properties of Two Novel Energetic Complexes Based on 3-Amino-1,2,4-triazole-5-carboxylic Acid." ACS Omega 7, no. 3 (January 11, 2022): 3024–29. http://dx.doi.org/10.1021/acsomega.1c06052.
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Kindra, Vladimir, Nikolay Rogalev, Andrey Rogalev, Olga Zlyvko, and Maksim Oparin. "Thermodynamic Analysis of Binary and Trinary Power Cycles Fueled with Methane–Hydrogen Blends." Inventions 7, no. 3 (August 30, 2022): 73. http://dx.doi.org/10.3390/inventions7030073.
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The development of hydrogen energetics is a possible way to reduce emissions of harmful substances into the atmosphere in the production of electricity. Its implementation requires the introduction of energy facilities capable of operating on environmentally safe fuel. At the same time, from a technological point of view, it is easier to implement a gradual shift to the use of hydrogen in power plants by burning methane–hydrogen blends. This paper presents the results of thermodynamic studies of the influence of the chemical composition of the methane–hydrogen blend on the performance of binary and trinary power units. It is shown that an increase in the hydrogen volume fraction in the fuel blend from 0 to 80% leads to a decrease in the Wobbe index by 16% and an increase in the power plant auxiliaries by almost 3.5 times. The use of a trinary CCGT unit with a single-circuit WHB and working fluid water condensation makes it possible to increase the net efficiency by 0.74% compared to a binary CCGT with a double-circuit WHB and a condensate gas heater.
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Verevkin, Sergey P., Artemiy A. Samarov, Sergey V. Vostrikov, Peter Wasserscheid, and Karsten Müller. "Comprehensive Thermodynamic Study of Alkyl-Cyclohexanes as Liquid Organic Hydrogen Carriers Motifs." Hydrogen 4, no. 1 (January 10, 2023): 42–59. http://dx.doi.org/10.3390/hydrogen4010004.
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Alkyl-cyclohexanes can be considered as suitable model compounds to understand the thermochemistry of aromatic compounds and their hydrogenated counterparts discussed as Liquid Organic Hydrogen Carrier systems. Thermochemical measurements on these hydrogen-rich compounds are thwarted by complications due to the 99.9 % purity limitation and sample size specific to these methods. However, the data on vaporisation and formation enthalpies are necessary to optimize the hydrogenation/dehydrogenation processes. In this work, various empirical and theoretical methods are described to reliably assess the gas phase enthalpies of formation and vaporization enthalpies of alkyl-substituted cyclohexanes. The empirical and quantum-chemical methods have been validated against reliable literature data and provide reasonable estimates with an accuracy comparable to that of the experimental data. The liquid phase enthalpies of formation of differently shaped alkyl-cyclohexanes were derived and used to estimate the energetics of their dehydrogenation reactions. The influence of alkyl substituents on the reaction enthalpy is discussed. The vapour pressures of typical hydrogen-rich compounds at technically relevant temperatures were calculated and compared to vapour pressures of biodiesel fuels measured in this work using the static method.
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Rajasekaran, Nandakumar, and Athi N. Naganathan. "A self-consistent structural perturbation approach for determining the magnitude and extent of allosteric coupling in proteins." Biochemical Journal 474, no. 14 (July 6, 2017): 2379–88. http://dx.doi.org/10.1042/bcj20170304.
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Elucidating the extent of energetic coupling between residues in single-domain proteins, which is a fundamental determinant of allostery, information transfer and folding cooperativity, has remained a grand challenge. While several sequence- and structure-based approaches have been proposed, a self-consistent description that is simultaneously compatible with unfolding thermodynamics is lacking. We recently developed a simple structural perturbation protocol that captures the changes in thermodynamic stabilities induced by point mutations within the protein interior. Here, we show that a fundamental residue-specific component of this perturbation approach, the coupling distance, is uniquely sensitive to the environment of a residue in the protein to a distance of ∼15 Å. With just the protein contact map as an input, we reproduce the extent of percolation of perturbations within the structure as observed in network analysis of intra-protein interactions, molecular dynamics simulations and NMR-observed changes in chemical shifts. Using this rapid protocol that relies on a single structure, we explain the results of statistical coupling analysis (SCA) that requires hundreds of sequences to identify functionally critical sectors, the propagation and dissipation of perturbations within proteins and the higher-order couplings deduced from detailed NMR experiments. Our results thus shed light on the possible mechanistic origins of signaling through the interaction network within proteins, the likely distance dependence of perturbations induced by ligands and post-translational modifications and the origins of folding cooperativity through many-body interactions.
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Guariento, Mara, Michael Assfalg, Serena Zanzoni, Dimitrios Fessas, Renato Longhi, and Henriette Molinari. "Chicken ileal bile-acid-binding protein: a promising target of investigation to understand binding co-operativity across the protein family." Biochemical Journal 425, no. 2 (December 23, 2009): 413–24. http://dx.doi.org/10.1042/bj20091209.
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Protein–bile acid interactions are crucial microscopic events at the basis of both physiological and pathological biochemical pathways. BABPs (bile-acid-binding proteins) are intracellular transporters able to bind ligands with different stoichiometry, selectivity and co-operativity. The molecular determinants and energetics of interaction are the observables that connect the microscopic to the macroscopic frameworks. The present paper addresses the study and proposes a mechanism for the multi-site interaction of bile acids with chicken I-BABP (ileal BABP) with the aim of elucidating the determinants of ligand binding in comparison with homologous proteins from different species and tissues. A thermodynamic binding model describing two independent consecutive binding sites is derived from isothermal titration calorimetry experiments and validated on the basis of both protein-observed and ligand-observed NMR titration data. It emerges that a singly bound protein is relatively abundant at low ligand/protein molar ratios assessing the absence of strong co-operativity. Both the measured energetics of binding and the distributed protein chemical-shift perturbations are in agreement with a first binding event triggering a global structural rearrangement. The enthalpic and entropic contributions associated with binding of the first ligand indicate that the interaction increases stability and order of the bound protein. The results described in the present study point to the presence of a protein scaffold which is able to establish long-range communication networks, but does not manifest positive-binding co-operativity, as observed for the human protein. We consider chicken I-BABP a suitable model to address the molecular basis for a gain-of-function on going from non-mammalian to mammalian species.
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Rossnagel, S. M., and J. J. Cuomo. "Ion-Beam-Assisted Deposition and Synthesis." MRS Bulletin 12, no. 2 (March 1987): 40–51. http://dx.doi.org/10.1557/s0883769400068391.
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Concurrent energetic particle bombardment during film deposition can strongly modify the structural and chemical properties of the resulting thin film. The interest in this technique, ion-assisted deposition, comes about because it can be used to produce thin films with properties not achievable by conventional deposition. Bombardment by low energy ions occurs during almost all plasma-based thin film deposition techniques. Bombardment of a growing film, particularly by accelerated ions, can also be combined with non-plasma-based deposition techniques, such as evaporation, to simulate some of the effects observed with sputtering. The bombarding particle flux is usually controllable so that the arrival rate, energy, and species can be independently varied from the depositing flux. Thus, a basic aspect of ion-beam-based deposition techniques is the “control” often absent in plasma-based techniques. In plasmas, the voltage, current, and pressure are all interdependent. The energetic bombardment at the substrate-film interface depends on the various properties of the plasma, as does the deposition rate. It is often difficult, or even impossible, to decouple these processes. With ion-beam-based deposition techniques, the ion bombardment is essentially independent of the deposition process, and both can be more easily controlled.The incident energetic particle contributes some of its energy or momentum to irreversibly change the dynamics of the film surface. The incident particle may also be incorporated into the growing film, changing the film's chemical nature. The changes induced by particle bombardment during deposition are often not characteristic of equilibrium thermodynamics because the incident particle's energy is often many times the local adsorption or binding energy.
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Knapczyk, Adrian, Sławomir Francik, Marcin Jewiarz, Agnieszka Zawiślak, and Renata Francik. "Thermal Treatment of Biomass: A Bibliometric Analysis—The Torrefaction Case." Energies 14, no. 1 (December 30, 2020): 162. http://dx.doi.org/10.3390/en14010162.
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The aim of the paper was to summarize and discuss current research trends in biomass thermal treatment (torrefaction process). Quantitative analyses were carried out, in which the main countries, research units and scientists were indicated. The analysis showed a clear upward trend in number of publications after 2010. Most scientists on selected topics come from China, USA, Canada, South Korea, Republic of China, Poland (Web od Science—Core Collection (WoS-CC) and Scopus databases). Quantitative analysis also showed that the most relevant WoS-CC categories in the summary are: Energy Fuels, Engineering Chemical, Agricultural Engineering, Biotechnology Applied Microbiology and Thermodynamics and Scopus Subject area: Energy, Chemical Engineering, Environmental Science, Engineering and Chemistry. Thematic analysis included research topics, process parameters and raw materials used. Thematic groups were separated: torrefaction process (temp.: 150–400 °C), hydrothermal carbonization process (HTC) (temp: 120–500 °C), pyrolysis process (temp.: 200–650 °C) and gasification and co-combustion process (temp.: 350–1600 °C). In the years 2015–2019, current research topics were: new torrefaction technologies (e.g., HTC), improvement of the physico-mechanical, chemical and energetic properties of produced fuel as well as the use of torrefied biomass in the process of pyrolysis, gasification and co-combustion. The raw materials used in all types of biomass thermal treatment were: energy crops, wood from fast-growing and exotic trees, waste from the agri-food industry, sewage sludge and microalgae.
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Demo, Pavel, Šárka Hošková, Marina Davydova, Petra Tichá, Alexej Sveshnikov, Jan Krňanský, and Zdeněk Kožíšek. "Nucleation on Polymer Nanofibers and their Controllable Conversion to Protective Layers: Preliminary Theoretical Study." Key Engineering Materials 466 (January 2011): 201–5. http://dx.doi.org/10.4028/www.scientific.net/kem.466.201.
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Nanofibers are very promising new type of material with a broad range of possible applications. The new NANOSPIDER technology opens a possibility to produce nanofabrics in an amount large enough for them to start being interesting as a construction material. There are many so-called passive applications of nanotextiles (including different types of filters and protective layers), and active applications, when the active chemical agent is incorporated in their structure. In the present paper, however, the new possible application of nanofabrics is proposed: as a base material on which technically interesting nanoclusters are heterogeneously nucleated. The basic thermodynamics of heterogeneous nucleation on nanofibers is considered. The extreme curvature of nanofibers manifests itself in an energetic barrier of nucleation, which is quite different from a case of nucleation on a flat surface. The expression for Gibbs energy of cluster formation is derived, taking into account the elastic strain resulting from a volume (or shape) changes during nucleation.
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Brunsteiner, Michael, Johannes Khinast, and Amrit Paudel. "Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study." Pharmaceutics 10, no. 3 (July 21, 2018): 101. http://dx.doi.org/10.3390/pharmaceutics10030101.
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Amorphous solid dispersions are considered a promising formulation strategy for the oral delivery of poorly soluble drugs. The limiting factor for the applicability of this approach is the physical (in)stability of the amorphous phase in solid samples. Minimizing the risk of reduced shelf life for a new drug by establishing a suitable excipient/polymer-type from first principles would be desirable to accelerate formulation development. Here, we perform Molecular Dynamics simulations to determine properties of blends of eight different polymer–small molecule drug combinations for which stability data are available from a consistent set of literature data. We calculate thermodynamic factors (mixing energies) as well as mobilities (diffusion rates and roto-vibrational fluctuations). We find that either of the two factors, mobility and energetics, can determine the relative stability of the amorphous form for a given drug. Which factor is rate limiting depends on physico-chemical properties of the drug and the excipients/polymers. The methods outlined here can be readily employed for an in silico pre-screening of different excipients for a given drug to establish a qualitative ranking of the expected relative stabilities, thereby accelerating and streamlining formulation development.
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IRLE, S., G. ZHENG, Z. WANG, and K. MOROKUMA. "THEORY–EXPERIMENT RELATIONSHIP OF THE "SHRINKING HOT GIANT" ROAD OF DYNAMIC FULLERENE SELF-ASSEMBLY IN HOT CARBON VAPOR." Nano 02, no. 01 (February 2007): 21–30. http://dx.doi.org/10.1142/s1793292007000362.
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Though subject to intensive studies, the formation mechanism of buckminsterfullerene C 60 and related higher fullerenes has long evaded discovery. To elucidate their atomistic self-assembly mechanism, we have performed high-temperature quantum chemical molecular dynamics simulations on carbon vapor model systems initially consisting of C 2 molecules. Our simulations reveal a coherent mechanism how highly ordered fullerene cages naturally self-assemble under nonequilibrium conditions, following a series of irreversible processes from the polymerization of C 2 molecules to vibrationally excited giant fullerenes, which then shrink by C 2 evaporation down to the smallest spherical, isolated pentagon rule obeying species C 70 and C 60 as the smallest and kinetically most stable species of the shrinking process. We show that the potential energy surface associated with giant fullerene cage growth, measured by an average cluster curvature, is downhill all the way, and in agreement with high-level energetics from density functional theory. This fullerene formation mechanism is a good example of dynamic self-assembly leading to dissipative structures far from thermodynamic equilibrium, and the "shrinking hot giant" road provides a natural explanation for the observed cage size distributions in a random optimization process consistent with several important experimental observations.
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Woledge, Roger C. "Douglas Robert Wilkie. 2 October 1922 – 21 May 1998." Biographical Memoirs of Fellows of the Royal Society 47 (January 2001): 481–95. http://dx.doi.org/10.1098/rsbm.2001.0029.
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D.R. Wilkie entered University College London (UCL), which was to be his lifelong academic home, in 1940 to study medicine on the shortened wartime course. He soon showed his great academic ability and won the Rockefeller Scholarship that took him to Yale University, New Haven, Connecticut, for the last year of his medical education, where he obtained his MD. He returned to University College Hospital as house physician in 1944 and, quite exceptionally, obtained his MRCP in that same academic year. The Physiology Department of UCL appointed him to an assistant lectureship in 1945 when he was 23 years old and, apart from a period of military service at the Institute of Aviation Medicine in Farnborough, from 1948 to 1950, he worked there until his retirement in 1988. During the period 1951–54 he held a Locke Fellowship of The Royal Society. In 1945 A.V. Hill, F.R.S., then nearly 60, had returned to his laboratories at UCL to resume the muscle research interrupted by the war. Wilkie evidently soon fell under his spell and he took up some of Hill's lifelong interests: the mechanics of muscle, its relation to human performance and the application of thermodynamics to muscle contraction. In addition, he adopted something of Hill's style of research, characterized by the application of basic principles and measurements from physics, mathematics and chemistry to the understanding of the behaviour of human or muscle, together with ingenuity in the invention of methods. Wilkie's research work started with the application of muscle mechanics to human movement. He critically tested the current theories of muscle mechanics and then took up the question of the supply of chemical energy for muscle contraction. Through initiating collaborations he brought together the experimental study of the chemical changes in muscle with that of the output of energy as heat and as work. These experiments, along with his 1960 review (12)*, put this subject of ‘chemical energetics of muscle contraction’ back on the thermodynamic rails from which it had strayed and allowed the subject to make further progress, exposing again the limitations of the current theories. In 1969 A.F. (later Sir Andrew) Huxley, F.R.S. (P.R.S. 1980–85), head of UCL's Physiology Department, stepped aside to take a Royal Society Chair and it was natural that Wilkie, by then holder of a personal chair and a major force in medical education, should be asked to lead the department. He filled that role conscientiously for 10 years. Although his personal involvement in scientific experimentation had consequently to be reduced during this period, his interest in muscle energy supply led to a new enthusiasm: the application of magnetic resonance spectroscopy, first to the study of isolated muscles, in collaboration with G.K. Radda (F.R.S. 1980) and D.G. Gadian in Oxford, and then, with his UCL colleagues R.H.T. Edwards (Medicine), D.T. Delpy (F.R.S. 1999) (Medical Physics) and E.O.R. Reynolds (F.R.S. 1993) (Paediatrics), to the study of the brains of newborn babies. Wilkie was elected to Fellowship of The Royal Society in 1971 and to Fellowship of UCL in 1972.
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Marinopoulos, A. G. "Binding and energetics of oxygen at the CuInSe2 chalcopyrite and the CuInSe2/CdS interface." Physica Scripta 97, no. 5 (April 14, 2022): 055810. http://dx.doi.org/10.1088/1402-4896/ac6462.
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Abstract The introduction of oxygen in thin-film solar cells based on the CuInSe2 compound and related CuInSe2/CdS devices has been known to affect their electrical properties, with a tendency of neutralizing part of the donor density and favoring a p-type behavior for the CuInSe2 (CIS) absorber material. The present study employed calculations based on density-functional theory supplemented with a hybrid-functional approach to determine the energetics of oxygen incorporation in the bulk CIS compound and the CIS/CdS heterojunction interface. The latter was represented by two distinct faceted interface variants. Oxygen atoms were assumed to exist both as interstitial and substitutional impurities, in the latter case occupying vacant selenium sites. The calculations identified the structural relaxation patterns and examined the thermodynamic stability of the impurity as a function of the electron and the elemental chemical potentials. Oxygen was found to incorporate favourably at the core of the CIS/CdS interfaces, in most cases by taking up a bridging position within the nearest In–In pair. The sites of the lowest-energy oxygen configurations were found to be associated with a copper-poor local environment, owing to the presence of copper vacancies or the relaxation-induced breaking of a copper-oxygen bond. The electronic structures of the CIS/CdS interfaces were also studied by analyzing the site-projected and layer-resolved densities of states for several layers within the interfacial cores. Oxygen introduced deep-lying nonbonding levels and impurity-host bonding states in the valence-energy region.
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De Bari, Benjamin, Dilip K. Kondepudi, and James A. Dixon. "Foraging Dynamics and Entropy Production in a Simulated Proto-Cell." Entropy 24, no. 12 (December 8, 2022): 1793. http://dx.doi.org/10.3390/e24121793.
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All organisms depend on a supply of energetic resources to power behavior and the irreversible entropy-producing processes that sustain them. Dissipative structure theory has often been a source of inspiration for better understanding the thermodynamics of biology, yet real organisms are inordinately more complex than most laboratory systems. Here we report on a simulated chemical dissipative structure that operates as a proto cell. The simulated swimmer moves through a 1D environment collecting resources that drive a nonlinear reaction network interior to the swimmer. The model minimally represents properties of a simple organism including rudimentary foraging and chemotaxis and an analog of a metabolism in the nonlinear reaction network. We evaluated how dynamical stability of the foraging dynamics (i.e., swimming and chemotaxis) relates to the rate of entropy production. Results suggested a relationship between dynamical steady states and entropy production that was tuned by the relative coordination of foraging and metabolic processes. Results include evidence in support of and contradicting one formulation of a maximum entropy production principle. We discuss the status of this principle and its relevance to biology.
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Miar, Marzieh, Abolfazl Shiroudi, Khalil Pourshamsian, Ahmad Oliaey, and Farhad Hatamjafari. "DFT study and NBO analysis of solvation/substituent effects of 3-phenylbenzo[d]thiazole-2(3H)-imine derivatives." Journal of the Serbian Chemical Society 85, no. 11 (2020): 1445–62. http://dx.doi.org/10.2298/jsc200421058m.
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In this work, to determine natural bond orbital (NBO) analysis, solvation and substituent effects for electron-releasing substituents (CH3, OH) and electron-withdrawing derivatives (Cl, NO2, CF3) in para positions on the molecular structure of the synthesized 3-phenylbenzo[d]thiazole-2(3H)-imine derivatives 1?6 (H (1), CH3 (2), Cl (3), OH (4), CF3 (5), NO2 (6)) in the selected solvents (acetone, toluene, and ethanol) and gas-phase employing polarizable continuum method (PCM) model were studied at the M06-2x/6- -311++G(d,p) level of theory. The relative stability of the studied compounds was affected by the possibility of intramolecular interactions between substituents and the electron donor/acceptor centers of the thiazole ring. Furthermore, atomic charges electron density, chemical thermodynamics, energetic properties, dipole moments, and the nucleus-independent chemical shifts (NICS) of the studied compounds and their relative stability are considered. The dipole moment values and the HOMO?LUMO energy gap reveal the different charge transfer possibilities within the considered molecules. Frontier molecular orbital (FMO) analysis revealed that compound 6 has very small HOMO-LUMO energy gaps in the considered phases, and thus is kinetically less stable. The obtained HOMO-LUMO energy gap corresponds to intramolecular hyperconjugative interactions ?? ?*. Finally, NBO analysis is carried out to demonstrate the charge transfer between localized bonds and lone pairs.
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Ers, Heigo, Liis Siinor, and Piret Pikma. "Visualizing the 2nd Layer: 4,4´-Bipyridine Adsorption on Sb(111) from EMImBF4." ECS Meeting Abstracts MA2022-01, no. 50 (July 7, 2022): 2124. http://dx.doi.org/10.1149/ma2022-01502124mtgabs.
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Room temperature ionic liquids (RTIL) have had a lot of attention in modern chemical research. Due to their high stability under applied electrode potential, the wide electrochemical window and dual usability as a solvent and an electrolyte RTILs have become very attractive in the field of applied electrochemistry and modern energetics [1]. Molecular self-assembly at solid surfaces, resulting in the formation of the nanostructures with well-controlled properties and functionality reveals fascinating perspectives in science and technology at nanoscale [2]. For instance, the smart tailoring of the structural properties of the functionalized electrodes enables SAMs to be used as protective coatings and for the fabrication of organic thin-film transistors and sensors, and as triggers of specific electrochemical processes. In this study the in situ STM and impedance spectroscopy methods have been applied to study the structure and properties of the electrochemically polished Sb(111) single crystal electrode | EMImBF4, and EMImBF4 + 1% 4,4´-bipyridine, interface. Using in situ scanning tunnelling microscopy, the adsorption/desorption of 4,4’-bipyridine was demonstrated and a dense underlying structure, formed below a sparse self-assembled monolayer, was visualized. The detection of two separate adsorbed layers indicates that the ordering of organic molecules could extend well beyond the monolayer on the electrode’s surface. These insights are of fundamental and practical importance in the development of nanoelectronics. References: [1] H. Ohno (Ed.), Electrochemical Aspects of Ionic Liquids, John Wiley & Sons, Inc., New Jersey, 2005, p.1. [2] T. Wandlowski, Phase Transitions in Two-dimensional Adlayers at Electrode Surfaces: Thermodynamics, Kinetics, and Structural Aspects, A.J. Bard, M. Stratmann (Eds.), Encyclopedia of Electrochemistry, Wiley VCH, Weinheim (2002) p. 383-471. Acknowledgments: This work was supported by the Estonian Research Council grant PSG249 and by the EU through the European Regional Development Fund under project TK141 (2014-2020.4.01.15-0011). For providing us with the computational resources, we would like to acknowledge the HPC Center of the University of Tartu.
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Lo, John M. H., Robert A. Marriott, Binod R. Giri, John M. Roscoe, and Mariusz Klobukowski. "A theoretical analysis of the kinetics of the reaction of atomic bromine with tetrahydrofuran." Canadian Journal of Chemistry 88, no. 11 (November 2010): 1136–45. http://dx.doi.org/10.1139/v10-092.
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The kinetic behaviour for the reaction of atomic bromine with tetrahydrofuran has been analysed using the information from quantum chemical calculations. Structures and energy profiles were first obtained using density functional theory (DFT) employing the Dunning’s basis sets of triple-zeta quality, and then for an accurate energetic description, single-point calculations were carried out at the coupled-cluster with single and double excitations (CCSD) and the fourth-order Møller–Plesset (MP4(SDQ)) levels of theory. The rate coefficients and the equilibrium constants for the potential reaction channels were obtained from the statistical rate theories and statistical thermodynamics, respectively, using the results of quantum chemical calculations; and the results were compared with our recently published experimental data. In terms of reaction mechanism, this reaction was found to be analogous to the reactions of the Br atom with 1,4-dioxane and with methanol, where the reaction proceeds via an addition–elimination mechanism. The dominant reaction channel involved coordination of the approaching Br atom to one of the hydrogen atoms adjacent to the ether oxygen atom, i.e., β-hydrogen abstraction is uncompetitive. Although the complexes formed by direct coordination of the Br atom to the ether oxygen atom appeared in the reaction mechanism, we were not able to link them specifically to any reaction. The density functional theory predicted an activation energy and enthalpy of reaction that were much smaller than the experimental values, which led to an overestimation of the theoretical rate coefficients. The source of this discrepancy could be attributed to the overbinding of the transition states and of the tetrahydrofuranyl radical by DFT. Single-point calculations at the DFT structures using the CCSD and MP4(SDQ) methods yielded an accurate energetic description of the reaction of tetrahydrofuran with bromine, resulting in rate coefficients that showed excellent agreement with the experimental values.