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1
Du, Quan, Zhen Wang, and Vern L. Schramm. "Human DNMT1 transition state structure." Proceedings of the National Academy of Sciences 113, no. 11 (February 29, 2016): 2916–21. http://dx.doi.org/10.1073/pnas.1522491113.
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Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys1226 to cytosine (Cyt) C6, methyl transfer from S-adenosyl-l-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys1226 attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.
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Williams, Ian H. "Catalysis: transition-state molecular recognition?" Beilstein Journal of Organic Chemistry 6 (November 3, 2010): 1026–34. http://dx.doi.org/10.3762/bjoc.6.117.
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The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.
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Lee, Sang Jin, and Tamer A. Zaki. "Simulations of natural transition in viscoelastic channel flow." Journal of Fluid Mechanics 820 (May 5, 2017): 232–62. http://dx.doi.org/10.1017/jfm.2017.198.
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Orderly, or natural, transition to turbulence in dilute polymeric channel flow is studied using direct numerical simulations of a FENE-P fluid. Three Weissenberg numbers are simulated and contrasted to a reference Newtonian configuration. The computations start from infinitesimally small Tollmien–Schlichting (TS) waves and track the development of the instability from the early linear stages through nonlinear amplification, secondary instability and full breakdown to turbulence. At the lowest elasticity, the primary TS wave is more unstable than the Newtonian counterpart, and its secondary instability involves the generation of $\unicode[STIX]{x1D6EC}$-structures which are narrower in the span. These subsequently lead to the formation of hairpin packets and ultimately breakdown to turbulence. Despite the destabilizing influence of weak elasticity, and the resulting early transition to turbulence, the final state is a drag-reduced turbulent flow. At the intermediate elasticity, the growth rate of the primary TS wave matches the Newtonian value. However, unlike the Newtonian instability mode which reaches a saturated equilibrium condition, the instability in the polymeric flow reaches a periodic state where its energy undergoes cyclical amplification and decay. The spanwise size of the secondary instability in this case is commensurate with the Newtonian $\unicode[STIX]{x1D6EC}$-structures, and the extent of drag reduction in the final turbulent state is enhanced relative to the lower elasticity condition. At the highest elasticity, the exponential growth rate of the TS wave is weaker than the Newtonian flow and, as a result, the early linear stage is prolonged. In addition, the magnitude of the saturated TS wave is appreciably lower than the other conditions. The secondary instability is also much wider in the span, with weaker ejection and without hairpin packets. Instead, streamwise-elongated streaks are formed and break down to turbulence via secondary instability. The final state is a high-drag-reduction flow, which approaches the Virk asymptote.
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Rico-Pasto, Marc, Annamaria Zaltron, and Felix Ritort. "Force Dependence of Proteins’ Transition State Position and the Bell–Evans Model." Nanomaterials 11, no. 11 (November 11, 2021): 3023. http://dx.doi.org/10.3390/nano11113023.
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Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and measure their free energy landscape. The force–extension curves of single proteins often present large hysteresis, with unfolding forces that are higher than refolding ones. Therefore, the high energy of the transition state (TS) in these molecules precludes kinetic rates measurements in equilibrium hopping experiments. In irreversible pulling experiments, force-dependent kinetic rates measurements show a systematic discrepancy between the sum of the folding and unfolding TS distances derived by the kinetic Bell–Evans model and the full molecular extension predicted by elastic models. Here, we show that this discrepancy originates from the force-induced movement of TS. Specifically, we investigate the highly kinetically stable protein barnase, using pulling experiments and the Bell–Evans model to characterize the position of its kinetic barrier. Experimental results show that while the TS stays at a roughly constant distance relative to the native state, it shifts with force relative to the unfolded state. Interestingly, a conversion of the protein extension into amino acid units shows that the TS position follows the Leffler–Hammond postulate: the higher the force, the lower the number of unzipped amino acids relative to the native state. The results are compared with the quasi-reversible unfolding–folding of a short DNA hairpin.
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Sihelniková, Lucie, Stanislav Kozmon, and Igor Tvaroška. "DFT and Docking Study of Potential Transition State Analogue Inhibitors of Glycosyltransferases." Collection of Czechoslovak Chemical Communications 73, no. 5 (2008): 591–607. http://dx.doi.org/10.1135/cccc20080591.
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Conformational behavior of the [(2S,3R,4R,5S)-3,4,5-trihydroxy-2-(phenylsulfanyl)tetrahydrofuran-2-yl]methyl sulfate anion (2), which is the potential transition state (TS) analogue of the inverting glycosyltransferases, was studied by means of two-dimensional potential-energy maps, using a density functional theory method at the B3LYP/6-31+G* level. The maps revealed the presence of eight low-energy domains which were refined at the B3LYP/6-311++G** level and led to six conformers in vacuum. In aqueous solution, two conformers dominate at equilibrium. The preferred conformers superimpose well with the transition state structure, as determined previously for glycosyltransferase GnT-I. The conformations of 2 in the active site of glycosyltransferase GnT-I were obtained by docking methods. It was found that one of the two best docking poses mimics the binding mode of TS. These results suggest that the proposed TS mimics 2 have the potential to be used as a scaffold for the design of TS analogue inhibitors.
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Martínez-Núñez, Emilio. "An automated transition state search using classical trajectories initialized at multiple minima." Physical Chemistry Chemical Physics 17, no. 22 (2015): 14912–21. http://dx.doi.org/10.1039/c5cp02175h.
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Ammal, Salai Cheettu, and Hiroshi Yamataka. "Linear free energy relationship and kinetic isotope effects as measures for the transition-state variation A case of the neophyl system." Canadian Journal of Chemistry 83, no. 9 (September 1, 2005): 1606–14. http://dx.doi.org/10.1139/v05-209.
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Ab initio calculations at the MP2/6-31G* level and density functional theory (B3LYP/6-311+G**) calculations have been performed on acid-catalyzed ionizations of substituted neophyl alcohols to investigate whether a variation of the transition-state (TS) structure is reflected in the kinetic isotope effects (KIE) and linear free energy relationship. The effect of substituents on KIEs, TS structures, and activation and reaction energies was calculated. This study revealed that a curved Brønsted-type plot could arise for a single-step process from the variation of TS structure with the substituent, whereas the Hammett plots with a dual-parameter treatment can not detect such TS variation. The variation of KIEs at various positions of neophyl alcohol reflects the variation of TS structures in a manner consistent with the More O'Ferrall Jencks type reaction diagram analyses.Key words: transition-state variation, substituent effect, kinetic isotope effect, linear free energy relationship.
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Wang, Chuan-Ming, Yang-Dong Wang, and Zai-Ku Xie. "General scaling relations and prediction of transition state energies in CHA/AlPO-34-structured zeolite catalysis related to the methanol-to-olefins conversion." Catalysis Science & Technology 9, no. 9 (2019): 2245–52. http://dx.doi.org/10.1039/c9cy00534j.
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Scaling relations of transition state (TS) energies with the acid strength were established. The inherent scaling relations and the acidity sensitivity dependence on charge variation enable fast prediction of TS energies in zeolite catalysis.
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Miton, Charlotte M., Stefanie Jonas, Gerhard Fischer, Fernanda Duarte, Mark F. Mohamed, Bert van Loo, Bálint Kintses, et al. "Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset." Proceedings of the National Academy of Sciences 115, no. 31 (July 16, 2018): E7293—E7302. http://dx.doi.org/10.1073/pnas.1607817115.
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The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Structural, kinetic, and in silico characterizations of the evolutionary intermediates revealed that two key mutations, T50A and M72V, locally reshaped the active site, improving access to the catalytic machinery for the phosphonate. Measured transition state (TS) charge changes along the trajectory suggest the creation of a new Michaelis complex (E•S, enzyme–substrate), with enhanced leaving group stabilization in the TS for the promiscuous phosphonate (βleavinggroup from −1.08 to −0.42). Rather than altering the catalytic machinery, evolutionary repurposing was achieved by fine-tuning the molecular recognition of the phosphonate in the Michaelis complex, and by extension, also in the TS. This molecular scenario constitutes a mechanistic alternative to adaptation solely based on enzyme flexibility and conformational selection. Instead, rapid functional transitions between distinct chemical reactions rely on the high reactivity of permissive active-site architectures that allow multiple substrate binding modes.
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BOUCHAREB, A., M. RAMÓN MEDRANO, and N. G. SÁNCHEZ. "SEMICLASSICAL (QFT) AND QUANTUM (STRING) ROTATING BLACK HOLES AND THEIR EVAPORATION: NEW RESULTS." International Journal of Modern Physics A 22, no. 08n09 (April 10, 2007): 1627–48. http://dx.doi.org/10.1142/s0217751x07035252.
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Combination of both quantum field theory (QFT) and string theory in curved backgrounds in a consistent framework, the string analogue model, allows us to provide a full picture of the Kerr–Newman black hole and its evaporation going beyond the current picture. We compute the quantum emission cross-section of strings by a Kerr–Newman black hole (KNbh). It shows the black hole emission at the Hawking temperature T sem in the early stage of evaporation and the new string emission featuring a Hagedorn transition into a string state of temperature Ts at the last stages. New bounds on J and Q emerge in the quantum string regime (besides the known ones of the classical/semiclassical QFT regime). The last state of evaporation of a semiclassical Kerr–Newman black hole with mass M > m Pl , angular momentum J and charge Q is a string state of temperature Ts, string mass Ms, J = 0 and Q = 0, decaying as usual quantum strings do into all kinds of particles. (Naturally, in this framework, there is no loss of information, (there is no paradox at all).) We compute the string entropy Ss(m, j) from the microscopic string density of states of mass m and spin mode j, ρ(m, j). (Besides the Hagedorn transition at Ts) we find for high j (extremal string states j → m2α′c), a new phase transition at a temperature [Formula: see text], higher than Ts. By precisely identifying the semiclassical and quantum (string) gravity regimes, we find a new formula for the Kerr black hole entropy S sem (M, J), as a function of the usual Bekenstein–Hawking entropy [Formula: see text]. For M ≫ m Pl and J < GM2/c, [Formula: see text] is the leading term, but for high angular momentum, (nearly extremal case J = GM2/c), a gravitational phase transition operates and the whole entropy S sem is drastically different from the Bekenstein–Hawking entropy [Formula: see text]. This new extremal black hole transition occurs at a temperature T sem J = (J/ℏ)T sem , higher than the Hawking temperature T sem .
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Beneitez, Miguel, Yohann Duguet, Philipp Schlatter, and Dan S. Henningson. "Edge tracking in spatially developing boundary layer flows." Journal of Fluid Mechanics 881 (October 24, 2019): 164–81. http://dx.doi.org/10.1017/jfm.2019.763.
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Recent progress in understanding subcritical transition to turbulence is based on the concept of the edge, the manifold separating the basins of attraction of the laminar and the turbulent state. Originally developed in numerical studies of parallel shear flows with a linearly stable base flow, this concept is adapted here to the case of a spatially developing Blasius boundary layer. Longer time horizons fundamentally change the nature of the problem due to the loss of stability of the base flow due to Tollmien–Schlichting (TS) waves. We demonstrate, using a moving box technique, that efficient long-time tracking of edge trajectories is possible for the parameter range relevant to bypass transition, even if the asymptotic state itself remains out of reach. The flow along the edge trajectory features streak switching observed for the first time in the Blasius boundary layer. At long enough times, TS waves co-exist with the coherent structure characteristic of edge trajectories. In this situation we suggest a reinterpretation of the edge as a manifold dividing the state space between the two main types of boundary layer transition, i.e. bypass transition and classical transition.
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Kalu, Georgina I., Collins I. Ubochi, and Ikenna Onyido. "Reactions of aryl dimethylphosphinothioate esters with anionic oxygen nucleophiles: transition state structure in 70% water–30% ethanol." RSC Advances 11, no. 15 (2021): 8833–45. http://dx.doi.org/10.1039/d0ra10759j.
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Erofeev, Dmitry, Artjoms Jablunovskis, and Elena Chukalina. "Optical spectroscopy of ErFe3(BO3)4: detection of phase transitions and crystal-field levels of the Er3+ ground multiplet." EPJ Web of Conferences 185 (2018): 07002. http://dx.doi.org/10.1051/epjconf/201818507002.
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High-resolution spectra of oriented ErFe3(BO3)4 single crystals are registered in the spectral range 500 – 8000 cm-1 at various temperatures (4 – 470 K). The temperature behaviour of the phonon mode at 976 cm-1 allowed us to register a structural phase transition at TS=431 K. The energies of crystal-field levels of the ground 4I15/2 and the first excited 4I13/2 multiplets of the Er3+ ion are determined in the paramagnetic state of ErFe3(BO3)4. The exchange splitting of the ground Kramers doublet in the magnetically ordered state was found to be Δ0=6.3±1 cm-1. The interference occurring due to birefringence in the single crystals was also registered. The temperature dependence of the position of the maximum of the interference band demonstrates two anomalies, at TN and TS, associated with the phase transitions in ErFe3(BO3)4.
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Wang, Q., P. Duan, J. Y. Wang, L. Chang, J. X. Deng, and A. J. Yuan. "Effects of different sintering temperatures on microstructural, transport, and magnetic properties of La0.93Sb0.07MnO3 compound." International Journal of Modern Physics B 28, no. 24 (August 5, 2014): 1450166. http://dx.doi.org/10.1142/s0217979214501665.
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Polycrystalline La 0.93 Sb 0.07 MnO 3 ceramics were synthesized using solid-state reaction method. The samples were sintered at different temperatures ranging from 1100°C to 1200°C. It is observed that microstructural, transport and magnetic properties of La 0.93 Sb 0.07 MnO 3 compounds strongly depend on sintering temperatures (TS). With TS increasing, the degree of lattice distortion has been weakened, the grain size has become larger and grain boundaries have decreased. Furthermore, the resistivity was reduced, and metal–insulator transition temperature was enhanced; the saturation magnetization per unit mass has decreased with TS increasing. These effects of different TS on physical properties can be explained by the structure distortion and grain boundary contributions for La 0.93 Sb 0.07 MnO 3 compounds.
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BOUCHAREB, A., M. RAMÓN MEDRANO, and N. G. SÁNCHEZ. "SEMICLASSICAL (QFT) AND QUANTUM (STRING) ANTI-DE SITTER REGIMES: NEW RESULTS." International Journal of Modern Physics A 22, no. 07 (March 20, 2007): 1395–416. http://dx.doi.org/10.1142/s0217751x07035008.
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We compute the quantum string entropy Ss(m, H) from the microscopic string density of states ρs(m, H) of mass m in Anti-de Sitter space–time. For high m, (high Hm → c/α′), no phase transition occurs at the Anti-de Sitter string temperature Ts = (1/2πkB)L cl c2/α′, which is higher than the flat space (Hagedorn) temperature ts. (L cl = c/H, the Hubble constant H acts as producing a smaller string constant α′ and thus, a higher tension). Ts is the precise quantum dual of the semiclassical (QFT) Anti-de Sitter temperature scale T sem = ℏc/(2πkBL cl ). We compute the quantum string emission σ string by a black hole in Anti-de Sitter (or asymptotically Anti-de Sitter) space–time (bhAdS). For T sem bhAdS ≪ Ts (early evaporation stage), it shows the QFT Hawking emission with temperature T sem bhAdS (semiclassical regime). For T sem bhAdS → Ts, it exhibits a phase transition into a Anti-de Sitter string state of size [Formula: see text], and Anti-de Sitter string temperature Ts. New string bounds on the black hole emerge in the bhAdS string regime. The bhAdS string regime determines a maximal value for H : H max = 0.841c/ls. The minimal black hole radius in Anti-de Sitter space–time turns out to be rg min = 0.841ls, and is larger than the minimal black hole radius in de Sitter space–time by a numerical factor equal to 2.304. We find a new formula for the full AdS entropy S sem (H), as a function of the usual Bekenstein–Hawking entropy [Formula: see text]. For L cl ≫ ℓ Planck , i.e. for low H ≪ c/ℓ Planck , or classical regime, [Formula: see text] is the leading term with its logarithmic correction, but for high H ≥ c/ℓ Planck or quantum regime, no phase transition operates, in contrast to de Sitter space, and the entropy S sem (H) is very different from the Bekenstein–Hawking term [Formula: see text].
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Gallardo-Fuentes, Sebastián, Ricardo A. Tapia, Renato Contreras, and Paola R. Campodónico. "Site activation effects promoted by intramolecular hydrogen bond interactions in SNAr reactions." RSC Adv. 4, no. 58 (2014): 30638–43. http://dx.doi.org/10.1039/c4ra04725g.
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The nucleophilic aromatic substitution reaction of benzohydrazide derivatives towards 2-chloro-5-nitropyrimidine is used as model system to experimentally and theoretically show that intramolecular hydrogen-bond formation operates as a perturbation that elicits a dual response at the reaction center of the transition state (TS) structure.
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Suggs, Kelvin, and Alfred Z. Msezane. "Doubly-Charged Negative Ions as Novel Tunable Catalysts: Graphene and Fullerene Molecules Versus Atomic Metals." International Journal of Molecular Sciences 21, no. 18 (September 13, 2020): 6714. http://dx.doi.org/10.3390/ijms21186714.
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The fundamental mechanism underlying negative-ion catalysis involves bond-strength breaking in the transition state (TS). Doubly-charged atomic/molecular anions are proposed as novel dynamic tunable catalysts, as demonstrated in water oxidation into peroxide. Density Functional Theory TS calculations have found a tunable energy activation barrier reduction ranging from 0.030 eV to 2.070 eV, with Si2−, Pu2−, Pa2− and Sn2− being the best catalysts; the radioactive elements usher in new application opportunities. C602− significantly reduces the standard C60− TS energy barrier, while graphene increases it, behaving like cationic systems. According to their reaction barrier reduction efficiency, variation across charge states and systems, rank-ordered catalysts reveal their tunable and wide applications, ranging from water purification to biocompatible antiviral and antibacterial sanitation systems.
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ZHU, Y. D., X. A. LI, H. H. LIAO, L. J. SUN, C. S. XIONG, and Y. H. XIONG. "ELECTRICAL-MAGNETIC TRANSPORT AND MAGNETORESISTANCE IN La0.7Ca0.3MnO3/Bi2O3 COMPOSITES." Modern Physics Letters B 24, no. 04n05 (February 20, 2010): 439–51. http://dx.doi.org/10.1142/s0217984910022512.
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The structure and electrical-magnetic transport properties of ( La 0.7 Ca 0.3 MnO 3)1-x/( Bi 2 O 3)x has been investigated systematically by conventional solid-state reaction method. The composite samples were obtained by pure La 0.7 Ca 0.3 MnO 3 (LCMO) and Bi 2 O 3 powders and sintered at different temperature (Ts) 800°C and 1300°C for 2 h. For Ts=800°C samples, the results of X-ray diffraction (XRD) and scanning electronic microscopy (SEM) indicate that Bi 2 O 3 and LCMO coexist in the composites and Bi 2 O 3 mainly segregates at the grain boundaries or grain surface of LCMO, and double peaks related to the metal-to-insulator (M–I) transition have been observed. Corresponding to the two M–I transition peaks, the curves of magnetoresistance (MR) against temperature also showed two peaks for all composites. But for Ts = 1300°C samples, Bi 3+ ions mainly enter into the lattice of LCMO to form reaction products layer La 0.7-x Bi x Ca 0.3 MnO 3, only one peak occurs around the M–I transition temperature and the MR around T P has been enhanced. The results also indicate that the added Bi 2 O 3 has an important effect on the LFMR. These phenomena can be explained by the double exchange (DE) mechanism, the grain boundary effect and the intrinsic transport properties together. And the grain surface state of the particles is a key factor influencing the magnetoresistance effects.
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Li, Xu, Ting Fan, Qingji Wang, and Tongfei Shi. "A Mechanistic Study of Asymmetric Transfer Hydrogenation of Imines on a Chiral Phosphoric Acid Derived Indium Metal-Organic Framework." Molecules 27, no. 23 (November 26, 2022): 8244. http://dx.doi.org/10.3390/molecules27238244.
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A density functional theory (DFT) study is reported to examine the asymmetric transfer hydrogenation (ATH) of imines catalyzed by an indium metal-organic framework (In-MOF) derived from a chiral phosphoric acid (CPA). It is revealed that the imine and reducing agent (i.e., thiazoline) are simultaneously adsorbed on the CPA through H-bonding to form an intermediate, subsequently, a proton is transferred from thiazoline to imine. The transition state TS-R and TS-S are stabilized on the CPA via H-bonding. Compared to the TS-S, the TS-R has shorter H-bonding distances and longer C-H···π distances, it is more stable and experiences less steric hindrance. Consequently, the TS-R exhibits a lower activation barrier affording to the (R)-enantiomer within 68.1% ee in toluene. Imines with substituted groups such as −NO2, −F, and −OCH3 are used to investigate the substitution effects on the ATH. In the presence of an electron-withdrawing group like −NO2, the electrophilicity of imine is enhanced and the activation barrier is decreased. The non-covalent interactions and activation-strain model (ASM) analysis reveal that the structural distortions and the differential noncovalent interactions of TSs in a rigid In-MOF provide the inherent driving force for enantioselectivity. For −OCH3 substituted imine, the TS-S has the strongest steric hindrance, leading to the highest enantioselectivity. When the solvent is changed from toluene to dichloromethane, acetonitrile, and dimethylsulfoxide with increasing polarity, the activation energies of transition state increase whereas their difference decreases. This implies the reaction is slowed down and the enantioselectivity becomes lower in a solvent of smaller polarity. Among the four solvents, toluene turns out to be the best for the ATH. The calculated results in this study are in fairly good agreement with experimental observations. This study provides a mechanistic understanding of the reaction mechanism, as well as substitution and solvent effects on the activity and enantioselectivity of the ATH. The microscopic insights are useful for the development of new chiral MOFs toward important asymmetric reactions.
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KOYAKUMARU, TAKATOSHI, and HIROFUMI NAKANO. "Effects of preincubation on the gelatinization of cassava and corn starch suspensions containing sodium hydroxide as a main component of corrugating adhesives." TAPPI Journal 18, no. 5 (June 1, 2019): 321–29. http://dx.doi.org/10.32964/tj18.5.321.
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Effects of the preincubation temperature and the caustic-ratio, the molar ratio of sodium hydroxide to starch glucose residue, on the gelatinization of cassava starch and corn starch suspensions were studied using differential scanning calorimetry in view of utilization for corrugating adhesives. The gelatinization temperature and enthalpy change of cassava starch suspensions after the preincubation at 30°C decreased as the caustic-ratio increased, similar to those of corn starch ones: The gelatinization starting temperature (Ts) decreased considerably more than the peak temperature and the conclusion temperature (Tc). Although Ts lowered and the width of gelatinization temperature expanded, compared with those of corn starch suspensions, the two starch suspensions with the same half gelatinization transition temperature showed similar gelatinization characteristics of almost the same Ts and Tc. During 1 h-preincubations at 30°C–50°C, the starch granules with Ts that were lowered considerably below each preincubation temperature by sodium hydroxide showed limited gelatinization. The gelatinization transition did not rapidly spread over the whole suspension, but progressed stepwise in response to the increase of the causticratio and the rise of the preincubation temperature. In a prolonged preincubation at a constant temperature, Ts gradually rose at higher caustic-ratios in which stepwise gelatinization commenced. Although the starch gelatinization was irreversible and not in a stable equilibrium state for a long time, we concluded that such stepwise gelatinization progress controlled the practical preparation and use of corrugating adhesives.
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Shan, Xiao, and David C. Clary. "Application of one-dimensional semiclassical transition state theory to the CH 3 OH + H ⇌ CH 2 OH/CH 3 O + H 2 reactions." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 376, no. 2115 (February 5, 2018): 20170147. http://dx.doi.org/10.1098/rsta.2017.0147.
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The rate constants of the two branches of H-abstractions from CH 3 OH by the H-atom and the corresponding reactions in the reverse direction are calculated using the one-dimensional semiclassical transition state theory (1D SCTST). In this method, only the reaction mode vibration of the transition state (TS) is treated anharmonically, while the remaining internal degrees of freedom are treated as they would have been in a standard TS theory calculation. A total of eight ab initio single-point energy calculations are performed in addition to the computational cost of a standard TS theory calculation. This allows a second-order Richardson extrapolation method to be employed to improve the numerical estimation of the third- and fourth-order derivatives, which in turn are used in the calculation of the anharmonic constant. Hindered-rotor (HR) vibrations are identified in the equilibrium states of CH 3 OH and CH 2 OH, and the TSs of the reactions. The partition function of the HRs are calculated using both a simple harmonic oscillator model and a more sophisticated one-dimensional torsional eigenvalue summation (1D TES) method. The 1D TES method can be easily adapted in 1D SCTST computation. The resulting 1D SCTST with 1D TES rate constants show good agreement to previous theoretical and experimental works. The effects of the HR on rate constants for different reactions are also investigated. This article is part of the theme issue ‘Modern theoretical chemistry’.
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Abell, Amy N., Deborah A. Granger, Nancy L. Johnson, Nicole Vincent-Jordan, Christopher F. Dibble, and Gary L. Johnson. "Trophoblast Stem Cell Maintenance by Fibroblast Growth Factor 4 Requires MEKK4 Activation of Jun N-Terminal Kinase." Molecular and Cellular Biology 29, no. 10 (March 16, 2009): 2748–61. http://dx.doi.org/10.1128/mcb.01391-08.
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ABSTRACT Trophoblast differentiation during placentation involves an epithelial-mesenchymal transition (EMT) with loss of E-cadherin and gain of trophoblast invasiveness. Mice harboring a point mutation that renders inactive the mitogen-activated protein kinase kinase kinase MEKK4 exhibit dysregulated placental development with increased trophoblast invasion. Isolated MEKK4 kinase-inactive trophoblast stem (TS) cells cultured under undifferentiating, self-renewing conditions in the presence of fibroblast growth factor 4 (FGF4) display increased expression of Slug, Twist, and matrix metalloproteinase 2 (MMP2), loss of E-cadherin, and hyperinvasion of extracellular matrix, each a hallmark of EMT. MEKK4 kinase-inactive TS cells show a preferential differentiation to Tpbpα- and Gcm1-positive trophoblasts, which are indicative of spongiotrophoblast and syncytiotrophoblast differentiation, respectively. FGF4-stimulated Jun N-terminal kinase (JNK) and p38 activity is markedly reduced in MEKK4 kinase-inactive TS cells. Chemical inhibition of JNK in wild-type TS cells induced a similar EMT response as loss of MEKK4 kinase activity, including inhibition of E-cadherin expression and increased expression of Slug, MMP2, Tpbpα, and Gcm1. Chromatin immunoprecipitation analyses revealed changes in AP-1 composition with increased Fra-2 and decreased Fra-1 and JunB binding to the regulatory regions of Gcm1 and MMP2 genes in MEKK4 kinase-inactive TS cells. Our results define MEKK4 as a signaling hub for FGF4 activation of JNK that is required for maintenance of TS cells in an undifferentiated state.
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Feder, J. N., C. J. Guidos, B. Kusler, C. Carswell, D. Lewis, and R. T. Schimke. "A cell cycle analysis of growth-related genes expressed during T lymphocyte maturation." Journal of Cell Biology 111, no. 6 (December 1, 1990): 2693–701. http://dx.doi.org/10.1083/jcb.111.6.2693.
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Fetal liver or bone marrow-derived T lymphocyte precursors undergo extensive, developmentally regulated proliferation in response to inductive signals from the thymic microenvironment. We have used neonatal mouse thymocytes size-separated by centrifugal elutriation to study the cell cycle stage-specific expression of several genes associated with cell proliferation. These include genes involved in the biosynthesis of deoxyribonucleotide precursors, such as dihydrofolate reductase (DHFR), thymidylate synthase (TS), and the M1 and M2 subunits of ribonucleotide reductase, as well as c-myc, a cellular oncogene of unknown function. Using nuclear run-on assays, we observed that the transcription rates for these genes, with the exception of TS, are essentially invariant not only throughout the cell cycle in proliferating cells, but also in noncycling (G0) cells. The TS gene showed a transient increase in transcription rate in cells which bordered between a proliferating and nonproliferating status. Studies of an elutriated T cell line, S49.1, yielded similar results, indicating that the process of immortalization has not affected the transcriptional regulation of these genes. Analysis of steady-state mRNA levels using an RNase protection assay demonstrated that the levels of DHFR and TS mRNA accumulate as thymocytes progress through the cell cycle. In contrast, only the M2 subunit of ribonucleotide reductase showed cyclic regulation. Finally, in contrast to cultured cell models, we observed an abrupt fivefold increase in the steady-state level of c-myc mRNA in the transition from G1 to S-phase. We conclude from these studies that the transcriptional regulation of specific genes necessary for cellular proliferation is a minor component of the developmental modulation of the thymocyte cell cycle.
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Ma, Xinyou, and William L. Hase. "Perspective: chemical dynamics simulations of non-statistical reaction dynamics." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 375, no. 2092 (March 20, 2017): 20160204. http://dx.doi.org/10.1098/rsta.2016.0204.
Full textAbstract:
Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’.
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Kahlert, Elin, Martina Blaschke, Knut Brockmann, Clemens Freiberg, Onno E. Janssen, Nikolaus Stahnke, Domenika Strik, et al. "Deficient knowledge in adult Turner syndrome care as an incentive to found Turner centers in Germany." Endocrine Connections 8, no. 11 (November 2019): 1483–92. http://dx.doi.org/10.1530/ec-19-0418.
Full textAbstract:
Objective Turner syndrome (TS) is characterized by the complete or partial loss of the second sex chromosome and associated with a wide range of clinical manifestations. We aimed to assess the medical care of adult patients with TS in Germany. Design Retrospective multicenter observational study. Methods Data were collected from medical records of 258 women with TS treated between 2001 and 2017 in five non-university endocrinologic centers in Germany. Results Mean age was 29.8 ± 11.6 years, mean height 152 ± 7.7 cm, and mean BMI 26.6 ± 6.3 kg/m2. The karyotype was known in 50% of patients. Information on cholesterol state, liver enzymes, and thyroid status was available in 81–98% of women with TS; autoimmune thyroiditis was diagnosed in 37%. Echocardiography was performed in 42% and cardiac MRI in 8.5%, resulting in a diagnosis of cardiovascular disorder in 28%. Data on growth hormone therapy were available for 40 patients (15%) and data concerning menarche in 157 patients (61%). Conclusion In 258 women with TS, retrospective analysis of healthcare data indicated that medical management was focused on endocrine manifestations. Further significant clinical features including cardiovascular disease, renal malformation, liver involvement, autoimmune diseases, hearing loss, and osteoporosis were only marginally if at all considered. Based on this evaluation and in accordance with recent guidelines, we compiled a documentation form facilitating the transition from pediatric to adult care and further medical management of TS patients. The foundation of Turner Centers in March 2019 will improve the treatment of TS women in Germany.
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Svensson, Peder, and Nils-Åke Bergman. "Isotope Effects and Concerted Two-Hydron-Transfer between Formamidine Molecules." Zeitschrift für Naturforschung A 44, no. 5 (May 1, 1989): 473–79. http://dx.doi.org/10.1515/zna-1989-0517.
Full textAbstract:
With the intention to assist mechanistic studies of two-hydron-transfer reactions using 1H/2H isotope effects we have carried out theoretical studies of the two-hydron-transfer reaction between formamidine molecules. The ab initio STO-3G potential energy surface has been calculated and all stationary points characterized by their force constant matrices. With this basis set the two hydrons are transferred concertedly and synchronously. The transition state (TS) has D2h symmetry. 1H/2H isotope effects were calculated using the Bebovib-IV program. Our results deviated from predictions made from common simple vibrational models. The isotope effects are dominated by the zero-pointenergy contribution. The effect due to the stretching vibrations of the initial state is to a small extent counteracted by stretching of the TS. The bending vibrations appear to play a dominant role in reducing the magnitude of the isotope effect for the two-hydron-transfer reaction to a value expected for a one-hydron-transfer reaction.
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Ma, Li, Zhi-Peng Wang, Guo-Hua Huang, Jin-Li Huang, Ping-Ying Tang, and Tou-Wen Fan. "Magnetic Phase Transition, Elastic and Thermodynamic Properties of L12-(Ni,Cu)3(Al,Fe,Cr) in 3d High-Entropy Alloys." Crystals 10, no. 12 (December 2, 2020): 1102. http://dx.doi.org/10.3390/cryst10121102.
Full textAbstract:
The phase stability and elastic properties of paramagnetic (PM), ferromagnetic (FM) and antiferromagnetic (AFM) phases in L12-(Ni,Cu)3(Al,Fe,Cr) alloy are first investigated using the exact muffin-tin orbitals (EMTO) method in combination with the coherent potential approximation (CPA). The result shows the AFM structure phase of the three is the most stable in the ground state. Calculated elastic constants show that all the phases are mechanically stable, and have uncovered that L12-(Ni,Cu)3(Al,Fe,Cr) can achieve good strength and ductility simultaneously. Then, crucial thermal properties are described satisfactorily using the Debye–Grüneisen model, showing heat capacity, Gibbs free energy G, the competitive contribution of entropy −TS and enthalpy H exhibiting significant temperature dependences. Moreover, the magnetic phase transition thermodynamics was studied, which suggests that −TS has a primary contribution to Gibbs free energy and may play a key role in the phase transition. The present results can benefit the understanding of the mechanical, thermodynamic and magnetic properties of the L12 structure phase in 3d high-entropy alloys.
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Rondeau, David, Yves Gimbert, Károly Vékey, Laszlo Dráhos, Mathieu Turbiez, Pierre Frère, and Jean Roncali. "Mass spectrometry evidence for self-rigidification of π-conjugated oligomers containing 3,4-ethylenedioxythiophene groups using RRKM theory and internal energy calibration." European Journal of Mass Spectrometry 25, no. 2 (April 2019): 239–50. http://dx.doi.org/10.1177/1469066718811712.
Full textAbstract:
The self-rigidification of ionized π-conjugated systems based on two combinations of thiophene (T) and 3,4-Ethylenedioxythiophene (E) is investigated using mass-analyzed ion kinetic energy spectrometry (MIKES) of ions produced from electron impact ionization at 70 eV. The m/z 446 radical cations of the two isomers ETTE and TEET lead to detect m/z 418 and 390 daughter ions. The MIKE spectra differ only by the intensities of these fragment ions. As the m/z 418 daughter ion is produced through a same retro-Diels Alder reaction whatever the fragmenting isomer, the difference in daughter ion intensities is interpreted in term of unimolecular dissociation rate constants ( k( Eint)) ratios. Considering that the transition state (TS) of such reaction is attributed to a quinoid form, equivalent vibration modes are assumed for the TS of both dissociating ETTE and TEET radical cations. As a result, by using the Rice–Ramsperger–Kassel–Marcus (RRKM) theory, the difference in daughter ion intensities is interpreted by considering that the fragmenting ion is more or less ordered in its ground state than at the transition state, resulting from the influence of the number of the S…O interactions in the planarization of the TEET ion toward the ETTE charged species. The comparison of this behavior in MIKES experiments is supported by the modeling of ion behavior in mass spectrometer and the calibration in internal energy of the radical cations produced in an EI source.
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da Silva, Jorge Alberto Valle, Ander Francisco Pereira, Steven R. LaPlante, Kamil Kuca, Teodorico Castro Ramalho, and Tanos Celmar Costa França. "Reactivation of VX-Inhibited Human Acetylcholinesterase by Deprotonated Pralidoxime. A Complementary Quantum Mechanical Study." Biomolecules 10, no. 2 (January 27, 2020): 192. http://dx.doi.org/10.3390/biom10020192.
Full textAbstract:
In the present work, we performed a complementary quantum mechanical (QM) study to describe the mechanism by which deprotonated pralidoxime (2-PAM) could reactivate human (Homo sapiens sapiens) acetylcholinesterase (HssAChE) inhibited by the nerve agent VX. Such a reaction is proposed to occur in subsequent addition–elimination steps, starting with a nucleophile bimolecular substitution (SN2) mechanism through the formation of a trigonal bipyramidal transition state (TS). A near attack conformation (NAC), obtained in a former study using molecular mechanics (MM) calculations, was taken as a starting point for this project, where we described the possible formation of the TS. Together, this combined QM/MM study on AChE reactivation shows the feasibility of the reactivation occurring via attack of the deprotonated form of 2-PAM against the Ser203-VX adduct of HssAChE.
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Nagahata, Yutaka, Rigoberto Hernandez, and Tamiki Komatsuzaki. "Phase space geometry of isolated to condensed chemical reactions." Journal of Chemical Physics 155, no. 21 (December 7, 2021): 210901. http://dx.doi.org/10.1063/5.0059618.
Full textAbstract:
The complexity of gas and condensed phase chemical reactions has generally been uncovered either approximately through transition state theories or exactly through (analytic or computational) integration of trajectories. These approaches can be improved by recognizing that the dynamics and associated geometric structures exist in phase space, ensuring that the propagator is symplectic as in velocity-Verlet integrators and by extending the space of dividing surfaces to optimize the rate variationally, respectively. The dividing surface can be analytically or variationally optimized in phase space, not just over configuration space, to obtain more accurate rates. Thus, a phase space perspective is of primary importance in creating a deeper understanding of the geometric structure of chemical reactions. A key contribution from dynamical systems theory is the generalization of the transition state (TS) in terms of the normally hyperbolic invariant manifold (NHIM) whose geometric phase-space structure persists under perturbation. The NHIM can be regarded as an anchor of a dividing surface in phase space and it gives rise to an exact non-recrossing TS theory rate in reactions that are dominated by a single bottleneck. Here, we review recent advances of phase space geometrical structures of particular relevance to chemical reactions in the condensed phase. We also provide conjectures on the promise of these techniques toward the design and control of chemical reactions.
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Rasmussen, Maria H., and Jan H. Jensen. "Fast and automatic estimation of transition state structures using tight binding quantum chemical calculations." PeerJ Physical Chemistry 2 (September 29, 2020): e15. http://dx.doi.org/10.7717/peerj-pchem.15.
Full textAbstract:
We present a method for the automatic determination of transition states (TSs) that is based on Grimme’s RMSD-PP semiempirical tight binding reaction path method (J. Chem. Theory Comput. 2019, 15, 2847–2862), where the maximum energy structure along the path serves as an initial guess for DFT TS searches. The method is tested on 100 elementary reactions and located a total of 89 TSs correctly. Of the 11 remaining reactions, nine are shown not to be elementary reactions after all and for one of the two true failures the problem is shown to be the semiempirical tight binding model itself. Furthermore, we show that the GFN2-xTB RMSD-PP barrier is a good approximation for the corresponding DFT barrier for reactions with DFT barrier heights up to about 30 kcal/mol. Thus, GFN2-xTB RMSD-PP barrier heights, which can be estimated at the cost of a single energy minimisation, can be used to quickly identify reactions with low barriers, although it will also produce some false positives.
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Martiník, O., B. Smetana, J. Dobrovská, A. Kalup, S. Zlá, M. Kawuloková, K. Gryc, P. Dostál, Ľ. Drozdová, and B. Baudisová. "Prediction and measurement of selected phase transformation temperatures of steels." Journal of Mining and Metallurgy, Section B: Metallurgy 53, no. 3 (2017): 391–98. http://dx.doi.org/10.2298/jmmb170711030m.
Full textAbstract:
The study deals with precise determination of phase transformation temperatures of steel. A series of experimental measurements were carried out by Differential Thermal Analysis (DTA) and Direct Thermal Analysis (TA) to obtain temperatures very close to the equilibrium temperatures. There are presented results from the high temperatures region, above 1000?C, with focus on the solidus temperatures (TS), peritectic transition (TP) and liquidus (TL) of multicomponent steels. The data obtained were verified by statistical evaluation and compared with computational thermodynamic and empirical calculations. The calculations were performed using 15 empirical equations obtained by literature research (10 for TL and 5 for TS), as well as by software InterDendritic Solidification (IDS) and Thermo-Calc (2015b, TCFE8; TC). It was verified that both thermo-analytical methods used are set correctly; the results are reproducible, comparable and close to equilibrium state.
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Alkorta, Ibon, Cristina Trujillo, Goar Sánchez-Sanz, and José Elguero. "Solvent and Substituent Effects on the Phosphine + CO2 Reaction." Inorganics 6, no. 4 (October 10, 2018): 110. http://dx.doi.org/10.3390/inorganics6040110.
Full textAbstract:
A theoretical study of the substituent and solvent effects on the reaction of phosphines with CO2 has been carried out by means of Møller-Plesset (MP2) computational level calculations and continuum polarizable method (PCM) solvent models. Three stationary points along the reaction coordinate have been characterized, a pre-transition state (TS) assembly in which a pnicogen bond or tetrel bond is established between the phosphine and the CO2 molecule, followed by a transition state, and leading finally to the adduct in which the P–C bond has been formed. The solvent effects on the stability and geometry of the stationary points are different. Thus, the pnicogen bonded complexes are destabilized as the dielectric constant of the solvent increases while the opposite happens within the adducts with the P–C bond and the TSs trend. A combination of the substituents and solvents can be used to control the most stable minimum.
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Zaccaria, Francesco, Roberta Cipullo, Andrea Correa, Peter H. M. Budzelaar, Vincenzo Busico, and Christian Ehm. "Separating Electronic from Steric Effects in Ethene/α-Olefin Copolymerization: A Case Study on Octahedral [ONNO] Zr-Catalysts." Processes 7, no. 6 (June 20, 2019): 384. http://dx.doi.org/10.3390/pr7060384.
Full textAbstract:
Four Cl/Me substituted [ONNO] Zr-catalysts have been tested in ethene/α-olefin polymerization. Replacing electron-donating methyl with isosteric but electron-withdrawing chlorine substituents results in a significant increase of comonomer incorporation. Exploration of steric and electronic properties of the ancillary ligand by DFT confirm that relative reactivity ratios are mainly determined by the electrophilicity of the metal center. Furthermore, quantitative DFT modeling of propagation barriers that determine polymerization kinetics reveals that electronic effects observed in these catalysts affect relative barriers for insertion and a capture-like transition state (TS).
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Hou, Li-Jie, Bo-Wan Wu, Yan-Xia Han, Chao Kong, Dong-Ping Chen, and Li-Guo Gao. "Density functional theoretical study on the reaction mechanism of SiHF radical with HNCO." Journal of Theoretical and Computational Chemistry 13, no. 07 (November 2014): 1450054. http://dx.doi.org/10.1142/s0219633614500540.
Full textAbstract:
The reaction mechanism of SiHF radical with HNCO has been investigated by the B3LYP method of density functional theory (DFT), while the geometries and harmonic vibration frequencies of reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311++G** level. To obtain more precise energy result, stationary point energies were calculated at the CCSD(T)/6-311++G**//B3LYP/6-311++G** level. In temperature range of 100 K to 1900 K, the statistical thermodynamics and Eyring transition state theory with Winger correction are used to study the thermodynamic and kinetic characters of the channel with low energy barrier at 1.0 Atm. SiHF + HNCO → IM 8 → TS 8 → SiFNHCHO ( P 3) was the main channel with low potential energy in the singlet state, SiFNHCHO was the main product. The analyses for the combining interaction between SiHF radical and HNCO with the atom-in-molecules (AIM) theory have been performed. There are three reaction channels in the triplet.
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Aliev, Amil R., Isa R. Akhmedov, Murad G. Kakagasanov, and Zakir A. Aliev. "ПРЕДПЕРЕХОДНЫЕ ЯВЛЕНИЯ В ОБЛАСТИ СТРУКТУРНОГО ФАЗОВОГО ПЕРЕХОДА В СУЛЬФАТЕ КАЛИЯ." Kondensirovannye sredy i mezhfaznye granitsy = Condensed Matter and Interphases 21, no. 3 (September 26, 2019): 350–57. http://dx.doi.org/10.17308/kcmf.2019.21/1148.
Full textAbstract:
Методами спектроскопии комбинационного рассеяния света исследованы структурно-динамические свойства и процессы молекулярной релаксации в кристаллическом сульфате калия K2SO4 в интервале температур от 293 до 900 К. Проанализированы температурные зависимости положения максимума v (частоты), ширины w и интенсивности I спектральной полосы, отвечающей полносимметричному колебанию v1(A) сульфат-иона SO4 2–, в спектральном интервале от 963 до 976 см–1. С ростом температуры частота колебания уменьшается. Примерно при 650 K имеют место определённые особенности температурной зависимости v(T). При дальнейшем увеличении температуры частота продолжает уменьшаться. В точке структурного фазового перехода первого рода (Ts = 854 K)уменьшение частоты приостанавливается. С ростом температуры ширина возрастает, а интенсивность уменьшается. Примерно при 650 K имеют место определённые особенности температурных зависимостей w(T) и I(T). Уменьшение интенсивности приостанавливается, и в интервале температур 650–850 K интенсивность остаётся почти постоянной. При структурном фазовом переходе первого рода (Ts = 854 K) интенсивность уменьшается. Рост ширины при температуре T ≈ 650 K приостанавливается, а затем снова ширина начинает увеличиваться. Ближе к структурному фазовому переходу первого рода (Ts = 854 K) рост ширины замедляется и в точке структурного фазового перехода первого рода (Ts = 854 K) имеет место уменьшение ширины. Установлено, что в кристаллическом сульфате калия K2SO4 структурный фазовый переход первого рода носит растянутый характер. При температуре фазового перехода (Ts = 854 К) ширина резко возрастает, а частота резко уменьшается, уменьшаясь и при дальнейшем увеличении температуры. Обнаружено существование предпереходной области в исследованном кристаллическом сульфате калия K2SO4. Эта предпереходная область имеет место в интервале температур от 650 К до Ts = 854 К.
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Aliev A. R., Akhmedov I. R., Kakagasanov M. G., Aliev Z. A., Gafurov M. M., Rabadanov K. Sh., Amirov A. M. Relaxation of vibrationally excited states in solid “nitrate – nitrite” binary systems. Opt. Spectrosc., 2017, vol. 123(4), pp. 587–589. https://doi.org/10.1134/S0030400X17100022
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Wang, Wei Dong, and Tetsuro Shimo. "Solid-State Photocycloaddition Reactions between Di-2-Pyrones Tethered by Arylalkyl Chain and Benzophenones." Advanced Materials Research 396-398 (November 2011): 2467–70. http://dx.doi.org/10.4028/www.scientific.net/amr.396-398.2467.
Full textAbstract:
Solid-state photocycloaddition reactions between di-2-pyrones (1a-d) with benzophenone (2a) gave the corresponding oxetane derivatives (3a-d; 1:2 adducts) with high site- and regioselectivity across the C5-C6 and C5′-C6′ double bonds in 1 via the triplet excited state of 2a. The reactions were inferred by MO methods to be initiated by electrostatic interaction between the C6 position of 1a-d and the carbonyl oxygen of 2a at their ground states, and the solid-state interaction may be enhanced by electron density at carbonyl oxygen of the triplet 2a. The transition state (TS) analysis of the [2+2] cycloaddition reactions also suggested some triplet complex, and the high regioselectivity. The hydrogen-bonding interaction between 2a and 1a-d and the triplet reaction mechanism were also explained by the IR analyses and the quenching experiments, respectively.
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Liu, Lin-Lin, Tong-Yong Zhang, and Song-Qi Hu. "DFT Calculations for the HONO Elimination Process of CL-20 Conformers." Journal of Chemistry 2021 (December 22, 2021): 1–6. http://dx.doi.org/10.1155/2021/3875282.
Full textAbstract:
The HONO elimination process is regarded to be an important initial decomposition process of energetic nitramines. Four CL-20 conformers based on the ε-CL-20 were obtained by the optimization at the m062x/cc-pvtz level in this study, and the Transition State (TS) and Intrinsic Reaction Coordinate (IRC) calculations were carried out at the same level. In addition, the rate coefficients and activation energy of the HONO elimination process were evaluated using conventional transition state theory (TST) and canonical variational transition state theory (CVT) with Eckart and small-curvature tunneling (SCT) methods to correct the transmission coefficients for the quantum tunneling effect. The calculation results have shown that the HONO elimination process concerning the nitro groups located on six numbered rings is the hardest to happen, and it seems that the longer distance between nitro groups and the adjacent hydrogen atom would result in the higher barrier energy; the HONO elimination process is most likely to happen for the axial positioning of nitro groups located on five numbered rings and most unlikely to happen for the ones located on six numbered rings; CL-20 II and CL-20 IV conformers are the most unstable one and most stable one concerning the reaction difficulty of the HONO elimination process.
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WAHAB, Olaide, Jide IGE, Grace OGUNLUSI, Lukman OLASUNKANMI, and Kayode SANUSI. "Oxatriquinane Derivatives: A Theoretical Investigation of SN1-SN2 Reactions Borderline." Walailak Journal of Science and Technology (WJST) 15, no. 6 (October 10, 2016): 439–53. http://dx.doi.org/10.48048/wjst.2018.2476.
Full textAbstract:
This study investigated the nucleophilic substitution reaction mechanisms of 5 oxatriquinane derivatives, namely: oxatriquinane (OTQ), 1,4,7-trimethyloxatriquinane (TMO), 1,4,7-triethyloxatriquinane (TEO), 1,4,7-tri-iso-propyloxatriquinane (TIO) and 1,4,7-tri-tert-butyloxatriquinane (TTO). In addition to the G3 conformation (one with the substituent groups at 1,4 and 7 positions pointing into the plane of the paper) originally proposed by the previous workers, Mascal et al. in 2008 and Gunbas et al. in 2013, one more geometrical isomer was considered again for each of the derivatives, the 2G1 isomer (one in which only 2 of the 3 substituent groups at 1,4 and 7 positions are into the paper plane). Geometry optimization and determination of transition state properties of the conformers corresponding to each molecule (in the presence of azide ion, N3-) provided theoretical evidences on the possible reaction mechanisms. The 2G1 conformer for TTO was found to be unstable. The reactions of OTQ, TMO and TEO with azide ion (N3-) followed SN2 pathway, with SN1mechanism completely lacking. This finding is in agreement with the first set of reports published on this subject in 2008 and 2010 by Mascal’s group. For TIO (in the presence of azide ion), only the presence of SN1 mechanism could be proved without any observation of transition state (TS), even though, it possesses a 2G1 conformer. TTO surprisingly, showed marked evidence of SN1 mechanism also without any evidence of TS. The results obtained showed that OTQ derivatives up to TEO undergo nucleophilic substitution predominantly via SN2, and above which (i.e. for TIO and TTO) the mechanisms predominantly become SN1.
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Kalpana, Padmanaban, and Lakshminarayanan Akilandeswari. "Can Aromaticity of Fused Aromatic Ring in 1,3-Pentadiene Modulate its Reactivity towards [1,5]-Halo Shift? - A DFT Study." Asian Journal of Chemistry 33, no. 2 (2021): 447–52. http://dx.doi.org/10.14233/ajchem.2021.23092.
Full textAbstract:
In (Z)-1,3-pentadienes, [1,5]-H migration is suprafacially allowed while fluorine shift in this system takes place by a Contra Hoffmann antarafacial pathway for which aromaticity is the driving force. If aromaticity of the transition structure (TS) can drive a reaction towards a disallowed pathway as found in the case of fluorine, the role of aromatic ring annealed to (Z)-1,3-pentadienes in determining the reaction pathway and barrier is worth noting. Hence, the combined role of aromaticity of transition state and the loss in aromaticity of the annealed ring has been explored during the [1,5]-X (X = H, F, Cl, Br) shifts in aromatic (benzene/naphthalene) annealed 1,3-pentadiene system. Notable correlations between various aromaticity index NICS(0,1) with activation barriers show that aromaticity of transition structure in pericyclic reaction can drive the stereochemical course of a reaction. The distinct effect of fluorine to other halogens is the antara migration while the other halogens (Cl & Br) prefer supramode.
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Vessally, E., Ehsan Fereyduni, M. Kamaee, and S. Moradi. "A theoretical study of the intramolecular proton transfer and calculation of the nucleus independent chemical shift in juglone and some of its derivatives." Journal of the Serbian Chemical Society 76, no. 6 (2011): 879–90. http://dx.doi.org/10.2298/jsc100930080v.
Full textAbstract:
In the present study, first, the intramolecular proton transfer (IPT) process of juglone and its derivatives were theoretically investigated in the gas phase and the effect of electron-withdrawing and electronreleasing substituents in different positions of the phenyl and benzoquinone rings of juglone on the IPT process was studied in which the geometries, energies and thermodynamic functions of the compounds were obtained using DFT calculations at the B3LYP/6-31+G(2d,p) level. Next, the influence of IPT on changing the aromaticity of the phenyl and benzoquinone rings was investigated. To determine the aromaticity of the rings, nuclear independent chemical shift (NICS) values were calculated for the ground state and transition state structures (GS1,TS,GS2) using the continues set of gauge transformations (CSGT) procedure at the B3LYP/6-311+G(2d,p) level.
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LÉCUÉ, FREDDY, ALEXANDRE DELTEIL, and ALAIN LÉGER. "TOWARDS A SEMANTIC STATE TRANSITION SYSTEM FOR AUTOMATED GENERATION OF DATA FLOW IN WEB SERVICE COMPOSITION." International Journal of Semantic Computing 03, no. 04 (December 2009): 499–526. http://dx.doi.org/10.1142/s1793351x09000896.
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Most of the work on automated web service composition has focused so far on composition of stateful web services. This level of composition so-called "Process Level" considers web services with their internal and complex behaviors. At process level formal models such as State Transition Systems (STS from now) or Interface Automata are the most appropriate models to represent the internal behavior of stateful web services. However such models focus only on semantics of their behaviors and unfortunately not on semantics of actions and their parameters. In this paper, we suggest to extend the STS model, by following the WSMO based annotation for Abstract State Machine. This semantic enhancement of STS so called S2 TS will enable to model semantics of internal behaviors and semantics of their actions together with their input and output parameters. Secondly, we will focus on automated generation of data flow (or the process to perform automated assignments between parameter of services involved in a composition). Thus we do not restrict to assignments of exact parameters (which is practically never used in industrial scenario) but extend assignments to semantically close parameters (e.g., through a subsumption matching) in the same ontology. Our system is implemented and interacting with web services dedicated to Telecommunication scenarios. The preliminary evaluation results showed high efficiency and effectiveness of the proposed approach.
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Salter, E. Alan, Andrzej Wierzbicki, and Richard E. Honkanen. "Quantum-Based Modeling of Dephosphorylation in the Catalytic Site of Serine/Threonine Protein Phosphatase-5 (PPP5C)." Catalysts 10, no. 6 (June 16, 2020): 674. http://dx.doi.org/10.3390/catal10060674.
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Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M1/M2), an associated bridge hydroxide (W1(OH−)), an M1-bound water/hydroxide (W2), and a highly conserved core sequence. The PPPs are presumed to share a common mechanism: The seryl/threonyl phosphoryl group of the phosphoprotein coordinates the metal ions, W1(OH−) attacks the central phosphorous atom, rupturing the antipodal phosphoester bond and releasing the phosphate-free protein. Also, a histidine/aspartate tandem is responsible for protonating the exiting seryl/threonyl alkoxide. Here, we employed quantum-based computations on a large section of the PP5 catalytic site. A 33-residue, ONIOM(UB3LYP/6-31G(d):UPM7) model was built to perform computations using methylphosphate dianion as a stand-in substrate for phosphoserine/phosphothreonine. We present a concerted transition state (TS) in which W1(OH−) attacks the phosphate center at the same time that the exiting seryl/threonyl alkoxide is protonated directly by the His304/Asp274 tandem, with W2 assigned as a water molecule: W2(H2O). Arg275, proximal to M1, stabilizes the substrate and TS by binding both the ester oxygen (Oγ) and a phosphoryl oxygen (O1) in a bidentate fashion; in the product state, Tyr451 aids in decoupling Arg275 from O1 of the product phosphate ion. The reaction is exothermic (ΔH = −2.0 kcal/mol), occurs in a single step, and has a low activation barrier (ΔH‡ = +10.0 kcal/mol). Our work is an improvement over an earlier computational study that also found bond rupture and alkoxide protonation to be concerted, but concluded that Arg275 is deprotonated during the reactant and TS stages of the pathway. In that earlier study, the critical electron-withdrawal role that Arg275 plays during the hydroxide attack was not correctly accounted for.
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Banerjee, Puja, and Biman Bagchi. "Dynamical control by water at a molecular level in protein dimer association and dissociation." Proceedings of the National Academy of Sciences 117, no. 5 (January 22, 2020): 2302–8. http://dx.doi.org/10.1073/pnas.1908379117.
Full textAbstract:
Water, often termed as the “lubricant of life,” is expected to play an active role in navigating protein dissociation–association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1–2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance RMM from ∼4 to ∼2 nm, orientation of monomers and hydrophobic hydration in the monomers. A quasistable, solvent-shared, protein monomer pair (SSPMP) forms at around 2 nm during association process which is a local free-energy minimum having ∼50–60% of native contacts. Simulations starting with arrangements sampled from the transition state (TS) of the dimer dissociation reveal that the final outcome depends on relative orientation of the backbone in the “hotspot” region.
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Kim, Sung Soo, Yu Zhu, In Seok Oh, and Chang Gyeong Lim. "Reactions of benzyl methyl substituted-benzyl phosphites with tert-butyl hypochlorite: "balanced TS" validating reactivity/selectivity principle." Canadian Journal of Chemistry 76, no. 6 (June 1, 1998): 836–42. http://dx.doi.org/10.1139/v98-081.
Full textAbstract:
Reactions of a series of several benzyl methyl substituted-benzyl phosphites with tert-butyl hypochlorite were investigated. The reactions produced phosphates, isobutene, alkyl chlorides, and benzyl chlorides via phosphonium chlorides as intermediates. Furthermore, the phosphates bearing a tert-butyl group underwent fragmentation to yield isobutene and another phosphates. Relative rates of formations of substituted benzyl and benzyl chloride (kY/kH) were measured at the temperatures (-20, 0, 20, 40°C). Logarithms of the rates (log kY/kH) were plotted against sigma + and 1/T, respectively. The former gave Hammett correlations to suggest a polar transition state (TS). The latter yielded differential activation parameters (ΔΔ Hdouble daggerY-H and ΔΔ Sdouble daggerY-H ), which indicate isokinetic relations and enthalpy control of rates. The selectivities (kY/kH) decrease with higher temperatures and thereby follow the reactivity/selectivity principle.Key words: phosphites, tert-butyl hypochlorite, Hammett correlations, differential activation terms, reactivity/selectivity principle.
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Massat, Pierre, Donato Farina, Indranil Paul, Sandra Karlsson, Pierre Strobel, Pierre Toulemonde, Marie-Aude Méasson, et al. "Charge-induced nematicity in FeSe." Proceedings of the National Academy of Sciences 113, no. 33 (August 1, 2016): 9177–81. http://dx.doi.org/10.1073/pnas.1606562113.
Full textAbstract:
The spontaneous appearance of nematicity, a state of matter that breaks rotation but not translation symmetry, is one of the most intriguing properties of the iron-based superconductors (Fe SC), and has relevance for the cuprates as well. Establishing the critical electronic modes behind nematicity remains a challenge, however, because their associated susceptibilities are not easily accessible by conventional probes. Here, using FeSe as a model system, and symmetry-resolved electronic Raman scattering as a probe, we unravel the presence of critical charge nematic fluctuations near the structural/nematic transition temperature, TS∼ 90 K. The diverging behavior of the associated nematic susceptibility foretells the presence of a Pomeranchuk instability of the Fermi surface with d-wave symmetry. The excellent scaling between the observed nematic susceptibility and elastic modulus data demonstrates that the structural distortion is driven by this d-wave Pomeranchuk transition. Our results make a strong case for charge-induced nematicity in FeSe.
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Повзнер, А. А., А. Г. Волков, Т. А. Ноговицына, and С. А. Бессонов. "Магнитообъемные эффекты и тепловое расширение в киральных геликоидальных ферромагнетиках Fe-=SUB=-1-x-=/SUB=-Co-=SUB=-x-=/SUB=-Si." Физика твердого тела 64, no. 8 (2022): 909. http://dx.doi.org/10.21883/ftt.2022.08.52681.336.
Full textAbstract:
Within the framework of the theory of band magnetism and the Heine model for the volume dependence of the electronic spectrum, an approach is being developed to study magneto-volume effects in chiral helical ferromagnets. Using Fe1-хCoxSi as an example, it was found that in the range of long-range order (at temperature Т<Tc) the magnetovolume effect is determined by the amplitude of helicoidal spin spirals and leads to the experimentally observed negative volume thermal expansion coefficient. In the region of phase transitions of the first order (from Тс to Тs) prolonged in temperature, a new mechanism of the magnetovolume effect is established due to the spatial fluctuations of spin spirals arising due to the difference in the Hubbard potentials of iron and cobalt. It is shown that the considered volume effects lead not only to the experimentally observed negative volume thermal expansion coefficient (VCTE) in the chiral spin short-range order phase, but also to a noticeable increase in the transition temperature to the paramagnetic state (Т>Ts).
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Повзнер, А. А., А. Г. Волков, Т. А. Ноговицына, and С. А. Бессонов. "Магнитообъемные эффекты и тепловое расширение в киральных геликоидальных ферромагнетиках Fe-=SUB=-1-x-=/SUB=-Co-=SUB=-x-=/SUB=-Si." Физика твердого тела 64, no. 8 (2022): 909. http://dx.doi.org/10.21883/ftt.2022.08.52681.336.
Full textAbstract:
Within the framework of the theory of band magnetism and the Heine model for the volume dependence of the electronic spectrum, an approach is being developed to study magneto-volume effects in chiral helical ferromagnets. Using Fe1-хCoxSi as an example, it was found that in the range of long-range order (at temperature Т<Tc) the magnetovolume effect is determined by the amplitude of helicoidal spin spirals and leads to the experimentally observed negative volume thermal expansion coefficient. In the region of phase transitions of the first order (from Тс to Тs) prolonged in temperature, a new mechanism of the magnetovolume effect is established due to the spatial fluctuations of spin spirals arising due to the difference in the Hubbard potentials of iron and cobalt. It is shown that the considered volume effects lead not only to the experimentally observed negative volume thermal expansion coefficient (VCTE) in the chiral spin short-range order phase, but also to a noticeable increase in the transition temperature to the paramagnetic state (Т>Ts).
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Cheikh, Wafaa, Zsófia Borbála Rózsa, Christian Orlando Camacho López, Péter Mizsey, Béla Viskolcz, Milán Szőri, and Zsolt Fejes. "Urethane Formation with an Excess of Isocyanate or Alcohol: Experimental and Ab Initio Study." Polymers 11, no. 10 (September 22, 2019): 1543. http://dx.doi.org/10.3390/polym11101543.
Full textAbstract:
A kinetic and mechanistic investigation of the alcoholysis of phenyl isocyanate using 1-propanol as the alcohol was undertaken. A molecular mechanism of urethane formation in both alcohol and isocyanate excess is explored using a combination of an accurate fourth generation Gaussian thermochemistry (G4MP2) with the Solvent Model Density (SMD) implicit solvent model. These mechanisms were analyzed from an energetic point of view. According to the newly proposed two-step mechanism for isocyanate excess, allophanate is an intermediate towards urethane formation via six-centered transition state (TS) with a reaction barrier of 62.6 kJ/mol in the THF model. In the next step, synchronous 1,3-H shift between the nitrogens of allophanate and the cleavage of the C–N bond resulted in the release of the isocyanate and the formation of a urethane bond via a low-lying TS with 49.0 kJ/mol energy relative to the reactants. Arrhenius activation energies of the stoichiometric, alcohol excess and the isocyanate excess reactions were experimentally determined by means of HPLC technique. The activation energies for both the alcohol (measured in our recent work) and the isocyanate excess reactions were lower compared to that of the stoichiometric ratio, in agreement with the theoretical calculations.
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Chu, Dezhang, Peter H. Wiebe, Nancy J. Copley, Gareth L. Lawson, and Velmurugu Puvanendran. "Material properties of North Atlantic cod eggs and early-stage larvae and their influence on acoustic scattering." ICES Journal of Marine Science 60, no. 3 (January 1, 2003): 508–15. http://dx.doi.org/10.1016/s1054-3139(03)00047-x.
Full textAbstract:
Abstract To study the acoustic signatures of Atlantic cod (Gadus morhua) at different biological stages from eggs to early-stage larvae (<37 days post-hatch), we conducted a series of experiments to estimate their sound-speed and density contrasts. A laboratory version of the “Acoustic Properties of Zooplankton” system was used. Sound speed was estimated by means of travel time between two transducers using a broadband acoustic signal (∼300–600 kHz). Density was estimated using a dual-density method in which two fluids of different densities were employed. It was found that the density contrasts of cod eggs and early-stage larvae were nearly all slightly less than unity (0.969–0.998), while the effective sound-speed contrasts were only slightly greater than unity (1.017–1.024) for eggs and yolk-sac stage larvae (<5 days post-hatch), and increased significantly (>1.130) for larvae older than 16 days. This change in sound-speed contrast reflected the transition of the swimbladder from an uninflated state to an inflated state. The regression relation between estimated target strength at 500 kHz and larval length in centimetres was found to be TS = 176.1 log10L − 82.4(dB). The inflation ratio of the swimbladder for early-stage larvae was an exponential function of time. The predicted period of time until full swimbladder inflation was 43.3 days.