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Journal articles on the topic 'Transition State Structure (TS)'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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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 (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. Experimen

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2

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 fo

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3

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 (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 substituen

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4

Zhao, Yongling, Chengwang Lei, and John C. Patterson. "The K-type and H-type transitions of natural convection boundary layers." Journal of Fluid Mechanics 824 (July 5, 2017): 352–87. http://dx.doi.org/10.1017/jfm.2017.354.

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The K-type and H-type transitions of a natural convection boundary layer of a fluid of Prandtl number 7 adjacent to an isothermally heated vertical surface are investigated by means of three-dimensional direct numerical simulation (DNS). These two types of transitions refer to different flow features at the transitional stage from laminar to turbulence caused by two different types of perturbations. To excite the K-type transition, superimposed Tollmien–Schlichting (TS) and oblique waves of the same frequency are introduced into the boundary layer. It is found that a three-layer longitudinal v

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5

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

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6

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 ins

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7

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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8

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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9

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 efficien

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10

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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11

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 (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 magnetiz

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12

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 (2020): 1102. http://dx.doi.org/10.3390/cryst10121102.

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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

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13

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 (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 peak

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14

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.

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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. Furthe

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15

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.

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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]-

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16

Chen, Kuan Yu, Yi Ting Kong, and Shyi Long Lee. "Theoretical Studies of Au₃^+/0/- Clusters Using Density Funtional Theory." Key Engineering Materials 862 (September 2020): 94–98. http://dx.doi.org/10.4028/www.scientific.net/kem.862.94.

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In this study, the PW91PW91 method with LANL2DZ level was carried out to settle the dispute about the most stable structure of Au3+/0/-. Molecular orbital analyses and Walsh diagram were adopted to rationalize our computational result about the ground state geometry of Au3+/0/-. Our results show that the most stable geometry of Au3 is bent structure (C2v) with bond angle 146.0°. The less stable structure is equilateral triangle structure (D3h) with relative energies of 1.74 eV. The D3h structure possesses multiplicity 4 while the C2v structure 2. In addition, the most stable geometry of Au3+ a

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17

Ryabov, Mikhail A., Thi Ngok Anh Vu, Olga V. Kovalchukova, and Dmitry S. Gusarov. "Quantum-chemical modeling of structure and properties of nitrogen derivatives of phloroglucinol." Butlerov Communications 57, no. 3 (2019): 51–57. http://dx.doi.org/10.37952/roi-jbc-01/19-57-3-51.

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The DFT/B3LYP quantum-chemical method has been used to simulate the structure of 2-((2-hydroxyphenyl) diazonyl) benzene-1,3,5-triol (L1) and 2-((2-hydroxy-4-nitrophenyl) diazonyl) benzene-1,3,5-triol (L2) molecules. The spatial and electronic structure of molecules in various tautomeric forms was determined. It was shown that the stability of these compounds is primarily due to the presence of strong intramolecular hydrogen bonds (IHB), which form six-membered cycles, and the isomerism of the molecule, which assume the formation of IHB. The structures where IHB form five-membered cycles, are l

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18

Aliev, Amil R., Isa R. Akhmedov, Murad G. Kakagasanov та Zakir A. Aliev. "ПРЕДПЕРЕХОДНЫЕ ЯВЛЕНИЯ В ОБЛАСТИ СТРУКТУРНОГО ФАЗОВОГО ПЕРЕХОДА В СУЛЬФАТЕ КАЛИЯ". Kondensirovannye sredy i mezhfaznye granitsy = Condensed Matter and Interphases 21, № 3 (2019): 350–57. http://dx.doi.org/10.17308/kcmf.2019.21/1148.

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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 дальне

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19

Zhou, Jin-Hui, Liang-Wen Zheng, Mao-Cai Yan, Mao-Jian Shi, Jing Liu, and Guo-Qiang Shangguan. "Synthesis, Crystal Structure, and DFT Study of Ethyl 1-(2-(Hydroxyimino)-2-phenylethyl)-3-phenyl-1H-pyrazole-5-carboxylate." Journal of Chemistry 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/6537402.

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The crystal structure of ethyl 1-(2-(hydroxyimino)-2-phenylethyl)-3-phenyl-1H-pyrazole-5-carboxylate has been determined by X-ray single crystal diffraction. The crystal of the title compound is the monoclinic space group P2/c with unit cell parameters of a=8.634(2) Å, b=9.616(2) Å, c=22.190(3) Å, β=99.2652°, V=1818.3(4) Å3, and Z=4. The dihedral angles formed by the planes of the central pyrazole ring and the adjacent benzene rings are 73.60(7)° and 3.55(7)°, respectively. The combination of the weak intermolecular C-H⋯O and N-H⋯O hydrogen-bonding interactions stabilizes the crystal packing.

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20

Plonska, Malgorzata, Wojciech A. Pisarski, and Joanna Pisarska. "Luminescence Properties of Ytterbium Activated PLZT Ceramics." Advances in Science and Technology 98 (October 2016): 64–69. http://dx.doi.org/10.4028/www.scientific.net/ast.98.64.

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In the present work the influence of co-doping with ytterbium ions (for 0, 0.5, 1.5, 2.5 wt.% of Yb3+) on physical properties of 8/65/35 PLZT was studied. The ceramic powders were synthesized by the modified sol-gel method, and underwent consolidation by the pressure-less sintering techniques, in Ts=1200°C/6h. Our investigations give a detailed account of the relationships between concentrations of trivalent ytterbium ions in PLZT matrix, on their structure, microstructure, as well as luminescence properties. Near-infrared luminescence spectra at about 1020 nm were registered, which correspond

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21

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.

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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 dete

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22

Um, Ik-Hwan, Ae-Ri Bae та Julian M. Dust. "Hydrazinolysis of aryl cinnamates and related esters: the α-effect arises from stabilization of five-membered cyclic transition state". Canadian Journal of Chemistry 97, № 1 (2019): 7–12. http://dx.doi.org/10.1139/cjc-2018-0290.

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A kinetic study is reported for nucleophilic substitution reactions of Y-substituted-phenyl cinnamates (1a–1h) with a series of primary amines including hydrazine in H2O containing 20 mol % DMSO at 25.0 °C. The Brønsted-type plot for the reaction of 2,4-dinitrophenyl cinnamate (1a) is linear with βnuc = 0.57 except hydrazine, which exhibits positive deviation from the linear correlation (i.e., the α-effect). The Brønsted-type plots for the reactions of 1a–1h with hydrazine and glycylglycine (glygly) are also linear with βlg = –0.71 and –0.87, respectively, when 1a is excluded from the linear c

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23

Zahedi, Ehsan, Safa Ali-Asgari, and Vahid Keley. "NBO and NICS analysis of the allylic rearrangements (the Cope and 3-aza-Cope rearrangements) of hexa-1,5-diene and N-vinylprop-2-en-1-amine: A DFT study." Open Chemistry 8, no. 5 (2010): 1097–104. http://dx.doi.org/10.2478/s11532-010-0084-1.

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AbstractIn this work, ab initio density functional theory (DFT) calculations have been performed on the 3,3-sigmatropic rearrangements of hexa-1,5-diene (Cope) and N-vinylprop-2-en-1-amine (3-aza-Cope) in the gas phase. The barrier heights and heats of reactions calculated at the B3LYP/6-311G** level of theory were in good agreement with experimental data. Transition states optimized with B3LYP/6-311G** theory were used for calculating the nucleus independent chemical shift (NICS) and, a natural bond orbital (NBO) analysis was also performed at the same level of theory. Our results indicate th

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24

Maré, George R. De. "Abinitio study of rotational isomerism in acrolein." Canadian Journal of Chemistry 63, no. 7 (1985): 1672–80. http://dx.doi.org/10.1139/v85-280.

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Analytic gradient (force) methods at the STO-3G, 3-21G, and 6-31G* basis set levels have been used to optimize the geometry of acrolein completely at each critical point (minima, maximum) in the torsional potential energy curves for rotation about the single C—C bond (dihedral angle θ). The STO-3G and 6-31G* optimizations predict the planar trans conformation (θ = 180°) to be more stable than the cis conformation (θ = 0°) by 1.87 and 6.97 kJ/mol, respectively. The 3-21G optimizations, in disagreement with experiment, place the planar cis structure below the trans by 4.5 J/mol. The predicted re

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25

Tzul, Franco O., Katrina L. Schweiker, and George I. Makhatadze. "Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling." Proceedings of the National Academy of Sciences 112, no. 3 (2015): E259—E266. http://dx.doi.org/10.1073/pnas.1410424112.

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The kinetics of folding–unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge–charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye–Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versu

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Jin, Feng, Le Wang, Anmin Zhang, et al. "Raman interrogation of the ferroelectric phase transition in polar metal LiOsO3." Proceedings of the National Academy of Sciences 116, no. 41 (2019): 20322–27. http://dx.doi.org/10.1073/pnas.1908956116.

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Ferroelectric (FE) distortions in a metallic material were believed to be experimentally inaccessible because itinerant electrons would screen the long-range Coulomb interactions that favor a polar structure. It has been suggested by Anderson and Blount [P. W. Anderson, E. I. Blount, Phys. Rev. Lett. 14, 217−219 (1965)] that a transition from paraelectric phase to FE phase is possible for a metal if, in the paraelectric phase, the electrons at the Fermi level are decoupled from the soft transverse optical phonons, which lead to ferroelectricity. Here, using Raman spectroscopy combined with mag

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Itoh, Kuniaki, Kazue Kitoh, and Shigehisa Kishimoto. "Concerted and stepwise mechanisms in the DielsAlder and Michael reactions of furans with methyl 3-nitroacrylate Experimental and theoretical studies." Canadian Journal of Chemistry 84, no. 3 (2006): 392–406. http://dx.doi.org/10.1139/v06-013.

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The DielsAlder reactions of the furans (1a1c) and methyl 3-nitroacrylate (2) produce the cycloadducts via a concerted mechanism. Then, the products subsequently undergo retro-DielsAlder reactions to give the Michael adducts via a stepwise mechanism. We have used both experimental and theoretical methods to investigate the mechanism for, and the regio- and stereo-selectivity in, the DielsAlder and Michael reactions. To account for the selectivity observed in these additions, we examined the frontier molecular orbitals involved, and to locate the transition states (TS), we employed a B3LYP/6

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Domingo, Luis R., Mar Ríos-Gutiérrez, and Patricia Pérez. "Unveiling the Lewis Acid Catalyzed Diels–Alder Reactions Through the Molecular Electron Density Theory." Molecules 25, no. 11 (2020): 2535. http://dx.doi.org/10.3390/molecules25112535.

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The effects of metal-based Lewis acid (LA) catalysts on the reaction rate and regioselectivity in polar Diels–Alder (P-DA) reactions has been analyzed within the molecular electron density theory (MEDT). A clear linear correlation between the reduction of the activation energies and the increase of the polar character of the reactions measured by analysis of the global electron density transfer at the corresponding transition state structures (TS) is found, a behavior easily predictable by analysis of the electrophilicity ω and nucleophilicity N indices of the reagents. The presence of a stron

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Carbajal-Franco, G., and M. F. Márquez-Quintana. "DFT Path Towards the Characterization of the SnO2-CH4 Gas Sensing Reactions." MRS Advances 2, no. 63 (2017): 3925–31. http://dx.doi.org/10.1557/adv.2018.82.

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Gas detecting and sensing is a largely studied field of knowledge, but total understanding is not yet achieved and the ideal device is still far in the future. Many experimental efforts have been devoted to find the minimum optimal temperature and operational conditions for SnO2 to sense hydrocarbons; different methods to build gas-detecting devices keep being developed all around the world, from paste-based bulk devices to nanostructured thick and thin films, but little effort has been aim to characterize the reactions by calculating their related enthalpies. Computational methods have been w

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Itoh, Kuniaki, Shigehisa Kishimoto та Kazuo Sagi. "Novel formation of isoxazoline N-oxide in addition to Michael adduct from the reaction of β-nitrostyrenes with 2-methoxyfuran — Experimental and theoretical studies". Canadian Journal of Chemistry 87, № 6 (2009): 760–74. http://dx.doi.org/10.1139/v09-068.

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2-Methoxyfuran reacts with β-nitrostyrenes to give Michael adducts. Interestingly, isoxazoline N-oxides were obtained in the reactions with β-nitrostyrenes possessing additional electron-withdrawing groups [COPh (2f) and CO2Et (2g)]. (Z)-Nitrostyrene (2g) gives trans-isoxazoline (4g) and (E)-nitrostyrene (2f) leads to the cis-form product 4f. We have used theoretical methods to investigate the mechanism and to probe the regio- and stereo-selectivity observed in the rearrangement and the Michael reactions. To account for the selectivity observed in these reactions, we examined the Fukui functio

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31

Hnatich, M., and D. Horváth. "Modified Self-Scaling Relation for the Inertial and Low Energy Containing Scales of Decaying Turbulence." International Journal of Modern Physics B 12, no. 04 (1998): 405–31. http://dx.doi.org/10.1142/s0217979298000272.

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The limits of a new form of scaling, named Extended Self Similarity (ESS) originally suggested [R. Benzi et al., Phys. Rev.E48 (1993), 29] for the inertial, dissipation and transition scales are discussed. A modification of the ESS concept is put forward using the model of decaying turbulence at high Reynolds numbers [L. Ts. Adzhemyan et al., Czech. J. Phys.45 (1995), 517]. In this model the statistical description is simplified by the hypotheses of homogeneity, isotropy, incompressibility and self-similarity, for the power law stage of decay the presence of a single scaling length — Karman sc

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32

Kotarba, Joseph A. "2124." Journal of Clinical and Translational Science 1, S1 (2017): 44. http://dx.doi.org/10.1017/cts.2017.159.

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OBJECTIVES/SPECIFIC AIMS: This report describes the evolution of scientific culture since the NIH/translational science (TS) mandate. The transition of the conduct of science to an increasingly translational model involves 2 dimensions of change. The first dimension consists of change in the structure and process of scientific work, in terms of factors such as funding, administration, application of new knowledge, and so forth. The second dimension consists of change in culture of scientific work. The culture of science is the set of values, assumptions, meanings, and traditions that inform th

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Alvarez, Maria, Edgardo Saavedra, Mónica Olivella, Fernando Suvire, Miguel Zamora, and Ricardo Enriz. "Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl." Open Chemistry 10, no. 1 (2012): 248–55. http://dx.doi.org/10.2478/s11532-011-0136-1.

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AbstractThe multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is

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Nutho, Bodee, Salila Pengthaisong, Anupong Tankrathok, et al. "Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7." Biomolecules 10, no. 6 (2020): 907. http://dx.doi.org/10.3390/biom10060907.

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β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosid

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Domingo, Luis R., Mar Ríos-Gutiérrez, and María José Aurell. "Unveiling the Intramolecular Ionic Diels–Alder Reactions within Molecular Electron Density Theory." Chemistry 3, no. 3 (2021): 834–53. http://dx.doi.org/10.3390/chemistry3030061.

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The intramolecular ionic Diels–Alder (IIDA) reactions of two dieniminiums were studied within the Molecular Electron Density Theory (MEDT) at the ωB97XD/6-311G(d,p) computational level. Topological analysis of the electron localization function (ELF) of dieniminiums showed that their electronic structures can been seen as the sum of those of butadiene and ethaniminium. The superelectrophilic character of dieniminiums accounts for the high intramolecular global electron density transfer taking place from the diene framework to the iminium one at the transition state structures (TSs) of these II

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Domingo, Luis R., Mar Ríos-Gutiérrez, and Patricia Pérez. "A Molecular Electron Density Theory Study of the Competitiveness of Polar Diels–Alder and Polar Alder-ene Reactions." Molecules 23, no. 8 (2018): 1913. http://dx.doi.org/10.3390/molecules23081913.

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The competitiveness of the BF3 Lewis acid (LA) catalyzed polar Diels–Alder (P-DA) and polar Alder-ene (P-AE) reactions of 2-methyl-1,3-butadiene, a diene possessing an allylic hydrogen, with formaldehyde has been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. Coordination of BF3 LA to the oxygen of formaldehyde drastically accelerates both reactions given the high electrophilic character of the BF3:formaldehyde complex. As a consequence, these reactions present a very low activation enthalpy—less than 2.2 kcal·mol−1—thus becoming comp

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Yateem, Ali Hussain. "Rotational Barrier and Conjugation: Theoretical Study of Resonance Stabilization of Various Substituents for the Donors NH₂ and OCH₃ in Substituted 1,3-Butadienes." Indonesian Journal of Chemistry 19, no. 4 (2019): 1055. http://dx.doi.org/10.22146/ijc.42850.

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The barrier to internal rotation around the central C2–C3 single bond of a series of (1E)-monosubstituted 1,3-butadienes and (1E,3E)-1-Y-4-X-disubstituted butadienes, with Y=NH2 or OCH3 and X=NO2, CHO, COOH, CN, CF3, Cl or F, were studied at the density functional w B97X-D/6-31G∗∗ level. The effect of substituents on π-conjugation in disubstituted 1,3-butadienes was studied by correlating the calculated internal rotational barriers with the difference in structural, atomic and molecular properties between the transition state TS and the s-trans conformers. The calculated differences in lengths

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Nguyen, Dang T., and Quan T. Pham. "A Theoretical and Experimental Study on Esterification of Citric Acid with the Primary Alcohols and the Hydroxyl Groups of Cellulose Chain (n = 1-2) in Parched Condition." Journal of Chemistry 2020 (November 12, 2020): 1–9. http://dx.doi.org/10.1155/2020/8825456.

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Esterification of citric acid (CA) with the primary alcohols and the hydroxyl groups of cellulose chain (n = 1-2) in parched condition were investigated by using density functional theory (DFT) method and a two-layer ONIOM approach. Geometry and energy of reactants, products, and transition state (TS) structures were optimized at B3LYP/6-311g (d, p) level and ONIOM (B3LYP/6-311g (d, p):PM3MM) level. The computational results show that the esterification occurs in the two main steps: the first step is the dehydration reaction of CA to form anhydrides of 5-membered ring and 6-membered ring and t

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Bérces, Attila, Dennis M. Whitfield, Tomoo Nukada, Iwona do Santos Z., Agnes Obuchowska, and Jiri J. Krepinsky. "Is acyl migration to the aglycon avoidable in 2-acyl assisted glycosylation reactions?" Canadian Journal of Chemistry 82, no. 7 (2004): 1157–71. http://dx.doi.org/10.1139/v04-059.

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This report unequivocally separates orthoester formation from acyl transfer for the first time and indicates possible routes to eliminate 2-O-acyl transfer during glycosylation reactions. Experimental evidence is shown that acyl transfer from 2-O-acyl-3,4,6-tri-O-benzyl-D-galactopyranose-derived glycosyl donors decreases in the order formyl > acetyl > pivaloyl. The 2-O-benzoyl derivatives are more variable, in some cases transferring easily, and in others not at all. Density functional theory (DFT) calculations of the structure and energetics of dioxolenium ion and related intermediates

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PRAVDIUK, Nataliia. "INFORMATION SUPPORT FOR STRATEGIC DEVELOPMENT OF AGRARIAN ENTERPRISES." "EСONOMY. FINANСES. MANAGEMENT: Topical issues of science and practical activity", no. 2 (56) (June 29, 2021): 49–63. http://dx.doi.org/10.37128/2411-4413-2021-2-4.

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Information tools for ensuring strategic development are investigated on the example of agricultural enterprises. The methodological foundations of the content of basic categories for the management of strategic development are revealed, the components of the structure of its information support are highlighted and it is determined that the information support of the strategic development of agricultural enterprises is scientifically grounded management of the process of constant growth of the volume of information and knowledge through traditional and new tools for processing and analyzing in

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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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Shi, Frank G. "Glass transition: A unified treatment." Journal of Materials Research 9, no. 7 (1994): 1908–16. http://dx.doi.org/10.1557/jmr.1994.1908.

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A unified kinetic and thermodynamic description of the glass transition in undercooled liquids at normal pressure is established. The following results are obtained for the first time: (1) The glass transition temperature Tg is determined to be in the range of Ts < Tg < Tn. Both Ts and Tn are material-dependent and each of them is characterized by a different Ω(T) = TΔslc(T)/Δslc(T) with Δhlc as the excess enthalpy and Δslc the excess entropy. (2) Being above Kauzmann's isentropic temperature, the lowest limit Ts is determined by Ω(Ts) = 1 −2/(3γ) with γ being the ratio between the total

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Journal, Baghdad Science. "Study the Band Energy Structure and Absorption Coefficient for PbSe Thin Films." Baghdad Science Journal 5, no. 1 (2008): 89–94. http://dx.doi.org/10.21123/bsj.5.1.89-94.

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The PbSe alloy was prepared in evacuated quarts tubs by the method of melt quenching from element, the PbSe thin films prepared by thermal evaporation method and deposited at different substrate temperature (Ts) =R.T ,373 and 473K . The thin films that deposited at room temperature (R.T=303)K was annealed at temperature, Ta= R.T, 373 and 473K . By depended on D.C conductivity measurements calculated the density of state (DOS), The density of extended state N(Eext) increases with increasing the Ts and Ta, while the density of localized state N(Eloc) is decreased . We investigated the absorption

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Tao, Wen, Charles Grubmeyer, and John S. Blanchard. "Transition State Structure ofSalmonella typhimuriumOrotate Phosphoribosyltransferase†." Biochemistry 35, no. 1 (1996): 14–21. http://dx.doi.org/10.1021/bi951898l.

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Lee, Vladimir Ya, Yuki Ito, Olga A. Gapurenko, et al. "Pentagermapyramidane: Crystallizing the “Transition-State” Structure." Angewandte Chemie 127, no. 19 (2015): 5746–49. http://dx.doi.org/10.1002/ange.201500731.

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Lee, Vladimir Ya, Yuki Ito, Olga A. Gapurenko, et al. "Pentagermapyramidane: Crystallizing the “Transition-State” Structure." Angewandte Chemie International Edition 54, no. 19 (2015): 5654–57. http://dx.doi.org/10.1002/anie.201500731.

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47

Liberman, David A. "Slater transition-state band-structure calculations." Physical Review B 62, no. 11 (2000): 6851–53. http://dx.doi.org/10.1103/physrevb.62.6851.

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Miton, Charlotte M., Stefanie Jonas, Gerhard Fischer, 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 (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

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Chakrabarty, Kuheli, Atanu Basak, Animesh Ghosh, and Gourab Kanti Das. "Ionic liquid supported acid additive stabilizes the transition structure of organocatalytic asymmetric direct aldol reaction by proton donation: A quantum mechanical study." Journal of Theoretical and Computational Chemistry 15, no. 06 (2016): 1650049. http://dx.doi.org/10.1142/s0219633616500498.

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ONIOM studies were performed on the transition structure (TS) of organocatalytic direct aldol reaction by using ionic liquid supported benzoic acid (ILS-PhCO2H) as an additive. Results obtained from this computation suggest direct involvement of ILS-PhCO2H in the TS as a proton donor. It has also come out from the present study that, the counter ion of the ILS-acid additive may also play significant role to maintain the proper TS geometry by holding the organocatalyst and the acid additive close together during the course of reaction.

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Journal, Baghdad Science. "The structure and optical properties of CdSe:Cu Thin Films." Baghdad Science Journal 6, no. 1 (2009): 141–49. http://dx.doi.org/10.21123/bsj.6.1.141-149.

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A polycrystalline CdSe thin films doped with (5wt%) of Cu was fabricated using vacuum evaporation technique in the substrate temperature range(Ts=RT-250)oC on glass substrates of the thickness(0.8?m). The structure of these films are determined by X-ray diffraction (XRD). The X-ray diffraction studies shows that the structure is polycrystalline with hexagonal structure, and there are strong peaks at the direction (200) at (Ts=RT-150) oC, while at higher substrate temperature(Ts=150-250) oC the structure is single crystal. The optical properties as a function of Ts were studied. The absorption,

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