Academic literature on the topic 'Transition state (TS)'
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Journal articles on the topic "Transition state (TS)"
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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.
Full textAbstract:
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.
Full textAbstract:
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.
Full textAbstract:
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.
Full textAbstract:
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.
Full textAbstract:
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 .
Dissertations / Theses on the topic "Transition state (TS)"
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Kinal, Armagan. "Theoretical Investigation Of Unimolecular Reactions Of Cyclic C5h6 Compounds By Ab Initio Quantum Chemical Methods." Phd thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/12605124/index.pdf.
Full textAbstract:
Thermodynamic stabilities of eighteen cyclic C5H6 isomers were explored computationally both on singlet and triplet state potential energy surfaces (PES). All isomers have singlet ground states except for bicyclo[2.1.0]pent-5-ylidene (B5) having no stable geometry on the singlet C5H6 PES. Cyclopenta-1,3-diene (M1) is the most stable cyclic C5H6 isomer while cyclopent-1,4-diylidene is the least stable one among all. Cyclopenta-1,2-diene (M2) and cyclopentyne (M3) have biradical characters of 46.9 and 21.5%, respectively.
Seven unimolecular isomerization reactions occurring among several of these molecules were investigated by DFT and ab initio methods. The conversion of bicyclo[2.1.0]pent-2-ene (B1) and tricyclo[2.1.0.02,5]-pentane (T1) into 1,3-cyclopentadiene (M1) are shown to be concerted processes whose reaction paths pass through TSs with a high degree of biradical character. The reaction enthalpies (DH0) are predicted to be -47.7 kcal/mol for B1 and -63.8 kcal/mol for T1 at UB3LYP/6-31G(d) level. The activation enthalpy (DH0¹) for the ring opening of B1 was calculated by the CR-CCSD(T) method to be 25.2 kcal/mol, in good agreement with experiment. Furthermore, the DH0¹
for the ring opening of T1 was obtained by the CR-CCSD(T) method to be 48.2 kcal/mol. The self-conversion of M1 via 1,5-hydrogen shift is a facile and concerted reaction with aromatic TS. The DH0¹
estimations of B3LYP and CC methods are 25.24 and 28.78 kcal/mol, respectively. For 1,2-hydrogen shift reactions of cyclopent-3-enylidene (M4) and cyclopenten-2-ylidene (M5), the single point CC calculations predicted the DH0¹
values of 3.13 and 10.12 kcal/mol, as well as, the DH0 values of -71.28 and -64.05 kcal/mol, respectively. The reason of M5 being more stable than M4 is due to the conjugation of the carbene carbon and the double bond in M5. The reaction path of cyclobutylidene methylene to cyclopentyne rearrangement is found to be rather shallow. The DH0¹
and DH0 values predicted by the RCCSD(T) method to be 3.65 and -5.72 kcal/mol, respectively. Finally, triplet state isomerization of bicyclo[2.1.0]pent-5-ylidene to cyclopenta-1,2-diene, as well as, its parent reaction, cyclopropylidene to 1,2-propadiene were investigated at several levels of theory including DFT, CASSCF and CC methods. The UCCSD(T) method estimated a moderate barrier whose value is 8.12 kcal/mol for the isomerization of 3B5 with the reaction enthalpy of -44.63 kcal/mol.
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Harman, David Grant. "Mechanisms of the Intriguing Rearrangements of Activated Organic Species." Phd thesis, 2003. http://hdl.handle.net/1885/47123.
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The β-acyloxyalkyl radical rearrangement has been known since 1967 but its mechanism is still not fully understood, despite considerable investigation. Since the migration of a β-trifluoroacetoxy group generally proceeds more rapidly and with more varied regiochemistry than its less electronegative counterparts, this reaction was studied in the hope of understanding more about the subtleties of the mechanism of the β- acyloxyalkyl radical rearrangement. The mechanism of the catalysed rearrangement of Nalkoxy- 2(1H)-pyridinethiones was also explored because preliminary studies indicated that the transition state (TS) for this process was isoelectronic with TSs postulated for the β-acyloxyalkyl radical and other novel rearrangements. ¶ ...
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Philion, Stephen E. "The discourse of workers democracy in China as a terrain of ideological struggle in the moment of transition from state socialism." 2004. http://proquest.umi.com/pqdweb?index=1&did=765924121&SrchMode=1&sid=1&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1233712301&clientId=23440.
Full textConference papers on the topic "Transition state (TS)"
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Gvozdkov, Alexander, and Olga Suslova. "Some Aspects of Improving the Efficiency of Air Treatment in the Contact Units of HVAC Systems." In Environmental Engineering. VGTU Technika, 2017. http://dx.doi.org/10.3846/enviro.2017.258.
Full textAbstract:
One of the main issues of improving the efficiency of air treatment in ventilation and air conditioning systems (HVAC systems) is development of methodology for the realization of energy-efficient air treatment processes in the contacting units. This paper investigates the thermodynamic models of “air-water” system, considering some features of the transition area at the interface, including surface phases and boundary layers of air and water. It has a great impact on the efficiency of processes of heat and moisture exchange in the contact units HVAC systems. The paper presents the results of experimental studies to determine the air-water interfaces temperature when achieving a state of thermodynamic balance condition in contacting media (air and water) in the working space of contact units. It was found that the surface temperature is determined by state of the surface phase and depends on the direction process of heat and moisture exchange (condensation or evaporation). The temperature factor k = Tdry/Ts as a criterion for determining the effect of the state transition area on the processes of heat and moisture exchange, was used. Processing of results from experimental researches in the processes of heat and mass transfer is presented in the form of criterial equations for Nu, Nu. Results of the performed research are the basis for the formulation of theoretical ideas about the energy efficient processes and the development of a new method for calculation of the contact units HVAC systems.