ライフサイエンスコーパス: transition state

1 agmentations proceeding through an inversion transition state.

2 0) moieties, which mimic the geometry of the transition state.

3 gen bond interactions form after the docking transition state.

4 pecies are not involved in the rate-limiting transition state.

5 to promote GTPase domain dimerization in the transition state.

6 avors one helicity of the electrocyclization transition state.

7 or to and after the formation of the docking transition state.

8 structure awaits, reached through a bicyclic transition state.

9 equilibrium geometry similar to the neutral transition state.

10 -H...F interactions, in the major R-inducing transition state.

11 to form an alkoxy group via a carbenium-ion transition state.

12 n via either an allylic cation or a cationic transition state.

13 tacking nucleophile (2.10 A) advanced at the transition state.

14 driven by stabilization of the axle-forming transition state.

15 nthalpy, owing to partial desolvation of the transition state.

16 stabilizes the open channel, relative to the transition state.

17 quantum mechanical calculations for the NSD2 transition state.

18 ay that they are primed to form the required transition state.

19 concerted, four-center (H3C...*...H...O*)() transition state.

20 ing of the electron and proton from the same transition state.

21 nal frontier molecular orbitals (MOs) at the transition state.

22 geometry of the presumed phosphoryl transfer transition state.

23 d for glycosides, and through a very similar transition state.

24 h almost no effect on the free energy of the transition state.

25 d Meisenheimer complex in the C-H activation transition state.

26 e binding while facilitating sampling of the transition state.

27 reaction is characterized by an advanced SN2 transition state.

28 could be used to energetically differentiate transition states.

29 ydrogen bonds are enhanced from reactants to transition states.

30 ions and distortion energies in the computed transition states.

31 he difficulty in predicting their accessible transition states.

32 selectivity by identifying stereocontrolling transition states.

33 ling axis in the respective rate-determining transition states.

34 on mechanisms but multiple stereocontrolling transition states.

35 stinct interactions within the corresponding transition states.

36 ism via the energetically favorable syn/endo-transition states.

37 set analyses to the computationally derived transition states.

38 stive quantum mechanical search for possible transition states (728 were found in total).

39 while computational studies on the reaction transition state allowed us to rationalize the stereoche

40 reactions proceed via a highly asynchronous transition state allowing easier bond formation between

41 Interesting phenomena such as a shift in a transition state along a reaction coordinate, a switch o

42 tant proton transfers and stabilize multiple transition states along a complex reaction coordinate.

43 ure of the arrested enzyme in complex with a transition state analog shows that catalytic sidechains

44 pt a high-affinity homodimer when bound to a transition-state analog.

45 thetic point of view: they act as amino acid transition state analogs and Horner-Wadsworth-Emmons rea

46 using collagen-model templates combined with transition state analogs produced a first generation of

47 mplex analogue AK:pAIE:Mg.ADP (PCA), and the transition state analogue AK:Arg:Mg.ADP:NO3(-) (TSA).

48 ealed that acyclic boronic acids can act as 'transition state analogue' inhibitors of nucleophilic se

49 ructure of zebrafish HDAC10 complexed with a transition-state analogue inhibitor reveals that a gluta

50 The 1994 structure of a transition-state analogue with AlF4(-) and GDP complexed

51 edge that should stimulate the design of new transition-state analogues for use as chemical biology t

52 Transition-state analogues of PNP bind with picomolar (p

53 H is highly favored in vivo We conclude that transition-state analogues with picomolar dissociation c

54 llvalene results in the stabilization of the transition state and a further lowering of the Cope barr

55 eventually formed can the protein reach the transition state and continue folding.

56 ed that this reaction proceeds via chairlike transition state and is exothermic.

57 arge on the nitro-substituted carbon in both transition state and product is the driving force for th

58 arily by lowering the energy of the directed transition state and reaction conformers.

59 atures that promote the stabilization of the transition state and slight variations in these interact

60 bmotif precedes the formation of the docking transition state and tertiary A-minor hydrogen bond inte

61 zabo models), we extract the position of the transition state and the height of the kinetic barrier m

62 nfection generates an epithelial-mesenchymal transition state and tumor-initiating cancer stem-like c

63 the intermediates, which could stabilize the transition states and facilitate the formation of 2-subs

64 the structures of folding intermediates and transition states and their associated energies.

65 Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement.

66 s, conformations, energies, strain energies, transition states, and activation energies of these rear

67 ediate, the degree of charge transfer in the transition states, and, in certain cases, secondary orbi

68 nism and revealed additional features of the transition states, anionic intermediates, and final neut

69 Bispericyclic transition states appear when two independent pericyclic

70 ven challenging 15- and 19-membered ligation transition states are suitable for information translati

71 The spin-crossover transition states are thoroughly investigated, revealing

72 ceed in a concerted fashion through a cyclic transition state-are among the most powerful synthetic t

73 y of Au-catalysts to the Bergman cyclization transition state as one of the key components of the lar

74 ion of the anhydride-methanol complex in the transition state as the factor leading to stereoselectiv

75 stabilization of a cobalt(III)-oxyl/propane transition state as the Lewis acidity of the promoter io

76 We used free energy of stable and transition states as independent fitting parameters and

77 determine the structural orientation of the transition states, as well as the presence/absence of an

78 zes the ozonide and lowers the energy of the transition state at neutral pH.

79 of binding that is indeed reflective of the transition state at the CARM1 active site.

80 echanism with a relatively short-lived polar transition state (average lifetime = 519 +/- 240 fs), wh

81 ts are hindered by computationally expensive transition state barrier calculations.

82 Prior to crossing the transition state barrier, hydrogen exchange protection f

83 ecay upon deuteration in the vicinity of the transition state barrier, which is confirmed by microcan

84 3,3] sigmatropic shift where the pericyclic "transition state" becomes the most stable species on the

85 he drive to minimize torsional strain in the transition state being coupled with assistance from hydr

86 of deactivation by primarily stabilizing the transition state between the activated and closed states

87 involving product-forming pathways with post-transition-state bifurcations.

88 new active sites by improving substrate and transition-state binding, through the sampling of many p

89 e sulfur to the 5'-C of ATP is 2.03 A at the transition state (bond order of 0.67).

90 here is a 6.7 kcal/mol stabilization of this transition state by 1.0 M guanidine cation (Gua(+)).

91 present an alternative approach (decrypting transition state by light = DTS-hnu), which enables the

92 he associated lone-pair stabilization of the transition state by Ox promotes cyclization of tradition

93 tent with a significant stabilization of the transition state by the ribozyme, and functional group s

94 Further analysis of the reaction transition states, by means of multidimensional correlat

95 reactivity predictions better than those of transition-state calculations for a concerted SNAr react

96 avior of sulfonylallenes was rationalized by transition-state calculations which enabled a semiquanti

97 n folding and other biopolymer processes and transition states can be determined from analysis of ure

98 iable contribution of MHC side-chains to the transition state complex, arguing against a two-step mec

99 for those enzymes reacting through the (4)H3 transition-state conformation.

100 roperties of these domains reveal that their transition states contain most of the internal solvent e

101 en the putative product-determining isomeric transition states (DeltaDeltaE(double dagger)) in both t

102 We found that the free-energy barrier at the transition state (DeltaF) correlates with nonnative-cont

103 h an increased residence time on InhA due to transition-state destabilization rather than ground-stat

104 e between the native state and the unfolding transition state-dictates the LC's unfolding rate.

105 cyclic 1-azadienes originate from increased transition state distortion energies and unfavorable int

106 itive charge at the benzylic position in the transition state during the degradation of acetals.

107 (550) and to stabilize the incipient anionic transition state during thioester exchange.

108 that involves a three-center (H3C...*...H)() transition state, during which a Ni-atom inserts into th

109 it has proven valuable to prepare and probe transition-state dynamics by the photodetachment of anio

110 that have enabled an extension of studies of transition-state dynamics to increasingly multidimension

111 bstitution, unimolecular decomposition, post-transition-state dynamics, mass spectrometry experiments

112 verview of the breakdown of ground-state and transition state effects in enzyme catalysis in unpreced

113 ing is more advanced than bond making at the transition state, electrophile-nucleophile electrostatic

114 and solvent molecules; (ii) modifications to transition state energies and structures relative to the

115 We develop scaling relations relating transition state energies to the carbon monoxide adsorpt

116 understanding of the regiochemistry based on transition-state energies is unsupported.

117 h in the pathways and dramatic shifts in the transition-state ensemble (TSE) in src SH3 domain as f i

118 recently determined that CD4-induced (CD4i) transition state epitopes in the HIV surface antigen, gp

119 of negative charge at the NSO3 moiety in the transition state, especially when the sulfonamide NH is

120 work reveals how shape and charge mimicry of transition state features can enable the rational design

121 governed by transient species, including the transition state for activated bimolecular reactions.

122 This indicates that the transition state for activation of carbonate is stabiliz

123 ws that the 31 kcal/mol stabilization of the transition state for decarboxylation of OMP provided by

124 lts in a 9.1 kcal/mol destabilization of the transition state for enzyme-catalyzed reduction of dihyd

125 Density functional theory predicts a transition state for H2 formation where the S-H(+) bond

126 Our results indicate that the transition state for hybridization is visited before the

127 complex is controlled by interactions in the transition state for inhibitor binding rather than the g

128 The transition state for MAT2A is more advanced along the re

129 The transition state for OMPDC-catalyzed decarboxylation of

130 n driving force are largely expressed at the transition state for proton transfer.

131 nnels, and a nucleophilic substitution (SN2) transition state for transmethylation.

132 The geometries of the transition states for nucleophilic substitutions on benz

133 d on AlF4(-) , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigon

134 opentene and cyclohexene, respectively, with transition states for pi-ligand exchange having barriers

135 opic mass in F159Y PNP causes more efficient transition state formation.

136 of crystallization theories reveals that the transition state from solution to crystalline aggregates

137 The transition states from both I1 and I2 to the native stat

138 tational methods can identify conformational transition states from structural changes, revealing com

139 uide the design of inhibitors that mimic the transition state geometry and charge.

140 al/mol) is required to achieve the concerted transition state geometry.

141 e a positively charged arene intermediate or transition state, giving rise to novel electrophilic aro

142 The transition state governs how chemical bonds form and cle

143 as the activation entropy suggested that the transition state has less structural freedom than that o

144 alytic speed on a cooler Earth-by exploiting transition-state heat capacity.

145 ddle of the box, and freezes what would be a transition state in its absence.

146 le states represent a chemical marker of the transition state in the eigenenergy spectrum.

147 The barrier creates a transition state in the free energy landscape that slows

148 the pi bond and an unsymmetrical perepoxide transition state in the hydroperoxide-forming step.

149 are thus preorganized closer to the assumed transition state in these glycosylation reactions.

150 A transition state in which atropisomerism occurs by a coo

151 zed in terms of the greater stability of the transition state in which the Ar and NO2 groups are anti

152 arboxylation of benzoylacetic acid support a transition state in which the proton transfer is complet

153 ble dagger) upon switching from the unpaired transition states in high solvent dielectric to ion pair

154 tes in high solvent dielectric to ion paired transition states in low solvent dielectric (Delta(Delta

155 of a water molecule in the rate determining transition state, in such a way that the preferential nu

156 umber of weak interactions are formed at the transition state, including nonnative interactions, and

157 of common warheads employed in the design of transition state inhibitors of serine and cysteine prote

158 the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolite

159 ermining step, and the possible turning of a transition state into a stable minimum are revealed by t

160 TS-hnu), which enables the decryption of the transition states involved in chiral phosphoric acids ca

161 rprint pattern is directly correlated to the transition states involved in the transformation.

162 n DFT calculations, an eight-membered cyclic transition state involving coordination of the lithium a

163 RO2 H-shift rate coefficients via transition states involving six- and seven-membered ring

164 preferentially through an open-shell singlet transition state: iron donates electron density to weake

165 The transition state is a late, asymmetric nucleophilic disp

166 n bonding, the dipole moment of the ion-pair transition state is an important factor.

167 most favored [3,3]-sigmatropic rearrangement transition state is bimodal, leading to two reaction int

168 This positively charged transition state is consistent with the relative degrada

169 This transition state is further supported by the KIEs, BIEs,

170 bond breaking and O-H bond formation in the transition state is minimized, and (b) when the electros

171 tereochemical information through an ordered transition state is obtained.

172 In the intramolecular oxidation of PDI, a transition state is only observed if hydrogen bond donor

173 gmatropic reaction featuring a bispericyclic transition state is reported for a cyclohexane featuring

174 The transition state is stabilized by an oxyanion hole forme

175 strates and catalyst in the C-S bond forming transition state is the key reason for stereoinduction i

176 ed acid catalysis, experimental insight into transition states is very rare, and most of the mechanis

177 show that this steric strain, present in the transition state, is responsible for the unusually high

178 3SiCl to the metal center via a six-membered transition state (IV) that leads to the intermediate, (e

179 is explained by a stabilizing effect on the transition state leading to the biradical intermediate.

180 between the substrate and the ligand in the transition state leading to the formation of the minor e

181 alone by stabilizing every intermediate and transition state leading up to and including the final s

182 interaction of the new catalyst with the SN2 transition state leads to a very important catalytic eff

183 eutrophils or macrophages, the nature of the transition states manifested in vivo, and the underlying

184 tates appear when two independent pericyclic transition states merge into one.

185 a route to their specific inhibition through transition-state mimicry.

186 ent nature of PRMT-substrate complexes, such transition state mimics represent valuable chemical tool

187 moiety as in the AdoMet cofactor to generate transition state mimics.

188 On the basis of these studies, a transition state model explaining the observed stereoche

189 The predicted DFT transition state model is also in agreement with the exp

190 In the most preferred transition states, more effective C-H...pi (between the

191 The transition state occurs when this activation strain is o

192 a sub-millisecond time scale through a late transition state of all four domains.

193 teracts with the nucleotide, stabilizing the transition state of GTP hydrolysis and compensating for

194 ct-like) than that from the near-symmetrical transition state of methionine adenosyltransferase from

195 of the lysine nucleophile and stabilizes the transition state of the ATP alpha phosphate; a second oc

196 ed by a secondary orbital interaction in the transition state of the formal H-atom transfer that driv

197 t to the electric field stabilization of the transition state of the LDE variants of the KE07 and KE7

198 These data indicate that the binding transition state of the nSH3 domain and PRM is accompani

199 h 2(COD)Ir(+) and 1(COD)Ir.POM(8-) yield the transition state of the rate-determining step of nucleat

200 o enable more efficient stabilization of the transition state of the reaction.

201 5)-eta(3) ligand slippage that occurs in the transition state of the selectivity-determining step.

202 izing energy of the Pd-Cu interaction in the transition state of the transmetalation step in Pd/Cu-ca

203 Here, we probe the transition state of this interaction experimentally thro

204 The transition states of aldol reactions catalyzed by vicina

205 Diels-Alder routes is blurred, and favorable transition states of both types may coexist.

206 ic field values relevant to the reactant and transition states of designed Kemp eliminases KE07 and K

207 tes and in the alternative Zimmerman-Traxler transition states of model compounds as shown by DFT cal

208 The relative energy levels of the possible transition states of the IMDA reaction of the camphanate

209 The cyclic transition states of these reactions involve nine-member

210 ning, the resulting stabilization of anionic transition states on fullerenes is shown to accelerate d

211 the structures of both the ground states and transition states on the binding reaction coordinate are

212 the recognition of anionic intermediates and transition states on this polarized pi surface, that is,

213 Application of a direct multidimensional transition state optimization to the hydride transfer st

214 structural change of the spring helix at the transition state, optimizing the interaction network cen

215 de group that either transfer protons at the transition state or trap the initially formed tetrahedra

216 dissociation and calculating the kinetic and transition state parameters.

217 namics and vibrational coupling to enzymatic transition state passage.

218 t the reactants into geometries they have in transition states plus the interaction energies between

219 ances and bound states supported by the post-transition state potential well.

220 ccur concertedly through highly asynchronous transition states, proceed with lower activation barrier

221 rine bond formation proceeds via a concerted transition state rather than a discrete Meisenheimer int

222 coincides with an increase in selectivity of transition-state recognition by up to -14.8 kJ mol(-1).

223 dicals, which have relatively early and late transition states, respectively, the difference in the d

224 racter of the Fe(IV) horizontal lineO at the transition states resulting from the weaker ligand field

225 revealed positive charge accumulation in the transition state (rho = -2.9).

226 nzyme to diminish motions that determine the transition state sampling in the native enzyme, in accor

227 group additivity fingerprints, combined with transition-state scaling relations and a simple classifi

228 ometric conformations that have a bearing on transition-state selection.

229 covalent modification of D244, requiring two transition-state species and is regulated by coordinatio

230 Transition state spectroscopy experiments based on negat

231 tope effects (KIEs), indicating very similar transition state stabilities and structures.

232 tion, while its direct electrostatic role in transition state stabilization is secondary.

233 ion in a manner that allows it to assist in transition state stabilization.

234 binding energy) and are the key factors for transition-state stabilization and molecular recognition

235 of protein side chain functional groups, and transition-state stabilization of the S(VI) exchange rea

236 pling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate

237 by creating a more favorable environment for transition-state stabilization.

238 O and Sn in the fragmentation as a specific transition state stabilizing effect.

239 vealed that ground state destabilization and transition state stabilizing effects contribute almost e

240 The transition state structure can be represented in a molec

241 um mechanical (QM) calculations to solve the transition state structure of human MAT2A.

242 e in the intrinsic KIEs, indicating the same transition state structure.

243 ting features of the reaction coordinate and transition-state structure has emerged as a powerful app

244 show that certain CD4i epitopes specific to transition state structures are exposed across the surfa

245 toluene and the N-oxyl aromatic rings in the transition state structures.

246 rge mimicry of the proposed intermediate and transition state structures.

247 Our calculations show that the transition-state structures vary smoothly across the ran

248 es and structural features for reactants and transition states support these conclusions.

249 Such a transition state supports a model in which the rate-limi

250 serves to stabilize the turnover-determining transition states (TDTSs) via strong N-H...O hydrogen-bo

251 arcus intrinsic barrier and over the earlier transition state than carboxylate that produces an anion

252 tial cycloaddition proceeds via an ambimodal transition state that can lead to both of the proposed [

253 more general ambimodal concept applied to a transition state that connects reactants with two or mor

254 predicted the structure of the rate-limiting transition state that controlled the time-dependent inhi

255 lysis and corresponds to the post-hydrolysis transition state that is stabilized by phosphorylation a

256 iled DFT study of equilibrium geometries and transition states that explains the stereochemical outco

257 Universality is key to the theory of phase transitions, stating that the equilibrium properties of

258 iclassical trajectories passing through this transition state, the new O-H bond after proton transfer

259 Conventional and variational transition state theories can predict neither the select

260 ed in further developments of reaction class transition state theory (RC-TST) for description of comp

261 macromolecular rate theory (MMRT), based on transition state theory (TST) for enzyme-catalyzed kinet

262 icle reviews the fundamentals of variational transition state theory (VTST), its recent theoretical d

263 strategy to quantify the error associated to transition state theory from the number of recrossings o

264 previous work found that canonical forms of transition state theory incorrectly predict the regiosel

265 e of the HT mechanism from that described by transition state theory to a regime controlled by solven

266 reaction rate theories, the applicability of transition state theory to the study of enzymatic reacti

267 dimensional tunneling (canonical variational transition state theory with small curvature tunneling),

268 Thus, the use of transition state theory, even with simplified reaction c

269 differ substantially from KIEs predicted by transition state theory, which suggests that IVR in this

270 ew development of a hybrid method of quantum transition state theory/improved kinetic gas theory, for

271 Here we present aspects of transition-state theory (TST) alongside with kinetic gas

272 and corresponding electronic-structure-based transition-state theory calculations.

273 room temperature it channels passage to the transition state, thereby determining the rate-limiting

274 lO4 is found to favor the C-C bond formation transition state to the S-E isomer in the case of MeQd a

275 e "normal" reaction proceeds through a tight transition state to yield H2 + CO but for which a high f

276 opulations and Eyrings rate constant for the transition state, to describe inactivation kinetics of e

277 l remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H(+) after the b

278 addition approaches of the sulfur ylide, the transition state (TS) energies for the formation of poss

279 data permit the identification of changes in transition state (TS) properties.

280 (5)Hsigma and (3)Hsigma) that possess linear transition state (TS) structures, and a triplet pi -path

281 At transition state (TS), a linkage of O-H-O involving O 2p

282 unavailable information about mechanisms and transition states (TS) of protein folding and binding is

283 ormational itineraries through B2,5 or (3)H4 transition-state (TS) conformations.

284 llow a reaction pathway involving sequential transition states (TS6 and TS8), for which reaction dyna

285 the expected addition product 21 as well as transition state TS8, directly forming the rearranged pr

286 The parameterization of the transition states (TSs) for the uncatalyzed reaction, th

287 he context of ground-state stabilization and transition-state tunneling.

288 To further characterize the binding transition state, we conducted the Eyring and linear fre

289 With the optimized geometries of the transition states, we found that the aromatic ring of th

290 In particular, the identity of the transition state, which determines the kinetics of the t

291 ading to two reaction intermediates from one transition state, which is confirmed by molecular dynami

292 hance the polarization of toluene during its transition state, which suggests that a polarizable char

293 l, we determined the elastic behavior of the transition state, which we find to be similar to that of

294 ferential electrostatic stabilization of the transition state with greater charge separation by the c

295 d by the experimentally inferred Im9 folding transition state with native packing most developed at t

296 that the transmetalation occurs via a cyclic transition state with retention of configuration at the

297 proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35-

298 omatization reactions, such crossings define transition states with energies defined by both the in-p

299 thered nucleophiles that required endocyclic transition states with small angles between the bond bei

300 athways in catalytic reactions often involve transition states with very different charge distributio