Restricted Transition State Research Articles

Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations

Experiments have compared the folding of proteins with different amino acid sequences but the same basic structure, or fold. Results indicate that folding is robust to sequence variations for proteins with some nonlocal folds, such as all-β, whereas the folding of more local, all-α proteins typically exhibits a stronger sequence dependence. Here, we use a coarse-grained model to systematically study how variations in sequence perturb the folding energy landscapes of three model sequences with 3α, 4β + α, and β-barrel folds, respectively. These three proteins exhibit folding features in line with experiments, including expected rank order in the cooperativity of the folding transition and stability-dependent shifts in the location of the free-energy barrier to folding. Using a generalized-ensemble simulation approach, we determine the thermodynamics of around 2000 sequence variants representing all possible hydrophobic or polar single- and double-point mutations. From an analysis of the subset of stability-neutral mutations, we find that folding is perturbed in a topology-dependent manner, with the β-barrel protein being the most robust. Our analysis shows, in particular, that the magnitude of mutational perturbations of the transition state is controlled in part by the size or “width” of the underlying conformational ensemble. This result suggests that the mutational robustness of the folding of the β-barrel protein is underpinned by its conformationally restricted transition state ensemble, revealing a link between sequence and topological effects in protein folding.

Microporous Zeolites as Catalysts for the Preparation of Decyl Glucoside from Glucose with 1-Decanol by Direct Glucosidation

The catalytic properties of microporous zeolite catalysts were evaluated in the synthesis of decyl glucoside from glucose with 1-decanol by direct glucosidation. The effects of the acidic properties and pore structure of the zeolite catalysts on the glucose conversions and decyl glucoside yields were investigated. The conversions of glucose on the H+ ion-exchanged FAU, MFI, and BEA zeolite catalysts were above 70%. The conversion increased with decreasing acid strength of the catalysts. The highest conversion and yield of decyl glucoside were exhibited on the H-FAU(3) zeolite catalyst. The catalytic activities were enhanced with increasing amounts of acid sites. The selectivity of decyl glucopyranoside increased with decreasing Si/Al values for the same zeolite catalysts. The pore structure of H-FAU zeolite would allow sufficient spatial restriction to produce decyl glucopyranoside through the isomerization of decyl glucofuranoside into decyl glucopyranoside in its extensive pore channels. The selectivities of the decyl glucoside isomers relied significantly on the restricted transition state to the primary products due to their pore topologies.

The isopropylation of biphenyl over transition metal substituted aluminophosphates: MAPO-5 (M: Co and Ni)

The isopropylation of biphenyl (BP) was examined over transition metal substituted aluminophosphates (MAPO-5; M: Co and Ni) with 12-membered (12-MR) oxygen ring pore-entrances of AFI topology. The MAPO-5 samples were synthesized by dry gel conversion method using trimethylamine as a structure directing agent, and their properties were characterized by XRD, XPS, SEM, N2 adsorption, NH3-TPD, pyridine adsorption, and o-xylene uptake. They are clear crystals without impurity phases and agglomerates, and found small amounts of Brønsted acid sites which are expecting active for acid catalysis. The isopropylation of BP over both of Co(5)APO-5 and Ni(5)APO-5 at 250°C gave the high selectivities for 4,4′-DIPB: 65–75%. 4-IPBP is almost exclusive precursor of 4,4′- and 3,4′-DIPB. 3-IPBP was not significantly concerned even though 3-IPBP was predominant among IPBP isomers at the late stages: the MAPO-5 channels allow preferential access of 4-IPBP, and prevent the access of 3-IPBP due to reactant selectivity mechanism. The selective formation of 4,4′-DIPB occurred by preferential exclusion of bulkier 3,4′-DIPB and other isomers through the steric interaction of transition states with the channels by the restricted transition state selectivity mechanism. MAPO-5 (M: Co and Ni) has the same level of the selectivities for 4,4′-DIPB to SSZ-24 and other MAPO-5 (M: Si, Mg, and Zn), and these selectivities were originated by the AFI channels. The selectivities for 4,4′-DIPB were kept 65–75% at low and moderate temperatures over MAPO-5 (M: Co and Ni); however, they were decreased by the isomerization to stable 3,4′-DIPB with the increase in temperature.

Shape-selective synthesis of para-diethylbenzene over pore-engineered ZSM-5: A kinetic study

Alkylation of ethylbenzene (EB) with ethanol was carried out in a fixed bed, continuous, down-flow, tubular reactor at atmospheric pressure and hydrogen as a carrier gas in vapor phase. A detailed kinetic study was conducted over ZSM-5 zeolite extrudates pore-engineered by phosphate modification. The reaction was performed at EB: ethanol mole ratio of 4:1 and with varying contact time at temperatures of 613, 633 and 653K. Due to the induced shape-selectivity in ZSM-5 by phosphate modification, para-diethylbenzene (PDEB) was formed as a major product and side products like benzene, meta-diethylbenzene (MDEB) and other isomers were formed in minor quantity. Langmuir–Hinselwood–Hougen–Watson (LHHW) method for dual site mechanism with an assumption of surface reaction controlling was applied to derive the rate equations. Activation energies for the ethylation of EB, dealkylation of EB and isomerization of PDEB were found to be 117.2, 186.0 and 298.6kJ/mol respectively. Adsorption energetics showed that EB is weakly adsorbed, whereas ethanol is strongly adsorbed over the catalyst surface. Activation energy of PDEB formation was found to be lower than that of MDEB. Considering that the alkylation takes place mostly inside the zeolite channels, the results support restricted transition state selective mechanism for EB alkylation with ethanol over phosphate modified ZSM-5. Based on the proposed kinetic model, calculated values of EB conversion and PDEB formation were found to be in good agreement with the experimental results.

Easy Access to Modified Cyclodextrins by an Intramolecular Radical Approach

A simple method to modify the primary face of cyclodextrins (CDs) is described. The 6I-O-yl radical of α-, β-, and γ-CDs regioselectively abstracts the H5II, located in the adjacent D-glucose unit, by an intramolecular 1,8-hydrogen-atom-transfer reaction through a geometrically restricted nine-membered transition state to give a stable 1,3,5-trioxocane ring. The reaction has been extended to the 1,4-diols of α- and β-CD to give the corresponding bis(trioxocane)s. The C2-symmetric bis(trioxocane) corresponding to the α-CD is a stable crystalline solid whose structure was confirmed by X-ray diffraction analysis. The calculated geometric parameters confirm that the primary face is severely distorted toward a narrower elliptical shape for this rim.

Easy access to modified cyclodextrins by an intramolecular radical approach.

A simple method to modify the primary face of cyclodextrins (CDs) is described. The 6(I)-O-yl radical of α-, β-, and γ-CDs regioselectively abstracts the H5(II), located in the adjacent D-glucose unit, by an intramolecular 1,8-hydrogen-atom-transfer reaction through a geometrically restricted nine-membered transition state to give a stable 1,3,5-trioxocane ring. The reaction has been extended to the 1,4-diols of α- and β-CD to give the corresponding bis(trioxocane)s. The C2-symmetric bis(trioxocane) corresponding to the α-CD is a stable crystalline solid whose structure was confirmed by X-ray diffraction analysis. The calculated geometric parameters confirm that the primary face is severely distorted toward a narrower elliptical shape for this rim.

The isopropylation of biphenyl over H-mordenite — Roles of 3- and 4-isopropylbiphenyls

The isopropylation of biphenyl (BP) and 3- and 4-isopropylbiphenyls (3- and 4-IPBPs) was examined over H-mordenites (MOR) to elucidate the mechanism of shape-selective formation of 4,4′-diisopropylbiphenyl (4,4′-DIPB). The isopropylation of BP occurred predominantly to form 4-isopropylbiphenyl (4-IPBP) from BP and 4,4′-DIPB from 4-IPBP. However, 3-IPBP, a minor isomer from BP, cannot participate effectively in the formation of 3,4′-DIPB due to steric restriction of its isopropyl moiety with MOR channels. Selective formation of 4,4′-DIPB was observed at low to moderate temperatures: 225–275 °C. However, the selectivities for 4,4′-DIPB were decreased at high temperatures, 300–350 °C under propene pressure, 0.8MPa, by the isomerization of 4,4′-DIPB at external acid sites. The isomerization of 4,4′-DIPB occurred under low propene pressure even at 250 °C. The roles of 3- and 4-IPBPs in the formation of DIPB isomers were examined in the isopropylation of their mixtures. 4-IPBP was consumed much faster than 3-IPBP in all cases examined. 4-IPBP was an exclusive precursor to DIPB isomers, particularly 4,4′-DIPB. 4,4′-DIPB was also found as a predominant isomer in encapsulated products at all conditions examined. These results show that 4-IPBP can preferentially establish active transition state with propene and acid site in MOR channels, resulting in selective formation of 4,4′-DIPB. It is concluded that the isopropylation of BP over MOR occurs through reactant selectivity mechanism and restricted transition state mechanism, but not through product selectivity mechanism.

Synthetic investigation on MCM-68 zeolite with MSE topology and its application for shape-selective alkylation of biphenyl

The synthesis of MCM-68 zeolite with MSE topology, which is a three-dimensional zeolite with 12 × 10 × 10 membered ring (MR) channel systems was tuned under the hydrothermal conditions using N, N, N′, N′-tetraethylbicyclo[2.2.2]oct-7-ene-2,3:5,6-dipyrrolidinium diiodide as SDA, and applied for the isopropylation of biphenyl (BP). The H + form zeolite (SiO 2/Al 2O 3=26) was obtained by the ion-exchange of as-synthesized sample (SiO 2/Al 2O 3 = 20) after the calcination, and the zeolites with SiO 2/Al 2O 3 = 70–263 were prepared by the dealumination of calcined sample (SiO 2/Al 2O 3 = 20) by 1 N hydrochloric acid. Catalytic activities in the isopropylation of BP were enhanced by the dealumination of MCM-68 zeolite, and maximized at SiO 2/Al 2O 3 = 70. However, further dealumination accompanies the decrease in the catalytic activity. The selectivity for 4,4′-diisopropylbiphenyl was ca 75–80% for all MCM-68 zeolites at moderate temperatures up to 300 °C. These high selectivities are due to restricted transition state mechanism inside the 12-MR straight channels: BP cannot easily enter into the 10-MR channels and cages of the zeolites. The selectivity for 4,4′-di- sec-butylbiphenyl and 4,4′-di- tert-butylbiphenyl improved in sec-butylation and tert-butylation of BP compared to the isopropylation. The exclusion of bulky isomers was enhanced by increasing the bulkiness of the alkylating agents.

The ethylation of biphenyl over H-mordenite: Reactivities of the intermediates in the catalysis

The ethylation of biphenyl (BP) with ethene was examined over dealuminated H-mordenite (MOR; SiO 2/Al 2O 3 = 206). The ethylation occurred non-shape-selectively, and gave a mixture of ethylbiphenyls (EBPs), diethylbiphenyls (DEBPs), and higher ethylates. The ethylation of BP to EBPs was yielded in the ratio, 2-EBP:3-EBP:4-EBP = 2:2:1 at the initial stages. The reaction occurs under kinetic control. The formation of 4,4′-DEBP was less selective than that of the other isomers; however, the combined selectivity for DEBPs with 4-ethyl groups was higher than 80% during the reaction. 4-EBP was consumed rapidly than the other EBPs in the ethylation of EBPs to DEBPs. Less bulky DEBPs, particularly, 4,4′-DEBP disappeared preferentially compared to the other DEBPs in the ethylation of EBPs to higher ethylates. These results show that the MOR channels are too large for the shape-selective formation of 4-EBP and 4,4′-DEBP by the “restricted transition state selectivity mechanism”. The reactivities of reaction intermediates in the ethylation of BP decreased in the order: 4,4′-DEBP > 4-EBP > BP ≫ 3-EBP ≫ 2-EBP. These three EBP isomers have quite different reactivities for the further ethylation: 4-EBP was preferentially consumed to yield DEBPs with 4-ethyl groups. 3-EBP partly participated in the ethylation to DEBPs, particularly, at high conversion; however, 2-EBP was not ethylated even at the high conversion. Further, 4,4′-DEBP was preferentially ethylated to higher ethylates because it is the most reactive among BP, EBPs, and DEBPs. These high reactivities of 4-EBP and 4,4′-DEBP among their isomers were due to the “reactant selectivity mechanism”. Molecular modeling of the diffusion of the products suggests that the MOR channels are too large for the selective formation of 4,4′-DEBP because all DEBPs can diffuse in the channels. The preferential disappearance of 4-EBP and 4,4′-DEBP is due to the difference of the diffusion in the channels among their isomers. These simulations are corresponding to the experimental results.

The Roles of 3- and 4-Isopropylbiphenyls in the Isopropylation of Biphenyl over a H-Mordenite

The isopropylation of mixtures of 3- and 4-isopropylbiphenyls (3- and 4-IPBPs) was examined over a dealuminated H-mordenite (HM) to elucidate the role of 3- and 4-IPBPs in the isopropylation of biphenyl (BP). 4-IPBP was consumed much faster than 3-IPBP in all cases. 4-IPBP was an exclusive precursor to diisopropylbiphenyls (DIPBs), particularly 4,4′-DIPB, and 4,4′-DIPB was found in encapsulated products during the reaction. These results show that 4-IPBP can allow establishment of an active complex with propylene and acid site in HM pores, whereas 3-IPBP cannot. It is concluded that the isopropylation of BP over HM occurs through a reactant selectivity mechanism, and through a restricted transition state mechanism, but not through a product selectivity mechanism.

Routes to Catalysis: Structure of a Catalytic Antibody and Comparison with Its Natural Counterpart

The three-dimensional structure of a catalytic antibody (1F7) with chorismate mutase activity has been determined to 3.0 A resolution as a complex with a transition state analog. The structural data suggest that the antibody stabilizes the same conformationally restricted pericyclic transition state as occurs in the uncatalyzed reaction. Overall shape and charge complementarity between the combining site and the transition state analog dictate preferential binding of the correct substrate enantiomer in a conformation appropriate for reaction. Comparison with the structure of a chorismate mutase enzyme indicates an overall similarity between the catalytic mechanism employed by the two proteins. Differences in the number of specific interactions available for restricting the rotational degrees of freedom in the transition state, and the lack of multiple electrostatic interactions that might stabilize charge separation in this highly polarized metastable species, are likely to account for the observed 10(4) times lower activity of the antibody relative to that of the natural enzymes that catalyze this reaction. The structure of the 1F7 Fab'-hapten complex provides confirmation that the properties of an antibody catalyst faithfully reflect the design of the transition state analog.

Binding of a high-energy substrate conformer in antibody catalysis.

Enzymes can substantially increase the probability of a reaction by exploiting binding energy to preorganize their substrates into reactive conformations. Similar effects are likely to be important in a wide variety of designed catalysts, including catalytic antibodies. Transferred nuclear Overhauser effects have been used here to investigate how an antibody possessing chorismate mutase activity binds its flexible substrate molecule chorismate. The conversion of chorismate to prephenate by way of a Claisen rearrangement requires the substrate to adopt an energetically disfavored diaxial conformation in which the enolpyruvyl side chain is positioned over the six-membered ring. The antibody, which was elicited by a conformationally restricted transition state analog for this reaction, appears to bind this high-energy substrate conformer preferentially, as judged by diagnostic intramolecular transferred nuclear Overhauser effects. Inhibitor studies with the transition state analog confirm that preorganization takes place exclusively at the antibody active site. These results thus provide strong physical evidence for a direct relationship between the properties of a catalytic antibody and the structure of the transition state analog originally used to elicit the immune response.

Reaction of Trimethylbenzene over Alumina‐Pillared Montmorillonite

AbstractThe reaction of trimethylbenzene (TMB) over alumina‐pillared montmorillonite (Al‐PM) had been investigated in a fixed‐bed flow reactor at 300 °C and atmospheric pressure. Al‐PM calcined in the range 300‐500 °C exhibited decreased layer distance, surface area and acid amount. The strong acid sites of Al‐PM calcined at 500 °C were greatly diminished according to measurements of ammonia temperature‐programmed desorption. Under our conditions the reaction proceeded mainly via isomerization and disproportionation with little dealkylation. The conversion of reactant decreased in the order 1,2,3‐TMB ≥ 1,2,4‐TMB > 1,3,5‐TMB and the selectivity of isomerization in the order 1,2,3‐TMB > 1,3,5‐TMB > 1,2,4‐TMB, corresponding to the order of diminishing thermal instability. Both the catalytic activity and the selectivity ratio of disproportionation to isomerization decreased with increased calcined temperature and time‐on‐stream. o‐Xylene content in the total xylene produced from 1,2,4‐TMB or 1,2,3‐TMB greatly exceeded the composition at thermodynamic equilibrium. These results arc consistent with the decrease of both the strong acid sites and the pore size of Al‐PM which exhibits the restricted transition state selectivity.

Catalysis by shape selective zeolites-science and technology

Abstract

Conversion of trimethylbenzenes over montmorillonites pillared by aluminium and zirconium oxides

On the pillared clays and H-Y catalysts, the reactivity of TrMB isomers decreased with increasing cross-sectional diameter. Especially on montmorillonite intercalated by aluminium oxide (Al-mont-2) of which the layer distance was 5.4 A(0.54nm), there was a remarkable difference in reactivity between the smallest 1,2,4-TrMB and other isomers. Pillared clays showed higher selectivity for disproportionation against isomerization of every TrMB isomers than H-Y. The selectivity of pillared clays was unaccountable on a basis of the interlayer spacing: montmorillonite intercalated by zirconium oxide (Zr-mont) of which the layer distance was 7.1 A and the Al-mont-2 showed higher disproportionation selectivity than an Al-mont-1 having layer distance of 8.5 A, probably due to the difference in acidic property. There was no appreciable difference in the distribution of products for disproportionation of 1,2,3- and 1,3,5-TrMB over the catalysts tested. On the other hand, 1,2,4,5-TeMB and o-xylene were the main products from 1,2,4-TrMB and the selectivity to these products depended on the type of catalysts to decrease in the order: Al-mont-2 >Zr-mont > Al-mont-1 > H-Y. A mechanistic consideration suggests that the preferential formation of 1,2,4,5-TeMB and o-xylene is due to the restricted transition state selectivity.

Functional monomers and polymers, 118. Asymmetric syntheses of 2‐alkylcyclohexanones using chiral polymers containing aminobornanol moieties

AbstractCis‐endo‐3‐amino‐endo‐2‐bornanol (5) and exo‐5‐amino‐endo‐2‐bornanol (2) (prepared from endo‐2‐hydroxy‐5‐bornanone (1)) were reacted with chloromethylated polystyrene. With the resulting chiral polymers 4 and 6 asymmetric syntheses of 2‐alkyl‐cyclohexanones were carried out. These reactions showed a high enantioselectivity particularly with the chiral polymer 6, which suggests a specific restricted transition state to be important for the asymmetric alkylation reaction.

Disproportionation of 1,2,4-trimethylbenzene over montmorillonite pillared by aluminium oxide

Disproportionation of 1,2,4-trimethylbenzene was investigated in a flow system at 200°C, using montmorillonite intercalated by aluminium chlorohydroxyl complex (Al-mont) as a catalyst. Calcination of the Al-mont at 4000C gave an interlayer spacing of 8.5 A. The Al-mont catalyst was selective for disproportionation to yield 1,2,4, 5-tetramethylbenzene (durene) and xylenes. o-Xylene was produced far more abundantly than expected from thermodynamical equilibrium. A mechanistic consideration suggested that the preferential formation of 1,2,4,5-tetramethylbenzene and o-xylene was a result of restricted transition state selectivity. The catalytic activity decreased with time on stream owing to coke deposition. The catalyst deactivation was, however, prevented by supporting a small amount of Pd on the catalyst and using H 2 as a carrier gas, probably as a result of hydrogen spill-over.

Reductive elimination of biaryl from diarylbis(phosphine)platinum(II) complexes in solution: kinetics and mechanism

The thermal decompositions of complexes cis-[PtR2L2][R = Ph or C6H4Me-4; L2=(PPh3)2, {P(C6H4Me-4)3}2, (PMePh2)2, Ph2PCH2PPh2, Ph2PCH2CH2PPh2, or Me2PCH2CH2PMe2] in toluene solution have been investigated. Their stability to thermolysis varies markedly with L2, and only complexes of monotertiary phosphines are labile at 60 °C. Reaction occurs via primary concerted unimolecular reductive elimination of biaryl, and conforms to a first-order kinetic rate law. Concurrent but independent secondary decomposition of [PtL2] generates both arene and biaryl as minor products. The elimination of 4,4′-bitolyl from cis-[Pt(C6H4Me-4)2(PPh3)2] exhibits a pronounced negative entropy of activation, suggestive of a conformationally restricted transition state. The inclusion of free PPh3 suppresses secondary processes and accelerates primary decay. Although itself inert under these conditions, [PtR2(Ph2PCH2PPh2)] also eliminates biaryl in a concerted and kinetically first-order manner when allowed to react in the presence of 10 equivs. of Ph2PCH2PPh2. These observations provide further evidence for the facilitation of reductive elimination by added nucleophiles.