Origins and predictions of stereoselective antibody catalysis: theoretical analysis of Diels-Alder catalysis by 39A11 and its germ-line antibody

The binding of enantiomeric haptens and transition states by the Schultz Diels-Alderase antibody 39A11 and its germ-line antibody were studied theoretically. The mechanisms by which one hapten and one transition state stereoisomer is recognized selectively are explored with docking simulations and quantum mechanical models. Transition states of the relevant Diels-Alder reaction were located with density functional theory. A prediction is made that the stereoselectivity of 39A11 will be achieved by two strategically placed hydrogen bonds and pi-stacking interactions of the maleimide with a binding-site tryptophan, arranged so as to coordinate one enantiomeric transition state. Binding of other ligands by antibody 39A11 and the germ-line antibody has also been investigated. The polyspecific nature of 39A11 and its germ-line precursor was found to originate from the general ability of the binding pockets to achieve hydrophobic binding of small organic substrates. Comparison of the highly homologous progesterone and Diels-Alderase antibodies (DB3, 1E9, and 39A11) highlights the fact that differences of several key residues in the binding pockets are sufficient to confer selectivity for different antigens.     

Broadening the Aldolase Catalytic Antibody Repertoire by Combining Reactive Immunization and Transition State Theory: New Enantio- and Diastereoselectivities

Nine efficient aldolase antibodies were generated by using hapten 1. This hapten unites reactive immunization and the transition state analogue approach in a single molecule. Characterization of two of these antibodies reveals that they are highly proficient (up to 1000-fold better than any other antibody catalyst) and enantioselective catalysts for aldol and retro-aldol reactions and exhibit enantio- and diastereoselectivities opposite to that of antibody 38C2.     

A catalysis-based selection for peroxidase antibodies with increased activity

A biotin-tyramine conjugate (1) was found to covalently cross-link with peroxidase antibody 7G12 upon the catalytic oxidation of the tyramine moiety in the presence of hydrogen peroxide (H2O2). On the basis of this observation, a novel strategy was developed to select mutants of 7G12 Fab with enhanced peroxidase activity from a library of phage displayed antibodies. In such a selection, tyramine is oxidized by hydrogen peroxide in a process catalyzed by peroxidase antibodies displayed on phage. Antibodies with higher peroxidase activity are preferentially labeled with biotin through irreversible adduct formation between oxidized biotin-linked tyramine molecules and phenolic side chains of the antibody. The corresponding phage particles can then be selected via biotin-streptavidin interactions. Using this strategy, phage displayed libraries of antibody 7G12 were selected for higher peroxidase activity. As a result, mutations of antibody 7G12 that led to 10 to 20-fold increases in the peroxidase activity (kcat/Km) were identified, suggesting the validity of this method for the evolution of peroxidase antibodies based directly on catalytic turnover.     

Unravelling Enzymatic Features in a Supramolecular Iridium Catalyst by Computational Calculations

Non-biological catalysts following the governing principles of enzymes are attractive systems to disclose unprecedented reactivities. Most of those existing catalysts feature an adaptable molecular recognition site for substrate binding that are prone to undergo conformational selection pathways. Herein, we present a non-biological catalyst that is able to bind substrates via the induced fit model according to in-depth computational calculations. The system, which is constituted by an inflexible substrate-recognition site derived from a zinc-porphyrin in the second coordination sphere, features destabilization of ground states as well as stabilization of transition states for the relevant iridium-catalyzed C−H bond borylation of pyridine. In addition, this catalyst appears to be most suited to tightly bind the transition state rather than the substrate. Besides these features, which are reminiscent of the action modes of enzymes, new elementary catalytic steps (i. e. C−B bond formation and catalyst regeneration) have been disclosed owing to the unique distortions encountered in the different intermediates and transition states.     

Theoretical analysis of transition states in the exchange reaction of hydrogen and methane involving σ-bond metathesis

Silica supported zirconium hydride species are used to model heterogeneous catalysts for industrially-relevant reactions such as hydrogenation of paraffins. This work explores the exchange reaction between methane and hydrogen in the presence of a silica-supported zirconium or titanium hydride catalyst in order to determine the preferred transition state. Calculations at the B3LYP/LanL2DZ level of theory are used to model two distinct pathways for the reaction. Orbital interactions are analyzed to elucidate the relative stability of the two transition states.     

The mechanism of ethylene polymerization by nickel salicylaldiminato catalysts - Agostic interactions and their kinetic isotope effects

The ethylene polymerization reaction of a neutral nickel catalyst was studied by DFT calculations at the Becke3LYP/6-31G(d) level of theory. As in related cases a β-agostic bond stabilizes the nickel alkyl ground states. Transition states for the insertion of the olefin show a distinct α-agostic interaction, which has not been observed for late metal polymerization catalysts before. An ethylene-alkyl complex was identified as the resting state of the reaction. The overall barrier height of the reaction amounts to 17.54 kcal/mol, which slightly increases to 17.60 kcal/mol for the polymerization of deuterated ethylene. Therefore, a small positive kinetic isotope effect (k_H/k_D = 1.09) can be calculated, which is caused by the α-agostic interaction in the transition state. A comparison to other late metal based polymerization systems reveals that the ethylene coordination step of highly active catalysts is significantly lower in energy compared to catalysts which are only moderately active.     

The roles of benzoic acid and water on the Michael reactions of pentanal and nitrostyrene catalyzed by diarylprolinol silyl ether

The roles of benzoic acid and water on the Michael reaction of pentanal and nitrostyrene catalyzed by diarylprolinol silyl ether are revealed by density functional theory calculations. The calculations demonstrate that the benzoic acid is ready to attack the catalysts and form a hydrogen bond between the hydrogen atom of the COOH of benzoic acid and one of the N atoms of the catalyst. The complex formed from pentanal, catalyst and benzoic acid attacks nitroalkene and forms transition states. Finally, the transition states hydrolyze and the products are formed. The calculations demonstrate that the stereoselectivity is dominated by the steric hindrance of the 2-substituent groups, and the benzoic acid can increase the reaction rate evidently by decreasing the activation energies; however, H(3)O(+) or strong acid may prevent the formation of the transition states between enamines and nitroalkenes. The employed solvent can decrease the activation energies and promote the proton transfer from benzoic acid onto the catalyst 2. The calculated enantiomeric excess values are in good agreement with the experimental results. These calculations also reveal that the role of benzoic acid is dependent on the sophisticated structures of the catalysts and provide a valuable index for the structural design of new catalysts and selection of additives or co-catalysts.     

Origin of enantioselectivity in the propargylation of aromatic aldehydes catalyzed by helical N-oxides

The enantioselective propargylation of aromatic aldehydes with allenyltrichlorosilanes catalyzed by bipyridine N-oxides was explored using density functional theory. Low-lying transition states for a highly enantioselective helical bipyridine N-oxide catalyst [Org. Lett. 2011, 13, 1654] were characterized at the B97-D/TZV(2d,2p) level of theory. Predicted free energy barrier height differences are in agreement with experimental ee's for the propargylation of benzaldehyde and substituted analogues. The origin of enantioselectivity was pinpointed through distortion-interaction analyses. The stereoselectivity arises in part from through-space electrostatic interactions of the carbonyl carbon with the Cl ligands bound to Si, rather than noncovalent aryl-aryl interactions between the aromatic aldehyde and the helix as previously proposed. Moreover, aryl-aryl interactions between the aldehyde and helix are predicted to favor transition states leading to the R enantiomer, and ultimately reduce the enantioselectivity of this reaction. (S)-2,2'-bipyridine N-oxide was studied as a model catalyst in order to quantify the inherent enantioselectivity arising from different chiral arrangements of ligands around the hexacoordinate silicon in the stereocontrolling transition state for these reactions. The predicted selectivities arising from different chiral octahedral silicon complexes provide guidelines for the development of transition state models for N-oxide-based alkylation catalysts.     

Stereocartography: a computational mapping technique that can locate regions of maximum stereoinduction around chiral catalysts

A hypothesis concerning asymmetric induction by chiral catalysts is posited, tested, and found to be valid. The hypothesis states that chiral catalysts that are efficient at inducing asymmetry will have their region of maximum stereoinduction spatially congruent with the site of chemistry but inefficient catalysts will not. A simple mapping strategy (stereocartography) is used to assess where the region of maximum stereoinduction is located around a given catalyst. The protocol compares interaction energies between mirror image probes at each point in space around the catalyst being considered. The probes are models of the actual transition states of the reaction being catalyzed by a particular catalyst. The hypothesis was tested on three Diels-Alder reactions. Seventeen of the eighteen catalysts conform to the hypothesis. The idea of using this as a catalyst design tool is presented.     

Cooperative Catalysis of Metal and O?H⋅⋅⋅O/sp3‐C?H⋅⋅⋅O Two‐Point Hydrogen Bonds in Alcoholic Solvents: Cu‐Catalyzed Enantioselective Direct Alkynylation of Aldehydes with Terminal Alkynes

Catalyst–substrate hydrogen bonds in artificial catalysts usually occur in aprotic solvents, but not in protic solvents, in contrast to enzymatic catalysis. We report a case in which ligand–substrate hydrogen‐bonding interactions cooperate with a transition‐metal center in alcoholic solvents for enantioselective catalysis. Copper(I) complexes with prolinol‐based hydroxy amino phosphane chiral ligands catalytically promoted the direct alkynylation of aldehydes with terminal alkynes in alcoholic solvents to afford nonracemic secondary propargylic alcohols with high enantioselectivities. Quantum‐mechanical calculations of enantiodiscriminating transition states show the occurrence of a nonclassical sp³‐C? H???O hydrogen bond as a secondary interaction between the ligand and substrate, which results in highly directional catalyst–substrate two‐point hydrogen bonding.     

Kinetics and mechanism of the Pudovik reaction in the azomethine series: III. Acid-catalyzed hydrophosphorylation of imines

A complex spectral (UV, IR, and ³¹P NMR), preparative, and kinetic investigation of the mechanism of the noncatalytic variant of the Pudovik reaction in the series of imines was carried out. The reaction proceeds through a four-center cyclic transition state. The transition state is highly labile, which determines its high sensitivity to the structure of the reagents, the nature of the solvent and catalyst, and some other factors. The necessary condition for the hydrophosphorylation of imines to occur is the participation of proton-donor reagents and acidic admixtures, specifically hydrolysis products of dialkyl hydrogen phosphites, such as monoalkyl dihydrogen phosphates and phosphorous acid, which act as acid catalysts. When the starting reagents are thoroughly purified and no such catalysts are present, the Pudovik reaction fails to occur in the imine series.     

Stepwise diels-alder: more than just an oddity? A computational mechanistic study

We have employed hybrid DFT and SCS-MP2 calculations at the SMD-PCM-6-311++G(2d,2p)//6-31+G(d) level to investigate the relationship between three possible channels for forming a Diels-Alder adduct from a highly nucleophilic diene and moderately to highly electrophilic dienophiles. We discuss geometries optimized using the B3LYP and M06-2X functionals with the 6-31+(d) basis set. The transition states and intermediates are characterized on the basis of geometric and electronic properties, and we also address the possibility of predicting detectability of a zwitterionic intermediate based on its relative stability. Our results show that a conventional Diels-Alder transition state conformation yields intermediates in all four investigated cases, but that these are too short-lived to be detected experimentally for the less activated reactants. The stepwise trans pathway, beginning with a conjugate addition-like transition state, becomes increasingly competitive with more activated reactants and is indeed favored for the most electrophilic dienophiles. Addition of a trans diene leads to a dead-end as the trans intermediates have insurmountable rotation barriers that prohibit formation of the second bond, unless another, heterocyclic intermediate is formed. We also show that introduction of a hydrogen bond donating catalyst favors a stepwise pathway even for less activated dienophiles.     

Experimental determination of the absolute enantioselectivity of an antibody-catalyzed Diels-Alder reaction and theoretical explorations of the origins of stereoselectivity

The exo and endo Diels-Alder adducts of p-methoxycarbonylbenzyl trans-1,3-butadiene-1-carbamate and N,N-dimethylacrylamide have been synthesized, and the absolute configurations of resolved enantiomers have been determined. On the basis of this information, the absolute enantioselectivities of the Diels-Alder reaction catalyzed by antibodies 13G5 and 4D5 as well as other catalytic antibodies elicited in the same immunizations have been established. The effects of different arrangements of catalytic residues on the structure and energetics of the possible Diels-Alder transition states were modeled quantum mechanically at the B3LYP/6-311++G**//B3LYP/6-31+G** level of theory. Flexible docking of these enantiomeric transition states in the antibody active site followed by molecular dynamics on the resulting complexes provided a prediction of the transition-state binding modes and an explanation of the origin of the observed enantioselectivity of antibody 13G5.     

Design and Synthesis of 6 α-Corticosteroid Haptens and Their Bovine Serum Albumin(BSA) Conjugates

The site of attachment of protein carrier to corticosteroids has great influence on the specificity of produced antibody.In order to obtain highly specific and accurate antibodies for bioimmunoassay determination of cortisol,different tether lengths of 60633－corticosteroid haptens and their BSA conjugates were designed and synthesized.     

Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9

Direct hydroxide attack on the scissile carbonyl of the substrate has been suggested as a likely mechanism for esterase antibodies elicited by phosphonate haptens, which mimic the transition states for the alkaline hydrolysis of esters.1 The unique amidase activity of esterase antibody 43C9 has been attributed to nucleophilic attack by an active-site histidine residue.2 Yet, the active site of 43C9 is strikingly similar to those of other esterase antibodies, particularly 17E8. We have carried out quantum mechanical calculations, molecular dynamics simulations, and free energy calculations to assess the mechanism involving direct hydroxide attack for 43C9. Results support this mechanism and suggest that the mechanism is plausible for other antiphosphonate antibodies that catalyze the hydrolysis of (p-nitro)phenyl esters.     

Temperature-programmed oxidation of equilibrium fluid catalytic cracking catalysts

Characterization of coke on equilibrium, fluid catalytic cracking (FCC) catalysts contaminated with metals was investigated using temperature-programmed oxidation (TPO). TPO spectra of spent equilibrium catalysts from cracking of sour imported heavy gas oil (SIHGO) were deconvoluted into four peaks (Peak K, L, M and N). The four peaks were assigned to different types of coke on the catalyst. Peak L in the TPO spectrum was assigned to the 'contaminant' coke in the vicinity of metals. The amount of contaminant coke (Peak L) correlates with metal-contaminant concentration. The size of Peak L which is related to amount of contaminant coke decreased significantly for the spent highly contaminated catalyst pretreated with hydrogen and methane prior to cracking reactions as compared to the non-pretreated catalysts. Since both hydrogen and methane pretreatment can reduce oxidation state of the vanadium that present at high concentrations on the equilibrium catalysts the decrease in the amount of contaminant-coke represented by Peak L was explained by the reduction of the oxidation state of vanadium. Less contaminant coke was produced after the equilibrium catalysts were pretreated using hydrogen and methane gases since reduced vanadium has lower dehydrogenation activity compared to oxidized vanadium. This revised version was published online in August 2006 with corrections to the Cover Date.     

水电解制氢非贵金属催化剂的研究进展

氢能作为零碳排放能源是被公认的最清洁能源之一,如何有效可持续地产氢是未来人类步入氢能经济首先要解决的问题。电解水技术基于电化学分解水的原理,利用可再生电能或太阳能驱动水分解为氢气和氧气,被认为是最有前途和可持续性的产氢途径。然而,无论是光解水还是电解水,均需要高活性、高稳定性的非贵金属氢析出和氧析出催化剂以使水电解反应经济节能。本文介绍了我们研究所近三年在水电解方面的研究进展,其中着重介绍了：（ⅰ）氢析出催化剂,包括利用低温磷化过渡金属（氢）氧化物的方法制备过渡金属磷化物,同时过渡金属硫化物、硒化物以及碳化物等均被成功合成并被应用为有效的阴极析氢催化剂;（ⅱ）氧析出催化剂,主要包括金属磷化物、硫化物、氧化物/氢氧化物等;（ⅲ）双功能催化剂,主要包括过渡金属磷化物、硒化物、硫化物等。最后,总结展望了发展水电解非贵金属催化剂所面临的挑战与未来发展方向。     

PROPERTIES OF Ni-Cu/SiO_2 BIMETALLIC CATALYSTSPREPARED BY SOLVATED METAL ATOM DISPERSION(SMAD) TECHNIQUE

IntroductionAsoneofthemethodsofpreparationofsupportedmetalcatalysts,solvatedmatalatomdispersion(SMAD)onoxidesupportsattractsmuchattentionnowadays.TIstechniquehasbeendevelopedbyKlabunde'SandOzin'sresearchgroups.Itprovidesanumberofadvantages,ascomparedwitht…     

An approach to sequence-specific antibody proteases

We describe here a novel strategy for the isolation of antibodies with sequence-specific protease activity: the synthesis of dipeptide haptens in which the targeted peptide bond has been replaced by a ring-strained or torsionally strained hydroxyethylene transition-state analog. Thus, the analogs mimic both a peptide bond in a distorted, reactive conformation and the transition state for peptide bond hydrolysis. In order to obtain sequence-specific antibody proteases, these analogs have been flanked with additional amino acid residues in preparation for immunization. In particular, we have synthesized peptides containing analogs such as 2-cis-amino-3-cis-hydroxycyclobutane carboxylic acid andendo-(3-amino-2-hydroxy)bicyclo[2.2.1]heptane-7-anti-carboxylic acid. We have also prepared a series of peptide derivatives containing analogs, such as 2-[3-amino-2-oxo-1-azetidinyl]-3-methylbutanoic acid, in which the targeted peptide bond has been incorporated into a β-lactam ring. Since the “peptide bond” has been left intact, these species mimic only a distorted ground state. At present, antibodies are being elicited against a number of the above peptide derivatives.     

Importance of Intermolecular Hydrogen Bonding for the Stereochemical Control of Allene–Enone (3+2) Annulations Catalyzed by a Bifunctional,Amino Acid Derived Phosphine Catalyst

The origin of stereoselectivity in the (3+2) annulation of allenes and enones catalyzed by an amino acid derived phosphine catalyst has been investigated by the use of dispersion‐corrected density functional theory. An intermolecular hydrogen bond between the intermediate zwitterion and the enone was found to be the key interaction in the two enantiomeric transition states. Additional stabilization is provided by intermolecular hydrogen‐bonding interactions between acidic positions on the catalyst backbone and the substrate. Enantioselectivity occurs because the intermolecular hydrogen bond in the transition state leading to the minor enantiomer is only possible at the expense of reactant distortion.