Quantum chemical modeling of enzyme active sites and reaction mechanisms

Density functional methods, in particular the B3LYP functional, together with the explosive enhancement of computational power, have in the last 5 years or so made it possible to model enzyme active sites and reaction mechanisms in a quite realistic way. Many mechanistic problems have indeed been addressed and solved. This review gives a brief account of the methods and models used to study enzyme active sites and their reaction mechanisms using quantum chemical methods. Examples are given from our recent work in this field. Future perspectives of the field are discussed.     

Methyl transfer in glycine N-methyltransferase. A theoretical study

Density functional theory calculations using the hybrid functional B3LYP have been performed to study the methyl transfer step in glycine N-methyltransferase (GNMT). This enzyme catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of glycine to form sarcosine. The starting point for the calculations is the recent X-ray crystal structure of GNMT complexed with SAM and acetate. Several quantum chemical models with different sizes, employing up to 98 atoms, were used. The calculations demonstrate that the suggested mechanism, where the methyl group is transferred in a single S(N)2 step, is thermodynamically plausible. By adding or eliminating various groups at the active site, it was furthermore demonstrated that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to the carboxylate group raise the barrier.     

The structure of the diazonium coupling products of phenacyl thiocyanate and phenacyl selenocyanate with diazotized 3-phenyl-5-aminopyrazole

The reaction of diazotized 3-phenyl-5-aminopyrazole with phenacyl thiocyanate 1a and phenacyl selenocyanate 1b afforded directly 2-imino-3-(3-phenyl-5-pyrazolyl)-5-benzoyl-2,3-dihydro-1,3,4-thiadiazole monohydrate 9a and 2-imino-3-(3-phenyl-5-pyrazolyl)-5-benzoyl-2,3-dihydro-1,3,4-selenadiazole monohydrate 9b , respectively. The products 9a and 9b were also obtained from the reaction of C-benzoyl-N-(3-phenyl-5-pyrazolyl)formohydrazidoyl bromide 10 with potassium thiocyanate and potassium selenocyanate, respectively. Acetylation, benzoylation, and nitrosation of 9 afforded the corresponding diacetyl, dibenzoyl, and nitroso derivatives 11-13 , respectively. Cyclization of C-benzoyl-N-(3-phenyl-5-pyrazolyl)-nitrilimine 6 was shown to give the pyrazolo [5,1-d]triazole 8 and not the pyrazolo[5,1-c]-as-triazine derivative 7 , as previously reported.     

Photo- and thermoinduced generation of 1,3-diaryl carbonyl ylides from 2,3-diaryloxiranes 1,3-dipolar cycloadditions to dipolarophiles

A group of symmetrically substituted 2,3-diaryloxiranes have been studied as photoprecursors for carbonyl ylides. The stereochemistry of the adducts obtained upon interception of these 4n pi-transient systems with a variety of dipolarophiles provides information on the mode(s) of electrocyclic opening of the oxiranes to carbonyl ylides, as well as the mechanism of the 4n + 2 cycloaddition process. The stereochemistry of the dipolarophiles is preserved in the cycloadducts, which is consistent with a concerted addition process; however, solvent effects, steric hindrance, and possibly secondary orbital overlap factors all may play a role in determining the product distribution.     

Arylation with Unsymmetrical Diaryliodonium Salts: A Chemoselectivity Study

Phenols, anilines, and malonates have been arylated under metal‐free conditions with twelve aryl(phenyl)iodonium salts in a systematic chemoselectivity study. A new “anti‐ortho effect” has been identified in the arylation of malonates. Several “dummy groups” have been found that give complete chemoselectivity in the transfer of the phenyl moiety, irrespective of the nucleophile. An aryl exchange in the diaryliodonium salts has been observed under certain arylation conditions. DFT calculations have been performed to investigate the reaction mechanism and to elucidate the origins of the observed selectivities. These results are expected to facilitate the design of chiral diaryliodonium salts and the development of catalytic arylation reactions that are based on these sustainable and metal‐free reagents.     

Atom‐Efficient Gold(I)‐Chloride‐Catalyzed Synthesis of α‐Sulfenylated Carbonyl Compounds from Propargylic Alcohols and Aryl Thiols: Substrate Scope and Experimental and Theoretical Mechanistic Investigation

Gold(I)‐chloride‐catalyzed synthesis of α‐sulfenylated carbonyl compounds from propargylic alcohols and aryl thiols showed a wide substrate scope with respect to both propargylic alcohols and aryl thiols. Primary and secondary aromatic propargylic alcohols generated α‐sulfenylated aldehydes and ketones in 60–97 % yield. Secondary aliphatic propargylic alcohols generated α‐sulfenylated ketones in yields of 47–71 %. Different gold sources and ligand effects were studied, and it was shown that gold(I) chloride gave the highest product yields. Experimental and theoretical studies demonstrated that the reaction proceeds in two separate steps. A sulfenylated allylic alcohol, generated by initial regioselective attack of the aryl thiol on the triple bond of the propargylic alcohol, was isolated, evaluated, and found to be an intermediate in the reaction. Deuterium labeling experiments showed that the protons from the propargylic alcohol and aryl thiol were transferred to the 3‐position, and that the hydride from the alcohol was transferred to the 2‐position of the product. Density functional theory (DFT) calculations showed that the observed regioselectivity of the aryl thiol attack towards the 2‐position of propargylic alcohol was determined by a low‐energy, five‐membered cyclic protodeauration transition state instead of the strained, four‐membered cyclic transition state found for attack at the 3‐position. Experimental data and DFT calculations supported that the second step of the reaction is initiated by protonation of the double bond of the sulfenylated allylic alcohol with a proton donor coordinated to gold(I) chloride. This in turn allows for a 1,2‐hydride shift, generating the final product of the reaction.     

Total synthesis of deamido bleomycin a(2), the major catabolite of the antitumor agent bleomycin

Metabolic inactivation of the antitumor antibiotic bleomycin is believed to be mediated exclusively via the action of bleomycin hydrolase, a cysteine proteinase that is widely distributed in nature. While the spectrum of antitumor activity exhibited by the bleomycins is believed to reflect the anatomical distribution of bleomycin hydrolase within the host, little has been done to characterize the product of the putative inactivation at a chemical or biochemical level. The present report describes the synthesis of deamidobleomycin demethyl A(2) (3) and deamido bleomycin A(2) (4), as well as the respective aglycones. These compounds were all accessible via the key intermediate N(alpha)-Boc-N(beta)-[1-amino-3(S)-(4-amino-6-carboxy-5-methylpyrimidin-2-yl)propion-3-yl]-(S)-beta-aminoalanine tert-butyl ester (16). Synthetic deamido bleomycin A(2) was shown to be identical to the product formed by treatment of bleomycin A(2) with human bleomycin hydrolase, as judged by reversed-phase HPLC analysis and (1)H NMR spectroscopy. Deamido bleomycin A(2) was found to retain significant DNA cleavage activity in DNA plasmid relaxation assays and had the same sequence selectivity of DNA cleavage as bleomycin A(2). The most significant alteration of function noted in this study was a reduction in the ability of deamido bleomycin A(2) to mediate double-strand DNA cleavage, relative to that produced by BLM A(2).     

Mechanisms of tetrazole formation by addition of azide to nitriles

It is well-known that azide salts can engage nitriles at elevated temperatures to yield tetrazoles; however, there is continued debate as to the mechanism of the reaction. Density functional theory calculations with the hybrid functional B3LYP have been performed to study different mechanisms of tetrazole formation, including concerted cycloaddition and stepwise addition of neutral or anionic azide species. The calculations presented here suggest a previously unsuspected nitrile activation step en route to an imidoyl azide, which then cyclizes to give the tetrazole. The activation barriers are found to correlate strongly with the electron-withdrawing potential of the substituent on the nitrile.     

Crystallization and stereocomplexation behavior of poly(D‐ and L‐lactide)‐b‐poly(N,N‐dimethylamino‐2‐ethyl methacrylate) block copolymers

The thermal properties, crystallization, and morphology of amphiphilic poly(D ‐lactide)‐b‐poly(N,N‐dimethylamino‐2‐ethyl methacrylate) (PDLA‐b‐PDMAEMA) and poly (L ‐lactide)‐b‐poly(N,N‐dimethylamino‐2‐ethyl methacrylate) (PLLA‐b‐PDMAEMA) copolymers were studied and compared to those of the corresponding poly(lactide) homopolymers. Additionally, stereocomplexation of these copolymers was studied. The crystallization kinetics of the PLA blocks was retarded by the presence of the PDMAEMA block. The studied copolymers were found to be miscible in the melt and the glassy state. The Avrami theory was able to predict the entire crystallization range of the PLA isothermal overall crystallization. The melting points of PLDA/PLLA and PLA/PLA‐b‐PDMAEMA stereocomplexes were higher than those formed by copolymer mixtures. This indicates that the PDMAEMA block is influencing the stability of the stereocomplex structures. For the low molecular weight samples, the stereocomplexes particles exhibited a conventional disk‐shape structure and, for high molecular weight samples, the particles displayed unusual star‐like shape morphology. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1397–1409, 2011     

Mechanism,reactivity, and selectivity of the iridium-catalyzed C(sp3)–H borylation of chlorosilanes

The iridium-catalyzed C(sp³)–H borylation of methylchlorosilanes is investigated by means of density functional theory, using the B3LYP and M06 functionals. The calculations establish that the resting state of the catalyst is a seven-coordinate Ir(v) species that has to be converted into an Ir(iii)tris(boryl) complex in order to effect the oxidative addition of the C–H bond. This is then followed by a C–B reductive elimination to yield the borylated product, and the catalytic cycle is finally completed by the regeneration of the active catalyst over two facile steps. The two employed functionals give somewhat different conclusions concerning the nature of the rate-determining step, and whether reductive elimination occurs directly or after a prior isomerization of the Ir(v) hydride intermediate complex. The calculations reproduce quite well the experimentally-observed trends in the reactivities of substrates with different substituents. It is demonstrated that the reactivity can be correlated to the Ir–C bond dissociation energies of the corresponding Ir(v) hydride intermediates. The effect of the chlorosilyl group is identified to originate from the α-carbanion-stabilizing effect of the silicon, which is further reinforced by the presence of an electron-withdrawing chlorine substituent. Furthermore, the source of selectivity for the borylation of primary over secondary C(sp³)–H can be explained on a steric basis, by repulsion between the alkyl group and the Ir/ligand moiety. Finally, the difference in the reactivity between C(sp³)–H and C(sp²)–H borylation is investigated and rationalized in terms of distortion/interaction analysis.