Theoretical study of the role of low-barrier hydrogen bonds in enzyme catalysis: a model of proton transfer in serine protease

 A model of low-barrier hydrogen bonds (LBHBs) in enzymes has been studied by ab initio quantum mechanical calculations including the self-consistent reaction field solvent model. The hydrogen-bond strengths and the deprotonation energies for the hydrogen-bonded and non-hydrogen-bonded cis-urocanic acid were calculated at the HF/6-31 + G(d,p) level at various dielectric constants. The same calculations were performed for the α,β-dihydrourocanic acid to model the catalytic dyad of serine protease. The deprotonation energy of N^ɛ2 in α,β-dihydrourocanic acid is increased by formation of LBHBs and depends very much on the dielectric constant. This study suggests that the formation of LBHBs increases the basicity of the dyad, and the polarity change near the reaction center in the active site could help the proton abstraction from Ser 195 and the donation to the leaving group. Both the LBHBs and the environment can play crucial roles in the enzyme catalysis. Received: 8 March 2000 / Accepted: 3 January 2001 / Published online: 3 May 2001     

Immobilization of MP-11 into a mesoporous metal-organic framework, MP-11@mesoMOF: a new platform for enzymatic catalysis

Microperoxidase-11 has for the first time been successfully immobilized into a mesoporous metal-organic framework (MOF) consisting of nanoscopic cages and it demonstrates superior enzymatic catalysis performances compared to its mesoporous silica counterpart.     

Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase

The ability of using wave function propagation approaches to simulate isotope effects in enzymes is explored, focusing on the large H/D kinetic isotope effect of soybean lipoxygenase-1 (SLO-1). The H/D kinetic isotope effect (KIE) is calculated as the ratio of the rate constants for hydrogen and deuterium transfer. The rate constants are calculated from the time course of the H and D nuclear wave functions. The propagations are done using one-dimensional proton potentials generated as sections from the full multidimensional surface of the reacting system in the protein. The sections are obtained during a classical empirical valence bond (EVB) molecular dynamics simulation of SLO-1. Since the propagations require an extremely long time for treating realistic activation barriers, it is essential to use an effective biasing approach. Thus, we develop here an approach that uses the classical quantum path (QCP) method to evaluate the quantum free energy change associated with the biasing potential. This approach provides an interesting alternative to full QCP simulations and to other current approaches for simulating isotope effects in proteins. In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction.     

Rate-promoting vibrations and coupled hydrogen-electron transfer reactions in the condensed phase: a model for enzymatic catalysis

A model is presented for coupled hydrogen-electron transfer reactions in condensed phase in the presence of a rate promoting vibration. Large kinetic isotope effects (KIEs) are found when the hydrogen is substituted with deuterium. While these KIEs are essentially temperature independent, reaction rates do exhibit temperature dependence. These findings agree with recent experimental data for various enzyme-catalyzed reactions, such as the amine dehydrogenases and soybean lipoxygenase. Consistent with earlier results, turning off the promoting vibration results in an increased KIE. Increasing the barrier height increases the KIE, while increasing the rate of electron transfer decreases it. These results are discussed in light of other views of vibrationally enhanced tunneling in enzymes.     

Colloid-chemical properties of ruthenium dioxide in relation to catalysis of the photochemical generation of hydrogen

A colloid of RuO₂, prepared by thermal decomposition of RuCl₃, was characterized with respect to its colloid-chemical properties and assessed as a catalyst for photochemical production of hydrogen. The RuO₂ proved to be unstable towards coagulation, even under conditions of low electrolyte concentration and in the presence of polymers. The sol manifested the same electric double layer characteristics as many other oxide dispersions. The point of zero charge (p.z.c.) in indifferent electrolyte was positioned at pH 5.75.Adsorption of methylviologen (MV²⁺), a commonly used electron relay in photochemical systems, at the RuO₂/solution interface is mainly a result of attractive coulombic interactions (above the p.z.c. of RuO₂). No indications have been found that it adsorbs on RuO₂ under the operational conditions of hydrogen production. In the hydrogen production system, the mass transfer of methylviologen radicals (MV⁺) is a rate-limiting factor. As a function of the methylviologen concentration, the catalytic production of hydrogen passes through a maximum.Dedicated to Professor Dr. Dr. h. c. Armin Weiss on the occasion of his 60th birthday.     

The influence of hydrogen bonding on the physical properties of ionic liquids

Potential applications of ionic liquids depend on the properties of this class of liquid material. To a large extent the structure and properties of these Coulomb systems are determined by the intermolecular interactions among anions and cations. In particular the subtle balance between Coulomb forces, hydrogen bonds and dispersion forces is of great importance for the understanding of ionic liquids. The purpose of the present paper is to answer three questions: Do hydrogen bonds exist in these Coulomb fluids? To what extent do hydrogen bonds contribute to the overall interaction between anions and cations? And finally, are hydrogen bonds important for the physical properties of ionic liquids? All these questions are addressed by using a suitable combination of experimental and theoretical methods including newly synthesized imidazolium-based ionic liquids, far infrared spectroscopy, terahertz spectroscopy, DFT calculations, differential scanning calorimetry (DSC), viscometry and quartz-crystal-microbalance measurements. The key statement is that although ionic liquids consist solely of anions and cations and Coulomb forces are the dominating interaction, local and directional interaction such as hydrogen bonding has significant influence on the structure and properties of ionic liquids. This is demonstrated for the case of melting points, viscosities and enthalpies of vaporization. As a consequence, a variety of important properties can be tuned towards a larger working temperature range, finally expanding the range of potential applications.     

A new mathematical model for the enzymatic kinetic resolution of racemates

A mathematical model is presented for the kinetic resolution of racemates. It takes all intermediate binding steps into account and assumes that such steps are reversible. The model describing dynamics of the chiral reaction products consists of two nonlinear differential equations. With this model, the enantioselectivity of enzyme has been studied. Mathematical and numerical simulation of the model show that there are several ways to control the enantiomeric ratio (E) but the affinity and the binding rates of the intermediate enzyme complex to the racemic substrates are the key steps for the enzyme enantioselectivity.     

Systemic approach in the physical and structural chemistry of enzyme catalysis: From primary structure to elementary event

The state of the art in enzyme catalysis is considered in terms of physical and structural chemistry. The main chemical kinetic and structural approaches are presented that can provide detailed information concerning the elementary processes making up the multistep catalytic cycle of molecular conversion at the active site of an enzyme. It is demonstrated that knowledge of the sequence of amino acids in a protein is sufficient to reconstruct the tertiary structure of this protein, to identify the catalytic groups, and to elucidate the molecular mechanism of catalysis. This approach is based on highly efficient information and computational technologies. The architecture of the active sites of enzymes is analyzed, including geometric invariants and the characteristic bond distances and angles of catalytic groups. The template method for identifying catalytic sites in the protein 4D structure is considered. The potential of molecular mechanics in the study of active sites is illustrated by the example of computer-simulated mutagenesis. Quantum chemical calculations applied to elementary events of the catalytic cycle are considered as a physical basis for understanding the catalytic mechanism and the origin of the efficiency and specificity of enzymes.     

Polyynes as a model for carbyne: synthesis, physical properties, and nonlinear optical response

With the Fritsch-Buttenberg-Wiechell rearrangement as a primary synthetic route, a series of conjugated, triisopropylsilyl end-capped polyynes containing 2-10 acetylene units has been assembled. In a few steps, significant quantities of the polyynes are made available, which allow for a thorough analysis of their structural, physical, and optical properties. Molecules in the series have been characterized in detail using (13)C NMR spectroscopy, differential scanning calorimetry, mass spectrometry, and, for four derivatives including octayne 6, X-ray crystallography. UV-vis spectroscopy of the polyynes 1-7 shows a consistent lowering of the HOMO-LUMO gap (E(g)) as a function of the number of acetylene units (n), fitting a power-law relationship of E(g) approximately n(-)(0.379)(+/-)(0.002). The third-order nonlinear optical (NLO) properties of the polyyne series have been examined, and the nonresonant molecular second hyperpolarizabilities (gamma) increase as a function of length according to the power-law gamma approximately n(4.28)(+/-)(0.13). This result exhibits an exponent that is larger than theoretically predicted for polyynes and higher than is observed for polyenes and polyenynes. The combined linear and nonlinear optical results confirm recent theoretical studies that suggest polyynes as model 1-D conjugated systems. On the basis of UV-vis spectroscopic analysis, the effective conjugation length for this series of polyynes is estimated to be ca. n = 32, providing insight into characteristics of carbyne.     

Analysis of a theoretical model for anisotropic enzyme membranes application to enzyme electrodes

A theoretical model of diffusion and reaction in an anisotropic enzyme membrane is presented with particular emphasis on the application of such membranes in enzyme electrodes. The dynamic response of systems in which the kinetics are linear, which comprises the practical operating regime for enzyme electrodes in analysis, is investigated via an analytic solution of the governing differential equations. The response is presented as a function of a single dimensionless group, Μ, that is the membrane modulus.     

The preparation and resolution of 2-phenyl-Quinazolinap,a new atropisomeric phosphinamine ligand for asymmetric catalysis

The preparation and resolution of an axially chiral quinazoline-containing phosphinamine ligand is described. The biaryl linkage was formed in a Pd-catalysed coupling of 4-chloro-2-phenylquinazoline 10 with 2-methoxy-1-naphthylboronic acid 11. Demethylation of the product ether 12 afforded alcohol 13 which was converted into the corresponding triflate 14 by treatment with trifluoromethanesulphonic anhydride. An Ni-catalysed phosphinylation gave the required phosphinamine ligand 9 as a racemate. Diastereomeric palladacycles 16, formed from 9 and (+)-di-μ-chlorobis[(R)-dimethyl(1-(1-naphthyl)ethyl)aminato-C₂,N]dipalladium(II) 15 were separated to give diastereomerically pure materials. An X-ray crystal structure of the (R,R)-16 palladacycle was determined and is discussed. Displacement of the resolving agent by reaction with 1,2-bis(diphenylphosphino)ethane gave enantiopure 2-phenyl-Quinazolinap 9, a new atropisomeric phosphinamine ligand for asymmetric catalysis.     

The proton‐coupled proton transfer mechanism,H2O catalysis,and hydrogen tunneling effects in the reaction of HNCH2 with HCOOH in the interstellar medium

The reaction HNCH₂ + HCOOH → H₂NCH₂COOH is supposed to be an important reaction related to the possible origin of amino acids on the early Earth. We find that it has an energy barrier of 87.37 kcal mol⁻¹ obtained with MP2/6‐311+G** in the gas phase, but it is likely enhanced to occur in the interstellar medium (ISM) through a proton‐coupled proton transfer reaction, initiated by HNCH₂ coupled with H₂⁺, H₃⁺, or H₃⁺O. H₂⁺, H₃⁺, and H₃⁺O serve as a donor of energy in the coupled reactions. H⁺, which is a key species to the coupled reactions, further, plays a catalytic role in reducing a barrier up to 14.14 kcal mol⁻¹. In the coupled reaction with H₃⁺O, H₂O, which can seize, transport, and deliver a proton from HCOOH to H₂NCH₂⁺, reduces a barrier up to 14.96 kcal mol⁻¹. A significant hydrogen‐tunneling pathway is predicted by the temperature dependences of k_H^CVT/SCT, calculated using the small curvature tunneling (SCT) approximation and canonical variational transition state theory (CVT). Hydrogen tunneling is another important mechanism to make the reaction happen in the ISM. The achieved results can be applied to discuss the origin of amino acids from the materials of the Earth itself. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling

The literature hypothesis that "the optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of quantum-mechanical tunneling" is experimentally tested herein for the first time. The system employed is the key to being able to provide this first experimental test of the "enhanced hydrogen tunneling" hypothesis, one that requires a comparison of the three criteria diagnostic of tunneling (vide infra) for the same, or nearly the same, reaction with and without the enzyme. Specifically, studied herein are the adenosylcobalamin (AdoCbl, also known as coenzyme B(12))-dependent diol dehydratase model reactions of (i). H(D)(*) atom abstraction from ethylene glycol-d(0) and ethylene glycol-d(4) solvent by 5'-deoxyadenosyl radical (Ado(*)) and (ii.) the same H(*) abstraction reactions by the 8-methoxy-5'-deoxyadenosyl radical (8-MeOAdo(*)). The Ado(*) and 8-MeOAdo(*) radicals are generated by Co-C thermolysis of their respective precursors, AdoCbl and 8-MeOAdoCbl. Deuterium kinetic isotope effects (KIEs) of the H(*)(D(*)) abstraction reactions from ethylene glycol have been measured over a temperature range of 80-120 degrees C: KIE = 12.4 +/- 1.1 at 80 degrees C for Ado(*) and KIE = 12.5 +/- 0.9 at 80 degrees C for 8-MeOAdo(*) (values ca. 2-fold that of the predicted maximum primary times secondary ground-state zero-point energy (GS-ZPE) KIE of 6.4 at 80 degrees C). From the temperature dependence of the KIEs, zero-point activation energy differences ([E(D) - E(H)]) of 3.0 +/- 0.3 kcal mol(-)(1) for Ado(*) and 2.1 +/- 0.6 kcal mol(-)(1) for 8-MeOAdo(*) have been obtained, both of which are significantly larger than the nontunneling, zero-point energy only maximum of 1.2 kcal mol(-)(1). Pre-exponential factor ratios (A(H)/A(D)) of 0.16 +/- 0.07 for Ado(*) and 0.5 +/- 0.4 for 8-MeOAdo(*) are observed, both of which are significantly less than the 0.7 minimum for nontunneling behavior. The data provide strong evidence for the expected quantum mechanical tunneling in the Ado(*) and 8-MeOAdo(*)-mediated H(*) abstraction reactions from ethylene glycol. More importantly, a comparison of these enzyme-free tunneling data to the same KIE, (E(D) - E(H)) and A(H)/A(D) data for a closely related, Ado(*)-mediated H(*) abstraction reaction from a primary CH(3)- group in AdoCbl-dependent methylmalonyl-CoA mutase shows the enzymic and enzyme-free data sets are identical within experimental error. The Occam's Razor conclusion is that at least this adenosylcobalamin-dependent enzyme has not evolved to enhance quantum mechanical tunneling, at least within the present error bars. Instead, this B(12)-dependent enzyme simply exploits the identical level of quantum mechanical tunneling that is available in the enzyme-free, solution-based H(*) abstraction reaction. The results also require a similar, if not identical, barrier width and height within experimental error for the H(*) abstraction both within, and outside of, the enzyme.     

Synthesis of a new bifunctionalised fluorescent label and physical properties of the bound form on model peptide of troponin C

A new bifunctional fluorescent label, BRos, was synthesised in order to monitor protein dynamics using fluorescence microscopy, and the photophysical properties were compared with those of bifunctionalised rhodamine, BRho. In a labelling experiment with a model peptide of troponin C, which regulates muscle contraction and relaxation, it was found that BRos was bound to the peptide through two linkages and provided a homogeneous compound, whereas BRho gave a pair of diastereomers having different physical properties in NMR and HPLC analyses.     

Protease catalysis mediated by a substrate mimetic: a novel enzymatic approach to the synthesis of carboxylic acid amides

We present a protease-based method for the coupling of non-coded and non-amino-acid-derived amines with carboxy components. The key feature of this approach is the combination of the substrate-mimetic strategy with the ability of the cysteine protease clostripain to accept a wide spectrum of amines. Firstly, we tested the use of the 4-guanidinophenyl ester leaving group to mediate acceptance of non-coded and non-amino-acid-derived acyl residues. This employed beta-amino acid and simple carboxylic acid moieties as acyl donors, and several amino acid and peptide units as acyl acceptors. The study was completed by the use of non-amino-acid-derived acyl acceptors comprising simple amines, amino alcohols, and diamines. The results indicate that the approach presented is a useful strategy for the synthesis of peptide isosteres, peptide analogues, and organic amides. These last open a new range of synthetic applications of proteases completely beyond peptide synthesis, achieving efficient and selective acylations of non-amino-acid-derived amines under extraordinarily mild reaction conditions.     

Synthesis, structure, and physical properties for a series of trigonal bipyramidal M(II)-Cl complexes with intramolecular hydrogen bonds

A series of transition metal chloro complexes with the tetradentate tripodal tris(2-amino-oxazoline)amine ligand (TAO) have been synthesized and characterized. X-Ray structural analyses of these compounds demonstrate the formation of the mononuclear complexes [M(II)(TAO)(Cl)](+), where M(II) = Cr, Mn, Fe, Co, Ni, Cu and Zn. These complexes exhibit distorted trigonal-bipyramidal geometry, coordinating the metal through an apical tertiary amine, three equatorial imino nitrogen atoms, and an axial chloride anion. All the complexes possess an intramolecular hydrogen-bonding (H-bonding) network within the cavity occupied by the metal-bound chloride ion. The metal-chloride bond distances are atypically long, which is attributed to the effects of the H-bonding network. Nuclear magnetic resonance (NMR) spectroscopy of the Zn complex suggests that the solid-state structures are representative of that observed in solution, and that the H-bonding interactions persist as well. Additionally, density functional theory (DFT) calculations were carried out to probe the electronic structures of the complexes.     

Synthesis,structure, and physical properties of the new layered ternary chalcogenide NbNiTe5

The new ternary chalcogenide NbNiTe₅ has been prepared. NbNiTe₅ crystallizes with four formula units in a cell with dimensions a = 3.656(5), b = 13.075(16), c = 15.111(19) Å in the orthorhombic system in space group D¹⁷_2h-Cmcm. The structure has been refined to a final R index on F²_o of 0.037 for 25 variables and 1405 observations. NbNiTe₅ forms in a new layered structural type. Each layer consists of bicapped trigonal prismatic niobium atoms and octahedral nickel atoms coordinated by tellurium atoms. Electrical conductivity measurements indicate that NbNiTe₅ is a metal; its conductivity at room temperature is about 1.3 × 10⁴ Ω⁻¹ cm⁻¹. Magnetic susceptibility measurements show that NbNiTe₅ is paramagnetic (X_rt ≈ 1.04 × 10⁻³ emu mole⁻¹).     

Synthesis, physicochemical properties, and hydrogen bonding of 4(5)-substituted 1-H-imidazole-2-carboxamide, a potential universal reader for DNA sequencing by recognition tunneling

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores.1 The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5)?position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH?6-10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC?dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.     

The innate reactivity of a membrane associated peptide towards lipids: acyl transfer to melittin without enzyme catalysis

The innate reactivity of the peptide melittin (H-GIGAVLKVLTTGLPALISWIKRKRQQ-NH(2)) towards membrane lipids has been explored using LC-MS methods. The high sensitivity afforded by LC-MS analysis enabled acyl transfer to the peptide to be detected, within 4 h, from membranes composed of phosphocholines (PCs). Acyl transfer from PCs was also observed from mixtures of PC with phosphoserine (PS) or phosphoglycerol (PG). In the latter case, transfer from PG was also detected. The half-lives for melittin conversion varied between 24 h and 75 h, being fastest for POPC and slowest for DOPC/DMPG mixtures. The order of reactivity for amino groups on the peptide was N-terminus > K23 ? K21 > K7. Products arising from double-acylation of melittin were detected as minor components, together with a putative component derived from transesterification involving S18 of the peptide.