Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics

Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G^** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-point-energy contributions are added. Our calculations allow the dynamic aspects of the ionization mechanism to be discussed by incorporating nonequilibrium effects. Received: 28 June 1999 / Accepted: 13 October 1999 / Published online: 14 March 2000     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.     

Theoretical study of environmental effects on proton transfer reaction through the peptide bond in a model system

This study considered the possibility of proton transfer reactions through the peptide bond under different environments using the dipeptide and the 12-mer polyglycine α-helix models, in which diglycine is substituted by the 12-mer polyglycine helix. Ab initio molecular orbital calculations were carried out at the B3LYP/6-31+G(d) level of theory. To evaluate the free energies in solution, calculations of the solvation energies were performed using PCM. The correction functions on the calculated solvation energies were provided to reproduce experimental pKa values. The proton transfer reactions through the peptide bond are concluded to be possible in the protein for a wide range of proton acceptors. His complex has two free energy minima along a putative proton transfer pathway in spite of one minimum in the other complexes. The α-helix is estimated to suppress the proton transfer reactions through the peptide bond at the termini of the helix, although it is possible to proceed when the proton affinity of the acceptor is low. Contribution to the Mark S. Gordon 65th Birthday Festschrift Issue.     

Theoretical studies of the proton transfer behaviors in molecular complexes analogous to catalytic triad of serine protease: Toward understanding the existence and significance of the low-barrier hydrogen-bond in enzymatic catalysis

A representative acetate-(5-methylimidazole)-methanol system has been employed as a model of catalytic triad in serine protease to validate the formation processes of low-barrier H-bonds (LBHB) at the B3LYP/6-311++G** level of theory, and variable H-bonding characters from conventional ones to LBHBs have been represented along with the proceedings of proton transfer. Solvent effect is an important factor in modulation of the existence of an LBHB, where an LBHB (or a conventional H-bond) in the gas phase can be changed into a non-LBHB (an LBHB) upon solvation. The origin of the additional stabilization energy arising from the LBHB may be attributed to the H-bonding energy difference before and after proton transfer because the shared proton can freely move between the proton donor and proton acceptor. Most importantly, the order of magnitude of the stabilization energy depends on the studied systems. Furthermore, the nonexistence of LBHBs in the catalytic triad of serine proteases has been verified in a more sophisticated model treated using the ONIOM method. As a result, only the single proton transfer mechanism in the catalytic triad has been confirmed and the origin of the powerful catalytic efficiency of serine proteases should be attributed to other factors rather than the LBHB. Supported by the National Natural Science Foundation of China (Grant Nos. 20633060 & 20573063), the Natural Science Foundation of Shandong Province (Grant No. Y2007B23), the Scientific Research Foundation of Qufu Normal University (Grant Nos. Bsqd2007003 and Bsqd2007008), and the State Key Laboratory of Physical Chemistry of Solid Surfaces (Xiamen University)     

Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase

Two different transition structures (TSs) have been located and characterized for the chorismate conversion to prephenate in Bacillus subtilis chorismate mutase by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations. GRACE software, combined with an AM1/CHARMM24/TIP3P potential, has been used involving full gradient relaxation of the position of ca. 3300 atoms. These TSs have been connected with their respective reactants and products by the intrinsic reaction coordinate (IRC) procedure carried out in the presence of the protein environment, thus obtaining for the first time a realistic enzymatic reaction path for this reaction. Similar QM/MM computational schemes have been applied to study the chemical reaction solvated by ca. 500 water molecules. Comparison of these results together with gas phase calculations has allowed understanding of the catalytic efficiency of the protein. The enzyme stabilizes one of the TSs (TS_OHout) by means of specific hydrogen bond interactions, while the other TS (TS_OHin) is the preferred one in vacuum and in water. The enzyme TS is effectively more polarized but less dissociative than the corresponding solvent and gas phase TSs. Electrostatic stabilization and an intramolecular charge-transfer process can explain this enzymatically induced change. Our theoretical results provide new information on an important enzymatic transformation and the key factors responsible for efficient selectivity are clarified. Received: 25 March 2000 / Accepted: 7 August 2000 / Published online: 23 November 2000     

Recent advances in quantum mechanical/molecular mechanical calculations of enzyme catalysis: hydrogen tunnelling in liver alcohol dehydrogenase and inhibition of elastase by α-ketoheterocycles

 Hybrid quantum mechanical (QM)/molecular mechanical (MM) calculations are used to study two aspects of enzyme catalysis, Kinetic isotope effects associated with the hydride ion transfer step in the reduction of benzyl alcohol by liver alcohol dehydrogenase are studied by employing variational transition-state theory and optimised multidimensional tunnelling. With the smaller QM region, described at the Hartree–Fock ab initio level, together with a parameterised zinc atom charge, good agreement with experiment is obtained. A comparison is made with the proton transfer in methylamine dehydrogenase. The origin of the large range in pharmacological activity shown by a series of α-ketoheterocycle inhibitors of the serine protease, elastase, is investigated by both force field and QM/MM calculations. Both models point to two different inhibition mechanisms being operative. Initial QM/MM calculations suggest that these are binding, and reaction to form a tetrahedral intermediate, the latter process occurring for only the more potent set of inhibitors. Recieved 3 October 2001 / Accepted: 6 September 2002 / Published online: 31 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: I. H. Hillier Acknowledgements. We thank EPSRC and BBSRC for support of the research and D.G. Truhlar for the use of the POLYRATE code.     

Theoretical study on the substituent effect of a Wittig reaction

The substituent effects of F, H and methyl (Me) in replacement of phenyl (Ph) groups bonding with the ylide phosphorus in Wittig reactions have been examined theoretically by performing ab intio calculations. It is shown that the energy barrier for the Wittig reaction with F as the substituent is much higher than that with H, Me and Ph. The Wittig reaction is found to be more favorable with the substituent in the order F<H<Ph<Me. The reactions are found to proceed through two transition states: the formation and the decomposition of oxaphosphetane. We conclude that only the model of the Wittig reaction in which Ph is simplified to Me can reasonably describe the real Wittig reaction. Received: 7 August 2001 / Accepted: 25 October 2001 / Published online: 22 March 2002     

Interaction of the important species HNO and HFSO2 in the atmosphere: Theoretical study of the N?H and S?H blue‐shifted hydrogen bonds

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the N? H…O and S? H…O blue‐shifted H‐bonds in the HNO…HFSO₂ complex. The geometric structures, vibrational frequencies, and interaction energies were calculated by both standard and CP‐corrected methods. Natural bond orbital (NBO) analysis was used to investigate the origin of blue‐shifted H‐bonds, showing that the decrease in the σ*(N? H) and σ*(S? H) is due to the electron density redistribution effect. The structure reorganization effect on the blue‐shifted hydrogen bonds was discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

FT-IR study of the proton polarizability of hydrogen bonds and of the hydrogen-bonded systems in a di-Mannich base of 5,5′-dimethoxy-2,2′-biphenol

The mono- as well as the di-Mannich bases of 5,5′-dimethoxy-2,2′-biphenol are studied by FT-IR spectroscopy. It is shown that in these bases the protons remain localized at the phenol O atom. This result is in contrast to those obtained earlier for more acidic biphenols in which the protons are not localized but fluctuate and the relevant hydrogen bonds show large polarizability. An intense infrared continuum in the FT-IR spectrum of the mono-protonated di-Mannich base of 5,5′-dimethoxy-2,2′-biphenol demonstrates that the intramolecular hydrogen bond in this compound shows large proton polarizability.     

Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes

The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.     

Proton dynamics in an extended array of hydrogen bonds: normal coordinates, proton transfer and macroscopic quantum entanglement in the ground state

After a brief introduction to neutron scattering techniques, illustrated with the scattering function for harmonic oscillators, some new aspects of proton dynamics in the KHCO₃ crystal are presented. The full scattering function for the proton modes measured on single crystals provides a graphic view of proton dynamics. Vibrational states are fully characterized with three quantum numbers. The effective oscillator mass of 1 amu confirms the decoupling of protons from the lattice. Combining infrared, Raman and inelastic neutron scattering techniques, the double minimum potential for the transfer of a single proton along hydrogen bonds is totally determined. Elastic neutron scattering techniques probe dynamics in the fully degenerate ground state. Quantum entanglement arising from normal coordinates gives rise to quantum interference. With diffraction techniques, the dynamical structure arising from large-scale quantum coherence is observed as ridges of intensity, well separated from Bragg's peaks. The vibrational wave function in the ground state must be regarded as a superposition of non-factorable macroscopic wave function.     

Electrostatic effects in enzyme catalysis: a quantum mechanics/molecular mechanics study of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined quantum mechanics/molecular mechanics molecular dynamics simulations have been carried out to study the cleavage of the carbon–chlorine bond in 1,2-dichloroethane catalysed by haloalkane dehalogenase from Xanthobacter Autotrophicus GJ10. The process has been compared with an adequate counterpart in aqueous solution, the nucleophilic attack of acetate anion on 1,2-dichloroethane. Within the limitations of the model, mainly due to the use of a semiempirical Hamiltonian, our results reproduce the magnitude and characteristics of the catalytic effect. Comparisons of the enzymatic and in solution potentials of mean force reveal that, irrespective of the reference state, the enzyme shows a larger affinity for the transition state. The origin of this increased affinity is found in the differences in the electrostatic pattern created by the environment in aqueous solution and in the enzyme.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Interstitial water and the formation of low barrier hydrogen bonds: A computational model study

The B3LYP/D95+(d,p) analysis of the uncharged low barrier hydrogen bond (LBHB) between 4‐methyl‐1H‐imidazole (Mim) and acetic acid (HAc) shows that uncharged LBHBs can be formed either by adding three water molecules around the cluster or by placing the Mim–HAc pair in a dielectric environment created by a polarizable continuum model with a permittivity larger than 20.7. The permittivity of environment around uncharged LBHB can be lowered significantly by including water molecules into the system. A Mim–HAc LBHB stabilized with one water molecule observed in diethyl ether (ε = 4.34), with two water molecules in toluene (ε = 2.38), and with three water molecules in vacuo (ε = 1). Solvation models with different numbers of water molecules predict average differences in the proton affinities of the hydrogen bonded bases (ΔPA) for stable uncharged LBHB systems in vacuo to be 91.5 kcal/mol being different from the ΔPA values close to zero in charge‐assisted LBHB systems. The results clearly indicate that small amounts of interstitial water molecules at the active site of enzymes do not preclude the existence of LBHBs in biological catalysis. Our results also show that interstitial water molecules provide a useful clue in the search for uncharged LBHBs in an enzymatic environment and the number of water molecules can be used as a relative measure for the polarity around the direct environment of LBHBs. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Self-consistent reaction field calculation of solvent reorganization energy in electron transfer: a dipole-reaction field interaction model

Based on the continuum dielectric model, this work has established the relationship between the solvent reorganization energy of electron transfer (ET) and the equilibrium solvation free energy. The dipole-reaction field interaction model has been proposed to describe the electrostatic solute-solvent interaction. The self-consistent reaction field (SCRF) approach has been applied to the calculation of the solvent reorganization energy in self-exchange reactions. A series of redox couples, O₂/O⁻ ₂, NO/NO⁺, O₃/O⁻ ₃, N₃/N⁻ ₃, NO₂/NO⁺ ₂, CO₂/CO⁻ ₂, SO₂/SO⁻ ₂, and ClO₂/ClO⁻ ₂, as well as (CH₂)₂C-(-CH₂-) _n -C(CH₂)₂ (n=1 ∼ 3) model systems have been investigated using ab initio calculation. For these ET systems, solvent reorganization energies have been estimated. Comparisons between our single-sphere approximation and the Marcus two-sphere model have also been made. For the inner reorganization energies of inorganic redox couples, errors are found not larger than 15% when comparing our SCRF results with those obtained from the experimental estimation. While for the (CH₂)₂C–(–CH₂–) _n –C(CH₂)₂ (n=1 ∼ 3) systems, the results reveal that the solvent reorganization energy strongly depends on the bridge length due to the variation of the dipole moment of the ionic solute, and that solvent reorganization energies for different systems lead to slightly different two-sphere radii. Received: 19 April 2000 / Accepted: 6 July 2000 / Published online: 27 September 2000     

A novel tubular hydrogen‐bond pattern in a new diazaphosphole oxide: a combination of X‐ray crystallography and theoretical study of hydrogen bonds

In the structure of 2‐(4‐chloroanilino)‐1,3,2λ⁴‐diazaphosphol‐2‐one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N—H)₂…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R ³₃(12) and R ₄³(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J _H–P coupling constant.     

Molecular dynamics study of the tautomeric equilibrium in the 4-nitro- and 2,4,6-trichloro derivatives of 2-(N,N-dialkyloaminomethyl)phenol

 Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric equilibrium of Mannich base in methanol solution. The values obtained for the free-energy difference are in good agreement with experimental data. However, the results from quantum mechanical calculations were not as good as the results of MDTI simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell of solvent molecules in the Tomasi model of the solvent reaction field. The radial distribution functions between solute atoms and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first solvation shell than is the molecular form. Received: 26 April 2002 / Accepted: 9 September 2002 / Published online: 31 March 2003     

Theoretical study of hydrogen bonded clusters of water and cyanic acid: Hydrogen bonding in terms of the molecular structure

Ab initio and density functional calculations were used to analyze the interaction between a molecule of cyanic acid (HOCN) and up to 4 molecules of water at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect (CE) is increased with the increasing size of the studied clusters. Red shifts of the H–O stretching frequency for complexes involving HOCN as an H-donor were predicted. The strength of the hydrogen bonds in terms of molecular structures could be deduced from a comparison of HOCN–H₂O with HCNO–H₂O, HONC–H₂O and HNCO–H₂O HB clusters. The atom in molecules (AIM) method was used to analyze the cooperative effects on topological parameters.     

A proton NMR study on aggregation of cationic surfactants in water: effects of the structure of the headgroup

 ¹H NMR chemical shifts of solutions of the following cationic surfactants in D₂O were determined as a function of their concentrations: cetyltrimethylammonium chloride, CTACl, a 1 : 1 molar mixture of CTACl and toluene, cetylpyridinium chloride, CPyCl, cetyldimethylphenylam-monium chloride, CDPhACl, cetyldimethylbenzylammonium chloride, CDBzACl, cetyldimethyl-2-phenylethylammonium chloride, CDPhEtACl, and cetyldimethyl-3-phenylpropylammonium chloride, CDPhPrACl. Plots of observed chemical shifts versus [surfactant] are sigmoidal, and were fitted to a model based on the mass-action law. Satisfactory fitting was obtained for the discrete protons of all surfactants. From these fits, we calculated the equilibrium constant for micelle formation, K, the critical micelle concentration, CMC and the chemical shifts of the monomer, δ_mon and the micelle δ_mic. ¹H NMR-based CMC values are in excellent agreement with those which we determined by surface tension measurements of surfactant solutions in H₂O, allowing for the difference in structure between D₂O and H₂O. Values of K increase as a function of increasing the size of the hydrophilic group, but the free energy of transfer per CH₂ group of the phenylalkyl moiety from bulk water to the micellar interface is approximately constant, 1.9±0.1 kJ mol^-1. Values of (δ_mic–δ_mon) for the surfactant groups at the interface, e.g., CH₃–(CH₂)₁₅–N+(CH₃)₂ and within the micellar core, e.g., CH₃–(CH₂)₁₅–N⁺ were used to probe the (average) conformation of the phenyl group in the interfacial region. The picture that emerges is that the aromatic ring is perpendicular to the interface in CDPhACl and is more or less parallel to it in CDBzACl, CDPhEtACl, and CDPhPrACl. Received: 23 February 1996 Accepted: 29 August 1996     

TD‐DFT study on the sensing mechanism of a fluorescent chemosensor for fluoride: Excited‐state proton transfer

An excited‐state proton transfer (ESPT) process, induced by both intermolecular and intramolecular hydrogen‐bonding interactions, is proposed to account for the fluorescence sensing mechanism of a fluoride chemosensor, phenyl‐1H‐anthra(1,2‐d)imidazole‐6,11‐dione. The time‐dependent density functional theory (TD‐DFT) method has been applied to investigate the different electronic states. The present theoretical study of this chemosensor, as well as its anion and fluoride complex, has been conducted with a view to monitoring its structural and photophysical properties. The proton of the chemosensor can shift to fluoride in the ground state but transfers from the proton donor (NH group) to a proton acceptor (neighboring carbonyl group) in the first singlet excited state. This may explain the observed red shifts in the fluorescence spectra in the relevant fluorescent sensing mechanism. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Blue‐shifted and red‐shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes

The blue‐shifted and red‐shifted H‐bonds have been studied in complexes CH₃CHO…HNO. At the MP2/6‐31G(d), MP2/6‐31+G(d,p) MP2/6‐311++G(d,p), B3LYP/6‐31G(d), B3LYP/6‐31+G(d,p) and B3LYP/6‐311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH₃CHO…HNO are calculated by both standard and CP‐corrected methods, respectively. Complex A exhibits simultaneously red‐shifted C? H…O and blue‐shifted N? H…O H‐bonds. Complex B possesses simultaneously two blue‐shifted H‐bonds: C? H…O and N? H…O. From NBO analysis, it becomes evident that the red‐shifted C? H…O H‐bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue‐shifted C? H…O H‐bond is a result of conjunct C? H bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue‐shifted N? H…O H‐bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the N? H stretching frequency is observed because the rehybridization dominates the hyperconjugation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006