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)     

A Multi‐Center Energy Analysis of the Tunable Proton Affinity of Hydrogen Bonded Cluster Ions

The proton affinity (PA) of the [Tca–H^βMim]^? ion (Tca^?: trichloroacetate ion, HMim: 4‐Methyl‐1H‐imidazole) is a nearly linear function of the position (r₃) of H^β using the rigid framework approximation. This useful property of the ion is caused by an unusually large four‐center interaction term revealed by the multi‐center energy (MCE) analysis of PA(r₃). The MCE analysis shows further that despite the general stabilization of the [Tca–HMim–HAc]^? ion by cooperative effects, the individual hydrogen bonds carry a strong anti‐cooperative element caused by the rivalry of the two bases for the proton linking them.     

Correlated proton motion in hydrogen bonded systems: tuning proton affinities

The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.     

A quantum description of the proton movement in an idealized NHN+ bridge

A series of model calculations was done to analyze the delocalization of the proton in the linking hydrogen bond of the (Dih)(2)H(+) cation (Dih: 4,5-dihydro-1H-imidazole). Standard quantum chemical calculations (B3LYP/D95+(d,p)) predict a low barrier hydrogen bond (LBHB) and thereby a delocalized proton in the NHN(+) hydrogen bridge. Explicit quantum calculations on the proton indicate that the delocalization of the proton does not provide enough energy to stabilize a permanent LBHB. Additional Born-Oppenheimer Molecular Dynamics (BOMD) simulations indicate further that the proton is localized at either side of the NHN(+) bridge and that a central proton position is the result of temporal averaging. The possibility of the proton to tunnel from one side to the other side of the NHN(+) bridge increases with the temperature as the trajectory of the (Dih)(2)H(+) cation runs through regions where the thermal excitation of Dih ring vibrations creates equal bonding opportunities for the proton on both sides of the bridge (vibrationally assisted proton tunneling). The quantum calculations for the proton in (Dih)(2)H(+) suggest further a broad peak for the 1 ← 0 transition with a maximum at 938 cm(-1) similar to that observed for LBHBs. Moreover, the asymmetric NHN(+) bridge in a thermally fluctuating environment is strong enough to create a significant peak at 1828 cm(-1) for the 2 ← 0 transition, while contributions from the 2 ← 1 are expected to be weak for the same reason.     

Hydrogen-bonding partner of the proton-conducting histidine in the influenza m2 proton channel revealed from (1)h chemical shifts

The influenza M2 protein conducts protons through a critical histidine (His) residue, His37. Whether His37 only interacts with water to relay protons into the virion or whether a low-barrier hydrogen bond (LBHB) also exists between the histidines to stabilize charges before proton conduction is actively debated. To address this question, we have measured the imidazole (1)H(N) chemical shifts of His37 at different temperatures and pH using 2D (15)N-(1)H correlation solid-state NMR. At low temperature, the H(N) chemical shifts are 8-15 ppm at all pH values, indicating that the His37 side chain forms conventional hydrogen bonds (H-bonds) instead of LBHBs. At ambient temperature, the dynamically averaged H(N) chemical shifts are 4.8 ppm, indicating that the H-bonding partner of the imidazole is water instead of another histidine in the tetrameric channel. These data show that His37 forms H-bonds only to water, with regular strength, thus supporting the His-water proton exchange model and ruling out the low-barrier H-bonded dimer model.     

Theoretical study of the symmetry of the (OH...O)- hydrogen bonds in vinyl alcohol-vinyl alcoholate systems

The interactions between substituted vinyl alcohols and vinyl alcoholates (X = NH(2), H, F, Cl, CN) are studied at the B3LYP/6-311++G(d,p) level of theory. In a first step, the conformation of the monomers is investigated and the proton affinities (PA(A(-))) of the enolates are calculated. The enols and enolates are held together by strong (OH...O)(-) hydrogen bonds, the hydrogen bond energies ranging from 19.1 to 34.6 kcal mol(-1). The optimized O...O distances are between 2.414 and 2.549 A and the corresponding OH distances from 1.134 and 1.023 A. The other geometry parameters such as C[double bond]C or CO distances also indicate that, in the minimum energy configuration, the hydrogen bonds are characterized by a double well potential. The Mulliken charges on the different atoms of the proton donors and proton acceptors and the frequencies of the nu(OH) stretching vibrations agree with this statement. All the data indicate that the hydrogen bonds are the strongest in the homomolecular complexes. The transition state for hydrogen transfer is located with the transition barrier estimated to be about zero. Upon addition of the zero-point vibration energies to the total potential energy, the barrier vanishes. This is a characteristic feature of low-barrier hydrogen bonds (LBHBs). The hydrogen bond energies are correlated to the difference 1.5 PA(AH) - PA(A(-)). The correlation predicts different energies for homomolecular hydrogen bonds, in agreement with the theoretical calculations. Our results suggest that a PA (or pK(a)) match is not a necessary condition for forming LBHBs in agreement with recent data on the intramolecular hydrogen bond in the enol form of benzoylacetone (J. Am. Chem. Soc. 1998, 120, 12117).     

Solvent‐Modulated Influence of Intramolecular Hydrogen‐Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study

Intramolecular hydrogen‐bonding (H‐bonding) is commonly regarded as a major determinant of the conformation of (bio)molecules. However, in an aqueous environment, solvent‐exposed H‐bonds are likely to represent only a marginal (possibly adverse) conformational driving as well as steering force. For example, the hydroxymethyl rotamers of glucose and galactose permitting the formation of an intramolecular H‐bond with the adjacent hydroxyl group are not favored in water but, in the opposite, least populated. This is because the solvent‐exposed H‐bond is dielectrically screened as well as subject to intense H‐bonding competition by the water molecules. In the present study, the effect of a decrease in the solvent polarity on this rotameric equilibrium is probed using molecular dynamics simulation. This is done by considering six physical solvents (H₂O, DMSO , MeOH , CHC l₃, CC l₄, and vacuum), along with 19 artificial water‐like solvent models for which the dielectric permittivity and H‐bonding capacity can be modulated independently via a scaling of the O–H distance and of the atomic partial charges. In the high polarity solvents, the intramolecular H‐bond is observed, but arises as an opportunistic consequence of the proximity of the H‐bonding partners in a given rotameric state. Only when the polarity of the solvent is decreased does the intramolecular H‐bond start to induce a conformational pressure on the rotameric equilibrium. The artificial solvent series also reveals that the effects of the solvent permittivity and of its H‐bonding capacity mutually enhance each other, with a slightly larger influence of the permittivity. The hydroxymethyl conformation in hexopyranoses appears to be particularly sensitive to solvent‐polarity effects because the H‐bond involving the hydroxymethyl group is only one out of up to five H‐bonds capable of forming a network around the ring.     

Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein

The role and existence of low-barrier hydrogen bonds (LBHBs) in enzymatic and protein activity has been largely debated. An interesting case is that of the photoactive yellow protein (PYP). In this protein, two short HBs adjacent to the chromophore, p-coumaric acid (pCA), have been identified by X-ray and neutron diffraction experiments. However, there is a lack of agreement on the chemical nature of these H-bond interactions. Additionally, no consensus has been reached on the presence of LBHBs in the active site of the protein, despite various experimental and theoretical studies having been carried out to investigate this issue. In this work, we perform a computational study that combines classical and density functional theory (DFT)-based quantum mechanical/molecular mechanical (QM/MM) simulations to shed light onto this controversy. Furthermore, we aim to deepen our understanding of the chemical nature and dynamics of the protons involved in the two short hydrogen bonds that, in the dark state of PYP, connect pCA with the two binding pocket residues (E46 and Y42). Our results support the existence of a strong LBHB between pCA and E46, with the H fully delocalized and shared between both the carboxylic oxygen of E46 and the phenolic oxygen of pCA. Additionally, our findings suggest that the pCA interaction with Y42 can be suitably described as a typical short ionic H-bond of moderate strength that is fully localized on the phenolic oxygen of Y42.     

Aqueous Heterogeneity at the Air/Water Interface Revealed by 2D‐HD‐SFG Spectroscopy

Water molecules interact strongly with each other through hydrogen bonds. This efficient intermolecular coupling causes strong delocalization of molecular vibrations in bulk water. We study intermolecular coupling at the air/water interface and find intermolecular coupling 1) to be significantly reduced and 2) to vary strongly for different water molecules at the interface—whereas in bulk water the coupling is homogeneous. For strongly hydrogen‐bonded OH groups, coupling is roughly half of that of bulk water, due to the lower density in the near‐surface region. For weakly hydrogen‐bonded OH groups that absorb around 3500 cm^?1, which are assigned to the outermost, yet hydrogen‐bonded OH groups pointing towards the liquid, coupling is further reduced by an additional factor of 2. Remarkably, despite the reduced structural constraints imposed by the interfacial hydrogen‐bond environment, the structural relaxation is slow and the intermolecular coupling of these water molecules is weak.     

Hydration state of nonionic surfactant monolayers at the liquid/vapor interface: structure determination by vibrational sum frequency spectroscopy

The OH stretching region of water molecules in the vicinity of nonionic surfactant monolayers has been investigated using vibrational sum frequency spectroscopy (VSFS) under the polarization combinations ssp, ppp, and sps. The surface sensitivity of the VSFS technique has allowed targeting the few water molecules present at the surface with a net orientation and, in particular, the hydration shell around alcohol, sugar, and poly(ethylene oxide) headgroups. Dramatic differences in the hydration shell of the uncharged headgroups were observed, both in comparison to each another and in comparison to the pure water surface. The water molecules around the rigid glucoside and maltoside sugar rings were found to form strong hydrogen bonds, similar to those observed in tetrahedrally coordinated water in ice. In the case of the poly(ethylene oxide) surfactant monolayer a significant ordering of both strongly and weakly hydrogen bonded water was observed. Moreover, a band common to all the surfactants studied, clearly detected at relatively high frequencies in the polarization combinations ppp and sps, was assigned to water species located in proximity to the surfactant hydrocarbon tail phase, with both hydrogen atoms free from hydrogen bonds. An orientational analysis provided additional information on the water species responsible for this band.     

Potential of mean force of hydrophobic association: dependence on solute size

The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.     

The charge density distribution in a model compound of the catalytic triad in serine proteases

Combined low temperature (28(1) K) X-ray and neutron diffraction measurements were carried out on the co-crystallised complex of betaine, imidazole, and picric acid (1). The experimental charge density was determined and compared with ab initio theoretical calculations at the B3LYP/6-311G(d,p) level of theory. The complex serves as a model for the active site in, for example, the serine protease class of enzymes, the so-called catalytic triad. The crystal contains three short strong N-H...O hydrogen bonds (HBs) with dN...O < 2.7 A. The three HBs have energies above 13 kcalmol(-1), although the hydrogen atoms are firmly localized in the "nitrogen wells". This suggests that low-barrier hydrogen bonding in catalytic enzyme reactions may be a sufficient, but not a necessary, condition for obtaining transition-state stabilization. Structural analysis (e.g., covalent N-H bond lengthening) indicates that the hydrogen bond between H3A and 08 of imidazole and betaine respectively (HB2) is slightly stronger than the bond between H1A and O1A of imidazole and picric acid (HB1), although HB1 is shorter than HB2: (dN...O(HB1)= 2.614(1) A, dN...O(HB2) = 2.684(1) A, dH...O(HB1) = 1.630(1) A, dH...O(HB2)= 1.635(1) A, dN-H(HB1) = 1.046(1) A, dN-H(HB2) = 1.057(1) A). Furthermore, the charge density analysis reveals that HB2 has a larger covalent character than HB1, with considerable polarization of the density towards the acceptor atom. The Gatti and Bader source function (S) is introduced to the analysis of strong HBs. The source function is found to be a sensitive measure for the nature of a hydrogen bond, and comparison with low-barrier and single-well hydrogen bonding systems (e.g., benzoylacetone and nitromalonamide) shows that the low-barrier hydrogen bond (LBHB) state is characterized by an enormously increased hydrogen atom source contribution to the bond critical point in the HB. In this context, HB2 can be characterized as intermediate between localized HBs and delocalized LBHBs.     

Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug

NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.     

Influence of 1-alkyl-3-methylimidazolium tetrafluoroborate on the lamellar liquid crystal formed by tetraethylene glycol lauryl ether and water

Lyotropic liquid crystals (LLCs) formed in tetraethylene glycol lauryl ether–water system by the addition of 1-alkyl-3-methylimidazolium tetrafluoroborate ([C _n Mim][BF₄], n?=?2, 4, 6, 8, 10) are characterised by polarised optical microscopy and small-angle X-ray scattering techniques. A small number of [C _n Mim][BF₄] molecules can be solubilised in the liquid crystal without changing the lamellar type. These imidazolium salts are considered as an ideal kind of modifiers for the ordered structure. With different lengths of alkyl chains, [C _n Mim][BF₄] molecules appear in various domains of ordered assemblies: in the water layer for [C₂Mim][BF₄], in the water layer as well as in the polar domain for [C₄Mim][BF₄] and in the apolar domain for the other imidazolium salts with long alkyl chains. Diverse distributions of [C _n Mim][BF₄] molecules in the inner structure bring about their specific influence on the lamellar phase. These results enlighten the use of diverse alkyl-substituted imidazolium salts in modulating LLC and other assemblies and also enrich the aggregation behaviour of these assemblies.     

High Selective Determination of Anionic Surfactant Using Its Parallel Catalytic Hydrogen Wave

IntroductionAnionicsurfactants (AS)arewidelyusedinhouse holdorindustrialcleaners ,cosmetics ,researchlaborato ries,textiles ,pharmacies ,etc .,solargeamountofASreleasedintotheenvironmentarecausingpollution .There foreitisnecessarytodevelopafast,simpleandcosteffec tivemethodforthedeterminationofAS .Theofficialmeth odsrecommendedforthedeterminationofASarespec trophotometryandpotentialtitration .SpectrophotometricmethodanditsvariationsarebasedonthemeasurementofthecoloredassociatesofASwithposi…     

From Single Molecule to Crystal: Mapping Out the Conformations of Tartaric Acids and Their Derivatives

Stereoisomers of one of the most important organic compounds, tartaric acid, optically active and meso as well as the ester or amide derivatives, can show diverse structures related to the rotation around the three carbon–carbon bonds. This study determines the controlling factors for conformational changes of these molecules in vacuo, in solution, and in the crystalline state using DFT calculations, spectroscopic measurements, and X‐ray diffraction. All structural variations can be logically accounted for by the possibility of formation and breaking of hydrogen bonds between the hydroxy or amide donors and oxygen acceptors, among these the hydrogen bonds that close five‐membered rings being the most stable. These findings are useful in designing molecular and crystal structures of highly polar, polyfunctional, chiral compounds.     

Lamellare Schichten auf der Grundlage von Wasserstoffbrücken und π‐Stapelung: Kristallstrukturen der Metall(II)‐Komplexe [Cd{C6H4(SO2)2N}2(H2O)4] und [Cu{C6H4(SO2)2N}2(H2O)4]·2 H2O

The title complexes, obtained by treating hot aqueous solutions of ortho‐benzenedisulfonimide with solid CdCO₃ or CuO, have been characterized by low‐temperature X‐ray diffraction (both triclinic, space group P&1macr;, Z = 1, metal ions on inversion centres). The cations have trans‐octahedral coordinations provided by two Cd‐N bonded or two Cu‐O bonded anions and four water molecules [Cd‐N 234.7(2) pm; Cu‐O(anion) 240.4(1) pm, elongated by Jahn‐Teller distortion]; the copper complex contains two further, non‐coordinating, water molecules per formula unit. In both structures, the uncharged zero‐dimensional building blocks are associated via strong hydrogen bonds O(W)‐H···A and one short C‐H···O bond to form two‐dimensional assemblies comprising an internal polar lamella of metal cations, (SO₂)₂N groups and water molecules, and hydrophobic peripheral regions consisting of vertically protruding benzo rings. Carbocycles drawn alternatingly from adjacent layers form π‐stacking arrays, in which the parallel aromatic rings display intercentroid distances in the range 365‐385 pm and vertical ring spacings in the range 345‐385 pm.     

基于2-氯-6-甲基苯甲酸和N-甲基咪唑铜(Ⅱ)配合物的合成、晶体结构和电化学性能(英文)

合成了标题配合物Cu(Cmba)2(Mim)2(Cmba为2-氯-6-甲基苯甲酸阴离子,Mim为N-甲基咪唑),并用X射线单晶衍射仪测定了其晶体结构。晶体属单斜晶系,P21/n空间群,晶胞参数为:a=0.7389(15)nm,b=2.1379(4)nm,c=0.8150(16)nm,β=112.41(3)°,V=1.1902(4)nm3,Z=2,Dc=1.582g.cm-3。最后精修结果为:R1=0.0682,wR2=0.1740。在配合物结构中每个Cu髤原子分别与来自2个羧酸根离子中的2个氧原子、2个N-甲基咪唑分子中的2个N原子进行配位,形成了1个平面四边形结构。电化学研究显示配合物中的Cu2+/Cu+对的氧化还原是一个准可逆的过程。     

Cooperative hydration of pyruvic acid in ice

About 3.5 +/- 0.3 water molecules are still involved in the exothermic hydration of 2-oxopropanoic acid (PA) into its monohydrate (2,2-dihydroxypropanoic acid, PAH) in ice at 230 K. This is borne out by thermodynamic analysis of the fact that QH(T) = [PAH]/[PA] becomes temperature independent below approximately 250 K (in chemically and thermally equilibrated frozen 0.1 < or = [PA]/M < or = 4.6 solutions in D2O), which requires that the enthalpy of PA hydration (DeltaHH approximately -22 kJ mol(-1)) be balanced by a multiple of the enthalpy of ice melting (DeltaHM = 6.3 kJ mol(-1)). Considering that: (1) thermograms of frozen PA solutions display a single endotherm, at the onset of ice melting, (2) the sum of the integral intensities of the 1deltaPAH and 1deltaPA methyl proton NMR resonances is nearly constant while, (3) line widths increase exponentially with decreasing temperature before diverging below approximately 230 K, we infer that PA in ice remains cooperatively hydrated within interstitial microfluids until they vitrify.     

Mapping Hydration Water around Alcohol Chains by THz Calorimetry

THz spectroscopy was used to probe changes that occur in the dynamics of the hydrogen bond network upon solvation of alcohol chains. The THz spectra can be decomposed into the spectrum of bulk water, tetrahedral hydration water, and more disordered (or interstitial) hydration water. The tetrahedrally ordered hydration water exhibits a band at 195 cm⁻¹ and is localized around the hydrophobic moiety of the alcohol. The interstitial component yields a band at 164 cm⁻¹ which is associated with hydration water in the first hydration shell. These temperature‐dependent changes in the low‐frequency spectrum of solvated alcohol chains can be correlated with changes of heat capacity, entropy, and free energy upon solvation. Surprisingly, not the tetrahedrally ordered component but the interstitial hydration water is found to be mainly responsible for the temperature‐dependent change in ΔC_p and ΔG. The solute‐specific offset in free energy is attributed to void formation and scales linearly with the chain length.