Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.     

Cu^2＋诱导甘氨酸质子迁移机理的理论研究

采用CCSD/6-31＋＋G＊＊//B3LYP/6-31＋＋G＊＊方法研究了Cu2＋诱导甘氨酸质子迁移的机理.优化得到了7个中性配合物和1个两性配合物,其中两性配合物最稳定,结合能为215.93 kcal mol-1.中性构型间通过分子内单键的旋转相互转化,C-N、C-C和C-O键旋转的能垒范围分别为1.62～2.49、0.27～7.80和2.27～16.97 kcal mol-1;中性构型N6经质子迁移变为两性构型,能垒为33.82 kcal mol-1.Cu2＋作用于甘氨酸,使甘氨酸N5原子负电荷减少超过0.5,降低了N5对H6原子的库仑吸引,钝化了共价键B（O3–H6）,动力学上不利于H6质子迁移;但是H6质子迁移后,形成的两性构型Z1却是热力学最稳定体系.     

Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength,aromaticity, and excited‐state intramolecular proton transfer reaction

The inequivalence of substitution pair positions of naphthalene ring has been investigated by a theoretical measurement of hydrogen bond strength, aromaticity, and excited state intramolecular proton transfer (ESIPT) reaction as the tools in three substituted naphthalene compounds viz 1‐hydroxy‐2‐naphthaldehyde (HN12), 2‐hydroxy‐1‐naphthaldehyde (HN21), and 2‐hydroxy‐3‐naphthaldehyde (HN23). The difference in intramolecular hydrogen bond (IMHB) strength clearly reflects the inequivalence of substitution pairs where the calculated IMHB strength is found to be greater for HN12 and HN21 than HN23. The H‐bonding interactions have been explored by calculation of electron density ρ(r) and Laplacian ?²ρ(r) at the bond critical point using atoms in molecule method and by calculation of interaction between σ* of OH with lone pair of carbonyl oxygen atom using NBO analysis. The ground and excited state potential energy surfaces (PESs) for the proton transfer reaction at HF (6‐31G**) and DFT (B3LYP/6‐31G**) levels are similar for HN12, HN21 and different for HN23. The computed aromaticity of the two rings of naphthalene moiety at B3LYP/6‐31G** method also predicts similarity between HN12 and HN21, but different for HN23. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Intramolecular proton transfer induced by divalent alkali earth metal cation in the gas state

Interactions between divalent alkali earth metal (DAEM) ions M (M?Be, Mg, Ca, Sr, Ba) and the second stable glycine conformer in the gas phase, which can transfer into the ground‐state glycine‐M²⁺ (except the glycine–Be²⁺) among each corresponding isomers when these divalent metal ions are bound, are studied at the hybrid three‐parameter B3LYP level with three different basis sets. Proton transfers from the hydroxyl to the amino nitrogen of the glycine without energy barriers have been first observed in the gas phase in these glycine–M²⁺ systems. The interaction between the glycine and these DAEM ions except beryllium and magnesium ion only create an amino hydrogen pointing to the original hydroxyl due to their weaker interaction relative to those divalent transition metal (DTM) ion‐bound glycine derivatives, being obviously different from that between the glycine and DTM ions, in which two amino hydrogens point to the original hydroxyl oxygen when these metal‐chelated glycine derivatives are produced. The interaction energy between the glycine and divalent magnesium would be the boundary of one or two amino hydrogens pointing to the hydrogyl oxygen, i.e., the ?170.3 kcal/mol of binding energy is a critical point. Similar intramolecular proton transfer has also been predicted for those DTM ion‐chelated glycine systems; however, that in the gas state has not been observed in the monovalent metal ion‐coordinated glycine systems. The binding energy between some monovalent TM ion and the glycine is similar to that of the glycine–Ba²⁺, which has the lowest binding strength among these DAEM–ion chelated glycine complexes. The difference among them only lies in the larger electrostatic and polarized effects in the latter, which favor the stability of the zwitterionic glycine form in the gas phase. According to these observations, we predict that the zwitterionic glycine would exist in the field of two positive charges in the gas phase. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 205–214, 2003     

Neutral and zwitterionic glycine.H(2)O complexes: A theoretical and matrix-isolation Fourier transform infrared study

The H-bond interaction between glycine and H2O has been studied by a combined theoretical (DFT(B3LYP)/6-31++G(**)) and experimental (matrix-isolation FT-IR) methodology. The 1:1 and 1:2 complexes of the most stable conformation (I) of glycine appear to be neutral complexes which have been vibrationally characterized in detail. The higher stoichiometry complexes (glycine).(H2O)n with n larger than 3 are demonstrated to be zwitterionic H-bonded complexes. A set of characteristic IR absorption bands for this zwitterionic structure has been observed in low-temperature Ar matrices. This would be the first experimental IR evidence for proton transfer occurring between the NH2 and COOH groups of amino acids by a H-bonded water molecular channel in isolated conditions.     

二水合甘氨酸两性离子复合体的结构和性能的理论研究

采用理论计算方法B3LYP, 在6-31++G**基组水平研究使甘氨酸质子化所需的最少水分子数目, 然后讨论水合两性离子复合体的结构和性能, 进而计算了二水合甘氨酸中性分子复合体(2W-GN)到二水合甘氨酸两性离子复合体(2W-GZ)的过渡态, 得到如下结论: (1)两个水分子可以使甘氨酸质子化, 能够形成稳定的二水合两性离子复合体. (2)甘氨酸与水分子之间通过氢键相互作用, 结合能较大, 复合体稳定; 在二水合甘氨酸复合体中, 水合甘氨酸中性分子比水合甘氨酸两性离子稳定. (3)由2W-GN到2W-GZ过程的反应活化能和氢键键能相近.     

Kinetics of the interaction of ketyl and semiquinone radicals with dioxygen. Concerted electron and proton transfer involving ketyl and semiquinone radicals

Kinetics of the interaction of ketyl and neutral semiquinone radicals with dioxygen was studied by the flash photolysis technique. The reactivity of neutral semiquinone radicals in the transfer of a hydrogen atom to O₂ is lower than that of ketyl radicals and increases as the reduction ability of the radicals increases, which give evidence for the charge transfer from the radicals to O₂ in the transition state of the reaction. The deuterium kinetic isotope effect of the reaction (up to 2.6) suggests considerable weakening of the O−H bond of the seminquinone radical in the transition state. A cyclic structure of the transition state similar to that in the reactions of ketyl radicals with hydrogen atom acceptors is proposed. In aprotic volvents, solvation has essentially no effect on the reactivity of neutral anthrasemiquinone radicals up to solvent nucleophilicityB≈240. In solvents with higher nucleophilicity and in protic solvents, their reactivity drops sharply. Hydrogen atom transfer reactions involving ketyl and neutral semiquinone radicals are shown to involve concerted electron and proton transfers, and to have transition states in which the partial transfer of an electron and a proton from the ketyl or semiquinone radical to an acceptor occurs. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1131–1137, June, 1997.     

Theoretical Studies on the Proton Transfer Mechanism in Four-water Hydrated Glycine Complexes

The mp2/6-31++g**//b3lyp/6-31++g** method has been employed to study the proton transfer mechanism in 4H2O-glycine complexes(4W-G).Compared with bare glycine the four-water hydrated neutral glycine complexes(4W-GN) can turn into the corresponding zwitterionic glycine(4W-GZ) through proton transfer.The most stable conformation of 4W-GZ has a "double water-chain" structure and is more stable than its corresponding precursor 4W-GN by 0.97 KJ/mol though it is less stable than the most stable 4W-GN by 7.80 KJ/mol.It is a spontaneous reaction to form the most stable conformation of 4W-GZ,and the potential barrier is only 1.97 KJ/mol,so the probability of this reaction is very high and the most stable 4W-GZ may be detected in experiment or in the early stage of experiment.     

Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer

The relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine-water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute-solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono- and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute-solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism.     

Solvent effects on glycine II. Water-assisted tautomerization

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.     

Investigating Alanine–Silica Interaction by Means of First‐Principles Molecular‐Dynamics Simulations

In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynamics technique. The simulations are carried out in vacuo as well as in the presence of water molecules. In the case of a negatively charged surface and an alanine cation, an indirect proton transfer from the alanine carboxylic group to the surface takes place. The transfer involves several water molecules revealing an alanine in its zwitterionic state interacting with the neutral surface through indirect hydrogen bonds mediated by water molecules. During the simulation of the zwitterionic state the ammonium group eventually establishes a direct ? N? H???O? Si interaction, suggesting that the surface–amino group interaction is stronger than the interaction between the surface and the carboxylic group. In vacuum simulations, the amino group exhibits clearly stronger interactions with the surface than the carboxylic group.     

The Role of Hydrogen Bond in Catalytic Triad of Serine Proteases

In order to investigate the origin of catalytic power for serine proteases, the role of the hydrogen bond in the catalytic triad was studied in the proteolysis process of the peptides chymotrypsin inhibitor 2 (CI2), MCTI-A, and a hexapeptide (SUB), respectively. We first calculated the free energy profile of the proton transfer between His and Asp residues of the catalytic triad in the enzyme-substrate state and transition state by employing QM/MM molecular dynamics simulations. The results show that a low-barrier hydrogen bond (LBHB) only forms in the transition state of the acylation of CI2, while it is a normal hydrogen bond in the acylation of MCTI-A or SUB. In addition, the change of the hydrogen bond strength is much larger in CI2 and SUB systems than in MCTI-A system, which decreases the acylation energy barrier significantly for CI2 and SUB. Clearly, a LBHB formed in the transition state region helps accelerate the acylation reaction. But to our surprise, a normal hydrogen bond can also help to decrease the energy barrier. The key to reducing the reaction barrier is the increment of hydrogen bond strength in the transition state state, whether it is a LBHB or not. Our studies cast new light on the role of the hydrogen bond in the catalytic triad, and help to understand the catalytic triad of serine proteases.     

Gas phase intramolecular proton transfer in cationized glycine and chlorine substituted derivatives (M-Gly, M = Na+, Mg2+, Cu+, Ni+, and Cu2+): existence of Zwitterionic structures?

The intramolecular proton transfer in cationized glycine and chlorine substituted derivatives with M = Na+, Mg2+, Ni+, Cu+, and Cu2+ has been studied with the three parameter B3LYP density functional method. The coordination of metal cations to the oxygens of the carboxylic group of glycine stabilizes the zwitterionic structure. For all monocations the intramolecular proton transfer occurs readily with small energy barriers (1-2 kcalmol(-1)). For the dication Mg2+ and Cu2+ systems, the zwitterionic structure becomes very stable. However, whereas for Mg2+, the proton transfer process takes place spontaneously, for Cu2+ the reaction occurs with an important energy barrier. The substitution of the hydrogens of the amino group by chlorine atoms decreases the basicity of nitrogen, which destabilizes the zwitterionic structure. For monosubstituted glycine complexed with Na+, the zwitterionic structure still exists as a minimum, but for disubstituted glycine no minimum appears for this structure. In contrast, for Mg2+ complexed to mono- and disubstituted glycine, the zwitterionic structure remains the only minimum, since the enhanced electrostatic interaction with the dication overcomes the destabilizing effect of the chlorine atoms.     

Insights into the excited state intramolecular proton transfer process and mechanism of the novel 3‐hydroxythioflavone system: A theoretical study

It is well known that the molecular excited state dynamical process plays important roles in designing and developing novel applications. In this work, based on density functional theory and time‐dependent density functional theory methods, we theoretically explored a novel 3‐hydroxythioflavone (3HTF). Through calculating the electrostatic potential surface of the 3HTF structure, we confirm the formation of intramolecular hydrogen bonding O2‐H3···O4. Our theoretically obtained dominating bond lengths and bond angles involved in hydrogen bonds demonstrate that the intramolecular hydrogen bonds should be strengthened in the S₁ state. Coupling with the simulated infrared vibrational spectra, we further verify the enhanced hydrogen bonding O2‐H3···O4 in the S₁ state. Upon photoexcitation, we found that the charge transfer characteristics around hydrogen bonding moieties play important roles in facilitating the excited state intramolecular proton transfer (ESIPT) process. Via constructing potential energy curves in both S₀ and S₁ states, we confirm the almost nonbarrier ESIPT reaction should be an ultrafast process that further explains the previous experimental phenomenon. At last, we search the S₁‐state transition state (TS) structure along with ESIPT path, based on which we simulate the intrinsic reaction coordinate path that further confirms the ESIPT mechanism. We hope that our theoretical work could guide novel applications based on the 3HTF system in future.     

Proton transfer at the carboxylic sites of amino acids: A single water molecule catalyzed process

Ab initio calculations at MP2 level of theory were used to study the proton transfer at the carboxylic sites of amino acids, in the isolated, mono‐ and di‐hydrated forms. In the case of water dimer, two interaction modes with glycine neutral structures (see Fig. 3 ) were explored, corresponding to the concerted and stepwise reaction pathways. Their transition states can be described as (H₂O? H? OH₂)⁺ [Fig. 4 (a)] and (H₂O‐‐‐H? OH₂)⁺ [Fig. 4 (b)], respectively. The energy analysis indicated that the concerted pathway is preferred. In the isolated, mono‐ and di‐hydrated glycine complexes, the activation barriers of the proton transfer at the carboxylic sites were calculated to be 34.49, 16.59, and 13.36 kcal mol^?1, respectively. It was thus shown that the proton transfer is significantly assisted and catalyzed by water monomer so that it can take place at room temperature. Instead, the further addition of water molecules plays solvent effects rather than catalytic effects to this proton transfer process. The above results obtained with discrete water molecules were supported by the solvent continuum calculated data. It was also observed that the heavy dependence of the solvent continuum models on dipole moments may produce misleading results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

FMO‐MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics

Full‐quantum mechanical fragment molecular orbital‐based molecular dynamics (FMO‐MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO‐MD simulations to give reactive trajectories spontaneously, a More O’Ferrall–Jencks‐type diagram was constructed from the statistical analysis of the FMO‐MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic‐like (ZW‐like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW‐like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO‐MD trajectories, water‐mediated cyclic proton transfers were observed in both reactions on the way from the ZW‐like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO‐MD simulations to obtain detailed information at a molecular level for solution reactions.     

Quantum chemical investigation on the reaction mechanism of tertiary phosphines with unsaturated carboxylic acids: An insight into kinetic data

The structures of intermediates and transition states in the reaction of tertiary phosphines with unsaturated carboxylic acids have been calculated at the B3LYP level of theory using the 6‐31+G(d,p) basis set. Analysis of the results shows that [1,3]‐intramolecular migration of carboxylic proton to carbanionic center of generated zwitterionic intermediate is strongly kinetically unfavorable, and external proton‐donor source is essential to complete quaternization. A molecular cluster of the intermediate with one molecule of water has been modeled for intermolecular reaction pathway, but even in this case, the proton transfer remains to be the rate‐determining step that is in a good agreement with previous kinetic investigations on this reaction. The data obtained for this reaction have much in common with recent studies on the mechanisms of the Morita–Baylis–Hillman reaction and phosphine‐catalyzed [3+2] cycloaddition, which revealed paramount importance of proton‐transfer steps. © 2013 Wiley Periodicals, Inc.     

Proton Transfer Influence on Geometry and Electron Density in Benzoic Acid–Pyridine Complexes

The influence of the proton transfer on the geometry of donor and acceptor molecule in benzoic acid–pyridine complexes is investigated by theoretical calculations at the B3LYP/6‐311++G** level of theory. Systematic shifts of the H‐atom in the H‐bond are reflected in the geometry of the COOH group and the lengths of aromatic ring bond lengths of the proton acceptor. Changes in electron densities have been studied by atoms in molecules analysis. A systematic natural bond orbital analysis has been performed to study the proton transfer mechanism. Two donor orbitals are engaged in the proton transfer process which is accompanied by a change in orbital delocalization of H‐atom that can switch between two donor orbitals so the path of proton transfer in intermolecular H‐bond is not determined by the orbital shape. Theoretical results have been confirmed by experimental results published previously.