The three states criterion of nucleophilic reactivity in the conjugate acid of an anionic nucleophile and some problems of proton partitioning: implications for the reactions of 2,2′-dipyridyl disulphide with papain and with L-ergothioneine

The circumstances in which observation of three reactive protonic states of a reaction, involving an electrophile that increases its reactivity consequent on protonation, may be regarded as compelling evidence of nucleophilic character in the conjugate acid of an anionic nucleophile (”three states criterion“) are delineated. Aspects of the reaction of papain with 2,2′-dipyridyl disulphide not previously reported suggest that this reaction at pH 4 is best described as an intracomplex thiol-disulphide interchange involving the unionized thiol group of the cysteine-25-histidine-159-asparagine-175 hydrogen bonded system of papain with 2,2′-dipyridyl disulphide hydrogen bonded at one nitrogen atom to the carboxyl group of aspartic acid-158. The reaction appears to involve pre-transition state proton transfer in the thiol-imidazole hydrogen bond; the protonation of the side chains of aspartate-158 and histidine-159 may be positively cooperative. Rate equations for reactions involving up to three reactive protonic states are presented in an appendix.     

2-巯基吡啶质子迁移过程的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了2-巯基吡啶分子硫醇式结构和硫酮式结构进行结构互变质子迁移过程中的4种可能途径:(a)分子内质子迁移,(b)水助质子迁移,(c)同种二聚体双质子迁移和(d)异种二聚体间双质子迁移.计算结果表明,途经c所需要的活化能最小(9.73 kJ.mol-1,逆反应则为55.28 kJ.mol-1),而过程a所需要的活化能最大(106.02 kJ.mol-1),途径b和d的活化能居中间(分别为32.05和15.91 kJ.mol-1).研究还表明,氢键在降低反应活化能方面起着重要的作用.     

Quino[7,8-h]quinoline,a New Type of “Proton Sponge”

So far, “proton sponges” have been defined as bis(dialkylamino)arenes whose dialkylamino groups are in close spatial proximity.^[1] The unusual basicity of these compounds is ascribed to the destabilizing overlap of the lone electron pairs on the nitrogen atoms, to the formation of especially strong hydrogen bonds in the monoprotonated diamines, and to the hydrophobic shielding of these hydrogen bonds. In order to differentiate and assess the relative importance of these factors, we were interested in quino[7,8-h]quinoline 1 , whose nitrogen atoms exhibit a mutual orientation similar to that in 1,8-bis(dimethylamino)naphthalene 2 (“proton sponge”). In contrast to 2 , however, 1 lacks the hydrophobic shielding of the hydrogen bonds of its monoprotonated derivative. This shielding is considered to be responsible for the low rates of proton transfer, which make the “proton sponges” reported so far unsuitable as auxiliary bases in chemical reactions.     

4(3H)-嘧啶酮及其类似物互变异构的理论研究

采用密度泛函理论,在B3LYP/6-311G**基组水平上,计算并考察了4(3H)-嘧啶酮及其类似物(5-氟-4(3H)-嘧啶酮、4-巯基嘧啶和5-氟-4-巯基嘧啶)醇式结构和酮式结构进行结构互变质子迁移过程中的2种可能途径:(a)分子内质子迁移;(b)水助质子迁移.计算结果表明,途经b所需要的活化能较小.研究还表明,氢键在降低反应活化能方面起着重要的作用.     

Relationships between NMR shifts and interaction energies in biphenyls,alkanes, aza-alkanes,and oxa-alkanes with X─H…H─Y and X─H…Z (X,Y = C or N; Z = N or O) hydrogen bonding

Hydrogen–hydrogen C─H^…H─C bonding between the bay-area hydrogens in biphenyls, and more generally in congested alkanes, very strained polycyclic alkanes, and cis-2-butene, has been investigated by calculation of proton nuclear magnetic resonance (NMR) shifts and atom–atom interaction energies. Computed NMR shifts for all protons in the biphenyl derivatives correlate very well with experimental data, with zero intercept, unit slope, and a root mean square deviation of 0.06 ppm. For some congested alkanes, there is generally good agreement between computed values for a selected conformer and the experimental data, when it is available. In both cases, the shift of a given proton or pair of protons tends to increase with the corresponding interaction energy. Computed NMR shift differences for methylene protons in polycyclic alkanes, where one is involved in a very short contact (“in”) and the other is not (“out”), show a rough correlation with the corresponding C─H^…H─C exchange energies. The “in” and “in,in” isomers of selected aza- and diaza-cycloalkanes, respectively, are X─H^…H─N hydrogen bonded, whereas the “out” and “in,out” isomers display X─H^…N hydrogen bonds (X = C or N). Oxa-alkanes and the “in” isomers of aza–oxa-alkanes are X─H^…O hydrogen bonded. There is a very good general correlation, including both N─H^…H─Y (Y = C or N) and N─H^…Z (Z = N or O) interactions, for NH proton shifts against the exchange energy. For “in” CH protons, the data for the different C─H^…H─Y and C─H^…Z interactions are much more dispersed and the overall shift/exchange energy correlation is less satisfactory.     

Theoretical study on the β−-decay effect in mono-tritiated two hydrogen bonded systems: proton transfer along the hydrogen bond direction

The effect of tritium β^?-decay on the “two” hydrogen bonds in mono-tritiated formamide dimer (A), formic acid dimer (B), and acetic acid-formic acid (C) was studied with ab initio MO calculations. The tritium β^?-decay in (A) and (B) is expected to result in spontaneous transfer of one proton along the hydrogen bond direction: no proton transfer takes place in (C).     

Exceptional Isotopic‐Substitution Effect: Breakdown of Collective Proton Tunneling in Hexagonal Ice due to Partial Deuteration

Multiple proton transfer controls many chemical reactions in hydrogen‐bonded networks. However, in contrast to well‐understood single proton transfer, the mechanisms of correlated proton transfer and of correlated proton tunneling in particular have remained largely elusive. Herein, fully quantized ab initio simulations are used to investigate H/D isotopic‐substitution effects on the mechanism of the collective tunneling of six protons within proton‐ordered cyclic water hexamers that are contained in proton‐disordered ice, a prototypical hydrogen‐bonded network. At the transition state, isotopic substitution leads to a Zundel‐like complex, [HO???D???OH], which localizes ionic defects and thus inhibits perfectly correlated proton tunneling. These insights into fundamental aspects of collective proton tunneling not only rationalize recent neutron‐scattering experiments, but also stimulate investigations into multiple proton transfer in hydrogen‐bonded networks much beyond ice.     

Hydrogen bonding in vitamin B6

Double-well potential energy surfaces for hydrogen bonding in crystalline vitamin B₆ have been associated with molecular environmental effects. New calculations, involving improved representations of a fragmentation model, include the introduction of a second pyridoxinium chloride system within the model in a “dimer-like” configuration. The new results confirm the double-well potential and the prediction of the experimentally observed position for the proton as being due essentially to environmental effects. Atomic difference maps are presented for the charge density distributions, which reflect the nature of the bonding as it depends on the proton position. Mulliken populations are examined particularly in relation to the “intermolecular” transfer of electrons.     

Sigma-Bonded Organochromium Compounds. Hydrogen Transfer Reactions

The preparation and properties of two classes of organochromium compounds and their interconversion have been studied actively in recent years. These are the σ-bonded organochromium compounds in which alkyl, aryl, or aralkyl groups are covalently bonded to chromium (II or III) and the π-arenechromium complexes in which “aromatic” nuclei are covalently bonded to chromium (0 or I). From certain reactions of the σ-bonded organochromium compounds, evidence has accumulated which shows that the chromium atom acts not only as a coordination center, but also as a hub for hydrogen transfer and H/D exchange^[1,2]. σ-Organochromium compounds may act as sources of radicals and carbanions. The present paper deals with the preparation and properties of σ-bonded organochromium compounds; particular attention is given to hydrogen transfer reactions and rearrangements to bis(π-arene)chromium complexes.     

A study on the proton transfer in the benzoic acid dimer by C high-resolution solid-state NMR and proton T1 measurements

By a solid-state ¹³C and proton NMR study of the hydrogen bonded dimer of benzoic acid, the rate of proton transfer, the height of the potential barrier for the transfer and the relative population of two different configurations were determined.     

Proton/Hydrogen‐Transfer Coordinate of 2,5‐Dihydroxybenzoic Acid Investigated in a Supersonic Beam: Combined IR/UV Spectroscopy in the S0, S1, and D0 States

As a model system for intramolecular proton/hydrogen‐transfer coordinates, the structure of 2,5‐dihydroxybenzoic acid is investigated for the ground, first electronically excited and also the ionic state. Combined IR/UV spectroscopy in molecular‐beam experiments is applied and the experimental results are interpreted by the application of DFT and CASPT2 methods. No proton or hydrogen transfer is observed, but evidence is given for a hydrogen dislocation of the intramolecular hydrogen bond in the S₁ state and to lesser extent in the D₀ state. To obtain direct information on the proton/hydrogen‐transfer coordinate, IR spectra are recorded both in the region of the OH and especially the CO stretching vibrations by also applying two new variants of combined IR/UV spectroscopy for the S₁ and D₀ states. The CO groups are directly involved in the hydrogen bond and, in contrast to the hydrogen‐bonded OH groups, the CO stretching frequencies can be observed in all electronic states.     

The Cyclic Hydrogen‐Bonded 6‐Azaindole Trimer and its Prominent Excited‐State Triple‐Proton‐Transfer Reaction

The compound 6‐azaindole undergoes self‐assembly by formation of N(1)?H???N(6) hydrogen bonds (H bonds), forming a cyclic, triply H‐bonded trimer. The formation phenomenon is visualized by scanning tunneling microscopy. Remarkably, the H‐bonded trimer undergoes excited‐state triple proton transfer (ESTPT), resulting in a proton‐transfer tautomer emission maximized at 435 nm (325 nm of the normal emission) in cyclohexane. Computational approaches affirm the thermodynamically favorable H‐bonded trimer formation and the associated ESTPT reaction. Thus, nearly half a century after Michael Kasha discovered the double H‐bonded dimer of 7‐azaindole and its associated excited‐state double‐proton‐transfer reaction, the triply H‐bonded trimer formation of 6‐azaindole and its ESTPT reaction are demonstrated.     

Anti‐Electrostatic Hydrogen Bonds

Ab initio and hybrid density functional techniques were employed to characterize a surprising new class of H‐bonded complexes between ions of like charge. Representative H‐bonded complexes of both anion–anion and cation–cation type exhibit appreciable kinetic stability and the characteristic theoretical, structural, and spectroscopic signatures of hydrogen bonding, despite the powerful opposition of Coulomb electrostatic forces. All such “anti‐electrostatic” H‐bond (AEHB) species confirm the dominance of resonance‐type covalency (“charge transfer”) interactions over the inessential (secondary or opposing) “ionic” or “dipole–dipole” forces that are often presumed to be essential for numerical modeling or conceptual explanation of the H‐bonding phenomenon.     

Solvent dependent excited state spectral properties of 4-hydroxyacridine: Evidence for only water mediated excited state proton transfer process

The possibility of ground and excited state proton transfer reaction across the five member intramolecular hydrogen bonded ring in 4-hydroxyacridine (4-HA) has been investigated spectroscopically and the experimental results have been correlated with quantum chemical calculations. The difference in the emissive behaviour of 4-HA in different types of solvents is due to the presence of different species in the excited state. In non-polar solvents, the species present is non-fluorescing in nature, whereas 4-HA molecule shows normal emission from intramolecularly hydrogen bonded closed conformer in polar aprotic solvents. In polar protic solvents like MeOH, EtOH, etc. (except water), a single broad emission band is attributed to the hydrogen bonded solvated form of 4-HA. However, in case of water, fluorescence from the tautomeric form of 4-HA is observed apart from emission from the solvated form. Emission from the tautomeric form may arise due to double proton transfer via a single water molecule bonded to 4-HA. Evaluation of the potential energy surfaces by quantum chemical calculations using density functional theory (DFT) and time dependent density functional theory (TDDFT), however, points towards the possibility of proton transfer—both intrinsic intramolecular as well as water mediated in the first excited state of 4-HA.     

The Host/Guest Type of Excited‐State Proton Transfer; a General Review

Contemporary progress regarding guest/host types of excited‐state double proton transfer has been reviewed, among which are the biprotonic transfer within doubly H‐bonded host/guest complexes, the transfer through a solvent bridge relay, the intramolecular double proton transfer and solvation dynamics coupled proton transfer. Of particular emphases are the photophysical and photochemical properties of excited‐state double proton transfer (ESDPT) in 7‐azaindole and its corresponding analogues. From the chemical aspect, two types of ESDPT reaction, namely the catalytic and non‐catalytic types of ESDPT, have been classified and reviewed separately. For the case of static host/guest hydrogen‐bonded complexes both hydrogen‐bonding strength and configuration (i.e. geometry) play key roles in accounting for the reaction dynamics. In addition to the dynamical concern, excited‐state thermodynamics are of importance to fine‐tune the proton transfer reaction in the non‐catalytic host/guest type of ESDPT. The mechanisms of protic solvent assisted ESDPT, depending on host molecules and proton‐transfer models, have been reviewed where the plausible resolution is deduced. Particular attention has been given to the excited‐state proton transfer dynamics in pure water, aiming at its future perspective in biological applications. Finally, the differentiation in mechanism between solvent diffusive reorganization and solvent relaxation to affect the host/guest ESPT dynamics is made and discussed in de tail.     

A Reversible Proton Relay Process Mediated by Hydrogen‐Bonding Interactions in [FeFe]Hydrogenase Modeling

A reversible and temperature‐dependent proton‐relay process is demonstrated for a Fe₂ complex possessing a terminal thiolate in the presence of nitrogen‐based acids. The terminal sulfur site (S^t) of the complex forms a hydrogen‐bond interaction with N,N‐dimethylanilinium acid at 183 K. The Fe₂ core, instead, is protonated to generate a bridging hydride at 298 K. Reversibility is observed for the tautomerization between the hydrogen‐bonded pair and the Fe–hydride species. X‐ray structural analysis of the hydrogen‐bonded species at 193 K reveals a short N(H)???S^t contact. Employment of pyridinium acid also results in similar behavior, with reversible proton–hydride interconversion. DFT investigation of the proton‐transfer pathways indicates that the pK_a value of the hydrogen‐bonded species is enhanced by 3.2 pK_a units when the temperature is decreased from 298 K to 183 K.     

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.     

HCN(HNC)与NH3, H2O和HF分子间相互作用的理论研究

在MP2/aug-cc-pVTZ水平上, 对HCN(HNC)与NH3, H2O和HF分子间可能存在的氢键型复合物进行了全自由度能量梯度优化, 通过在相同水平上的频率验证分析发现了稳定的分子间相互作用形式是HCN(HNC)作为质子供体或作为质子受体形成的复合物. 基组重叠误差对总相互作用能的影响均小于3.34 kJ/mol. 通过自然键轨道(NBO)分析, 研究了单体和复合物中的原子电荷和电荷转移对分子间相互作用的影响. 对称性匹配微扰理论(SAPT, Symmetry Adapted Perturbation Theory)能量分解结果表明, 在分子间相互作用中, 静电作用与诱导作用占主导地位, 而诱导作用与复合物的电荷转移之间具有良好的正相关性.     

H2S·HOH or H2O·HSH, which is more stable in the water-hydrogen sulfide complex?

High-level ab initio calculations are carried out to study the relative stability of the two hydrogen bonded structures of water-hydrogen sulfide complex, one with water as the proton donor (A) and the other with hydrogen sulfide as the proton donor (B). The results show that structure A is considerably more stable than B at the correlated level, which is in contrast with previous results obtained from Hartree-Fock calculations.