Density functional computations of proton affinity and gas-phase basicity of proline

The proton affinity and gas-phase basicity of proline were evaluated by using density functional theory coupling the B3-LYP hybrid functional with the extended 6--311++G** basis set. Cis and trans conformations of the carboxyl moiety for both exo and endo ring structures were considered for the neutral proline. The results show that the most stable structure of proline has the endo ring conformation with the carboxyl group in the cis position. The structure at the global minimum is stabilized by an intramolecular hydrogen bond. The nitrogen of the ring in the exo form is the preferred protonation site. The calculated proton affinity (924.3 kJ mol(-1)) and gas-phase basicity (894.4 kJ mol(-1)) are in very good agreement with the experimental counterparts.     

Excited-state proton transfer through water bridges and structure of hydrogen-bonded complexes in 1H-pyrrolo[3,2-h]quinoline: adiabatic time-dependent density functional theory study

Proton transfer reaction is studied for 1H-pyrrolo[3,2-h]quinoline-water complexes (PQ-(H(2)O)(n), n = 0-2) in the ground and the lowest excited singlet states at the density functional theory (DFT) level. Cyclic hydrogen-bonded complexes are considered, in which water molecules form a bridge connecting the proton donor (pyrrole NH group) and acceptor (quinoline nitrogen) atoms. To understand the effect of the structure and length of water bridges on the excited-state tautomerization in PQ, the potential energy profile of the lowest excited singlet state is calculated adiabatically by the time-dependent DFT (TDDFT) method. The S(0) --> S(1) excitation of PQ is accompanied by significant intramolecular transfer of electron density from the pyrrole ring to the quinoline fragment, so that the acidity of the N-H group and the basicity of the nitrogen atom of the quinoline moiety are increased. These excited-state acid-base changes introduce a driving force for the proton transfer reaction. The adiabatic TDDFT calculations demonstrate, however, that the phototautomerization requires a large activation energy in the isolated PQ molecule due to a high energy barrier separating the normal form and the tautomer. In the 1:1 cyclic PQ-H(2)O complex, the energy barrier is dramatically reduced, so that upon excitation of this complex the tautomerization can occur rapidly in one step as concerted asynchronous movements of the two protons assisted by the water molecule. In the PQ-(H(2)O)(2) solvate two water molecules form a cyclic bridge with sterically strained and unfavorable hydrogen bonds. As a result, some extra activation energy is needed for initiating the proton dislocation along the longer hydrogen-bond network. The full tautomerization in this complex is still possible; however, the cooperative proton transfer is found to be highly asynchronous. Large relaxation and reorganization of the hydrogen-bonded water bridge in PQ-(H(2)O)(2) are required during the proton translocation from the pyrrole NH group to the quinoline nitrogen; this may block the complete tautomerization in this type of solvate.     

Water dimer proton affinity from the kinetic method: dissociation energy of the water dimer

The proton affinity of water dimer was measured, using the kinetic method with nitrile reference bases, to be 808 +/- 6 kJ mol(-1). The difference between the measured value and the proton affinity of a single water molecule (690 +/- 4 kJ mol(-1)) reflects the difference in solvation energy for two neutral water molecules (the hydrogen bond energy of water dimer), and the energy for solvation of hydronium cation and water. Using the measured proton affinity of the dimer along with ancillary data yields an experimental value of the hydrogen bond energy of neutral water dimer, 18 +/- 9 kJ mol(-1), in good agreement with previous experimental and theoretical values. The proton affinity of the dimer measured by using alcohol references is ca 100 kJ mol(-1) too low, likely because the structure of the protonated cluster is not well-suited for kinetic method measurements. These results highlight the importance of choosing reference bases that form cluster ions consisting of a proton bound complex between the water dimer and the reference base.     

On the reduced form of (imidazole-N)(N-salicylidene-alaninato-O,N,O′) copper(II)

The geometries of the (imidazole-N³)(N-salicylidene-alaninato-O,N,O′) copper(II) and of its anion as well as of six models of its neutral hydrogenated form with the additional hydrogen at oxygen or nitrogen sites modeling its reduced copper(I) form are optimized using the gaussian 98 program package at B3LYP/6-31G* level of theory. Energy data indicate the highest stability of the structures with additional hydrogen bonded to some of carboxyl oxygens with released (or significantly weakened) Cu–O(carboxyl) bond. Hydrogen atom is inserted into this bond in the second most stable model system (with ca. 1 kJ/mol higher energy).     

Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides

Some of the most prominent "neutral losses" in peptide ion fragmentation are the loss of ammonia and water from N-terminal glutamine. These processes are studied by electrospray ionization mass spectrometry in singly- and doubly-protonated peptide ions undergoing collision-induced dissociation in a triple quadrupole and in an ion trap instrument. For this study, four sets of peptides were synthesized: (1) QLLLPLLLK and similar peptides with K replaced by R, H, or L, and Q replaced by a number of amino acids, (2) QLnK (n = 0, 1, 3, 5, 7, 9, 11), (3) QLnR (n = 0, 1, 3, 5, 7, 9), and (4) QLn (n = 1, 2, 3, 4, 8). The results for QLLLPLLLK and QLLLPLLLR show that the singly protonated ions undergo loss of ammonia and to a smaller extent loss of water, whereas the doubly protonated ions undergo predominant loss of water. The fast fragmentation next to P (forming the y5 ion) occurs to a larger extent than the neutral losses from the singly protonated ions but much less than the water loss from the doubly protonated ions. The results from these and other peptides show that, in general, when N-terminal glutamine peptides have no "mobile protons", that is, the number of charges on the peptide is no greater than the number of basic amino acids (K, R, H), deamination is the predominant neutral loss fragmentation, but when mobile protons are present the predominant process is the loss of water. Both of these processes are faster than backbone fragmentation at the proline. These results are rationalized on the basis of resonance stabilization of the two types of five-membered ring products that would be formed in the neutral loss processes; the singly protonated ion yields the more stable neutral pyrrolidinone ring whereas the doubly protonated ion yields the protonated aminopyrroline ring (see Schemes). The generality of these trends is confirmed by analyzing an MS/MS spectra library of peptides derived from tryptic digests of yeast. In the absence of mobile protons, glutamine deamination is the most rapid neutral loss process. For peptides with mobile protons, dehydration from glutamine is far more rapid than from any other amino acid. Most strikingly, end terminal glutamine is by far the most labile source of neutral loss in excess-proton peptides, but not highly exceptional when mobile protons are not available. In addition, rates of deamination are faster in lysine versus arginine C-terminus peptides and 20 times faster in positively charged than negatively charged peptides, demonstrating that these formal neutral loss reactions are not "neutral reactions" but depend on charge state and stability.     

Coupling of intramolecular hydrogen bonding to the cis-to-trans isomerization of a proline imide bond of small model peptides

A relationship between intramolecular hydrogen bonding and the cis-trans isomerization of a proline imide bond for proline-containing short peptides were studied by proton NMR and infrared spectroscopy using DMSO-d6/CDCl3 mixed solvents. The percentage of the trans form increases with increasing fraction of CDCl3 in the mixed solvents except for compounds without possibility of intramolecular hydrogen bonding. Chemical shift variations of amide protons with solvent mixing ratios were found to be useful for judging whether the amide protons take part in the intramolecular hydrogen bonding to a considerable degree or not. These results and infrared spectra were used to specify intramolecularly hydrogen bonded structures of the peptides. Formation of the 10-membered or 13-membered hydrogen bonded ring which includes the carbonyl group precedent to the prolyl residue facilitates the cis-to-trans isomerization and these hydrogen bonded rings are strong enough to restrict the proline imide bond to the trans form in CDCl3 solution. On the other hand, a 7-membered hydrogen bonded ring is not so effective in restricting the proline imide bond.     

Ab initio and NMR studies on the effect of hydration on the chemical shift of hydroxy protons in carbohydrates using disaccharides and water/methanol/ethers as model systems

Density functional theory (DFT) and Hartree-Fock (HF) quantum mechanical calculations have been performed on the disaccharides, [small beta]-l-Fucp-(1[rightward arrow]4)-[small alpha]-d-Galp-OMe, [small beta]-l-Fucp-(1[rightward arrow]4)-[small alpha]-d-Glcp-OMe, and [small beta]-l-Fucp-(1[rightward arrow]3)-[small alpha]-d-Glcp-OMe. The [capital Delta][small delta]-values (difference between the chemical shift in the disaccharide and the corresponding monosaccharide methyl glycoside) for the exchangeable hydroxy protons have been calculated and compared to experimental values previously measured by NMR spectroscopy for samples in aqueous solutions. The calculations performed on molecules in vacuum showed that hydroxy protons hydrogen bonded to the neighboring ring oxygens have large positive [capital Delta][small delta]-values, indicating that they are deshielded relative to those in the corresponding methyl glycoside. The NMR experiments showed instead that these hydroxy protons close to the neighboring ring oxygens were shielded. This discrepancy between calculated and experimental data was attributed to solvent effects, and this hypothesis has been confirmed in this work by monitoring the chemical shift of the hydroxy proton of methanol in water, ethers and water/ether solutions. Shielding of the hydroxy proton of methanol is observed for increased ether concentrations, whereas deshielding is observed for increased concentration of water. The shielding observed for hydroxy protons in disaccharides is a consequence of reduced hydration due to intermolecular hydrogen bonding or steric effects. In strongly hydrated systems such as carbohydrates, the hydration state of a hydroxy proton is the key factor determining the value of the chemical shift of its NMR signal, and the [capital Delta][small delta] will be a direct measure of the change in hydration state.     

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.     

Evolution of Organized Lariat Ether Alcohol and Diol Hydrate Macrostructures in the Solid State

Lariat ether alcohols and diols derived from dibenzo-14-crown-4crystallize in the anhydrous form or as hydrogen-bondedmonohydrates or networks depending upon thepolyether ring substitutents and the composition of the aqueous organic crystallization solvent. Supramolecular structures are created when the lariat ether alcohol sym-(hydroxy)dibenzo-14-crown-4 (1) with ``sticky ends' of ether oxygens and hydroxyl protons, hydrogen bond to each other via bridging water molecules to form three-dimensional networks. For crystallization of 1 from 30% aqueous acetonitrile, this self-association is sufficiently strong to spontaneously generate a supramolecular structure with water channels.     

One-step versus stepwise mechanism in protonated amino acid-promoted electron-transfer reduction of a quinone by electron donors and two-electron reduction by a dihydronicotinamide adenine dinucleotide analogue. Interplay between electron transfer and hydrogen bonding

Semiquinone radical anion of 1-(p-tolylsulfinyl)-2,5-benzoquinone (TolSQ(*-)) forms a strong hydrogen bond with protonated histidine (TolSQ(*-)/His x 2 H(+)), which was successfully detected by electron spin resonance. Strong hydrogen bonding between TolSQ(*-) and His x 2 H(+) results in acceleration of electron transfer (ET) from ferrocenes [R2Fc, R = C5H5, C5H4(n-Bu), C5H4Me] to TolSQ, when the one-electron reduction potential of TolSQ is largely shifted to the positive direction in the presence of His x 2 H(+). The rates of His x 2 H(+)-promoted ET from R2Fc to TolSQ exhibit deuterium kinetic isotope effects due to partial dissociation of the N-H bond in His x 2 H(+) at the transition state, when His x 2 H(+) is replaced by the deuterated compound (His x 2 D(+)-d6). The observed deuterium kinetic isotope effect (kH/kD) decreases continuously with increasing the driving force of ET to approach kH/kD = 1.0. On the other hand, His x 2 H(+) also promotes a hydride reduction of TolSQ by an NADH analogue, 9,10-dihydro-10-methylacridine (AcrH2). The hydride reduction proceeds via the one-step hydride-transfer pathway. In such a case, a large deuterium kinetic isotope effect is observed in the rate of the hydride transfer, when AcrH2 is replaced by the dideuterated compound (AcrD2). In sharp contrast to this, no deuterium kinetic isotope effect is observed, when His x 2 H(+) is replaced by His x 2 D(+)-d6. On the other hand, direct protonation of TolSQ and 9,10-phenanthrenequinone (PQ) also results in efficient reductions of TolSQH(+) and PQH(+) by AcrH2, respectively. In this case, however, the hydride-transfer reactions occur via the ET pathway, that is, ET from AcrH2 to TolSQH(+) and PQH(+) occurs in preference to direct hydride transfer from AcrH2 to TolSQH(+) and PQH(+), respectively. The AcrH2(*+) produced by the ET oxidation of AcrH2 by TolSQH(+) and PQH(+) was directly detected by using a stopped-flow technique.     

A neutron scattering study of strong-symmetric hydrogen bonds in potassium and cesium hydrogen bistrifluoroacetates: Determination of the crystal structures and of the single-well potentials for protons

The crystal structures of potassium and cesium bistrifluoroacetates, KH(CF(3)COO)(2) and CsH(CF(3)COO)(2), respectively, were determined at room and cryogenic temperatures with the single crystal neutron diffraction technique. The crystals belong to the monoclinic space groups, I2a and A2a, respectively, and there is no evidence of any structural phase transition. In both crystals, trifluoroacetate entities in centrosymmetric dimers are linked by very short hydrogen bonds lying across a center of inversion. The thermal parameters provide no evidence of any double minimum potential for hydrogen bond protons. Single-minimum potentials were determined via best fitting to the inelastic neutron scattering spectral profiles of the stretching vibrations. They comprise a narrow well for the ground state and a very broad quasiharmonic well for excited states. The spread out of the wave functions of these states shows that protons are no longer confined between the oxygens. Presumably, they are attracted by the lone pairs of oxygen atoms. These potentials emphasize the covalent nature of the OO bond and the ionic character of the hydrogen bond proton.     

Effects of microsolvation and aqueous solvation on the tautomers of histidine: a computational study on energy, structure and IR spectrum

Microsolvation and combined microsolvation-continuum approaches are employed to investigate the structures and energies of canonical and zwitterionic histidine conformers. The effect of hydration on the relative conformational stability is examined. The strategy of exploring singly and doubly hydrated structures and the possible microsolvation patterns are described. We find that bonding water molecule may significantly change the relative conformational stabilities. In gas phase, the singly and doubly hydrated canonical forms are more stable than their zwitterionic counterparts. In solution, the continuum solvent model shows that bare zwitterionic form is more stable than bare canonical form by 1.1 kcal/mol. This energy separation is increased to 2.2 and 3.4 kcal/mol with inclusion of one and two explicit water molecules, respectively. We have also observed that the doubly hydrated structures obtained by combining two water molecules simultaneously to the solute molecule are preferred over the stepwise hydration. Hydrogen bond energies for the most stable hydrated histidine tautomers are determined by the atoms in molecules theory. The infrared (IR) spectra for the most stable singly and doubly hydrated structures of both histidine tautomers in gas phase are characterized. The stretching frequencies for NH of imidazole ring and OH of COOH are red shifted due to the hydrations. The IR spectra for the most stable zwitterionic tautomers in solution are also presented and discussed in connection with the comparison to the experiments. The pKa values obtained for the ring protonated zwitterions with two explicit water molecules appear to be in good agreement with the experiments.     

An exploration of mechanisms for the transformation of 8-oxoguanine to guanidinohydantoin and spiroiminodihydantoin by density functional theory

The potential energy surface for formation of 2-amino-5-hydroxy-7,9-dihydropurine-6,8-dione (5-OH-OG), guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) from 8-oxoguanine (8-oxoG) has been mapped out using B3LYP density functional theory, the aug-cc-pVTZ and 6-31+G(d,p) basis sets and the IEF-polarizable continuum model (PCM) solvation model. Three pathways for formation of 5-OH-OG from 8-oxoG were evaluated: (A) stepwise loss of two electrons and two protons to form the quinonoid intermediate 2-amino-7,9-dihydro-purine-6,8-dione (8-oxoG(ox)) followed by hydration; (B) stepwise loss of two electrons and one proton and net addition of hydroxide, in which the key step is nucleophilic addition to the 8-oxoG radical cation; and (C) stepwise loss of one electron and one proton and addition of hydroxyl radical to the 8-oxoG radical cation. The data suggest that all three pathways are energetically feasible mechanisms for the formation of 5-OH-OG, however, Pathway A may be kinetically favored over Pathway B. Although lower in energy, Pathway C may be of limited biological significance since it depends on the local concentration of hydroxyl radical. Pathways for hydrolysis and decarboxylation of 5-OH-OG to form Gh via either a carboxylic acid or substituted carbamic acid intermediate have been evaluated with the result that cleavage of the N1-C6 bond is clearly favored over that of the C5-C6 bond. Formation of Sp from 5-OH-OG via stepwise proton transfer and acyl migration or ring opening followed by proton transfer and ring closure have also been explored and suggest that deprotonation of the hydroxyl group facilitates a 1,2 acyl shift. Results of the calculations are consistent with experimental studies showing dependence of the Gh/Sp product ratio on pH. Under neutral and basic conditions, the data predict that formation of Sp is kinetically favored over the pathways for formation of Gh. Under acidic conditions, Gh is predicted to be the kinetically favored product.     

Reaction of Phenanthrene‐9,10‐dione with Phenanthrene‐9,10‐diol: Synthesis and Characterization of the First ortho‐Quinhydrone Derivative

Treatment of phenanthrene‐9,10‐dione (PQ) with phenanthrene‐9,10‐diol (PQH₂), as prepared by catalytic hydrogenation of PQ, in toluene solution or in the solid state afforded crystalline ‘9,10‐phenanthrenequinhydrone’ (PQH), the first example of an ortho‐quinhydrone. PQH was characterized by analytical and spectroscopic methods, including X‐ray and CP/MAS ¹³C‐NMR analyses. The crystal structure of PQH showed pairs of planar molecules linked by H‐bonds and organized in columns parallel to the crystallographic axis a. The solid‐state structure of PQH was compared with those of the parent compounds, PQ and PQH₂, the latter being reported for the first time. PQH was found to be stable in the solid state only, the components PQ and PQH₂ being formed upon dissolution in media of even low polarity such as toluene.     

Probing the N(5)-H bond of the isoalloxazine moiety of flavin radicals by X- and W-band pulsed electron-nuclear double resonance.

An X- (9.7 GHz and W-band (94 GHz) pulsed electron-nuclear double resonance (ENDOR) study of the flavin cofactor of Escherichia coli DNA photolyase in its neutral radical form is presented. Through proton and deuteron ENDOR measurements at T = 80 K, we detect and characterize the full anisotropy of the hyperfine coupling (hfc) tensor of the proton or deuteron bound to N(5) of the isoalloxazine ring. Scaling of the anisotropic proton hfc components by multiplication with the quotient of the magnetogyric ratio of a deuteron and a proton, chiD/chiH, reveals subtle differences compared to the respective deuteron couplings obtained by 95-GHz deuterium ENDOR spectroscopy on an H-->D buffer-exchanged sample. These differences can be attributed to the different lengths of N(5)-H and N(5)-D bonds arising from the different masses of protons and deuterons. From the R(-3) dependence of the dipolar hyperfine splitting, we estimated that the N(5)-D bond is about 2.5% shorter than the respective N(5)-H bond. That such subtle bond-length differences can be resolved by pulsed ENDOR spectroscopy suggests that this method may be favorably used to probe the geometry of hydrogen bonds between the H(5) of the paramagnetic flavin and the protein backbone. Such information is only obtained with difficulty by other types of spectroscopy.     

Effect of axial ligands and macrocyclic structure on redox potentials and electron-transfer mechanisms of SnIV porphyrins

The electrochemical properties of dichloro- and dihydroxo-SnIV porphyrins with three different macrocycles were examined in CH2Cl2 containing 0.1 or 0.2 M tetra-n-butylammonium perchlorate as supporting electrolyte. The investigated compounds are represented as (TPP)SnX2, (P)Sn(X)2, and (PQ)Sn(X)2, where TPP = 5,10,15,20-tetraphenylporphyrin, P = 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin, PQ = 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)quinoxalino[2,3-b']porphyrin, and X = Cl or OH. Each porphyrin can be electroreduced in two one-electron-transfer steps with the half-wave potentials and stability of the eletroreduced compounds being dependent upon the type of coordinated axial ligand and specific macrocyclic structure. All reductions of (TPP)Sn(OH)2, (P)Sn(OH)2, and (PQ)Sn(OH)2 are reversible under the given experimental conditions and lead to the expected porphyrin pi-anion radicals and dianions, which were characterized by thin-layer UV-vis spectroelectrochemistry. This contrasts with what occurs upon the reduction of (PQ)SnCl2, which undergoes a chemical reaction with trace H2O in solution, leading to the formation of (PQ)Sn(OH)2 as well as to a protonated form of the quinoxalinoporphyrin, (PQH)Sn(OH)2, under the application of an applied potential. A protonation of the Q group breaks the conjugation between the fused quinoxaline unit and the porphyrin macrocycle, thus effectively giving a compound whose reduction properties resemble that of the metalloporphyrin in the absence of the fused ring. The electrooxidation of each neutral SnIV porphyrin was also investigated, and the effect of axial ligand and fused quinoxaline ring on the redox potentials and products of electron transfer are discussed.     

Effect of the surface on charge reduction and desorption kinetics of soft landed peptide ions

Charge reduction and desorption kinetics of ions and neutral molecules produced by soft-landing of mass-selected singly and doubly protonated Gramicidin S (GS) on different surfaces was studied using time dependant in situ secondary ion mass spectrometry (SIMS) integrated in a specially designed Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) research instrument. Soft-landing targets utilized in this study included inert self-assembled monolayers (SAMs) of 1-dodecane thiol (HSAM) and its fluorinated analog (FSAM) on gold and hydrophilic carboxyl-terminated (COOH-SAM) and amine-terminated (NH₂-SAM) surfaces. We observed efficient neutralization of soft-landed ions on the COOH-SAM surface, partial retention of only one proton on the HSAM surface, and efficient retention of two protons on the FSAM surface. Slow desorption rates measured experimentally indicate fairly strong binding between peptide molecules and SAM surfaces with the binding energy of 20–25 kcal/mol.     

Electron-capture induced dissociation of doubly charged dipeptides: on the neutral losses and N-Cα bond cleavages

Electron capture by doubly charged peptide cations leads to neutral losses in addition to N-C(α) bond cleavages that give c and z fragments. In this work we discuss the influence of amino acid sequence on hydrogen versus ammonia loss and the propensity for subsequent partial side-chain cleavage after ammonia loss to give w fragment ions. Experiments were done on two series of doubly protonated dipeptides, [XK+2H](2+) and [XR+2H](2+), where X is one of the twenty common amino acid residues, excluding aspartic acid (D), and K and R are lysine and arginine, respectively. While it was previously established that NH(3) is lost exclusively from the N-terminal ammonium group and not from side-chain ammonium groups, we find here that ammonia can be lost from guanidinium radicals as well. The ratio between H loss and NH(3) loss reveals some information on internal ionic hydrogen bonds and peptide conformation since proton sharing between the N-terminal ammonium group and a basic side chain decreases the probability for NH(3) loss due to a lower recombination energy and as a result reduced capture probability. The abundance of w ions was found to correlate with the reaction energy for their formation; highest yield was found for CK and lowest for AK and HK. The survival rate of charge-reduced species was higher for XR than for XK, which is likely linked to the formation of long-lived C(α) radicals in the latter case. The probability for N-C(α) bond cleavage is smaller on average for XR than for XK which indicates that hydrogen transfer from the ε-ammonium radical to the amide group triggers some of the cleavages, or is a result of the different distances between the amide group and the charges in XR and XK. Finally, our data support the previous concept that charge partitioning between c and z fragments can be explained by competition between the two fragments for the proton.     

Phonon driven proton transfer in crystals with short strong hydrogen bonds

Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.     

Gas phase retro‐Michael reaction resulting from dissociative protonation: fragmentation of protonated warfarin in mass spectrometry

A mass spectrometric study of protonated warfarin and its derivatives (compounds 1 to 5) has been performed. Losses of a substituted benzylideneacetone and a 4‐hydroxycoumarin have been observed as a result of retro‐Michael reaction. The added proton is initially localized between the two carbonyl oxygens through hydrogen bonding in the most thermodynamically favorable tautomer. Upon collisional activation, the added proton migrates to the C‐3 of 4‐hydroxycoumarin, which is called the dissociative protonation site, leading to the formation of the intermediate ion‐neutral complex (INC). Within the INC, further proton transfer gives rise to a proton‐bound complex. The cleavage of one hydrogen bond of the proton‐bound complex produces the protonated 4‐hydroxycoumarin, while the separation of the other hydrogen bond gives rise to the protonated benzylideneacetone. Theoretical calculations indicate that the 1, 5‐proton transfer pathway is most thermodynamically favorable and support the existence of the INC. Both substituent effect and the kinetic method were utilized for explaining the relative abundances of protonated 4‐hydroxycoumarin and protonated benzylideneacetone derivative. For monosubstituted warfarins, the electron‐donating substituents favor the generation of protonated substituted benzylideneacetone, whereas the electron‐withdrawing groups favor the formation of protonated 4‐hydroxycoumarin. Copyright © 2012 John Wiley & Sons, Ltd.