Carbon protonation of 2,4,6-triaminopyrimidines: synthesis, NMR studies, and theoretical calculations

Several C5-substituted 2,4,6-triaminopyrimidine derivatives and their HBF4 salts were synthesized to study the carbon protonation of the pyrimidine ring. NMR investigations in DMSO-d6 prove experimentally that, in addition to the usual protonation at N1, the compounds can be protonated at C5 as well. We present several new stable cationic sigma-complexes in the pyrimidine series, where C5 protonation predominates over N1 protonation. Quantum chemical calculations using the B3LYP/cc-pVDZ method were utilized in the gas phase and also in DMSO solvent with the polarized continuum model (PCM) method to rationalize the observed protonation behavior. Results of the calculations accord with the experimental observations and prove that combined steric and electronic effects are responsible for the observed C5 protonation and for sigma-complex stability. We demonstrate that C5 protonation is a general feature of the 2,4,6-triaminopyrimidine system.     

Photophysics and photochemistry of nalidixic acid

The photophysics and photochemistry of nalidixic acid (NA) were studied as function of pH and solvent properties. The ground state of NA exhibits different protonated forms in the range of pH 1.8-10.0. Fluorescence studies showed that the same species exist at the lowest singlet excited state. Absorption experiments were carried out with NA and with the methylated analog of nalidixic acid (MNE) in different organic solvents and water pH 3, where the main species corresponds to that protonated at the carboxylic group. These studies and the DFT calculation of torsional potential energy profiles suggest that the most stable conformation of the NA in nonprotic solvents corresponds to a closed structure caused by the existence of intramolecular hydrogen bond. Absorption and fluorescence spectra were studied in sulfuric acid solution. The pK value (Ho -1.0) found in these conditions was attributed to the protonation of the 4' keto oxygen atom of the heterocyclic ring. Theoretical calculations (DFT/B3LYP/6-311G*) of the energies of the different monoprotonated forms of the NA and Fukui indexes (f(x)-) showed that the species with the proton attached to 4' keto oxygen atom is the most stable of all the cationic forms. MNE and enoxacin also showed the protonation of the 4' keto oxygen atom with similar pK values. The photodecomposition of NA is dependent on the medium properties. Faster decomposition rates were obtained in strong acid solution. In nonprotic solvents, a very slow decomposition rate was observed.     

Protonation Preferentially Stabilizes Minor Tautomers of the Halouracils: IRMPD Action Spectroscopy and Theoretical Studies

Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics, potentially inducing errors during DNA and RNA replication. The gas-phase structures of protonated complexes of five halouracils, including 5-fluorouracil, 5-chlorouracil, 5-bromouracil, 5-iodouracil, and 6-chlorouracil are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. IRMPD action spectra were measured for each complex in the IR fingerprint region extending from ~1000 to 1900?cm(-1) using the free electron laser (FELIX). Correlations are made between the measured IRMPD action spectra and the linear IR spectra for the stable low-energy tautomeric conformations computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory. Absence of an intense band(s) in the IRMPD spectrum arising from the carbonyl stretch(es) that are expected to appear near 1825?cm(-1) provides evidence that protonation induces tautomerization and preferentially stabilizes alternative, noncanonical tautomers of these halouracils where both keto functionalities are converted to hydroxyl groups upon binding of a proton. The weak, but measurable absorption, which does occur for these systems near 1835?cm(-1) suggests that in addition to the ground-state conformer, very minor populations of excited, low-energy conformers that contain keto functionalities are also present in these experiments.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

An ab initio study of excited states of guanine in the gas phase and aqueous media: Electronic transitions and mechanism of spectral oscillations

Ground state geometries of the four tautomeric forms keto‐N9H, keto‐N7H, enol‐N9H, and enol‐N7H of guanine were optimized in the gas phase at the RHF level using a mixed basis set consisting of the 4‐31G basis set for all the atoms except the nitrogen atom of the amino group for which the 6‐311+G* basis set was used. These calculations were also extended to hydrogen‐bonded complexes of three water molecules with each of the keto‐N9H (G9‐3W) and keto‐N7H (G7‐3W) forms of guanine. Relative stabilities of the four above‐mentioned tautomers of guanine as well as those of G9‐3W and G7‐3W complexes in the ground state in the gas phase were studied employing the MP2 correlation correction. In aqueous solution, relative stabilities of these systems were studied using the MP2 correlation correction and polarized continuum model (PCM) or the isodensity surface polarized continuum model (IPCM) of the self‐consistent reaction field (SCRF) theory. Geometry optimization in the gas phase at the RHF level using the 6‐31+G* basis set for all atoms and the solvation calculations in water at the MP2 level using the same basis set were also carried out for the nonplanar keto‐N9H and keto‐N7H forms of guanine. Thus, it is shown that among the different tautomers of guanine, the keto‐N7H form is most stable in the gas phase, while the keto‐N9H form is most stable in aqueous solution. It appears that both the keto‐N9H and keto‐N7H forms of guanine would be present in the ground state, particularly near the aqueous solution–air interface. Vertical excitation and excited state geometry optimization calculations were performed using configuration interaction involving single electron excitation (CIS). It is found that the absorption spectrum of guanine would arise mainly due to its keto‐N9H form but the keto‐N7H form of the same would also make some contribution to it. The enol‐N9H and enol‐N7H forms of the molecule are not expected to occur in appreciable abundance in the gas phase or aqueous media. The normal fluorescence spectrum of guanine in aqueous solution with a peak near 332 nm seems to originate from the lowest singlet excited state of the keto‐N7H form of the molecule while the fluorescence of oxygen‐rich aqueous solutions of guanine with a peak near 450 nm appears to originate from the lowest singlet excited state of the keto‐N9H form of the molecule. The origin of the slow damped spectral oscillation observed in the absorption spectrum of guanine has been explained. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 826–846, 2000     

Reduction pathway of end-on terminally coordinated dinitrogen. V. N-N bond cleavage in Mo/W hydrazidium complexes with diphosphine coligands. Comparison with triamidoamine systems

N-N cleavage of the dialkylhydrazido complex [W(dppe)2(NNC5H10)] (B(W)) upon treatment with acid, leading to the nitrido/imido complex and piperidine, is investigated experimentally and theoretically. In acetonitrile and at room temperature, B(W) reacts orders of magnitude more rapidly with HNEt3BPh4 than its Mo analogue, [Mo(dppe)2(NNC5H10)] (B(Mo)). A stopped-flow experiment performed for the reaction of B(W) with HNEt3BPh4 in propionitrile at -70 degrees C indicates that protonation of B(W) is completed within the dead time of the stopped-flow apparatus, leading to the primary protonated intermediate B(W)H+. Propionitrile coordination to this species proceeds with a rate constant k(obs(1)) of 1.5 +/- 0.4 s(-1), generating intermediate RCN-B(W)H+ (R = Et) that rapidly adds a further proton at Nbeta and then mediates N-N bond splitting in a slower reaction (k(obs(2)) = 0.35 +/- 0.08 s(-1), 6 equiv of acid). k(obs(1)) and k(obs(2)) are found to be independent of the acid concentration. The experimentally observed reactivities of B(Mo) or B(W) with acids in nitrile solvents are reproduced by DFT calculations. In particular, geometry optimization of models of solvent-coordinated, Nbeta-protonated intermediates is found to lead spontaneously to separation into the nitrido/imido complexes and piperidine/piperidinium, corresponding to activationless heterolytic N-N bond cleavage processes. Moreover, DFT indicates a spontaneous cleavage of nonsolvated B(W) protonated at Nbeta. In the second part of this article, a theoretical analysis of the N-N cleavage reaction in the Mo(III) triamidoamine complex [HIPTN3N]Mo(N2) is presented (HIPTN3N = hexaisopropylterphenyltriamidoamine). To this end, DFT calculations of the Mo(III)N2)triamidoamine complex and its protonated and reduced derivatives are performed. Calculated structural and spectroscopic parameters are compared to available experimental data. N-N cleavage most likely proceeds by one-electron reduction of the Mo(V) hydrazidium intermediate [HIPTN3N]Mo(NNH3)+, which is predicted to have an extremely elongated N-N bond. From an electronic-structure point of view, this reaction is analogous to that of Mo/W hydrazidium complexes with diphos coligands. The general implications of these results with respect to synthetic N2 fixation are discussed.     

Density functional theory studies of N-protonation of the free base phthalocyanine

The structures and relative energies of twenty-two N-protonated species of the free base phthalocyanine (H₂Pc) have been systematically studied with the density functional theory at the B3LYP/6-31G(d) level of theory. The calculations demonstrated that the N-protonation tends to increase the N–C bonds and the C–N–C angles on the protonation sites. The inner protonation at the isoindole-nitrogen atoms causes significant out-of-plane deformation of the macrocycle, ascribed to the steric hindrance of the central cavity. The relative energies of various protonated species were calculated and compared to deduce the preferred sites for protonation. It was revealed that the outer protonation at the meso-nitrogen atoms is energetically more favorable than the inner protonation at the isoindole-nitrogen atoms. Among the studied twenty-two protonated species, the most stable one is H₆Pc⁴⁺(IS1), for which all the outer meso-nitrogen atoms are protonated. TDDFT calculations have been performed for selected species, and the results were used to analysis the UV–visible spectrum of the concentrated sulfuric acid solution of the free base phthalocyanine.     

Proton migration and tautomerism in protonated triglycine.

Proton migration in protonated glycylglycylglycine (GGG) has been investigated by using density functional theory at the B3LYP/6-31++G(d,p) level of theory. On the protonated GGG energy hypersurface 19 critical points have been characterized, 11 as minima and 8 as first-order saddle points. Transition state structures for interconversion between eight of these minima are reported, starting from a structure in which there is protonation at the amino nitrogen of the N-terminal glycyl residue following the migration of the proton until there is fragmentation into protonated 2-aminomethyl-5-oxazolone (the b(2) ion) and glycine. Individual free energy barriers are small, ranging from 4.3 to 18.1 kcal mol(-)(1). The most favorable site of protonation on GGG is the carbonyl oxygen of the N-terminal residue. This isomer is stabilized by a hydrogen bond of the type O-H.N with the N-terminal nitrogen atom, resulting in a compact five-membered ring. Another oxygen-protonated isomer with hydrogen bonding of the type O-H.O, resulting in a seven-membered ring, is only 0.1 kcal mol(-)(1) higher in free energy. Protonation on the N-terminal nitrogen atom produces an isomer that is about 1 kcal mol(-)(1) higher in free energy than isomers resulting from protonation on the carbonyl oxygen of the N-terminal residue. The calculated energy barrier to generate the b(2) ion from protonated GGG is 32.5 kcal mol(-)(1) via TS(6-->7). The calculated basicity and proton affinity of GGG from our results are 216.3 and 223.8 kcal mol(-)(1), respectively. These values are 3-4 kcal mol(-)(1) lower than those from previous calculations and are in excellent agreement with recently revised experimental values.     

Local structure of nitrogen atoms in a porphine ring of mesophenyl substituted porphyrin with an electron-withdrawing group using X-ray photoelectron spectroscopy and X-ray absorption spectroscopy.

This study investigated the protonation of nitrogen atoms in porphyrins with meso-phenyl p-substituted by an electron-withdrawing group using N 1s X-ray photoelectron spectroscopy (XPS), the N K X-ray absorption near-edge structure (XANES), and the discrete variational (DV)-Xalpha molecular orbital (MO) method. Both tetraphenylporphyrin (TPP) and tetrakis(p-sulfonatophenyl)porphyrin (TSPP) have a single structure: the former has two protonated and two non-protonated N atoms in the porphine ring; the latter has four protonated N atoms in the porphine ring. In contrast, a combination of XPS, XANES, and DV-Xalpha MO calculations shows that tetrakis(p-carboxyphenyl)porphyrin (TCPP) has a dual structure: one structure has two protonated and two non-protonated N atoms; the other has four protonated N atoms. Furthermore, this result was also considered based on the protonation constants of N atoms in the porphyrins. The correlation between the strength of electron-withdrawing groups and protonation to N atoms in porphyrins can be described using the spectral patterns of the N 1s XPS and N K XANES spectra.     

Experimental and theoretical studies of the structures and interactions of vancomycin antibiotics with cell wall analogues

Surface-induced dissociation (SID) of the singly protonated complex of vancomycin antibiotic with cell wall peptide analogue (N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala) was studied using a 6 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) specially configured for SID experiments. The binding energy between the vancomycin and the peptide was obtained from the RRKM modeling of the time- and energy-resolved fragmentation efficiency curves (TFECs) of the precursor ion and its fragments. Molecular dynamics simulations of the vancomycin, peptide, and vancomycin-peptide complex were carried out to explore the low energy conformations. Density functional theory (DFT) calculations of the geometries, proton affinities, and binding energies were performed for several model systems including vancomycin (V), vancomycin aglycon (VA), N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala, and noncovalent complexes of VA with N-acetyl-D-Ala-D-Ala and V with N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala. Comparison between the experimental and computational results suggests that the most probable structure of the complex observed in our experiments corresponds to the neutral peptide bound to the vancomycin protonated at the primary amine of the disaccharide group. The experimental binding energy of 30.9 +/- 1.8 kcal/mol is in good agreement with the binding energy of 36.3-42.0 kcal/mol calculated for the model system representing the preferred structure of the complex.     

Probing Protonation Sites of Isolated Flavins Using IR Spectroscopy: From Lumichrome to the Cofactor Flavin Mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B₂), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm^?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.     

Mechanisms of HNO and NO production from Angeli's salt: density functional and CBS-QB3 theory predictions

The mechanism of decomposition of Angeli's salt, Na(2)N(2)O(3), was explored with B3LYP and CBS-QB3 computational methods. Angeli's salt produces both nitroxyl (HNO) and nitric oxide (NO), depending upon the pH of the solution. These calculations show that protonation on N(2), while less favorable than O protonation, leads spontaneously to HNO production, while diprotonation at O(3) leads to NO generation. K(a) values for protonation at different centers and rate constants have been found which reproduce experimental data satisfactorily.     

Fragmentations of protonated arginine, lysine and their methylated derivatives: concomitant losses of carbon monoxide or carbon dioxide and an amine

The fragmentation pathways of protonated arginine, protonated N(alpha),N(alpha)-dimethylarginine, the N(alpha),N(alpha),N(alpha)-trimethylarginine ion, three protonated N(epsilon),N(epsilon)-dimethyllysines, and three permanent lysine ions in which the charge is fixed by trimethylation are reported. Ion assignment was facilitated by (15)N-labeling and deuterium substitution. The chemistries are dominated by charge-induced elimination of the amino groups as neutrals, including dimethylamine, trimethylamine and guanidine. Competitive losses of the alpha-amino and side-chain amino groups were observed; these losses led to intermediates that had different structures and different subsequent dissociation reactions. Concomitant losses of CO or CO(2) with these amines were also commonly observed. However, the ionic products of amine losses did not subsequently lose CO or CO(2), suggesting strongly that in these concomitant eliminations, it is the CO or CO(2) that was first eliminated, followed immediately by the loss of the amine. Results of density functional theory calculations on protonated arginine and protonated N(alpha),N(alpha)-dimethylarginine reveal that, in such concomitant eliminations, the dissociating complex is vibrationally hot and the intermediate ion formed by losing CO or CO(2) can immediately dissociate to eliminate the amine.     

Ligand versus metal protonation of an iron hydrogenase active site mimic

The protonation behavior of the iron hydrogenase active-site mimic [Fe2(mu-adt)(CO)4(PMe3)2] (1; adt=N-benzyl-azadithiolate) has been investigated by spectroscopic, electrochemical, and computational methods. The combination of an adt bridge and electron-donating phosphine ligands allows protonation of either the adt nitrogen to give [Fe2(mu-Hadt)(CO)4(PMe3)2]+ ([1 H]+), the Fe-Fe bond to give [Fe2(mu-adt)(mu-H)(CO)4(PMe3)2]+ ([1 Hy]+), or both sites simultaneously to give [Fe2(mu-Hadt)(mu-H)(CO)4(PMe3)2]2+ ([1 HHy]2 +). Complex 1 and its protonation products have been characterized in acetonitrile solution by IR, (1)H, and (31)P NMR spectroscopy. The solution structures of all protonation states feature a basal/basal orientation of the phosphine ligands, which contrasts with the basal/apical structure of 1 in the solid state. Density functional calculations have been performed on all protonation states and a comparison between calculated and experimental spectra confirms the structural assignments. The ligand protonated complex [1 H]+ (pKa=12) is the initial, metastable protonation product while the hydride [1 Hy]+ (pKa=15) is the thermodynamically stable singly protonated form. Tautomerization of cation [1 H]+ to [1 Hy]+ does not occur spontaneously. However, it can be catalyzed by HCl (k=2.2 m(-1) s(-1)), which results in the selective formation of cation [1 Hy]+. The protonations of the two basic sites have strong mutual effects on their basicities such that the hydride (pK(a)=8) and the ammonium proton (pK(a)=5) of the doubly protonated cationic complex [1 HHy]2+ are considerably more acidic than in the singly protonated analogues. The formation of dication [1 HHy]2+ from cation [1 H]+ is exceptionally slow with perchloric or trifluoromethanesulfonic acid (k=0.15 m(-1) s(-1)), while the dication is formed substantially faster (k>10(2) m(-1) s(-1)) with hydrobromic acid. Electrochemically, 1 undergoes irreversible reduction at -2.2 V versus ferrocene, and this potential shifts to -1.6, -1.1, and -1.0 V for the cationic complexes [1 H]+, [1 Hy]+, and [1 HHy]2+, respectively, upon protonation. The doubly protonated form [1 HHy]2+ is reduced at less negative potential than all previously reported hydrogenase models, although catalytic proton reduction at this potential is characterized by slow turnover.     

Theoretical investigation of the binding of small molecules and the intramolecular agostic interaction at tungsten centers with carbonyl and phosphine ligands

The factors controlling both the binding of small molecules to several tungsten complexes and agostic bonding in the W(CO)3(PCy3)2 complex have been examined through B3LYP hybrid density functional theory and ab initio MP2 calculations with and without basis set superposition error (BSSE) corrections. This approach attempts to isolate insofar as possible the separate effects of intrinsic bonding interactions, electron induction by ligands, and steric hindrance and strain. An important conclusion from this study is that for bimolecular reactions, BSSE corrections must be included for quantitative predictions. There is a reasonably good correlation between the BSSE-corrected B3LYP and MP2 results for bond dissociation enthalpies (BDEs) of very small molecules (H2, N2, and CO), but generally B3LYP BDEs tend to be smaller than the corresponding MP2 values. In the few cases where a comparison with experimental data can be appropriately made, it appears that the BSSE-corrected MP2 BDEs are more reliable. Using N2 as a probe molecule, the strength of the agostic bond in W(CO)3(PCy3)2 has been examined by calculating the BDE of N2 in a series of tungsten complexes with increasing electron inducing effect without agostic bonding, then extrapolating the expected trend to the case of agostically bonded W(CO)3(PCy3)2. Comparison of the extrapolated value to the calculated BDE of W(CO)3(PCy3)2(N2) yields an estimated strength of the agostic bond of from 7 to 9 kcal mol-1. Approximately 5 kcal mol-1 of the interaction is assigned to the net agostic interaction associated with moving from a nonagostic local minimum configuration of the PCy3 ligands to the agostically bonded global minimum.     

Isolation and Structural Characterization of Eightfold Protonated Octacyanometalates [M(CNH)8]4+ (M=MoIV,WIV) from Superacids

Octacyanometalates K₄[Mo(CN)₈] and K₄[W(CN)₈] are completely protonated in superacidic mixtures of anhydrous hydrogen fluoride and antimony pentafluoride. The resulting hydrogen isocyanide complexes [Mo(CNH)₈]⁴⁺ [SbF₆]^?₄ and [W(CNH)₈]⁴⁺ [SbF₆]^?₄ are the first examples of eight‐coordinate homoleptic metal complexes containing hydrogen isocyanide (CNH) ligands. The complexes were crystallographically characterized, revealing hydrogen‐bonded networks with short N???H???F contacts. Low‐temperature NMR measurements in HF confirmed rapid proton exchange even at ?40 °C. Upon protonation, ν(C≡N) increases of about 50 cm^?1 which is in agreement with DFT calculations.     

Evidence for basic ferryls in cytochromes P450

Using a combination of M?ssbauer spectroscopy and density functional calculations, we have determined that the ferryl forms of P450(BM3) and P450cam are protonated at physiological pH. Density functional calculations were performed on large active-site models of these enzymes to determine the theoretical M?ssbauer parameters for the ferryl and protonated ferryl (Fe(IV)OH) species. These calculations revealed a significant enlargement of the quadrupole splitting parameter upon protonation of the ferryl unit. The calculated quadrupole splittings for the protonated and unprotonated ferryl forms of P450(BM3) are DeltaE(Q) = 2.17 mm/s and DeltaE(Q) = 1.05 mm/s, respectively. For P450cam, they are DeltaE(Q) = 1.84 mm/s and DeltaE(Q) = 0.66 mm/s, respectively. The experimentally determined quadrupole splittings (P450(BM3), DeltaE(Q) = 2.16 mm/s; P450cam, DeltaE(Q) = 2.06 mm/s) are in good agreement with the values calculated for the protonated forms of the enzymes. Our results suggest that basic ferryls are a natural consequence of thiolate-ligated hemes.     

Spectroscopic identification of carbenium and ammonium isomers of protonated aniline (AnH+): IR spectra of weakly bound AnH+ -Ln clusters (L = Ar, N2)

Infrared photodissociation (IRPD) spectra of mass-selected clusters composed of protonated aniline (C6H8N+ = AnH+) and a variable number of neutral ligands (L = Ar, N2) are obtained in the N-H stretch range. The AnH+ -Ln complexes (n < or = 3) are produced by chemical ionization in a supersonic expansion of An, H2, and L. The IRPD spectra of AnH+-Ln feature the unambiguous fingerprints of at least two different AnH+ nucleation centers, namely, the ammonium isomer (5) and the carbenium ions (1 and/or 3) corresponding to protonation at the N atom and at the C atoms in the para and/or ortho positions, respectively. Protonation at the meta and ipso positions is not observed. Both classes of observed AnH+-Ln isomers exhibit very different photofragmentation behavior upon vibrational excitation arising from the different interaction strengths of the AnH+ cores with the surrounding neutral ligands. Analysis of the incremental N-H stretch frequency shifts as a function of cluster size shows that microsolvation of both 5 and 1/3 in Ar and N2 starts with the formation of intermolecular H bonds of the ligands to the acidic NH protons and proceeds by intermolecular pi bonding to the aromatic ring. The analysis of both the photofragmentation branching ratios and the N-H stretch frequencies demonstrates that the N-H bonds in 5 are weaker and more acidic than those in 1/3, leading to stronger intermolecular H bonds with L. The interpretation of the spectroscopic data is supported by density functional calculations conducted at the B3LYP level using the 6-31G* and 6-311G(2df,2pd) basis sets. Comparison with clusters of neutral aniline and the aniline radical cation demonstrates the drastic effect of protonation and ionization on the acidity of the N-H bonds and the topology of the intermolecular potential, in particular on the preferred aromatic substrate-nonpolar ligand recognition motif.     

Energetics and structural elucidation of mechanisms for gas phase H/D exchange of protonated peptides

Hydrogen/deuterium exchange reactions involving protonated triglycine and deuterated ammonia (ND(3)) have been examined in the gas phase using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Ab initio and density functional theory (DFT) calculations have been carried out to model the exchanges and to obtain energetics and vibrational frequencies for molecules involved in the proposed exchange mechanisms. Structural optimization and frequency calculations have been performed at the B3LYP level of theory with the 6-311+G(d,p) basis set. Transition states have been calculated at the same level of theory and basis set as above using the QST2 and QST3 methods. Single-point energy calculations have been performed at the MP2/6-311+G(d,p) level. Six labile sites of protonated triglycine were found to undergo H/D exchange. Of these six labile hydrogens, two are amide, three are ammonium, and one is carboxyl. Detailed mechanisms for each of these transfers are proposed. Qualitative onium ion and tautomer mechanisms for the exchanges of ammonium and amide hydrogens, respectively, using semiempirical calculations were suggested in previous studies by Beauchamp et al. As shown by the current ab initio and DFT calculations completed during this study, the mechanisms proposed in that study are notionally correct; however, the tautomer mechanisms are shown here to be the result of the fact that a second stable isomer of protonated triglycine exists in which the amide1 carbonyl oxygen is protonated. The exchange of the carboxyl hydrogen is found to proceed via a transition state resembling an ammonium ion interacting with a carboxylate moiety via two hydrogen bonds. The current work thus provides significant mechanistic and structural detail for a considerably more in-depth understanding of the processes involved in gas phase H/D exchange of peptides.     

Molekülstrukturen von Kupfer(II)- und Eisen(III)-Chlorokomplexen mit di- und monoprotoniertem N-(Pyrid-2-ylmethyl)ethylendiamin-N,N′,N′-triacetat (H2pedta−; Hpedta2−)

Molecular Structures of Copper(II) and Iron(III) Chloro Complexes with di- and monoprotonated N-(pyrid-2-ylmethyl)ethylenediamine-N,N′,N′-triacetate (H₂pedta^?; Hpedta^2?) The molecular structures of two complexes of di- and monoprotonated N-(pyrid-2-ylmethyl)ethylenediamine-N,N′,N′ -triacetate (pedta^3?) with Cu^II and Fe^III as central atoms have been determined by single crystal X-ray diffraction methods. Both complexes have a distorted octahedral coordination with H₂pedta^? and Hpedta^2? as pentadentate ligands and a chloride ion occupying the sixth coordination site. The different oxidation states of the central atoms result in a completely different coordination behaviour of the carboxyl groups. In both complexes one of the ? CH₂? COOH groups is uncoordinated. In the Fe^III complex, the central atom is coordinated by the hydroxylic O atoms of the deprotonated carboxyl groups. Contrary to this in the Cu^II complex, the central atom is coordinated by the carbonylic O atoms. One of the coordinated carboxyl groups is protonated and the other is deprotonated. All protonated carboxyl groups in both complexes form intermolecular hydrogen bonds.