Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy.

The binding motifs in the halide adducts with tyrosine ([Tyr + X]-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]- and [nitroTyr + X]-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]-, where the anion is placed above the face of the aromatic ring.

Mode-specific fragmentation of amino acid-containing clusters.

A combination of infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations have been employed to study the structures and mode-specific dissociation pathways of the proton-bound dimer of 3-trifluoromethylphenylalanine (3-CF3-Phe) and trimethylamine (TMA). Three structural motifs are identified: canonical (charge-solvated), zwitterionic (charge-separated), and TMA-bridged. In the 1000-1350 cm(-1) region, similar spectra are observed in the TMA·H(+) and 3-CF3-Phe·H(+) product channels. At wavenumbers above 1350 cm(-1), infrared excitation of charge-solvated structures leads exclusively to production of protonated TMA, while excitation of zwitterionic or TMA-bridged structures results exclusively in production of protonated 3-CF3-Phe. The cluster potential energy landscape is topologically mapped and mechanisms for isomerization and mode-selective dissociation are proposed. In particular, cluster transparency as a result of IR-induced isomerization is implicated in deactivation of some IRMPD channels.

Gas-phase solvation of protonated amino acids by methanol.

The enthalpy and entropy changes for the formation of the 1:1 complexes of methanol with various gaseous protonated amino acids have been measured using pulsed-ionization high-pressure mass spectrometry. The enthalpy changes for formation of the clusters Gly(MeOH)H(+), Ala(MeOH)H(+), Val(MeOH)H(+), Leu(MeOH)H(+), Ile(MeOH)H(+), and Pro(MeOH)H(+) have been determined to be -92.0, -83.3, -82.4, -79.5, -78.7, and -73.6 kJ mol(-1), respectively. These values agree very well with the energetic values computed at the MP2(full)/6-311++G(2d,2p)//B3LYP/6-311+G(d,p) level of theory for the lowest energy adducts in each system. Both experimental observations and computational determinations of the potential energy surface for the glycine system suggest that a mixture of low-lying isomers may be present for each of the cluster systems examined. The primary structural motif for these clusters is the coordination of the methanol molecule to the ammonium group of the protonated amino acid via a strong ionic hydrogen bond. For the amino acids studied here, computational results reveal that one methanol molecule does not sufficiently stabilize any zwitterionic structure such that no appreciable extent of proton transfer from the amino acid to methanol was observed.

Persistent Intramolecular C-H···X (X = O or S) Hydrogen-Bonding in Benzyl Meldrum's Acid Derivatives.

C-H···X (where X = O or S) intramolecular hydrogen bonding is investigated in three benzyl Meldrum's acid derivatives using a combination of solution phase NMR spectroscopy, gas phase infrared multiple photon dissociation spectroscopy, and density functional theory calculations. In one compound, an abnormally large C-H···S hydrogen bond energy of 30.4 kJ mol-1 is calculated with a natural bond orbital analysis. Intramolecular C-H···O hydrogen bonding is found to persist in the gas phase. Gibbs energy decomposition pathways are calculated.

Insight into the gas-phase structure of a copper(II) L-histidine complex, the agent used to treat Menkes disease.

Copper(II) L-histidine is used in the treatment of a rare neurological disease called Menkes disease. An infrared multiple photon dissociation (IRMPD) vibrational spectrum of the gas-phase copper(II) L-histidine complex has been obtained. This spectrum was compared to lowest-energy computational spectra obtained at the B3LYP/6-311+G** level of theory. Two species, CuHis1 and CuHis2, are very close in Gibbs free energy, and both have computed vibrational spectra in good agreement with the experimentally observed IRMPD spectrum. The first structure exhibits four histidine-copper interactions in the same plane and a fifth out-of-plane interaction. The second structure exhibits four histidine-copper interactions in the same plane. The fact that the experimental and computational spectra are found to be in good agreement adds considerable insight into the gas-phase structure of the copper(II) L-histidine complex.

Structural investigation of protonated azidothymidine and protonated dimer.

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.

Proton-bound 3-cyanophenylalanine trimethylamine clusters: isomer-specific fragmentation pathways and evidence of gas-phase zwitterions.

The structures and dissociation pathways of the proton-bound 3-cyanophenylalanine·trimethylamine cluster have been studied using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations. Three isomer motifs are identified: charge-solvated, zwitterionic, and trimethylamine (TMA)-bridged. While the TMA-bridged structures fragment to yield protonated TMA (channel 1) and protonated 3-cyanophenylalanine (channel 2), charge-solvated species exclusively fragment via channel 1 and zwitterionic species exclusively fragment via channel 2. Mechanisms are proposed.

Weak ion-molecule interactions in the gas phase: a high-pressure mass spectrometry and computational study of chloride-alkane interactions.

High-pressure mass spectrometric equilibrium experiments and electronic structure calculations have been carried out to investigate the energetics of the interactions of chloride ion with a series of normal alkanes and cycloalkanes in the gas phase. The structures of the complexes obtained from the electronic structure calculations provide considerable insight into the nature of the interaction between the negatively charged ion and the alkanes, which has the character of a purely ion-induced dipole interaction. The structural information also shows how the charged species affect the confirmation of the normal alkanes.

Consecutive fragmentation mechanisms of protonated ferulic acid probed by infrared multiple photon dissociation spectroscopy and electronic structure calculations.

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm(-1). The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

Experimental and theoretical investigation of the proton-bound dimer of lysine.

The structure of the proton-bound lysine dimer has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. The structures of different possible isomers of the proton-bound lysine dimer have been optimized at the B3LYP/6-31 + G(d) level of theory and IR spectra calculated using the same computational method. Based on relative Gibbs free energies (298 K) calculated at the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d) level of theory, LL-CS01, and followed closely (1.1 kJ mol(-1)) by LL-CS02 are the most stable non-zwitterionic isomers. At the MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + (d,p) levels of theory, isomer LL-CS02 is favored by 3.0 and 2.3 kJ mol(-1), respectively. The relative Gibbs free energies calculated by the aforementioned levels of theory for LL-CS01 and LL-CS02 are very close and strongly suggest that diagnostic vibrational signatures found in the IRMPD spectrum of the proton-bound dimer of lysine can be attributed to the existence of both isomers. LL-ZW01 is the most stable zwitterionic isomer, in which the zwitterionic structure of the neutral lysine is well stabilized by the protonated lysine moiety via a very strong intermolecular hydrogen bond. At the MP2/aug-cc-pVTZ//B3LYP/6-31 + G(d), MP2/aug-cc-pVTZ//6-31 + G(d) and MP2/aug-cc-pVTZ//6-31 + G(d,p) levels of theory, the most stable zwitterionic isomer (LL-ZW01) is less favored than LL-CS01 by 7.3, 4.1 and 2.3 kJ mol(-1), respectively. The experimental IRMPD spectrum also confirms that the proton-bound dimer of lysine largely exists as charge-solvated isomers. Investigation of zwitterionic and charge-solvated species of amino acids in the gas phase will aid in a further understanding of structure, property, and function of biological molecules.

Tridentate ionic hydrogen-bonding interactions of the 5-fluorocytosine cationic dimer and other 5-fluorocytosine analogues characterized by IRMPD spectroscopy and electronic structure calculations.

Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.

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.

Infrared vibrational spectra as a structural probe of gaseous ions formed by caffeine and theophylline.

Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and the two protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using infrared multiphoton dissociation (IRMPD) spectroscopy and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. The proton-bound dimer (PBD) of caffeine and ammonia exhibits a low binding energy and was found to be elusive under the experimental conditions due, most probably, to collision-induced dissociation of the complex with helium buffer gas before IRMPD irradiation. The IRMPD spectrum of a PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also been obtained. The spectrum of protonated caffeine showed dominant protonation at the N(9) site, whereas the spectrum of protonated theophylline showed a mixture of two isomers. The first protonated isomer of theophylline exhibits protonation at the N(9) site and the second isomer demonstrated protonation at the C(6) carbonyl oxygen. The protonated carbonyl isomer of theophylline cannot be produced as a result of direct protonation and is thus suggested to be a consequence of proton-transport catalysis (PTC) initiated by the electrostatic interaction between water and N(9) protonated theophylline. Calculated anharmonic spectra have been simulated at the B3LYP/6-311+G(d,p) level of theory. It is shown that calculated anharmonic frequencies significantly outperform calculated harmonic frequencies in providing simulated IRMPD spectra in all cases.

Protonation sites and conformations of peptides of glycine (Gly(1-5)H(+)) by IRMPD spectroscopy.

The protonation sites and conformations of protonated glycine and its peptides (Gly(1-5)) have been investigated using infrared multiple photon dossociation (IRMPD) spectroscopy in combination with theoretical calculations. For small peptides, protonation is generally presumed to occur at the amine nitrogen of the N-terminus or a nitrogen of a basic side chain. However, for triglycine, the experimental and calculated results indicate that one of the main species is an isomer in which the proton is bound to an amide oxygen. The amide II vibrational mode is found to be very sensitive to the protonation site. When the protonation site is at the amine nitrogen, the amide II mode appears around 1540 cm(-1) for diglycine, tetraglycine, pentaglycine, and one of the main isomers of triglycine (GGGH02). When the proton is bound to an amide oxygen, the amide II mode is blue-shifted to 1590 cm(-1), as seen in GGGH01. IR spectra have been obtained to provide direct evidence that an amide oxygen may serve as the protonation site in a peptide. An analogous result is found for the tripeptide of alanine. In the progression from glycine to pentaglycine, the corresponding conformations of the most stable isomers vary from linear to cyclic structures. Both glycine and diglycine are linear structures, while the most stable isomers of the tetra- and pentapeptides are both cyclic structures. For triglycine, the linear and cyclic isomers are found to coexist. The carbonyl stretches also directly reflect the conformational changes. For the linear isomers of the di- and tripeptides of glycine, two well-separated bands are observed. The amide I modes appear slightly above 1700 cm(-1), but as a result of the fact that the C horizontal lineO bond in the carboxylic acid moiety is stronger than those of the amide carbonyls, the corresponding band appears near 1800 cm(-1). However, for the cyclic isomers of the tri-, tetra-, and pentapeptides, the carbonyl oxygen in the carboxylic acid group acts as a proton acceptor to form a very strong intramolecular hydrogen bond with the protonated amine terminus. This results in a weakening of the C horizontal lineO bond, such that the amide I modes are nearly identical in frequency to the carbonyl stretch of the carboxylic acid group.

Structures, energetics, and dynamics of gas phase ions studied by FTICR and HPMS.

Both Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and high-pressure mass spectrometry (HPMS) are very powerful tools in the field of gas phase ion chemistry. Many experimental method developments based on FTICR-MS and HPMS are summarized, including the coupling of a high-pressure external ion source to a FTICR mass spectrometer, blackbody infrared radiative dissociation (BIRD), coupling laser desorption ionization with HPMS, infrared multiple photon dissociation (IRMPD), radiative association and bimolecular routes to gas phase cluster ion formation. An abundance of thermochemical data, such as proton affinities, gas phase acidities, methyl cation affinities and metal cation affinities, have been obtained. Some of these data are the basis of the standard data listed in the NIST thermochemical databases. Ion-molecule interactions, energetics, reactivities, and structures of molecules have been extensively investigated using the methods developed based on HPMS and FTICR mass spectrometric techniques.

Investigations of strong hydrogen bonding in (ROH)n...FHF- (n = 1, 2 and R = H, CH3, C2H5) clusters via high-pressure mass spectrometry and quantum calculations.

An examination of strong hydrogen bonds found in (ROH)(n)...FHF(-) clusters (n = 1 and 2; R = H, CH(3), C(2)H(5)) is presented. Excellent agreement is observed between thermochemical values obtained from high-pressure mass spectrometric measurements and those predicted from MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations. Calculated structures are examined, and insight into the geometric nature of the bonding for these systems is obtained. In the case of water binding to FHF(-), it was found that the large entropic advantage of one particular structure, which was not the most enthalpically favored, was significant enough to make it the predominant species within the ion source. In the case of methanol solvation, no evidence of secondary interaction of the methyl group and any other moiety could be found. The structural details revealed from calculations of the ethanol-solvated clusters indicate that secondary interactions between the terminal methyl group and FHF(-) have an impact on the length of the FHF and OHF bonds.

Effects of isomerization on the measured thermochemical properties of deprotonated glycine/protic-solvent clusters.

The thermochemical properties associated with the formation of an isomeric distribution of ROHNH(2)CH(2)COO(-) clusters (R=H, CH(3), C(2)H(5)) are measured by using high-pressure mass spectrometry. A comparison of the measured properties with calculated values provides new insights into the thermochemical effects arising from the isomeric nature of this clustering system. When the distribution of isomers is correctly accounted for, the measured values of DeltaH degrees , DeltaS degrees , and DeltaG degrees (298) consistently agree, to a very high degree of accuracy, with those predicted by MP2(full)/6-311++G(d,p)//B3LYP/6-311++G(d,p) calculations.

An investigation of protonation sites and conformations of protonated amino acids by IRMPD spectroscopy.

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic-structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free-electron laser (FEL) and an electrospray-ion-trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6-311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the alpha-amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol(-1)) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side-chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the alpha-amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol(-1) higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760-1800 cm(-1) is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.

Investigation of cation-pi interactions in biological systems.

Noncovalent interactions, such as van der Waals interactions, hydrogen bonds, salt bridge and cation-Pi interactions play extremely important roles in biological systems and, in contrast to covalent bonds, many such noncovalent interactions are not well understood. In the present work a new protocol has been developed to measure the enhancement of binding energies due to cation-Pi interactions between aromatic amino acids and organic or metal ions. Investigation of the cation-Pi interactions will provide further insight into the structure and function of biological molecules.