The structures and properties of anionic tryptophan complexes.

The physicochemical properties of [Trpn-H]- and [TrpnCl]- (n = 1, 2) have been investigated in a combined computational and experimental infrared multiple dissociation (IRMPD) study. IRMPD spectra within the 850-1900 cm-1 region indicate that deprotonation is localized on the carboxylic acid moiety in [Trpn-H]- clusters. A combination of hydrogen bonding and higher order charge-quadrupole interactions appear to influence cluster geometries for all investigated systems. Calculated global minimum and low energy geometries of [TrpCl]- and [Trp2Cl]- clusters favour coordination of the halide by the indole NH. [Trp2-H]- and [Trp2Cl]- exhibit additional π-π interactions between the heterocyclic side chains.

Infrared-Driven Charge-Transfer in Transition Metal-Containing B12X122- (X = H, F) Clusters.

Density functional theory (DFT) calculations and infrared multiple photon dissociation (IRMPD) spectroscopy are employed to probe [TM·(B12H12)]- and [TM·(B12H12)2]2- clusters [TM = Ag(I), Cu(I), Co(II), Ni(II), Zn(II), Cd(II)]. A comparison is made between the charge-transfer properties of the clusters containing the hydrogenated dodecaborate dianions, B12H122-, and the fluorinated analogues, B12F122-, for clusters containing Cd(II), Co(II), Ni(II), and Zn(II). IRMPD of the [TM·(B12H12)]- and [TM·(B12H12)2]2- species yields B12H11- via hydride abstraction and B12H12- in all cases. To further explore the IR-induced charge-transfer properties of the B12X122- (X = H, F) cages, mixed-cage [TM(B12H12)(B12F12)]2- [TM = Co(II), Ni(II), Zn(II), Cd(II)] clusters were investigated. IRMPD of the mixed-cage species yielded appreciable amounts of B12F12- and B12H12- in most cases, indicating that charge-transfer to the central TM cation is a favorable process; formation of B12F12- is the dominant process for the Co(II) and Ni(II) mixed-cage complexes. In contrast, the Zn(II) and Cd(II) mixed-cage complexes preferentially produced fragments of the form B xH yF z-/2-, suggesting that H/F scrambling and/or fusion of the boron cages occurs along the IRMPD pathway.

Mode-Selective Laser Control of Palladium Catalyst Decomposition.

It is generally assumed that molecules behave ergodically during chemical reactions, that is, reactivities depend only on the total energy content and not on the initial state of the molecule. While there are a few examples of nonergodic behavior in small (usually electronically excited) species, to date there have been no reports of such behavior in larger covalently bound species composed of several tens of atoms. Here, we demonstrate vibrational mode-selective behavior in a series of palladium catalysts. When we excite solvent-tagged gas-phase Pd catalysts with an infrared laser that is tuned to be resonant with specific molecular vibrations, depending on which vibration we excite, we can select different reaction pathways. We also demonstrate that this behavior can be "turned off" via chemical substitution.

Interaction of B12F122- with All-cis 1,2,3,4,5,6 Hexafluorocyclohexane in the Gas Phase.

Clusters of all-cis 1,2,3,4,5,6-hexafluorocyclohexane and the dodecafluorododecaboron dianion, [C6F6H6]n[B12F12]2- (n = 0-4), are investigated in a combined experimental and computational study. DFT calculations and IRMPD spectra in the region of 800-2000 cm-1 indicate that C6H6F6 binds to open trigonal faces of B12F122- via a three-point interlocking binding motif. Calculated binding interactions reveal substantial contributions from C-H···F hydrogen bonding and binding energies that are among the strongest observed for a neutral-anion system.

Intramolecular cation-π interactions in protonated phenylalanine derivatives.

The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000-2000 cm-1 region show that protonation is localized on the amine group in all cases. Intramolecular cation-π interactions between the ammonium group and the phenyl ring heavily influence molecular geometries and properties such as gas phase basicity and proton affinity. By varying substituents on the phenyl ring, one can sensitively tune the cation-π interaction and, therefore, the molecular structure and properties. Variations in molecular structures and properties as a function of phenyl ring substitution are shown to correlate with substituent Hammett parameters.

Changes in Tricarbastannatrane Transannular N-Sn Bonding upon Complexation Reveal Lewis Base Donicities.

Hypercoordinated complexes involving tricarbastannatrane cation [N(CH2CH2CH2)3Sn]+ with various Lewis bases are investigated in the gas and solution phases using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, NMR spectroscopy, and density functional theory calculations. Coordination is found to occur at the apical position leading to a pentacoordinated Sn center. Strongly electron donating Lewis bases disrupt the N···Sn transannular interaction and induce higher degrees of geometric distortion at the metal center than weakly donating Lewis bases, an effect that manifests as anharmonic shifts in the vibrational spectra. Once characterized in the gas phase, [N(CH2CH2CH2)3Sn(Lewis base)]+ structures were embedded in a dichloroethane polarizable continuum model to investigate solution phase properties. Calculated 119Sn NMR chemical shifts were found to be in good agreement with those measured experimentally, thus suggesting that the bonding properties of [N(CH2CH2CH2)3Sn]+ are essentially the same in the gas and solution phases.

Janus Face Aspect of All-cis 1,2,3,4,5,6-Hexafluorocyclohexane Dictates Remarkable Anion and Cation Interactions In the Gas Phase.

Experiments have been carried out in which electrospray ionization has been used to generate ionic complexes of all-cis 1,2,3,4,5,6 hexafluorocyclohexane. These complexes were subsequently mass isolated in a quadrupole ion trap mass spectrometer and then irradiated by the tunable infrared output of a free electron laser in the 800-1600 cm(-1) range. From the frequency dependence of the fragmentation of the complexes, vibrational signatures of the complexes were obtained. Computational work carried out in parallel reveals that the complexes formed are very strongly bound and are among the most strongly bound complexes of Na(+) and Cl(-) ever observed with molecular species. The dipole moment calculated for the heaxafluorocyclohexane is very large (∼7 D), and it appears that the bonding in each of the complexes has a significant electrostatic contribution.

The structures and properties of proton- and alkali-bound cysteine dimers.

The proton-, lithium-, and sodium-bound cysteine dimers have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000-2000 cm(-1) region show that protonation is localized on an amine group, and that intermolecular hydrogen bonding occurs between the protonated amine and the carbonyl oxygen of the neutral Cys moiety. Alkali-bound dimers adopt structures reminiscent of those observed for the monomeric Cys·Li(+) and Cys·Na(+) species. Calculations of the heavier Cys2·M(+) (M = K, Rb or Cs) species suggest that these are significantly less strongly bound than the lighter (M = H, Li, or Na) dimers.

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.

Structures and Energetics of Protonated Clusters of Methylamine with Phenylalanine Analogs, Characterized by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations.

Gas-phase clusters of protonated methylamine and phenylalanine (Phe) derivatives have been studied using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. Experiments were performed on several Phe derivatives including 4-chloro-l-phenylalanine (4Chloro-Phe), 4-nitro-l-phenylalanine (4Nitro-Phe), 3-cyano-l-phenylalanine (3Cyano-Phe), and 3-trifluoromethyl-l-phenylalanine (3CF3-Phe). Through comparisons between experimental IRMPD spectra and stimulated spectra obtained by electronic structure calculations, charge-solvated structures were found to be prevalent in both 4Chloro-Phe and 4Nitro-Phe, whereas 3Cyano-Phe favored zwitterionic structures and 3-CF3-Phe likely have both zwitterionic and charge-solvated structures present.

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.

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.

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.

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.