Glycine in a basket: protonated complexes of 1,1,n,n-tetramethyl[n](2,11)teropyrenophane (n = 7, 8, 9) with glycine in the gas-phase.

Protonated complexes composed of a basket-like host molecule 1,1,n,n-tetramethyl[n](2,11)teropyrenophanes (TMnTP) (n = 7, 8, 9) and glycine as a guest were studied in the gas phase by experimental and computational methods. Blackbody infrared radiative dissociation (BIRD) experiments of [(TMnTP)(Gly)]H+ not only provided the observed Arrhenius parameters (activation energies, Eobsa, and frequency factors, A) but also suggested the existence of two populations of isomeric complexes of [(TMnTP)(Gly)]H+, termed fast dissociating (FD) and slow dissociating (SD), due to their relative BIRD rate constants. Master equation modeling was conducted to obtain the threshold dissociation energies E0 of the host-guest complexes. The relative stabilities of the most stable of the n = 7, 8, or 9 [(TMnTP)(Gly)]H+ complexes followed the trend SD-[(TM7TP)(Gly)]H+ > SD-[(TM8TP)(Gly)]H+ > SD-[(TM9TP)(Gly)]H+ by both BIRD and energy resolved sustained off-resonance irradiation collision-induced dissociation experiments (ER-SORI-CID). Computed structures and energies of [(TMnTP)(Gly)]H+ were obtained using B3LYP-D3/6-31+G(d,p) and for all TMnTP molecules, the lowest-energy structures were ones where protonated glycine was within the cavity of the TMnTP, despite the TMnTP molecules having a proton affinity 100 kJ mol-1 higher than glycine. An independent gradient model based on the Hirshfeld partition (IGMH) and natural energy decomposition analysis (NEDA) were applied to visualize and reveal the nature of interactions between hosts and guest. The NEDA analysis suggested that the polarization (POL) component which described interactions between induced multipoles contributed the most to the [(TMnTP)(Gly)]H+ (n = 7, 8, 9) complexes.

A vibrational spectroscopic and computational study of the structures of protonated imidacloprid and its fragmentation products in the gas phase.

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments in the 600-2000 cm-1 region and computational chemistry studies were combined with the aim of elucidating the structures of protonated imidacloprid (pIMI), and its unimolecular decomposition products. The computed IR spectra for the lowest energy structures for pIMI as well as for protonated desnitrosoimidacloprid, corresponding to the loss of NO radical (pIMI-NO), and protonated imidacloprid urea corresponding to the loss of N2O (pIMIU) were found to reproduce the experimental IRMPD spectrum quite well. The complex IRMPD spectrum for protonated desnitroimidaclpride (pDIMI), resulting from the loss of NO2 radical from pIMI, was explained as a contribution from several computed structures, including those involving simple loss of NO2 radical and some isomerization. However, based on a comparison of the computed IR spectrum for the lowest energy structure of pDIMI and the IRMPD spectrum, it was concluded that the lowest energy structure is a minor contributor to the experimental spectrum. This observation is rationalized as being due to the energy requirement for isomerization to the lowest energy structure, being substantially higher than that for simple loss of NO2 radical. Experimental mass spectrometry fragmentation results indicated that the loss of N, O2, H was the result of a loss of NO radical followed by loss of OH radical. A comparison of the experimental IRMPD and computed IR spectra revealed that following NO radical loss, the structure entailing a hydride shift from the methylene bridge to the guanidine moiety followed by OH radical elimination, generated the best match with the experimental IRMPD spectrum. This was consistent with the computed potential energy surfaces showing this structure as having the lowest energy requirement.

Top-down lignomics analysis of the French oak lignin by atmospheric pressure photoionization and electrospray ionization quadrupole time-of-flight tandem mass spectrometry: Identification of a novel series of lignans.

We report herein the top-down lignomic analysis of virgin released lignin (VRL) extracted from the French oak wood using atmospheric pressure photoionization quadrupole orthogonal time-of-flight mass spectrometry (APPI-QqTOF-MS) (+ ion mode). Eight major protonated lignin oligomers were identified using the APPI-QqTOF-MS/MS of this complex VRL mixture without any kind of purification. This series of protonated oligomer ions were identified as neolignan cedrusin (1), five different aryltetralin lignans dimers (2-6), one lignan-dehydroshikimic acid complex (7), and a lignan trimer (8). Similarly, electrospray ionization (ESI)-QqTOF-MS (+ ion mode) allowed us to identify three extra aryltetralin lignan derivatives (9-11). The Kendrick mass defect analysis was used for the simplification of this complex APPI-QqTOF-MS into a compositional map, which displayed clustering points of associated ions possessing analogous elemental composition. This series of novel protonated molecules were selected and subjected to low-energy collision-induced dissociation (CID)-MS/MS analyses. The obtained gas-phase fragmentation patterns helped to tentatively assign their most likely structures. Also, it was found that the use of different APPI and ESI ambient ionization techniques enhances the ionization of different types of lignin oligomers.

Top-down lignomics analysis of the French pine lignin by atmospheric pressure photoionization quadrupole time-of-flight tandem mass spectrometry: Identification of a novel series of lignin-carbohydrate complexes.

RATIONALE: We report the top-down lignomics analysis of the virgin released lignin (VRL) extracted from French pine wood by using atmospheric pressure photoionization quadrupole time-of-flight mass spectrometry (APPI-QqTOF-MS) and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS). METHODS: We used APPI-QqTOF-MS (positive ion mode) for the analysis of the complex mixture of VRL oligomers extracted from French pine wood. Some of the major precursor ions were fished out from the complex VRL oligomeric mixture and subjected to low-energy CID-MS/MS analyses. RESULTS: Fourteen novel lignin-carbohydrate complexes (LCCs) were identified using APPI-QqTOF-MS/MS of the very complex mixture of virgin released lignins (VRLs), directly extracted from French pine wood without any kind of purification. The low-energy CID-MS/MS analyses allowed us to establish the fragmentation patterns of the precursor ions and to identify the complex structures of the identified LCC molecules. These novel identified series of LCCs were composed of one or two carbohydrate rings to which one, two, or three lignin units were covalently attached. In addition to the fourteen LCCs, acetyl eugenol was identified in the French pine VRL sample. The identification of acetyl eugenol indicates possible lignin degradation and modification (acetylation) during the mild extraction method developed by the Compagnie Industrielle de la Matière Végétale (CIMV). CONCLUSIONS: The top-down lignomics analysis of the French pine VRLs using APPI-QqTOF-MS and low energy CID-MS/MS allowed us to identify acetylated eugenol and a novel series of fourteen LCCs. These series of LCCs provide evidence that lignins are covalently linked to carbohydrates in the native wood network and act as cross-linkers between cellulose and hemicellulose components of wood.

A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs.

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M+, where M+ = Li+, Na+, K+, Rb+, Cs+ as well as the protonated complex, (9eG:1mC)H+, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H+, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H+, forming much more (1mC)H+ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M+; M = Li+, Na+, K+, Rb+, Cs+ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li+, the lowest energy structure is one in which Li+ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na+, K+, and Rb+, similar binding of the metal cation to 1mC is calculated but, unlike Li+, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs+ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.

Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (negative ion mode) of French Oak lignin: A novel series of lignin and tricin derivatives attached to carbohydrate and shikimic acid moieties.

RATIONALE: We report the top-down lignomic analysis of the virgin released lignin (VRL) small oligomers obtained from French Oak wood. METHODS: We have used MALDI-TOF-MS in the negative ion mode for the analysis of the complex mixture of lignin oligomers extracted from French Oak wood. High-energy CID-TOF/TOF-MS/MS analyses were used to support the postulated precursor ion structures. RESULTS: Twenty compounds were identified using MALDI-TOF-MS/MS of the VRL extracted from French Oak wood: seven tricin derivatives and/or flavonoids, three syringylglycerol derivatives, two syringol derivatives, two flavonolignin derivatives, and six miscellaneous compounds: luteoferol, lariciresinol isomer, 5-hydroxy guaiacyl derivative, syringyl -C10 H10 O2 dimer, trihydroxy benzaldehyde derivative, and aryl tetralin lignan derivative. Most of the identified compounds were in the form of carbohydrate and/or shikimic acid complexes. CONCLUSIONS: The analysis of this complex mixture led to the identification of a series of lignin dimers, novel lignin-carbohydrate complexes (LCC), and unique tricin derivatives linked to different types of carbohydrates and shikimic acid moieties. This finding supports the presence of lignin-carbohydrate complexes in the isolated VRL. These analyses also showed that French Oak lignin is abundant in syringol moieties present in the lignin syringyl units or tricin derivatives. Moreover, the identification of some lignin-carbohydrate and/or flavonoid-shikimic acid complexes could provide new insight into the relationship between the biosynthesis of lignin and tricin.

Demystifying and unravelling the molecular structure of the biopolymer sporopollenin.

RATIONALE: We report the unsolved molecular structure of the complex biopolymer sporopollenin exine extracted from Lycopodium clavatum pollen grains. METHODS: TOF-SIMS and CID-MS/MS, MALDI-TOF-MS and CID-TOF/TOF-MS/MS were used for the analysis of this complex biopolymer sporopollenin exine extracted from Lycopodium clavatum pollen grains. Solid-state 1 H- and 13 C-NMR, 2D 1 H-1 H NOESY, Rotor-synchronized 13 C{1 H} HSQC, and 13 C{1 H} multi CP-MAS NMR experiments were used to confirm the structural assigments revealed by MS and MS/MS studies. Finally, high-resolution XPS was used to check for the presence of aromatic components in sporopollenin. RESULTS: The combined MS and NMR analyses showed that sporopollenin contained poly(hydroxy acid) dendrimer-like networks with glycerol as a core unit, which accounted for the sporopollenin empirical formula. In addition, these analyses showed that the hydroxy acid monomers forming this network contained a ß-diketone moiety. Moreover, MALDI-TOF-MS and MS/MS allowed us to identify a unique macrocyclic oligomeric unit composed of polyhydroxylated tetraketide-like monomers. Lastly, high-resolution X-ray photoelectron spectroscopy (HR-XPS) showed the absence of aromaticity in sporopollenin. CONCLUSIONS: We report for the first time the two main building units that form the Lycopodium clavatum sporopollenin exine. The first building unit is a macrocyclic oligomer and/or polymer composed of polyhydroxylated tetraketide-like monomeric units, which represents the main rigid backbone of the sporopollenin biopolymer. The second building unit is the poly(hydroxy acid) network in which the hydroxyl end groups can be covalently attached by ether links to the hydroxylated macrocyclic backbone to form the sporopollenin biopolymer, a spherical dendrimer. Such spherical dendrimers are a typical type of microcapsule that have been used for drug delivery applications. Finally, HR-XPS indicated the total absence of aromaticity in the sporopollenin exine.

An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase.

Infrared multiple photon dissociation (IRMPD) spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Computational chemistry has been used to determine the relative energies and compute the infrared spectra of these complexes. By comparing the IRMPD spectra with the computed spectra, in all cases, it was possible to deduce that what was observed experimentally were the lowest energy computed structures. The protonated complex between 9eG and 1-methylthymine (1mT) is protonated at N7 of 9eG-the most basic site of all three bases in this study-and bound in a Hoogsteen type structure with two hydrogen bonds. The experimental IRMPD spectrum for the protonated complex between 9eG and 9-methyladenine (9mA) is described as arising from a combination of the two lowest energy structures, both which are protonated at N1 of adenine and each containing two hydrogen bonds with 9eG being the acceptor of both. The protonated dimer of 9eG is protonated at N7 with an N7-H+-N7 ionic hydrogen bond. It also contains an interaction between a C-H of protonated guanine and the O6 carbonyl of neutral guanine which is manifested in a slight red shift of that carbonyl stretch. The protonated 9eG/9mA structures have been previously identified by X-ray crystallography in RNA and are contained within the protein database.

The K2(9-ethylguanine)122+ quadruplex is more stable to unimolecular dissociation than the K(9-ethylguanine)8+ quadruplex in the gas phase: a BIRD, energy resolved SORI-CID, IRMPD spectroscopic, and computational study.

A combination of experimental trapped-ion mass spectrometric studies and computational chemistry has been used in the present work to assess the intrinsic properties of the potassiated 9-ethylguanine (9eG) self-assembled quadruplex, K2(9eG)122+, in the gas phase. Infrared multiple photon dissociation (IRMPD) spectroscopy in the N-H/C-H stretching region (2700-3800 cm-1) revealed that this G-quadruplex is a sandwich-type structure with two G-tetrads sandwiching each of the two K+, very similar to the structure determined previously for the K(9eG)8+ complexes. The stability of K2(9eG)122+ toward unimolecular dissociation and its binding energy were examined using energy-resolved sustained off-resonance collision induced dissociation (SORI-CID) and blackbody infrared radiative dissociation (BIRD) kinetics experiments. SORI-CID experiments showed that the self-assembled K2(9eG)122+ complex undergoes charge separation forming K(9eG)8+ and K(9eG)4+ compared to K(9eG)8+ which loses neutral 9eG. More interestingly, K2(9eG)122+ is more stable toward unimolecular dissociation activated by SORI-CID than the K(9eG)8+ complex. Temperature dependent BIRD kinetics for K2(9eG)122+ were consistent with energy-resolved SORI-CID results showing K2(9eG)122+ to have an activation energy of 225 ± 15 kJ mol-1, approximately 50 kJ mol-1 greater than that determined for K(9eG)8+. The extra stability of K2(9eG)122+ is apparently not thermodynamic stability, but most likely due to an energy barrier for dissociation.

Hydrogen bonding in alkali metal cation-bound i-motif-like dimers of 1-methyl cytosine: an IRMPD spectroscopic and computational study.

The structures of alkali metal cation bound 1-methylcytosine (1-mCyt) dimers were explored using vibrational spectroscopy in the form of infrared multiple photon dissociation (IRMPD) spectroscopy and by computational methods. For the smaller alkali metal cations, Li+ and Na+, only non-hydrogen bonded symmetric anti-parallel structures were observed in agreement with the lowest energy computed structures. For K+, Rb+, and Cs+ the vibrational spectra in the N-H stretch region showed strong evidence for hydrogen bonding in agreement with the lowest energy structures which contained hydrogen bonding interactions between the amine group of one cytosine and the carbonyl oxygen of the other cytosine. The lowest energy structures for these complexes were compared to previously studied cytosine complexes [(Cyt)2M]+ where M = Li, Na, and K. The calculations are in agreement that only the non-hydrogen bonded structures would be observed for these cytosine complexes.

Top-down lignomic matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis of lignin oligomers extracted from date palm wood.

RATIONALE: We report for the first time the top-down lignomic analysis of the virgin released lignin (VRL) oligomers obtained from the Saudi date palm wood (SDPW), using a matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) instrument. In addition, we are proposing new collision-induced dissociation tandem mass spectrometry (CID-MS/MS) fragmentation routes for this series of unreported VRL oligomers. METHODS: We have used direct MALDI-TOF-MS analysis of the mixture of lignin oligomers without any chromatographic pre-separation. High-energy CID-MS/MS analyses were used to confirm the precursor ion structures. RESULTS: Six protonated lignin oligomer molecules were identified: [C19 H24 O8  + H]+ as H(8-O-4')G; [C50 H52 O19  + H]+ as H(8-O-4')H(8-O-4'')S(8-O-4''')S(8-O-4'''')G; [C58 H54 O18 + H]+ as H(8-O-4')H(8-O-4'')H(8-O-4''')G(8-O-4'''')S(8-O-4''''')G; [C58 H54 O19  + H]+ as H(8-O-4')H(8-O-4'')H(8-O-4''')S(8-O-4'''')S(8-O-4''''')G; [C61 H68 O25  + H]+ as H(8-O-4')G(8-O-4'')G(8-O-4''')S(8-O-4'''')S(8-O-4''''')G; and [C61 H68 O26  + H]+ as C(8-O-4')G(8-O-4'')G(8-O-4''')S(8-O-4'''')S(8-O-4''''')G units (H = coniferyl, S = sinapyl, and G = p-coumaryl). Two distonic cations were identified as [C39 H43 O15  + H]+• and [C40 H43 O16  + H]+• deriving from two tetrameric lignin oligomers. The high-energy MS/MS analyses allowed the confirmation of the proposed structures of this series of lignin oligomers. CONCLUSIONS: To our knowledge, this is the first elucidation of the lignin structure of the Saudi seedling date palm wood that was accomplished using a top-down lignomic strategy that has not previously been published. The complex high-energy CID-MS/MS fragmentations presented herein are novel and have never been described before.

Strong intramolecular hydrogen bonding in protonated ß-methylaminoalanine: A vibrational spectroscopic and computational study.

The gas-phase structure of protonated ß-methylaminoalanine was investigated using infrared multiple photon dissociation spectroscopy in the C-H, N-H, O-H stretching region (2700-3800 cm-1) and the fingerprint region (1000-1900 cm-1). Calculations using density functional theory methods show that the lowest energy structures prefer protonation of the secondary amine. Formation of hydrogen bonds between the primary and secondary amine, and the secondary amine and carboxylic oxygen further stabilize the lowest energy structure. The infrared spectrum of the lowest energy structure originating with harmonic density functional theory has features that generally match the positions of the experimental spectra; however, the overall agreement with the experimental spectrum is poor. Molecular dynamics calculations were used to generate a gas-phase infrared spectrum. With these calculations a reasonable match with the experimental spectrum, especially in the high-energy region, was obtained. The results of the molecular dynamics simulation support the density functional theory calculations, with protonation of the secondary amine and the formation of a hydrogen bond between the protonated secondary amine and the primary amine. This work shows the importance of accounting for anharmonic effects in systems with very strong intramolecular hydrogen bonding.

Endo or Exo? Structures of Gas-Phase Alkali Metal Cation/Aromatic Half-Belt Complexes.

1,1,9,9-Tetramethyl[9](2,11)teropyrenophane (TM9TP), a belt-shaped molecule, has a sizable cavity that molecules or ions could occupy. In this study, the question of whether TM9TP forms gas-phase ion-molecule complexes with metal cations (K+ , Rb+ , Cs+ ) situated inside or outside the TM9TP cavity was addressed using both experimental and computational methods. Complexes were trapped in a Fourier transform ion cyclotron resonance mass spectrometer and their structures were explored by some novel physical chemistry/mass spectrometry methods. Blackbody infrared radiative dissociation kinetics reveal two populations of ions, a fast dissociating fraction and a persistent fraction. Infrared multiphoton dissociation spectra (vibrational spectra) provide very strong evidence that the most abundant population is a complex where the metal cation is inside the TM9TP cavity, endo-TM9TP. Red-shifted C-H stretching bands present in the gas-phase vibrational spectra of these ionic complexes show that there is an interaction between the metal cation and bridge C-H bonds due to the cation sitting inside the cavity of TM9TP. B3LYP/6-31+G(d,p) calculations showed the endo complexes to be the lowest in energy; about 60 kJ mol-1 more thermodynamically stable and more than 120 kJ mol-1 kinetically more stable than the exo complex.

Structural investigation by tandem mass spectrometry analysis of a heterogeneous mixture of Lipid An isolated from the lipopolysaccharide of Aeromonas hydrophila SJ-55Ra.

RATIONALE: We report herein the electrospray ionization mass spectrometry (ESI-MS) negative ion mode and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) analysis of a mixture of lipid An isolated from the lipopolysaccharide (LPS) of a rough-resistant wild strain of the Gram-negative bacteria Aeromonas hydrophila grown in the presence of phages (SJ-55Ra). This investigation indicates that the presence of a mixture of lipid A acylated disaccharides, whose molecular structures were not relatively conserved, resulted from the incomplete LPS biosynthesis caused by the phage treatment. METHODS: The heterogeneous lipid An mixture from the LPS-SJ55Ra was obtained following growth of the Gram-negative bacteria Aeromonas hydrophila (SJ-55R) in the presence of phages and isolation by the aqueous phenol method. Following hydrolysis and purification of the lipopolysaccharide, ESI-MS and low-energy CID-MS/MS analyses were performed on a triple-quadrupole (QqQ) and a Fourier transform ion cyclotron resonance (FTICR) instrument. RESULTS: ESI-MS analysis suggested that this lipid An mixture contained eight molecular disaccharide anions and three monosaccharide anions. This series of lipid An was asymmetrically substituted with ((R)-14:0(3-OH)) fatty acids located at O-3 and N-2 and with branched fatty acids: (Cl4:0(3-(R)-O-C14:0)) and (C12:0(3-(R)-O-(14:0)) at the O-3' and N-2' positions. CONCLUSIONS: Tandem mass spectrometric analyses allowed the exact determination of the fatty acid acylation locations on the D-GlcpN disaccharide. The MS/MS results established that it was possible to selectively cleave C-O, C-N, and C-C bonds, together with glycosidic C-O and cross-ring cleavages, affording excellent structural analysis of lipid A biomolecules.

Self-assembled uracil complexes containing tautomeric uracils: an IRMPD spectroscopic and computation study of the structures of gaseous uracilnCa2+ (n = 4, 5, or 6) complexes.

The structures of doubly-charged uracil (U) complexes with Ca2+, UnCa2+ (n = 4, 5, 6), were studied by infrared multiple photon dissociation (IRMPD) spectroscopy and computational methods. The ions were produced by electrospray ionization (ESI) and were isolated in the gas phase in a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). The recorded IRMPD spectra in both the fingerprint and the C-H/N-H/O-H stretching regions, combined with computed vibrational spectra, reveal that the structures present in the greatest abundance consist of both canonical uracil as well as the lactam (or colloquially "enol") tautomer of uracil. U4Ca2+ consists of two hydrogen-bonded dimers of uracil, one canonical and one tautomer, with each uracil interacting with Ca2+ through a carbonyl oxygen. The structures most consistent with the vibrational spectrum of U6Ca2+ consist of two hydrogen-bonded uracil trimers, each composed of two canonical and one enolic uracil, with each uracil also interacting with Ca2+ through carbonyl oxygen. U5Ca2+ consists of one of the aforementioned trimers and dimers, each containing one enol tautomerized uracil. The computed structures whose vibrational spectra best agree with the experimental vibrational spectra are also the lowest-energy structures for all three complexes. This study clearly shows that some uracils adopt the normally very high energy enol tautomer in the lowest energy gas phase complexes of uracil with a doubly-charged ion like Ca2+.

Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH3)]+ by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd).

The structures of deprotonated d-block metal dication bound uracil dimers, solvated by a single ammonia molecule, were explored in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance-mass spectrometer. The IRMPD spectra were then compared with computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31+G(d,p) basis set for all atoms, with the exception of Cd, for which the LANL2DZ basis set with relativistic core potentials was used. The calculations were then repeated using the def2-TZVPP basis set on all atoms and were compared to the first set of calculations. The lowest-energy structures are those in which one uracil is deprotonated at the N3 position and, aside from the Cu complex, the intact uracil is a tautomer in which the N3 hydrogen is at the O4 carbonyl oxygen. The metal displays a tetradentate interaction to the uracil moieties, with the exception of Cu, which is tridentate, and the ammonia molecule is bound directly to the metal center. In the Cu complex, a square planar geometry is observed about the metal center, consistent with Jahn-Teller distortions commonly observed in Cu(II) complexes, and the intact uracil assumes its canonical tautomer. All other metal cation complexes are five-coordinate, square pyramidal complexes, with the intact uracil adopting a tautomer in which the N3 hydrogen is on O4. The IRMPD spectroscopic data are consistent with the computed infrared spectra for the lowest-energy structures in all cases.

Distinguishing Isomeric Peptides: The Unimolecular Reactivity and Structures of (LeuPro)M+ and (ProLeu)M+ (M = Alkali Metal).

The unimolecular chemistries and structures of gas-phase (ProLeu)M+ and (LeuPro)M+ complexes when M = Li, Na, Rb, and Cs have been explored using a combination of SORI-CID, IRMPD spectroscopy, and computational methods. CID of both (LeuPro)M+ and (ProLeu)M+ showed identical fragmentation pathways and could not be differentiated. Two of the fragmentation routes of both peptides produced ions at the same nominal mass as (Pro)M+ and (Leu)M+, respectively. For the litiated peptides, experiments revealed identical IRMPD spectra for each of the m/z 122 and 138 ions coming from both peptides. Comparison with computed IR spectra identified them as the (Pro)Li+ and (Leu)Li+, and it is concluded that both zwitterionic and canonical forms of (Pro)Li+ exist in the ion population from CID of both (ProLeu)Li+ and (LeuPro)Li+. The two isomeric peptide complexes could be distinguished using IRMPD spectroscopy in both the fingerprint and the CH/NH/OH regions. The computed IR spectra for the lowest energy structures of each charge solvated complexes are consistent with the IRMPD spectra in both regions for all metal cation complexes. Through comparison between the experimental spectra, it was determined that in lithiated and sodiated ProLeu, metal cation is bound to both carbonyl oxygens and the amine nitrogen. In contrast, the larger metal cations are bound to the two carbonyls, while the amine nitrogen is hydrogen bonded to the amide hydrogen. In the lithiated and sodiated LeuPro complexes, the metal cation is bound to the amide carbonyl and the amine nitrogen while the amine nitrogen is hydrogen bonded to the carboxylic acid carbonyl. However, there is no hydrogen bond in the rubidiated and cesiated complexes; the metal cation is bound to both carbonyl oxygens and the amine nitrogen. Details of the position of the carboxylic acid C═O stretch were especially informative in the spectroscopic confirmation of the lowest energy computed structures.

Structures, Unimolecular Fragmentations, and Reactivities of the Self-Assembled Multimetallic/Peptide Complexes [Mnn (GlyGly-H)2n-1 ](+) and [Mnn+1 (GlyGly-H)2n ](2.).

Complexes of Mn(2+) with deprotonated GlyGly are investigated by sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiple-photon dissociation spectroscopy, ion-molecule reactions, and computational methods. Singly [Mnn (GlyGly-H)2n-1 ](+) and doubly [Mnn+1 (GlyGly-H)2n ](2+) charged clusters are formed from aqueous solutions of MnCl2 and GlyGly by electrospray ionization. The most intense ion produced was the singly charged [M2 (GlyGly-H)3 ](+) cluster. Singly charged clusters show extensive fragmentations of small neutral molecules such as water and carbon dioxide as well as dissociation pathways related to the loss of NH2 CHCO and GlyGly. For the doubly charged clusters, however, loss of GlyGly is observed as the main dissociation pathway. Structure elucidation of [Mn3 (GlyGly-H)4 ](2+) clusters has also been done by IRMPD spectroscopy as well as DFT calculations. It is shown that the lowest energy structure of the [Mn3 (GlyGly-H)4 ](2+) cluster is deprotonated at all carboxylic acid groups and metal ions are coordinated with carbonyl oxygen atoms, and that all amine nitrogen atoms are hydrogen bonded to the amide hydrogen. A comparison of the calculated high-spin (sextet) and low-spin (quartet) state structures of [Mn3 (GlyGly-H)4 ](2+) is provided. IRMPD spectroscopic results are in agreement with the lowest energy high-spin structure computed. Also, the gas-phase reactivity of these complexes towards neutral CO and water was investigated. The parent complexes did not add any water or CO, presumably due to saturation at the metal cation. However, once some of the ligand was removed via CO2 laser IRMPD, water was seen to add to the complex. These results are consistent with high-spin Mn(2+) complexes.

Structures of [M(Ura-H)(H2 O)n ](+) (M = Mg, Ca, Sr, Ba; n = 1-3) complexes in the gas phase by IRMPD spectroscopy and theoretical studies.

The structures of singly and doubly (and for Mg, triply) hydrated group 2 metal dications bound to deprotonated uracil were explored in the gas phase using infrared multiple photon dissociation spectroscopy in the mid-infrared region (1000-1900 cm(-1) ) and the O-H/N-H stretching region (2700-3800 cm(-1) ) in a Fourier transform ion cyclotron resonance mass spectrometer. The infrared multiple photon dissociation spectra were then compared with the computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31 + G(d,p) basis set for all atoms except Ba(2+) and Sr(2+) , for which the LANL2DZ or the def2-TZVPP basis sets with relativistic core potentials were used. Atoms-in-molecules analysis was conducted for all lowest energy structures. The lowest energy isomers in all cases are those in which the one uracil is deprotonated at the N3 position, and the metal is coordinated to the N3 and O4 of uracil. Regardless of the degree of solvation, all water molecules are bound to the metal ion and participate in a hydrogen bond with a carbonyl of the uracil moiety.

Tandem mass spectrometry determination of the putative structure of a heterogeneous mixture of Lipid As isolated from the lipopolysaccharide of the Gram-negative bacteria Aeromonas liquefaciens SJ-19a.

RATIONALE: We report herein the electrospray ionization mass spectrometry (ESI-MS) and low-energy collision-induced dissociation tandem mass spectrometry analysis (CID-MS/MS) of a mixture of lipid As isolated from the rough lipopolysaccharide (LPS) of the mutant wild strain of the Gram-negative bacteria Aeromonas liquefaciens (SJ-19a, resistant) grown in the presence of phages. The interaction between the phages and the Gram-negative bacteria regulates host specificity and the heterogeneity of the lipid A component of the LPS. METHODS: The heterogeneous mixture of lipid As was isolated by the aqueous phenol method from the LPS of the rough wild strain of Gram-negative bacteria Aeromonas liquefaciens (SJ-19a). Hydrolysis of the LPS was with 1% acetic acid, and purification was by chromatography using Sephadex G-50 and Sephadex G-15. ESI-MS and low-energy CID-MS/MS analyses were performed with a triple-quadrupole (QqQ) and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. RESULTS: Preliminary analysis of the lipid As mixture was conducted by ESI-MS in the negative ion mode and the spectrum obtained suggested that the lipid A SJ-19a was composed of a heterogeneous mixture of different lipid A molecules. CID-MS/MS experiments confirmed the identities of the various mono-phosphorylated ß-D-GlcpN-(1→6)-α-D-GlcpN disaccharide entities. This lipid As mixture was asymmetrically substituted with fatty acids such as ((R)-14:0(3-OH)), (14:0(3-(R)-(O-12:0)) and (14:0(3-(R)-O-(14:0)) located on the O-3, O-3', N-2 and N-2' positions, respectively. CONCLUSIONS: Low-energy collision-induced dissociation tandem mass spectrometry in-space (QqQ-MS/MS) and in-time (FTICR-MS/MS) allowed the exact determination of the fatty acid acylation positions on the H2 PO3 →4-O'-ß-D-GlcpN-(1→6)-α-D-GlcpN disaccharide backbones of this heterogeneous mixture of lipid As , composed inter alia of seven different substituted lipid As , formed from the incomplete biosynthesis of their respective LPS.