Fragmentation reactions of protonated peptides containing glutamine or glutamic acid

A variety of protonated dipeptides and tripeptides containing glutamic acid or glutamine were prepared by electrospray ionization or by fast atom bombardment ionization and their fragmentation pathways elucidated using metastable ion studies, energy-resolved mass spectrometry and triple-stage mass spectrometry (MS(3)) experiments. Additional mechanistic information was obtained by exchanging the labile hydrogens for deuterium. Protonated H-Gln-Gly-OH fragments by loss of NH(3) and loss of H(2)O in metastable ion fragmentation; under collision-induced dissociation (CID) conditions loss of H-Gly-OH + CO from the [MH - NH(3)](+) ion forms the base peak C(4)H(6)NO(+) (m/z 84). Protonated dipeptides with an alpha-linkage, H-Glu-Xxx-OH, are characterized by elimination of H(2)O and by elimination of H-Xxx-OH plus CO to form the glutamic acid immonium ion of m/z 102. By contrast, protonated dipeptides with a gamma-linkage, H-Glu(Xxx-OH)-OH, do not show elimination of H(2)O or formation of m/z 102 but rather show elimination of NH(3), particularly in metastable ion fragmentation, and elimination of H-Xxx-OH to form m/z 130. Both the alpha- and gamma-dipeptides show formation of [H-Xxx-OH]H(+), with this reaction channel increasing in importance as the proton affinity (PA) of H-Xxx-OH increases. The characteristic loss of H(2)O and formation of m/z 102 are observed for the protonated alpha-tripeptide H-Glu-Gly-Phe-OH whereas the protonated gamma-tripeptide H-Glu(Gly-Gly-OH)-OH shows loss of NH(3) and formation of m/z 130 as observed for dipeptides with the gamma-linkage. Both tripeptides show abundant formation of the y(2)' ion under CID conditions, presumably because a stable anhydride neutral structure can be formed. Under metastable ion conditions protonated dipeptides of structure H-Xxx-Glu-OH show abundant elimination of H(2)O whereas those of structure H-Xxx-Gln-OH show abundant elimination of NH(3). The importance of these reaction channels is much reduced under CID conditions, the major fragmentation mode being cleavage of the amide bond to form either the a(1) ion or the y(1)' ion. Particularly when Xxx = Gly, under CID conditions the initial loss of NH(3) from the glutamine containing dipeptide is followed by elimination of a second NH(3) while the initial loss of H(2)O from the glutamic acid dipeptide is followed by elimination of NH(3). Isotopic labelling shows that predominantly labile hydrogens are lost in both steps. Although both [H-Gly-Glu-Gly-OH]H(+) and [H-Gly-Gln-Gly-OH]H(+) fragment mainly to form b(2) and a(2) ions, the latter also shows elimination of NH(3) plus a glycine residue and formation of protonated glycinamide. Isotopic labelling shows extensive mixing of labile and carbon-bonded hydrogens in the formation of protonated glycinamide.     

Characteristic negative ion fragmentations of deprotonated peptides containing post-translational modifications: mono-phosphorylated Ser, Thr and Tyr. A joint experimental and theoretical study

Peptides and proteins may contain post-translationally modified phosphorylated amino acid residues, in particular phosphorylated serine (pSer), threonine (pThr) and tyrosine (pTyr). Following earlier work by Lehmann et al., the [M-H]- anions of peptides containing pSer and pThr functionality show loss of the elements of H3PO4. This process, illustrated for Ser (and using a model system), is CH3CONH-C(CH2OPO3H2)CONHCH(3) --> [CH3CONHC(==CH2)CONHCH3 (-OPO3H2)] (a) --> [CH3CONHC(==CH2)CONHCH3-H]- + H3PO4, a process endothermic by 83 kJ mol(-1) at the MP2/6-31++G(d,p)//HF/6-31++G(d,p) level of theory. In addition, intermediate (a) may decompose to yield CH3CONHC(==CH2)CONHCH3 + H2PO4 - in a process exothermic by 3 kJ mol(-1). The barrier to the transition state for these two processes is 49 kJ mol(-1). Characteristic cleavages of pSer and pThr are more energetically favourable than the negative ion backbone cleavages of peptides described previously. In contrast, loss of HPO3 from [M-H]- is characteristic of pTyr. The cleavage [NH2CH(CH2-C6H4-OPO3H-)CO2H] --> [NH2C(CH2-C6H4-O-)CO2H (HPO3)] (b) --> NH2CH(CH2-C6H4-O-)CO2H + HPO3 is endothermic by 318 kJ mol(-1) at the HF/6-31+G(d)//AM1 level of theory. In addition, intermediate (b) also yields NH2CH(CH2-C6H4-OH)CO2H + PO3 - (reaction endothermic by 137 kJ mol(-1)). The two negative ion cleavages of pTyr have a barrier to the transition state of 198 kJ mol(-1) (at the HF/6-31+G(d)//AM1 level of theory) comparable with those already reported for negative ion backbone cleavages.     

Metal aminocarboxylate coordination polymers with chain and layered structures

The synthesis and structures of metal aminocarboxylates prepared in acidic, neutral, or alkaline media have been explored with the purpose of isolating coordination polymers with linear chain and two-dimensional layered structures. Metal glycinates of the formulae [CoCl2(H2O)2(CO2CH2NH3)] (I), [MnCl2(CO2CH2NH3)2] (II), and [Cd3Cl6(CO2CH2NH3)4] (III) with one-dimensional chain structures have been obtained by the reaction of the metal salts with glycine in an acidic medium under hydro/solvothermal conditions. These chain compounds contain glycine in the zwitterionic form. 4-Aminobutyric acid transforms to a cyclic amide under such reaction conditions, and the amide forms a chain compound of the formula [CdBr2(C4H7NO)2] (IV). Glycine in the zwitterionic form also forms a two-dimensional layered compound of the formula [Mn(H2O)2(CO2CH2NH3)2]Br2 (V). 6-Aminocaproic acid under alkaline conditions forms layered compounds with metals at room temperature, the metal being coordinated both by the amino nitrogen and the carboxyl oxygen atoms. Of the two layered compounds [Cd{CO2(CH2)5NH2}2]2 H2O (VI) and [Cu{CO2(CH2)5NH2}2]2 H2O (VII), the latter has voids in which water molecules reside.     

Simple <Emphasis Type="Italic">b</Emphasis> ions have cyclic oxazolone structures. A neutralization-reionization mass spectrometric and computational study of oxazolone radicals

The 2-methyloxazol-5-on-2-yl radical (3) and its deuterium labeled analogs were generated in the gas-phase by femtosecond electron-transfer and studied by neutralization-reionization mass spectrometry and quantum chemical calculations. Radical 3 undergoes fast dissociation by ring opening and elimination of CO and CH(3)CO. Loss of hydrogen is less abundant and involves hydrogen atoms from both the ring and side-chain positions. The experimental results are corroborated by the analysis of the potential energy surface of the ground electronic state in 3 using density functional, perturbational, and coupled-cluster theories up to CCSD(T) and extrapolated to the 6-311 ++ G(3df,2p) basis set. RRKM calculations of radical dissociations gave branching ratios for loss of CO and H that were k(CO)/k(H) > 10 over an 80-300 kJ mol(-1) range of internal energies. The driving force for the dissociations of 3 is provided by large Franck-Condon effects on vertical neutralization and possibly from involvement of excited electronic states. Calculations also provided the adiabatic ionization energy of 3, IE(adiab) = 5.48 eV and vertical recombination energy of cation 3(+), RE(vert) = 4.70 eV. The present results strongly indicate that oxazolone structures can explain fragmentations of b-type peptide ions upon electron capture, contrary to previous speculations.     

Intramolecular condensation reactions in protonated dipeptides: Carbon monoxide,water, and ammonia losses in competition

The elimination of carbon monoxide and water from a series of protonated dipeptides, [XxxYyy + H](+), is investigated by tandem mass spectrometry experiments and density functional theory. The combined results show that CO loss occurs on the a(1)-y(1) pathway, which begins by rearrangement of the added proton to the amide N-atom and creates the proton-bound dimer of an amino acid (Yyy) and an imine (that from Xxx residue). The loss of H(2)O is initiated from a tautomer in which the added proton has migrated to the hydroxyl group of the C-terminus, thereby promoting the formation of an ion with protonated oxazolone structure (a nominal b(2) ion). The highest yields of [XxxYyy + H - CO](+) and [XxxYyy + H - H(2)O](+) are observed at threshold energies. As the internal energy of the protonated dipeptides increases, these primary products are depleted by consecutive dissociations yielding mostly backbone fragments. Specifically, [XxxYyy + H - CO](+) decomposes to y(1) (protonated Yyy) and a(1) (immonium ion of Xxx residue), while [XxxYyy + H - H(2)O](+) produces a(2) and the immonium ions of residues Xxx (a(1)) and Yyy ("internal" immonium ion). Water loss takes place more efficiently when the more basic residue is at the C-terminal position. Increasing the basicity of the N-terminal residue enhances the extent of CO versus H(2)O loss and introduces the competitive elimination of NH(3). The dissociations leading to eliminations of small neutrals (CO, H(2)O, etc.) generally proceed over transition states that lie higher in energy than the corresponding dissociation products. The excess energy is disposed of either in translational or rovibrational modes of the products, depending on the stability of the incipient noncovalent assemblies emerging during the cleavage of the small neutrals.     

Fragmentation characteristics of b(n) (n=2-15) ions from protonated peptides

The fragmentation reactions of protonated oligoalanines (trialanine, tetraalanine and pentaalanine) and the fragments present in the electrospray ionization (ESI) mass spectrum of polyalanine have been studied by collisionally activated dissociation (CAD) mass spectrometry (MS(2) and MS(3) experiments). The MS(n) experiments provided strong evidence that the m/z 71n+1 ion series in the ESI mass spectrum of polyalanine is a b(n) series. These ions are formed via the b(n) -y(m) pathway of amide bond cleavage, which results in the formation of a proton-bound complex of an oxazolone and a peptide/amino acid. Also, the MS(2) spectra of the b(n) series from polyalanine revealed that the chain length of b(n) ions influences significantly the dissociations taking place. For example, b(n) ions start losing H(2)O at n ≥5 and the losses of CO and CO+NH(3) decrease in intensity from b(2) to b(15). The elimination of H(2)O+NH(3) and the elimination of 61 mass (HN=C=O+H(2)O) commence with b(6); their abundances initially increase up to ~ b(8)-b(9) and then gradually decrease until b(15) (largest fragment studied). The tandem mass spectrometry experiments help to elucidate the dissociation mechanisms of the observed structures of biopolymer fragments.     

Theoretical calculation of the dehydrogenation of ethanol on a Rh/CeO2(111) surface

We applied periodic density-functional theory (DFT) to investigate the dehydrogenation of ethanol on a Rh/CeO2 (111) surface. Ethanol is calculated to have the greatest energy of adsorption when the oxygen atom of the molecule is adsorbed onto a Ce atom in the surface, relative to other surface atoms (Rh or O). Before forming a six-membered ring of an oxametallacyclic compound (Rh-CH2CH2O-Ce(a)), two hydrogen atoms from ethanol are first eliminated; the barriers for dissociation of the O-H and the beta-carbon (CH2-H) hydrogens are calculated to be 12.00 and 28.57 kcal/mol, respectively. The dehydrogenated H atom has the greatest adsorption energy (E(ads) = 101.59 kcal/mol) when it is adsorbed onto an oxygen atom of the surface. The dehydrogenation continues with the loss of two hydrogens from the alpha-carbon, forming an intermediate species Rh-CH2CO-Ce(a), for which the successive barriers are 34.26 and 40.84 kcal/mol. Scission of the C-C bond occurs at this stage with a dissociation barrier Ea = 49.54 kcal/mol, to form Rh-CH(2(a)) + 4H(a) + CO(g). At high temperatures, these adsorbates desorb to yield the final products CH(4(g)), H(2(g)), and CO(g).     

Molybdenum amido complexes with single Mo-N bonds: synthesis,structure, and reactivity

Reactions of the complex [MoCl(eta(3)-C(3)H(4)-Me-2)(CO)(2)(phen)] (1) (phen=1,10-phenanthroline) with potassium arylamides were used to synthesize the amido complexes [Mo(N(R)Ar)(eta(3)-C(3)H(4)-Me-2)(CO)(2)(phen)] (R=H, Ar=Ph, 2 a; R=H, Ar=p-tolyl, 2 b; R=Me, Ar=Ph; 2 c). For 2 b the Mo-N(amido) bond length (2.105(4) A) is consistent with it being a single bond, with which the metal attains an 18-electron configuration. The reaction of 2 b with HOTf affords the amino complex [Mo(eta(3)-C(3)H(4)-Me-2)(NH(2)(p-tol))(CO)(2)(phen)]OTf (3-OTf). Treatment of 3-OTf with nBuLi or KN(SiMe(3))(2) regenerates 2 b. The new amido complexes react with CS(2), arylisothiocyanates and maleic anhydride. A single product corresponding to the formal insertion of the electrophile into the Mo-N(amido) bond is obtained in each case. For maleic anhydride, ring opening accompanied the formation of the insertion product. The reaction of 2 b with maleimide affords [Mo(eta(3)-C(3)H(4)-Me-2)[NC(O)CH=CHC(O)](CO)(2)(phen)] (7), which results from simple acid-base metathesis. The reaction of 2 b with (p-tol)NCO affords [[Mo(eta(3)-C(3)H(4)-Me-2)(CO)(2)(phen)](2)(eta(2)-MoO(4))] (8), which corresponds to oxidation of one third of the metal atoms to Mo(VI). Complex 8 was also obtained in the reactions of 2 b with CO(2) or the lactide 3,6-dimethyl-1,4-dioxane-2,5-dione. The structures of the compounds 2 b, 3-OTf, [Mo(eta(3)-C(3)H(4)-Me-2)[SC(S)(N(H)Ph)](CO)(2)(phen)] (4), [Mo(eta(3)-C(3)H(4)-Me-2)[SC(N(p-tol))(NH(p-tol))](CO)(2)(phen)] (5 a), and [Mo(eta(3)-C(3)H(4)-Me-2)[OC(O)CH=CHC(O)(NH(p-tol))](CO)(2)(phen)] (6), 7, and 8 (both the free complex and its N,N'-di(p-tolyl)urea adduct) were determined by X-ray diffraction.     

Ammonium, alkylammonium, and amino acid complexes of a hexacopper fluoro-metallacrown cavitand

Reaction of CuF2 with one equivalent of 3{5}-(pyrid-2-yl)-5{3}-(tertbutyl)pyrazole (HL) and excess NH4OH in MeOH affords crystalline [NH4{Cu(micro-F)(microL)}6(CH2Cl2)2]HF2 in moderate yield. This compound contains the 12-MC-6 metallacrown [{Cu(micro-F)(micro-L)}6] (1) with a NH4 + ion at its center, and CH2Cl2 molecules complexed in bowl-shaped cavities above and below the Cu6F6 ring. Similar reactions using the bases MeNH2, glycine, l-alanine or beta-alanine afforded solvated crystals of [1(H3NMe)2]Cl2, [1(gly)2], [1(l-ala)2], and [1(beta-ala)2], respectively. The metallacrown 1 in these products contains methylammonium and zwitterionic amino-acid guests in its two bowl-shaped cavities; each of the amino acids hydrogen-bonds to three F atoms. A related reaction using 1,6-diaminohexane resulted in fixation of CO2 from the air to give solvated [1(H3NC6H12NHCO2)2], again with a zwitterionic guest. NMR, ESI-MS and UV/vis measurements suggest that the metallacrown 1 retains its integrity in several organic solvents, although it is unclear to what extent guest binding takes place in solution.     

Investigation of the neutral loss of a full amino acid mass during collision-induced dissociation of the b(3)+ ion derived from a model peptide containing a 4-aminobutyric acid residue

In a previous study we found that a dominant fragmentation pathway observed for collision-induced dissociation (CID) of b(3)+ derived from peptides with sequence AXAG, where X is gamma-aminobutyric acid (gammaAbu) or epsilon-aminocaproic acid (Cap), involved the loss of 89 mass units (u). A neutral loss of 89 u corresponded to the free acid mass of an alanine (A) residue. This specific pathway was studied in greater detail here using a series of A(gammaAbu)AG peptides with strategic positioning of (15)N, (13)C and (2)H isotope labels. Based on the extensive labeling, several possible routes to the net elimination of 89 u are proposed. One is based on initial elimination of either aziridinone or imine and CO, followed by opening of an oxazolinone, tautomerization and elimination of H2O. Another involves formation of an aziridinone by cleavage of the N-terminal amide bond, and transfer of O and H atoms to this fragment via an H-bonded ion-molecule complex to complete the loss of 89 u. Both types of pathway include the transfer/migration of H atoms from the alpha-carbon position of gammaAbu or A residues.     

Gas-phase electrophilic addition promoted by CH(3)S(+)=CH(2) ions on aromatic systems

The gas-phase methylenation reaction between CH(3)S(+)=CH(2) and alkylbenzenes, aniline, phenol and alkyl phenyl ethers, which yields [M + CH](+) and CH(3)SH, has been studied by Fourier transform ion cyclotron resonance (FT-ICR) techniques and computational chemistry at the DFT level. The methylthiomethyl cation is less reactive than methoxymethyl and, unlike the latter, is unreactive toward benzene. The calculations suggest that reaction with toluene should proceed primarily by addition at the para and ortho positions resulting in a benzyl-type ion. Reaction with aniline-2,3,4,5,6-d(5) reveals that elimination of CH(3)SD is kinetically favored by a factor of 5 over elimination of CH(3)SH. Experiments with C(6)H(6)ND(2) and theoretical calculations suggest that methylenation at the nitrogen atom is energetically favorable and likely, but the observed results may reflect some H/D scrambling, which occurs after attack at a ring position. By comparison, reaction with phenol-2,3,4,5,6-d(5) reveals that methylenation followed by elimination of CH(3)SD is kinetically favored by a factor of 3.8 over elimination of CH(3)SH. For phenol, the theoretical calculations suggest that attack by CH(3)S(+)=CH(2) at the para or ortho position is the only low-energy pathway for methylenation. However, a low-energy pathway for hydrogen scrambling is predicted by the calculations originating from the exit complex, [CH(3)SH(...) CH(2)=C(6)H(4)=OH](+), of reaction at a ring position.     

丹参酮与胺类化合物的反应研究

研究了隐丹参酮与氨、甲胺、乙胺等有机胺的作用。发现丹参酮二氢呋喃环部分在氨及NaOH的作用下发生亲核开环,且亲核加成反应与开环反应协同进行。与甲胺、乙胺等有机胺作用则分别生成丹参酮的咪唑环及恶唑环衍生物。探讨了可能的反应历程。     

Characterization by theory of H-transfers and onium reactions of CH<Subscript>3</Subscript>CH<Subscript>2</Subscript>CH<Subscript>2</Subscript>N<Superscript>+</Superscript>H=CH<Subscript>2</Subscript>

H-transfers by 4-, 5-, and 6-membered ring transition states to the pi-bonded methylene of CH3CH2CH2NH+=CH2 (1) are characterized by theory and compared with the corresponding transfers in cation radicals. Four-membered ring H-transfers converting 1 to CH3CH2CH=N+HCH3 (2) and CH3N+H=CH2 to CH2=NH+CH3 are high-energy processes involving rotation of the source and destination RHC= groups (R = H or C2H5) to near bisection by skeletal planes; migrating hydrogens move near these planes. The H-transfer 1 --> CH3C+HCH2NHCH3 (3) has a higher energy transition-state than 1 --> 2, in marked contrast to the corresponding relative energies of 4- and 5-membered ring H-transfers in cation-radicals. Six-membered ring H-transfer-dissociation (1 --> CH2=CH2 + CH2=N+HCH3) is a closed shell analog of the McLafferty rearrangement. It has a lower energy transition-state than either 1 --> 2 or 1 --> 3, but is still a much higher energy process than 6-membered ring H-transfers in aliphatic cation radicals. In contrast to the stepwise McLafferty rearrangement in cation radicals, H-transfer and CC bond breaking are highly synchronous in 1 --> CH3N+H=CH2 + CH2=CH2. H-transfers in propene elimination from 1 are ion-neutral complex-mediated: 1--> [CH3CH2CH2+ ---NH=CH2] --> [CH3C+HCH3 NH=CH2] --> CH3CH = CH2 + CH2=NH2+. Intrinsic reaction coordinate tracing demonstrated that a slight preference for H-transfer from the methyl containing the carbon from which CH2=NH is cleaved is due to CH2=NH passing nearer this methyl than the other on its way to abstracting H, i.e., some memory of the initial orientation of the partners accompanies this reaction.     

The "missing link": the gas-phase generation of platinum-methylidyne clusters Pt(n)CH+ (n=1, 2) and their reactions with hydrocarbons and ammonia

Electrospray ionization (ESI) of tetrameric platinum(II) acetate, [Pt(4)(CH(3)COO)(8)], in methanol generates the formal platinum(III) dimeric cation [Pt(2)(CH(3)COO)(3)(CH(2)COO)(MeOH)(2)](+), which, upon harsher ionization conditions, sequentially loses the two methanol ligands, CO(2), and CH(2)COO to form the platinum(II) dimer [Pt(2)(CH(3)COO)(2)(CH(3))](+). Next, intramolecular sequential double hydrogen-atom transfer from the methyl group concomitant with the elimination of two acetic acid molecules produces Pt(2)CH(+) from which, upon even harsher conditions, PtCH(+) is eventually generated. This degradation sequence is supported by collision-induced dissociation (CID) experiments, extensive isotope-labeling studies, and DFT calculations. Both PtCH(+) and Pt(2)CH(+) react under thermal conditions with the hydrocarbons C(2)H(n) (n=2, 4, 6) and C(3)H(n) (n=6, 8). While, in ion-molecule reactions of PtCH(+) with C(2) hydrocarbons, the relative rates decrease with increasing n, the opposite trend holds true for Pt(2)CH(+). The Pt(2)CH(+) cluster only sluggishly reacts with C(2)H(2), but with C(2)H(4) and C(2)H(6) dihydrogen loss dominates. The reactions with the latter two substrates were preceded by a complete exchange of all of the hydrogen atoms present in the adduct complex. The PtCH(+) ion is much less selective. In the reactions with C(2)H(2) and C(2)H(4), elimination of H(2) occurs; however, CH(4) formation prevails in the decomposition of the adduct complex that is formed with C(2)H(6). In the reaction with C(2)H(2), in addition to H(2) loss, C(3)H(3)(+) is produced, and this process formally corresponds to the transfer of the cationic methylidyne unit CH(+) to C(2)H(2), accompanied by the release of neutral Pt. In the ion-molecule reactions with the C(3) hydrocarbons C(3)H(6) and C(3)H(8), dihydrogen loss occurs with high selectivity for Pt(2)CH(+), but in the reactions of these substrates with PtCH(+) several reaction routes compete. Finally, in the ion-molecule reactions with ammonia, both platinum complexes give rise to proton transfer to produce NH(4)(+); however, only the encounter complex generated with PtCH(+) undergoes efficient dehydrogenation of the substrate, and the rather minor formation of CNH(4)(+) indicates that C-N bond coupling is inefficient.     

Influence of "alternative" C-terminal amino acids on the formation of [b3 + 17 + Cat]+ products from metal cationized synthetic tetrapeptides

The aim of this study was to investigate the dissociation patterns, and in particular the relative abundance of [b(3) + 17 + Cat](+), for peptides with C-termini designed to allow transfer of the -OH required to generate the product ion, but not necessarily as the most favored pathway. Working with the hypothesis that formation of a five-membered ring intermediate, including intramolecular nucleophilic attack by a carbonyl oxygen atom, is an important mechanistic step, several model peptides with general sequence AcFGGX were synthesized, metal cationized by electrospray ionization and subjected to collision-induced dissociation (CID). The amino acid at position X was one that either required a larger ring intermediate (beta-alanine, gamma-aminobutyric acid and epsilon-amino-n-caproic acid to generate six-, seven- or nine- membered rings, respectively) to transfer -OH, lacked a structural element required for nucleophilic attack (aminoethanol) or prohibited cyclization because of the inclusion of a rigid ring (p- and m-aminobenzoic acid). For Ag(+), Li(+) and Na(+) cationized peptides, our results show that amino acids requiring the adoption of larger ring intermediates suppressed the formation of [b(3) + 17 + Cat](+), while amino acids that prohibit cyclization eliminated the reaction pathway completely. Formation of [b(3) - 1 + Cat](+) from the alkali metal cationized versions was not a favorable process upon suppression or elimination of the [b(3) + 17 + Cat](+) pathway: the loss of H(2)O to form [M - H(2)O + Cat](+) was instead the dominant dissociation reaction observed. Multiple-stage dissociation experiments suggest that [M - H(2)O + Cat](+) is not [b(4) - 1 + Cat](+) arising from the loss of H(2)O from the C-terminus, but may instead be a species that forms via a mechanism involving the elimination of an oxygen atom from an amide group.     

Structure and unimolecular chemistry of protonated sulfur betaines, (CH3)2S(+)(CH2)(n)CO2H (n = 1 and 2)

The fixed charge zwitterionic sulfur betaines dimethylsulfonioacetate (DMSA) (CH(3))(2)S(+)CH(2)CO(2)(-) and dimethylsulfoniopropionate (DMSP) (CH(3))(2)S(+)(CH(2))(2)CO(2)(-) have been synthesized and the structures of their protonated salts (CH(3))(2)S(+)CH(2)CO(2)H···Cl(-) [DMSA.HCl] and (CH(3))(2)S(+)(CH(2))(2)CO(2)H···Pcr(-) [DMSP.HPcr] (where Pcr = picrate) have been characterized using X-ray crystallography. The unimolecular chemistry of the [M+H](+) of these betaines was studied using two techniques; collision-induced dissociation (CID) and electron-induced dissociation (EID) in a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer. Results from the CID study show a richer series of fragmentation reactions for the shorter chain betaine and contrasting main fragmentation pathways. Thus while (CH(3))(2)S(+)(CH(2))(2)CO(2)H fragments via a neighbouring group reaction to generate (CH(3))(2)S(+)H and the neutral lactone as the most abundant fragmentation channel, (CH(3))(2)S(+)CH(2)CO(2)H fragments via a 1,2 elimination reaction to generate CH(3)S(+)=CH(2) as the most abundant fragment ion. To gain insights into these fragmentation reactions, DFT calculations were carried out at the B3LYP/6-311++G(2d,p) level of theory. For (CH(3))(2)S(+)CH(2)CO(2)H, the lowest energy pathway yields CH(3)S(+)=CH(2)via a six-membered transition state. The two fragment ions observed in CID of (CH(3))(2)S(+)(CH(2))(2)CO(2)H are shown to share the same transition state and ion-molecule complex forming either (CH(3))(2)S(+)H or (CH(2))(2)CO(2)H(+). Finally, EID shows a rich and relatively similar fragmentation channels for both protonated betaines, with radical cleavages being observed, including loss of ˙CH(3).     

Theoretical survey of the gas-phase reactions of allylamine with Co+

Density functional theory calculations have been carried out to survey the gas-phase reactions of allylamine with Co+. The geometries and bonding characteristics of all the stationary points involved in the reactions have been investigated at the B3LYP/6-311++G(d,p) level. Final energies are obtained by means of the B3LYP/6-311+G(2df,2pd) single-point calculations. The performance of these theoretical methods is valuated with respect to the available thermochemical data. Co+ strongly binds allylamine by forming a chelated structure in which the metal cation binds concomitantly to the two functional groups of the neutral molecule. Various mechanisms leading to the loss of NH3, NH2, C2H2, and H2 are analyzed in terms of the topology of the potential energy surface. The most favorable mechanism corresponds to the loss of NH3, through a process of C-N activation followed by a concerted beta-H shift. The accompanying NH2 elimination is also discussed. The loss of C2H2 is also favorable, through C-C activation and stepwise beta-H shift, giving Co+(NH2CH3) and Co+H(NH2CH2) as the product ions. Various possible channels for the loss of H2 are considered. The most favorable mechanism of the H2 loss corresponds to a pathway through which the metal acts as a carrier, connecting a hydrogen atom from the methylidyne group of allylamine with a hydrogen atom of the terminal methylene group. The product ion of this pathway has a tricoordinated structure in which Co+ binds to the terminal two Cs and N atoms of the NH2CH2CCH moiety.     

A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations

We propose a new DFT-based mechanism for methane production using the full F430 cofactor of MCR (methyl-coenzyme M reductase) along with a coordinated O=CH2CH2C(H)NH2C(H)O (surrogate for glutamine) as a model of the active site for conversion of CH3SCoM(-) (CH3SCH2CH2SO3(-)) + HSCoB to methane plus the corresponding heterodisulfide. The cycle begins with the protonation of F430, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH3SCoM(-) to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring nitrogens. The movement of Ni (and the attached CH3 and SCH2CH2SO3(2-) ligands) toward the SCoB(-) (deprotonated HSCoB) cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The concerted elimination of methane, where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen, has a very small calculated activation barrier (5.4 kcal/mol). The NPA charge on Ni for the various reaction steps indicates that the oxidation state changes occur largely on the attached ligands.     

Decomposition of protonated noradrenaline and normetanephrine assisted by NH2 migration studied by electrospray tandem mass spectrometry and molecular orbital calculations

As part of a research program on neurotransmitters in a biological fluid, the fragmentations characterising catecholamines protonated under electrospray ionisation (ESI) conditions, under low collision energy in a triple-quadrupole mass spectrometer, were investigated. The decompositions of protonated noradrenaline (VH) and normetanephrine (VIH) were studied. Both precursor ions eliminate first H2O at very low collision energy, and the fragmentations of [MH-H2O]+ occur at higher collision energy. The breakdown graphs of [MH-H2O]+ ions, with collision energy varying from 0-40 eV in the laboratory frame, are presented. [VIH-H2O]+ ions lose competitively NH3 and CH3OH. For [VH-H2O]+ the loss of NH3 is dominant while H2O is eliminated at very low abundance at all collision energies. All of these secondary fragmentations are followed at higher collision energies by elimination of CO. These fragmentations are interpreted by means of ab initio calculations up to the B3LYP/6-311+G(2d,2p) level of theory. The elimination of H2O requires first the isomerisation of N-protonated forms, chosen as energy references, to O-protonated forms. The isomerisation barriers are calculated to be lower than 81 kJ/mol above the N-protonated forms. The elimination of NH3 from [MH-H2O]+ requires first the migration, via a cyclisation, of the amine function from the linear chain to the aromatic ring in order to prevent the formation of unstable disubstituted carbocations in the ring. The barriers associated with the loss of NH3 are located 220 and 233 kJ/mol above VH and 219 kJ/mol above VIH. The energy barrier for the loss of ROH is located 236 and 228 kJ/mol above VH and VIH, respectively. The absence of ions corresponding to [VH-2H2O]+ is due to a parasitic mechanism with an activation barrier lower than 236 kJ/mol that leads to a stable species unable to fragment, thus preventing the second loss of H2O. Losses of CO following the secondary fragmentations involve activation barriers higher than 330 kJ/mol.     

Magnesium monocationic complexes: a theoretical study of metal ion binding energies and gas-phase association kinetics

Bond dissociation energies (BDEs) for complexes of ground state Mg+ (2S) with several small oxygen- and nitrogen-containing ligands (H2O, CO, CO2, H2CO, CH3OH, HCOOH, H2CCO, CH3CHO, c-C2H4O, H2CCHOH, CH3CH2OH, CH3OCH3, NH3, HCN, H2CNH, CH3NH2, CH3CN, CH3CH2NH2, (CH3)2NH, H2NCN, and HCONH2) have been calculated at the CP-dG2thaw level of theory. These BDE values, as well as counterpoise-corrected MP2(thaw)/6-311+G(2df,p) calculations on the Mg+ complexes of several larger ligands, augment and complement existing experimental or theoretical determinations of gas-phase Mg+/ligand bond strengths. The reaction kinetics of complex formation are also investigated via variational transition state theory (VTST) calculations using the computed ligand and molecular ion parameters. Radiative association rate coefficients for most of these systems increase by approximately 1 order of magnitude with every 3-fold reduction in temperature from 300 to 10 K. Several of the largest molecules surveyed-notably, CH3COOH, (CH3)2CO, and CH3CH2CN-exhibit comparatively efficient radiative association with Mg+ (k(RA) > or = 1.0 x 10(-10) cm3 molecule(-1) s(-1)) at temperatures as high as 100 K, implying that these processes may have a considerable influence on the metal ion chemistry of warm molecular astrophysical environments known to contain these potential ligands. Our calculations also identify the infrared chromophoric brightness of various functional groups as a significant factor influencing the efficiency of the radiative association process.