tert-Butylaminium 2-carboxy-4,5-dichlorobenzoate

In the structure of the title anhydrous salt C4H12N+ C8H3Cl2O4-, the 4,5-dichlorophthalate monoanions have the common 'planar' conformation with the carboxyl groups close to coplanar with the benzene ring and with a short intramolecular carboxylic acid O-H...O hydrogen bond. A two-dimensional sheet structure is formed through aminium N-H...O(carboxyl) hydrogen-bonding associations.

rac-4-Carbamoylpiperidinium cis-2-carboxycyclohexane-1-carboxylate

In the title salt, racemic C6H12N2O+ C8H11O4- from the reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with isonipecotamide, the cations are linked into duplex chain substructures through both centrosymmetric cyclic head-to-head 'amide motif' hydrogen-bonding associations [graph set R2/2(8)] and 'side-by-side' R2/2(14) associations. The anions are incorporated into the chains through cyclic R3/4(10) interactions involving amide and piperidinium N-H...O(carboxyl) hydrogen bonds which, together with inter-anion carboxylic acid O-H...O(carboxyl) hydrogen bonds, give a two-dimensional layered structure extending along (011).

Bis(benzylaminium) 4,5-dichlorobenzene-1,2-dicarboxylate monohydrate

In the structure of the title salt 2C7H10N+.C8H2Cl2O4(2-) .H2O the two benzylaminium anions have different conformations, one being essentially planar the other having the side-chain rotated out of the benzene plane (minimum ring to side-chain C-C-C-N torsion angles = -3.6(6) and 50.1(5)\%, respectively). In the 4,5-dichlorophthalate dianion the carboxyl groups make ihedral angles of 23.0(2) and 76.5(2)\% with the benzene ring. Aminium N-H...O and water O-H...O hydrogen-bonding associations with carboxyl O-atom acceptors give a two-dimensional duplex sheet structure which extends along the (011) plane. Weak pi-pi interactions are also present between the benzene ring and one of the cation rings [minimum ring centroid separation = 3.749(3)Ang.

Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism

Significant cleavage by hammerhead ribozymes requires activation by divalent metal ions. Several models have been proposed to account for the influence of metal ions on hammerhead activity. A number of recent papers have presented data that have been interpreted as supporting a one-metal-hydroxide-ion mechanism. In addition, a solvent deuterium isotope effect has been taken as evidence against a proton transfer in the rate-limiting step of the cleavage reaction. We propose that these data are more easily explained by a two-metal-ion mechanism that does not involve a metal hydroxide, but does involve a proton transfer in the rate-limiting step.

Hydrogen-bonding in the structures of the 1:1 salts of isonipecotamide with a set of four polyfunctional monocyclic heteroaromatic carboxylic acids

The crystal structures of the 1:1 proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with the monocyclic heteroaromatic carboxylic acids, isonicotinic acid, picolinic acid, dipicolinic acid and pyrazine-2,3-dicarboxylic acid have been determined at 200 K and their hydrogen-bonding patterns examined. The compounds are respectively anhydrous 4-carbamoylpiperidinium pyridine-4-carboxylate (1), the partial hydrate 4-carbamoylpiperidinium pyridine-2-carboxylate 0.25 water (2), the solvate 4-carbamoylpiperidinium 6-carboxypyridine-2-carboxylate methanol monosolvate (3), and anhydrous 4-carbamoylpiperidinium 3-carboxypyrazine-2-carboxylate (4). In compounds 1 and 3, hydrogen-bonding interactions give two-dimensional sheet structures which feature enlarged cyclic ring systems, while in compounds 2 and 4, three-dimensional structures are found. The previously described cyclic R2/2(8) hydrogen-bonded amide-amide dimer is present in 2 and 3. The hydrogen-bonding in 2 involves the partial-occupancy water molecule while the structure of 4 is based on inter-linked homomolecular hydrogen-bonded cation-cation and anion-anion associated chains comprising head-to-tail interactions. This work further demonstrates the utility of the isonipecotamide cation in the generation of chemically stable hydrogen-bonded systems, particularly with aromatic carboxylate anions, providing crystalline solids.

2-(4-Aminobenzenesulfonamido)-4,6-dimetylpyrimidin-1-ium 2-carboxy-4,6-dinitrophenolate

In the structure of the of the phenolate salt of the sulfa drug sulfamethazine with 3,5-dinitrosalicylic acid, C12H15N4O2S+ C7H3N2O7-, the dihedral angle between the pyrimidine and phenyl rings of the cation is 59.70(17)\%. Cation--anion hydrogen-bonding interactions involving pyrimidine N+-H...O(carboxyl) and amine N-H...O(carboxyl) pairs give a cyclic R2/2(8) motif while secondary N-H...O hydrogen bonds between the aniline group and both sulfone and nitro O-atom acceptors give a two-dimensional structure extending along (001).

Charge carrier exchange at chemically modified graphene edges: A density functional theory study

Heteroatom doping on the edge of graphene may serve as an effective way to tune chemical activity of carbon-based electrodes with respect to charge carrier transfer in an aqueous environment. In a step towards developing mechanistic understanding of this phenomenon, we explore herein mechanisms of proton transfer from aqueous solution to pristine and doped graphene edges utilizing density functional theory. Atomic B-, N-, and O- doped edges as well as the native graphene are examined, displaying varying proton affinities and effective interaction ranges with the H3O+ charge carrier. Our study shows that the doped edges characterized by more dispersive orbitals, namely boron and nitrogen, demonstrate more energetically favourable charge carrier exchange compared with oxygen, which features more localized orbitals. Extended calculations are carried out to examine proton transfer from the hydronium ion in the presence of explicit water, with results indicating that the basic mechanistic features of the simpler model are unchanged.

Molecular cocrystals of 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine: hydrogen bonding in the structures of the 1:1 adduct with 2-(naphthalen-2-yloxy)acetic acid and the salt with 3,5-dinitrobenzoic acid

The structures of the anhydrous products from the interaction of 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazole with (2-naphthoxy)acetic acid, the 1:1 adduct C8H6BrN3S . C12H10O3 (I) and 3,5-dinitrobenzoic acid, the salt C8H7BrN3S+ C7H3N2O6- (II) have been determined. In the adduct (I), a heterodimer is formed through a cyclic hydrogen-bonding motif [graph set R2/2(8)], involving carboxylic acid O-H...N(hetero)and amine N-H...O(carboxyl) interactions. The heterodimers are essentially planar with a thiadiazole to naphthyl ring dihedral angle of 15.9(2)deg. and the intramolecular thiadiazole to phenyl ring angle of 4.7(2)deg. An amine N-H...N(hetero) hydrogen bond between the heterodimers generates a one-dimensional chain structure extending down [001]. Also present are weak benzene-benzene and naphthalene-naphthalene pi-pi stacking interactions down the b axis [minimum ring centroid separation, 3.936(3) Ang.]. With the salt (II), the cation-anion association is also through a cyclic R2/2(8) motif but involving duplex N-H...O(carboxyl) hydrogen bonds, giving a heterodimer which is close to planar [dihedral angles between the thiadiazole ring and the two benzene rings, 5.00(16)deg. (intra) and 7.23(15)deg. (inter)]. A secondary centrosymmetric cyclic N-H...O(carboxyl) hydrogen-bonding association involving the second amino H-atom generates a heterotetramer. Also present in the crystal are weak pi-pi i-\p interactions between thiadiazolium rings [minimum ring centroid separation, 3.936(3)Ang.], as well as a short Br...O(nitro) interaction [3.314(4)Ang.]. The two structures reported here now provide a total of three crystallographically characterized examples of co-crystalline products from the interaction of 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazole with carboxylic acids, of which only one involves proton-transfer.

Gas-Phase Transformation of Phosphatidylcholine Cations to Structurally Informative Anions via Ion/Ion Chemistry

Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC16:0/18:1) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC18:1/16:0), were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, \[PC + PDPA - H](-). Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating \[PC - CH3](-). Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low-abundance acyl neutral losses as free acids and ketenes. Product ion spectra of \[PC - CH3](-) suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry. Grant Number ARC/CE0561607, ARC/DP120102922

A comparison of the gas phase acidities of phospholipid headgroups: Experimental and computational studies

Proton-bound dimers consisting of two glycerophospholipids with different headgroups were prepared using negative ion electrospray ionization and dissociated in a triple quadrupole mass spectrometer. Analysis of the tandem mass spectra of the dimers using the kinetic method provides, for the first time, an order of acidity for the phospholipid classes in the gas phase of PE < PA << PG < PS < PI. Hybrid density functional calculations on model phospholipids were used to predict the absolute deprotonation enthalpies of the phospholipid classes from isodesmic proton transfer reactions with phosphoric acid. The computational data largely support the experimental acidity trend, with the exception of the relative acidity ranking of the two most acidic phospholipid species. Possible causes of the discrepancy between experiment and theory are discussed and the experimental trend is recommended. The sequence of gas phase acidities for the phospholipid headgroups is found to (1) have little correlation with the relative ionization efficiencies of the phospholipid classes observed in the negative ion electrospray process, and (2) correlate well with fragmentation trends observed upon collisional activation of phospholipid \[M - H](-) anions. (c) 2005 American Society for Mass Spectrometry.

Reactions of simple and peptidic alpha-carboxylate radical anions with dioxygen in the gas phase

alpha-Carboxylate radical anions are potential reactive intermediates in the free radical oxidation of biological molecules (e. g., fatty acids, peptides and proteins). We have synthesised well-defined alpha-carboxylate radical anions in the gas phase by UV laser photolysis of halogenated precursors in an ion-trap mass spectrometer. Reactions of isolated acetate ((center dot)CH(2)CO(2)) and 1-carboxylatobutyl (CH(3)CH(2)CH(2)(center dot)CHCO(2)(-)) radical anions with dioxygen yield carbonate (CO(3)(center dot-)) radical anions and this chemistry is shown to be a hallmark of oxidation in simple and alkyl-substituted cross-conjugated species. Previous solution phase studies have shown that C(alpha)-radicals in peptides, formed from free radical damage, combine with dioxygen to form peroxyl radicals that subsequently decompose into imine and keto acid products. Here, we demonstrate that a novel alternative pathway exists for two alpha-carboxylate C(alpha)-radical anions: the acetylglycinate radical anion (CH(3)C(O)NH(center dot)CHCO(2)(-)) and the model peptide radical anion, YGGFG(center dot-). Reaction of these radical anions with dioxygen results in concerted loss of carbon dioxide and hydroxyl radical. The reaction of the acetylglycinate radical anion with dioxygen reveals a two-stage process involving a slow, followed by a fast kinetic regime. Computational modelling suggests the reversible formation of the C(alpha) peroxyl radical facilitates proton transfer from the amide to the carboxylate group, a process reminiscent of, but distinctive from, classical proton-transfer catalysis. Interestingly, inclusion of this isomerization step in the RRKM/ME modelling of a G3SX level potential energy surface enables recapitulation of the experimentally observed two-stage kinetics.

Bond dissociation energies of organic molecules

In this Account we have compiled a list of reliable bond energies that are based on a set of critically evaluated experiments. A brief description of the three most important experimental techniques for measuring bond energies is provided. We demonstrate how these experimental data can be applied to yield the heats of formation of organic radicals and the bond enthalpies of more than 100 representative organic molecules.

4-Methoxyanilinium 2-carboxy-4,5-dichlorobenzoate

In the structure of the title salt C7H10NO+ C8H3Cl2O4- the benzene planes of the cation and anion are essentially parallel [inter-ring dihedral angle 4.8(2)deg]. In the anion the carboxylic acid and carboxylate groups make dihedral angles of 19.0(2) and 79.5(2)\%, respectively, with the benzene ring. Aminium N-H...O, carboxylic acid O-H...O and weak aromatic C-H...O hydrogen-bonding associations with carboxyl O-atom acceptors together with cation-anion pi-pi ring interactions [minimum ring centroid separation = 3.734(3)Ang] give a two-dimensional sheet structure which lies parallel to (001).

4-(4-Aminophenylsulfonyl)anilinium toluene-4-sulfonate

In the title p-toluenesulfonate salt of the drug dapsone, C12H13N2O2S+ C7H7O3S-, the dihedral angle between the two aromatic rings of the dapsone monocation is 70.19(17)deg. and those between these rings and that of the p-toluenesulfonate anion are 72.34(17) and 46.43(17)deg. All amine and aminium H-atoms are involved in intermolecular N-H...O hydrogen-bonding associations with sulfonyl O-atom acceptors as well as one of the sulfone O-atoms, giving a three-dimensional structure.

Photoelectron spectroscopy of HCCN- and HCNC- reveals the quasilinear triplet carbenes, HCCN and HCNC

Negative ion photoelectron spectroscopy has been used to study the HCCN- and HCNC- ions. The electron affinities (EA) of cyanocarbene have been measured to be EA(HCCN (X) over tilde (3)Sigma(-)=2.003+/-0.014 eV and EA(DCCN (X) over tilde (3)Sigma(-))=2.009+/-0.020 eV. Photodetachment of HCCN- to HCCN (X) over tilde (3)Sigma(-) shows a 0.4 eV long vibrational progression in nu(5), the H-CCN bending mode; the HCCN- photoelectron spectra reveal excitations up to 10 quanta in nu(5). The term energies for the excited singlet state are found to be T-0(HCCN (a) over tilde (1)A('))=0.515+/-0.016 eV and T-0(DCCN (a) over tilde (1)A('))=0.518+/-0.027 eV. For the isocyanocarbene, the two lowest states switch and HCNC has a singlet ground state and an excited triplet state. The electron affinities are EA(HCNC (X) over tilde (1)A('))=1.883+/-0.013 eV and EA((X) over tilde (1)A(') DCNC)=1.877+/-0.010 eV. The term energy for the excited triplet state is T-0(HCNC (a) over tilde (3)A("))=0.050+/-0.028 eV and T-0(DCNC (a) over tilde (3)A("))=0.063+/-0.030 eV. Proton transfer kinetics in a flowing afterglow apparatus were used to re-measure the enthalpy of deprotonation of CH3NC to be Delta(acid)H(298)(CH3NC)=383.6+/-0.6 kcal mol(-1). The acidity/EA thermodynamic cycle was used to deduce D-0(H-CHCN)=104+/-2 kcal mol(-1) [Delta(f)H(0)(HCCN)=110+/-4 kcal mol(-1)] and D-0(H-CHNC)=106+/-4 kcal mol(-1) [Delta(f)H(0)(HCNC)=133+/-5 kcal mol(-1)]. (C) 2002 American Institute of Physics.