Ahmed M. Hamid

Structure and hydration of the C4H4•+ ion formed by electron impact ionization of acetylene clusters

Here we report ion mobility experiments and theoretical studies aimed at elucidating the identity of the acetylene dimer cation and its hydrated structures. The mobility measurement indicates the presence of more than one isomer for the C(4)H(4)(●+) ion in the cluster beam. The measured average collision cross section of the C(4)H(4)(●+) isomers in helium (38.9 ± 1 Å(2)) is consistent with the calculated cross sections of the four most stable covalent structures calculated for the C(4)H(4)(●+) ion [methylenecyclopropene (39.9 Å(2)), 1,2,3-butatriene (41.1 Å(2)), cyclobutadiene (38.6 Å(2)), and vinyl acetylene (41.1 Å(2))]. However, none of the single isomers is able to reproduce the experimental arrival time distribution of the C(4)H(4)(●+) ion. Combinations of cyclobutadiene and vinyl acetylene isomers show excellent agreement with the experimental mobility profile and the measured collision cross section. The fragment ions obtained by the dissociation of the C(4)H(4)(●+) ion are consistent with the cyclobutadiene structure in agreement with the vibrational predissociation spectrum of the acetylene dimer cation (C(2)H(2))(2)(●+) [R. A. Relph, J. C. Bopp, J. R. Roscioli, and M. A. Johnson, J. Chem. Phys. 131, 114305 (2009)]. The stepwise hydration experiments show that dissociative proton transfer reactions occur within the C(4)H(4)(●+)(H(2)O)(n) clusters with n ≥ 3 resulting in the formation of protonated water clusters. The measured binding energy of the C(4)H(4)(●+)H(2)O cluster, 38.7 ± 4 kJ/mol, is in excellent agreement with the G3(MP2) calculated binding energy of cyclobutadiene(●+)·H(2)O cluster (41 kJ/mol). The binding energies of the C(4)H(4)(●+)(H(2)O)(n) clusters change little from n = 1 to 5 (39-48 kJ/mol) suggesting the presence of multiple binding sites with comparable energies for the water-C(4)H(4)(●+) and water-water interactions. A significant entropy loss is measured for the addition of the fifth water molecule suggesting a structure with restrained water molecules, probably a cyclic water pentamer within the C(4)H(4)(●+)(H(2)O)(5) cluster. Consequently, a drop in the binding energy of the sixth water molecule is observed suggesting a structure in which the sixth water molecule interacts weakly with the C(4)H(4)(●+)(H(2)O)(5) cluster presumably consisting of a cyclobutadiene(●+) cation hydrogen bonded to a cyclic water pentamer. The combination of ion mobility, dissociation, and hydration experiments in conjunction with the theoretical calculations provides strong evidence that the (C(2)H(2))(2)(●+) ions are predominantly present as the cyclobutadiene cation with some contribution from the vinyl acetylene cation.

Formation of nitrogen-containing polycyclic cations by gas-phase and intracluster reactions of acetylene with the pyridinium and pyrimidinium ions.

Here, we present evidence from laboratory experiments for the formation of nitrogen-containing complex organic ions by sequential reactions of acetylene with the pyridinium and pyrimidinium ions in the gas phase and within ionized pyridine-acetylene binary clusters. Additions of five and two acetylene molecules onto the pyridinium and pyrimidinium ions, respectively, at room temperature are observed. Second-order rate coefficients of the overall reaction of acetylene with the pyridinium and pyrimidinium ions are measured as 9.0 × 10(-11) and 1.4 × 10(-9) cm(3) s(-1), respectively, indicating reaction efficiencies of about 6% and 100%, respectively, at room temperature. At high temperatures, only two acetylene molecules are added to the pyridinium and pyrimidinium ions, suggesting covalent bond formation. A combination of ion dissociation and ion mobility experiments with DFT calculations reveals that the addition of acetylene into the pyridinium ion occurs through the N-atom of the pyridinium ion. The relatively high reaction efficiency is consistent with the absence of a barrier in the exothermic N-C bond forming reaction leading to the formation of the C(7)H(7)N(•+) covalent adduct. An exothermic addition/H-elimination reaction of acetylene with the C(7)H(7)N(•+) adduct is observed leading to the formation of a bicyclic quinolizinium cation (C(9)H(8)N(+)). Similar chemistry is observed in the sequential reactions of acetylene with the pyrimidinium ion. The second acetylene addition onto the pyrimidinium ion involves an exclusive addition/H-elimination reaction at room temperature leading to the formation of a bicyclic pyrimidinium cation (C(8)H(7)N(2)(+)). The high reactivity of the pyridinium and pyrimidinium ions toward acetylene is in sharp contrast to the very low reactivity of the benzene cation, which has a reaction efficiency of 10(-4)-10(-5). This indicates that the presence of a nitrogen atom within the aromatic ring enhances the ring growth mechanism by the sequential addition of acetylene to form nitrogen-containing polycyclic hydrocarbon ions. The observed reactions could explain the possible formation of nitrogen-containing complex organics by gas-phase ion-molecule reactions involving the pyridinium and pyrimidinium ions with acetylene under a wide range of temperatures and pressures in astrochemical environments such as the nitrogen-rich Titans atmosphere. The current results suggest searching for spectroscopic evidence for these organics in Titans atmosphere.

Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations

Ion mobility (IM) separations have a broad range of analytical applications, but insufficient resolution often limits their utility. Here, we report on ion mobility separations in a structures for lossless ion manipulations (SLIM) serpentine ultralong path with extended routing (SUPER) traveling wave (TW) ion mobility (IM) module in conjunction with mass spectrometry (MS). Ions were confined in the SLIM by rf fields in conjunction with a DC guard bias, enabling essentially lossless TW transmission over greatly extended paths. The extended routing utilized multiple passes (e.g., ∼1094 m over 81 passes through the 13.5 m serpentine path) and was facilitated by the introduction of a lossless ion switch that allowed ions to be directed to either the MS detector or for another pass through the serpentine separation region, allowing theoretically unlimited IM path lengths. The multipass SUPER IM-MS provided resolution approximately proportional to the square root of the number of passes (or total path length). More than 30-fold higher IM resolution (∼340 vs ∼10) for Agilent tuning mix m/z 622 and 922 ions was achieved for 40 passes compared to commercially available drift tube IM and other TWIM-based platforms. An initial evaluation of the isomeric sugars lacto-N-hexaose and lacto-N-neohexaose showed the isomeric structures to be baseline resolved, and a new conformational feature for lacto-N-neohexaose was revealed after 9 passes. The new SLIM SUPER high resolution TWIM platform has broad utility in conjunction with MS and is expected to enable a broad range of previously challenging or intractable separations.

Evidence for the Formation of Pyrimidine Cations from the Sequential Reactions of Hydrogen Cyanide with the Acetylene Radical Cation.

Herein, we report the first direct evidence for the formation of pyrimidine ion isomers by sequential reactions of HCN with the acetylene radical cation in the gas phase at ambient temperature using the mass-selected variable temperature and pressure ion mobility technique. The formation and structures of the pyrimidine ion isomers are theoretically predicted via coupled cluster and density functional theory calculations. This ion-molecule synthesis may indicate that pyrimidine is produced in the gas phase in space environments before being incorporated into condensed-phase ices and transformed into nucleic acid bases such as uracil.

Unconventional hydrogen bonding to organic ions in the gas phase: Stepwise association of hydrogen cyanide with the pyridine and pyrimidine radical cations and protonated pyridine

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N(+·)(HCN)n and C4H4N2 (+·)(HCN)n clusters, respectively, with n = 1-4. For comparison, the binding of 1-4 HCN molecules to the protonated pyridine C5H5NH(+)(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). The pyridine and pyrimidine radical cations form unconventional carbon-based ionic hydrogen bonds with HCN (CH(δ+)⋯NCH). Protonated pyridine forms a stronger ionic hydrogen bond with HCN (NH(+)⋯NCH) which can be extended to a linear chain with the clustering of additional HCN molecules (NH(+)⋯NCH··NCH⋯NCH) leading to a rapid decrease in the bond strength as the length of the chain increases. The lowest energy structures of the pyridine and pyrimidine radical cation clusters containing 3-4 HCN molecules show a strong tendency for the internal solvation of the radical cation by the HCN molecules where bifurcated structures involving multiple hydrogen bonding sites with the ring hydrogen atoms are formed. The unconventional H-bonds (CH(δ+)⋯NCH) formed between the pyridine or the pyrimidine radical cations and HCN molecules (11-12 kcal/mol) are stronger than the similar (CH(δ+)⋯NCH) bonds formed between the benzene radical cation and HCN molecules (9 kcal/mol) indicating that the CH(δ+) centers in the pyridine and pyrimidine radical cations have more effective charges than in the benzene radical cation.

Stepwise Association of Hydrogen Cyanide and Acetonitrile with the Benzene Radical Cation: Structures and Binding Energies of (C6H6•+)(HCN)n, n = 1–6, and (C6H6•+)(CH3CN)n, n = 1–4, Clusters

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise association of HCN and CH(3)CN molecules with the benzene radical cation in the C(6)H(6)(•+)(HCN)(n) and C(6)H(6)(•+)(CH(3)CN)(n) clusters with n = 1-6 and 1-4, respectively. The binding energy of CH(3)CN to the benzene cation (14 kcal/mol) is stronger than that of HCN (9 kcal/mol) mostly due to a stronger ion-dipole interaction because of the large dipole moment of acetonitrile (3.9 D). However, HCN can form hydrogen bonds with the hydrogen atoms of the benzene cation (CH(δ+)···NCH) and linear hydrogen bonding chains involving HCN···HCN interaction. HCN molecules tend to form externally solvated structures with the benzene cation where the ion is hydrogen bonded to the exterior of HCN chains. For the C(6)H(6)(•+)(CH(3)CN)(n) clusters, internally solvated structures are formed where the acetonitrile molecules are directly interacting with the benzene cation through ion-dipole and hydrogen bonding interactions. The lack of formation of higher clusters with n > 4, in contrast to HCN, suggests the formation of a solvent shell at n = 4, which is attributed to steric interactions among the acetonitrile molecules attached to the benzene cation and to the presence of the blocking CH(3) groups, both effects make the addition of more than four acetonitrile molecules less favorable.

Formation of Complex Organics in the Gas Phase by Sequential Reactions of Acetylene with the Phenylium Ion

In this paper, we report a study on the reactivity of the phenylium ion with acetylene, by measuring product yield as a function of pressure and temperature using mass-selected ion mobility mass spectrometry. The reactivity is dominated by a rapid sequential addition of acetylene to form covalently bonded C8H7(+) and C10H9(+) ions with an overall rate coefficient of 7-5 × 10(-10) cm(3) s(-1), indicating a reaction efficiency of nearly 50% at room temperature. The covalent bonding nature of the product ions is confirmed by high temperature studies where enhanced production of these ions is observed at temperatures as high as 660 K. DFT calculations at the UPBEPBE/6-31++G** level identify the C8H7(+) adduct as 2-phenyl-ethenylium ion, the most stable C8H7(+) isomer that maintains the phenylium ion structure. A small barrier of 1.6 kcal/mol is measured and attributed to the formation of the second adduct C10H9(+) containing a four-membered ring connected to the phenylium ion. Evidence for rearrangement of the C10H9(+) adduct to the protonated naphthalene structure at temperatures higher than 600 K is provided and suggests further reactions with acetylene with the elimination of an H atom and an H2 molecule to generate 1-naphthylacetylene or acenaphthylene cations. The high reactivity of the phenylium ion toward acetylene is in sharp contrast to the low reactivity of the benzene radical cation with a reaction efficiency of 10(-4)-10(-5), confirming that the first step in the cation ring growth mechanism is the loss of an aromatic H atom. The observed reactions can explain the formation of complex organics by gas phase ion-molecule reactions involving the phenylium ion and acetylene under a wide range of temperatures and pressures in astrochemical environments.

Hydration of the pyrimidine radical cation and stepwise solvation of protonated pyrimidine with water, methanol, and acetonitrile.

Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH(+)(H2O) consistent with the formation of a weak carbon-based CH(δ+)··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH(+)··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH(+)(CH3OH) and pyrimidineH(+)(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton affinities and dipole moments of acetonitrile and methanol as compared to water. The measured collisional cross sections of the proton-bound dimers provide experimental-based support for the DFT calculated structures at the M06-2x/6-311++G (d,p) level. The calculations show that the hydrated pyrimidine radical cation clusters form internally solvated structures in which the water molecules are bonded to the C4N2H4(●+) ion by weak CH(δ+)··OH2 hydrogen bonds. The hydrated protonated pyrimidine clusters form externally solvated structures where the water molecules are bonded to each other and the ion is external to the water cluster. Dissociative proton transfer reactions C4N2H4(●+)(H2O)(n-1) + H2O → C4N2H3(●) + (H2O)(n)H(+) and C4N2H5(+)(H2O)(n-1) + H2O → C4N2H4 + (H2O)(n)H(+) are observed for n ≥ 4 where the reactions become thermoneutral or exothermic. The absence of the dissociative proton transfer reaction within the C4N2H5(+)(CH3CN)n clusters results from the inability of acetonitrile molecules to form extended hydrogen bonding structures such as those formed by water and methanol due to the presence of the methyl groups which block the extension of hydrogen bonding networks.

Substituent effects on noncovalent bonds: complexes of ionized benzene derivatives with hydrogen cyanide.

Here, we report the first experimental and computational study of the noncovalent binding energies and structures of ionized benzenes containing electron-withdrawing substituents solvated by one to four HCN molecules. Measured by ion mobility mass spectrometric equilibrium studies, the bond dissociation enthalpies of the first HCN molecule to the fluorobenzene (C6H5F(•+)), 1,4-difluorobenzene (C6H4F2(•+)), and benzonitrile (C6H5CN(•+)) ions (11.2, 11.2, and 9.2 kcal/mol, respectively) are similar to those of HCN with the benzene (C6H6(•+)) and phenyacetylene (C6H5CCH(•+)) radical cations (9.2 and 10.5 kcal/mol, respectively). DFT calculations at the B3LYP/6-311++G(d,p) level show that HCN can form in-plane hydrogen bonds to ring hydrogens, or bind electrostatically to positively charged carbon centers in the ring. The electron-withdrawing substituents increase the bond energy by increasing the partial positive charge on the ring hydrogens that form CH(δ+)---NCH bonds, and by creating a π hole, as evidenced by positive charge centers on the fluorinated ring carbons for electrostatically bonded isomers. In the complexes of benzonitrile(•+), similar to benzene(•+), hydrogen bonded planar isomers have the lowest energy. In the complexes of (fluorinated benzene)(•+), the lowest energy isomers are electrostatically bonded where HCN is perpendicular to the ring and its dipole points to a positively charged ring carbon. However, in all cases the planar hydrogen-bonded and vertical electrostatic isomers have similar binding energies within 1 kcal/mol, although HCN interacts with different sites of the ionized benzenes in these isomers, suggesting that the observed cluster populations are mixtures of the planar and vertical isomers. Further HCN molecules can bind directly to unoccupied ring CH hydrogens or bind to the first-shell HCN molecules to form linear HCN---HCN--- hydrogen bonded chains. The binding energies decrease stepwise to about 6-7 kcal/mol by 4 HCN molecules, approaching the macroscopic enthalpy of vaporization of liquid HCN (6.0 kcal/mol).