In this dissertation, the ion mobility mass spectrometry technique is used to study the possible mechanisms of formation of polyaromatic hydrocarbons (PAHs) and polyaromatic nitrogen-containing hydrocarbons (PANHs) via the ion-molecule reactions of acetylene neutrals with different aromatic cations, in order to infer the possible mechanisms of formation of PAHs and PANHs in different environments such as interstellar media under different ionizing conditions. Furthermore, this technique is used to probe structures, address the thermochemistry, and measure the kinetics of the product ions originated from these reactions. Reactions of benzene radical cations with acetylene produce styrene and naphthalene-type cations at high temperatures. The second order rate constant of this reaction is found to be in the order of 10-14 cm3.s-1 with a barrier of 3.5 kcal.mol-1. Under low temperature regime, benzene radical cation acts as a catalyst to initiate the formation of higher complex hydrocarbons through the associative charge transfer to the acetylene clusters, (C2H2)n+, n= 6-10. Phenylium cation reactions with acetylene is found to be four orders of magnitudes faster than those of benzene radical cation, as predicted theoretically. In these systems the second addition of acetylene molecule is found to follow the Bittner-Howard mechanism. Phenylacetylene and styrene radical cations reactions with acetylene are also studied and the addition of one acetylene molecule to the radical cation is observed. The second order rate constant of the product ions is found to be in the order of 10-13 and 10-14 cm3.s-1 for the phenylacetylene and styrene radical cations respectively. Ion molecule reactions of pyridine cation, benzonitrile cation and pyrimidine radical cation with acetylene are studied. Formation of complex organics with fused nitrogen atom in an aromatic ring is reported. Condensation products of acetylene via the ion-molecule reactions are observed with pyridine cation of up to five acetylene molecules onto the pyridine cation at room temperature. Meanwhile, condensation of only two acetylene molecules is observed for benzonitrile cation and pyrimidine radical cation respectively. In the later case, these condensation reactions are observed with hydrogen abstraction. Ion mobility measurements, collisional induced dissociation (CID) and ab initio calculations are combined to probe the possible structures of the reaction products. Formation of PAHs over nanoparticle surfaces is carried out by studying polymerization of acetylene over Pd nanocatalyst and supported Pd nanocatalyst over MgO and CeO2 prepared by the LVCC technique under different temperature conditions. C8H10 species are formed at 400 oC. However, at 600 oC, production of C16H10 (pyrene isomer) is found to be the major catalytic product. Self polymerization of acetylene at different temperatures is presented as well. Our results of the ion-molecule reactions, associative charge transfer (ACT) and catalytic polymerization over catalysts surfaces’ of acetylene interacting with different aromatic and heterocyclic cations could explain the different possible pathways of formation of complex organics in different ionizing environments in carbon-rich interstellar media in space.

The syntheses and characterization of the palladium complexes [Pd(accp)2] (7), [Pd(acch)2] (8), [Pd(η3-CH2CMeCH2)(accp)] (11), [Pd(η3-CH2CMeCH2)(acch)] (12), [Pd(η3-CH2CtBuCH2)(accp)] (13) and [Pd(η3-CH2CtBuCH2)(acch)] (14) (accp = 2-acetylcyclopentanoate; acch = 2-acetylcyclohexanoate) are reported. These complexes are available by the reaction of Haccp (2-acetylcyclopentanone) and Hacch (2-acetylcyclohexanone) with Na2[Pd2Cl6] forming 7 and 8 or with [(Pd(η3-CH2CRCH2)(μ-Cl))2] (9, R = Me; 10, R = tBu) forming 11–14. The molecular structures of 7, 8 and 14 are discussed. Complexes 7 and 8 consist of a square-planar coordinated Pd atom with two trans-positioned bidentate β-diketonate ligands. The asymmetric unit of 14 exhibits one molecule of the palladium complex and a half molecule of water. The thermal behavior of 7, 8 and 11–14 and their vapor pressure data were investigated to show, if the appropriate complexes are suited as CVD precursors for palladium layer formation. Thermogravimetric studies showed the evaporation of the complexes at atmospheric pressure upon heating. The vapor pressure of 7, 8 and 11–14 was measured by using thermogravimetric analysis, giving vapor pressure values ranging from 0.62 to 2.22 mbar at 80 °C. Chemical vapor deposition studies were carried out applying a vertical cold wall CVD reactor. Either oxygen or forming gas (N2/H2, ratio 90/10, v/v) was used as reactive gas. Substrate temperatures of 350 and 380 °C were utilized. With 11–14 dense and conformal as well as particulate palladium films were obtained, as directed by SEM studies, whereas 7 and 8 failed to give thin films, which is probably attributed to their high thermal stability in the gas phase. For all deposited layers, XPS measurements confirmed the partial oxidation of palladium to palladium(II) oxide at 380 °C, when oxygen was used as reactive gas. In contrast, thin layers of solely metallic palladium were obtained utilizing forming gas during the deposition experiments. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Neste trabalho, as fragmentações de 2-aroilbenzofuranos e de neolignanas diidrobenzofurânicas (NDB) foram investigadas empregando espectrometria de massas sequencial com ionização por eletrospray (ESI-MS/MS). Os compostos estudados foram sintetizados e, em seguida, suas vias de fragmentação em condições de dissociação induzida por colisão (CID) foram associadas às suas respectivas estruturas. Além das relações estrutura-fragmentação, espectrometria de massas de múltiplos estágios (MSn) e dados termoquímicos, obtidos por Química Quântica Computacional, foram também utilizados para a elucidação das vias de fragmentação. Para os 2-aroilbenzofuranos protonados, os resultados demonstraram que dois íons acílios, provenientes de rearranjos de hidrogênio competitivos, são os mais intensos nos espectros de íons produtos. O íon acílio [M+HC6H6]+ foi o mais intenso para todos os 2-aroilbenzofuranos investigados devido ao fato de que sua decomposição requerer energia crítica maior que a de outras vias de fragmentação competitivas. No caso das NDBs, os resultados indicaram que perdas de CH3OH e CO são comuns aos compostos analisados, tanto na forma protonada como na forma desprotonada. Entretanto, as perdas de CH3OH a partir de NDB protonadas envolvem migração de carga, enquanto que para moléculas desprotonadas, a perda de metanol é um processo remoto à carga. A perda de ceteno (C2H2O) diretamente da molécula protonada é uma via diagnóstica das NDB acetiladas, enquanto que os íons produtos [M+HC3H6O2]+ ou [M+HC6H6O]+ são diagnósticos das NDB que apresentam saturação entre C7 e C8. Para NDBs desprotonadas, íons produtos formados por perdas de CH3 são diagnósticos de grupos metoxila ligados ao anel aromático. A presença do grupo acetil também levou à formação de alguns íons diagnósticos devido à mudança no sítio de desprotonação. Por sua vez, clivagens da cadeia lateral remotas à carga são fragmentações diagnósticas de NDBs que apresentam saturação entre C-7 e C-8. As estruturas dos íons propostos foram suportadas por dados termoquímicos (entalpia e energia de Gibbs). Os resultados deste trabalho contribuem para o conhecimento da química em fase gasosa desses compostos e auxiliarão na identificação dos mesmos diretamente de misturas. / In this work, the fragmentation of 2-aroylbenzofuran and dihydrobenzofuran neolignans (DBN) was investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS). The studies compounds were synthesized and their fragmentation pathways under collision-induced dissociation (CID) were associated with their respective structures. Besides the structure-fragmentation correlations, multiple-stage mass spectrometry (MSn) and thermochemical data, which were estimated by Quantum Computational Chemistry, were also employed in the elucidation of the fragmentation pathways. For protonated 2-aroylbenzofuran, the results demonstrated that two acylium ions, which arises from two competitive hydrogen rearrangements, are the most intense in the product ion spectra. The acylium ion [M+HC6H6]+ was the most intense for all the investigated 2-aroylbenzofuran, since its decomposition requires a higher critical energy as compared to other competitive fragmentation processes. In the case of DBNs, our results indicated that eliminations of CH3OH e CO are common to the analyzed compounds in their protonated and deprotonated forms. However, eliminations of CH3OH from protonated DBNs involve charge migration, whereas elimination of CH3OH from deprotonated DBNs is a fragmentation remote to the charge site. Elimination of ketene (C2H2O) directly from the protonated molecule is diagnostic for acetylated DBNs, whereas the product ions [M+HC3H6O2]+ or [M+HC6H6O]+ are diagnostic for DBNs displaying a saturated bond between C7 and C8. For deprotonated DBNs, product ions resulting of CH3 losses are diagnostic for methoxyl groups attached to the aromatic ring. The presence of the acetyl group also led to the formation of some diagnostic ions due to the change of the deprotonation site. For compounds that display a saturated bond between C-7 and C-8, cleavages of the side chain of DBNs are also diagnostic. The structures of the proposed ions were supported by thermochemical data (enthalpy and Gibbs energy). The results of this work will contribute to the knowledge of the gas-phase ion chemistry of these compounds and will aid in their identification directly from mixtures.

A presente tese tem por objetivo inicial estudar a reatividade de ésteres de Si, N, S e seus análogos em fase gasosa para obter informações detalhadas do mecanismo destas espécies quando submetidas a ataque nucleofílico, sobretudo no que tange a competição entre as vias de substituição nesses centros e no carbono. Esses estudos são realizados experimentalmente através da técnica de espectrometria de massas por transformada de Fourier e ressonância ciclotrônica de íons (FT-ICR) e amparados por cálculos de estrutura eletrônica. Os resultados obtidos indicam que, para o Si, as alcoxissilanas reagem com os nucleófilos através de um aduto pentacoordenado que desloca, preferencialmente, um alcóxido. De forma minoritária, pode ocorrer o deslocamento de outro ligante gerando silóxidos ou carbânions. Neste estudo, foi caracterizada uma reação inédita de troca de Me por F nos silóxidos mediada por NF3. Os estudos dos ésteres de nitrogênio indicam que as reações de eliminação são mais favoráveis que as de substituição e que a substituição no nitrogênio, apesar de ser considerada mais favorável pelos cálculos, não é observada. Esse comportamento foi elucidado através do uso de dinâmica molecular e indica que o complexo de entrada para a via de reação no nitrogênio não é formado devido à repulsão sofrida pelo nucleófilo pelos oxigênios que rodeiam o centro de N. Resultados teóricos semelhantes foram encontrados para os ésteres de enxofre e, em adição aos resultados experimentais disponíveis, indicam que não só a dinâmica de reação exerce um papel importante nesses sistemas, como também sugerem uma compensação entre o caráter dinâmico e a termoquímica destes sistemas. Para nucleófilos fracos que não são favoráveis do ponto de vista termoquímico, a formação do complexo de entrada não é impedida pela repulsão, dado que esses nucleófilos não costumam ter centros nucleofílicos com carga muito localizada. O oposto ocorre com nucleófilos fortes, que procederiam pelo caminho de substituição no S por uma via praticamente sem barreira, mas não o fazem já que a repulsão do nucleófilo é muito intensa. Em uma segunda etapa a solvatação dos íons F-, Br- e I- foram estudadas na fase gasosa a partir da espectroscopia dissociação no infravermelho. A partir da formação por uma fonte de eletrospray de agregados altamente solvatados, foi possível determinar o efeito dos íons na organização das moléculas de solvente, determinar a mudança da solvatação interna para solvatação de superfície e determinar o número de hidratação em fase gasosa para os íons Br- e F-. Além disso, tanto os resultados experimentais quanto teóricos mostram que a natureza do íon influencia a primeira camada de solvatação e que a carga formal tem um efeito predominante em longo alcance, podendo organizar até centenas de moléculas de solventes. Por fim, realizamos a adaptação do sistema de aquisição do FT-ICR do laboratório. Isso não só confere um sistema atualizado ao nosso instrumento, como possibilita que novos experimentos, como a espectroscopia de íons, possam ser realizados no nosso grupo de pesquisa. / This thesis comprises the study of the reactivity of gas-phase ions in the gas-phase and the structural modifications observed for gas-phase ions as a function of progressive solvation by spectroscopic techniques. In the first part, we describe the gas-phase reactivity of Si, N, and S esters and their analogs towards simple nucleophiles and a detailed analysis of the competition between different reaction channels namely substitution vs. elimination. These studies were carried out by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR) and supported by theoretical calculations. Our results suggest that alkoxysilanes react with nucleophiles via a pentacoordinated adduct that results in alkoxide displacement as the major reaction channel. The displacement of other ligands can also occur to yield siloxides or carbanions. As part of these studies, we also report a Me/F exchange reaction in siloxide ions mediated by NF3. Results obtained for the nitrogen esters show elimination-type reactions to be the most favorable pathway followed by nucleophilic displacement. No displacement was observed at the nitrogen center in spite of the fact that calculations predict this channel to be the most favorable pathway. This behavior was further explored by ab initio molecular dynamics calculations that show that the entrance complex for the nitrogen pathway is avoided because of the strong electrostatic repulsion exerted by the oxygen atoms as the nucleophile approaches the N center. Similar theoretical results were obtained for the sulfur esters. Comparison of these calculations with the experimental results also suggests that the reaction dynamics play an important role in these systems. Furthermore, we propose that a combination of thermochemical and dynamic balance hinders substitution at the heteroatom. For strong nucleophiles that could undergo substitution at the S center via a barrierless pathway, the reaction is hindered by the strong repulsion experienced by these nucleophiles. In the second part, we study the structure of gas-phase solvated F-, Br- and I- by infrared dissociation spectroscopy. The highly solvated clusters were generated by electrospray ionization and their structures probed to gather information regarding the short and long-range effect of these ions on the solvation network. Solvation parameters such as the number of water molecules needed for a switch from internal to surface solvation and the hydration numbers for F- and Br- were determined. Theoretical and experimental results show that the solvation pattern of the first solvation shell for these ions depends on the nature of the ion while the ion charge prevails in determining the long-range pattern. This pattern effect is shown to prevail up to hundreds of solvent molecules. Finally, a new data acquisition and control system is described for our FT-ICR spectrometer. This system not only updates the original instrument but it also brings in new capabilities to the spectrometer such as the ability to carry out gas-phase ion dissociation spectroscopy.

Non-covalent interactions in solution are subject to modulation by surrounding solvent molecules. This thesis presents two experimental molecular balances that have been used to quantify solvent effects on non-covalent interactions, including electrostatic and dispersion interactions. The first chapter introduces literature where non-covalent interactions have been studied in a range of solvents, particularly those where the effects of aqueous or fluorous solvents have been investigated. These solvents are of particular interest as they both invoke solvophobic effects on organic molecules, but have differing chemical and physical properties. The second chapter describes the adaptation of the Wilcox molecular torsion balance to study interactions between organic and fluorinated carbon chains in a range of solvents. Solvent cohesion was found to be the principle force driving both the alkyl and fluorous chains together in aqueous solvents, where no contribution to the interaction energy arising from dispersion forces could be detected. In fluorous and polar organic solvents evidence was found for weak favourable dispersion interactions between the alkyl chains. In contrast dispersion forces between the chains were found to be disrupted by competitive van der Waals interactions with surrounding solvent molecules in apolar organic solvents. Association of the fluorous chains was found to be solely driven by solvent cohesion. The final chapter describes the design and synthesis of a novel synthetic molecular-balance framework and describes its application to simultaneously measure solvent and substituent effects on the position of conformational equilibria. Despite the simplicity of the model system, surprisingly complicated behaviour emerged from the interplay of conformational, intramolecular and solvent effects. Nonetheless, a large data set of experimental equilibrium constants was analysed using a simple solvent model, which was able to account for both the intuitive and more unusual patterns observed. A means of dissecting electrostatic and solvent effects to reveal pseudo gas-phase behaviour has resulted from the analysis of experimental data obtained in many solvents.

The microcantilever (MC) has become a common transducer for chemical and biological sensing in gas phase and liquid phase during recent years. MC sensors provide superior mass sensitivity by converting weak chemical and biological stimuli into high mechanical response. Moreover, other advantages such as small size, low cost and array format have made MCs more attractive than other comparable sensors. Selectivity in MC sensors can be enhanced by creating a differentially functionalized MC array (MCA) with responsive phases (RPs). A well-designed array should incorporate RPs exhibiting a variety of possible interactions with the analytes, and a specific analyte should induce a distinctive response pattern demonstrated by the array. The first major division of the dissertation research work focused on enhancing selectivity of MC sensor by creating a differentiating MCA. The MCs within the array were nanostructured in a previously developed manner. A self-designed capillary array was set up to chemically functionalize different ligands onto individual MCs in an array for metal ion sensing in liquid phase. Another array was prepared by selectively vapor depositing different organic RPs onto nanostructured MCs and applied to landfill siloxane sensing in gas phase. Both of the arrays demonstrated response diversity to the target analytes. The second major division of the dissertation research work focused on developing a new method to modify MC surfaces with a function nanostructure. Aluminium oxide nanoparticles (AONP) were uniformly dispersed onto MC and a roughened surface with high surface area was achieved as stable sensor platform. Alkoxysilyl compounds were then grafted onto this platform as RPs. For demonstration, a MCA functionalized with three different alkoxysilanes was prepared for volatile organic compound sensing in gas phase. Additionally, another MCA was functionalized with anti-human immunoglobulin G and anti-biotin for bio-sensing in liquid phase. Both of the arrays were prepared with the aforementioned capillary array setup. Selective responses of specific analytes, as well as good sensitivity, were obtained from each type of AONP MCA.

This thesis summarises experimental results on the molecular spectroscopy of gas phase molecules excited by synchrotron radiation in the VUV and soft X-ray regions. We have used three different detection techniques, photon induced fluorescence spectroscopy, photoionisation mass spectroscopy and near edge X-ray absorption fine structure spectroscopy to study molecular deuterium, hydrogen sulphide, ammonia, methanol, pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, and 2-deoxy-D-ribose, the last one also known as the DNA sugar. Out of this variety of techniques and molecules we have shown that: (1) high resolution dispersed fluorescence allows us to identify vibrational and rotational bands in molecular deuterium, as well as to estimate the predissociation probability of the same molecule [paper I]; (2) the main species fluorescing after core excitation of methane, ammonia [paper III], hydrogen sulphide [paper II], pyridine, pyrimidine and s-triazine is H Balmer α, followed by fluorescence from ionised species, molecular bands and Balmer β, γ , δ; (3) the Rydberg enhancement seen in fluorescence measurements of water [Melero et al. PRL 96 (2006) 063003], corroborated later in H2S [paper II], NH3 [paper III] and CH4 [paper III] and postulated as general behaviour for molecules formed by low-Z atoms, is also seen in larger organic cyclic molecules, e.g. azabenzenes; (4) when dissociative ionisation of pyridine, pyridazine, pyrimidine, pyrazine, s-triazine and 2-deoxy-D-ribose occurs, concerted bond rearrangement and nuclear motion takes place as opposed to stepwise dissociation [papers V and VI]. / QC 20100916

Degassing and in situ formation of a mobile gas phase takes place when an aqueous phase equilibrated with a gas at a pressure higher than the subsurface pressure is injected in water-saturated porous media. This process, which has been termed supersaturated water injection (SWI), is a novel and hitherto unexplored means of introducing a gas phase into the subsurface. Herein is a first macroscopic account of the SWI process on the basis of continuum scale simulations and column experiments with CO2 as the dissolved gas. A published empirical mass transfer correlation (Nambi and Powers, Water Resour Res, 2003) is found to adequately describe the non-equilibrium transfer of CO2 between the aqueous and gas phases. Remarkably, the dynamics of gas-water two-phase flow, observed in a series of SWI experiments in homogeneous columns packed with silica sand or glass beads, are accurately predicted by traditional two-phase flow theory which allows the corresponding gas phase relative permeability to be determined. A key consequence of the finding, that the displacement of the aqueous phase by gas is compact at the macroscopic scale, is consistent with pore scale simulations of repeated mobilization, fragmentation and coalescence of large gas clusters (i.e., large ganglion dynamics) driven entirely by mass transfer. The significance of this finding for the efficient delivery of a gas phase below the water table in relation to the alternative process of in-situ air sparging and the potential advantages of SWI are discussed. SWI has been shown to mobilize a previously immobile oil phase in the subsurface of 3-phase systems (oil, water and gas). A macroscopic account of the SWI process is given on the basis of continuum-scale simulations and column experiments using CO2 as the dissolved gas and kerosene as the trapped oil phase. Experimental observations show that the presence of oil ganglia in the subsurface alters gas phase mobility from 2-phase predictions. A corresponding 3-phase gas relative permeability function is determined, whereas a published 3-phase relative permeability correlation (Stone, Journal of Cana Petro Tech, 1973) is found to be inadequate for describing oil phase flow during SWI. A function to predict oil phase relative permeability is developed for use during SWI at high aqueous phase saturations with a disconnected oil phase and quasi-disconnected gas phase. Remarkably, the dynamics of gas-water-oil 3-phase flow, observed in a series of SWI experiments in homogeneous columns packed with silica sand or glass beads, are accurately predicted by traditional continuum-scale flow theory. The developed relative permeability function is compared to Stone’s Method and shown to approximate it in all regions while accurately describing oil flow during SWI. A published validation of Stone’s Method (Fayers and Matthews, Soc of Petro Eng Journal, 1984) is cited to validate this approximation of Stone’s Method.

Copper ions (Cu⁺, Cu²⁺) play important roles in many biological processes (i.e., oxidation, dioxygen transport, and electron transfer); many of the functions in these processes result from copper ions interacting with proteins and peptides. Previous studies using matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) have shown that Cu⁺ ions preferentially bind to electron rich groups in gas phase (i.e., N-terminal amino group, the side-chains of lysine, histidine and arginine). For peptides with more than one Cu⁺ ligand, the interaction between Cu⁺ ions and ligands is described in terms of competitive binding; however, Cu⁺ coordination chemistry for multiple Cu⁺-containing proteins and peptides in gas phase is still not fully understood. In addition, no studies on the fragmentation chemistry for multiple Cu⁺-binding peptides, such as [M + 2Cu - H]⁺ ions, have been reported. The synthesized dinuclear copper complex (alpha-cyano-4-hydroxycinnamic acid (CHCA) copper salt (CHCA)₄Cu₂) enhances the ion abundances for [M + xCu - (x-1)H]⁺ (x = 1-6) ions in gas-phase when used as a MALDI matrix. Using this matrix we have investigated site-specific copper binding of several peptides using fragmentation chemistry of [M + Cu]⁺ and [M + 2Cu - H]⁺ ions. The fragmentation studies reveal that the binding of a single Cu⁺ ion and two Cu⁺ ions are different, and these differences are explained in terms of intramolecular interactions of the peptide-Cu ionic complex. The competitive Cu⁺ binding to C-terminus (i.e., amide, carboxyl, methyl ester) versus lysine, as well as cysteine (SH/SO₃H) versus arginine (guanidino), was also examined by MALDI MS and theoretical calculations (Density Functional Theory (DFT)). For example, results from theoretical and experimental (fragmentation reactions) studies on [M + Cu]⁺ and [M + 2Cu - H]⁺ ions suggest that cysteine side chains (SH/SO₃H) are important Cu⁺ ligands. Note that, the proton of the SH/SO₃H group is mobile and can be transferred to the arginine guanidino group. For [M + 2Cu - H]⁺ ions, deprotonation of the -SH/SO₃H group is energetically more favorable than that of the carboxyl group, and the resulting thiolate/sulfonate group plays an important role in the coordination structure of [M + 2Cu - H]⁺ ions.

IM-MS is a 2-D technique which provides separations based on ion shape (ion-neutral collision cross-section, Ω) and mass (m/z ratio). Ion structures can be deduced from the measured collision cross-section (Ωmeas) by calculating the collision cross-sections (Ωcalc) of candidates generated by molecular dynamics (MD) and compared with the experiment results. A database of Ωs for singly-charged peptide ions is presented. Standard proteins are digested using different enzymes (trypsin, chymotrypsin and pepsin), resulting in peptides that differ in amino acid composition. The majority (63%) of the peptide ion correlates well with the globular structures, but some exhibit Ωs that are significantly larger or smaller than the average correlation. Of the peptide ions having larger Ωs, approximately 71% are derived from trypsin digestion and most of the peptide ions that have smaller Ωs are derived from pepsin digestion (90%). We use computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH2-Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI and compare the structures of MIFAGIK derivatives to test the ‘sensitivity’ of the cluster analysis method. Cluster analysis suggests that [MIFAGIK + H]+ ions formed by MALDI have a predominantly turn structure even though the low energy ions prefer partial helical conformers. Although the ions formed by ESI have Ωs that are different from those formed by MALDI, the results of cluster analysis indicate that the ions backbone structures are similar. Chemical modifications (N-acetyl, methylester, as well as addition of Boc or Fmoc groups) of MIFAGIK alter the distribution of various conformers, the most dramatic changes are observed for the [M + Na]+ ion, which show a strong preference for random coil conformers owing to the strong solvation by the backbone amide groups. Ωmeas of oligodeoxynucleotides in different length have been measured in both positive and negative modes. For a given molecular weight and charge state, Ωmeas of the oligodeoxynucleotide ions are smaller than those of the peptides, indicating their different packing efficiency. A novel generalized non-Boltzman sampling MD has been utilized to investigate the gas-phase ion conformations of dGGATC based on the free energy values. Theory predicts only one low-energy conformer for the zwitterionic form of dGGATC- while dGGATC+ ions have several stable conformers in both canonical and zwitterionic form in the gas phase, in good agreement with the experiment.