Methanol Clusters Research Articles

Scrubbing Ions with Molecules: Kinetic Studies of Chemical Noise Reduction in Mass Spectrometry Using Ion−Molecule Reactions with Dimethyl Disulfide

The kinetics and product distributions of the reactions of dimethyl disulfide (DMDS) have been investigated with a group of chemical background ions commonly observed in atmospheric pressure ionization (API) mass spectrometry (MS) in order to assess the value of this molecule in filtering (or "scrubbing") these ions by changing their mass/charge (m/z) ratio. The measurements were taken with a novel electrospray ionization/selected ion flow tube/QqQ tandem mass spectrometer. The background ions studied include those with m/z 42 (protonated acetonitrile, ACN), 83 (protonated ACN dimer), 99 (protonated phosphoric acid), 117 (water cluster of m/z 99), 131 (methanol cluster of m/z 99), 149 (protonated phthalic anhydride, formed from the phthalates), and 327 (protonated triphenyl phosphate). In addition, reactions of DMDS have been studied with two model analytes--protonated caffeine and doubly protonated bradykinin--in order to assess the selectivity of DMDS reactivity. All the measurements were taken at 295 +/- 2 K in helium buffer gas at a pressure of 0.35 +/- 0.01 Torr. DMDS was observed to react efficiently with m/z 42 (ACNH+), 149 (from phthalates), and 99 (protonated phosphoric acid), with k/kc=0.91, 0.47, and 0.38, respectively. Only proton transfer was observed with ACNH+, followed by the secondary reaction of [DMDSH]+ with DMDS to yield [CH3S-S(CH3)-SCH3]+. Ligation of DMDS was the dominant primary channel observed for the reaction of the m/z 149 background ion; however, some proton transfer also was observed. Both of these primary product ions react further with DMDS to yield [CH3S-S(CH3)-SCH3]+, the structure of which we have determined computationally using DFT calculations. Only the sequential ligation with two DMDS molecules was observed for the reaction of the m/z 99 ion. Reactions of DMDS with m/z 117 [H3PO4 + H + H2O]+ and m/z 131 [H3PO4 + H + MeOH]+ were observed to proceed with k/kc=0.71 and 0.058, respectively. Ligand substitution of DMDS for H2O predominated ( approximately 94%) over DMDS ligation ( approximately 6%) in the reaction with m/z 117, while only DMDS ligation was observed for the reaction of m/z 131 with DMDS. In contrast, the reactions of DMDS with ions of m/z 83 (protonated dimer of ACN) and 327 (protonated triphenyl phosphate) were extremely inefficient, with k/kc=0.0042 and 0.0079, respectively. The higher reactivity of DMDS toward ACNH+ (m/z 42) compared to (ACN)2H+ (m/z 83) is attributed to the lower proton affinity of the unsolvated ACN. The reactivity of DMDS toward the two model analyte ions studied-protonated caffeine and doubly protonated bradykinin-was negligible, with k/kc=0.0073 and 0.010, for the respective reactions. These results suggest that, under appropriate reagent pressure conditions, DMDS can be an appropriate reagent for chemically filtering out many common API-MS background ions, without significantly affecting the observed intensity of analyte peaks.

A possible mechanism underlying the anomalous dielectric response in concentrated methanol-in-carbon tetrachloride mixtures

The association of CCl4 with the non-donating ends of open (chain-like)methanol aggregates, is shown to be relevant in the occurrence of positive deviations of the static dielectric constant with respect to ideality in methanol/CCl4 mixtures. This interaction tends to reduce in fact the fraction of methanol aggregated in cyclic clusters. This hypothesis is suggested by the comparison with the data of lattice calculations for the equilibrium distribution of methanol clusters.

Structural, Energetic, and Infrared Spectra Insights into Methanol Clusters (CH3OH)n, for n = 2-12, 16, 20. ONIOM as an Efficient Method of Modeling Large Methanol Clusters.

An investigation of gas-phase methanol clusters (CH3OH)n, where n = 2-12, 16, and 20, was completed with a range of computational methods: PM3, Hartree-Fock, B3LYP, MP2, and their combination using an ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) method. Geometries, binding energies, and vibrational frequencies are reported. For all ab initio optimized structures, the cyclic isomer was found to be the most stable structure of all isomers investigated. The scaled OH frequency shift for n = 1-4 is found to be in good agreement with experimentally measured shifts. An ONIOM method, with the methyl group calculated at the low level and the hydroxyl group at the high level, proved to be an excellent way of reducing computational expense. The calculated enthalpies, geometries, and infrared spectra using an ONIOM method were comparable to that of a high-level calculation. Clusters were solvated using the integral equation formalism for the polarized continuum model method to compare with the microsolvation studies.

Synthesis and X-ray crystallographic investigation of a novel indole-based cryptand: structure of a sandwiched cyclic S 6 hexameric methanol cluster

Synthesis of a novel cryptand with an indole moiety in its architecture is described. Crystal structures of this newly synthesized cryptand and its trialdehyde precursor have been investigated. In the case of the cryptand molecule, a discrete cyclic S 6-symmetric hexameric methanol cluster sandwiched between the hydrophobic ends of two cryptand units was characterized crystallographically. Moreover, a hexameric cyclic chair conformation composed of methanol and secondary nitrogen atoms from the cryptand skeleton was also identified.

Irradiation Effects of Methanol Cluster Ion Beams on Solid Surfaces

AbstractIn order to investigate the interactions of methanol cluster ion beams with solid surfaces, Si substrates and SiO2 films were irradiated at different acceleration voltages. The sputtered depth increased with increase of the acceleration voltage. When the acceleration voltage was 9 kV, the sputtered depths of Si and SiO2 at a dose of 1×1016ions/cm2 were 1497.1 nm and 147.8 nm, respectively. The selectivity between Si and SiO2 surfaces arose from the volatility of the reaction products. Furthermore, the sputtering yield for the Si surface was approximately seven hundreds times larger than that by Ar monomer ion beams. This suggested that chemical sputtering was predominant for the methanol cluster ion irradiation. In addition, the etching and cleaning process by the methanol cluster ion irradiation was performed on the Si surfaces contaminated with a small amount of metal particles such as Au and Al. Thus, methanol cluster ion beams have unique characteristics such as surface etching and cleaning with high sputtering yield and smooth surface.

APPI-MS: Effects of Mobile Phases and VUV Lamps on the Detection of PAH Compounds

The technique of atmospheric pressure photoionization (APPI) has several advantages over electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), including efficient ionization of nonpolar or low charge affinity compounds, reduced susceptibility to ion suppression, high sensitivity, and large linear dynamic range. These benefits are greatest at low flow rates (i.e., <or=100 microL/min), while at a higher flow, photon absorption and ion-molecule reactions become significant. Under certain circumstances, APPI signal and S/N have been observed to excel at higher flow, which may be due to a nonphotoionzation mechanism. To better understand APPI at higher flow rates, we have selected three lamps (Xe, Kr, and Ar) and four mobile phases typical for reverse-phase, high-pressure liquid chromatography: acetonitrile, methanol, (1:1) acetonitrile:water and (1:1) methanol:water. As test compounds, three polyaromatic hydrocarbons are studied: benzo[a]pyrene, indeno[1,2,3-c, d]pyrene and benz[a]anthracene. We find that solvent photoabsorption cross-section is not the only parameter in explaining relative signal intensity, but that solvent photo-ion chemistry can also play a significant role. Three conclusions from this investigation are: (1) methanol photoionization leads to protonated methanol clusters that can result in chemical ionization of analyte molecule; (2) use of the Ar lamp often results in greater signal and S/N; (3) acetonitrile photoionization is less efficient and resulting clusters are too strongly bound to chemically ionize the analyte efficiently, so that analyte ion formation is dominated by direct photoionization.

Nanostructured Thermosensitive Polymers with Radical Scavenging Ability

The thermosensitive [60]fullerene end-capped poly(N-isopropylacrylamide) was successfully synthesized by the reaction of C(60) with dithiobenzoate-terminated poly(N-isopropylacrylamide), which was prepared by reversible addition-fragmentation chain-transfer (RAFT) polymerization in the presence of azobisisobutyronitrile (AIBN). Its structure was determined by FTIR, UV/Vis, and carbon and proton NMR spectroscopy as well as by size exclusion chromatography (SEC). The novel fullerenated polymer retained the thermosensitivity of poly(N-isopropylacrylamide). Moreover, it is soluble in water and most of the common organic solvents. Interestingly, it was able to form nanoparticle clusters in methanol and exhibited significant radical scavenging ability in cell viability and metabolic activity tests with fibroblasts and NOR-3 radicals.

Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide.

The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion-solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of -263.5, -260.2, and -273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the solvents mentioned above.

Formation of H 3O + by the soft X-ray ionization of ethanol clusters

Time-of-flight mass spectra have been measured for inner-shell ionization of ethanol molecules, its clusters, and methanol clusters at the oxygen K-edge regions. Only in the case of the ethanol clusters, a fairly intense signal corresponding to H 3O + has been observed. The measurements for ethanol- d 1 (C 2H 5OD) suggest that at least one H atom in the H 3O + ion originates from the C 2H 5 group of neighbouring ethanol. It is proposed that in addition to the O–H⋯OH type hydrogen bonding in the ethanol clusters, the H in the C 2H 5 group and OH interact with each other.

A Density Functional Study of Methanol Clusters.

The potential energy surfaces of methanol clusters, (CH3OH)n, n = 2-12, have been studied using density functional theory at the B3LYP/6-31G(d) and higher levels of theory. Cyclic clusters in which n methanol molecules are joined in a ring structure formed by n hydrogen bonds are shown to be more stable than structures of the same number of methanol molecules where one or more methanol molecules are outside the ring and are hydrogen-bonded to oxygens of methanols in rings of n - 1, n - 2, and so forth. So-called chain structures are generally even less stable. Furthermore, the hydrogen-bonding energy per methanol molecule of the n-ring clusters is shown to converge to an asymptotic value of about 27 kJ/mol at B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) after five to six methanols are included in the cluster. As expected, there are many minima on the potential energy surfaces of the methanol clusters, the number increasing rapidly with n. A cyclic cluster of five to six methanol molecules appears to be sufficient to mimic liquid behavior as far as vibrational frequencies are concerned.

Two size regimes of methanol clusters produced by adiabatic expansion

Free neutral methanol clusters produced by adiabatic expansion have been studied by photoelectron spectroscopy and line shape modeling. The results show that clusters belonging to two distinct size regimes can be produced by changing the expansion conditions. While the larger size regime can be well described by line shapes calculated for clusters consisting of hundreds of molecules, the smaller size regime corresponds to methanol oligomers, predominantly of cyclic structure. There is little contribution from dimers to the spectra.

Photoelectron imaging of large anionic methanol clusters: (MeOH)n− (n∼70–460)

Electron solvation in methanol anion clusters, (MeOH)(n) (-) (n approximately 70-460), is studied by photoelectron imaging. Two isomers are observed: methanol I, with vertical binding energies (VBE) ranging from 2-2.5 eV, and methanol II, with much lower VBE's between 0.2 and 0.5 eV. The VBE's of the two isomers depend linearly on n(-1/3) with nearly identical slopes. We propose that the excess electron is internally solvated in methanol I clusters, whereas in methanol II it resides in a dipole-bound surface-state. Evidence of an excited state accessible at 1.55 eV is observed for methanol I.

Cooperative organic hydrogen bonds: The librational modes of cyclic methanol clusters

Intermolecular hydrogen bond libration modes of isolated cyclic methanol trimers (approximately 613 cm(-1)) and tetramers (695 and 760 cm(-1)) are observed in pulsed jet Fourier transform infrared spectra and found to exhibit sizeable anharmonicity and mode coupling effects, opening the way for a microscopic interpretation of the broad librational bands of alcohols. The correlation of experimental OH stretching and OH libration band intensities provides important constraints for theoretical band strengths, cluster densities, and size assignments.

Infrared plus vacuum ultraviolet spectroscopy of neutral and ionic methanol monomers and clusters: New experimental results

We present new observations of the infrared (IR) spectrum of neutral methanol and neutral and protonated methanol clusters employing IR plus vacuum ultraviolet (vuv) spectroscopic techniques. The tunable IR light covers the energy ranges of 2500-4500 cm(-1) and 5000-7500 cm(-1). The CH and OH fundamental stretch modes, the OH overtone mode, and combination bands are identified in the vibrational spectrum of supersonic expansion cooled methanol (2500-7500 cm(-1)). Cluster size selected IR plus vuv nonresonant infrared ion-dip infrared spectra of neutral methanol clusters, (CH(3)OH)(n) (n=2,[ellipsis (horizontal)],8), demonstrate that the methanol dimer has free and bonded OH stretch features, while clusters larger than the dimer display only hydrogen bonded OH stretch features. CH stretch mode spectra do not change with cluster size. These results suggest that all clusters larger than the dimer have a cyclic structure with OH groups involved in hydrogen bonding. CH groups are apparently not part of this cyclic binding network. Studies of protonated methanol cluster ions (CH(3)OH)(n)H(+) n=1,[ellipsis (horizontal)],7 are performed by size selected vuv plus IR photodissociation spectroscopy in the OH and CH stretch regions. Energies of the free and hydrogen bonded OH stretches exhibit blueshifts with increasing n, and these two modes converge to approximately 3670 and 3400 cm(-1) at cluster size n=7, respectively.

Reactions of Laser Ablation-magnesium Plasma with Methanol Clusters

The laser ablation-molecular beam(LA-MB) method is useful for studying the reactions of metal ions with molecular clusters. Reactions of magnesium plasma with methanol clusters were studied by using this method. A specially designed reaction cell was used as a fast flow reactor operated under thermal conditions, and the reaction products were measured with a time-of-flight(TOF) mass spectrometer. Surprisingly, several series of cluster ions with complex sizes and intensity distributions were obtained when the laser ablating was applied to different parts of the molecular beam. In the front part of the molecular beam, strong Mg+ (CH3OH)n(n = 0–5) and weak H+ (CH3OH)n (n = 0–5) cluster ions were observed with relatively small cluster sizes; in the middle part of the molecular beam, the main cluster ions were H+ (CH3OH)n(n = 6–17) and H+ (H3O)2 (CH3OH)n(n = 6–17) with a relatively large cluster size and a weak intensity; in the back part of the molecular beam, two new series of cluster ions, MgO+ (H2O)(CH3OH)n(n = 6–10) and MgOCH3+ (CH3OH)n(n = 6–10), were obtained and accompanied by weak H+ (CH3OH)n(n = 4–7) and H+ (H2O)2 (CH3OH)n(n = 3–6). The formation mechanisms and speed characteristics of the cluster ions are discussed in this article.

Heterogeneous Association in Methanol−Carbon Tetrachloride Mixtures

A lattice model developed for the calculation of the equilibrium distribution of molecular clusters in methanol-carbon tetrachloride mixtures is modified in order to account for an entropy component associated to the binding of CCl(4) with the nondonating end of methanol clusters. This entropy contribution is shown to affect significantly the H-bonding energy estimates based on the use of the model for the analysis of both the static dielectric response and the Raman O-H stretching spectra of these mixtures. The agreement with some results from numerical simulations turns out to be improved. In particular, the new value of approximately 6.2 kcal/mol found for the H-bonding energy (to be compared with approximately 3.2 kcal/mol yielded by the previous version of the model) is close to the results of simulation (approximately 5.5 kcal/mol). The H-bonding energy is also estimated by fitting the excess mixing enthalpy with an empirical polynomial expansion, complemented by an association contribution derived from the model. The agreement is good in this case, too.

Chain conformation and solvent partitioning in reversed-phase liquid chromatography: Monte Carlo simulations for various water/methanol concentrations

Many structural models for the stationary phase in reversed-phase liquid chromatography (RPLC) systems have been suggested from thermodynamic and spectroscopic measurements and theoretical considerations. To provide a molecular picture of chain conformation and solvent partitioning in a typical RPLC system, a particle-based Monte Carlo simulation study is undertaken for a dimethyl octadecyl (C 18) bonded stationary phase on a model siliceous substrate in contact with mobile phases having different methanol/water concentrations. Following upon previous simulations for gas–liquid chromatography and liquid–liquid phase equilibria, the simulations are conducted using the configurational-bias Monte Carlo method in the Gibbs ensemble and the transferable potentials for phase equilibria force field. The simulations are performed for a chain surface density of 2.9 μ mol/m 2, which is a typical bonded-phase coverage for mono-functional alkyl silanes. The solvent concentrations used here are pure water, approximately 33 and 67% mole fraction of methanol and pure methanol. The simulations show that the chain conformation depends only weakly on the solvent composition. Most chains are conformationally disordered and tilt away from the substrate normal. The interfacial width increases with increasing methanol content and, for mixtures, the solvent shows an enhancement of the methanol concentration in a 10 Å region outside the Gibbs dividing surface. Residual surface silanol groups are found to provide hydrogen bonding sites that lead to the formation of substrate bound water and methanol clusters, including bridging clusters that penetrate from the solvent/chain interfacial region all the way to the silica surface.

Dynamics and fragmentation of van der Waals clusters: (H2O)n, (CH3OH)n, and (NH3)n upon ionization by a 26.5eV soft x-ray laser

A tabletop soft x-ray laser is applied for the first time as a high energy photon source for chemical dynamics experiments in the study of water, methanol, and ammonia clusters through time of flight mass spectroscopy. The 26.5 eV/photon laser (pulse time duration of approximately 1 ns) is employed as a single photon ionization source for the detection of these clusters. Only a small fraction of the photon energy is deposited in the cluster for metastable dissociation of cluster ions, and most of it is removed by the ejected electron. Protonated water, methanol, and ammonia clusters dominate the cluster mass spectra. Unprotonated ammonia clusters are observed in the protonated cluster ion size range 2< or =n< or =22. The unimolecular dissociation rate constants for reactions involving loss of one neutral molecule are calculated to be (0.6-2.7)x10(4), (3.6-6.0)x10(3), and (0.8-2.0)x10(4) s(-1) for the protonated water (9< or =n< or =24), methanol (5< or =n< or =10), and ammonia (5< or =n< or =18) clusters, respectively. The temperatures of the neutral clusters are estimated to be between 40 and 200 K for water clusters (10< or =n< or =21), and 50-100 K for methanol clusters (6< or =n< or =10). Products with losses of up to five H atoms are observed in the mass spectrum of the neutral ammonia dimer. Large ammonia clusters (NH(3))(n) (n>3) do not lose more than three H atoms in the photoionization/photodissociation process. For all three cluster systems studied, single photon ionization with a 26.5 eV photon yields near threshold ionization. The temperature of these three cluster systems increases with increasing cluster size over the above-indicated ranges.

NMR study of hydrogen bonding in methanol – carbon tetrachloride solutions

The nuclear magnetic resonance (NMR) frequencies of the hydroxyl protons of methanol clusters in carbon tetrachloride were measured as a function of concentration between 245.4 and 320.2 K. The size of the methanol cluster (n) and the enthalpy and entropy of methanol self-association were obtained from nonlinear least-squares fittings to a model that assumed that only one dominant cluster was in equilibrium with the monomer at each temperature. The chemical shift measurements at 273 and 299.1 K fit best to theoretical curves calculated for a monomer–tetramer equilibrium. However, at higher and lower temperatures, the analyses indicate that the most dominant clusters are smaller and larger, respectively.Key words: alcohol liquid solutions, structure, hydrogen bonding, thermodynamics of self-association, nuclear magnetic resonance.

Resonance Raman Spectrum of the Solvated Electron in Methanol: Simulation within a Cluster Model

The microsolvation of the CH(3)OH(2) hypervalent radical in methanol clusters has been investigated by density functional theory. It is shown that the CH(3)OH(2) radical spontaneously decomposes within methanol clusters into protonated methanol and a localized solvated electron cloud. The geometric and electronic structures of these clusters as well as their vibrational frequencies have been characterized. Resonance Raman intensities, associated with the s --> p transition of the unpaired electron, have been estimated for CH(3)OH(2)M(n) (M = CH(3)OH, n = 1-3) clusters. It is shown that with increasing cluster size the simulated spectra converge toward the resonance Raman spectrum of the solvated electron in methanol measured recently by Tauber and Mathies (J. Am. Chem. Soc. 2004, 126, 3414). The results suggest that CH(3)OH(2)M(n) clusters are useful finite-size model systems for the computational investigation of the spectroscopic properties of the solvated electron in liquid methanol.