Association patterns in (HF)(m)(H2O)(n) (m + n = 2-8) clusters

In an attempt to understand the phase behavior of aqueous hydrogen fluoride, the clustering in the mixture is investigated at the molecular level. The study is performed at the mPW1B95/6-31+G(d,p) level of theory. Several previous studies attempted to describe the dissociation of HF in water, but in this investigation, the focus is only on the association patterns that are present in this binary mixture. A total of 214 optimized geometries of (HF)n(H2O)m clusters, with m + n as high as 8, were investigated. For each cluster combination, several different conformations are investigated, and the preferred conformations are presented. Using multiple linear regressions, the average strengths of the four possible H-bonding interactions are obtained. The strongest H-bond interaction is reported to be the H2O...H-F interaction. The most probable distributions of mixed clusters as a function of composition are also deduced. It is found that the larger (HF)n(H2O)m clusters are favored both energetically and entropically compared to the ones that are of size m + n < or = 3. Also, the clusters with equimolar contributions of HF and H2O are found to have the strongest interactions.     

Photoabsorption and photofragmentation of isolated cationic silver cluster-tryptophan hybrid systems

We present a theoretical study of the size and structure selective absorption properties of cationic silver cluster-tryptophan Trp-Ag(n)(+) (n = 2-5,9) hybrid systems supported by photofragmentation experiments. Our time-dependent density functional theory calculations provide insight into the nature of excitations in interacting nanoparticle-biomolecule subunits and allow to determine characteristic spectral features as fingerprints of two different classes of structures: charge solvated and zwitterionic. Moreover, different types of charge transfer transitions have been identified. Charge transfer from pi system of tryptophan to silver cluster occurs for charge solvated structures while charge transfer from silver to the NH(3) (+) group takes place for zwitterionic structures. This has been confirmed by experimentally measured photofragmentation channels and molecular dynamics simulations. Our findings provide fundamental insight into the structure- and size-dependent mechanism responsible for the enhanced absorption and emission in nanoparticle-biomolecular hybrid systems.     

Conformer-dependent proton-transfer reactions of ubiquitin ions

The conformations of ubiquitin ions before and after being exposed to proton transfer reagents have been studied by using ion mobility/mass spectrometry techniques. Ions were produced by electrospray ionization and exposed to acetone, acetophenone, n-butylamine, and 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene. Under the conditions employed, the +4 to +13 charge states were formed and a variety of conformations, which we have characterized as compact, partially folded, and elongated, have been observed. The low charge state ions have cross sections that are similar to those calculated for the crystal conformation. High charge states favor unfolded conformations. The ion mobility distributions recorded after ions have been exposed to each base show that the lowest charge state that is formed during proton-transfer reactions favors a compact conformation. More open conformations are observed for the higher charge states that remain after reaction. The results show that for a given charge state, the apparent gas-phase acidities of the different conformations are ordered as compact < partially folded < elongated.     

Resolution and structural transitions of elongated states of ubiquitin

Electrospray ionization, combined with two-dimensional ion mobility spectrometry and mass spectrometry, is used to produce, select, and activate distributions of elongated ions, [M + 11H]11+ to [M + 13H]13+, of ubiquitin. The analysis makes it possible to examine state-to-state transitions for structural types, and transition diagrams associated with the efficiencies of structural changes are presented. The +11 and +12 charge states can form four resolvable states while only one state is formed for [M + 13H]13+. Some conformations, which appear to belong to the same family based on mobility analysis of different charge states, undergo similar transitions, others do not. Activation of ions that exist in low-abundance conformations, having mobilities that fall in between sharp peaks associated with higher abundances species, shows that the low-abundance forms undergo efficient (approximately 90 to 100%) conversion into states associated with well-defined peaks. This efficiency is significantly higher than the approximately 10 to 60% efficiency of transitions of structures associated with well-defined peaks. The formation of sharp features from a range of low-intensity species with different cross sections indicates that large regions of conformation space must be unfavorable or inaccessible in the gas phase. These results are compared with several previous IMS measurements of this system as well as information about gas-phase structure provided by other techniques.     

盐水溶液中离子与丙氨酸极性基团间的作用对丙氨酸缔合的影响:密度泛函理论与分子动力学模拟

采用密度泛函理论和经典分子动力学模拟研究了盐水溶液中Na⁺、Cu²⁺、Zn²⁺、Cl^-与丙氨酸分子间的相互作用对丙氨酸分子缔合的影响. 密度泛函理论的计算结果显示丙氨酸分子与Na⁺、Cu²⁺、Zn²⁺、Cl^-之间的相互作用可增强其电荷分离. 经典分子动力学模拟结果显示在水溶液中两性离子形式的丙氨酸存在三种缔合结构.盐水溶液中, 阳离子、阴离子与丙氨酸间的相互作用均能一定程度上减弱丙氨酸分子的缔合. 但是阳离子与丙氨酸间的相互作用明显受离子水合作用的影响. 由于Cu²⁺水合作用较强, 虽在气相中Cu²⁺与丙氨酸分子之间相互作用明显比Na⁺强, 但是在水溶液中则情况刚好相反. 在ZnCl₂稀溶液中, Zn²⁺与丙氨酸间的相互作用被其第一水合壳层隔开. 但这种相互作用仍能明显影响丙氨酸分子的缔合, 这与Zn²⁺的水合壳层特征有关. 另外, 离子与丙氨酸之间的相互作用, 不仅会削弱丙氨酸的缔合, 也可导致丙氨酸分子间的缔合结构发生转变. 离子浓度也会影响其与丙氨酸分子间的缔合形式以及丙氨酸的缔合结构.     

Interaction of low-energy ions and atoms of light elements with a fluorinated carbon molecular lattice

The mechanism of interaction of low-energy atoms and ions of light elements (H, H+, He, Li, the kinetic energy of the particles 2-40 eV) with C6H6, C6F12, C60, and C60F48 molecules was studied by ab initio MD simulations and quantum-chemical calculations. It was shown that starting from 6 A from the carbon skeleton for the "C6H6 + proton" and "C60 + proton" systems, the electronic charge transfer from the aromatic molecule to H+ occurs with a probability close to 1. The process transforms the H+ to a hydrogen atom and the neutral C6H6 and C60 molecules to cation radicals. The mechanism of interaction of low-energy protons with C6F12 and C60F48 molecules has a substantially different character and can be considered qualitatively as the interaction between a neutral molecule and a point charge. The Coulomb perturbation of the system arising from the interaction of the uncompensated proton charge with the Mulliken charges of fluorine atoms results in an inversion of the energies of the electronic states localized on the proton and on the C6F12 and C60F48 molecules and makes the electronic charge transfer energetically unfavorable. On the different levels of theory, the barriers of the proton penetration for the C6F12 and C60F48 molecules are from two to four times lower than those for the corresponding parent systems (C6H6 and C60). The penetration barriers of the He atom and Li+ ion depend mainly on the effective radii of the bombarding particles. The theoretical penetration and escaped barriers for the "Li+ + C60" process qualitatively explain the experimental conditions of synthesis of the Li@C60 complex.     

Theoretical-experimental study of formic acid photofragmentation in the valence region

Photoionization and photofragmentation studies of formic acid (HCOOH) are performed for the valence shell electron ionization process. The total and partial ion yield of gaseous HCOOH were collected as a function of photon energy in the ultraviolet region, between 11.12 and 19.57 eV. Measurements of the total and partial ion yield of gaseous formic acid molecule are performed with a time-of-flight mass spectrometer at the Synchrotron Light Brazilian Laboratory. Density functional theory and time dependent density functional theory are employed to calculate the ground and excited electronic state energies of neutral and ionic formic acid as well as their fragments and normal vibration modes. The ionization potential energies, the stability of electronic excited states of HCOOH(+), and the energies of opening fragmentation channels are estimated from theoretical-experimental analysis. Additionally, the main formic acid photofragmentation pathways by exposition of photons within that energy range are determined experimentally. These produced ions primarily have the following mass/charge ratios: 46 (HCOOH(+)), 45 (COOH(+)), 29 (HCO(+)), and 18 (H(2)O(+)).     

Structure and interaction of adsorbing symmetrical triblock polyampholyte solution between two planes

In this paper, the continuum self-consistent field theory(SCFT) is applied to study the structure and the interaction of the adsorption of symmetrical ABA polyampholytes(PAs) between two neutral planes. It is found that the amounts of all the conformations decrease with the increase of the charge fraction of polymer chain, and increase with the increase of the bulk salt concentration and become saturated at high bulk salt concentration. The effective interaction between the two planes presented a long-range repulsion. Splitting it into various components and relating with the dependence of the variations of the conformations on environment parameters, we try to find the origin of the total long-range interaction between the two planes.     

Generation and detection of alkyl peroxy radicals in a supersonic jet expansion

Alkyl peroxy radicals are synthesized in a supersonic jet expansion by the initial production of alkyl radicals and subsequent reaction with molecular oxygen. Parent ions CH3OO+/CD3OO+ are observed employing vacuum ultraviolet (VUV) single photon ionizationtime-of-flight mass spectroscopy (TOFMS). Employing infrared (IR) + VUV photofragmentation detected spectroscopy, rotationally resolved infrared spectra of jet-cooled CH3OO and CD3OO radicals are recorded for the A 2A' <-- X 2A" transition by scanning the IR laser frequency while monitoring the CH3 + and CD3 + ion signals generated by the VUV laser. The band origins of the A 2A'<--X 2A" transition for CH3OO and CD3OO are identified at 7381 and 7371 cm(-1), respectively. Rotational simulation for the CH3OO and CD3OO 0(0) 0 transitions of A<--X yields a rotational temperature for these radicals of approximately 30 K. With the aid of ab initio calculations, two and five vibrational modes for the A 2A' excited electronic state are assigned for CH3OO and CD3OO radicals, respectively. Both experimental and theoretical results suggest that the ground electronic state of the ions of ethyl and propyl peroxy radicals are not stable although their ionization energies (IE) are less than 10.5 eV. The C2H5OO+/C3H7OO+ cations can readily decompose to C2H5 +/C3H7 + and O2. This is partially responsible for the inability of IR+VUV photofragmentation spectroscopy to detect the near IR A<--X electronic transition for these radicals.     

The energy landscape of unsolvated peptides: the role of context in the stability of alanine/glycine helices

Ion mobility measurements have been used to examine the conformations present for unsolvated Ac-(AG)(7)A+H(+) and (AG)(7)A+H(+) peptides (Ac = acetyl, A = alanine, and G = glycine) over a broad temperature range (100-410 K). The results are compared to those recently reported for Ac-A(4)G(7)A(4)+H(+) and A(4)G(7)A(4)+H(+), which have the same compositions but different sequences. Ac-(AG)(7)A+H(+) shows less conformational diversity than Ac-A(4)G(7)A(4)+H(+); it is much less helical than Ac-A(4)G(7)A(4)+H(+) at the upper end of the temperature range studied, and at low temperatures, one of the two Ac-A(4)G(7)A(4)+H(+) features assigned to helical conformations is missing for Ac-(AG)(7)A+H(+). Molecular dynamics simulations suggest that the different conformational preferences are not due to differences in the stabilities of the helical states, but differences in the nonhelical states: it appears that Ac-(AG)(7)A+H(+) is more flexible and able to adopt lower energy globular conformations (compact random looking three-dimensional structures) than Ac-A(4)G(7)A(4)+H(+). The helix to globule transition that occurs for Ac-(AG)(7)A+H(+) at around 250-350 K is not a direct (two-state) process, but a creeping transition that takes place through at least one and probably several intermediates.     

Theoretical Study on the Formation of H‐ and O‐Atoms,HONO, OH,NO, and NO2 from the Lowest Lying Singlet and Triplet States in Ortho‐Nitrophenol Photolysis

The photolysis of nitrophenols was proposed as a source of reactive radicals and NOx compounds in polluted air. The S₀ singlet ground state and T₁ first excited triplet state of nitrophenol were investigated to assess the energy dependence of the photofragmentation product distribution as a function of the reaction conditions, based on quantum chemical calculations at the G3SX//M06–2X/aug‐cc‐pVTZ level of theory combined with RRKM master equation calculations. On both potential energy surfaces, we find rapid isomerization with the aci‐nitrophenol isomer, as well as pathways forming NO, NO₂, OH, HONO, and H‐, and O‐atoms, extending earlier studies on the T₁ state and in agreement with available work on other nitroaromatics. We find that accessing the lowest photofragmentation channel from the S₀ ground state requires only 268 kJ/mol of activation energy, but at a pressure of 1 atm collisional energy loss dominates such that significant fragmentation only occurs at internal energies exceeding 550 kJ/mol, making this surface unimportant for atmospheric photolysis. Intersystem crossing to the T₁ triplet state leads more readily to fragmentation, with dissociation occurring at energies of ～450 kJ/mol above the singlet ground state even at 1 atm. The main product is found to be OH + nitrosophenoxy, followed by formation of hydroxyphenoxy + NO and phenyloxyl + HONO. The predictions are compared against available experimental data.     

Extreme stability of an unsolvated alpha-helix

High-temperature ion mobility measurements have been performed for alpha-helical Ac-A15K+H+ and globular Ac-KA15+H+ peptides. The alpha-helical and globular conformations do not melt into random coils as the temperature is raised. Instead, both conformations survive to the point where the peptide signals vanishes due to fragmentation. This occurs at 600 K for the globular Ac-KA15+H+ peptide and at 725 K for the alpha-helical Ac-A15K+H+. For the helical Ac-A15K+H+ peptide it appears that fragmentation is triggered by disruption of the helical conformation.     

Gas-phase photofragmentation of tris(methyl vinyl ketone) tungsten(0) and the relationship to laser-assisted CVD of tungsten oxide thin films

The gas-phase laser-induced photofragmentation of tris(methyl vinyl ketone) tungsten(0) is studied, and the photoproducts are identified by time-of-flight mass spectroscopy. The initially populated excited electronic state of the complex is attributed to metal-to-ligand charge transfer by analysis of the electronic and preresonance Raman spectra. The major metal-containing photofragmentation products are W(+) and WO(+); smaller amounts of WC(+) and W(C(2)H(2))(+) are also observed. Intramolecular ligand coupling occurs, and dimeric products and their fragments are identified. Reaction pathways that explain the observed products are proposed. Thin films on silicon substrates are produced by laser-assisted chemical vapor deposition. The films consist of polycrystalline tungsten oxide with less than 10% tungsten carbide and are characterized by X-ray diffraction, SEM, and Auger electron spectroscopy. Relationships between the composition of the gas-phase photofragments and that of the solid films are discussed.     

Spectroscopy of isolated, mass-selected tryptophan-Ag3 complexes: a model for photoabsorption enhancement in nanoparticle-biomolecule hybrid systems

We wish to show that gas-phase studies of small metal cluster-biomolecule complexes provide fundamental insights into the mechanism leading to enhanced optical absorption in nanoparticle-biomolecular hybrid systems. Here we present, for the first time, a joint experimental and theoretical study of photoabsorption and photofragmentation of the silver trimer-tryptophan cation complex ([Trp.Ag3]+). We demonstrate that binding the metal cluster to a biomolecule leads to a remarkably high optical absorption as compared to the bare tryptophan or the [Trp.Ag]+ complex. As calculations show this arises due to coupling between the excitations in the metallic subunit with a charge transfer excitation to the tryptophan molecule.     

Interaction of ionic biomolecular building blocks with nonpolar solvents: acidity of the imidazole cation (Im+) probed by IR spectra of Im+-Ln complexes (L = Ar, N2; n < or = 3)

The intermolecular interaction between the imidazole cation (Im+ = C3N2H4+) and nonpolar ligands is characterized in the ground electronic state by infrared photodissociation (IRPD) spectroscopy of size-selected Im+-Ln complexes (L = Ar, N2) and quantum chemical calculations performed at the UMP2/6-311G(2df,2pd) and UB3LYP/6-311G(2df,2pd) levels of theory. The complexes are created in an electron impact cluster ion source, which predominantly produces the most stable isomers of a given cluster ion. The analysis of the size-dependent frequency shifts of both the N-H and the C-H stretch vibrations and the photofragmentation branching ratios provides valuable information about the stepwise microsolvation of Im+ in a nonpolar hydrophobic environment, including the formation of structural isomers, the competition between various intermolecular binding motifs (H-bonding and pi-bonding) and their interaction energies, and the acidity of both the CH and NH protons. In line with the calculations, the IRPD spectra show that the most stable Im+-L dimers feature planar H-bound equilibrium structures with nearly linear H-bonds of L to the acidic NH group of Im+. Further solvation occurs at the aromatic ring of Im+ via the formation of intermolecular pi-bonds. Comparison with neutral Im-Ar demonstrates the drastic effect of ionization on the topology of the intermolecular potential, in particular in the preferred aromatic substrate-nonpolar recognition motif, which changes from pi-bonding to H-bonding. .     

Photofragmentation of phase-transferred gold nanoparticles by intense pulsed laser light

Gold nanoparticles with an average diameter of approximately 20 nm were prepared in an aqueous solution by a wet chemistry method. The parent gold nanoparticles were then capped with a 4-aminothiophenol protecting layer and transferred into toluene by tuning the surface charge of the modified nanoparticles. Gold nanoparticles before and after phase transfer were subjected to photofragmentation by a pulsed 532 nm laser. The effects of solvent properties and surface chemistry on the photofragmentation of the gold nanoparticles have been investigated. Fast photofragmentation has been observed in the organic solvent in which the dielectric constant, heat capacity, and thermal conductivity are lower. The results suggest new approaches for the preparation of very small gold clusters from gold nanoparticles.     

Elastic and charge transfer processes in H+ + CO collisions

Proton and hydrogen atom time-of-flight spectra in collision energy range of E(trans) = 9.5-30 eV show that the endoergic charge transfer process in the H+ + CO system is almost an order of magnitude less probable than the elastic scattering [G. Niedner-Schatteburg and J. P. Toennies, Adv. Chem. Phys. LXXXII, 553 (1992)]. Ab initio computations at the multireference configuration interaction level have been performed to obtain the ground- and several low-lying excited electronic state potential energy curves in three different molecular orientations namely, H+ approaching the O-end and the C-end (collinear), and H+ approaching the CO molecule in perpendicular configuration with fixed CO internuclear distance. Nonadiabatic coupling terms between the ground electronic state (H+ + CO) and the three low-lying excited electronic states (H + CO+) have been computed and the corresponding diabatic potentials have been obtained. A time-dependent wavepacket dynamics study is modeled first involving only the ground and the first excited states and then involving the ground and the three lowest excited states at the collision energy of 9.5 eV. The overall charge transfer probability have been found to be approximately 20%-30% which is in qualitative agreement with the experimental findings.     

Time‐dependent Density Functional Theory Study on the Hydrogen‐bonded Dimers Formed by Gauche‐1PA and Trans‐1PA

Three hydrogen bonding complexes of the gauche‐1PA dimer (GG), trans‐1PA dimer (TT) and mixed dimer (GT) have been calculated for the geometry conformations and excited‐state energies. The electron distribution at the site of C‐O of H‐donor moiety in HOMO transfers to the direction of O‐H of H‐acceptor moiety in LUMO. The hydrogen bond between two 1PAs is the bridge of the intermolecular charge transfer. By the Zhao and Han's excited‐state hydrogen bonding dynamics rule, the first excited‐state hydrogen bonding change has been discussed without optimizing the excited‐state geometry conformations. According to the distinct difference between GT and GG (TT), we concluded that two gauche‐1PA monomers of one dimer are transformed at the same time to two trans‐1PA monomers.     

Spectroscopic identification of carbenium and ammonium isomers of protonated aniline (AnH+): IR spectra of weakly bound AnH+ -Ln clusters (L = Ar, N2)

Infrared photodissociation (IRPD) spectra of mass-selected clusters composed of protonated aniline (C6H8N+ = AnH+) and a variable number of neutral ligands (L = Ar, N2) are obtained in the N-H stretch range. The AnH+ -Ln complexes (n < or = 3) are produced by chemical ionization in a supersonic expansion of An, H2, and L. The IRPD spectra of AnH+-Ln feature the unambiguous fingerprints of at least two different AnH+ nucleation centers, namely, the ammonium isomer (5) and the carbenium ions (1 and/or 3) corresponding to protonation at the N atom and at the C atoms in the para and/or ortho positions, respectively. Protonation at the meta and ipso positions is not observed. Both classes of observed AnH+-Ln isomers exhibit very different photofragmentation behavior upon vibrational excitation arising from the different interaction strengths of the AnH+ cores with the surrounding neutral ligands. Analysis of the incremental N-H stretch frequency shifts as a function of cluster size shows that microsolvation of both 5 and 1/3 in Ar and N2 starts with the formation of intermolecular H bonds of the ligands to the acidic NH protons and proceeds by intermolecular pi bonding to the aromatic ring. The analysis of both the photofragmentation branching ratios and the N-H stretch frequencies demonstrates that the N-H bonds in 5 are weaker and more acidic than those in 1/3, leading to stronger intermolecular H bonds with L. The interpretation of the spectroscopic data is supported by density functional calculations conducted at the B3LYP level using the 6-31G* and 6-311G(2df,2pd) basis sets. Comparison with clusters of neutral aniline and the aniline radical cation demonstrates the drastic effect of protonation and ionization on the acidity of the N-H bonds and the topology of the intermolecular potential, in particular on the preferred aromatic substrate-nonpolar ligand recognition motif.     

Water soluble cryptophanes showing unprecedented affinity for xenon: candidates as NMR-based biosensors

Cryptophanes bearing OCH(2)COOH groups in place of the methoxy groups represent a new class of xenon-carrier molecules soluble in water at biological pH. By using (1)H and (129)Xe NMR (thermally- and laser-polarized dissolved gas), the structural and dynamical behaviors of these host molecules as well as their interaction with xenon are studied. They are shown to exist in aqueous solution under different conformations in very slow exchange. A saddle form present for one of these conformations could explain the (1)H NMR spectra. Whereas the cryptophanes in such a conformation are unable to complex xenon, unprecedented high binding constants are found for cryptophanes in the other canonical crown-crown conformation. These host molecules could therefore be valuable candidates for biosensing using (129)Xe MRI.