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Sample records for gas-phase protein structure

  1. Amphipols Outperform Dodecylmaltoside Micelles in Stabilizing Membrane Protein Structure in the Gas Phase

    PubMed Central

    2014-01-01

    Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied. PMID:25495802

  2. Determinants of Gas-Phase Disassembly Behavior in Homodimeric Protein Complexes with Related yet Divergent Structures

    PubMed Central

    Dodds, Eric D.; Blackwell, Anne E.; Jones, Christopher M.; Holso, Katie L.; O’Brien, Dawne J.; Cordes, Matthew H. J.; Wysocki, Vicki H.

    2011-01-01

    The overall structure of a protein-protein complex reflects an intricate arrangement of non-covalent interactions. While intramolecular interactions confer secondary and tertiary structure to individual subunits, intermolecular interactions lead to quaternary structure - the ordered aggregation of separate polypeptide chains into multi-subunit assemblies. The specific ensemble of non-covalent contacts dictates the stability of subunit folds, enforces protein-protein binding specificity, and determines multimer stability. Consequently, non-covalent architecture is likely to play a role in the gas-phase dissociation of these assemblies during tandem mass spectrometry (MS/MS). To further advance the applicability of MS/MS to analytical problems in structural biology, a better understanding of the interplay between the structures and fragmentation behaviors of non-covalent protein complexes is essential. The present work constitutes a systematic study of model protein homodimers (bacteriophage N15 Cro; bacteriophage λ Cro; bacteriophage P22 Arc) with related but divergent structures, both in terms of subunit folds and protein-protein interfaces. Because each of these dimers has a well-characterized structure (solution and / or crystal structure), specific non-covalent features could be correlated with gas-phase disassembly patterns as studied by collision-induced dissociation, surface-induced dissociation, and ion mobility. Of the several respects in which the dimers differed in structure, the presence or absence of intermolecular electrostatic contacts exerted the most significant influence on the gas-phase dissociation behavior. This is attributed to the well-known enhancement of ionic interactions in the absence of bulk solvent. Because salt bridges are general contributors to both intermolecular and intramolecular stability in protein complexes, these observations are broadly applicable to aid in the interpretation or prediction of dissociation spectra for non

  3. Applying ion-molecule reactions to studies of gas-phase protein structure

    SciTech Connect

    Ogorzalek Loo, R.R.; Loo, J.A.; Smith, R.D.

    1992-06-01

    Whether solution phase differences in protein higher order structure persist in the gas phase, is examined by means of proton transfer reactions on ions generated by electrospray ionization of different solution conformations. Ion-molecule reactions were carried out in the atmosphere-vacuum interface of a quadrupole mass spectrometer with a Y-shaped capillary inlet-reactor. An amine (dimethyl-, trimethyl-, or diethyl-) were delivered to one inlet arm. Reactivities of bovine cytochrome c ions sprayed from denatured and native solutions were determined; the ions generated shifted to about the same charge states. Addition of equal amounts of amine to ions generated from different solution conformations of bovine ubiquitin also yielded similar final charge states; however, the average charge state increased with temperature. Myoglobin and apomyoglobin also yielded similar final charge states. The results suggest that for the non-disulfide linked proteins, either there are not significant differences in gas phase higher order structure, or proton transfer reactions are not sensitive enough to detect higher order structural differences arising from noncovalent interactions. 2 refs, 2 figs. (DLC)

  4. Stepwise evolution of protein native structure with electrospray into the gas phase, 10(-12) to 10(2) s.

    PubMed

    Breuker, Kathrin; McLafferty, Fred W

    2008-11-25

    Mass spectrometry (MS) has been revolutionized by electrospray ionization (ESI), which is sufficiently "gentle" to introduce nonvolatile biomolecules such as proteins and nucleic acids (RNA or DNA) into the gas phase without breaking covalent bonds. Although in some cases noncovalent bonding can be maintained sufficiently for ESI/MS characterization of the solution structure of large protein complexes and native enzyme/substrate binding, the new gaseous environment can ultimately cause dramatic structural alterations. The temporal (picoseconds to minutes) evolution of native protein structure during and after transfer into the gas phase, as proposed here based on a variety of studies, can involve side-chain collapse, unfolding, and refolding into new, non-native structures. Control of individual experimental factors allows optimization for specific research objectives.

  5. Exploring salt bridge structures of gas-phase protein ions using multiple stages of electron transfer and collision induced dissociation.

    PubMed

    Zhang, Zhe; Browne, Shaynah J; Vachet, Richard W

    2014-04-01

    The gas-phase structures of protein ions have been studied by electron transfer dissociation (ETD) and collision-induced dissociation (CID) after electrospraying these proteins from native-like solutions into a quadrupole ion trap mass spectrometer. Because ETD can break covalent bonds while minimally disrupting noncovalent interactions, we have investigated the ability of this dissociation technique together with CID to probe the sites of electrostatic interactions in gas-phase protein ions. By comparing spectra from ETD with spectra from ETD followed by CID, we find that several proteins, including ubiquitin, CRABP I, azurin, and β-2-microglobulin, appear to maintain many of the salt bridge contacts known to exist in solution. To support this conclusion, we also performed calculations to consider all possible salt bridge patterns for each protein, and we find that the native salt bridge pattern explains the experimental ETD data better than nearly all other possible salt bridge patterns. Overall, our data suggest that ETD and ETD/CID of native protein ions can provide some insight into approximate location of salt bridges in the gas phase.

  6. Gas-Phase Photoionization Of A Protein

    NASA Astrophysics Data System (ADS)

    Milosavljevic, A. R.; Giuliani, A.; Nicolas, C.; Gil, J.-F.; Lemaire, J.; Refregiers, M.; Nahon, L.

    2010-07-01

    We present preliminary results on gas phase photoionization of electrosprayproduced multiply protonated cytochrome c protein (104 amino acids; ˜12.4 kDa), which has been achieved with a newly developed experimental system for spectroscopy of electrosprayed ions in a linear quadrupole ion trap using a monochromatized vacuum ultraviolet (VUV) synchrotron radiation and tandem mass spectrometry method. The investigation of proteins in the gas phase, where they are free of the influence of counterions and solvent molecules, offer a possibility to understand their intrinsic molecular properties. However, due to limited both ion densities and available number of photons, the use of synchrotron radiation for the trapped ions spectroscopy is a rather challenging task. The feasibility of coupling a Fourier transform ion cyclotron resonance ion trap with soft x-ray synchrotron beamline and the first successful use of synchrotron radiation for spectroscopy of electrosprayed negative ions stored in a three-dimensional quadrupole ion trap have been demonstrated only recently (R. Thissen et al., 2008, Phys. Rev. Lett., 100, 223001; A. Giulliani et al., Proc. 57th ASMS Conf., Philadelphia, 2009). The present results are the first reported on photoionization of kDa species in the gas phase and are valuable regarding both a fundamental interest of accessing physical properties of large biological ions isolated in vacuo and potential development of a new technique for proteomics.

  7. The Electronic Structure, Ionization Potential and Electron Affinity of the Enzyme Cofactor (6R)-5,6,7,8-Tetrahydrobiopterin in Gas Phase, Solution and Protein Environment

    PubMed Central

    Gogonea, Valentin; Shy, Jacinto M.; Biswas, Pradip K.

    2008-01-01

    (6R)-5,6,7,8-tetrahydrobiopterin (BH4) is a key cofactor involved in the electron transfer to P450 heme of nitric oxide synthase. We calculated the electronic structure of the neutral, cation and anion forms of BH4 in gas phase, solution (both dielectric and explicit water), and in the protein environment using the density functional theory method (B3LYP/6-31+G(d,p)). Subsequently, we derived the ionization potential (IP) and electron affinity (EA) of the cofactor in these chemical environments. We found that the electronic structure of BH4 is susceptible to the presence of an external electric field, and that conformational changes in the structure of BH4 alone do not affect its electronic structure significantly. In gas phase, water, and protein environment the neutral BH4 is the most stable species, while, in dielectric, the anion becomes the most stable species. The IP of BH4 in the protein environment is about half of that in gas phase and its EA isabout five times smaller than in gas phase. Our results indicate that changes in the external electric field created by moving charged amino acid residues around BH4 may lead to configurations that have the BH4 ion as stable as, or more stable than the neutral form, thus facilitating the electron transfer. PMID:17092038

  8. Effects of polarity on the structures and charge states of native-like proteins and protein complexes in the gas phase.

    PubMed

    Allen, Samuel J; Schwartz, Alicia M; Bush, Matthew F

    2013-12-17

    Native mass spectrometry and ion mobility spectrometry were used to investigate the gas-phase structures of selected cations and anions of proteins and protein complexes with masses ranging from 6 to 468 kDa. Under the same solution conditions, the average charge states observed for all native-like anions were less than those for the corresponding cations. Using an rf-confining drift cell, similar collision cross sections were measured in positive and negative ion mode suggesting that anions and cations have very similar structures. This result suggests that for protein and protein complex ions within this mass range, there is no inherent benefit to selecting a specific polarity for capturing a more native-like structure. For peptides and low-mass proteins, polarity and charge-state dependent structural changes may be more significant. The charged-residue model is most often used to explain the ionization of large macromolecules based on the Rayleigh limit, which defines the upper limit of charge that a droplet can hold. Because ions of both polarities have similar structures and the Rayleigh limit does not depend on polarity, these results cannot be explained by the charged-residue model alone. Rather, the observed charge-state distributions are most consistent with charge-carrier emissions during the final stages of analyte desolvation, with lower charge-carrier emission energies for anions than the corresponding cations. These results suggest that the observed charge-state distributions in most native mass spectrometry experiments are determined by charge-carrier emission processes; although the Rayleigh limit may determine the gas-phase charge states of larger species, e.g., virus capsids.

  9. From Compact to String—The Role of Secondary and Tertiary Structure in Charge-Induced Unzipping of Gas-Phase Proteins

    NASA Astrophysics Data System (ADS)

    Warnke, Stephan; Hoffmann, Waldemar; Seo, Jongcheol; De Genst, Erwin; von Helden, Gert; Pagel, Kevin

    2016-12-01

    In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues.

  10. Capturing Polyradical Protein Cations after an Electron Capture Event: Evidence for their Stable Distonic Structures in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Baba, Takashi; Campbell, J. Larry

    2015-08-01

    We report on the formation and "capture" of polyradical protein cations after an electron capture event. Performed in a unique electron-capture dissociation (ECD) instrument, these experiments can generate reduced forms of multiply protonated proteins by sequential charge reduction using electrons with ~1 eV. The true structures of these possible polyradicals is considered: Do the introduced unpaired electrons recombine quickly to form a new two-electron bond, or do these unpaired electrons exist as radical sites with appropriate chemical reactivity? Using an established chemical probe—radical quenching with molecular oxygen—we demonstrate that these charge-reduced protein cations are indeed polyradicals that form adducts with up to three molecules of oxygen (i.e., tri-radical protein cations) that are stable for at least 100 ms.

  11. Visible and ultraviolet spectroscopy of gas phase protein ions.

    PubMed

    Antoine, Rodolphe; Dugourd, Philippe

    2011-10-06

    Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids

  12. Host-guest chemistry in the gas phase: selected fragmentations of CB[6]-peptide complexes at lysine residues and its utility to probe the structures of small proteins.

    PubMed

    Heo, Sung Woo; Choi, Tae Su; Park, Kyung Man; Ko, Young Ho; Kim, Seung Bin; Kim, Kimoon; Kim, Hugh I

    2011-10-15

    The gas phase host-guest chemistry between cucurbit[6]uril (CB[6]) and peptide is investigated using electrospray ionization mass spectrometry (ESI-MS). CB[6] exhibits a high preference to interacting with a Lys residue in a peptide forming a CB[6]-peptide complex. Collisionally activated CB[6] complexes of peptides yield a common highly selective fragment product at m/z 549.2, corresponding to the doubly charged CB[6] complex of 5-iminiopentylammonium (5IPA). The process involves the formation of an internal iminium ion, which results from further fragments to an a-type ion from a y-type ion, and the resulting 5IPA ion threads through CB[6]. Numerous peptides are investigated to test the generality of the observed unique host-guest chemistry of CB[6]. Its potential utility in probing protein structures is demonstrated using CB[6] complexes of ubiquitin. Low-energy collision induced dissociation yields CB[6] complex fragments, and further MS(n) spectra reveal details of the CB[6] binding sites, which allow us to deduce the protein structure in the solution phase. The mechanisms and energetics of the observed reactions are evaluated using density functional theory calculations.

  13. Relating gas phase to solution conformations: Lessons from disordered proteins

    PubMed Central

    Beveridge, Rebecca; Phillips, Ashley S.; Denbigh, Laetitia; Saleem, Hassan M.; MacPhee, Cait E.

    2015-01-01

    In recent years both mass spectrometry (MS) and ion mobility mass spectrometry (IM‐MS) have been developed as techniques with which to study proteins that lack a fixed tertiary structure but may contain regions that form secondary structure elements transiently, namely intrinsically disordered proteins (IDPs). IM‐MS is a suitable method for the study of IDPs which provides an insight to conformations that are present in solution, potentially enabling the analysis of lowly populated structural forms. Here, we describe the IM‐MS data of two IDPs; α‐Synuclein (α‐Syn) which is implicated in Parkinson's disease, and Apolipoprotein C‐II (ApoC‐II) which is involved in cardiovascular diseases. We report an apparent discrepancy in the way that ApoC‐II behaves in the gas phase. While most IDPs, including α‐Syn, present in many charge states and a wide range of rotationally averaged collision cross sections (CCSs), ApoC‐II presents in just four charge states and a very narrow range of CCSs, independent of solution conditions. Here, we compare MS and IM‐MS data of both proteins, and rationalise the differences between the proteins in terms of different ionisation processes which they may adhere to. PMID:25920945

  14. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum

    NASA Astrophysics Data System (ADS)

    Jhingree, Jacquelyn R.; Bellina, Bruno; Pacholarz, Kamila J.; Barran, Perdita E.

    2017-07-01

    Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge.

  15. Flavin Adenine Dinucleotide Structural Motifs: From Solution to Gas Phase

    PubMed Central

    2015-01-01

    Flavin adenine dinucleotide (FAD) is involved in important metabolic reactions where the biological function is intrinsically related to changes in conformation. In the present work, FAD conformational changes were studied in solution and in gas phase by measuring the fluorescence decay time and ion-neutral collision cross sections (CCS, in a trapped ion mobility spectrometer, TIMS) as a function of the solvent conditions (i.e., organic content) and gas-phase collisional partner (i.e., N2 doped with organic molecules). Changes in the fluorescence decay suggest that FAD can exist in four conformations in solution, where the abundance of the extended conformations increases with the organic content. TIMS-MS experiments showed that FAD can exist in the gas phase as deprotonated (M = C27H31N9O15P2) and protonated forms (M = C27H33N9O15P2) and that multiple conformations (up to 12) can be observed as a function of the starting solution for the [M + H]+ and [M + Na]+molecular ions. In addition, changes in the relative abundances of the gas-phase structures were observed from a “stack” to a “close” conformation when organic molecules were introduced in the TIMS cell as collision partners. Candidate structures optimized at the DFT/B3LYP/6-31G(d,p) were proposed for each IMS band, and results showed that the most abundant IMS band corresponds to the most stable candidate structure. Solution and gas-phase experiments suggest that the driving force that stabilizes the different conformations is based on the interaction of the adenine and isoalloxazine rings that can be tailored by the “solvation” effect created with the organic molecules. PMID:25222439

  16. The 'sticky business' of cleaning gas-phase membrane proteins: a detergent oriented perspective.

    PubMed

    Borysik, Antoni J; Robinson, Carol V

    2012-11-14

    In recent years the properties of gas-phase detergent clusters have come under close scrutiny due in part to their participation in the analysis of intact membrane protein complexes by mass spectrometry. The detergent molecules that cover the protein complex are removed in the gas-phase by thermally agitating the ions by collision-induced dissociation. This process however, is not readily controlled and can frequently result in the disruption of protein structure. Improved methods of releasing proteins from detergent clusters are clearly required. To facilitate this the structural properties of detergent clusters along with the mechanistic details of their dissociation need to be understood. Pivotal to understanding the properties of gas-phase detergent clusters is the technique of ion mobility mass spectrometry. This technique can be used to assign polydisperse detergent clusters and provide information about their geometries and packing densities. In this article we consider the shapes of detergent clusters and show that these clusters possess geometries that are inconsistent with those in solution. We analyse the distributions of clusters in detail using tandem mass spectrometry and suggest that the mean charge of clusters formed from certain detergents is governed by electrostatic repulsion. We discuss the dissociation of detergent clusters and propose that detergent evaporation it a key process in the protection of protein complexes during high energy collisions in the gas-phase.

  17. Structure and dynamics of oligonucleotides in the gas phase.

    PubMed

    Arcella, Annalisa; Dreyer, Jens; Ippoliti, Emiliano; Ivani, Ivan; Portella, Guillem; Gabelica, Valérie; Carloni, Paolo; Orozco, Modesto

    2015-01-07

    By combining ion-mobility mass spectrometry experiments with sub-millisecond classical and ab initio molecular dynamics we fully characterized, for the first time, the dynamic ensemble of a model nucleic acid in the gas phase under electrospray ionization conditions. The studied oligonucleotide unfolds upon vaporization, loses memory of the solution structure, and explores true gas-phase conformational space. Contrary to our original expectations, the oligonucleotide shows very rich dynamics in three different timescales (multi-picosecond, nanosecond, and sub-millisecond). The shorter timescale dynamics has a quantum mechanical nature and leads to changes in the covalent structure, whereas the other two are of classical origin. Overall, this study suggests that a re-evaluation on our view of the physics of nucleic acids upon vaporization is needed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Uridine Nucleoside Thiation: Gas-Phase Structures and Energetics

    NASA Astrophysics Data System (ADS)

    Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

    2016-06-01

    The naturally occurring thiated uridine nucleosides, 4-thiouridine (s4Urd) and 2-thiouridine (s2Urd), play important roles in the function and analysis of a variety of RNAs. 2-Thiouridine and its C5 modified analogues are commonly found in tRNAs and are believed to play an important role in codon recognition possibly due to their different structure, which has been shown by NMR to be predominantly C3'-endo. 2-Thiouridine may also play an important role in facilitating nonenzymatic RNA replication and transcription. 4-Thiouridine is a commonly used photoactivatable crosslinker that is often used to study RNA-RNA and RNA-protein cross-linking behavior. Differences in the base pairing between uracil and 4-thiouracil with adenine and guanine are an important factor in their role as a cross linker. The photoactivity of s4Urd may also aid in preventing near-UV lethality in cells. An understanding of their intrinsic structure in the gas-phase may help further elucidate the roles these modified nucleosides play in the regulation of RNAs. In this work, infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of s2Urd and s4Urd were collected in the IR fingerprint region. Structural information is determined by comparison with theoretical linear IR spectra generated from density functional theory calculations using molecular modeling to generate low-energy candidate structures. Present results are compared with analogous results for the protonated forms of uridine and 2'-deoxyuridine as well as solution phase NMR data and crystal structures.

  19. Surface induced dissociation: dissecting noncovalent protein complexes in the gas phase.

    PubMed

    Zhou, Mowei; Wysocki, Vicki H

    2014-04-15

    The quaternary structures of proteins are both important and of interest to chemists, because many proteins exist as complexes in vivo, and probing these structures allows us to better understand their biological functions. Conventional structural biology methods such as X-ray crystallography and nuclear magnetic resonance provide high-resolution information on the structures of protein complexes and are the gold standards in the field. However, other emerging biophysical methods that only provide low-resolution data (e.g. stoichiometry and subunit connectivity) on the structures of the protein complexes are also becoming more important to scientists. Mass spectrometry is one of these approaches that provide lower than atomic structural resolution, but the approach is higher throughput and provides not only better mass information than other techniques but also stoichiometry and topology. Fragile noncovalent interactions within the protein complexes can be preserved in the gas phase of MS under gentle ionization and transfer conditions. Scientists can measure the masses of the complexes with high confidence to reveal the stoichiometry and composition of the proteins. What makes mass spectrometry an even more powerful method is that researchers can further isolate the protein complexes and activate them in the gas phase to release subunits for more structural information. The caveat is that, upon gas-phase activation, the released subunits need to faithfully reflect the native topology so that useful information on the proteins can be extracted from mass spectrometry experiments. Unfortunately, many proteins tend to favor unfolding upon collision with neutral gas (the most common activation method in mass spectrometers). Therefore, this typically results in limited insights on the quaternary structure of the precursor without further manipulation of other experimental factors. Scientists have observed, however, that valuable structural information can be obtained

  20. Native biomolecules in the gas phase? The case of green fluorescent protein.

    PubMed

    Frankevich, Vladimir; Barylyuk, Konstantin; Chingin, Konstantin; Nieckarz, Robert; Zenobi, Renato

    2013-04-02

    Green fluorescent protein (GFP) was ionized by native electrospray ionization and trapped for many seconds in high vacuum, allowing fluorescence emission to be measured as a probe of its biological function, to answer the question whether GFP exists in the native form in the gas phase or not. Although a narrow charge-state distribution, a collision cross-section very close to that expected for correctly folded GFP, and a large stability against dissociation all support a near-native gas-phase structure, no fluorescence emission was observed. The loss of the native form is attributed to the absence of residual water in the gas phase, which normally stabilizes the para-hydroxybenzylidene imidazolone chromophore of GFP.

  1. Gas-phase IR spectra of intact [alpha]-helical coiled coil protein complexes

    NASA Astrophysics Data System (ADS)

    Pagel, Kevin; Kupser, Peter; Bierau, Frauke; Polfer, Nicolas C.; Steill, Jeffrey D.; Oomens, Jos; Meijer, Gerard; Koksch, Beate; von Helden, Gert

    2009-06-01

    Electrospray ionization (ESI) is the softest ionization method that is currently available and it is widely accepted, that ESI generated ions of proteins and protein assemblies at certain conditions retain characteristic aspects of their solution-state conformation. ESI mass spectrometry (MS) therefore evolved as a useful tool to obtain information on composition, stoichiometry, and dynamics of non-covalently associated protein complexes. While tertiary structure information of proteins can be obtained from ion mobility spectrometry (IMS), only a few techniques yield direct information on the secondary structure of gas-phase peptides and proteins. We present here the mid-IR spectroscopic secondary structural analysis of three de novo designed [alpha]-helical coiled coil model peptides and their non-covalently associated complexes in the gas-phase. The conformational stability of such coiled coil peptides in solution is primarily driven by aggregation. Isolated monomers usually remain unfolded. Two of the investigated peptides were designed to assemble into stable [alpha]-helical complexes in acidic solution, while the third one remains monomeric and unfolded at these conditions. Monomer ions of all three peptides show comparable photodissociation IR spectra and therefore suggest an unfolded conformation in the gas phase. In contrast, considerable CO stretch (amide-I) and N-H bend (amide-II) band shifts have been observed for the dimers which is consistent with an elevated H-bond content. These findings provide evidence that at least a fraction of the condensed phase [alpha]-helical structure is retained in the gas-phase coiled coil complexes.

  2. Mass Spectrometry of Protein-Ligand Complexes: Enhanced Gas Phase Stability of Ribonuclease-Nucleotide Complexes

    PubMed Central

    Yin, Sheng; Xie, Yongming; Loo, Joseph A.

    2008-01-01

    Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS). Ligand binding stoichiometry can be determined easily by the ESI-MS method. The ability to detect noncovalent protein-ligand complexes depends, however, on the stability of the complexes in the gas phase environment. Solution binding affinities may or may not be accurate predictors of their stability in vacuo. Complexes composed of cytidine nucleotides bound to ribonuclease A (RNase A) and ribonuclease S (RNase S) were detected by ESI-MS and were further analyzed by MS/MS. RNase A and RNase S share similar structures and biological activity. Subtilisin-cleavage of RNase A yields an S-peptide and an S-protein; the S-peptide and S-protein interact through hydrophobic interactions with a solution binding constant in the nanomolar range to generate an active RNase S. Cytidine nucleotides bind to the ribonucleases through electrostatic interactions with a solution binding constant in the micromolar range. Collisionally activated dissociation (CAD) of the 1:1 RNase A-CDP and CTP complexes yields cleavage of the covalent phosphate bonds of the nucleotide ligands, releasing CMP from the complex. CAD of the RNase S-CDP and CTP complexes dissociates the S-peptide from the remaining S-protein/nucleotide complex; further dissociation of the S-protein/nucleotide complex fragments a covalent phosphate bond of the nucleotide with subsequent release of CMP. Despite a solution binding constant favoring the S-protein/S-peptide complex, CDP/CTP remains electrostatically bound to the S-protein in the gas phase dissociation experiment. This study highlights the intrinsic stability of electrostatic interactions in the gas phase and the significant differences in solution and gas phase stabilities of noncovalent complexes that can result. PMID:18565758

  3. Stabilities and structures of gas phase MgO clusters

    SciTech Connect

    Ziemann, P.J.; Castleman, A.W. Jr. )

    1991-01-01

    Gas phase (MgO){sup +}{sub {ital n}} and (MgO){sub {ital n}}Mg{sup +} clusters ({ital n}{le}90) were produced in a gas aggregation source and studied by using laser-ionization time-of-flight mass spectrometry. The abundance maxima observed in the mass spectra indicate that the clusters form compact cubic structures similar to pieces of the MgO crystal lattice. The abundance maxima of the metal-rich clusters show an interesting dependence on the ionization wavelength that appears to be due to different fragmentation pathways for the cluster ions and neutrals, and may be indicative of excess electron behavior analogous to that observed in solid state color centers. Calculations of cluster structures and stabilities made with an ionic model were useful in obtaining qualitative information about the primary fragmentation channels and cluster electronic properties, but also indicate that covalent bonding interactions must be included to obtain quantitatively accurate results.

  4. Four Structures of Tartaric Acid Revealed in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Cortijo, Vanessa; Díez, Verónica; Alonso, Elena R.; Mata, Santiago; Alonso, José L.

    2017-06-01

    The tartaric acid, one of the most important organic compounds, has been transferred into the gas phase by laser ablation of its natural crystalline form (m.p.174°C) and probed in a supersonic expansion by chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW). Four stable structures, two with an extended (trans) disposition of the carbon chain and two with a bent (gauche) disposition, have been unequivocally identified on the basis of the experimental rotational constants in conjunction with ab initio predictions. The intramolecular interactions that govern the conformational preferences are dominated by cooperative O-H...O=C type and O-H?O hydrogen bonds extended along the entire molecule. The observation of only μc- type spectra for one "trans" and one "gauche" conformers, support the existence of a C2 symmetry for each structure.

  5. Hydrophobic protein-ligand interactions preserved in the gas phase.

    PubMed

    Liu, Lan; Bagal, Dhanashri; Kitova, Elena N; Schnier, Paul D; Klassen, John S

    2009-11-11

    the cavity. The loss of ligand from the closed structure would require both the cleavage of the H-bonds and the nonpolar contacts. Taken together, these results suggest that the aliphatic chain of the FA remains bound within the hydrophobic cavity in the gas phase (Lg + FA)(7-) ions. Furthermore, the barrier to dissociation of the (Lg + FA)(f)(7-) ions reflects predominantly the cleavage of the nonpolar intermolecular interactions, while for the (Lg + FA)(s)(7-) ions the FA is stabilized by both nonpolar interactions and H-bonds.

  6. Detergent release prolongs the lifetime of native-like membrane protein conformations in the gas-phase.

    PubMed

    Borysik, Antoni J; Hewitt, Dominic J; Robinson, Carol V

    2013-04-24

    Recent studies have suggested that detergents can protect the structure of membrane proteins during their transition from solution to the gas-phase. Here we provide mechanistic insights into this process by interrogating the structures of membrane protein-detergent assemblies in the gas-phase using ion mobility mass spectrometry. We show a clear correlation between the population of native-like protein conformations and the degree of detergent attachment to the protein in the gas-phase. Interrogation of these protein-detergent assemblies, by tandem mass spectrometry, enables us to define the mechanism by which detergents preserve native-like protein conformations in a solvent free environment. We show that the release of detergent is more central to the survival of these conformations than the physical presence of detergent bound to the protein. We propose that detergent release competes with structural collapse for the internal energy of the ion and permits the observation of transient native-like membrane protein conformations that are otherwise lost to structural rearrangement in the gas-phase.

  7. Gas phase structures of peroxides: experiments and computational problems.

    PubMed

    Oberhammer, Heinz

    2015-02-02

    Gas-phase structures of several organic and inorganic peroxides X-O-O-X and X-O-O-X', which have been determined experimentally by gas electron diffraction and/or microwave spectroscopy, are discussed. The OO bond length in these peroxides varies from 1.481(8) Å in Me3 SiOOSiMe3 to 1.214(2) Å in FOOF and the dihedral angle ϕ(XO-OX) between 0° in HC(O)O-OH and near 180° in Bu(t) O-OBu(t) . Some of the peroxides cause problems for quantum chemistry, since several computational methods fail to reproduce the experimental structures. Extreme examples are MeO-OMe and FO-OF. In the case of MeO-OMe only about half of the more than 100 computational methods reported in the literature reproduce the experimentally determined double-minimum shape of the torsional potential around the OO bond correctly. For FO-OF only a small number of close to 200 computational methods reproduce the OO and OF bond lengths better than ±0.02 Å.

  8. Microwave spectrum and the gas phase structure of phthalimide

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Lin, Wei; Oncer, Onur; Kukolich, Stephen G.

    2015-11-01

    The microwave spectrum of phthalimide (PhI) was measured in the 4.8-9.5 GHz range using a Flygare-Balle type, pulsed-beam Fourier transform microwave spectrometer. Rotational transitions were measured for the parent and all unique single 13C substituted isotopologues. The rotational (MHz), centrifugal distortion (kHz), and quadrupole coupling constants (MHz) were determined for the parent to be A = 1745.6655(10), B = 1199.3309(6), C = 711.0864(3), DJ = 0.012(7), DJK = -0.05(9), 1.5χaa = 2.719(11), and 0.25(χbb - χcc) = 1.236(3). Using the measured rotational constants of the isotopologues, a nonlinear least squares fit was performed to obtain the best fit gas phase structure. The inertial defect is Δ = -0.175 amu Å2, indicating a planar structure for PhI. Calculations using B3LYP/aug-cc-pVQZ provided rotational constants which are much closer to the experimental values compared to the MP2/6-311++G∗∗ calculated values.

  9. Microwave spectrum and gas phase structure of maleimide

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Oncer, Onur; Kang, Lu; Kukolich, Stephen G.

    2016-01-01

    The rotational spectrum of maleimide was measured in the 5-12 GHz range using a Flygare-Balle type, pulsed-beam Fourier transform microwave spectrometer. Rotational transitions were measured for the parent, all unique singly substituted 13C isotopologues, and an sbnd ND, deuterium substituted isotopologue. The parent (or normal isotopologue) rotational constants, centrifugal distortion constants, and quadrupole coupling constants are A = 6815.3251(12) MHz, B = 2361.85011(64) MHz, C = 1754.32750(64) MHz, DJ = 0.232(24) kHz, DJK = 0.546(54) kHz, 1.5χaa = 2.4227(53) MHz, and 0.25(χbb-χcc) = 1.3679(15) MHz. A best fit gas phase structure was determined using the experimental rotational constants of the isotopologues and some parameters from calculations. The inertial defect is Δ = -0.054 amu Å2, indicating a planar structure for maleimide, with no large amplitude motions observed on the sbnd NH hydrogen atom. Calculations using B3LYP/aug-cc-pVTZ provided rotational constants which are much closer (within 1-2%) to the experimental values compared to the MP2/aug-cc-pVTZ calculated values.

  10. Probing the Binding Interfaces of Protein Complexes Using Gas-Phase H/D Exchange Mass Spectrometry.

    PubMed

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

    2016-02-02

    Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub-millisecond time span after electrospray ionization by ND3 gas can provide structural insights into protein conformers present in solution. Here, we have explored the use of gas-phase HDX-MS for probing the higher-order structure and binding interfaces of protein complexes originating from native solution conditions. Lysozyme ions bound by an oligosaccharide incorporated less deuterium than the unbound ion. Similarly, trypsin ions showed reduced deuterium uptake when bound by the peptide ligand vasopressin. Our results are in good agreement with crystal structures of the native protein complexes, and illustrate that gas-phase HDX-MS can provide a sensitive and simple approach to measure the number of heteroatom-bound non-amide side-chain hydrogens involved in the binding interface of biologically relevant protein complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Investigating gas phase dissociation pathways of crosslinked peptides : application to protein complex determination.

    SciTech Connect

    Young, Malin M.; Gaucher, Sara P.; Hadi, Masood Z.

    2005-02-01

    Chemical crosslinking is an important tool for probing protein structure and protein-protein interactions. The approach usually involves crosslinking of specific amino acids within a folded protein or protein complex, enzymatic digestion of the crosslinked protein(s), and identification of the resulting crosslinked peptides by liquid chromatography/mass spectrometry (LC/MS). In this manner, distance constraints are obtained for residues that must be in close proximity to one another in the native structure or complex. As the complexity of the system under study increases, for example, a large multi-protein complex, simply measuring the mass of a crosslinked species will not always be sufficient to determine the identity of the crosslinked peptides. In such a case, tandem mass spectrometry (MS/MS) could provide the required information if the data can be properly interpreted. In MS/MS, a species of interest is isolated in the gas phase and allowed to undergo collision induced dissociation (CID). Because the gas-phase dissociation pathways of peptides have been well studied, methods are established for determining peptide sequence by MS/MS. However, although crosslinked peptides dissociate through some of the same pathways as isolated peptides, the additional dissociation pathways available to the former have not been studied in detail. Software such as MS2Assign has been written to assist in the interpretation of MS/MS from crosslinked peptide species, but it would be greatly enhanced by a more thorough understanding of how these species dissociate. We are thus systematically investigating the dissociation pathways open to crosslinked peptide species. A series of polyalanine and polyglycine model peptides have been synthesized containing one or two lysine residues to generate defined inter- and intra-molecular crosslinked species, respectively. Each peptide contains 11 total residues, and one arginine residue is present at the carboxy terminus to mimic species

  12. Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS.

    PubMed

    Devine, Paul W A; Fisher, Henry C; Calabrese, Antonio N; Whelan, Fiona; Higazi, Daniel R; Potts, Jennifer R; Lowe, David C; Radford, Sheena E; Ashcroft, Alison E

    2017-05-08

    Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.

  13. Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS

    NASA Astrophysics Data System (ADS)

    Devine, Paul W. A.; Fisher, Henry C.; Calabrese, Antonio N.; Whelan, Fiona; Higazi, Daniel R.; Potts, Jennifer R.; Lowe, David C.; Radford, Sheena E.; Ashcroft, Alison E.

    2017-09-01

    Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. [Figure not available: see fulltext.

  14. Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS

    NASA Astrophysics Data System (ADS)

    Devine, Paul W. A.; Fisher, Henry C.; Calabrese, Antonio N.; Whelan, Fiona; Higazi, Daniel R.; Potts, Jennifer R.; Lowe, David C.; Radford, Sheena E.; Ashcroft, Alison E.

    2017-05-01

    Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds.

  15. Titanium defect structure change after gas-phase hydrogenation at different temperatures and cooling rates

    NASA Astrophysics Data System (ADS)

    Mikhaylov, Andrey A.; Laptev, Roman S.; Kudiiarov, Viktor N.; Volokitina, Tatiana L.

    2016-11-01

    Influence of gas-phase hydrogenation temperature and cooling rate on defect structure of commercially pure titanium alloy was experimentally studied by means of positron annihilation spectroscopy. The change of temperature in the process of gas-phase hydrogenation was in the range of 500-700°C, while the change of cooling rate was in the range of 0.4-10.4°C/min. With increasing of gas-phase hydrogenation temperature, significant increase of hydrogen sorption rate was found. High temperature gas-phase hydrogenation of commercially pure titanium alloy lead to the formation of vacancy and hydrogen-vacancy complexes. For the same concentration of hydrogen, temperature variation or variation of cooling rate had no effect on the type of defect. However, this variation provides significant changes in defect concentration.

  16. Ensemble Methods Enable a New Definition for the Solution to Gas-Phase Transfer of Intrinsically Disordered Proteins.

    PubMed

    Borysik, Antoni J; Kovacs, Denes; Guharoy, Mainak; Tompa, Peter

    2015-11-04

    Intrinsically disordered proteins (IDPs) are important for health and disease, yet their lack of net structure precludes an understanding of their function using classical methods. Gas-phase techniques provide a promising alternative to access information on the structure and dynamics of IDPs, but the fidelity to which these methods reflect the solution conformations of these proteins has been difficult to ascertain. Here we use state of the art ensemble techniques to investigate the solution to gas-phase transfer of a range of different IDPs. We show that IDPs undergo a vast conformational space expansion in the absence of solvent to sample a conformational space 3-5 fold broader than in solution. Moreover, we show that this process is coupled to the electrospray ionization process, which brings about the generation of additional subpopulations for these proteins not observed in solution due to competing effects on protein charge and shape. Ensemble methods have permitted a new definition of the solution to gas-phase transfer of IDPs and provide a roadmap for future investigations into flexible systems by mass spectrometry.

  17. Resonance Energy Transfer Relates the Gas-Phase Structure and Pharmacological Activity of Opioid Peptides.

    PubMed

    Kopysov, Vladimir; Boyarkin, Oleg V

    2016-01-11

    Enkephalins are efficient pain-relief drugs that bind to transmembrane opioid receptors. One key structural parameter that governs the pharmacological activity of these opioid peptides and is typically determined from condensed-phase structures is the distance between the aromatic rings of their Tyr and Phe residues. We use resonance energy transfer, detected by a combination of cold ion spectroscopy and mass spectrometry, to estimate the Tyr-Phe spacing for enkephalins in the gas phase. In contrast to the condensed-phase structures, these distances appear to differ substantially in enkephalins with different pharmacological efficiencies, suggesting that gas-phase structures might be a better pharmacophoric metric for ligand peptides.

  18. High resolution ion mobility measurements for gas phase proteins: correlation between solution phase and gas phase conformations

    NASA Astrophysics Data System (ADS)

    Hudgins, Robert R.; Woenckhaus, Jürgen; Jarrold, Martin F.

    1997-11-01

    Our high resolution ion mobility apparatus has been modified by attaching an electrospray source to perform measurements for biological molecules. While the greater resolving power permits the resolution of more conformations for BPTI and cytochrome c, the resolved features are generally much broader than expected for a single rigid conformation. A major advantage of the new experimental configuration is the much gentler introduction of ions into the drift tube, so that the observed gas phase conformations appear to more closely reflect those present in solution. For example, it is possible to distinguish between the native state of cytochrome c and the methanol-denatured form on the basis of the ion mobility measurements; the mass spectra alone are not sensitive enough to detect this change. Thus this approach may provide a quick and sensitive tool for probing the solution phase conformations of biological molecules.

  19. Insights into diastereoisomeric characterization of tetrahydropyridazine amino acid derivatives: crystal structures and gas phase ion chemistry.

    PubMed

    Giorgi, Gianluca; Favi, Gianfranco; Attanasi, Orazio A

    2013-08-14

    Structural, conformational properties, and gas phase reactivity of two representative diastereoisomeric members of a series of α,α-tetrahydropyridazine amino acid derivatives have been investigated by using X-ray crystallography, tandem mass spectrometry and theoretical calculations. Both diastereoisomers show an unusual screw-boat conformation of the tetrahydropyridazine ring. While protonated molecules mainly decompose in the gas phase by loss of acetamide, the main reactivity of the [M + Na](+) species consists of loss of PhNCO followed by acetamide and it is strictly dependent upon the stereochemistry of the parent compound. The most stable energy minimized structures obtained by theoretical calculations are in full agreement with the experimental data and allowed us to rationalize the gas phase reaction pathways.

  20. Communications: The structure of Rh(8) (+) in the gas phase.

    PubMed

    Harding, D J; Walsh, T R; Hamilton, S M; Hopkins, W S; Mackenzie, S R; Gruene, P; Haertelt, M; Meijer, G; Fielicke, A

    2010-01-07

    The geometric structure of the Rh(8) (+) cation is investigated using a combination of far-infrared multiple photon dissociation spectroscopy and density functional theory (DFT) calculations. The energetic ordering of the different structural motifs is found to depend sensitively on the choice of pure or hybrid exchange functionals. Comparison of experimental and calculated spectra suggests the cluster to have a close-packed, bicapped octahedral structure, in contrast to recent predictions of a cubic structure for the neutral cluster. Our findings demonstrate the importance of including some exact exchange contributions in the DFT calculations, via hybrid functionals, when applied to rhodium clusters, and cast doubt on the application of pure functionals for late transition metal clusters in general.

  1. The gas phase structure of coulombically stretched polyethylene glycol ions.

    PubMed

    Larriba, Carlos; de la Mora, Juan Fernandez

    2012-01-12

    Prior ion-mobility mass-spectrometry (IMS-MS) studies of polyethylene glycol (PEG) ions have identified only two out of many sharply different observed structures: Linear shapes with several individually solvated singly charged cations at high charge states z (beads on a string), and single multiply charged globules at low z. The present study is devoted to assign all other existing structures of PEG ions, for the first time reaching masses of 100 kDa and charge states up to z = 10. There are at most z different structures at charge state z. All involve a single globule carrying n charges, tied to one or several appendices bearing z - n separate charges in a beads-on-a-string configuration. All sharp shape transitions observed at decreasing ion mass involve ejection of one elementary charge (sometimes two) from the shrinking globule into the growing linear appendage. This picture is supported by molecular dynamics simulations and approximate calculations of electrical mobilities for computed structures.

  2. Gas-phase concentration, purification, and identification of whole proteins from complex mixtures.

    PubMed

    Reid, Gavin E; Shang, Hao; Hogan, Jason M; Lee, Gil U; McLuckey, Scott A

    2002-06-26

    Five proteins present in a relatively complex mixture derived from a whole cell lysate fraction of E. coli have been concentrated, purified, and dissociated in the gas phase, using a quadrupole ion trap mass spectrometer. Concentration of intact protein ions was effected using gas-phase ion/ion proton-transfer reactions in conjunction with mass-to-charge dependent ion "parking" to accumulate protein ions initially dispersed over a range of charge states into a single lower charge state. Sequential ion isolation events interspersed with additional ion parking ion/ion reaction periods were used to "charge-state purify" the protein ion of interest. Five of the most abundant protein components present in the mixture were subjected to this concentration/purification procedure and then dissociated by collisional activation of their intact multiply charged precursor ions. Four of the five proteins were subsequently identified by matching the uninterpreted product ion spectra against a partially annotated protein sequence database, coupled with a novel scoring scheme weighted for the relative abundances of the experimentally observed product ions and the frequency of fragmentations occurring at preferential cleavage sites. The identification of these proteins illustrates the potential of this "top-down" protein identification approach to reduce the reliance on condensed-phase chemistries and extensive separations for complex protein mixture analysis.

  3. Gas Phase Structure of Amino Acids: La-Mb Studies

    NASA Astrophysics Data System (ADS)

    Mata, I. Pena S.; Sanz, M. E.; Vaquero, V.; Cabezas, C.; Perez, C.; Blanco, S.; López, J. C.; Alonso, J. L.

    2009-06-01

    Recent improvements in our laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectrometer such as using Laval-type nozzles and picoseconds Nd:YAG lasers (30 to 150 ps) have allowed a major step forward in the capabilities of this experimental technique as demonstrated by the last results in serine cysteine and threonine^a for which seven, six and seven conformers have been respectively identified. Taking advantage of these improvements we have investigated the natural amino acids metionine, aspartic and glutamic acids and the γ-aminobutyric acid (GABA) with the aim of identify and characterize their lower energy conformers. Searches in the rotational spectra have lead to the identification of seven conformers of metionine, six and five of aspartic and glutamic acids, respectively, and seven for the γ-aminobutyric. These conformers have been unambiguously identified by their spectroscopic constants. In particular the ^{14}N nuclear quadrupole coupling constants, that depend heavily on the orientation of the amino group with respect to the principal inertial axes of the molecule, prove to be a unique tool to distinguish unambigously between conformations with similar rotational constants. For the γ-aminobutyric acid two of the seven observed structures are stablized by an intramolecular interaction n-π*. Two new conformers of proline have been identified together with the two previously observed. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys.Chem.Chem.Phys., 2009, 11, 617. D. B. Atkinson, M. A. Smith, Rev. Sci. Instrum. 1995, 66, 4434 S. Blanco, M. E. Sanz, J. C. López, J. L. Alonso, Proc. Natl. Acad. Sci. USA2007, 104, 20183. M. E. Sanz, S. Blanco, J. C. López, J. L. Alonso, Angew. Chem. Int. Ed.,2008, 120, 6312. A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J.C. López, J. L. Alonso, Angew. Chem. Int. Ed. , 2002, 41, 4673

  4. Microsequence analysis of peptides and proteins. IX. Manual gas-phase microsequencing of multiple samples.

    PubMed

    Haniu, M; Shively, J E

    1988-09-01

    A novel apparatus for performing manual gas-phase Edman chemistry on protein and peptide samples is described. Edman chemistry is performed in 6 to 10 Teflon continuous flow reactors (CFR), previously described by J.E. Shively et al. (1987) Anal. Biochem. 163, 517-529). The CFRs are packed with 10-15 mg of Polybrene-coated spherical silica (Porasil B, Waters Associates). The gas-phase coupling reagent and cleavage reagent are 5% aqueous triethylamine and anhydrous trifluoroacetic acid, respectively, delivered by a stream of argon gas. The delivery of the gas-phase reagents is manually controlled with Hamilton 3-way valves and 2-way valves, and that of the solvents, ethyl acetate and butyl chloride, by syringe pipetting. The average cycle time is 15-20 min for 6 to 10 samples run simultaneously. Conversion of the anilinothiazolinone to phenylthiohydantoin (PTH) amino acid derivatives is accomplished manually with 25% aqueous trifluoroacetic acid. The PTH amino acids are analyzed by reversed-phase HPLC using an autosampler for handling multiple samples. Excellent results were obtained in the 100-200 pmol range. Protein samples can be sequenced from 15-20 cycles, and peptide samples usually to the COOH terminus. Initial yields ranged from 30 to 60% and repetitive yields ranged from 90 to 96%. The sample washout and size of background peaks are significantly reduced, compared to older methods of manual sequence analysis. The yields and background signal to noise are comparable to automated gas-phase Edman chemistry. The improved manual Edman described represents a low cost alternative to automated sequence analysis, and has the advantage being able to process multiple samples simultaneously.

  5. Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry.

    PubMed

    Haverland, Nicole A; Skinner, Owen S; Fellers, Ryan T; Tariq, Areeba A; Early, Bryan P; LeDuc, Richard D; Fornelli, Luca; Compton, Philip D; Kelleher, Neil L

    2017-06-01

    Fragmentation of intact proteins in the gas phase is influenced by amino acid composition, the mass and charge of precursor ions, higher order structure, and the dissociation technique used. The likelihood of fragmentation occurring between a pair of residues is referred to as the fragmentation propensity and is calculated by dividing the total number of assigned fragmentation events by the total number of possible fragmentation events for each residue pair. Here, we describe general fragmentation propensities when performing top-down mass spectrometry (TDMS) using denaturing or native electrospray ionization. A total of 5311 matched fragmentation sites were collected for 131 proteoforms that were analyzed over 165 experiments using native top-down mass spectrometry (nTDMS). These data were used to determine the fragmentation propensities for 399 residue pairs. In comparison to denatured top-down mass spectrometry (dTDMS), the fragmentation pathways occurring either N-terminal to proline or C-terminal to aspartic acid were even more enhanced in nTDMS compared with other residues. More generally, 257/399 (64%) of the fragmentation propensities were significantly altered (P ≤ 0.05) when using nTDMS compared with dTDMS, and of these, 123 were altered by 2-fold or greater. The most notable enhancements of fragmentation propensities for TDMS in native versus denatured mode occurred (1) C-terminal to aspartic acid, (2) between phenylalanine and tryptophan (F|W), and (3) between tryptophan and alanine (W|A). The fragmentation propensities presented here will be of high value in the development of tailored scoring systems used in nTDMS of both intact proteins and protein complexes. Graphical Abstract ᅟ.

  6. Gas-Phase Intramolecular Protein Crosslinking via Ion/Ion Reactions: Ubiquitin and a Homobifunctional sulfo-NHS Ester

    PubMed Central

    Webb, Ian K.; Mentinova, Marija; McGee, William M.; McLuckey, Scott A.

    2013-01-01

    Gas-phase intra-molecular crosslinking of protein ubiquitin cations has been demonstrated via ion/ion reactions with anions of a homobifunctional N-hydroxysulfosuccinimide (sulfo-NHS) ester reagent. The ion/ion reaction between multiply-protonated ubiquitin and crosslinker monoanions produces a stable, charge reduced complex. Covalent crosslinking is indicated by the consecutive loss of two molecules of sulfo-NHS under ion trap collisional activation conditions. Covalent modification is verified by the presence of covalently crosslinked sequence ions produced by ion-trap collision-induced dissociation of the ion generated from the losses of sulfo-NHS. Analysis of the crosslinked sequence fragments allows for the localization of crosslinked primary amines, enabling proximity mapping of the gas-phase 3-D structures. The presence of two unprotonated reactive sites within the distance constraint of the crosslinker is required for successful crosslinking. The ability to covalently crosslink is therefore sensitive to protein charge state. As the charge state increases, fewer reactive sites are available and protein structure is more likely to become extended due to intramolecular electrostatic repulsion. At high charge states, the reagent shows little evidence for covalent crosslinking but does show evidence for ‘electrostatic crosslinking’ in that the binding of the sulfonate groups to the protein is sufficiently strong that backbone cleavages are favored over reagent detachment under ion trap collisional activation conditions. PMID:23463545

  7. Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

    NASA Astrophysics Data System (ADS)

    Prentice, Boone M.; Stutzman, John R.; McLuckey, Scott A.

    2013-07-01

    Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the `cost' of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10 + 3H]3+ and the reagent cluster [5R5Na - Na]-). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

  8. Reagent Cluster Anions for Multiple Gas-phase Covalent Modifications of Peptide and Protein Cations

    PubMed Central

    Prentice, Boone M.; Stutzman, John R.; McLuckey, Scott A.

    2013-01-01

    Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated here using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used here to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the ‘cost’ of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K10+3H]3+ and the reagent cluster [5R5Na-Na]−). This type of gas phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anions which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included here as illustrative of the results obtained for the clusters comprised of 2–6 reagent molecules. PMID:23702708

  9. Is it biologically relevant to measure the structures of small peptides in the gas-phase?

    NASA Astrophysics Data System (ADS)

    Barran, Perdita E.; Polfer, Nick C.; Campopiano, Dominic J.; Clarke, David J.; Langridge-Smith, Patrick R. R.; Langley, Ross J.; Govan, John R. W.; Maxwell, Alison; Dorin, Julia R.; Millar, Robert P.; Bowers, Michael T.

    2005-02-01

    Recent developments in sample introduction of biologically relevant molecules have heralded a new era for gas-phase methods of structural determination. One of the biggest challenges is to relate gas-phase structures, often measured in the absence of water and counter ions, with in vivo biologically active structures. An advantage of gas-phase based techniques is that a given peptide can be analysed in a variety of different forms, for example, as a function of charge state, or with additional water molecules. Molecular modelling can provide insight into experimental findings and help elucidate the differences between structural forms. Combining experiment and theory provides a thorough interrogation of candidate conformations. Here two important naturally occurring peptide systems have been examined in detail and results are assessed in terms of their biological significance. The first of these is gonadotropin-releasing hormone (GnRH), a decapeptide which is the central regulator of the reproductive system in vertebrates. We have examined several naturally occurring variants of this peptide using Ion Mobility Mass Spectrometry and Electron Capture Dissociation (ECD) in conjunction with Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS). Candidate conformations are modelled using the AMBER force field. Single amino acid changes, for example Gly6 --> Ala6, or Ala6 --> D-Ala6, have observable effects on the gas phase structure of GnRH. It has been shown that evolutionary primary sequence variations are key to the biological activity of GnRH, and it is thought that this is due to different binding affinities at target receptors. This work provides strong evidence that this activity is structurally based. The second system examined is the relationship between the quaternary structure and activity of two novel [beta]-defensins. FT-ICR mass spectrometry has been employed to characterize di-sulphide bridging and dissociation based experiments utilised to

  10. Gas-Phase Structure Determination of Dihydroxycarbene, One of the Smallest Stable Singlet Carbenes

    NASA Astrophysics Data System (ADS)

    Womack, Carrie; Crabtree, Kyle N.; McCaslin, Laura; Martinez, Oscar, Jr.; Field, Robert W.; Stanton, John F.; McCarthy, Michael C.

    2014-06-01

    Carbenes (R1-C-R2) are a reactive class of compounds, usually characterized by an electron-deficient divalent carbon atom, found in applications ranging from organic synthesis to gas phase oxidation chemistry. Carbenes with 2- or 3-atom substituents often undergo rapid unimolecular isomerization, but may be stabilized if these substituents are electron-donating. Dihydroxycarbene (HO-C-OH) is one of the smallest singlet carbenes to be afforded this stability, due to its two electron-donating hydroxyl groups. We report the first gas-phase detection and structural characterization of this reactive species, using a combination of Fourier transform microwave spectroscopy and high level electronic structure calculations. Detection in the gas phase indicates that it is fairly stable relative to its isomers, formic acid (HCOOH) and the simplest Criegee intermediate (CH_2OO), the latter of which has recently received a great deal of attention for its role in the atmospheric ozonolysis of alkenes. Our experimental results yield a precise structure of HO-C-OH, and we comment on upcoming experiments investigating its stability and reactivity with other common atmospheric species.

  11. Infrared Action Spectroscopy of Low-Temperature Neutral Gas-Phase Molecules of Arbitrary Structure

    NASA Astrophysics Data System (ADS)

    Yatsyna, Vasyl; Bakker, Daniël J.; Salén, Peter; Feifel, Raimund; Rijs, Anouk M.; Zhaunerchyk, Vitali

    2016-09-01

    We demonstrate a technique for IR action spectroscopy that enables measuring IR spectra in a background-free fashion for low-temperature neutral gas-phase molecules of arbitrary structure. The method is exemplified experimentally for N -methylacetamide molecules in the mid-IR spectral range of 1000 - 1800 cm-1 , utilizing the free electron laser FELIX. The technique involves the resonant absorption of multiple mid-IR photons, which induces molecular dissociation. The dissociation products are probed with 10.49 eV vacuum ultraviolet photons and analyzed with a mass spectrometer. We also demonstrate the capability of this method to record, with unprecedented ease, mid-IR spectra for the molecular associates, such as clusters and oligomers, present in a molecular beam. In this way the mass-selected spectra of low-temperature gas-phase dimers and trimers of N -methylacetamide are measured in the full amide I-III range.

  12. Gas-phase acidities of tetrahedral oxyacids from ab initio electronic structure theory

    SciTech Connect

    Rustad, J.R.; Dixon, D.A.; Kubicki, J.D.; Felmy, A.R.

    2000-05-04

    Density functional calculations have been performed on several protonation states of the oxyacids of Si, P, V, As, Cr, and S. Structures and vibrational frequencies are in good agreement with experimental values where these are available. A reasonably well-defined correlation between the calculated gas-phase acidities and the measured pK{sub a} in aqueous solution has been found. The pK{sub a}/gas-phase acidity slopes are consistent with those derived from previous molecular mechanics calculations on ferric hydrolysis and the first two acidity constants for orthosilicic acid. The successive deprotonation of other H{sub n}TO{sub 4} species, for a given tetrahedral anion T are roughly consistent with this slope, but not to the extent that there is a universal correlation among all species.

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

    PubMed Central

    Stutzman, John R.; Blanksby, Stephen J.; McLuckey, Scott A.

    2013-01-01

    Gas-phase transformation of synthetic phosphatidylcholine (PC) monocations to structurally informative anions is demonstrated via ion/ion reactions with doubly deprotonated 1,4-phenylenedipropionic acid (PDPA). Two synthetic PC isomers, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC16:0/18:1) and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (PC18:1/16:0) were subjected to this ion/ion chemistry. The product of the ion/ion reaction is a negatively charged complex, [PC+PDPA-H]−. Collisional activation of the long-lived complex causes transfer of a proton and methyl cation to PDPA, generating [PC-CH3]−. Subsequent collisional activation of the demethylated PC anions produces abundant fatty acid carboxylate anions and low abundance acyl neutral losses as free acids and ketenes. Product ion spectra of [PC-CH3]− suggest favorable cleavage at the sn-2 position over the sn-1 due to distinct differences in the relative abundances. In contrast, collisional activation of PC cations is absent of abundant fatty acid chain-related product ions and typically indicates only the lipid class via formation of the phosphocholine cation. A solution phase method to produce the gas-phase adducted PC anion is also demonstrated. Product ion spectra derived from the solution phase method are similar to the results generated via ion/ion chemistry. This work demonstrates a gas-phase means to increase structural characterization of phosphatidylcholines via ion/ion chemistry. PMID:23469867

  14. Gas-phase transformation of phosphatidylcholine cations to structurally informative anions via ion/ion chemistry.

    PubMed

    Stutzman, John R; Blanksby, Stephen J; McLuckey, Scott A

    2013-04-02

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

  15. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.

    PubMed

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J

    2017-05-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.

  16. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J.

    2017-03-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions.

  17. Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation

    NASA Astrophysics Data System (ADS)

    Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J.

    2017-05-01

    Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions.

  18. Description and control of dissociation channels in gas-phase protein complexes

    NASA Astrophysics Data System (ADS)

    Thachuk, Mark; Fegan, Sarah K.; Raheem, Nigare

    2016-08-01

    Using molecular dynamics simulations of a coarse-grained model of the charged apo-hemoglobin protein complex, this work expands upon our initial report [S. K. Fegan and M. Thachuk, J. Am. Soc. Mass Spectrom. 25, 722-728 (2014)] about control of dissociation channels in the gas phase using specially designed charge tags. Employing a charge hopping algorithm and a range of temperatures, a variety of dissociation channels are found for activated gas-phase protein complexes. At low temperatures, a single monomer unfolds and becomes charge enriched. At higher temperatures, two additional channels open: (i) two monomers unfold and charge enrich and (ii) two monomers compete for unfolding with one eventually dominating and the other reattaching to the complex. At even higher temperatures, other more complex dissociation channels open with three or more monomers competing for unfolding. A model charge tag with five sites is specially designed to either attract or exclude charges. By attaching this tag to the N-terminus of specific monomers, the unfolding of those monomers can be decidedly enhanced or suppressed. In other words, using charge tags to direct the motion of charges in a protein complex provides a mechanism for controlling dissociation. This technique could be used in mass spectrometry experiments to direct forces at specific attachment points in a protein complex, and hence increase the diversity of product channels available for quantitative analysis. In turn, this could provide insight into the function of the protein complex in its native biological environment. From a dynamics perspective, this system provides an interesting example of cooperative behaviour involving motions with differing time scales.

  19. Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c.

    PubMed

    Allen, Samuel J; Eaton, Rachel M; Bush, Matthew F

    2017-07-18

    Ion mobility (IM) is a gas-phase separation technique that is used to determine the collision cross sections of native-like ions of proteins and protein complexes, which are in turn used as restraints for modeling the structures of those analytes in solution. Here, we evaluate the stability of native-like ions using tandem IM experiments implemented using structures for lossless ion manipulations (SLIM). In this implementation of tandem IM, ions undergo a first dimension of IM up to a switch that is used to selectively transmit ions of a desired mobility. Selected ions are accumulated in a trap and then released after a delay to initiate the second dimension of IM. For delays ranging from 16 to 33 231 ms, the collision cross sections of native-like, 7+ cytochrome c ions increase monotonically from 15.1 to 17.1 nm(2). The largest products formed in these experiments at near-ambient temperature are still far smaller than those formed in energy-dependent experiments (∼21 nm(2)). However, the collision cross section increases by ∼2% between delay times of 16 and 211 ms, which may have implications for other IM experiments on these time scales. Finally, two subpopulations from the full population were each mobility selected and analyzed as a function of delay time, showing that the three populations can be differentiated for at least 1 s. Together, these results suggest that elements of native-like structure can have long lifetimes at near-ambient temperature in the gas phase but that gas-phase dynamics should be considered when interpreting results from IM.

  20. The effect of molecular dynamics sampling on the calculated observable gas-phase structures.

    PubMed

    Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V

    2016-07-21

    In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory.

  1. Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration

    NASA Astrophysics Data System (ADS)

    Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.

    2013-10-01

    -ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.

  2. On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions

    PubMed Central

    Marchese, Roberto; Grandori, Rita; Carloni, Paolo; Raugei, Simone

    2010-01-01

    Determining the total number of charged residues corresponding to a given value of net charge for peptides and proteins in gas phase is crucial for the interpretation of mass-spectrometry data, yet it is far from being understood. Here we show that a novel computational protocol based on force field and massive density functional calculations is able to reproduce the experimental facets of well investigated systems, such as angiotensin II, bradykinin, and tryptophan-cage. The protocol takes into account all of the possible protomers compatible with a given charge state. Our calculations predict that the low charge states are zwitterions, because the stabilization due to intramolecular hydrogen bonding and salt-bridges can compensate for the thermodynamic penalty deriving from deprotonation of acid residues. In contrast, high charge states may or may not be zwitterions because internal solvation might not compensate for the energy cost of charge separation. PMID:20463874

  3. UV/Vis Action Spectroscopy and Structures of Tyrosine Peptide Cation Radicals in the Gas Phase.

    PubMed

    Viglino, Emilie; Shaffer, Christopher J; Tureček, František

    2016-06-20

    We report the first application of UV/Vis photodissociation action spectroscopy for the structure elucidation of tyrosine peptide cation radicals produced by oxidative intramolecular electron transfer in gas-phase metal complexes. Oxidation of Tyr-Ala-Ala-Ala-Arg (YAAAR) produces Tyr-O radicals by combined electron and proton transfer involving the phenol and carboxyl groups. Oxidation of Ala-Ala-Ala-Tyr-Arg (AAAYR) produces a mixture of cation radicals involving electron abstraction from the Tyr phenol ring and N-terminal amino group in combination with hydrogen-atom transfer from the Cα positions of the peptide backbone.

  4. Gas-phase hydrogen/deuterium exchange in a travelling wave ion guide for the examination of protein conformations

    PubMed Central

    Rand, Kasper D.; Pringle, Steven D.; Murphy, James P.; Fadgen, Keith E.; Brown, Jeff; Engen, John R.

    2009-01-01

    Accumulating evidence suggests that solution-phase conformations of small globular proteins and large molecular protein assemblies can be preserved for milliseconds after electrospray ionization. Thus, the study of proteins in the gas-phase on this time-scale is highly desirable. Here we demonstrate that a travelling wave ion guide (TWIG) of a Synapt mass spectrometer offers a highly suitable environment for rapid and efficient gas-phase hydrogen/deuterium exchange (HDX). Gaseous ND3 was introduced into either the source TWIG or the TWIG located just after the ion mobility cell, such that ions underwent HDX as they passed through the ND3 on the way to the time-of-flight analyzer. The extent of deuterium labeling could be controlled by varying the quantity of ND3 or the speed of the travelling wave. The gas-phase HDX of model peptides corresponded to labeling of primarily fast exchanging sites due to the short labeling times (ranging from 0.1 to 10 ms). In addition to peptides, gas-phase HDX of ubiquitin, cytochrome c, lysozyme and apomyoglobin were examined. We conclude that HDX of protein ions in a TWIG is highly sensitive to protein conformation, enables the detection of conformers present on sub-milliseconds timescales and can readily be combined with ion mobility spectrometry. PMID:19921790

  5. Gas-phase hydrogen/deuterium exchange in a traveling wave ion guide for the examination of protein conformations.

    PubMed

    Rand, Kasper D; Pringle, Steven D; Murphy, James P; Fadgen, Keith E; Brown, Jeff; Engen, John R

    2009-12-15

    Accumulating evidence suggests that solution-phase conformations of small globular proteins and large molecular protein assemblies can be preserved for milliseconds after electrospray ionization. Thus, the study of proteins in the gas phase on this time scale is highly desirable. Here we demonstrate that a traveling wave ion guide (TWIG) of a Synapt mass spectrometer offers a highly suitable environment for rapid and efficient gas-phase hydrogen/deuterium exchange (HDX). Gaseous ND(3) was introduced into either the source TWIG or the TWIG located just after the ion mobility cell, such that ions underwent HDX as they passed through the ND(3) on the way to the time-of-flight analyzer. The extent of deuterium labeling could be controlled by varying the quantity of ND(3) or the speed of the traveling wave. The gas-phase HDX of model peptides corresponded to labeling of primarily fast exchanging sites due to the short labeling times (ranging from 0.1 to 10 ms). In addition to peptides, gas-phase HDX of ubiquitin, cytochrome c, lysozyme, and apomyoglobin were examined. We conclude that HDX of protein ions in a TWIG is highly sensitive to protein conformation, enables the detection of conformers present on submilliseconds time scales, and can readily be combined with ion mobility spectrometry.

  6. Structural Isomerization of the Gas Phase 2-NORBORNYL Cation Revealed with Infrared Spectroscopy and Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Mauney, Daniel; Mosley, Jonathan; Duncan, Michael A.

    2014-06-01

    The non-classical structure of the 2-norborny cation (C_7H11+) which was at the center of "the most heated chemical controversy of our time" has been observed in the condensed phase and recently using X-ray crystallography. However, no gas phase vibrational spectrum has been collected. The C_7H11+ cation is produced via H_3+ protonation of norbornene by pulsed discharge in a supersonic expansion of H_2/Ar. Ions are mass-selected and probed using infrared photodissociation spectroscopy. Due to high exothermicity, protonation via H_3+ leads to a structural isomerization to the global minimum structure 1,3-dimethylcyclopentenyl (DMCP+). Experiments are currently being conducted to find softer protonation techniques that could lead to the authentic 2-norbornyl cation. Schleyer,P.v.R. et. al.; Stable Carbocation Chemistry, John Wiley & Sons,Inc.; New York, 1997, Chapter 2

  7. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries.

    PubMed

    Prentice, Boone M; McLuckey, Scott A

    2013-02-01

    Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field.

  8. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries

    PubMed Central

    Prentice, Boone M.

    2013-01-01

    Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field. PMID:23257901

  9. The structures of tellurium(IV) halides in the gas phase and as solvated molecules.

    PubMed

    Shlykov, Sergey A; Giricheva, Nina I; Titov, Anton V; Szwak, Małgorzata; Lentz, Dieter; Girichev, Georgiy V

    2010-04-07

    The structures of molecular tellurium tetrafluoride and tellurium tetrachloride were determined by a combination of gas-phase electron diffraction, mass spectrometry and quantum chemical calculations. The combined GED/MS experiments showed no evidence of decomposition of TeF(4) and TeCl(4). No ions of oligomeric (dimeric, trimeric, etc.) or any other composition were found in the mass spectra. The monomeric molecules possess a pseudo trigonal bipyramidal structure (C(2v) symmetry) with the equatorial Te-X distances being shorter than the axial ones. The fluorine atoms are bent away from the lone pair resulting in X(eq)-Te-X(eq) and X(eq)-Te-X(ax) bond angles smaller than 120 and 90 degrees, respectively. The structure of solvates TeF(4) (THF)(2), TeF(4) (dioxane) TeF(4) (DME)(2), TeF(4)(Et(2)O) TeF(4)(toluene), TeCl(4)(CH(3)CN)(2), TeCl(4)(DME)(2) and TeCl(4)(dioxane) were determined by X-ray diffraction. The structures of tellurium tetrafluoride solvates are strongly influenced by the choice of the solvent molecules. Monomeric TeF(4) units were obtained with THF, DME and dioxane whereas fluoride bridged coordination polymers were formed using diethyl ether or toluene. All tellurium tetrachloride solvates studied contain monomeric TeCl(4) units with coordinated solvent molecules. Coordination numbers range from four in the gas phase to eight in the TeF(4) dimethoxyethane solvate. Geometric parameters of the TeX(4) molecules in the crystal, solvates and gas phase were compared. DFT, MP2, CCSD, CCSD(T) methods were applied for calculation of geometric and vibrational characteristics of free TeX(4) molecules (X = F, Cl). The pseudorotation barriers were estimated and an NBO analysis was performed. It was shown that both, GED and theoretical, quantitative results are in agreement with the qualitative results of the VSEPR model.

  10. Possibilities of gas-phase synthesis of diamond structures from mixtures of hydrogen and hydrocarbons

    NASA Astrophysics Data System (ADS)

    Rebrov, A. K.

    2017-02-01

    To date, there is no universally recognized notion of diamond structure formation from the gas phase. The set of fragments determining this process differs for different methods of activation. Information on elementary processes of the interaction of hydrogen and hydrocarbon molecules with a surface for activation and deposition can be found in the literature, but it is scarce. Scientific problems of thermal activation relate not only to carbon structure synthesis; the description of non?equilibrium processes in channel flows with heterogeneous chemical reactions has unquestionable importance. In this review, the modern state of studies on the interaction of hydrogen and methane molecules and their fragments with high-temperature tungsten surfaces and diamond surfaces at temperatures close to 1300 K is considered, and accessible results are presented.

  11. Accurate Structure Parameters for Tunneling Ionization Rates of Gas-Phase Linear Molecules

    NASA Astrophysics Data System (ADS)

    Zhao, Song-Feng; Li, Jian-Ke; Wang, Guo-Li; Li, Peng-Cheng; Zhou, Xiao-Xin

    2017-03-01

    In the molecular Ammosov-Delone-Krainov (MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402], the ionization rate depends on the structure parameters of the molecular orbital from which the electron is removed. We determine systematically and tabulate accurate structure parameters of the highest occupied molecular orbital (HOMO) for 123 gas-phase linear molecules by solving time-independent Schrödinger equation with B-spline functions and molecular potentials which are constructed numerically using the modified Leeuwen-Baerends (LBα) model. Supported by National Natural Science Foundation of China under Grant Nos. 11664035, 11674268, 11465016, 11364038, 11364039, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001 and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  12. Electronic Structure and Gas-Phase Behaviour of the Heaviest Elements

    SciTech Connect

    Pershina, V.; Anton, J.; Jacob, T.; Borschevsky, A.

    2010-04-30

    Electronic structures and gas-phase adsorption behaviour of the heaviest elements 112, 113 and 114 and of their lighter homologs Hg, Tl and Pb is studied on the basis of ab initio Dirac-Coulomb atomic and four-component Density Functional Theory molecular and cluster calculations. The heaviest elements were shown to have low adsorption enthalpies on Teflon and should, therefore, be well transported through Teflon capillaries from the target chamber to the chemistry set up. Adsorption enthalpies of these elements on the Au(111) surface are predicted as -44.5 kJ/mol, -158.6 kJ/mol and -68.5 kJ/mol, respectively, giving the following sequence in the adsorption temperatures 113>114>112.

  13. Noble metal alloy clusters in the gas phase derived from protein templates: unusual recognition of palladium by gold

    NASA Astrophysics Data System (ADS)

    Baksi, Ananya; Pradeep, T.

    2013-11-01

    Matrix assisted laser desorption ionization of a mixture of gold and palladium adducts of the protein lysozyme (Lyz) produces naked alloy clusters of the type Au24Pd+ in the gas phase. While a lysozyme-Au adduct forms Au18+, Au25+, Au38+ and Au102+ ions in the gas phase, lysozyme-Pd alone does not form any analogous cluster. Addition of various transition metal ions (Ag+, Pt2+, Pd2+, Cu2+, Fe2+, Ni2+ and Cr3+) in the adducts contributes to drastic changes in the mass spectrum, but only palladium forms alloys in the gas phase. Besides alloy formation, palladium enhances the formation of specific single component clusters such as Au38+. While other metal ions like Cu2+ help forming Au25+ selectively, Fe2+ catalyzes the formation of Au25+ over all other clusters. Gas phase cluster formation occurs from protein adducts where Au is in the 1+ state while Pd is in the 2+ state. The creation of alloys in the gas phase is not affected whether a physical mixture of Au and Pd adducts or a Au and Pd co-adduct is used as the precursor. The formation of Au cores and AuPd alloy cores of the kind comparable to monolayer protected clusters implies that naked clusters themselves may be nucleated in solution.Matrix assisted laser desorption ionization of a mixture of gold and palladium adducts of the protein lysozyme (Lyz) produces naked alloy clusters of the type Au24Pd+ in the gas phase. While a lysozyme-Au adduct forms Au18+, Au25+, Au38+ and Au102+ ions in the gas phase, lysozyme-Pd alone does not form any analogous cluster. Addition of various transition metal ions (Ag+, Pt2+, Pd2+, Cu2+, Fe2+, Ni2+ and Cr3+) in the adducts contributes to drastic changes in the mass spectrum, but only palladium forms alloys in the gas phase. Besides alloy formation, palladium enhances the formation of specific single component clusters such as Au38+. While other metal ions like Cu2+ help forming Au25+ selectively, Fe2+ catalyzes the formation of Au25+ over all other clusters. Gas phase cluster

  14. Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation.

    PubMed

    Konermann, Lars

    2017-08-31

    Molecular dynamics (MD) simulations have become a key tool for examining the properties of electrosprayed protein ions. Traditional force fields employ static charges on titratable sites, whereas in reality, protons are highly mobile in gas-phase proteins. Earlier studies tackled this problem by adjusting charge patterns during MD runs. Within those algorithms, proton redistribution was subject to energy minimization, taking into account electrostatic and proton affinity contributions. However, those earlier approaches described (de)protonated moieties as point charges, neglecting charge solvation, which is highly prevalent in the gas phase. Here, we describe a mobile proton algorithm that considers the electrostatic contributions from all atoms, such that charge solvation is explicitly included. MD runs were broken down into 50 ps fixed-charge segments. After each segment, the electrostatics was reanalyzed and protons were redistributed. Challenges associated with computational cost were overcome by devising a streamlined method for electrostatic calculations. Avidin (a 504-residue protein complex) maintained a nativelike fold over 200 ns. Proton transfer and side chain rearrangements produced extensive salt bridge networks at the protein surface. The mobile proton technique introduced here should pave the way toward future studies on protein folding, unfolding, collapse, and subunit dissociation in the gas phase.

  15. Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine

    PubMed Central

    Bythell, Benjamin J.; Csonka, István P.; Suhai, Sándor; Barofsky, Douglas F.; Paizs, Béla

    2010-01-01

    The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b2 ions or facilely rearrange to form anhydrides from which both b2 and b2+H2O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b2 and b2+H2O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc., 2009, 131, 14057–14065.). In addition to these findings we also report on the mechanisms for the formation of the b1 ion, neutral loss (H2O, NH3, guanidine) fragment ions and the d3 ion. PMID:20973555

  16. Posttranslational modification of Birch and Ragweed allergen proteins by common gas phase pollutants, NO2 and O3

    NASA Astrophysics Data System (ADS)

    Mahmood, M. A.; Pope, F.; Bloss, W.

    2015-12-01

    The global incidence of hay fever has been rising for decades, however, the underlying reasons behind this rise remain unclear. It is hypothesized that exposure of pollen to common gas phase pollutants, such as nitrogen dioxide (NO2) and ozone (O3), increases the allergenicity of the pollen and thus increases hay fever incidence. Since atmospheric pollutants tend to have greater concentrations within urban areas (in particular NO2) the hypothesis suggests that greater allergenicity should occur in urban areas. Indeed, several studies do suggest higher hay fever incidence within urban areas compared to rural areas. Previous published work suggests a link between increased allergies with changes in the chemical composition of the pollen protein via posttranslational modification of the protein. This study investigates the posttranslational modification of two highly allergenic pollen species (Birch and Ragweed) that are common in Europe. Within the laboratory, we expose pollen grains to atmospherically relevant exposures of gas phase NO2, O3 and other common gas phase oxidants under a range of environmentally relevant conditions. The effects of the environmentally relevant exposures on the biochemistry of the pollen grains were probed using a proteomic approach (liquid chromatography coupled ultra-high resolution spectrometer). Our findings indicate the interaction between gas phase pollutants and pollen cause protein specific modifications; in particular, nitration occurs upon tyrosine residues and nitrosylation on cysteine residues. Possibly, these modifications may affect the immune response of the pollen protein, which may suggest a possible reason for increased allergies in reaction to such biologically altered protein. The laboratory-derived results will be supported with a time series analysis of asthma incidence rates for the London area, which take into account the pollen count, and pollutant concentrations. The implications of the results will be discussed

  17. Synthesis, structure and bonding of actinide disulphide dications in the gas phase.

    PubMed

    Lucena, Ana F; Bandeira, Nuno A G; Pereira, Cláudia C L; Gibson, John K; Marçalo, Joaquim

    2017-04-11

    Actinide disulphide dications, AnS2(2+), were produced in the gas phase for An = Th and Np by reaction of An(2+) cations with the sulfur-atom donor COS, in a sequential abstraction process of two sulfur atoms, as examined by FTICR mass spectrometry. For An = Pu and Am, An(2+) ions were unreactive with COS and did not yield any sulphide species. High level multiconfigurational (CASPT2) calculations were performed to assess the structures and bonding of the new AnS2(2+) species obtained for An = Th, Np, as well as for An = Pu to examine trends along the An series, and for An = U to compare with a previous experimental study and DFT computational scrutiny of US2(2+). The CASPT2 results showed that, like in the case of uranium, the new AnS2(2+) ions have ground states with triangular geometries, corresponding to the presence of a persulphide in the case of thorium that formally leads to a stable Th(IV)S2(2+) species, while a supersulphide appears to be present in the case of U, Np and Pu, formally leading to a An(III)S2(2+) species. The computations also revealed that linear thioactinyl structures are higher in energy, with a difference that increases fourfold upon moving from U to Pu, apparently indicating that it will be even more pronounced for Am.

  18. Structurally integrated organic light emitting device-based sensors for gas phase and dissolved oxygen.

    PubMed

    Shinar, Ruth; Zhou, Zhaoqun; Choudhury, Bhaskar; Shinar, Joseph

    2006-05-24

    A compact photoluminescence (PL)-based O2 sensor utilizing an organic light emitting device (OLED) as the light source is described. The sensor device is structurally integrated. That is, the sensing element and the light source, both typically thin films that are fabricated on separate glass substrates, are attached back-to-back. The sensing elements are based on the oxygen-sensitive dyes Pt- or Pd-octaethylporphyrin (PtOEP or PdOEP, respectively), which are embedded in a polystyrene (PS) matrix, or dissolved in solution. Their performance is compared to that of a sensing element based on tris(4,7-diphenyl-l,10-phenanthroline) Ru II (Ru(dpp)) embedded in a sol-gel film. A green OLED light source, based on tris(8-hydroxy quinoline Al (Alq3), was used to excite the porphyrin dyes; a blue OLED, based on 4,4'-bis(2,2'-diphenylviny1)-1,1'-biphenyl, was used to excite the Ru(dpp)-based sensing element. The O2 level was monitored in the gas phase and in water, ethanol, and toluene solutions by measuring changes in the PL lifetime tau of the O2-sensitive dyes. The sensor performance was evaluated in terms of the detection sensitivity, dynamic range, gas flow rate, and temperature effect, including the temperature dependence of tau in pure Ar and O2 atmospheres. The dependence of the sensitivity on the preparation procedure of the sensing film and on the PS and dye concentrations in the sensing element, whether a solid matrix or solution, were also evaluated. Typical values of the detection sensitivity in the gas phase, S(g) identical with tau(0% O2)/tau(100% O2), at 23 degrees C, were approximately 35 to approximately 50 for the [Alq3 OLED[/[PtOEP dye] pair; S(g) exceeded 200 for the Alq3/PdOEP sensor. For dissolved oxygen (DO) in water and ethanol, S(DO) (defined as the ratio of tau in de-oxygenated and oxygen-saturated solutions) was approximately 9.5 and approximately 11, respectively, using the PtOEP-based film sensor. The oxygen level in toluene was measured with Pt

  19. Mass spectrometric evaluation of the gas phase structure of noncovalent quadruplex DNA obtained by electrospray ionization

    SciTech Connect

    Edmonds, C.G.; Cheng, Xueheng; Bakhtiar, R.; Van Orden, S.; Smith, R.D.; Schlegel, C.; Camp, D.G. II

    1994-12-31

    A number of quanine-rich DNA sequences have been recognized which assemble into quadrupole-helical non-Watson/Crick hybridized structures. These sequences have been localized in a number of key regions in chromosomal DNA including telomers and transcriptional promoters. The preservation of this tetrameric association in the gas phase following electrospray ionization (ESI) has been reported in this laboratory. The authors have extended these studies by the preparation of four candidate quadruplex oligomers. Three of these (I, 5{prime}-dCGC GGG GCG-3{prime}; II, 5{prime}dCGC GGGG GCG-3{prime} and III, 5{prime}-dCGC GGGGG GCG-3{prime}) differ in the number of quanine residues available for G-quartet stacking in the quadruplex array and a fourth (HG, 5{prime}-dCGC AGGG GCG03{prime}) is a sequence prominent in human telomeric DNA. During their preparation, the authors observed remarkable stability of the multimeric species in the condensed phase including intact migration in HPLC under apparently {open_quotes}denaturing{close_quotes} conditions. Under standard conditions (aqueous solution of oligonucleotide samples and nozzle-skimmer interface) on a linear quadrupole mass spectrometer oligonucleotide samples showed the typical distribution of charge states for unassociated oligonucleotides. ESI from phosphate-EDTA buffered solutions with the utilization of a capillary/skimmer interface arrangement which provides mild conditions for transfer of ions through the atmosphere/vacuum interface afforded spectra which show prominent contributions from species with quadrupole stoichiometry together monomeric materials.

  20. Gas Phase Spectra and Structural Determination of Glucose 6 Phosphate Using Cryogenic Ion Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kregel, Steven J.; Voss, Jonathan; Marsh, Brett; Garand, Etienne

    2014-06-01

    Glucose-6-Phosphate (G6P) is one member of a class of simple phosphorylated sugars that are relevant in biological processes. We have acquired a gas phase infrared spectrum of G6P- using cryogenic ion vibrational spectroscopy (CIVS) in a home-built spectrometer. The experimental spectrum was compared with calculated vibrational spectra from a systematic conformer search. For both of the α and β anomers, results show that only the lowest energy conformers are present in the gas phase. If spectral signatures for similar sugars could be cataloged, it would allow for conformer-specific determination of mixture composition, for example, for glycolyzation processes.

  1. The structure of the 1H-imidazol-3-ium lawsonate salt aided by ab initio gas-phase calculations.

    PubMed

    Ribeiro, Marcos Antônio; Oliveira, Willian Xerxes Coelho; Stumpf, Humberto Osório; Pinheiro, Carlos Basílio

    2013-04-01

    For the new organic salt 1H-imidazol-3-ium 1,4-dioxo-1,4-dihydronaphthalen-2-olate, C3H5N2(+)·C10H5O3(-), ab initio calculations of the gas-phase structures of the lawsonate and imidazolium ions were performed to help in the interpretation of the structural features observed. Three different types of hydrogen bond are responsible for the three-dimensional packing of the salt.

  2. High-sensitivity gas phase sequence analysis of proteins and peptides on PVDF membranes using short cycle times.

    PubMed

    Reim, D F; Speicher, D W

    1993-10-01

    An optimized sequencer program with a cycle time of 38 min which is specifically tailored for analysis using polyvinylidene difluoride (PVDF) membranes has been developed. The program was developed using a pulsed liquid-phase instrument which was converted to gas-phase acid delivery. Gas-phase acid delivery minimized sample extraction from PVDF membranes and improved tryptophan yields in at least some cases. Other modifications which contributed to reliable high sensitivity sequencer performance included use of a Blott cartridge, substitution of ethyl acetate:heptane (1:1, v/v) instead of butyl chloride as the extraction solvent, use of a modified 100-microliters injection loop with an internal restrictor to reliably inject nearly 90% of the sample, and an HPLC gradient which resolved tryptophan from diphenylurea. These shortened cycle times were achieved at the conventional gas-phase reaction temperature. A slight increase in lag or carryover at prolines was compensated by reduced background from nonspecific acid cleavage which facilitated extended and/or high sensitivity sequencing of large proteins. Reproducible high initial and repetitive cycle yields were obtained with a wide range of experimental peptides which were electroblotted from either 1D or 2D polyacrylamide gels onto high retention PVDF membranes. Initial yields of the majority of the experimental samples analyzed with this program were less than 5 pmol. In addition, most samples with initial yields below 1-2 pmol yielded sufficient sequence information to identify the protein by comparison to protein sequence data-bases or to design oligonucleotide probes.

  3. Toluene gas phase biofiltration by Paecilomyces lilacinus and isolation and identification of a hydrophobin protein produced thereof.

    PubMed

    Vigueras, Gabriel; Shirai, Keiko; Martins de Souza, Daniel; Martins, Daniel; Franco, Telma Teixeira; Fleuri, Luciana Francisco; Revah, Sergio

    2008-08-01

    Paecilomyces lilacinus consumed toluene as the sole carbon source in a gas-phase biofilter packed with perlite obtaining an average elimination capacity of 50 g m(-3) h(-1), a removal efficiency of 53%, and a final biomass of 31.6 mg biomass g dry support(-1). Hydrophobin proteins from the mycelium produced in the biofilter were purified by formic acid extraction and precipitated by electrobubbling, and the molecular weight was found to be 10.6 +/- 0.3 kDa. The peptide mass fingerprinting analysis of the purified hydrophobin by matrix-assisted laser desorption/ionization time-of-flight resulted in the identification of two peptides that presented high homology with sequences of class I hydrophobin proteins from other ascomycetous fungi when compared against the National Center for Biotechnology Information database. The yield of hydrophobin (PLHYD) from P. lilacinus was 1.1 mg PLHYD g biomass(-1). These proteins modified the hydrophobicity of Teflon by lowering the contact angle from 130.1 (+/-2) degrees to 57.0 (+/-5) degrees supporting hot sodium dodecyl sulfate washing. This work is the first report about biodegradation of toluene by the nematophagous fungus P. lilacinus in a gas-phase biofilter and the identification of its hydrophobin protein.

  4. Gas phase characterization of the noncovalent quaternary structure of cholera toxin and the cholera toxin B subunit pentamer.

    PubMed

    Williams, Jonathan P; Smith, Daniel C; Green, Brian N; Marsden, Brian D; Jennings, Keith R; Roberts, Lynne M; Scrivens, James H

    2006-05-01

    Cholera toxin (CTx) is an AB5 cytotonic protein that has medical relevance in cholera and as a novel mucosal adjuvant. Here, we report an analysis of the noncovalent homopentameric complex of CTx B chain (CTx B5) using electrospray ionization triple quadrupole mass spectrometry and tandem mass spectrometry and the analysis of the noncovalent hexameric holotoxin usingelectrospray ionization time-of-flight mass spectrometry over a range of pH values that correlate with those encountered by this toxin after cellular uptake. We show that noncovalent interactions within the toxin assemblies were maintained under both acidic and neutral conditions in the gas phase. However, unlike the related Escherichia coli Shiga-like toxin B5 pentamer (SLTx B), the CTx B5 pentamer was stable at low pH, indicating that additional interactions must be present within the latter. Structural comparison of the CTx B monomer interface reveals an additional alpha-helix that is absent in the SLTx B monomer. In silico energy calculations support interactions between this helix and the adjacent monomer. These data provide insight into the apparent stabilization of CTx B relative to SLTx B.

  5. Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules.

    PubMed

    Boll, Rebecca; Rouzée, Arnaud; Adolph, Marcus; Anielski, Denis; Aquila, Andrew; Bari, Sadia; Bomme, Cédric; Bostedt, Christoph; Bozek, John D; Chapman, Henry N; Christensen, Lauge; Coffee, Ryan; Coppola, Niccola; De, Sankar; Decleva, Piero; Epp, Sascha W; Erk, Benjamin; Filsinger, Frank; Foucar, Lutz; Gorkhover, Tais; Gumprecht, Lars; Hömke, André; Holmegaard, Lotte; Johnsson, Per; Kienitz, Jens S; Kierspel, Thomas; Krasniqi, Faton; Kühnel, Kai-Uwe; Maurer, Jochen; Messerschmidt, Marc; Moshammer, Robert; Müller, Nele L M; Rudek, Benedikt; Savelyev, Evgeny; Schlichting, Ilme; Schmidt, Carlo; Scholz, Frank; Schorb, Sebastian; Schulz, Joachim; Seltmann, Jörn; Stener, Mauro; Stern, Stephan; Techert, Simone; Thøgersen, Jan; Trippel, Sebastian; Viefhaus, Jens; Vrakking, Marc; Stapelfeldt, Henrik; Küpper, Jochen; Ullrich, Joachim; Rudenko, Artem; Rolles, Daniel

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

  6. Gas-phase structures and thermochemistry of neutral histidine and its conjugated acid and base.

    PubMed

    Riffet, Vanessa; Bouchoux, Guy

    2013-04-28

    Extensive exploration of the conformational space of neutral, protonated and deprotonated histidine has been conducted at the G4MP2 level. Theoretical protonation and deprotonation thermochemistry as well as heats of formation of gaseous histidine and its ionized forms have been calculated at the G4 level considering either the most stable conformers or an equilibrium population of conformers at 298 K. These theoretical results were compared to evaluated experimental determinations. Recommended proton affinity and protonation entropy deduced from these comparisons are PA(His) = 980 kJ mol(-1) and ΔpS(His) ∼ 0 J mol(-1) K(-1), thus leading to a gas-phase basicity value of GB(His) = 947.5 kJ mol(-1). Similarly, gas phase acidity parameters are ΔacidH(o)(His) = 1373 kJ mol(-1), ΔacidS(His) ∼ 10 J mol(-1) K(-1) and ΔacidG(o)(His) = 1343 kJ mol(-1). Computed G4 heats of formation values are equal to -290, 265 and -451 kJ mol(-1) for gaseous neutral histidine and its protonated and deprotonated forms, respectively. The present computational data correct, and complete, previous thermochemical parameter estimates proposed for gas-phase histidine and its acido-basic properties.

  7. Structure of olefin-imidacloprid and gas-phase fragmentation chemistry of its protonated form.

    PubMed

    Fusetto, Roberto; White, Jonathan M; Hutton, Craig A; O'Hair, Richard A J

    2016-02-07

    One of the major insect metabolites of the widely used neonicotinoid insecticide imidacloprid, 1 (1-[(6-chloro-3-pyridinyl)methyl]-N-nitro-1H-imidazol-2-amine), is the olefin 2. To better understand how the structure of olefin 2 relates to the gas-phase fragmentation of its protonated form, 2H(+), X-ray crystallography, tandem mass spectrometry experiments and DFT calculations were carried out. Olefin 2 was found to be in a tautomeric form where the proton is on the N(1) position of the imidazole ring and forms a hydrogen bond to one of the oxygen atoms of the coplanar nitroamine group. Under conditions of low-energy collision-induced dissociation (CID) in a linear ion trap, 2H(+), formed via electrospray ionization (ESI), fragments via a major loss of water, together with minor competing losses of HNO2 and NO2•.This contrasts with 1H+, which mainly undergoes bond homolysis via NO2• loss. Thus, installation of the double bond in 2 plays a key role in facilitating the loss of water. DFT calculations, carried out using the B3LYP/6-311G++(d,p) level of theory, revealed that loss of water was energetically more favourable compared to HNO2 and NO2• loss. Three multistep, energetically accessible mechanisms were identified for loss of water from 2H(+), and these have the following barriers: (I) direct proton transfer from N(5) of the pyridine to O(1) on the NO2 group (119 kJ mol(-1)); (II) rotation of the N(2)-N(4) bond (117 kJ mol(-1)); (III) 1,3-intramolecular proton transfer between the two oxygen atoms of the NO2 group (145 kJ mol(-1)). Given that the lowest barrier for the losses of HNO2 and NO2• is 156 kJ mol(-1), it is likely that all three water loss mechanisms occur concurrently.

  8. Going clean: structure and dynamics of peptides in the gas phase and paths to solvation

    NASA Astrophysics Data System (ADS)

    Baldauf, Carsten; Rossi, Mariana

    2015-12-01

    The gas phase is an artificial environment for biomolecules that has gained much attention both experimentally and theoretically due to its unique characteristic of providing a clean room environment for the comparison between theory and experiment. In this review we give an overview mainly on first-principles simulations of isolated peptides and the initial steps of their interactions with ions and solvent molecules: a bottom up approach to the complexity of biological environments. We focus on the accuracy of different methods to explore the conformational space, the connections between theory and experiment regarding collision cross section evaluations and (anharmonic) vibrational spectra, and the challenges faced in this field.

  9. Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation.

    PubMed

    Saikusa, Kazumi; Fuchigami, Sotaro; Takahashi, Kyohei; Asano, Yuuki; Nagadoi, Aritaka; Tachiwana, Hiroaki; Kurumizaka, Hitoshi; Ikeguchi, Mitsunori; Nishimura, Yoshifumi; Akashi, Satoko

    2013-04-16

    The minimum structural unit of chromatin is the nucleosome core particle (NCP), consisting of 146 bp of DNA wrapped around a histone octamer, which itself contains two H2A/H2B dimers and one (H3/H4)2 tetramer. These multimers possess functionally important tail regions that are intrinsically disordered. In order to elucidate the mechanisms behind NCP assembly and disassembly processes, which are highly related to gene expression, structural characterization of the H2A/H2B dimer and (H3/H4)2 tetramer will be of importance. In the present study, human histone multimers with disordered tail regions were characterized by electrospray ionization (ESI) ion mobility-mass spectrometry (IM-MS) and molecular dynamics (MD) simulation. Experimentally obtained arrival times of these histone multimer ions showed rather wide distributions, implying that multiple conformers exist for each histone multimer in the gas phase. To examine their structures, MD simulations of the histone multimers were performed first in solution and then in vacuo at four temperatures, resulting in a variety of histone multimer structures. Theoretical collision cross-section (CCS) values calculated for the simulated structures revealed that structural models with smaller CCS values had more compact tail regions than those with larger CCS values. This implied that variation of the CCS values of the histone multimers were primarily due to the random behaviors of the tail regions in the gas phase. The combination of IM-MS and MD simulation enabled clear and comprehensive characterization of the gas-phase structures of histone multimers containing disordered tails.

  10. Controlling hydrogen scrambling in multiply charged protein ions during collisional activation: implications for top-down hydrogen/deuterium exchange MS utilizing collisional activation in the gas phase.

    PubMed

    Abzalimov, Rinat R; Kaltashov, Igor A

    2010-02-01

    Hydrogen exchange in solution combined with ion fragmentation in the gas phase followed by MS detection emerged in recent years as a powerful tool to study higher order protein structure and dynamics. However, a certain type of ion chemistry in the gas phase, namely, internal rearrangement of labile hydrogen atoms (the so-called hydrogen scrambling), is often cited as a factor limiting the utility of this experimental technique. Although several studies have been carried out to elucidate the roles played by various factors in the occurrence and the extent of hydrogen scrambling, there is still no consensus as to what experimental protocol should be followed to avoid or minimize it. In this study we employ fragmentation of mass-selected subpopulations of protein ions to assess the extent of internal proton mobility prior to dissociation. A unique advantage of tandem MS is that it not only provides a means to map the deuterium content of protein ions whose overall levels of isotope incorporation can be precisely defined by controlling the mass selection window, but also correlates this spatial isotope distribution with such global characteristic as the protein ion charge state. Hydrogen scrambling does not occur when the charge state of the precursor protein ions selected for fragmentation is high. Fragment ions derived from both N- and C-terminal parts of the protein are equally unaffected by scrambling. However, spatial distribution of deuterium atoms obtained by fragmenting low-charge-density protein ions is consistent with a very high degree of scrambling prior to the dissociation events. The extent of hydrogen scrambling is also high when multistage fragmentation is used to probe deuterium incorporation locally. Taken together, the experimental results provide a coherent picture of intramolecular processes occurring prior to the dissociation event and provide guidance for the design of experiments whose outcome is unaffected by hydrogen scrambling.

  11. Controlling hydrogen scrambling in multiply charged protein ions during collisional activation: Implications for top-down HDX MS utilizing collisional activation in the gas phase

    PubMed Central

    Abzalimov, Rinat R.; Kaltashov, Igor A.

    2010-01-01

    Hydrogen exchange in solution combined with ion fragmentation in the gas phase followed by MS detection emerged in recent years as a powerful tool to study higher order protein structure and dynamics. However, certain type of ion chemistry in the gas phase, namely internal rearrangement of labile hydrogen atoms (the so-called hydrogen scrambling), is often cited as a factor limiting the utility of this experimental technique. Although several studies have been carried out to elucidate the roles played by various factors in the occurrence and the extent of hydrogen scrambling, there is still no consensus as to what experimental protocol should be followed in order to avoid or minimize it. In this study we employ fragmentation of mass-selected subpopulations of protein ions to assess the extent of internal proton mobility prior to dissociation. A unique advantage of tandem MS is that not only does it provide a means to map deuterium content of protein ions whose overall levels of isotope incorporation can be precisely defined by controlling mass selection window, but also correlates this spatial isotope distributions with such global characteristic as the protein ion charge state. Hydrogen scrambling does not occur when the charge state of the precursor protein ions selected for fragmentation is high. Fragment ions derived from both N- and C-terminal parts of the protein are equally unaffected by scrambling. However, spatial distribution of deuterium atoms obtained by fragmenting low charge-density protein ions is consistent with a very high degree of scrambling prior to the dissociation events. The extent of hydrogen scrambling is also high when multi-stage fragmentation is used to probe deuterium incorporation locally. Taken together, the experimental results provide a coherent picture of intra-molecular processes occurring prior to the dissociation event and provide guidance for the design of experiments whose outcome is unaffected by hydrogen scrambling. PMID

  12. Ergothioneine and related histidine derivatives in the gas phase: tautomer structures determined by IRMPD spectroscopy and theory.

    PubMed

    Peckelsen, Katrin; Martens, Jonathan; Czympiel, Lisa; Oomens, Jos; Berden, Giel; Gründemann, Dirk; Meijer, Anthony J H M; Schäfer, Mathias

    2017-08-30

    l-Ergothioneine (ET) is a sulfur-containing derivative of the amino acid histidine that offers unique antioxidant properties. The enzyme independent redox-chemistry of ET relies on the availability of the thiol tautomer to allow oxidative formation of disulfide bridges, i.e., the tautomeric equilibrium. To study the intrinsic properties of ET the tautomeric equilibrium is studied in the gas-phase by infrared multiphoton dissociation (IRMPD) spectroscopy. The IR ion spectra of isolated molecular ions of ET and of the biosynthetic precursors of ET, i.e., hercynine and Nε-methyl-hercynine are acquired. The analyte structures are independently investigated by density functional theory (DFT) and computed linear IR-spectra of tautomer ion structures are compared with the gas-phase spectra for identification. For the molecular ion of ET the simulated IR spectra of thione and thiol structures match the recorded IRMPD spectrum and that prevents an individual structure assignment. On the other hand, theory suggests that ET adopts a thione tautomer in MeOH solution which could be carried over from the condensed phase to gas phase and could be kinetically trapped after effective electrospray phase transfer and desolvation. Such a non-thermal behavior is also found for the molecular ions of protonated hercynine and Nε-methyl-hercynine. Contrary to that, the sodium complex ions of ET, hercynine and Nε-methyl-hercynine adopt the respective ground structures predicted by theory, which are reliably identified spectroscopically. For ET the thione tautomer is by far the most stable isomer in the sodium complex molecular ion.

  13. Molecular structure of CeI 3 from gas-phase electron diffraction and vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Molnár, Judit; Konings, Rudy J. M.; Kolonits, Mária; Hargittai, Magdolna

    1996-02-01

    CeI 3 was investigated by electron diffraction and infrared spectroscopy, both in the gas phase, at high temperature (around 1270 K). The geometrical parameters are: r g( CeI) 2.948 ± 0.009 Å and r g( I⋯I) 4.943 ± 0.032 Å. One absorption band was detected in the stretching region of the spectrum and we have assigned it to the asymmetric stretch, v3 = 191 ± 10 cm -1. The unusually large uncertainty is due to the large population of excited vibrational and rotational levels. From the very low intensity band at the lower detection limit of the spectrometer, we can conclude that neither v2 nor v4 is above 35 cm -1. From the analysis of electron diffraction data and vibrational spectra we conclude that the molecule is very likely planar or at most slightly pyramidal (quasiplanar).

  14. Effects of metal ion adduction on the gas-phase conformations of protein ions.

    PubMed

    Flick, Tawnya G; Merenbloom, Samuel I; Williams, Evan R

    2013-11-01

    Changes in protein ion conformation as a result of nonspecific adduction of metal ions to the protein during electrospray ionization (ESI) from aqueous solutions were investigated using traveling wave ion mobility spectrometry (TWIMS). For all proteins examined, protein cations (and in most cases anions) with nonspecific metal ion adducts are more compact than the fully protonated (or deprotonated) ions with the same charge state. Compaction of protein cations upon nonspecific metal ion binding is most significant for intermediate charge state ions, and there is a greater reduction in collisional cross section with increasing number of metal ion adducts and increasing ion valency, consistent with an electrostatic interaction between the ions and the protein. Protein cations with the greatest number of adducted metal ions are no more compact than the lowest protonated ions formed from aqueous solutions. These results show that smaller collisional cross sections for metal-attached protein ions are not a good indicator of a specific metal-protein interaction in solution because nonspecific metal ion adduction also results in smaller gaseous protein cation cross sections. In contrast, the collisional cross section of α-lactalbumin, which specifically binds one Ca(2+), is larger for the holo-form compared with the apo-form, in agreement with solution-phase measurements. Because compaction of protein cations occurs when metal ion adduction is nonspecific, elongation of a protein cation may be a more reliable indicator that a specific metal ion-protein interaction occurs in solution.

  15. Effects of Metal Ion Adduction on the Gas-Phase Conformations of Protein Ions

    PubMed Central

    Flick, Tawnya G.; Merenbloom, Samuel I.; Williams, Evan R.

    2013-01-01

    Changes in protein ion conformation as a result of nonspecific adduction of metal ions to the protein during electrospray ionization (ESI) from aqueous solutions were investigated using traveling wave ion mobility spectrometry (TWIMS). For all proteins examined, protein cations (and in most cases anions) with nonspecific metal ion adducts are more compact than the fully protonated (or deprotonated) ions with the same charge state. Compaction of protein cations upon nonspecific metal ion binding is most significant for intermediate charge state ions, and there is a greater reduction in collisional cross section with increasing number of metal ion adducts and increasing ion valency, consistent with an electrostatic interaction between the ions and the protein. Protein cations with the greatest number of adducted metal ions are no more compact than the lowest protonated ions formed from aqueous solutions. These results show that smaller collisional cross sections for metal-attached protein ions are not a good indicator of a specific metal-protein interaction in solution, because nonspecific metal ion adduction also results in smaller gaseous protein cation cross sections. In contrast, the collisional cross section of α-lactalbumin, which specifically binds one Ca2+, is larger for the holo-form compared to the apo-form, in agreement with solution-phase measurements. Because compaction of protein cations occurs when metal ion adduction is nonspecific, elongation of a protein cation may be a more reliable indicator that a specific metal ion-protein interaction occurs in solution. PMID:23733259

  16. Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    PubMed Central

    KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

    2014-01-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

  17. Development of a Polarizable Force Field for Proteins Via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    SciTech Connect

    Kaminski, George A.; Stern, Harry A.; Berne, Bruce J.; Friesner, Richard A.; Cao, Yixiang; Murphy, Robert B.; Zhou, Ruhong; Halgren, Thomas A.

    2002-12-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.

  18. Structures and aggregation states of fluoromethyllithium and chloromethyllithium carbenoids in the gas phase and in ethereal solvent.

    PubMed

    Pratt, Lawrence M; Ramachandran, Bala; Xidos, James D; Cramer, Christopher J; Truhlar, Donald G

    2002-11-01

    Using high-level quantum mechanical calculations and various models to account for solvation effects, monomers and dimers of fluoromethyllithium and chloromethyllithium carbenoids are studied in the gas phase and in dimethyl ether solvent. A combination of explicit microsolvation and a continuum reaction field is required to account fully for the structural and energetic effects of solvation. One important effect of solvent is the stabilization of charge-separated structures in which the lithium-halogen distance is much greater than in the gas-phase structures. At the most complete level of theory the 173 K standard-state free energy of dimerization of fluoromethyllithium in dimethyl ether is predicted to be -0.9 kcal mol(-)(1), while that for chloromethyllithium in the same solvent is predicted to be 3.7 kcal mol(-)(1). This suggests that, under typical experimental conditions, dimers of chloroalkyllithiums will not be observed, while dimers of fluoroalkyllithiums may contribute to the equilibrium population at a detectable level.

  19. Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

    PubMed

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

    2014-12-02

    Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

  20. Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

    PubMed

    Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

    2017-02-15

    We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala)nn ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala)2, as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

  1. Microwave spectra and gas phase structural parameters for N-hydroxypyridine-2(1H)-thione.

    PubMed

    Daly, Adam M; Mitchell, Erik G; Sanchez, Daniel A; Block, Eric; Kukolich, Stephen G

    2011-12-22

    The microwave spectrum for N-hydroxypyridine-2(1H)-thione (pyrithione) was measured in the frequency range 6-18 GHz, providing accurate rotational constants and nitrogen quadrupole coupling strengths for three isotopologues, C(5)H(4)(32)S(14)NOH, C(5)H(4)(32)S(14)NOD, and C(5)H(4)(34)S(14)NOH. Pyrithione was found to be in a higher concentration in the gas phase than the other tautomer, 2-mercaptopyridine-N-oxide (MPO). Microwave spectroscopy is best suited to determine which structure predominates in the gas phase. The measured rotational constants were used to accurately determine the coordinates of the substituted atoms and provided sufficient data to determine some of the important structural parameters for pyrithione, the only tautomer observed in the present work. The spectra were obtained using a pulsed-beam Fourier transform microwave spectrometer, with sufficient resolution to allow accurate measurements of the (14)N nuclear quadrupole hyperfine interactions. Ab initio calculations provided structural parameters and quadrupole coupling strengths that are in very good agreement with measured values. The experimental rotational constants for the parent compound are A = 3212.10(1), B = 1609.328(7), and C = 1072.208(6) MHz, yielding the inertial defect Δ(0) = -0.023 amu·Å(2) for the C(5)H(4)(32)S(14)NOH isotopologue. The observed near zero inertial defect clearly indicates a planar structure. The least-squares fit structural analysis yielded the experimental bond lengths R(O-H) = 0.93(2) Å, R(C-S) = 1.66(2) Å, and angle (N-O-H) = 105(4)° for the ground state structure.

  2. Synthesis, structural and conformational properties, and gas phase reactivity of 1,4-dihydropyridine ester and ketone derivatives.

    PubMed

    Giorgi, Gianluca; Adamo, Mauro F A; Ponticelli, Fabio; Ventura, Antonio

    2010-12-07

    A new series of 4-aryl-2,6-dimethyl-1,4-dihydropyridines, characterized by ester or ketone functions at positions 3 and 5, has been synthesized. Structural and conformational properties, concerning the dihydropyridine ring and the orientation (synplanar/antiperiplanar) of the substituents have been investigated in their crystal structure and in solution by nuclear magnetic resonance. Evaluation of intermolecular and hydrogen bonding interactions as well as packing features, have been also carried out, evidencing interesting packing motifs. Their gas phase reactivity, as protonated and deprotonated molecules, has been investigated by electrospray ionization, high resolution and collision-induced dissociation multiple stage mass spectrometry. Deydrogenation reactions have been observed as a function of the capillary voltage.

  3. The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.

    PubMed

    Davari, Mehdi D; Ferrer, Francisco J Avila; Morozov, Dmitry; Santoro, Fabrizio; Groenhof, Gerrit

    2014-10-20

    In this work we present the vibrationally resolved optical absorption spectrum of p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI), the green fluorescent protein (GFP) chromophore, computed at several levels of theory, including time-dependent DFT with various functionals and basis sets, CASSCF, CASPT2 and XMCQDPT2. We also investigated what happens to the spectrum if the ground- and excited-state geometries are optimized at different levels of theory (mixed approach), as has been used previously. The vibrationally resolved absorption spectra obtained by DFT, CASPT2 and XMCQDPT2 are very similar and consist of a main absorption peak and a shoulder that is ∼1500 cm(-1) higher in energy. The vibrational progression increases moderately with temperature. These spectra are in qualitative agreement with experimental action spectra, but much narrower and lack the long tail in the blue, even at high temperatures. Because our calculated emission spectra, which are equally narrow, are in good agreement with the emission of green fluorescent protein at 253 K, we argue that the action spectrum are too broad to be considered as the absorption spectrum. The CASSCF method and the mixed approaches overestimate the vibrational progressions with respect to CAM-B3LYP, CASPT2 and XMCQDPT2, due to inaccuracies in the geometric S0 →S1 displacements. Finally, we computed the vibronic spectra of four chromophore analogues with different substitutions on the rings and found that these substitutions hardly affect the lineshape in vacuum.

  4. Controlling dissociation channels of gas-phase protein complexes using charge manipulation.

    PubMed

    Fegan, Sarah K; Thachuk, Mark

    2014-05-01

    Coarse-grained simulations with charge hopping were performed for a positively charged tetrameric transthyretin (TTR) protein complex with a total charge of +20. Charges were allowed to move among basic amino acid sites as well as N-termini. Charge distributions and radii of gyration were calculated for complexes simulated at two temperatures, 300 and 600 K, under different scenarios. One scenario treated the complex in its normal state allowing charge to move to any basic site. Another scenario blocked protonation of all the N-termini except one. A final scenario used the complex in its normal state but added a basic-site containing tether (charge tag) near the N-terminus of one chain. The differences in monomer unfolding and charging were monitored in all three scenarios and compared. The simulation results show the importance of the N-terminus in leading the unfolding of the monomer units; a process that follows a zipper-like mechanism. Overall, experimentally modifying the complex by adding a tether or blocking the protonation of N-termini may give the potential for controlling the unraveling and subsequent dissociation of protein complexes.

  5. Reagent Anions for Charge Inversion of Polypeptide/Protein Cations in the Gas Phase

    PubMed Central

    He, Min; Emory, Joshua F.; McLuckey, Scott A.

    2005-01-01

    Various reagent anions capable of converting polypeptide cations to anions via ion/ion reactions have been investigated. The major charge inversion reaction channels include multiple proton transfer and adduct formation. Dianions composed of sulfonate groups as the negative charge carriers show essentially exclusive adduct formation in converting protonated peptides and proteins to anions. Dianions composed of carboxylate groups, on the other hand, show far more charge inversion via multiple proton transfer, with the degree of adduct formation dependent upon both the size of the polypeptide and the spacings between carboxylate groups in the dianion. More highly charged carboxylate-containing anions, such as those derived from carboxylate-terminated polyamidoamine half-generation dendrimers show charge inversion to give anion charges as high in magnitude as −4, with the degree of adduct formation being inversely related to dendrimer generation. All observations can be interpreted on the basis of charge inversion taking place via a long-lived chemical complex. The lifetime of this complex is related to the strengths and numbers of the interactions of the reactants in the complex. Calculations with model systems are fully consistent with sulfonate groups giving rise to more stable complexes. The kinetic stability of the complex can also be affected by the presence of electrostatic repulsion if it is multiply charged. In general, this situation destabilizes the complex and reduces the likelihood for observation of adducts. The findings highlight the characteristics of multiply charged anions that play roles in determining the nature of charge inversion products associated with protonated peptides and proteins. PMID:15889906

  6. Gas phase studies of the Pesci decarboxylation reaction: synthesis, structure, and unimolecular and bimolecular reactivity of organometallic ions.

    PubMed

    O'Hair, Richard A J; Rijs, Nicole J

    2015-02-17

    CONSPECTUS: Decarboxylation chemistry has a rich history, and in more recent times, it has been recruited in the quest to develop cheaper, cleaner, and more efficient bond-coupling reactions. Thus, over the past two decades, there has been intense investigation into new metal-catalyzed reactions of carboxylic substrates. Understanding the elementary steps of metal-mediated transformations is at the heart of inventing new reactions and improving the performance of existing ones. Fortunately, during the same time period, there has been a convergence in mass spectrometry (MS) techniques, which allows these catalytic processes to be examined efficiently in the gas phase. Thus, electrospray ionization (ESI) sources have been combined with ion-trap mass spectrometers, which in turn have been modified to either accept radiation from tunable OPO lasers for spectroscopy based structural assignment of ions or to allow the study of ion-molecule reactions (IMR). The resultant "complete" gas-phase chemical laboratories provide a platform to study the elementary steps of metal-catalyzed decarboxylation reactions in exquisite detail. In this Account, we illustrate how the powerful combination of ion trap mass spectrometry experiments and DFT calculations can be systematically used to examine the formation of organometallic ions and their chemical transformations. Specifically, ESI-MS allows the transfer of inorganic carboxylate complexes, [RCO2M(L)n](x), (x = charge) from the condensed to the gas phase. These mass selected ions serve as precursors to organometallic ions [RM(L)n](x) via neutral extrusion of CO2, accessible by slow heating in the ion trap using collision induced dissociation (CID). This approach provides access to an array of organometallic ions with well-defined stoichiometry. In terms of understanding the decarboxylation process, we highlight the role of the metal center (M), the organic group (R), and the auxiliary ligand (L), along with cluster nuclearity, in

  7. Structural isomerization of the gas-phase 2-norbornyl cation revealed with infrared spectroscopy and computational chemistry.

    PubMed

    Mosley, Jonathan D; Young, Justin W; Agarwal, Jay; Schaefer, Henry F; Schleyer, Paul v R; Duncan, Michael A

    2014-06-02

    In an attempt to produce the 2-norbornyl cation (2NB(+)) in the gas phase, protonation of norbornene was accomplished in a pulsed discharge ion source coupled with a supersonic molecular beam. The C7H11(+) cation was size-selected in a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy using the method of "tagging" with argon. The resulting vibrational spectrum, containing sharp bands in the C-H stretching and fingerprint regions, was compared to that predicted by computational chemistry. However, the measured spectrum did not match that of 2NB(+), prompting a detailed computational study of other possible isomers of C7H11(+). This study finds five isomers more stable than 2NB(+). The spectrum obtained corresponds to the 1,3-dimethylcyclopentenyl cation, the global minimum-energy structure for C7H11(+), which is produced through an unanticipated ring-opening rearrangement path.

  8. To the limit of gas-phase electron diffraction: Molecular structure of magnesium octa(m-trifluoromethylphenyl)porphyrazine

    NASA Astrophysics Data System (ADS)

    Zhabanov, Yuriy A.; Zakharov, Alexander V.; Giricheva, Nina I.; Shlykov, Sergey A.; Koifman, Oscar I.; Girichev, Georgiy V.

    2015-07-01

    The gas-phase molecular structure of the magnesium octa(m-trifluoromethylphenyl)porphyrazine (MgC72H32N8F24) has been studied by a synchronous gas-phase electron diffraction and mass spectrometric experiment at T = 667(10) K in combination with DFT calculations using B3LYP hybrid method and triple-ζ valence basis sets. The molecule has an equilibrium structure of D4 symmetry. The following values of selected internuclear distances have been determined: rh1, Å: r(Mg-N) = 1.979(5), r(N-C) = 1.363(3), r(Nmezo-C) = 1.334(4), r(Cpyr-CPh) = 1.469(3), r(CPh-CF3) = 1.510(5), r(C-F) = 1.349(3), r(Cα-Cβ) = 1.466(3), r(Cβ-Cβ) = 1.380(7). A slight (less than 1 to 2 degrees) twisting deformation of the macrocycle from planarity, caused by the presence of the eight bulky PhCF3 substituents, planes of which are turned by 132.6(9) degrees relative to the adjacent pyrrole rings, has been found. The deviation of phenyl ring planes from 90 degrees orientation is caused by stabilizing donor-acceptor interactions between π-natural orbitals of pyrrole and phenyl moieties. Substitution effects and coordination bonding in magnesium porphyrazine complexes, MgPz, MgPzPh8 and MgPz(CF3Ph)8, are discussed. Sensitivity of GED data to long range interatomic distances of large molecules has been shown.

  9. An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine

    SciTech Connect

    Bokatzian, Samantha S.; Stover, Michele L.; Plummer, Chelsea E.; Dixon, David A.; Cassady, Carolyn J.

    2014-11-06

    Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at the phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol.

  10. An experimental and computational investigation into the gas-phase acidities of tyrosine and phenylalanine: three structures for deprotonated tyrosine.

    PubMed

    Bokatzian, Samantha S; Stover, Michele L; Plummer, Chelsea E; Dixon, David A; Cassady, Carolyn J

    2014-11-06

    Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at the phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol.

  11. Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism--a gas-phase ab initio study.

    PubMed

    Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M

    2015-02-14

    The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter

  12. Application of structured illumination to gas phase thermometry using thermographic phosphor particles: a study for averaged imaging

    NASA Astrophysics Data System (ADS)

    Zentgraf, Florian; Stephan, Michael; Berrocal, Edouard; Albert, Barbara; Böhm, Benjamin; Dreizler, Andreas

    2017-07-01

    Structured laser illumination planar imaging (SLIPI) is combined with gas phase thermometry measurements using thermographic phosphor (TGP) particles. The technique is applied to a heated jet surrounded by a coflow which is operated at ambient temperature. The respective air flows are seeded with a powder of BaMgAl10O17:Eu2+ (BAM) which is used as temperature-sensitive gas phase tracer. Upon pulsed excitation in the ultraviolet spectral range, the temperature is extracted based on the two-color ratio method combined with SLIPI. The main advantage of applying the SLIPI approach to phosphor thermometry is the reduction of particle-to-particle multiple light scattering and diffuse wall reflections, yielding a more robust calibration procedure as well as improving the measurement accuracy, precision, and sensitivity. For demonstration, this paper focuses on sample-averaged measurements of temperature fields in a jet-in-coflow configuration. Using the conventional approach, which in contrast to SLIPI is based on imaging with an unmodulated laser light sheet, we show that for the present setup typically 40% of the recorded signal is affected by the contribution of multiply scattered photons. At locations close to walls even up to 75% of the apparent signal is due to diffuse reflection and wall luminescence of BAM sticking at the surface. Those contributions lead to erroneous temperature fields. Using SLIPI, an unbiased two-color ratio field is recovered allowing for two-dimensional mean temperature reconstructions which exhibit a more realistic physical behavior. This is in contrast to results deduced by the conventional approach. Furthermore, using the SLIPI approach it is shown that the temperature sensitivity is enhanced by a factor of up to 2 at 270 °C. Finally, an outlook towards instantaneous SLIPI phosphorescence thermometry is provided.

  13. Infrared Spectroscopy of Cationized Arginine in the Gas Phase: Direct Evidence for the Transition from Nonzwitterionic to Zwitterionic Structure

    PubMed Central

    Bush, Matthew F.; O'Brien, Jeremy T.; Prell, James S.; Saykally, Richard J.; Williams, Evan R.

    2009-01-01

    The gas-phase structures of protonated and alkali metal cationized arginine (Arg) and arginine methyl ester (ArgOMe) are investigated with infrared spectroscopy and ab initio calculations. Infrared spectra, measured in the hydrogen-stretch region, provide compelling evidence that arginine changes from its nonzwitterionic to zwitterionic form with increasing metal ion size, with the transition in structure occurring between lithium and sodium. For sodiated arginine, evidence for both forms is obtained from spectral deconvolution, although the zwitterionic form is predominant. Comparisons of the photodissociation spectra with spectra calculated for low-energy candidate structures provide additional insights into the detailed structures of these ions. Arg•Li+, ArgOMe•Li+, and ArgOMe•Na+ exist in nonzwitterionic forms in which the metal ion is tricoordinated with the amino acid, whereas Arg•Na+ and Arg•K+ predominately exist in a zwitterionic form where the protonated side chain donates one hydrogen bond to the N terminus of the amino acid and the metal ion is bicoordinated with the carboxylate group. Arg•H+ and ArgOMe•H+ have protonated side chains that form the same interaction with the N terminus as zwitterionic, alkali metal cationized arginine, yet both are unambiguously determined to be nonzwitterionic. Calculations indicate that for clusters with protonated side chains, structures with two strong hydrogen bonds are lowest in energy, in disagreement with these experimental results. This study provides new detailed structural assignments and interpretations of previously observed fragmentation patterns for these ions. PMID:17249666

  14. Tuning structural motifs and alloying of bulk immiscible Mo-Cu bimetallic nanoparticles by gas-phase synthesis

    NASA Astrophysics Data System (ADS)

    Krishnan, Gopi; Verheijen, Marcel A.; Ten Brink, Gert H.; Palasantzas, George; Kooi, Bart J.

    2013-05-01

    Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape.Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still

  15. PIV Measurement of Transient 3-D (Liquid and Gas Phases) Flow Structures Created by a Spreading Flame over 1-Propanol

    NASA Technical Reports Server (NTRS)

    Hassan, M. I.; Kuwana, K.; Saito, K.

    2001-01-01

    In the past, we measured three-D flow structure in the liquid and gas phases that were created by a spreading flame over liquid fuels. In that effort, we employed several different techniques including our original laser sheet particle tracking (LSPT) technique, which is capable of measuring transient 2-D flow structures. Recently we obtained a state-of-the-art integrated particle image velocimetry (IPIV), whose function is similar to LSPT, but it has an integrated data recording and processing system. To evaluate the accuracy of our IPIV system, we conducted a series of flame spread tests using the same experimental apparatus that we used in our previous flame spread studies and obtained a series of 2-D flow profiles corresponding to our previous LSPT measurements. We confirmed that both LSPT and IPIV techniques produced similar data, but IPIV data contains more detailed flow structures than LSPT data. Here we present some of newly obtained IPIV flow structure data, and discuss the role of gravity in the flame-induced flow structures. Note that the application of IPIV to our flame spread problems is not straightforward, and it required several preliminary tests for its accuracy including this IPIV comparison to LSPT.

  16. Molecular structure of phthalocyaninatotin(II) studied by gas-phase electron diffraction and high-level quantum chemical calculations.

    PubMed

    Strenalyuk, Tatyana; Samdal, Svein; Volden, Hans Vidar

    2008-10-09

    The molecular structure of phthalocyaninatotin(II), Sn(II)Pc, is determined by density functional theory (DFT/B3LYP) calculations using various basis sets and gas-phase electron diffraction (GED). The quantum chemical calculations show that Sn(II)Pc has C4V symmetry, and this symmetry is consistent with the structure obtained by GED at 427 degrees C. GED locates the Sn atom at h(Sn) ) 112.8(48) pm above the plane defined by the four isoindole N atoms, and a N-Sn bond length of 226.0(10) pm is obtained. Calculation at the B3LYP/ccpVTZ/cc-pVTZ-PP(Sn) level of theory gives h(Sn) ) 114.2 pm and a N-Sn bond length of 229.4 pm. The phthalocyanine (Pc) macrocycle has a slightly nonplanar structure. Generally, the GED results are in good agreement with the X-ray structures and with the computed structure; however, the comparability between these three methods has been questioned. The N-Sn bond lengths determined by GED and X-ray are significantly shorter than those from the B3LYP predictions. Similar trends have been found for C-Sn bonds for conjugated organometallic tin compounds. Computed vibrational frequencies give five low frequencies in the range of 18-54 cm-1, which indicates a flexible molecule.

  17. Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

    NASA Astrophysics Data System (ADS)

    Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

    2017-02-01

    Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

  18. The structure of the gas-phase tyrosine-glycine dipeptide

    NASA Astrophysics Data System (ADS)

    Toroz, Dimitrios; van Mourik, Tanja

    The structural preferences of the neutral dipeptide Tyr-Gly have been investigated using a hierarchical selection scheme. This scheme consists of a hierarchy of increasingly more accurate electronic structure methods (single-point HF/3-21G* energy calculation, HF/3-21G* geometry optimization, B3LYP/6-31+G* geometry optimization, MP2/6-31+G* single-point energy calculation, and MP2/6-31+G* geometry optimization). The conformers are sorted according to their single-point or optimized energy, and only the most stable conformers according to one level are taken through to the next level of calculation. The defining structural characteristics in the 20 most stable Tyr-Gly conformers are the presence or absence of a folded arrangement of the peptide backbone ('book') and an OH···O hydrogen bond between the C-terminal hydroxyl group and the carbonyl oxygen of tyrosine ('OHO'). The most stable conformer is of the book/OHO type. MP2 geometry optimization significantly alters the structure of the book-type conformers, increasing their degree of foldedness. Thus, care has to be taken when applying standard density functionals like B3LYP in structural studies of peptides with aromatic side chains.

  19. Probing the structures of gas-phase rhodium cluster cations by far-infrared spectroscopy

    SciTech Connect

    Harding, D. J.; Gruene, P.; Haertelt, M.; Meijer, G.; Fielicke, A.; Hamilton, S. M.; Hopkins, W. S.; Mackenzie, S. R.; Neville, S. P.; Walsh, T. R.

    2010-12-07

    The geometric structures of small cationic rhodium clusters Rh{sub n}{sup +} (n = 6-12) are investigated by comparison of experimental far-infrared multiple photon dissociation spectra with spectra calculated using density functional theory. The clusters are found to favor structures based on octahedral and tetrahedral motifs for most of the sizes considered, in contrast to previous theoretical predictions that rhodium clusters should favor cubic motifs. Our findings highlight the need for further development of theoretical and computational methods to treat these high-spin transition metal clusters.

  20. Gas-Phase Structures of Linalool and Coumarin Studied by Microwave Spectroscopy

    NASA Astrophysics Data System (ADS)

    Nguyen, H. V. L.; Stahl, W.; Grabow, J.-U.

    2013-06-01

    The microwave spectra of two natural substances, linalool and coumarin, were recorded in the microwave range from 9 to 16 GHz and 8.5 to 10.5 GHz, respectively.Linalool is an acyclic monoterpene and the main component of lavender oil. It has a structure with many possible conformations. The geometry of the lowest energy conformer has been determined by a combination of microwave spectroscopy and quantum chemical calculations. Surprisingly, a globular rather than a prolate shape was found. This structure is probably stabilized by a π interaction between two double bonds which are arranged in two stacked layers of atoms within the molecule. A-E splittings due to the internal rotation of one methyl group could be resolved and the barrier to internal rotation was determined to be 400.20(64) cm^{-1}. The standard deviation of the fit was close to experimental accuracy. For an identification of the observed conformer not only the rotational constants but also the internal rotation parameters of one of the methyl groups were needed. Coumarin is a widely used flavor in perfumery as sweet woodruff scent. The aromatic structure allows solely for one planar conformer, which was found under molecular beam conditions and compared to other molecules with similar structures. Here, the rotational spectrum could be described by a set of parameters including the rotational constants and the centrifugal distortion constants using a semi-rigid molecule Hamiltonian. Furthermore, the rotational transitions of all nine ^{13}C isotopologues were measured in natural abundance. As a consequence, the microwave structure of coumarin could be almost completely determined.

  1. The conformational structures and dipole moments of ethyl sulfide in the gas phase

    NASA Astrophysics Data System (ADS)

    Plusquellic, D. F.; Suenram, R. D.; Maté, B.; Jensen, J. O.; Samuels, A. C.

    2001-08-01

    The pure rotational spectrum of ethyl sulfide has been measured from 12 to 21 GHz in a 1 K jet-cooled expansion using a Fourier-transform microwave (FTMW) spectrometer. Prominent features in the spectrum are assigned to transitions from three conformational isomers. Additional assignments of the 13C and 34S isotopomer spectra of these conformers effectively account for all of the remaining transitions in the spectrum. Accurate "heavy-atom" substitution structures are obtained via a Kraitchman analysis of 14 rotational parameter sets, permitting definitive identification of the molecular structures of the three conformers. Two of the structures designated as the gauche-gauche (GG) and trans-trans (TT) conformers have symmetric forms with C2 and C2v symmetries, respectively, and the third trans-gauche (TG) configuration is asymmetric. The components of the electric dipole moment along the principal inertial axes have been determined from Stark measurements and are consistent with these structural assignments. Detailed comparisons are made with the calculated geometries, dipole moments, and energy-level ordering at both the HF (Hartree-Fock)/6-31* and MP2 (second-order Møller-Plesset)/6-311** levels of theory. Significant discrepancies are found, which are mainly attributed to errors in the calculated dihedral angles that define the different conformations. A graphical-user-interface computer program has aided in the identification and assignment of entangled hybrid-band spectra from the different conformers and isotopomers in this study. The program includes features that enable real-time refinement of rotational constants and hybrid band intensities through visual comparisons of the experimental data with simulated spectra. Capacities also exist to rapidly assign quantum number labels for least-squares fitting purposes.

  2. Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

    PubMed

    Somogyi, Arpád

    2008-12-01

    The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

  3. Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

    2017-01-01

    Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

  4. The molecular structure of tris(dipivaloylmethanato) thulium: Gas-phase electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Pimenov, Oleg A.; Belova, Natalya V.; Sliznev, Valery V.

    2017-03-01

    The molecular structure of tris-2,2,6,6-tetramethyl-heptane-3,5-dione thulium, or Tm(thd)3, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both the DFT(PBE0) calculations and the GED data collected at 400(8) K indicate that the molecules have D3 symmetry with a distorted antiprismatic TmO6 coordination geometry. According to GED refinements the twist angle θ, i.e. the angle of rotation of the upper O3 triangles relative to their position in regular prism is θ = 16.9(2.0)0. This value is close to both the equilibrium value obtained from the DFT calculations and to the thermal average value at the temperature of the GED experiment obtained by integration over the DFT potential energy surface. The bond distances (rh1) in the chelate ring are Tmsbnd O = 2.214(5) Å, Csbnd O = 1.278(4) Å, and Csbnd C = 1.404(3) Å. The DFT calculations yielded structure parameters in close agreement with those found experimentally. As an alternative to conventional Lewis model which was realized in NBO the topological analysis of ρ(r) in the frame of Bader's quantum theory of atoms in molecule (QTAIM) was performed.

  5. Investigation of the gas-phase structure and rotational barrier of trimethylsilyl trifluoromethanesulfonate and comparison with covalent sulfonates

    NASA Astrophysics Data System (ADS)

    Defonsi Lestard, María E.; Tuttolomondo, María E.; Varetti, Eduardo L.; Wann, Derek A.; Robertson, Heather E.; Rankin, David W. H.; Altabef, Aida Ben

    2010-12-01

    The molecular structure of trimethylsilyl trifluoromethanesulfonate, CF 3SO 2OSi(CH 3) 3, has been determined in the gas phase from electron-diffraction data supplemented by ab initio (MP2) and DFT calculations using 6-31G(d), 6-311++G(d,p) and 6-311G++(3df,3pd) basis sets. Both experimental and theoretical data indicate that only one gauche conformer is possible by rotating about the O-S bond. The anomeric effect is a fundamental stereoelectronic interaction and presents a profound influence on the electronic geometry. We have investigated the origin of the anomeric effect by means of NBO and AIM analysis. A natural bond orbital analysis showed that the lpπ[O bonded to Si)] → σ *[C-S] hyperconjugative interaction favors the gauche conformation. In addition, comparison of the structural and stereoelectronic properties of the title molecule with those of silyl trifluoromethanesulfonate and methyl trifluoromethanesulfonate has been carried out.

  6. Pronounced Size Dependence in Structure and Morphology of Gas-Phase Produced, Partially Oxidized Cobalt Nanoparticles under Catalytic Reaction Conditions

    SciTech Connect

    Bartling, Stephan; Yin, Chunrong; Barke, Ingo; Oldenburg, Kevin; Hartmann, Hannes; von Oeynhausen, Viola; Pohl, Marga-Martina; Houben, Kelly; Tyo, Eric C.; Seifert, Sönke; Lievens, Peter; Meiwes-Broer, Karl-Heinz; Vajda, Stefan

    2015-06-23

    It is generally accepted that optimal particle sizes are key for efficient nanocatalysis. Much less attention is paid to the role of morphology and atomic arrangement during catalytic reactions. Here we unravel the structural, stoichiometric, and morphological evolution of gas-phase produced cobalt nanoparticles in a broad size range. Particles with diameters between 1.4 nm and 22nm generated in cluster sources are size selected and deposited on amorphous alumina (Al2O3) and ultrananocrystalline diamond (UNCD) films. A combination of different techniques is employed to monitor particle properties at the stages of production, exposure to ambient conditions, and catalytic reaction, in this case the oxidative dehydrogenation of cyclohexane at elevated temperatures. A pronounced size dependence is found, naturally classifying the particles into three size regimes. While small and intermediate clusters essentially retain their compact morphology, large particles transform into hollow spheres due to the nanoscale Kirkendall effect. Depending on the substrate an isotropic (Al2O3) or anisotropic (UNCD) Kirkendall effect is observed. The latter results in dramatic lateral size changes. Our results shed light on the interplay between chemical reactions and the catalyst's structure and provide an approach to tailor the cobalt oxide phase composition required for specific catalytic schemes.

  7. Gas-phase synthesis and structure of monomeric ZnOH: a model species for metalloenzymes and catalytic surfaces.

    PubMed

    Zack, Lindsay N; Sun, Ming; Bucchino, Matthew P; Clouthier, Dennis J; Ziurys, Lucy M

    2012-02-16

    Monomeric ZnOH has been studied for the first time using millimeter and microwave gas-phase spectroscopy. ZnOH is important in surface processes and at the active site of the enzyme carbonic anhydrase. In the millimeter-wave direct-absorption experiments, ZnOH was synthesized by reacting zinc vapor, produced in a Broida-type oven, with water. In the Fourier-transform microwave measurements, ZnOH was produced in a supersonic jet expansion of CH(3)OH and zinc vapor, created by laser ablation. Multiple rotational transitions of six ZnOH isotopologues in their X(2)A' ground states were measured over the frequency range of 22-482 GHz, and splittings due to fine and hyperfine structure were resolved. An asymmetric top pattern was observed in the spectra, showing that ZnOH is bent, indicative of covalent bonding. From these data, spectroscopic constants and an accurate structure were determined. The Zn-O bond length was found to be similar to that in carbonic anhydrase and other model enzyme systems.

  8. Rotational spectra and gas phase structure of the maleimide - Formic acid doubly hydrogen bonded dimer

    NASA Astrophysics Data System (ADS)

    Pejlovas, Aaron M.; Kukolich, Stephen G.

    2016-03-01

    Rotational transitions were measured for the maleimide - formic acid doubly hydrogen bonded dimer using a Flygare-Balle type pulsed-beam Fourier transform microwave spectrometer. No splittings caused by possible concerted double proton tunneling motion were observed. Experimental rotational constants (MHz), quadrupole coupling constants (MHz), and centrifugal distortion constants (kHz) were determined for the parent and three deuterium substituted isotopologues. The values for the parent are A = 2415.0297(10), B = 784.37494(38), C = 592.44190(33), DJ = 0.0616(64), DJK = -0.118(35), DK = -1.38(15), 1.5χaa = 2.083(14), and 0.25(χbb-χcc) = 1.1565(29). The hydrogen bond lengths were determined using a nonlinear least squares structure fitting program. Rotational constants for this complex are consistent with a planar structure, with an inertial defect of Δ = -0.528 amu Å2. The B3LYP calculation yielded rotational constants within 0.1% of the experimental values.

  9. The trans influence of CF 3: gas phase structure of CF 3SF 5

    NASA Astrophysics Data System (ADS)

    Marsden, Colin J.; Christen, Dines; Oberhammer, Heinz

    1985-11-01

    The molecular structure of CF 3SF 5 has been determined by gas electron diffraction. The microwave spectrum was recorded in the frequency range 18-32 GHz. Superimposed on the essentially symmetric top transitions are found perturbations due to the large amplitude torsional motion of the CF 3 group. Therefore, a joint analysis of the electron diffraction intensities and rotational constant was not attempted. An approximate valence force field has been derived and used to calculate vibrational amplitudes. The structure is based on a slightly distorted octahedron with the following zkeletal parameters (r a values, 2σ in parentheses): SF a = 1.562(7) A, SF e = 1.572(2) A, SC = 1.887(8) A and CSF e = 90.5(2)°. The axial SF bond ( trans to CF 3) in shorter by 1.010(7) A than the equational bonds and the mean SF distances are longer by 0.008(2) A than the bonds in SF 0. The SF bond lengths are discussed together with analogous bond lengths in other XSF 5 derivatives on the basis of the VSEPR model and " trans influence" concept. The variation of the SCF 3 distance with the sulfur oxidation state is analyzed.

  10. Conformational Transformation of Five-Membered Rings: the Gas Phase Structure of 2-METHYLTETRAHYDROFURAN

    NASA Astrophysics Data System (ADS)

    Van, Vinh; Nguyen, Ha Vinh Lam; Stahl, Wolfgang

    2015-06-01

    2-Methyltetrahydrofuran (2-MeTHF) is a promising environmentally friendly solvent and biofuel component which is derived from renewable resources. Following the principles of Green Chemistry, 2-MeTHF has been evaluated in various fields like organometallics, metathesis, and biosynthesis on the way to more eco-friendly syntheses. Cyclopentane as the prototype of five-membered rings is well-known to exist as twist or envelope structures. However, the conformational analysis of its heterocyclic derivative 2-methyl-tetrahydrothiophene (MTTP) yielded two stable twist conformers and two envelope transition states. Here, we report on the heavy atom r_s structure of the oxygen-analog of MTTP, 2-MeTHF, studied by a combination of molecular beam Fourier transform microwave spectroscopy and quantum chemistry. One conformer of 2-MeTHF was observed and highly accurate molecular parameters were determined using the XIAM program. In addition, all 13C-isotopologues were assigned in natural abundance of 1%. A structural determination based on the r_s positions of all carbon atoms was achieved via Kraitchman's equations. The methyl group in 2-MeTHF undergoes internal rotation and causes A-E splittings of the rotational lines. The barrier was calculated to be 1142 wn at the MP2/6-311++G(d,p) level of theory, which is rather high. Accordingly, narrow A-E splittings could be observed for only a few transitions. However, the barrier height could be fitted while the angles between the internal rotor axis and the principal axes of inertia were taken from the experimental geometry. V. Pace, P. Hoyos, L. Castoldi, P. Domínguez de María, A. R. Alcántara, ChemSusChem 5 (2012), 1369-1379. a) D. F. Aycock, Org. Process Res. Dev. 11 (2007),156-159. b) M. Smoleń, M. Kȩdziorek, K. Grela, Catal. Commun. 44 (2014), 80-84. V. Van, C. Dindic, H.V.L. Nguyen, W. Stahl, ChemPhysChem 16 (2015), 291-294. H. Hartwig, H. Dreizler, Z. Naturforsch. A 51 (1996), 923-932. J. Kraitchman, Am. J. Phys. 21

  11. The molecular structure and conformational composition of epichlorohydrin as determined by gas phase electron diffraction

    NASA Astrophysics Data System (ADS)

    Shen, Quang

    1985-09-01

    The molecular structure of gaseous epichlorohydrin has been investigated using electron diffraction data obtained at 67°C. The conformational composition at this temperature is such that the molecules exist predominantly in a gauche-2 conformer (where the CCl bond is 160° away from the CO) bond). Refinements showed that 33% (σ = 4) of the molecule exist in the gauche-1 form. The important distances ( rg) and angle (∠α) with the associated uncertainties are r(CH) = 1.095(5) Å, r(CO) = 1.442(3) Å, r(CC) = 1.475(8) Å, r(CC M) = 1.523(7) Å, r(CCl) = 1.788(2) Å, ∠CCO = 114° (1), ∠CCC M = 119°(1), ∠ClCC = 108.9° (7), and Tau(ClCCO) = -150°(10) ( gauche-2) and Tau(ClCCO) = 78° (10) ( gauche-1).

  12. Gas phase chemistry in comets

    NASA Technical Reports Server (NTRS)

    Oppenheimer, M.

    1976-01-01

    The significance of gas phase reactions in determining the nuclear structure of comets is discussed. The sublimation of parent molecules such as H2O, CH4, CO2, and NH3 from the surface of the nucleus and their subsequent photodissociation and ionization in forming observed cometary molecular species are elaborated.

  13. Photodecarbonylation mechanism of cyclopropenone in the gas phase: electronic structure calculation and AIMS dynamics simulation.

    PubMed

    Liu, Lihong; Xia, Shuhua; Fang, Wei-Hai

    2014-10-02

    In this article, structures and energies of cyclopropenone in the low-lying electronic states have been determined by the CASSCF and MS-CASPT2 calculations with different basis sets. Two minimum-energy conical intersections (CI-1 and CI-2) between S0 and S1 were obtained and their topographic characters were characterized by the SA4-CAS(10,9) calculated energy gradients and nonadiabatic coupling vectors. The AIMS method was used to carry out nonadiabatic dynamics simulation with ab initio calculation performed at the SA4-CAS(10,9) level. On the basis of time evolution of wave functions simulated here, the S1 lifetime is fitted to be 125 fs with a pure exponential decay for the S1 electronic population. The CI-1 intersection is mainly responsible for ultrafast S1→S0 nonadiabatic transition and the photoinduced decarbonylation is a sequential process, where the first C-C bond is broken in the S1 state and fission of the second C-C bond occurs in the S0 state as a result of the S1→S0 internal conversion via the CI-1 region. As a minor channel through the CI-2 region, the decarbonylation proceeds in an asynchronous concerted way. Effects of the S1 excess energies and the S1-S0 energy gap on the nonadiabatic dynamics were examined, which reveals that the S1→S0 nonadiabatic transition occurs within a small energy gap and high-energy conical intersection regions can play an important role. The present study provides new insights into mechanistic photochemistry of cyclopropenones and reveals that the AIMS dynamics simulation at a high-accuracy ab initio level is a powerful tool for exploring a mechanism of an ultrafast photochemical reaction.

  14. Structure and conformational behavior of N-phenylpiperidine studied by gas-phase electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Shlykov, Sergey A.; Phien, Tran D.; Gao, Yan; Weber, Peter M.

    2017-03-01

    Molecular structure and conformational behavior of N-phenylpiperidine (NPhP) were investigated by synchronous gas-phase electron diffraction/mass spectrometry (GED/MS) and quantum chemistry. Due to influence of steric repulsion and hyperconjugation, NPhP may exist in two conformers, equatorial and axial chair forms. Both experiment and theoretical calculations suggest a C1 symmetry of the conformers, with the plane perpendicular to the phenyl group turned by ca. 30-40° (equatorial) and 0-20° (axial) about the plane perpendicular to the piperidine ring symmetry plane. According to the QC calculations, NPhP may exist as two conformers, equatorial and axial, with a ratio of Eq:Ax = 92:8 (B3LYP), 87:13 (B3LYP-GD3), 84:16 (M06-2X), 83:17 (MP2/6-311G**) and 76:24% (MP2/cc-pVTZ). Except for the latter, these values are in good agreement with the experimental GED data of 90(10):10(10)%. A comparative analysis of similar compounds, phenylcyclohexane and 1-phenylheterocyclohexanes, was performed. Conformational properties depend on the CPhsbnd X bond distance and hyperconjugation between the phenyl ring and the lone pair on the heteroatom. The contribution of the axial form of 1-phenylcyclohexane derivatives increases in the series of the heteroatom X in the cyclohexane ring: C → N → Si → P.

  15. The molecular structure and conformation of trans-1,2,3-trichloropropene as determined by gas-phase electron diffraction

    NASA Astrophysics Data System (ADS)

    Shen, Quang

    1989-09-01

    The gas-phase molecular structure of trans-1,2,3-trichloropropene has been studied by electron diffraction at a nozzle-tip temperature of 110°C. The data are consistent with the presence of only a conformation with a torsional angle of 110° (8), where 0° corresponds to the eclipsing of the CCl and CC bonds. The principal geometrical parameter values ( rg and ∠ α) obtained from least squares refinement are: r(CH) = 1.06(3) Å, r(CC) = 1.365(12) Å, r(CC) = 1.467(15) Å, r(C 1Cl) = 1.733(25) Å, r(C 2Cl) = 1.727(25) Å, r(C 3Cl) = 1.800(9) Å, ∠ CCC = 124(2)°, ∠ ClC 1C 2 = 124(2)°, ∠ ClC 2C 1 = 115.2(14)°, ∠ClC 3C 2 = 110.9(13)°, and τ (ClC 3C 2C 1) = 110(8)°.

  16. Gas Phase Nanoparticle Synthesis

    NASA Astrophysics Data System (ADS)

    Granqvist, Claes; Kish, Laszlo; Marlow, William

    This book deals with gas-phase nanoparticle synthesis and is intended for researchers and research students in nanomaterials science and engineering, condensed matter physics and chemistry, and aerosol science. Gas-phase nanoparticle synthesis is instrumental to nanotechnology - a field in current focus that raises hopes for environmentally benign, resource-lean manufacturing. Nanoparticles can be produced by many physical, chemical, and even biological routes. Gas-phase synthesis is particularly interesting since one can achieve accurate manufacturing control and hence industrial viability.

  17. Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies.

    PubMed

    Rodgers, Mary T; Armentrout, Peter B

    2016-01-01

    Quantitative insight into the structures and thermodynamics of alkali metal cations interacting with biological molecules can be obtained from studies in the gas phase combined with theoretical work. In this chapter, the fundamentals of the experimental and theoretical techniques are first summarized and results for such work on complexes of alkali metal cations with amino acids, small peptides, and nucleobases are reviewed. Periodic trends in how these interactions vary as the alkali metal cations get heavier are highlighted.

  18. Effects of London dispersion correction in density functional theory on the structures of organic molecules in the gas phase.

    PubMed

    Grimme, Stefan; Steinmetz, Marc

    2013-10-14

    A benchmark set of 25 rotational constants measured in the gas phase for nine molecules (termed ROT25) was compiled from available experimental data. The medium-sized molecules with 18-35 atoms cover common (bio)organic structure motifs including hydrogen bonding and flexible side chains. They were each considered in a single conformation. The experimental B0 values were back-corrected to reference equilibrium rotational constants (Be) by computation of the vibrational corrections ΔBvib. Various density functional theory (DFT) methods and Hartree-Fock with and without dispersion corrections as well as MP2 type methods and semi-empirical quantum chemical approaches are investigated. The ROT25 benchmark tests their ability to describe covalent bond lengths, longer inter-atomic distances, and the relative orientation of functional groups (intramolecular non-covalent interactions). In general, dispersion corrections to DFT and HF increase Be values (shrink molecular size) significantly by about 0.5-1.5% thereby in general improving agreement with the reference data. Regarding DFT methods, the overall accuracy of the optimized structures roughly follows the 'Jacobs ladder' classification scheme, i.e., it decreases in the series double-hybrid > (meta)hybrid > (meta)GGA > LDA. With B2PLYP-D3, SCS-MP2, B3LYP-D3/NL, or PW6B95-D3 methods and extended QZVP (def2-TZVP) AO basis sets, Be values, accurate to about 0.3-0.6 (0.5-1)% on average, can be computed routinely. The accuracy of B2PLYP-D3/QZVP with a mean deviation of only 3 MHz and a standard deviation of 0.24% is exceptional and we recommend this method when highly accurate structures are required or for problematic conformer assignments. The correlation effects for three inter-atomic distance regimes (covalent, medium-range, long) and the performance of minimal basis set (semi-empirical) methods are discussed.

  19. Structures of protonated thymine and uracil and their monohydrated gas-phase ions from ultraviolet action spectroscopy and theory.

    PubMed

    Pedersen, Sara Øvad; Byskov, Camilla Skinnerup; Turecek, Frantisek; Brøndsted Nielsen, Steen

    2014-06-19

    The strong UV chromophores thymine (Thy) and uracil (Ura) have identical heteroaromatic rings that only differ by one methyl substituent. While their photophysics has been elucidated in detail, the effect on the excited states of base protonation and single water molecules is less explored. Here we report gas-phase absorption spectra of ThyH(+) and UraH(+) and monohydrated ions and demonstrate that the substituent is not only responsible for spectral shifts but also influences the tautomer distribution, being different for bare and monohydrated ions. Spectra interpretation is aided by calculations of geometrical structures and transition energies. The lowest free-energy tautomer (denoted 178, enol-enol form) accounts for 230-280 nm (ThyH(+)) and 225-270 nm (UraH(+)) bands. ThyH(+) hardly absorbs above 300 nm, whereas a discernible band is measured for UraH(+) (275-320 nm), ascribed to the second lowest free-energy tautomer (138, enol-keto form) comprising a few percent of the UraH(+) population at room temperature. Band widths are similar to those measured of cold ions in support of very short excited-state lifetimes. Attachment of a single water increases the abundance of 138 relative to 178, 138 now clearly present for ThyH(+). 138 resembles more the tautomer present in aqueous solution than 178 does, and 138 may indeed be a relevant transition structure. The band of ThyH(+)(178) is unchanged, that of UraH(+)(178) is nearly unchanged, and that of UraH(+)(138) blue-shifts by about 10 nm. In stark contrast to protonated adenine, more than one solvating water molecule is required to re-establish the absorption of ThyH(+) and UraH(+) in aqueous solution.

  20. Vibrational structure of n-π* transition of the UV absorption spectrum of acryloyl fluoride in the gas phase.

    PubMed

    Koroleva, Lidiya A; Tyulin, Vladimir I; Matveev, Vladimir K; Pentin, Yuriy A

    2014-03-25

    UV absorption spectrum of acryloyl fluoride molecule in the gas phase has been obtained in the region at 32600-35500 cm(-1) with the purpose of the investigation of the hindered internal rotation. The resolved vibrational structure of this spectrum consists of 92 absorption bands, each of which corresponds to a certain transition from the ground (S0) to excited (S1) electronic state. The assignment of all bands has been made. The values ν00trans=34831.8 cm(-1) and ν00cis=34679.2 cm(-1) have been determined. Several Deslandres Tables (DTs) have been constructed for torsional vibration of s-trans- and s-cis-isomers of investigated molecule. The origins in these DTs correspond to bands assigned to ν00 and to fundamental frequencies of each isomer in the S0 and S1 states. These DTs have been used to determine the harmonic frequencies ωe, anharmonicity coefficients x11, and frequencies of the torsional vibration transitions (0-υ) up to high values of the vibrational quantum number υ of s-trans- and s-cis-isomers in the both electronic states. The frequencies of torsional vibrations are ν1(″)=116.5cm(-1) for s-trans-isomer and ν1(″)=101.2 cm(-1) for s-cis-isomer in the S0 state. The frequencies of ones are ν1(')=170.4 cm(-1) for s-trans-isomer and ν1(')=139.7 cm(-1) for s-cis-isomer in the S1 state. The fundamental vibrational frequencies set has been found for isomers in the S0 and S1 states.

  1. Structural effect of the in situ generated titania on its ability to oxidize and capture the gas-phase elemental mercury.

    PubMed

    Lee, Tai Gyu; Hyun, Jung Eun

    2006-01-01

    Structural effect of the in situ generated TiO(2) sorbent particle was examined for its ability to capture elemental mercury under UV irradiation in a simulated combustion flue gas. Titania particles were prepared by thermal gas-phase oxidation of Titanium (IV) isopropoxide (TTIP) using a high temperature electric furnace reactor. The structural characteristics of the in situ generated TiO(2) at various synthesis temperatures were investigated; size distribution and the geometric mean diameter were measured using a scanning mobility particle sizer, while fractal dimension and radius of gyration were evaluated from the transmission electron microscopy images. Results from the Hg(0) capture experiment show that with increasing titania synthesis temperature, the overall aggregate size increases and the morphology becomes more open-structured to gas-phase Hg(0) and UV light, resulting in the improved mercury removal capability.

  2. Effects of Select Anions from the Hofmeister Series on the Gas-Phase Conformations of Protein Ions Measured with Traveling-Wave Ion Mobility Spectrometry/Mass Spectrometry

    PubMed Central

    Merenbloom, Samuel I.; Flick, Tawnya G.; Daly, Michael P.; Williams, Evan R.

    2011-01-01

    The gas-phase conformations of ubiquitin, cytochrome c, lysozyme, and ↦-lactalbumin ions, formed by electrospray ionization (ESI) from aqueous solutions containing 5 mM ammonium perchlorate, ammonium iodide, ammonium sulfate, ammonium chloride, ammonium thiocyanate, or guanidinium chloride, are examined using traveling-wave ion mobility spectrometry (TWIMS) coupled to time-of-flight (TOF) mass spectrometry (MS). For ubiquitin, cytochrome c, and ↦-lactalbumin, adduction of multiple acid molecules results in no significant conformational changes to the highest and lowest charge states formed from aqueous solutions, whereas the intermediate charge states become more compact. The transition to more compact conformers for the intermediate charge states occurs with fewer bound H2SO4 molecules than HClO4 or HI molecules, suggesting ion-ion or salt-bridge interactions are stabilizing more compact forms of the gaseous protein. However, the drift time distributions for protein ions of the same net charge with the highest levels of adduction of each acid are comparable, indicating that these protein ions all adopt similarly compact conformations or families of conformers. No change in conformation is observed upon the adduction of multiple acid molecules to charge states of lysozyme. These results show that the attachment of HClO4, HI, or H2SO4 to multiply protonated proteins can induce compact conformations in the resulting gas-phase protein ions. In contrast, differing Hofmeister effects are observed for the corresponding anions in solution at higher concentrations. PMID:21952780

  3. The structure and conformations of piracetam (2-oxo-1-pyrrolidineacetamide): Gas-phase electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Ksenafontov, Denis N.; Moiseeva, Natalia F.; Khristenko, Lyudmila V.; Karasev, Nikolai M.; Shishkov, Igor F.; Vilkov, Lev V.

    2010-12-01

    The geometric structure of piracetam was studied by quantum chemical calculations (DFT and ab initio), gas electron diffraction (GED), and FTIR spectroscopy. Two stable mirror symmetric isomers of piracetam were found. The conformation of pyrrolidine ring is an envelope in which the C4 atom deviates from the ring plane, the angle between the planes (C3 sbnd C4 sbnd C5) and (C2 sbnd C3 sbnd C5) is 154.1°. The direction of the deviation is the same as that of the side acetamide group. The piracetam molecule is stabilized in the gas phase by an intramolecular hydrogen bond between the N9H 2 group and the oxygen O6, bonded to C2. The principal structural parameters ( re, Å and ∠e, degrees; uncertainties are 3 σLS values) were found to be: r(С3 sbnd С4) = 1.533(1), r(C4 sbnd C5) = 1.540(1), r(N1 sbnd C5) = 1.456(1), r(C2 sbnd C3) = 1.520(1), r(N1 sbnd C7) = 1.452(1), r(C7 sbnd C8) = 1.537(1), r(N1 sbnd C2) = 1.365(2), r(C8 sbnd N9) = 1.360(2), r(C2 dbnd O6) = 1.229(1), r(C8 dbnd O10) = 1.221(1), ∠C2 sbnd N1 sbnd C5 = 113.4(6), ∠N1 sbnd C2 sbnd C3 = 106.9(6), ∠N1 sbnd C7 sbnd C8 = 111.9(6), ∠C7 sbnd C8 sbnd N9 = 112.5(6), ∠N1 sbnd C2 sbnd O6 = 123.0(4), ∠C3 sbnd N1 sbnd C7 = 120.4(4), ∠C7 sbnd C8 sbnd O10 = 120.2(4), ∠C5 sbnd N1 sbnd C2 sbnd O6 = 170(6), ∠C3 sbnd C2 sbnd N1 sbnd C7 = 178(6), ∠C2 sbnd N1 sbnd C7 sbnd C8 = 84.2, ∠N1 sbnd C7 sbnd C8 sbnd O10 = 111.9.

  4. Accurate gas-phase structure of para-dioxane by fs Raman rotational coherence spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Den, Takuya; Menzi, Samuel; Frey, Hans-Martin; Leutwyler, Samuel

    2017-08-01

    p-Dioxane is non-polar, hence its rotational constants cannot be determined by microwave rotational coherence spectroscopy (RCS). We perform high-resolution gas-phase rotational spectroscopy of para-dioxane-h8 and -d8 using femtosecond time-resolved Raman RCS in a gas cell at T = 293 K and in a pulsed supersonic jet at T ˜130 K. The inertial tensor of p-dioxane-h8 is strongly asymmetric, leading to a large number of asymmetry transients in its RCS spectrum. In contrast, the d8-isotopomer is a near-oblate symmetric top that exhibits a much more regular RCS spectrum with few asymmetry transients. Fitting the fs Raman RCS transients of p-dioxane-h8 to an asymmetric-top model yields the ground-state rotational constants A0 = 5084.4(5) MHz, B0 = 4684(1) MHz, C0 = 2744.7(8) MHz, and (A0 + B0)/2 = 4884.5(7) MHz (±1 σ ). The analogous values for p-dioxane-d8 are A0 = 4083(2) MHz, B0 = 3925(4) MHz, C0 = 2347.1(6) MHz, and (A0 + B0)/2 = 4002.4(6) MHz. We determine the molecular structure with a semi-experimental approach involving the highly correlated coupled-cluster singles, doubles and iterated triples method and the cc-pCVXZ basis set series from double- to quadruple-zeta (X = D, T, Q). Combining the calculated vibrationally averaged rotational constants A0c a l c(X ) ,B0c a l c(X ) ,C0c a l c(X ) for increasing basis-set size X with non-linear extrapolation to the experimental constants A0e x p,B0e x p,C0e x p allows to determine the equilibrium ground state structure of p-dioxane. For instance, the equilibrium C-C and C-O bond lengths are re(CC) = 1.5135(3) Å and re(CO) = 1.4168(4) Å, and the four axial C-H bond lengths are 0.008 Å longer than the four equatorial ones. The latter is ascribed to the trans-effect (anomeric effect), i.e., the partial delocalization of the electron lone-pairs on the O atoms that are oriented trans, relative to the axial CH bonds.

  5. Molecular Structure of 9H-Adenine Tautomer: Gas-Phase Electron Diffraction and Quantum-Chemical Studies

    NASA Astrophysics Data System (ADS)

    Vogt, Natalja; Dorofeeva, Olga V.; Sipachev, Victor A.; Rykov, Anatolii N.

    2009-10-01

    Molecular geometry of 9H-adenine tautomer was calculated by MP2 method using several basis sets (up to cc-pVQZ). According to the results of all quantum-chemical calculations, the molecule has an essentially planar heavy-atom skeleton and a quasi-planar amino group. Since the bond lengths of adenine are of similar magnitude, the structural problem could not be solved by the gas-phase electron diffraction (GED) method alone. Therefore the differences between similar bond lengths derived from ab initio geometry and rotational constants from microwave (MW) spectroscopic study (Brown, R. D.; et al. Chem. Phys. Lett. 1989, 156, 61) were used as supplementary data. To bring the data of the different experimental methods to the same basis (equilibrium structure), GED internuclear distances ra and MW rotational constants B0(i) (i = A, B, C) were corrected for vibrational effects. Harmonic and anharmonic corrections were estimated using quadratic and cubic force constants from MP2/cc-pVTZ calculations. Anharmonic corrections to ra distances were calculated using improved theoretical approximation. The molecular structure of 9H-adenine is determined experimentally for the first time. Since the GED intensities are not sensitive to hydrogen positions, and small deviations of skeleton cannot be determined with appropriate uncertainty, the molecular configuration of adenine was asumed to be planar (Cs symmetry) in the GED analysis. The main equilibrium structural parameters determined from GED data supplemented by rotational constants and results of MP2/cc-pVTZ calculations are the following (bond lengths in angstroms and bond angles in degrees with 3σ in parentheses): re(C2-N1) = 1.344(3), re(C2-N3) = 1.330(3), re(C4-N3) = 1.333(3), re(C4-C5) = 1.401(3), re(C5-C6) = 1.409(3), re(C6-N1) = 1.332(3), re(C5-N7) = 1.380(4), re(C8-N7) = 1.319(3), re(C8-N9) = 1.371(4), re(C4-N9) = 1.377(4), re(C6-N10) = 1.357(4), ∠e(N1-C2-N3) = 129.0(1), ∠e(C2-N3-C4) = 111.0(1), ∠e(N3-C4-C5

  6. Molecular structure of 9H-adenine tautomer: gas-phase electron diffraction and quantum-chemical studies.

    PubMed

    Vogt, Natalja; Dorofeeva, Olga V; Sipachev, Victor A; Rykov, Anatolii N

    2009-12-10

    Molecular geometry of 9H-adenine tautomer was calculated by MP2 method using several basis sets (up to cc-pVQZ). According to the results of all quantum-chemical calculations, the molecule has an essentially planar heavy-atom skeleton and a quasi-planar amino group. Since the bond lengths of adenine are of similar magnitude, the structural problem could not be solved by the gas-phase electron diffraction (GED) method alone. Therefore the differences between similar bond lengths derived from ab initio geometry and rotational constants from microwave (MW) spectroscopic study (Brown, R. D.; et al. Chem. Phys. Lett. 1989, 156, 61) were used as supplementary data. To bring the data of the different experimental methods to the same basis (equilibrium structure), GED internuclear distances r(a) and MW rotational constants B(0)((i)) (i = A, B, C) were corrected for vibrational effects. Harmonic and anharmonic corrections were estimated using quadratic and cubic force constants from MP2/cc-pVTZ calculations. Anharmonic corrections to r(a) distances were calculated using improved theoretical approximation. The molecular structure of 9H-adenine is determined experimentally for the first time. Since the GED intensities are not sensitive to hydrogen positions, and small deviations of skeleton cannot be determined with appropriate uncertainty, the molecular configuration of adenine was assumed to be planar (C(s) symmetry) in the GED analysis. The main equilibrium structural parameters determined from GED data supplemented by rotational constants and results of MP2/cc-pVTZ calculations are the following (bond lengths in angstroms and bond angles in degrees with 3sigma in parentheses): r(e)(C2-N1) = 1.344(3), r(e)(C2-N3) = 1.330(3), r(e)(C4-N3) = 1.333(3), r(e)(C4-C5) = 1.401(3), r(e)(C5-C6) = 1.409(3), r(e)(C6-N1) = 1.332(3), r(e)(C5-N7) = 1.380(4), r(e)(C8-N7) = 1.319(3), r(e)(C8-N9) = 1.371(4), r(e)(C4-N9) = 1.377(4), r(e)(C6-N10) = 1.357(4), angle(e)(N1-C2-N3) = 129

  7. The molecular structure of 1,1-dichlorosilacyclopentane as obtained from gas-phase electron diffraction and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Dakkouri, Marwan; Typke, Volker

    2010-08-01

    The molecular structure of 1,1-dichlorosilacyclopentane (DCSCP) has been investigated by means of gas-phase electron diffraction and quantum mechanical calculation. We applied both a pseudorotation model to account for the dynamic and large amplitude motion in DCSCP, and a one-conformer model of C1 symmetry. Using the computational results we analyzed the dependency of the ring geometrical parameters and vibrational mean amplitudes on the phase angle φ. The joint electron diffraction and ab initio study has led to the following ra structural parameters of DCSCP ( C1 conformer): r(Si-Cl) = 2.047(2) Å, r(Si-C) = 1.867(4) Å, average r(C-C) ring = 1.548(4) Å, average r(C-H) = 1.103(7) Å, <(C-Si-C) = 97.4(6)°, <(Cl-Si-Cl) = 104.8(10)°, and effective phase angle φ = 74.8(58)°. The puckering amplitude for the five-membered ring was determined to be q = 0.480(24) Å. The quantum mechanical calculations were performed by utilizing the UHF, B3LYP, and MP2 methods in combination with basis sets 6-311++G(2df,2pd), 6-311++G(df,pd), 6-311++G(p,d), 6-311+G(d,p), 6-311G(d,p) and Dunning double and triple zeta (with and without augmentation). All these methods have consistently shown that the C2 conformer is more stable than the C s symmetric form. For all calculations we used the MOLPRO and Gaussian03 packages. NBO and AIM analyses were also carried out to explore the bond/anti-bond hyperconjugative interactions and the topological properties of the charge density distribution in DCSCP. NBO scheme including second-order perturbation analysis has shown that the major orbital stabilizing interactions are between the chlorine lone pair ( nπ) Cl and the low-lying σSi-C2∗ and σSi-C5∗ antibonding orbitals. It was found that remote σSi-C → σC-H∗ interactions are stabilized by 4.4 kcal mol -1 and contribute to the stabilization of the C2 conformer in DCSCP. Deletion analysis was performed using various deletion algorithms like NOSTAR, NOVIC, NOGEM (see text). The

  8. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization.

    PubMed

    Pepin, Robert; Laszlo, Kenneth J; Marek, Aleš; Peng, Bo; Bush, Matthew F; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-10-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions. Graphical Abstract ᅟ.

  9. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

    NASA Astrophysics Data System (ADS)

    Pepin, Robert; Laszlo, Kenneth J.; Marek, Aleš; Peng, Bo; Bush, Matthew F.; Lavanant, Helène; Afonso, Carlos; Tureček, František

    2016-10-01

    Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions.

  10. The gas-phase molecular structure of 1-thia-spiro [2.5] octane: A microwave and molecular mechanics study

    NASA Astrophysics Data System (ADS)

    Boulebnane, Hassane; Roussy, Georges; Villamañan, Rosa M.; Alami, Waffi; Iratcabal, Pierre

    1988-11-01

    This paper describes the results on the gas-phase molecular structure of 1-thia-spiro [2.5] octane probed by a combination of microwave experiments and molecular mechanics calculations. Of the two theoretically predicted conformational isomers only one has been detected experimentally showing a pseudoequatorial orientation for the sulfur atom. A set of geometrical parameters which gives a good fit to the rotational constants has been derived. In agreement with molecular mechanics predictions, we conclude that the cyclohexane ring has a slightly flattened chair conformation.

  11. Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Rankin, David W H

    2007-07-05

    A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).

  12. Insight into the gas-phase structure of a copper(II) L-histidine complex, the agent used to treat Menkes disease.

    PubMed

    Ziegler, Blake E; Marta, Richard A; Burt, Michael B; McMahon, Terry B

    2014-03-03

    Copper(II) L-histidine is used in the treatment of a rare neurological disease called Menkes disease. An infrared multiple photon dissociation (IRMPD) vibrational spectrum of the gas-phase copper(II) L-histidine complex has been obtained. This spectrum was compared to lowest-energy computational spectra obtained at the B3LYP/6-311+G** level of theory. Two species, CuHis1 and CuHis2, are very close in Gibbs free energy, and both have computed vibrational spectra in good agreement with the experimentally observed IRMPD spectrum. The first structure exhibits four histidine-copper interactions in the same plane and a fifth out-of-plane interaction. The second structure exhibits four histidine-copper interactions in the same plane. The fact that the experimental and computational spectra are found to be in good agreement adds considerable insight into the gas-phase structure of the copper(II) L-histidine complex.

  13. Structure and chemistry of the heteronuclear oxo-cluster [VPO4]•+: a model system for the gas-phase oxidation of small hydrocarbons.

    PubMed

    Dietl, Nicolas; Wende, Torsten; Chen, Kai; Jiang, Ling; Schlangen, Maria; Zhang, Xinhao; Asmis, Knut R; Schwarz, Helmut

    2013-03-06

    The heteronuclear oxo-cluster [VPO4](•+) is generated via electrospray ionization and investigated with respect to both its electronic structure as well as its gas-phase reactivity toward small hydrocarbons, thus permitting a comparison to the well-known vanadium-oxide cation [V2O4](•+). As described in previous studies, the latter oxide exhibits no or just minor reactivity toward small hydrocarbons, such as CH4, C2H6, C3H8, n-C4H10, and C2H4, while substitution of one vanadium by a phosphorus atom yields the reactive [VPO4](•+) ion; the latter brings about oxidative dehydrogenation (ODH) of saturated hydrocarbons, e.g., propane and butane as well as oxygen-atom transfer (OAT) to unsaturated hydrocarbons, e.g. ethene, at thermal conditions. Further, the gas-phase structure of [VPO4](•+) is determined by IR photodissociation spectroscopy and compared to that of [V2O4](•+). DFT calculations help to elucidate the reaction mechanism. The results underline the crucial role of phosphorus in terms of C-H bond activation of hydrocarbons by mixed VPO clusters.

  14. Gas-phase peptide structures unraveled by far-IR spectroscopy: combining IR-UV ion-dip experiments with Born-Oppenheimer molecular dynamics simulations.

    PubMed

    Jaeqx, Sander; Oomens, Jos; Cimas, Alvaro; Gaigeot, Marie-Pierre; Rijs, Anouk M

    2014-04-01

    Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. Although the far-IR region (<500 cm(-1)) may contain a wealth of structural information, as recognized in condensed phase studies, DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two γ-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide A features. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  16. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  17. Cryogenic neon matrix-isolation FTIR spectroscopy of evaporated ionic liquids: geometrical structure of cation-anion 1:1 pair in the gas phase.

    PubMed

    Akai, Nobuyuki; Parazs, David; Kawai, Akio; Shibuya, Kazuhiko

    2009-04-09

    Low-temperature infrared spectra of thermally evaporated ionic liquids, 1-ethyl- and 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide and bis(trifluoromethanesulfonyl)amide have been measured in a cryogenic Ne matrix. The experimental IR spectrum of bis(trifluoromethanesulfonyl)amide can be reproduced theoretically by not B3LYP/6-31G* but MP2/6-31G* calculation, which suggests that the vibrational analysis for ionic liquids composed of bis(trifluoromethanesulfonyl)imide anion would be more successfully performed using the MP2 calculation. By comparison of the matrix-isolation spectra of the ionic liquids with the MP2 calculation, their geometrical structures in the gas phase are determined to be of C(2-position)-H(+)...N(-) interaction structure, which corresponds to the geometry of the energetically second-lowest ion-pair structure. The present study may provide a valuable clue to understand a vaporization mechanism of ionic liquid.

  18. Gas-phase structures of Pb(2+)-cationized phenylalanine and glutamic acid determined by infrared multiple photon dissociation spectroscopy and computational chemistry.

    PubMed

    Burt, Michael B; Fridgen, Travis D

    2013-02-14

    Infrared multiple photon dissociation (IRMPD) spectroscopy in the 3200-3800 cm(-1) region was used to determine the gas-phase structures of bare and monohydrated [Pb(Phe-H)](+) and [Pb(Glu-H)](+). These experiments were supported by infrared spectra calculated at the B3LYP/6-31+G(d,p) level of theory as well as 298 K enthalpies and Gibbs energies determined using the MP2(full)/6-311++G(2d,2p)//B3LYP/6-31+G(d,p) method. The gas-phase structure of [Pb(Phe-H)](+) has Pb(2+) bound in a tridentate fashion between Phe's amine nitrogen, one oxygen of the deprotonated carboxyl group, and the aromatic ring. The IRMPD spectrum of [Pb(Glu-H)](+) can be assigned to a structure where the side chain carboxyl group is deprotonated. The structure of [Pb(Phe-H)H(2)O](+) is simply the hydrated analogue of [Pb(Phe-H)](+) where water attaches to Pb(2+) in the same hemisphere as the ligated amino acid. The spectrum of [Pb(Glu-H)H(2)O](+) could not be assigned a unique structure. The IRMPD spectrum shows features attributed to symmetric and antisymmetric O-H stretching of water and a broad band characteristic of a hydrogen bonded O-H stretching vibration. These features can only be explained by the presence of at least two isomers and agree with the computational results that predict the four lowest energy structures to be within 6 kJ mol(-1) of one another.

  19. Alkali metal ion binding to amino acids versus their methyl esters: affinity trends and structural changes in the gas phase.

    PubMed

    Talley, Jody M; Cerda, Blas A; Ohanessian, Gilles; Wesdemiotis, Chrys

    2002-03-15

    The relative alkali metal ion (M(+)) affinities (binding energies) between seventeen different amino acids (AA) and the corresponding methyl esters (AAOMe) were determined in the gas phase by the kinetic method based on the dissociation of AA-M(+)-AAOMe heterodimers (M=Li, Na, K, Cs). With the exception of proline, the Li(+), Na(+), and K(+) affinities of the other aliphatic amino acids increase in the order AAAAOMe is already observed for K(+). Proline binds more strongly than its methyl ester to all M(+) except Li(+). Ab initio calculations on the M(+) complexes of alanine, beta-aminoisobutyric acid, proline, glycine methyl ester, alanine methyl ester, and proline methyl ester show that their energetically most favorable complexes result from charge solvation, except for proline which forms salt bridges. The most stable mode of charge solvation depends on the ligand (AA or AAOMe) and, for AA, it gradually changes with metal ion size. Esters chelate all M(+) ions through the amine and carbonyl groups. Amino acids coordinate Li(+) and Na(+) ions through the amine and carbonyl groups as well, but K(+) and Cs(+) ions are coordinated by the O atoms of the carboxyl group. Upon consideration of these differences in favored binding geometries, the theoretically derived relative M(+) affinities between aliphatic AA and AAOMe are in good overall agreement with the above given experimental trends. The majority of side chain functionalized amino acids studied show experimentally the affinity order AAAAOMe. The latter ranking is attributed to salt bridge formation.

  20. The fragmentation pathways of protonated Amiton in the gas phase: towards the structural characterisation of organophosphorus chemical warfare agents by electrospray ionisation tandem mass spectrometry.

    PubMed

    Ellis-Steinborner, Simon; Ramachandran, Aravind; Blanksby, Stephen J

    2006-01-01

    Amiton (O,O-diethyl-S-[2-(diethylamino)ethyl] phosphorothiolate), otherwise known as VG, is listed in schedule 2 of the Chemical Weapons Convention (CWC) and has a structure closely related to VX (O-ethyl-S-(2-diisopropylamino)ethylmethylphosphonothiolate). Fragmentation of protonated VG in the gas phase was performed using electrospray ionisation ion trap mass spectrometry (ESI-ITMS) and revealed several characteristic product ions. Quantum chemical calculations provide the most probable structures for these ions as well as the likely unimolecular mechanisms by which they are formed. The decomposition pathways predicted by computation are consistent with deuterium-labeling studies. The combination of experimental and theoretical data suggests that the fragmentation pathways of VG and analogous organophosphorus nerve agents, such as VX and Russian VX, are predictable and thus ESI tandem mass spectrometry is a powerful tool for the verification of unknown compounds listed in the CWC.

  1. Gas-phase separations of protein and peptide ion fragments generated by collision-induced dissociation in an ion trap.

    PubMed

    Badman, Ethan R; Myung, S; Clemmer, David E

    2002-10-01

    Ion mobility/time-of-flight mass spectrometry techniques have been used to examine distributions of fragment ions generated by collision-induced dissociation (CID) in a quadrupole ion trap. The mobility-based separation step prior to mass-to-charge (m/z) analysis reduces spectral congestion and provides information that complements m/z-based assignments of peaks. The approach is demonstrated by examining fragmentation patterns of insulin chain B (a 30-residue peptide), and ubiquitin (a protein containing 76 amino acids). Some fragments of ubiquitin show evidence for multiple stable conformations.

  2. Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian.

    PubMed

    Wlodek, S; Skillman, A G; Nicholls, A

    2010-07-13

    A method of rapid entropy estimation for small molecules in vacuum, solution, and inside a protein receptor is proposed. We show that the Hessian matrix of second derivatives built by a quasi-Newton optimizer during geometry optimization of a molecule with a classical molecular potential in these three environments can be used to predict vibrational entropies. We also show that a simple analytical solvation model allows for no less accurate entropy estimation of molecules in solution than a physically rigorous but computationally more expensive model based on Poisson's equation. Our work also suggests that scaled particle theory more precisely estimates the hydrophobic part of solvation entropy than the using a simple surface area term.

  3. Time dependent density functional theory study of the near-edge x-ray absorption fine structure of benzene in gas phase and on metal surfaces.

    PubMed

    Asmuruf, Frans A; Besley, Nicholas A

    2008-08-14

    The near-edge x-ray absorption fine structure of benzene in the gas phase and adsorbed on the Au(111) and Pt(111) surfaces is studied with time dependent density functional theory. Excitation energies computed with hybrid exchange-correlation functionals are too low compared to experiment. However, after applying a constant shift the spectra are in good agreement with experiment. For benzene on the Au(111) surface, two bands arising from excitation to the e(2u)(pi(*)) and b(2g)(pi(*)) orbitals of benzene are observed for photon incidence parallel to the surface. On Pt(111) surface, a broader band arises from excitation to benzene orbitals that are mixed with the surface and have both sigma(*)(Pt-C) and pi(*) characters.

  4. Electronic structure of BiGay(-) semiconductor clusters and the special stability of BiGa2- - A gas phase Zintl analogue

    NASA Astrophysics Data System (ADS)

    Gupta, Ujjwal; Ulises Reveles, J.; Melko, Joshua J.; Khanna, Shiv N.; Castleman, A. W., Jr.

    2009-01-01

    Here we present evidence that the gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gap) can be tuned (1.12-1.89 eV) by changing the Ga composition of Bi 3Ga y anionic and neutral clusters, some of which display special stability. Collaboratively, mass spectrometry, photoelectron spectroscopy and computational results show that BiGa2- is a very stable cluster with a large calculated HOMO-LUMO gap of 1.89 eV, and can be viewed as a gas phase Zintl analogue of Sn52-, already synthesized in the solution phase. The stability of BiGa2- is further attributed to the fact that it has 12 valence electrons and possesses a closo structure in agreement with Wade's rules.

  5. Electronic Structure of Bi3Gay^- Semiconductor Clusters and the Special Stability of Bi3Ga2^- - A Gas Phase Zintl Analogue

    NASA Astrophysics Data System (ADS)

    Ulises Reveles, Jose; Gupta, Ujjwal; Melko, Joshua J.; Khanna, Shiv N.; Castleman, A. W., Jr.

    2009-03-01

    Here we present evidence that the gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gap) can be tuned (1.12eV-1.89eV) by changing the Ga composition of Bi3Gay neutral and anionic clusters, some of which display special stability. Collaboratively, mass spectrometry, photoelectron spectroscopy and computational results show that Bi3Ga2^- is a very stable cluster with a large calculated HOMO-LUMO gap of 1.89 eV, and can be viewed as a gas phase Zintl analogue of Sn5^2-, already synthesized in the solution phase. The stability of Bi3Ga2^- is further attributed to the fact that it has 12 valence electrons and possesses a closo structure in agreement with Wade's rules.

  6. Gas-phase oligosaccharide nonreducing end (GONE) sequencing and structural analysis by reversed phase HPLC/mass spectrometry with polarity switching.

    PubMed

    Chen, Xiaoyu; Flynn, Gregory C

    2009-10-01

    Here we describe a technique to obtain all the N-linked oligosaccharide structures from a single reversed-phase (RP) HPLC run using on-line tandem MS in both positive and negative ion modes with polarity switching. Oligosaccharides labeled with 2-aminobenzamide (2AB) were used because they generated good ionization efficiency in both ion polarities. In the positive ion mode, protonated oligosaccharide ions lose sugar residues sequentially from the nonreducing end with each round of MS fragmentation, revealing the oligosaccharide sequence from greatly simplified tandem MS spectra. In the negative ion mode, diagnostic ions, including those from cross-ring cleavages, are readily observed in the MS2 spectra of deprotonated oligosaccharide ions, providing detailed structural information, such as branch composition and linkage positions. Both positive and negative ion modes can be programmed into the same LC/MS experiment through polarity switching of the MS instrument. The gas-phase oligosaccharide nonreducing end (GONE) sequencing data, in combination with the diagnostic ions generated in negative ion tandem MS, allow both sequence and structural information to be obtained for all eluting species during a single RP-HPLC chromatographic run. This technique generates oligosaccharide analyses at high speed and sensitivity, and reveals structural features that can be difficult to obtain by traditional methods.

  7. Low symmetry in molecules with heavy peripheral atoms. The gas-phase structure of perfluoro(methylcyclohexane), C6F11CF3.

    PubMed

    Kafka, Graeme R; Masters, Sarah L; Wann, Derek A; Robertson, Heather E; Rankin, David W H

    2010-10-21

    When refining structures using gas electron diffraction (GED) data, assumptions are often made in order to reduce the number of required geometrical parameters. Where these relate to light, peripheral atoms there is little effect on the refined heavy-atom structure, which is well defined by the GED data. However, this is not the case when heavier atoms are involved. We have determined the gas-phase structure of perfluoro(methylcyclohexane), C(6)F(11)CF(3), using three different refinement methods and have shown that our new method, which makes use of both MP2 and molecular mechanics (MM) calculations to restrain the peripheral-atom geometry, gives a realistic structure without the need for damaging constraints. Only the conformer with the CF(3) group in an equatorial position was considered, as ab initio calculations showed this to be 25 kJ mol(-1) lower in energy than the axial conformer. Refinements combining both high-level and low-level calculations to give constraints were superior both to those based only on molecular mechanics and to those in which assumptions about the geometry were imposed.

  8. A carbon foam with a bimodal micro–mesoporous structure prepared from larch sawdust for the gas-phase toluene adsorption

    SciTech Connect

    Liu, Shouxin; Huang, Zhanhua; Wang, Rui

    2013-07-15

    Highlights: ► Network carbon foam containing a bimodal pore distribution was prepared from Larch. ► Liquefaction route was used for the preparation of morphology controllable carbon. ► Pore structure of carbon foam was controlled through KOH activation. - Abstract: A carbon foam with a bimodal micro–mesopore distribution, was prepared by submitting larch sawdust to liquefaction, resinification, foaming, carbonization and KOH activation. The morphology, pore texture and crystal microstructure was characterized by scanning and transmission electron microscopy, nitrogen adsorption analysis and X-ray powder diffraction. A honeycomb structure with adjacent cells was observed for the precursor of carbon foam. After KOH activation, the cell wall of precursor shrunk and broke. This lead to the formation of a well-connected 3D network and developed ligament pore structure (surface area of 554–1918 m{sup 2}/g) containing bimodal pores, 2.1 and 3.9 nm in diameter. The porous carbon foam prepared at 700 °C exhibited a much higher gas-phase toluene removal than commercial activated carbon fiber owing to the 3D network and bimodal pore structure.

  9. Irmpd Action Spectroscopy and Computational Approaches to Elucidate Gas-Phase Structures and Energetics of 2'-DEOXYCYTIDINE and Cytidine Sodium Complexes

    NASA Astrophysics Data System (ADS)

    Zhu, Yanlong; Hamlow, Lucas; He, Chenchen; Gao, Juehan; Oomens, Jos; Rodgers, M. T.

    2016-06-01

    The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with cations. In order to determine the effects of Na+ cationization on the gas-phase structures of 2'-deoxycytidine, [dCyd+Na]+, and cytidine, [Cyd+Na]+, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides are measured over the range extending from 500 to 1850 wn using the FELIX free electron laser. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations, frequency analyses, and IR spectra of these species are determined at the B3LYP/6-311+G(d,p) level of theory. Single-point energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory to determine the relative stabilities of these conformations. Comparison of the measure IRMPD action spectra and computed linear IR spectra enable the conformations accessed in the experiments to be elucidated. For both cytosine nucleosides, tridentate binding of the Na+ cation to the O2, O4' and O5' atoms of the nucleobase and sugar is observed. Present results for the sodium cationized nucleosides are compared to results for the analogous protonated forms of these nucleosides to elucidate the effects of multiple chelating interactions with the sodium cation vs. hydrogen bonding interactions in the protonated systems on the structures and stabilities of these nucleosides.

  10. Semi-experimental equilibrium structure of pyrazinamide from gas-phase electron diffraction. How much experimental is it?

    NASA Astrophysics Data System (ADS)

    Tikhonov, Denis S.; Vishnevskiy, Yury V.; Rykov, Anatolii N.; Grikina, Olga E.; Khaikin, Leonid S.

    2017-03-01

    A semi-experimental equilibrium structure of free molecules of pyrazinamide has been determined for the first time using gas electron diffraction method. The refinement was carried using regularization of geometry by calculated quantum chemical parameters. It is discussed to which extent is the final structure experimental. A numerical approach for estimation of the amount of experimental information in the refined parameters is suggested. The following values of selected internuclear distances were determined (values are in Å with 1σ in the parentheses): re(Cpyrazine-Cpyrazine)av = 1.397(2), re(Npyrazine-Cpyrazine)av = 1.332(3), re(Cpyrazine-Camide) = 1.493(1), re(Namide-Camide) = 1.335(2), re(Oamide-Camide) = 1.219(1). The given standard deviations represent pure experimental uncertainties without the influence of regularization.

  11. Gas-phase chemical dynamics

    SciTech Connect

    Weston, R.E. Jr.; Sears, T.J.; Preses, J.M.

    1993-12-01

    Research in this program is directed towards the spectroscopy of small free radicals and reactive molecules and the state-to-state dynamics of gas phase collision, energy transfer, and photodissociation phenomena. Work on several systems is summarized here.

  12. Structure and Gas-Phase Thermochemistry of a Pd/Cu Complex: Studies on a Model for Transmetalation Transition States.

    PubMed

    Oeschger, Raphael J; Chen, Peter

    2017-01-25

    A heterobimetallic Pd(II)/Cu(I) complex was prepared and characterized by X-ray diffraction analysis. The crystal structure shows a remarkably short Pd-Cu bond and a trigonal ipso carbon atom. The Pd-Cu interaction, as determined by energy-resolved collision-induced dissociation cross-section experiments, models the net stabilizing energy of the Pd-Cu interaction in the transition state of the transmetalation step in Pd/Cu-catalyzed cross-coupling reactions. The bonding situation in the bimetallic dinuclear complex has been studied by atoms-in-molecules analysis.

  13. Prioritizing testing of organic compounds detected as gas phase air pollutants: structure-activity study for human contact allergens.

    PubMed Central

    Johnson, R; Macina, O T; Graham, C; Rosenkranz, H S; Cass, G R; Karol, M H

    1997-01-01

    Organic compounds that are used or generated anthropogenically in large quantities in cities can be identified through their presence in the urban atmosphere and in air pollutant source emissions. Compounds identified by this method were screened to evaluate their potential to act as contact allergens. The CASE and MULTICASE computer programs, which are based on the detection of structure-activity relationships (SAR), were used to evaluate this potential. These relationships first are determined by comparing chemical structures to biological activity within a learning set comprised of 458 compounds, each of which had been tested experimentally in human trials for its sensitization potential. Using the information contained in this learning set, CASE and MULTICASE predicted the activity of 238 compounds found in the atmosphere for their ability to act as contact allergens. The analysis finds that 21 of 238 compounds are predicted to be active contact allergens (probability >0.5), with potencies ranging from mild to very strong. The compounds come from chemical classes that include chlorinated aromatics and chlorinated hydrocarbons, N-containing compounds, phenols, alkenes, and an S-containing compound. Using the measured airborne concentrations or emission rates of these compounds as an indication of the extent of their use, together with their predicted potencies, provides an efficient method to prioritize the experimental assessment of contact sensitization of untested organic compounds that can be detected as air pollutants. Images Figure 1. PMID:9300925

  14. Prioritizing testing of organic compounds detected as gas phase air pollutants: structure-activity study for human contact allergens.

    PubMed

    Johnson, R; Macina, O T; Graham, C; Rosenkranz, H S; Cass, G R; Karol, M H

    1997-09-01

    Organic compounds that are used or generated anthropogenically in large quantities in cities can be identified through their presence in the urban atmosphere and in air pollutant source emissions. Compounds identified by this method were screened to evaluate their potential to act as contact allergens. The CASE and MULTICASE computer programs, which are based on the detection of structure-activity relationships (SAR), were used to evaluate this potential. These relationships first are determined by comparing chemical structures to biological activity within a learning set comprised of 458 compounds, each of which had been tested experimentally in human trials for its sensitization potential. Using the information contained in this learning set, CASE and MULTICASE predicted the activity of 238 compounds found in the atmosphere for their ability to act as contact allergens. The analysis finds that 21 of 238 compounds are predicted to be active contact allergens (probability >0.5), with potencies ranging from mild to very strong. The compounds come from chemical classes that include chlorinated aromatics and chlorinated hydrocarbons, N-containing compounds, phenols, alkenes, and an S-containing compound. Using the measured airborne concentrations or emission rates of these compounds as an indication of the extent of their use, together with their predicted potencies, provides an efficient method to prioritize the experimental assessment of contact sensitization of untested organic compounds that can be detected as air pollutants.

  15. Gas-phase structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene: cog-wheel-type vs. independent internal rotation and influence of dispersion interactions.

    PubMed

    Otlyotov, Arseniy A; Lamm, Jan-Hendrik; Blomeyer, Sebastian; Mitzel, Norbert W; Rybkin, Vladimir V; Zhabanov, Yuriy A; Tverdova, Natalya V; Giricheva, Nina I; Girichev, Georgiy V

    2017-05-24

    The gas-phase structure of 1,8-bis[(trimethylsilyl)ethynyl]anthracene (1,8-BTMSA) was determined by a combined gas electron diffraction (GED)/mass spectrometry (MS) experiment as well as by quantum-chemical calculations (QC). DFT and dispersion corrected DFT calculations (DFT-D3) predicted two slightly different structures for 1,8-BTMSA concerning the mutual orientation of the two -C-C[triple bond, length as m-dash]C-SiMe3 units: away from one another or both bent to the same side. An attempt was made to distinguish these structures by GED structural analysis. To probe the structural rigidity, a set of Born-Oppenheimer molecular dynamics (BOMD) calculations has been performed at the DFT-D level. Vibrational corrections Δr = ra - re were calculated by two BOMD approaches: a microcanonically (NVE) sampled ensemble of 20 trajectories (BOMD(NVE)) and a canonical (NVT) trajectory thermostated by the Noose-Hoover algorithm (BOMD(NVT)). In addition, the conventional approach with both, rectilinear and curvilinear approximations (SHRINK program), was also applied. Radial distribution curves obtained with models using both MD approaches provide a better description of the experimental data than those obtained using the rectilinear (SHRINK) approximation, while the curvilinear approach turned out to lead to physically inacceptable results. The electronic structure of 1,8-BTMSA was investigated in terms of an NBO analysis and was compared with that of the earlier studied 1,8-bis(phenylethynyl)anthracene. Theoretical and experimental results lead to the conclusion that the (trimethylsilyl)ethynyl (TMSE) groups in 1,8-BTMSA are neither restricted in rotation nor in bending at the temperature of the GED experiment.

  16. Gas-phase chemistry of ethynylamine, -phosphine and -arsine. Structure and stability of their Cu+ and Ni+ complexes.

    PubMed

    Galiano, Luis; Alcamí, Manuel; Mó, Otilia; Yáñez, Manuel

    2003-01-13

    The Cu+ and Ni+ binding energies of ethynylamine, ethynylphosphine and ethynylarsine have been calculated at the B3LYP/6-311 + G(2df,2p)//B3LYP/6-311G(d,p) level of theory. Significant differences between nitrogen-containing and phosphorus- or arsenic-containing compounds have been found regarding structural effects upon metal cation association. While for ethynylamine the global minimum of the potential energy surface corresponds to the complex in which the metal cation binds to the beta-carbon, for ethynylphosphine the most favourable process corresponds to phosphorus attachment. For ethynylarsine, the conventional pi-complex is the most stable one. This behavior resembles that found for the corresponding vinyl analogues, with the only exception being the arsenic derivative. The calculated Cu+ and Ni+ binding energies for attachment to the heteroatom follow a different trend, P > As > N, to that predicted for the corresponding proton affinities, P > N > As. Cu+ and Ni+ binding energies are almost identical when the metal cation binds to the heteroatom. However, Ni+ binding energies are slightly larger than Cu+ binding energies when the metal cation interacts with the C identical to C bond.

  17. Approaching the gas-phase structures of [AgS8]+ and [AgS16]+ in the solid state.

    PubMed

    Cameron, T Stanley; Decken, Andreas; Dionne, Isabelle; Fang, Min; Krossing, Ingo; Passmore, Jack

    2002-08-02

    Upon treating elemental sulfur with [AgSbF(6)], [AgAl(hfip)(4)], [AgAl(pftb)(4)] (hfip=OCH(CF(3))(2), pftb =OC(CF(3))(3)) the compounds [Ag(S(8))(2)][SbF(6)] (1), [AgS(8)][Al(hfip)(4)] (2), and [Ag(S(8))(2)](+)[[Al(pftb)(4)](-) (3) formed in SO(2) (1), CS(2) (2), or CH(2)Cl(2) (3). Compounds 1-3 were characterized by single-crystal X-ray structure determinations: 1 by Raman spectroscopy, 2 and 3 by solution NMR spectroscopy and elemental analyses. Single crystals of [Ag(S(8))(2)](+)[Sb(OTeF(5))(6)](-) 4 were obtained from a disproportionation reaction and only characterized by X-ray crystal structure analysis. The Ag(+) ion in 1 coordinates two monodentate SbF(6) (-) anions and two bidentate S(8) rings in the 1,3-position. Compound 2 contains an almost C(4v)-symmetric [AgS(8)](+) moiety; this is the first example of an eta(4)-coordinated S(8) ring (d(Agbond;S)=2.84-3.00 A). Compounds 3 and 4, with the least basic anions, contain undistorted, approximately centrosymmetric Ag(eta(4)-S(8))(2) (+) cations with less symmetric eta(4)-coordinated S(8) rings (d(Agbond;S)=2.68-3.35 A). The thermochemical radius and volume of the undistorted Ag(S(8))(2) (+) cation was deduced as r(therm)(Ag(S(8))(2) (+))=3.378+ 0.076/-0.120 A and V(therm)(Ag(S(8))(2) (+))=417+4/-6 A(3). AgS(8) (+) and several isomers of the Ag(S(8))(2) (+) cation were optimized at the BP86, B3LYP, and MP2 levels by using the SVP and TZVPP basis sets. An analysis of the calculated geometries showed the MP2/TZVPP level to give geometries closest to the experimental data. Neither BP86 nor B3LYP reproduced the longer weak dispersive Agbond;S interactions in Ag(eta(4)-S(8))(2) (+) but led to Ag(eta(3)-S(8))(2) (+) geometries. With the most accurate MP2/TZVPP level, the enthalpies of formation of the gaseous [AgS(8)](+) and [Ag(S(8))(2)](+) cations were established as Delta(f)H(298)([Ag(S(8))(2)](+), g)=856 kJ mol(-1) and Delta(f)H(298)([AgS(8)](+), g)=902 kJ mol(-1). It is shown that the [AgS(8)](+) moiety in 2

  18. Assigning structures to gas-phase peptide cations and cation-radicals. An infrared multiphoton dissociation, ion mobility, electron transfer, and computational study of a histidine peptide ion.

    PubMed

    Moss, Christopher L; Chamot-Rooke, Julia; Nicol, Edith; Brown, Jeffery; Campuzano, Iain; Richardson, Keith; Williams, Jonathan P; Bush, Matthew F; Bythell, Benjamin; Paizs, Bela; Turecek, Frantisek

    2012-03-15

    Infrared multiphoton dissociation (IRMPD) spectroscopy, using a free-electron laser, and ion mobility measurements, using both drift-cell and traveling-wave instruments, were used to investigate the structure of gas-phase peptide (AAHAL + 2H)(2+) ions produced by electrospray ionization. The experimental data from the IRMPD spectra and collisional cross section (Ω) measurements were consistent with the respective infrared spectra and Ω calculated for the lowest-energy peptide ion conformer obtained by extensive molecular dynamics searches and combined density functional theory and ab initio geometry optimizations and energy calculations. Traveling-wave ion mobility measurements were employed to obtain the Ω of charge-reduced peptide cation-radicals, (AAHAL + 2H)(+●), and the c(3), c(4), z(3), and z(4) fragments from electron-transfer dissociation (ETD) of (AAHAL + 2H)(2+). The experimental Ω for the ETD charge-reduced and fragment ions were consistent with the values calculated for fully optimized ion structures and indicated that the ions retained specific hydrogen bonding motifs from the precursor ion. In particular, the Ω for the doubly protonated ions and charge-reduced cation-radicals were nearly identical, indicating negligible unfolding and small secondary structure changes upon electron transfer. The experimental Ω for the (AAHAL + 2H)(+●) cation-radicals were compatible with both zwitterionic and histidine radical structures formed by electron attachment to different sites in the precursor ion, but did not allow their distinction. The best agreement with the experimental Ω was found for ion structures fully optimized with M06-2X/6-31+G(d,p) and using both projection approximation and trajectory methods to calculate the theoretical Ω values.

  19. Gas-Phase Structure of Amyloid-β (12 - 28) Peptide Investigated by Infrared Spectroscopy, Electron Capture Dissociation and Ion Mobility Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Le, Thi Nga; Poully, Jean Christophe; Lecomte, Frédéric; Nieuwjaer, Nicolas; Manil, Bruno; Desfrançois, Charles; Chirot, Fabien; Lemoine, Jerome; Dugourd, Philippe; van der Rest, Guillaume; Grégoire, Gilles

    2013-12-01

    The gas-phase structures of doubly and triply protonated Amyloid-β12-28 peptides have been investigated through the combination of ion mobility (IM), electron capture dissociation (ECD) mass spectrometry, and infrared multi-photon dissociation (IRMPD) spectroscopy together with theoretical modeling. Replica-exchange molecular dynamics simulations were conducted to explore the conformational space of these protonated peptides, from which several classes of structures were found. Among the low-lying conformers, those with predicted diffusion cross-sections consistent with the ion mobility experiment were further selected and their IR spectra simulated using a hybrid quantum mechanical/semiempirical method at the ONIOM DFT/B3LYP/6-31 g(d)/AM1 level. In ECD mass spectrometry, the c/z product ion abundance (PIA) has been analyzed for the two charge states and revealed drastic differences. For the doubly protonated species, N - Cα bond cleavage occurs only on the N and C terminal parts, while a periodic distribution of PIA is clearly observed for the triply charged peptides. These PIA distributions have been rationalized by comparison with the inverse of the distances from the protonated sites to the carbonyl oxygens for the conformations suggested from IR and IM experiments. Structural assignment for the amyloid peptide is then made possible by the combination of these three experimental techniques that provide complementary information on the possible secondary structure adopted by peptides. Although globular conformations are favored for the doubly protonated peptide, incrementing the charge state leads to a conformational transition towards extended structures with 310- and α-helix motifs.

  20. Quantum chemical calculations on the structure and stability of Mg2+XH3OH complexes in the gas phase (X = C, Si, and Ge)

    NASA Astrophysics Data System (ADS)

    El-Nahas, Ahmed M.; El-Demerdash, Safinaz H.; El-Shereefy, El-Sayed E.

    2007-06-01

    The structure and stability of Mg2+XH3OH complexes in gas phase (X = C, Si and Ge) have been studied using the B3LYP/6-31 + G(d) and CBS-QB3 levels of theory. Several dissociation pathways for Mg2+XH3OH complexes have been investigated. The complexes are thermodynamically stable with respect to the loss of H+, OH+, XH3, XH4, and XH4+ but thermodynamically unstable toward the loss of XH3+, XH3OH+, and XH3O+ ions. The presence of sizable kinetic energy barriers (25-81 kcal/mol) for unimolecular dissociation hinders the exothermic processes. This indicates that Mg2+XH3OH complexes can form metastable species and is likely observed under appropriate experimental conditions. On the other hand, endothermic channels are unlikely occurred under mild experimental conditions. Binding energies in the investigated complexes parallel charge transfer from ligands to the Mg2+ ion. Comparison between B3LYP and CBS-QB3 results is also presented.

  1. Spectroscopic study on the structural isomers of 7-azaindole(ethanol)n (n=1-3) and multiple-proton transfer reactions in the gas phase

    NASA Astrophysics Data System (ADS)

    Sakota, Kenji; Komure, Noriyuki; Ishikawa, Wataru; Sekiya, Hiroshi

    2009-06-01

    The resonance-enhanced two-photon ionization (RE2PI) and laser-induced fluorescence excitation spectra were recorded for the S1-S0(ππ ∗) region of the 7-azaindole(ethanol)n (n =1-3) [7AI(EtOH)n (n =1-3)] clusters in the gas phase to investigate the geometrical structures and the multiple-proton/hydrogen atom transfer reaction dynamics. Four and two structural isomers were identified for 7AI(EtOH)2 and 7AI(EtOH)3, respectively. Density functional theory calculations at the B3LYP/6-31++G∗∗/6-31G∗ level predicted four different conformations of the ethyl group for 7AI(EtOH)2, in good agreement with the observation of the four structural isomers in the RE2PI spectra. Visible fluorescence from the tautomeric forms was observed in the S1 states for all isomers of 7AI(EtOH)2, but no sign of double-proton/hydrogen atom transfer and quadruple-proton/hydrogen atom transfer has been obtained in the electronic spectra of 7AI(EtOH)1 and 7AI(EtOH)3, respectively. These results suggest that the multiple-proton transfer reaction is cluster-size selective, and the triple-proton/hydrogen atom transfer potential is dominated by the cyclic hydrogen-bonded network in 7AI(EtOH)2. The excitation of the in-phase intermolecular stretching vibration prominently enhances the excited-state triple-proton/hydrogen atom transfer reaction.

  2. Gas-Phase Molecular Structure of Nopinone and its Water Complexes Studied by Microwave Fourier Transform Spectroscopy and Quantum Chemical Calculations

    NASA Astrophysics Data System (ADS)

    Neeman, Elias M.; Aviles Moreno, Juan-Ramon; Huet, T. R.

    2016-06-01

    Several monoterpenes and terpenoids are biogenic volatile organic compounds which are emitted in the atmosphere, where they react with OH, O_3 and NO_x etc. to give rise to several oxidation and degradation products. Their decomposition products are a major source of secondray organic aerosol (SOA). Spectroscopic information on these atmospheric species is still very scarce. The rotational spectrum of nopinone (C_9H14O) one of the major oxidation products of β-pinene, and of its water complexes were recorded in a supersonic jet expansion with a Fourier transform microwave spectrometer over the range 2-20 GHz. The structure of the unique stable conformer of the nopinone was optimized using density functional theory and ab initio calculations. Signals from the parent species and from the 13C and 18O isotopomers were observed in natural abundance. A magnetic hyperfine structure associated with the pairs of hydrogen nuclei in the methylene groups was observed and modeled. The structures of several conformers of the nopinone-water complexes with up to three molecules of water were optimized using density functional theory and ab initio calculations. The energetically most stable of calculated conformers were observed and anlyzed. The rotational and centrifugal distortion parameters were fitted to a Watson's Hamiltonian in the A-reduction. The present work provides the first spectroscopic characterization of nopinone and its water complexes in the gas phase. A. Calogirou, B.R. Larsen, and D. Kotzias, Atmospheric Environment, 33, 1423-1439, (1999) P. Paasonen et al., Nat. Geosci., 6, 438-442 (2013) D. Zhang and R. Zhang The Journal of Chemical Physics, 122, 114308, (2005) R. Winterhalter et al. Journal of Atmospheric Chemistry, 35, 165-197, (2000)

  3. Gas phase synthesis, structure and unimolecular reactivity of silver iodide cluster cations, Ag(n)I(m)(+) (n = 2-5, 0 < m < n).

    PubMed

    Khairallah, George N; O'Hair, Richard A J

    2008-06-14

    Multistage mass spectrometry (MS(n)) experiments reveal that gas phase silver iodide cluster cations, Ag(n)I(m)(+), are readily built up in a stepwise fashion via ion-molecule reactions between mass selected silver (Ag(3)(+) and Ag(5)(+)) or silver hydride (Ag(2)H(+) and Ag(4)H(+)) cluster cations and allyl iodide, in contrast to their reactions with methyl iodide, which solely result in ligation of the clusters. The stoichiometries of these clusters range from 1 < or = n < or = 5 and 1 < or = m < or = 4, indicating the formation of several new subvalent silver iodide clusters. Collision induced dissociation (CID) experiments were carried out on each of these clusters to shed some light on their possible structures. The products arising from CID of the Ag(n)I(m)(+) clusters are highly dependent on the stoichiometry of the cluster. Thus the odd-electron clusters Ag(4)I(2)(+) and Ag(5)I(+) fragment via loss of a silver atom. In contrast, the even-electron cluster ions all fragment via loss of AgI. In addition, Ag(2)I(2) loss is observed for the Ag(4)I(3)(+) and Ag(5)I(2)(+) clusters, while loss of Ag(3)I(3) occurs for the stoichiometric Ag(5)I(4)(+) cluster. DFT calculations were carried out on these Ag(n)I(m)(+) clusters as well as the neutrals associated with the ion-molecule and CID reactions. A range of different isomeric structures were calculated and their structures are described. A noteworthy aspect is that ligation of these silver clusters by I can have a profound effect on the geometry of the silver cluster. For example, D(3h) Ag(3)(+) becomes C(2v) Ag(3)I(+), which in turn becomes C(2h) Ag(3)I(2)(+). Finally, the DFT predicted thermochemistry supports the different types of reaction channels observed in the ion-molecule reactions and CID experiments.

  4. The gas-phase bis-uranyl nitrate complex [(UO2)(2)(NO3)(5)](-): infrared spectrum and structure

    SciTech Connect

    Gary S. Groenewold; Michael J. van Stipdonk; Jos Oomens; Wibe de Jong; Michael E. McIlwain

    2011-12-01

    The infrared spectrum of the bis-uranyl nitrate complex [(UO{sub 2}){sub 2}(NO{sub 3}){sub 5}]{sup -} was measured in the gas phase using multiple photon dissociation (IRMPD). Intense absorptions corresponding to the nitrate symmetric and asymmetric vibrations, and the uranyl asymmetric vibration were observed. The nitrate nu3 vibrations indicate the presence of nitrate in a bridging configuration bound to both uranyl cations, and probably two distinct pendant nitrates in the complex. The coordination environment of the nitrate ligands and the uranyl cations were compared to those in the mono-uranyl complex. Overall, the uranyl cation is more loosely coordinated in the bis-uranyl complex [(UO{sub 2}){sub 2}(NO{sub 3}){sub 5}]{sup -} compared to the mono-complex [UO{sub 2}(NO{sub 3}){sub 3}]{sup -}, as indicated by a higher O-U-O asymmetric stretching (nu3) frequency. However, the pendant nitrate ligands are more strongly bound in the bis-complex than they are in the mono-uranyl complex, as indicated by the {nu}{sub 3} frequencies of the pendant nitrate, which are split into nitrosyl and O-N-O vibrations as a result of bidentate coordination. These phenomena are consistent with lower electron density donation per uranyl by the nitrate bridging two uranyl centers compared to that of a pendant nitrate in the mono-uranyl complex. The structure was calculated using density functional theory (B3LYP functional), which produced a structure in which the two uranyl molecules bridged by a single nitrate coordinated in a bis-bidentate fashion. Each uranyl molecule was coordinated by two pendant nitrate ligands. The corresponding vibrational spectrum was in excellent agreement with the IRMPD measurement, confirming the structural assignment.

  5. The gas-phase bis-uranyl nitrate complex [(UO2)2(NO3)5]-: infrared spectrum and structure

    SciTech Connect

    Groenewold, G. S.; van Stipdonk, Michael J.; Oomens, Jos; De Jong, Wibe A.; McIIwain, Michael E.

    2011-12-01

    The infrared spectrum of the bis-uranyl nitrate complex [(UO2)2(NO3)5]- was measured in the gas phase using multiple photon dissociation (IRMPD). Intense absorptions corresponding to the nitrate symmetric and asymmetric vibrations, and the uranyl asymmetric vibration were observed. The nitrate v3 vibrations indicate the presence of nitrate in a bridging configuration bound to both uranyl cations, and probably two distinct pendant nitrates in the complex. The coordination environment of the nitrate ligands and the uranyl cations were compared to those in the mono-uranyl complex. Overall, the uranyl cation is more loosely coordinated in the bis-uranyl complex [(UO2)2(NO3)5]- compared to the mono-complex [UO2(NO3)3]-, as indicated by a higher O-U-O asymmetric stretching (v3) frequency. However, the pendant nitrate ligands are more strongly bound in the bis-complex than they are in the mono-uranyl complex, as indicated by the v3 frequencies of the pendant nitrate, which are split into nitrosyl and O-N-O vibrations as a result of bidentate coordination. These phenomena are consistent with lower electron density donation per uranyl by the nitrate bridging two uranyl centers compared to that of a pendant nitrate in the mono-uranyl complex. The lowest energy structure predicted by density functional theory (B3LYP functional) calculations was one in which the two uranyl molecules bridged by a single nitrate coordinated in a bis-bidentate fashion. Each uranyl molecule was coordinated by two pendant nitrate ligands. The corresponding vibrational spectrum was in excellent agreement with the IRMPD measurement, confirming the structural assignment.

  6. Mass spectrometry study of multiply negatively charged, gas-phase NaAOT micelles: how does charge state affect micellar structure and encapsulation?

    PubMed

    Fang, Yigang; Liu, Fangwei; Liu, Jianbo

    2013-01-01

    We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na(n-z)AOT(n)](z-) (n = 1-18 and z = 1-2). Solvation by water was detected only for small aggregates [Na(n-1)AOT(n)H(2)O](-) of n = 3-9. Incorporation of glycine and tryptophan into [Na(n-z)AOT(n)](z-) aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na(n-z)AOT(n)](z-) of n ≥ 7, and at most two glycine molecules could be hosted in that of n ≥ 13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n ≥ 6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na(n+z)AOT(n)](z+) aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.

  7. GAS PHASE MOLECULAR DYNAMICS

    SciTech Connect

    SEARS,T.J.; HALL,G.E.; PRESES,J.M.; WESTON,R.E.,JR.

    1999-06-09

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution, high-sensitivity, laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule. The work of group members Fockenberg and Muckerman is described in separate abstracts of this volume.

  8. The C 1s and N 1s near edge x-ray absorption fine structure spectra of five azabenzenes in the gas phase

    SciTech Connect

    Vall-llosera, G.; Gao, B.; Kivimaeki, A.; Coreno, M.; Alvarez Ruiz, J.; Simone, M. de; Aagren, H.; Rachlew, E.

    2008-01-28

    Near edge x-ray absorption fine structure spectra have been measured and interpreted by means of density functional theory for five different azabenzenes (pyridine, pyridazine, pyrimidine, pyrazine, and s-triazine) in the gas phase. The experimental and theoretical spectra at the N 1s and C 1s edges show a strong resonance assigned to the transition of the 1s electron in the respective N or C atoms to the lowest unoccupied molecular orbital with {pi}* symmetry. As opposed to the N 1s edge, at the C 1s edge this resonance is split due to the different environments of the core hole atom in the molecule. The shift in atomic core-level energy due to a specific chemical environment is explained with the higher electronegativity of the N atom compared to the C atom. The remaining resonances below the ionization potential (IP) are associated to {sigma} or {pi} orbitals with mixed valence/Rydberg character. Upon N addition, a reduction of intensity is observed in the Rydberg region at both edges as compared to the intensity in the continuum. Above the IP one or more resonances are seen and ascribed here to transitions to {sigma}* orbitals. Calculating the experimental and theoretical {delta}{sub {pi}} term values at both edges, we observe that they are almost the same within {+-}1 eV as expected for isoelectronic bonded pairs. The term values of the {pi}* and {sigma}* resonances are discussed in terms of the total Z number of the atoms participating in the bond.

  9. Structure and conformation of 1,4-difluorobutane as determined by gas-phase electron diffraction, and by molecular mechanics and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Krosley, Kevin; Hagen, Kolbjørn; Hedberg, Kenneth

    1995-06-01

    Gas-phase electron diffraction data at 23°C together with molecular mechanics (MM3) and ab initio (HF/6-31G∗, gaussian 86) calculations have been used to determine the structure and conformations of 1,4-difluorobutane. The object was to ascertain whether effects similar to the gauche effect in 1,2-difluoroethane, which serves to stabilize the gauche form with the fluorine atoms in close proximity, could also operate in 1,4-difluorobutane. It was found both theoretically and experimentally that the proportion of those conformers having close fluorine atoms was small, implying the absence of effects similar to the gauche effect. The conformational composition estimated from the theoretical calculations is in good agreement with the experimental data. The experimental electron diffraction results constrained by assumptions drawn from the theoretical calculations, ED/MM3 [ED/ab initio], for the principal distances ( {r g}/{Å}) and angles ( {∠ α}/{deg}) with estimated 2σ uncertainties are as follows: r(CH) = 1.105(3) [1.106(3)], r(CF) = 1.398(2) [1.398(2)], r(C 1C 2) = 1.513(2) [1.516(2)], r(C 2C 3) = 1.537(2) [1.532(2)], ∠FCC = 110.9(3) [111.1(3)], ∠CCC = 112.9(4) [112.9(4)], and ∠HCH = 100(3) [100(3)].

  10. Substituent effect on electron affinity, gas-phase basicity, and structure of monosubstituted propynyl radicals and their anions: a theoretical study.

    PubMed

    Lee, Gab-Yong

    2009-11-15

    The substituent effect of electron-withdrawing groups on electron affinity and gas-phase basicity has been investigated for substituted propynl radicals and their corresponding anions. It is shown that when a hydrogen of the alpha-CH(3) group in the propynyl system is substituted by an electron-withdrawing substituent, electron affinity increases, whereas gas-phase basicity decreases. These results can be explained in terms of the natural atomic charge of the terminal acetylene carbon of the systems. The calculated electron affinities are 3.28 eV (*C=C-CH(2)F), 3.59 eV (*C[triple bond]C-CH(2)Cl) and 3.73 eV (*C[triple bond]C-CH(2)Br), and the gas-phase basicities of their anions are 359.5 kcal/mol ((-):C[triple bond]C-CH(2)F), 354.8 kcal/mol (:C[triple bond]C-CH(2)Cl) and 351.3 kcal/mol ((-):C[triple bond]C-CH(2)Br). It is concluded that the larger the magnitude of electron-withdrawing, the greater is the electron affinity of radical and the smaller is the gas-phase basicity of its anion.

  11. Understanding the structure and dynamic of odorants in the gas phase using a combination of microwave spectroscopy and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Mouhib, Halima

    2014-07-01

    This tutorial is an introduction for PhD students and researchers who intend to start their future work in the field of microwave spectroscopy to investigate structural and dynamical aspects of isolated molecular systems in the gas phase. Although the presented case studies are related to odorants, i.e., volatile molecules that possess a noticeable scent, the background and applications of the method can be transferred to any other resembling molecular system. In the early days, microwave spectroscopy was mainly related to the structure determination of very small systems such as OCS or ammonia, where the bond lengths could be determined with high accuracy by measuring the different isotopic species of the molecules. Nowadays, the method is far more advanced and is also used to tackle various fundamental molecular problems in different fields such as physical chemistry and molecular physics. Interesting questions that can be investigated concern, e.g., the molecular structure, i.e., the different conformations, not only of the isolated molecule but also of van der Waals complexes with water, noble gases or other molecules. The dynamical and intra- or intermolecular effects can be straightforwardly observed without the influence of the environment as in the condensed phase. This evolution was only achieved by using quantum chemical methods as a complementary tool to elude the necessity of isotopologues for structure determination, which cannot be realized for large systems (>5 atoms). The combination of microwave spectroscopy and quantum chemical calculations is the method of choice when it comes to sampling the conformational space of molecules. This is particularly the case when small energy differences make it difficult to determine the conformers of the lowest energy using computational methods alone. Although quantum chemical calculations are important for the validation of microwave spectra, the focus of the tutorial is set on the experimental part of the

  12. Gas-phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation, structures and electron capture dissociation.

    PubMed

    Afonso, Carlos; Tabet, Jean-Claude; Giorgi, Gianluca; Tureček, František

    2012-02-01

    Copper complexes with a cyclic D-His-β-Ala-L-His-L-Lys and all-L-His-β-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06-2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side-chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c-HAHK + H)](2+) and [Cu(c-HAHK - H)](2+) type with closed electronic shells followed similar orders when treated by the B3LYP and M06-2X functionals. Large differences between relative energies calculated by these methods were obtained for open-shell complexes of the [Cu(c-HAHK)](2+) type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c-HAHK - H)](2+) complexes, solution H/D exchange involved only the N-H protons, resulting in the exchange of up to seven protons, as established by ultra-high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas-phase ions that were deprotonated at the peptide C(α) positions.

  13. Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect.

    PubMed

    Cembran, Alessandro; Gonzalez-Luque, Remedios; Altoè, Piero; Merchan, Manuela; Bernardi, Fernando; Olivucci, Massimo; Garavelli, Marco

    2005-07-28

    The low-lying singlet states (i.e. S0, S1, and S2) of the chromophore of rhodopsin, the protonated Schiff base of 11-cis-retinal (PSB11), and of its all-trans photoproduct have been studied in isolated conditions by using ab initio multiconfigurational second-order perturbation theory. The computed spectroscopic features include the vertical excitation, the band origin, and the fluorescence maximum of both isomers. On the basis of the S0-->S1 vertical excitation, the gas-phase absorption maximum of PSB11 is predicted to be 545 nm (2.28 eV). Thus, the predicted absorption maximum appears to be closer to that of the rhodopsin pigment (2.48 eV) and considerably red-shifted with respect to that measured in solution (2.82 eV in methanol). In addition, the absorption maxima associated with the blue, green, and red cone visual pigments are tentatively rationalized in terms of the spectral changes computed for PSB11 structures featuring differently twisted beta-ionone rings. More specifically, a blue-shifted absorption maximum is explained in terms of a large twisting of the beta-ionone ring (with respect to the main conjugated chain) in the visual S-cone (blue) pigment chromophore. In contrast, the chromophore of the visual L-cone (red) pigment is expected to have a nearly coplanar beta-ionone ring yielding a six double bond fully conjugated framework. Finally, the M-cone (green) chromophore is expected to feature a twisting angle between 10 and 60 degrees. The spectroscopic effects of the alkyl substituents on the PSB11 spectroscopic properties have also been investigated. It is found that they have a not negligible stabilizing effect on the S1-S0 energy gap (and, thus, cause a red shift of the absorption maximum) only when the double bond of the beta-ionone ring conjugates significantly with the rest of the conjugated chain.

  14. Mimicking Trimeric Interactions in the Aromatic Side Chains of the Proteins: a Gas Phase Study of INDOLE...(PYRROLE)_2 Heterotrimer

    NASA Astrophysics Data System (ADS)

    Das, Aloke; Kumar, Sumit

    2012-06-01

    Aromatic trimeric interactions are extremely important in the stabilization of the specific structures of the proteins as well as protein-protein, and protein-ligand interactions. Here I will present a direct evidence of the observation of a cyclic asymmetric structure of indole...(pyrrole)_2 trimer bound by three N-H...π hydrogen bonding interactions in a supersonic jet. The experiment has been performed by using resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques. Density functional theory (DFT) calculations nicely corroborate the experimental results showing one weakly allowed IR-active band due to symmetric stretch of the N-H bonds and two strongly allowed IR-active bands due to two types of asymmetric stretches of the N-H bonds in the trimer. The most significant finding of the present investigation is that there is a direct IR spectral signature for the determination of the geometry of a trimer if it has a cyclic asymmetric structure.

  15. Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase.

    PubMed Central

    Gao, J; Wu, Q; Carbeck, J; Lei, Q P; Smith, R D; Whitesides, G M

    1999-01-01

    This paper describes the use of electrospray ionization-Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic anhydrase II (CAII, EC 4.2.1.1) and benzenesulfonamide inhibitors in the gas phase. Sustained off-resonance irradiation collision-induced dissociation (SORI-CID) was used to determine the energetics of dissociation of these CAII-sulfonamide complexes in the gas phase. When two molecules of a benzenesulfonamide (1) were bound simultaneously to one molecule of CAII, one of them was found to exhibit significantly weaker binding (DeltaE50 = 0.4 V, where E50 is defined as the amplitude of sustained off-resonance irradiation when 50% of the protein-ligand complexes are dissociated). In solution, the benzenesulfonamide group coordinates as an anion to a Zn(II) ion bound at the active site of the enzyme. The gas phase stability of the complex with the weakly bound inhibitor was the same as that of the inhibitor complexed with apoCAII (i.e., CAII with the Zn(II) ion removed from the binding site). These results indicate that specific interactions between the sulfonamide group on the inhibitor and the Zn(II) ion on CAII were preserved in the gas phase. Experiments also showed a higher gas phase stability for the complex of para-NO2-benzenesulfonamide-CAII than that for ortho-NO2-benzenesulfonamide-CAII complex. This result further suggests that steric interactions of the inhibitors with the binding pocket of CAII parallel those in solution. Overall, these results are consistent with the hypothesis that CAII retains, at least partially, the structure of its binding pocket in the gas phase on the time scale (seconds to minutes) of the ESI-FTICR measurements. PMID:10354450

  16. The gas-phase molecular structure of 1,1-diethynylsilacyclobutane as determined by means of electron diffraction and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Dakkouri, Marwan; Grosser, Martin

    2002-06-01

    As a continuation of our systematic investigation of the effect of substituents on the ring geometry and dynamics in silacyclobutanes and in order to explore the role of the silicon atom as a mediator for electronic interactions between the attached fragments, we studied the molecular structure of 1,1-diethynylsilacyclobutane (DESCB) by means of gas-phase electron diffraction and ab initio calculations. The structural refinement of the electron diffraction data yielded the following bond lengths (ra) and bond angles (uncertainties are 3σ): r(Si-C)=1.874(2) Å,r(Si-Ctbnd)=1.817(1) Å,r(-Ctbnd C-)=1.209(1)Å,r(C-C)=1.563(2)Å, ∠(C-Si-C)=79.2(6)°, ∠(tbnd C-Si-Ctbnd)=106.5(6)°. The geminal Si-Ctbnd C moieties were found to be bent outwards by 3.1(15)° and the puckering angle was determined to be 30.0(15)°. The evidently short Si-Ctbnd bond length, which was also reproduced by the ab initio calculations, could be rationalized as being the consequence of the electronic interaction between the outer π charges of the triple bond and the 3pπ orbitals at the silicon atom. It is also likely that the conjugation of the geminal ethynyl groups leads to an enhancement of this bond contraction. Electrostatic interactions and the subsequent reduction of the covalent radius of the silicon atom may also contribute to this bond shortening. It has been found that the endocyclic Si-C bond length fits nicely within a scheme describing a monotonous decrease of the Si-C bond length with the increase of the electronegativity of the substituent in various geminally substituted silacyclobutanes. A series of related silacyclobutanes and acyclic diethynylsilanes have been studied by applying various ab initio methods and their optimized structures were compared to the structure of DESCB. Among these compounds are 1,1-dicyanosilacyclobutane (DCYSCB), which is isoelectronic to DESCB, 1,1-diethynylcyclobutane (DECB) which is isovalent to DESCB, monoethynylsilacyclobutane (MESCB) and

  17. Liquid phase separation of proteins based on electrophoretic effects in an electrospray setup during sample introduction into a gas-phase electrophoretic mobility molecular analyzer (CE-GEMMA/CE-ES-DMA).

    PubMed

    Weiss, Victor U; Kerul, Lukas; Kallinger, Peter; Szymanski, Wladyslaw W; Marchetti-Deschmann, Martina; Allmaier, Günter

    2014-09-02

    Nanoparticle characterization is gaining importance in food technology, biotechnology, medicine, and pharmaceutical industry. An instrument to determine particle electrophoretic mobility (EM) diameters in the single-digit to double-digit nanometer range receiving increased attention is the gas-phase electrophoretic mobility molecular analyzer (GEMMA) separating electrophoretically single charged analytes in the gas-phase at ambient pressure. A fused-silica capillary is used for analyte transfer to the gas-phase by means of a nano electrospray (ES) unit. The potential of this capillary to separate analytes electrophoretically in the liquid phase due to different mobilities is, at measurement conditions recommended by the manufacturer, eliminated due to elevated pressure applied for sample introduction. Measurements are carried out upon constant feeding of analytes to the system. Under these conditions, aggregate formation is observed for samples including high amounts of non-volatile components or complex samples. This makes the EM determination of individual species sometimes difficult, if not impossible. With the current study we demonstrate that liquid phase electrophoretic separation of proteins (as exemplary analytes) occurs in the capillary (capillary zone electrophoresis, CE) of the nano ES unit of the GEMMA. This finding was consecutively applied for on-line desalting allowing EM diameter determination of analytes despite a high salt concentration within samples. The present study is to our knowledge the first report on the use of the GEMMA to determine EM diameters of analytes solubilized in the ES incompatible electrolyte solutions by the intended use of electrophoresis (in the liquid phase) during sample delivery. Results demonstrate the proof of concept of such an approach and additionally illustrate the high potential of a future on-line coupling of a capillary electrophoresis to a GEMMA instrument. Copyright © 2014 The Authors. Published by Elsevier B

  18. Development of a new Structure-Activity Relationship (SAR) for gas-phase reactions of NO3 radicals with organic compounds

    NASA Astrophysics Data System (ADS)

    Kerdouci, J.; Picquet-Varrault, B.; Doussin, J.

    2010-12-01

    kinetic database on NO3-oxidation rate constants. This allowed us to develop a new SAR for the gas-phase reactions of NO3 with organic compounds which is based exclusively on correlations between the molecular structures and the rate constants. This new SAR is based on experimental rate constants of 150 molecules and has been developed for alkanes, alkenes (simple and cyclic alkenes, dienes and terpenes) and saturated and unsaturated oxygenated species (alcohols, carbonyls, ethers and esters). Results and performances of this SAR will be discussed here. References [1] Geyer, A., et al., J. Geophys. Res., 108 (2003), 4368. [2] Grosjean, D. and E.L. Williams, Atmospheric Environment. Part A. General Topics, 26 (1992), 1395-1405. [3] Pfrang, C., et al., Atmospheric Environment, 40 (2006), 1180-1186. [4] Kwok, E.S.C. and R. Atkinson, Atmospheric Environment, 29 (1995), 1685-1695. [5] Jenkin, M.E., S.M. Saunders, and M.J. Pilling, Atmospheric Environment, 31(1997), 81-104. [6] Aumont, B., S. Szopa, and S. Madronich, Atmospheric Chemistry and Physics, 5 (2005), 2497-2517.

  19. Density functional theory investigations on the structure and dissolution mechanisms for cellobiose and xylan in an ionic liquid: gas phase and cluster calculations.

    PubMed

    Payal, Rajdeep Singh; Bharath, R; Periyasamy, Ganga; Balasubramanian, S

    2012-01-19

    Density functional theory (DFT) calculations have been carried out for cellobiose and xylan chosen as models for cellulose and hemicellulose, respectively, in gas phase, implicit and explicit solvent (water, methanol, and the ionic liquid, 1,3-dimethylimidazolium acetate) media using plane wave and atom centered basis set approaches in order to find out lowest energy conformers and configurations. Geometry, vibrational properties, and (1)H and (13)C NMR chemical shift values have been discussed under all three conditions. Calculations predict that inter- and intramolecular hydrogen bonding play an important role in the dissolution processes. In the gas phase and in implicit solvent, the anti-anti conformer of cellobiose and the anti-syn conformer of xylan are the most stable due to the formation of a large number of intramolecular hydrogen bonds. However, in the cluster calculations containing ion pairs of the ionic liquid (IL) surrounding the cellulosic units, the anti-syn conformer of cellobiose is more stable as intramolecular hydrogen bonds are substituted by intermolecular ones formed with the ions of the IL. The complexes of cellobiose (or of xylan) with the ions of the ionic liquid are stable with large negative binding energies ranging between -21 and -55 kcal mol(-1). The predicted (1)H NMR values of the lowest energy cellobiose conformers are in good agreement with the experimental value. Xylan binds stronger with the IL than cellobiose does by 20 kcal mol(-1). Furthermore, the two pentose rings in xylan are rotated by 60° to each other in contrast to their coplanarity in cellobiose, which can explain the higher solubility and the amorphous nature of hemicellulose in ionic liquids. The fewer number of hydroxyl groups in xylan (relative to cellobiose) does not affect the number of cations present in its first solvation shell while the number of anions is reduced.

  20. Rate processes in gas phase

    NASA Technical Reports Server (NTRS)

    Hansen, C. F.

    1983-01-01

    Reaction-rate theory and experiment are given a critical review from the engineers' point of view. Rates of heavy-particle, collision-induced reaction in gas phase are formulated in terms of the cross sections and activation energies for reaction. The effect of cross section function shape and of excited state contributions to reaction both cause the slope of Arrhenius plots to differ from the true activation energy, except at low temperature. The master equations for chemically reacting gases are introduced, and dissociation and ionization reactions are shown to proceed primarily from excited states about kT from the dissociation or ionization limit. Collision-induced vibration, vibration-rotation, and pure rotation transitions are treated, including three-dimensional effects and conservation of energy, which have usually been ignored. The quantum theory of transitions at potential surface crossing is derived, and results are found to be in fair agreement with experiment in spite of some questionable approximations involved.

  1. Gas-Phase Chemistry of Multiply Charged Bioions in Analytical Mass Spectrometry

    PubMed Central

    Huang, Teng-Yi; McLuckey, Scott A.

    2011-01-01

    Ion chemistry has long played an important role in molecular mass spectrometry (MS), as it is central to the use of MS as a structural characterization tool. With the advent of ionization methods capable of producing gaseous ions from large biomolecules, the chemistry of gaseous bioions has become a highly active area of research. Gas-phase biomolecule-ion reactions are usually driven by interactions with neutral molecules, photons, electrons, ions, or surfaces. Ion dissociation or transformation into different ion types can be achieved. The types of reaction products observed depend on the characteristics of the ions, the transformation methods, and the time frame of observation. This review focuses on the gas-phase chemistries of ions derived from the electrospray ionization of peptides, proteins, and oligonucleotides, with particular emphasis on their utility in bioanalysis. Various ion-transformation strategies, which further facilitate structural interrogation by converting ions from one type to another, are also summarized. PMID:20636047

  2. Gas phase kinetics during normal combustion

    NASA Technical Reports Server (NTRS)

    Price, C. F.; Boggs, T. L.; Eisel, J. L.; Atwood, A. I.; Zurn, D. E.

    1980-01-01

    The role of gas phase kinetics during combustion was explored in the steady state modeling efforts and in the analysis of ignition phenomena. In both cases it was shown that the combustion characteristics of some high energy ingredients and propellants are strongly affected, if not dictated, by the gas phase reactions which take place.

  3. Structure and energetics of gas phase halogen-bonding in mono-, bi-, and tri-dentate anion receptors as studied by BIRD.

    PubMed

    Gillis, Elizabeth A L; Demireva, Maria; Sarwar, Mohammed G; Chudzinski, Michael G; Taylor, Mark S; Williams, Evan R; Fridgen, Travis D

    2013-05-28

    Complexes of mono-, bi- (RB), and tridentate (RT) receptors with a range of anions (Cl(-), Br(-), I(-), NO3(-), H2PO4(-), HSO4(-), and tosylate (TsO(-))) have been studied in the gas phase by both experimental and theoretical methods. Temperature dependent blackbody infrared radiative dissociation (BIRD) experiments were performed on complexes of C8F17I with Br(-) and I(-), RB with I(-), NO3(-), HSO4(-), H2PO4(-), and TsO(-), and RT with I(-), HSO4(-) and TsO(-) and the observed Arrhenius parameters are reported here. Master equation modeling of the BIRD kinetics data was carried out to determine threshold dissociation energies. Geometry optimizations and thermochemistry calculations were performed using the B3LYP/6-31+G(d,p) level of theory. Additional single point energies were calculated using MP2/6-311++G(2d,p). Results were examined in terms of the binding order of various anions as well as the added binding strength from additional halogen bonding (XB) interactions. The relative binding energies of ions were generally consistent with the ordering previously reported from solution phase experiments; however, the relatively strong binding of H2PO4(-) to the bidentate receptor contrasted the solution phase observation of oxoanions having weaker interactions when compared to halides. An increase in the energy required to remove the same anion from the tridentate receptor when compared to the bidentate and monodentate receptors is explained as being due to the increase in halogen bonding interactions. The possibility of mixed halogen and hydrogen bonded complexes were considered.

  4. Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein.

    PubMed

    Rocha-Rinza, Tomás; Sneskov, Kristian; Christiansen, Ove; Ryde, Ulf; Kongsted, Jacob

    2011-01-28

    Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA(-)) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More specifically, it is found that the change in the excitation energy as a consequence of the disruption of the planarity of pCA(-) inside PYP is nearly canceled out by the shift induced by the intermolecular interactions of the chromophore and the protein as a whole. These results provide important insights about the primary absorption and the tuning of the chromophore by the protein environment in PYP.

  5. The Dipeptide Ala-Gly in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Bermúdez, Celina; Varela, Marcelino; Cabezas, Carlos; Peña, Isabel; Alonso, José L.

    2014-06-01

    The dipeptide Ala-Gly has been examined in gas phase by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy in the frequency region 3-12 GHz. Three rotamers have been detected in the supersonic expansion. The quadrupole hyperfine structure of two 14N (I=1) nuclei has been totally resolved allowing the conclusive identification of one conformer.

  6. Quantifying the stabilizing effects of protein–ligand interactions in the gas phase

    PubMed Central

    Allison, Timothy M.; Reading, Eamonn; Liko, Idlir; Baldwin, Andrew J.; Laganowsky, Arthur; Robinson, Carol V.

    2015-01-01

    The effects of protein–ligand interactions on protein stability are typically monitored by a number of established solution-phase assays. Few translate readily to membrane proteins. We have developed an ion-mobility mass spectrometry approach, which discerns ligand binding to both soluble and membrane proteins directly via both changes in mass and ion mobility, and assesses the effects of these interactions on protein stability through measuring resistance to unfolding. Protein unfolding is induced through collisional activation, which causes changes in protein structure and consequently gas-phase mobility. This enables detailed characterization of the ligand-binding effects on the protein with unprecedented sensitivity. Here we describe the method and software required to extract from ion mobility data the parameters that enable a quantitative analysis of individual binding events. This methodology holds great promise for investigating biologically significant interactions between membrane proteins and both drugs and lipids that are recalcitrant to characterization by other means. PMID:26440106

  7. Laserspray Ionization, a New Atmospheric Pressure MALDI Method for Producing Highly Charged Gas-phase Ions of Peptides and Proteins Directly from Solid Solutions*

    PubMed Central

    Trimpin, Sarah; Inutan, Ellen D.; Herath, Thushani N.; McEwen, Charles N.

    2010-01-01

    The first example of a matrix-assisted laser desorption/ionization (MALDI) process producing multiply charged mass spectra nearly identical to those observed with electrospray ionization (ESI) is presented. MALDI is noted for its ability to produce singly charged ions, but in the experiments described here multiply charged ions are produced by laser ablation of analyte incorporated into a common MALDI matrix, 2,5-dihydroxybenzoic acid, using standard solvent-based sample preparation protocols. Laser ablation is known to produce matrix clusters in MALDI provided a threshold energy is achieved. We propose that these clusters (liquid droplets) are highly charged, and under conditions that produce sufficient matrix evaporation, ions are field-evaporated from the droplets similarly to ESI. Because of the multiple charging, advanced mass spectrometers with limited mass-to-charge range can be used for protein characterization. Thus, using an Orbitrap mass spectrometer, low femtomole quantities of proteins produce full-range mass spectra at 100,000 mass resolution with <5-ppm mass accuracy and with 1-s acquisition. Furthermore, the first example of protein fragmentation using electron transfer dissociation with MALDI is presented. PMID:19955086

  8. Laserspray ionization, a new atmospheric pressure MALDI method for producing highly charged gas-phase ions of peptides and proteins directly from solid solutions.

    PubMed

    Trimpin, Sarah; Inutan, Ellen D; Herath, Thushani N; McEwen, Charles N

    2010-02-01

    The first example of a matrix-assisted laser desorption/ionization (MALDI) process producing multiply charged mass spectra nearly identical to those observed with electrospray ionization (ESI) is presented. MALDI is noted for its ability to produce singly charged ions, but in the experiments described here multiply charged ions are produced by laser ablation of analyte incorporated into a common MALDI matrix, 2,5-dihydroxybenzoic acid, using standard solvent-based sample preparation protocols. Laser ablation is known to produce matrix clusters in MALDI provided a threshold energy is achieved. We propose that these clusters (liquid droplets) are highly charged, and under conditions that produce sufficient matrix evaporation, ions are field-evaporated from the droplets similarly to ESI. Because of the multiple charging, advanced mass spectrometers with limited mass-to-charge range can be used for protein characterization. Thus, using an Orbitrap mass spectrometer, low femtomole quantities of proteins produce full-range mass spectra at 100,000 mass resolution with <5-ppm mass accuracy and with 1-s acquisition. Furthermore, the first example of protein fragmentation using electron transfer dissociation with MALDI is presented.

  9. Negative ion gas-phase chemistry of arenes.

    PubMed

    Danikiewicz, Witold; Zimnicka, Magdalena

    2016-01-01

    Reactions of aromatic and heteroaromatic compounds involving anions are of great importance in organic synthesis. Some of these reactions have been studied in the gas phase and are occasionally mentioned in reviews devoted to gas-phase negative ion chemistry, but no reviews exist that collect all existing information about these reactions. This work is intended to fill this gap. In the first part of this review, methods for generating arene anions in the gas phase and studying their physicochemical properties and fragmentation reactions are presented. The main topics in this part are as follows: processes in which gas-phase arene anions are formed, measurements and calculations of the proton affinities of arene anions, proton exchange reactions, and fragmentation processes of substituted arene anions, especially phenide ions. The second part is devoted to gas-phase reactions of arene anions. The most important of these are reactions with electrophiles such as carbonyl compounds and α,β-unsaturated carbonyl and related compounds (Michael acceptors). Other reactions including oxidation of arene anions and halogenophilic reactions are also presented. In the last part of the review, reactions of electrophilic arenes with nucleophiles are discussed. The best known of these is the aromatic nucleophilic substitution (SN Ar) reaction; however, other processes that lead to the substitution of a hydrogen atom in the aromatic ring are also very important. Aromatic substrates in these reactions are usually but not always nitroarenes bearing other substituents in the ring. The first step in these reactions is the formation of an anionic σ-adduct, which, depending on the substituents in the aromatic ring and the structure of the attacking nucleophile, is either an intermediate or a transition state in the reaction path. In the present review, we attempted to collect the results of both experimental and computational studies of the aforementioned reactions conducted since the

  10. Gas-phase Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scrambling

    PubMed Central

    Jia, Chenxi; Wu, Zhe; Lietz, Christopher B.; Liang, Zhidan; Cui, Qiang; Li, Lingjun

    2014-01-01

    Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M→cb) pathway is less energetically (or kinetically) favored. PMID:24313304

  11. Gas-phase ion isomer analysis reveals the mechanism of peptide sequence scrambling.

    PubMed

    Jia, Chenxi; Wu, Zhe; Lietz, Christopher B; Liang, Zhidan; Cui, Qiang; Li, Lingjun

    2014-03-18

    Peptide sequence scrambling during mass spectrometry-based gas-phase fragmentation analysis causes misidentification of peptides and proteins. Thus, there is a need to develop an efficient approach to probing the gas-phase fragment ion isomers related to sequence scrambling and the underlying fragmentation mechanism, which will facilitate the development of bioinformatics algorithm for proteomics research. Herein, we report on the first use of electron transfer dissociation (ETD)-produced diagnostic fragment ions to probe the components of gas-phase peptide fragment ion isomers. In combination with ion mobility spectrometry (IMS) and formaldehyde labeling, this novel strategy enables qualitative and quantitative analysis of b-type fragment ion isomers. ETD fragmentation produced diagnostic fragment ions indicative of the precursor ion isomer components, and subsequent IMS analysis of b ion isomers provided their quantitative and structural information. The isomer components of three representative b ions (b9, b10, and b33 from three different peptides) were accurately profiled by this method. IMS analysis of the b9 ion isomers exhibited dynamic conversion among these structures. Furthermore, molecular dynamics simulation predicted theoretical drift time values, which were in good agreement with experimentally measured values. Our results strongly support the mechanism of peptide sequence scrambling via b ion cyclization, and provide the first experimental evidence to support that the conversion from molecular precursor ion to cyclic b ion (M → (c)b) pathway is less energetically (or kinetically) favored.

  12. Correlation of the structural information obtained for europium-chelate ensembles from gas-phase photoluminescence and ion-mobility spectroscopy with density-functional computations and ligand-field theory.

    PubMed

    Greisch, Jean-François; Chmela, Jiří; Harding, Michael E; Wunderlich, Dirk; Schäfer, Bernhard; Ruben, Mario; Klopper, Wim; Schooss, Detlef; Kappes, Manfred M

    2017-02-22

    We report a combined investigation of europium(iii)9-oxo-phenalen-1-one (PLN) coordination complexes, [Eu(PLN)4AE](+) with AE = Mg, Ca, and Sr, using gas-phase photoluminescence, trapped ion-mobility spectrometry and density-functional computations. In order to sort out the structural impact of the alkali earth dications on the photoluminescence spectra, the experimental data are compared to the predicted ligand-field splittings as well as to the collision cross-sections for different isomers of [Eu(PLN)4AE](+). The best fitting interpretation is that one isomer family predominantly contributes to the recorded luminescence. The present work demonstrates the complexity of the coordination patterns of multicenter lanthanoid chelates involved in dynamical equilibria and the pertinence of using isolation techniques to elucidate their photophysical properties.

  13. Hydrated metal ions in the gas phase.

    PubMed

    Beyer, Martin K

    2007-01-01

    Studying metal ion solvation, especially hydration, in the gas phase has developed into a field that is dominated by a tight interaction between experiment and theory. Since the studied species carry charge, mass spectrometry is an indispensable tool in all experiments. Whereas gas-phase coordination chemistry and reactions of bare metal ions are reasonably well understood, systems containing a larger number of solvent molecules are still difficult to understand. This review focuses on the rich chemistry of hydrated metal ions in the gas phase, covering coordination chemistry, charge separation in multiply charged systems, as well as intracluster and ion-molecule reactions. Key ideas of metal ion solvation in the gas phase are illustrated with rare-gas solvated metal ions.

  14. Intramolecular photoelectron diffraction in the gas phase

    NASA Astrophysics Data System (ADS)

    Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Ayuso, D.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

    2013-09-01

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  15. Intramolecular photoelectron diffraction in the gas phase.

    PubMed

    Ueda, K; Miron, C; Plésiat, E; Argenti, L; Patanen, M; Kooser, K; Ayuso, D; Mondal, S; Kimura, M; Sakai, K; Travnikova, O; Palacios, A; Decleva, P; Kukk, E; Martín, F

    2013-09-28

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  16. Gas phase hydration of organic ions.

    PubMed

    Momoh, Paul O; El-Shall, M Samy

    2008-08-28

    In this work, we study the hydration phenomenon on a molecular level in the gas phase where a selected number of water molecules can interact with the organic ion of interest. The stepwise binding energies (DeltaH degrees (n-1,n)) of 1-7 water molecules to the phenyl acetylene cation are determined by equilibrium measurements using an ion mobility drift cell. The stepwise hydration energies DeltaH degrees (n-1,n) are nearly constant at 39.7 +/- 6.3 kJ mol(-1) from n = 1 to 7. The entropy change is larger in the n = 7 step, suggesting cyclic or cage-like water structures. No water addition is observed on the ionized phenyl acetylene trimer consistent with cyclization of the trimer ion to form triphenyl benzene cations C(24)H(18) (+) which are expected to interact weakly with the water molecules due to steric interactions and the delocalization of the charge on the large organic ion. The work demonstrates that hydration studies of organic ions can provide structural information on the organic ions.

  17. Scopine Isolated in the Gas Phase.

    PubMed

    Écija, Patricia; Vallejo-López, Montserrat; Uriarte, Iciar; Basterretxea, Francisco J; Lesarri, Alberto; Fernández, José A; Cocinero, Emilio J

    2016-10-05

    The rotational spectrum of the tropane alkaloid scopine is detected by Fourier transform microwave spectroscopy in a pulsed supersonic jet. A nonconventional method for bringing the molecules intact into the gas phase is used in which scopine syrup is mixed with glycine powder and the solid mixture is vaporized with an ultrafast UV laser beam. Laser vaporization prevents the easy isomerization to scopoline previously observed with conventional heating methods. A single conformer is unambiguously observed in the supersonic jet and corresponds to the energetically most stable species according to quantum chemical calculations. Rotational and centrifugal distortion constants are accurately determined. The spectrum shows fine and hyperfine structure due to the hindered rotation of the methyl group and the presence of a quadrupolar nucleus ((14) N), respectively. This additional information allows the angle of N-methyl inversion between the N-CH3 bond and the bicyclic C-N-C plane to be determined (131.8-137.8°), as well as the internal rotation barrier of the methyl group (6.235(1) kJ mol(-1) ). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Solvation-induced σ-complex structure formation in the gas phase: a revisit to the infrared spectroscopy of [C6H6-(CH3OH)2]+.

    PubMed

    Mizuse, Kenta; Suzuki, Yuta; Mikami, Naohiko; Fujii, Asuka

    2011-10-20

    Structures of the [C(6)H(6)-(CH(3)OH)(2)](+) cluster cation are investigated with infrared (IR) spectroscopy. While the noncovalent type structure has been confirmed for the n = 1 cluster of [C(6)H(6)-(CH(3)OH)(n)](+), only contradictory interpretations have been given for the spectra of n = 2, in which significant changes have been observed with the Ar tagging. In the present study, we revisit IR spectroscopy of the n = 2 cluster from the viewpoint of the σ-complex structure, which includes a covalent bond formation between the benzene and methanol moieties. The observed spectral range is extended to the lower-frequency region, and the spectrum is measured with and without Ar and N(2) tagging. A strongly hydrogen-bonded OH stretch band, which is characteristic to the σ-complex structure, is newly found with the tagging. The remarkable spectral changes with the tagging are interpreted by the competition between the σ-complex and noncovalent complex structures in the [C(6)H(6)-(CH(3)OH)(2)](+) system. This result shows that the microsolvation only with one methanol molecule can induce the σ-complex structure formation.

  19. A Uranyl Peroxide Dimer in the Gas Phase.

    PubMed

    Dau, Phuong D; Dau, Phuong V; Rao, Linfeng; Kovács, Attila; Gibson, John K

    2017-04-03

    The gas-phase uranyl peroxide dimer, [(UO2)2(O2)(L)2](2+) where L = 2,2'-trifluoroethylazanediyl)bis(N,N'-dimethylacetamide), was synthesized by electrospray ionization of a solution of UO2(2+) and L. Collision-induced dissociation of this dimer resulted in endothermic O atom elimination to give [(UO2)2(O)(L)2](2+), which was found to spontaneously react with water via exothermic hydrolytic chemisorption to yield [(UO2)2(OH)2(L)2](2+). Density functional theory computations of the energies for the gas-phase reactions are in accord with observations. The structures of the observed uranyl dimer were computed, with that of the peroxide of particular interest, as a basis to evaluate the formation of condensed phase uranyl peroxides with bent structures. The computed dihedral angle in [(UO2)2(O2)(L)2](2+) is 145°, indicating a substantial deviation from the planar structure with a dihedral angle of 180°. Energies needed to induce bending in the most elementary gas-phase uranyl peroxide complex, [(UO2)2(O2)](2+), were computed. It was found that bending from the lowest-energy planar structure to dihedral angles up to 140° required energies of <10 kJ/mol. The gas-phase results demonstrate the inherent stability of the uranyl peroxide moiety and support the notion that the uranyl-peroxide-uranyl structural unit is intrinsically planar, with only minor energy perturbations needed to form the bent structures found in studtite and uranyl peroxide nanostructures.

  20. Structure and mechanism of the formation of core–shell nanoparticles obtained through a one-step gas-phase synthesis by electron beam evaporation

    PubMed Central

    Bardakhanov, Sergey P; Schreiber, Makoto; Bazarova, Dashima G; Romanov, Nikolai A; Baldanov, Boris B; Radnaev, Bair R; Syzrantsev, Viacheslav V

    2015-01-01

    Summary The structure of core–shell Cu@silica and Ag@Si nanoparticles obtained in one-step through evaporation of elemental precursors by a high-powered electron beam are investigated. The structure of the core and shell of the particles are investigated in order to elucidate their mechanisms of formation and factors affecting the synthesis. It is proposed that the formation of Cu@silica particles is mainly driven by surface tension differences between Cu and Si while the formation of Ag@Si particles is mainly driven by differences in the vapour concentration of the two components. PMID:25977857

  1. Structure and mechanism of the formation of core-shell nanoparticles obtained through a one-step gas-phase synthesis by electron beam evaporation.

    PubMed

    Nomoev, Andrey V; Bardakhanov, Sergey P; Schreiber, Makoto; Bazarova, Dashima G; Romanov, Nikolai A; Baldanov, Boris B; Radnaev, Bair R; Syzrantsev, Viacheslav V

    2015-01-01

    The structure of core-shell Cu@silica and Ag@Si nanoparticles obtained in one-step through evaporation of elemental precursors by a high-powered electron beam are investigated. The structure of the core and shell of the particles are investigated in order to elucidate their mechanisms of formation and factors affecting the synthesis. It is proposed that the formation of Cu@silica particles is mainly driven by surface tension differences between Cu and Si while the formation of Ag@Si particles is mainly driven by differences in the vapour concentration of the two components.

  2. Retrospective hit-deconvolution of mixed metal oxides: spotting structure-property-relationships in gas phase oxidation catalysis through high throughput experimentation.

    PubMed

    Schunk, Stephan Andreas; Sundermann, Andreas; Hibst, Hartmut

    2007-01-01

    Complex multi-element lead structures of mixed metal oxides that may be identified as hits during high throughput experimentation (HTE) campaigns, can be deconvoluted retrospectively on the basis of simple binary and ternary oxides as illustrated in the current example of a hit found in an ammoxidation reaction. On the basis of the performance of the simple binary and ternary mixed metal oxides structure property relationships can be established, that give insight into the roles of the different components of the complex mixed metal oxides and may also help in establishing a reaction mechanism and converting the hit into a development candidate.

  3. Computational study of gas-phase molecular structure and substitution effects in para-substituted nickelabenzenes ( p-XC5H4)Ni(CO)2F

    NASA Astrophysics Data System (ADS)

    Hakimioun, Amir Hossein; Makkipour, Peymaneh; Ghiasi, Hossein; Pasdar, Hoda

    2015-09-01

    The structure and properties of nickelabenzene complex were examined by the Modified Perdew-Wang Exchange and Correlation method (mpw1pw91). The para-substitutions effect on the structure, frontier orbital energies, aromaticity and electronic spectra has been studied. Nucleus independent chemical shift (NICS) values show that these species are aromatic. Time dependent density functional theory (TD-DFT) was used to calculate the energy, oscillator strength and absorption maxima wavelength (λmax) of various electronic transitions and their nature within molecules.

  4. Sugars in the gas phase

    NASA Astrophysics Data System (ADS)

    Jockusch, Rebecca

    2006-03-01

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition is immense. Characterizing the three-dimensional structures of carbohydrates and glycoconjugates and their interactions with other molecules, particularly the ubiquitous solvent, water, are key starting points on the road towards the understanding of these processes. A new strategy, combining electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is being exploited to characterize carbohydrate conformations and hydrated structures, the hydrogen-bonded networks they support (or which support them) and the specificity of their interactions with other molecules. The spectral features of monosaccharide residues can be used to refine the assignment of larger, oligosaccharide structures - a supplementary `building-block' approach to the study of complex structures based upon an `alphabet' of established IR spectral signatures of different conformations of the monosaccharide units - when their spectroscopic patterns are retained. When their patterns are altered the changes may be understood by analyzing the modification of the hydrogen-bonded networks, eg., the retention (or disruption) of the secondary structural motifs generated by intra-residue hydrogen-bonding. Feedback from the increasing body of experimental data will also help to inform and guide future theoretical conformational searches.

  5. Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S1 states.

    PubMed

    Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Cabellos, José Luis; Yi, John T; Pratt, David W; Schmitt, Michael; Merino, Gabriel; Álvarez-Valtierra, Leonardo

    2015-09-07

    The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, but it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent   -OH and   -OCH3 groups plays a major role in these dynamics.

  6. Intramolecular structure and dynamics of mequinol and guaiacol in the gas phase: Rotationally resolved electronic spectra of their S{sub 1} states

    SciTech Connect

    Ruiz-Santoyo, José Arturo; Rodríguez-Matus, Marcela; Álvarez-Valtierra, Leonardo E-mail: gmerino@mda.cinvestav.mx; Cabellos, José Luis; Merino, Gabriel E-mail: gmerino@mda.cinvestav.mx; Yi, John T.; Pratt, David W.; Schmitt, Michael

    2015-09-07

    The molecular structures of guaiacol (2-methoxyphenol) and mequinol (4-methoxyphenol) have been studied using high resolution electronic spectroscopy in a molecular beam and contrasted with ab initio computations. Mequinol exhibits two low frequency bands that have been assigned to electronic origins of two possible conformers of the molecule, trans and cis. Guaiacol also shows low frequency bands, but in this case, the bands have been assigned to the electronic origin and vibrational modes of a single conformer of the isolated molecule. A detailed study of these bands indicates that guaiacol has a vibrationally averaged planar structure in the ground state, but it is distorted along both in-plane and out-of-plane coordinates in the first electronically excited state. An intramolecular hydrogen bond involving the adjacent   –OH and   –OCH{sub 3} groups plays a major role in these dynamics.

  7. Measuring Complementary Electronic Structure Properties of both Deposited and Gas Phase Clusters using STM, UPS, and PES: Size-Selected Clusters on Surfaces

    SciTech Connect

    Bowen, Kit H.

    2014-03-05

    In this project, we studied size-selected cluster interactions with surfaces, with other clusters on surfaces, and with external stimuli. These studies focused on mobility as a function of cluster size, surface morphologies as a function of composition and coverage, ion-induced modification and reactivity of clusters as a function of composition, the structural evolution of cluster cuboids culminating in the characterization of theoretically-predicted “baby crystal” clusters, and unusual fractal pattern formation due to deposition.

  8. Observation of gas-phase anionic bismuth zintl ions

    SciTech Connect

    Farley, R.W.; Castleman, A.W. Jr. )

    1989-03-29

    The authors report in this communication the first observation of gas-phase anionic Zintl ions of bismuth. Laser-ionization time-of-flight mass spectra of mixed bismuth/alkali clusters produced by a gas aggregation source were investigated in their laboratory and found to exhibit maxima for clusters corresponding to reported Zintl ions. Bonding in homoatomic clusters is a topic of fundamental as well as practical importance. The electronic and geometric structure of metal clusters in particular is currently the subject of intense investigation among a great number of researchers. Magic numbers corresponding to particularly abundant gas-phase cluster ions are observed to depend on the identity of the metal or alloy and on the ionization conditions. Reasons for the exceptional stabilities of such magic numbers have been ascribed to preferred electronic and structural configurations for either the neutral or ionic species.

  9. Hydration of Gas-Phase Ions Formed by Electrospray Ionization

    PubMed Central

    Rodriguez-Cruz, Sandra E.; Klassen, John S.; Williams, Evan R.

    2005-01-01

    The hydration of gas-phase ions produced by electrospray ionization was investigated. Evidence that the hydrated ions are formed by two mechanisms is presented. First, solvent condensation during the expansion inside the electrospray source clearly occurs. Second, some solvent evaporation from more extensively solvated ions or droplets is apparent. To the extent that these highly solvated ions have solution-phase structures, then the final isolated gas-phase structure of the ion will be determined by the solvent evaporation process. This process was investigated for hydrated gramicidin S in a Fourier-transform mass spectrometer. Unimolecular dissociation rate constants of isolated gramicidin S ions with between 2 and 14 associated water molecules were measured. These rate constants increased from 16 to 230 s−1 with increasing hydration, with smaller values corresponding to magic numbers. PMID:10497808

  10. Synthesis, structure and gas-phase reactivity of the mixed silver hydride borohydride nanocluster [Ag3(μ3-H)(μ3-BH4)LPh3]BF4 (LPh = bis(diphenylphosphino)methane)

    NASA Astrophysics Data System (ADS)

    Zavras, Athanasios; Ariafard, Alireza; Khairallah, George N.; White, Jonathan M.; Mulder, Roger J.; Canty, Allan J.; O'Hair, Richard A. J.

    2015-10-01

    Borohydrides react with silver salts to give products that span multiple scales ranging from discrete mononuclear compounds through to silver nanoparticles and colloids. The cluster cations [Ag3(H)(BH4)L3]+ are observed upon electrospray ionization mass spectrometry of solutions containing sodium borohydride, silver(i) tetrafluoroborate and bis(dimethylphosphino)methane (LMe) or bis(diphenylphosphino)methane (LPh). By adding NaBH4 to an acetonitrile solution of AgBF4 and LPh, cooled to ca. -10 °C, we have been able to isolate the first mixed silver hydride borohydride nanocluster, [Ag3(μ3-H)(μ3-BH4)LPh3]BF4, and structurally characterise it via X-ray crystallography. Combined gas-phase experiments (LMe and LPh) and DFT calculations (LMe) reveal how loss of a ligand from the cationic complexes [Ag3(H)(BH4)L3]+ provides a change in geometry that facilitates subsequent loss of BH3 to produce the dihydride clusters, [Ag3(H)2Ln]+ (n = 1 and 2). Together with the results of previous studies (Girod et al., Chem. - Eur. J., 2014, 20, 16626), this provides a direct link between mixed silver hydride/borohydride nanoclusters, silver hydride nanoclusters, and silver nanoclusters.Borohydrides react with silver salts to give products that span multiple scales ranging from discrete mononuclear compounds through to silver nanoparticles and colloids. The cluster cations [Ag3(H)(BH4)L3]+ are observed upon electrospray ionization mass spectrometry of solutions containing sodium borohydride, silver(i) tetrafluoroborate and bis(dimethylphosphino)methane (LMe) or bis(diphenylphosphino)methane (LPh). By adding NaBH4 to an acetonitrile solution of AgBF4 and LPh, cooled to ca. -10 °C, we have been able to isolate the first mixed silver hydride borohydride nanocluster, [Ag3(μ3-H)(μ3-BH4)LPh3]BF4, and structurally characterise it via X-ray crystallography. Combined gas-phase experiments (LMe and LPh) and DFT calculations (LMe) reveal how loss of a ligand from the cationic complexes [Ag

  11. The conformation and molecular structure of a 2,3-diazacyclohepta-1,3-diene derivative. A gas-phase electron diffraction study of perfluoro-(1,4-dimethyl-2,3-diazacyclohepta-1,3-diene)

    NASA Astrophysics Data System (ADS)

    Beagley, B.; Pritchard, R. G.

    1985-08-01

    The molecular structure of the perfluoro-(1,4-dimethyl-2,8-diazacyclohepta-1,3-diene) molecule has been studied using gas-phase electron diffraction data collected on the Balzers KDG2 instrument at UMIST. The data are compatible with a C2 conformer with a torsion angle around the single NN bond of 52.4° ( gauche-diene geometry). The NNC(C 2) fragments are planar; each of these olefin planes also contains a CF bond of a -CF 3 group, with torsion angle NCCF = 0°. The ring conformation closely resembles that of the cyclohepta-1,3-diene ring in 1-hydroxy-2,3-dicarbomethyoxycyclohepta-1,3-diene, rather than that of the parent hydrocarbon. The principal structural parameters are NN = 1.349(19) Å, NC = 1.257(11) Å, CC(mean) = 1.536(3) Å, CF(mean) = 1.340(2) Å, ∠NNC = 121.9(7)°, ∠NCC(F 2) = 124.0(6)°, ∠NCC(F 3) = 117.8(7)°, ∠CCF(CF 3) = 111.1(3)°, ∠FCF(CF 2) = 107.8(6)°.

  12. Structures of membrane proteins

    PubMed Central

    Vinothkumar, Kutti R.; Henderson, Richard

    2010-01-01

    In reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class. PMID:20667175

  13. Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

    SciTech Connect

    Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S. E-mail: hochlaf@univ-mlv.fr; Linguerri, Roberto; Hochlaf, Majdi E-mail: hochlaf@univ-mlv.fr

    2013-11-07

    Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

  14. OH radical formation from the gas-phase reaction of ozone with terminal alkenes and the relationship between structure and mechanism

    SciTech Connect

    Paulson, S.E.; Chung, M.Y.; Hasson, A.S.

    1999-10-14

    The reactions of ozone with alkenes have been shown recently to lead to the direct production of OH radicals in quantities that vary from 7 to 100% depending on the structure of the alkene. OH radicals are the most important oxidizing species in the lower atmosphere, and the OH-alkene reaction is a large source of new OH radicals, important in urban and rural air during both day and night. Evidence for OH formation comes both from low-pressure direct measurements and from tracer experiments at high pressure. With the goal of measuring OH formation yields with good precision, a small-ratio relative rate technique was developed. This method uses small amounts of fast-reacting aromatics and aliphatic ethers to trace OH formation yields. Here, the authors report OH formation yields for a series of terminal alkenes reacting with ozone. Measured OH yields were 0.29 {+-} 0.05, 0.24 {+-} 0.05, 0.18 {+-} 0.04, and 0.10 {+-} 0.03 for 1-butene, 1-pentene, 1-hexene, and 1-octene, respectively. For the methyl-substituted terminal alkenes methyl propene and 2-methyl-1-butene, OH yields were 0.72 {+-} 0.12 and 0.67 {+-} 0.12, respectively. The results are discussed both in terms of their atmospheric implications and the relationship between structure and OH formation.

  15. Photoionization of cold gas phase coronene and its clusters: Autoionization resonances in monomer, dimer, and trimer and electronic structure of monomer cation

    SciTech Connect

    Bréchignac, Philippe Falvo, Cyril; Parneix, Pascal; Pino, Thomas; Pirali, Olivier; Garcia, Gustavo A.; Nahon, Laurent; Joblin, Christine; Kokkin, Damian; Bonnamy, Anthony; Mulas, Giacomo

    2014-10-28

    Polycyclic aromatic hydrocarbons (PAHs) are key species encountered in a large variety of environments such as the Interstellar Medium (ISM) and in combustion media. Their UV spectroscopy and photodynamics in neutral and cationic forms are important to investigate in order to learn about their structure, formation mechanisms, and reactivity. Here, we report an experimental photoelectron-photoion coincidence study of a prototypical PAH molecule, coronene, and its small clusters, in a molecular beam using the vacuum ultraviolet (VUV) photons provided by the SOLEIL synchrotron facility. Mass-selected high resolution threshold photoelectron (TPES) and total ion yield spectra were obtained and analyzed in detail. Intense series of autoionizing resonances have been characterized as originating from the monomer, dimer, and trimer neutral species, which may be used as spectral fingerprints for their detection in the ISM by VUV absorption spectroscopy. Finally, a full description of the electronic structure of the monomer cation was made and discussed in detail in relation to previous spectroscopic optical absorption data. Tentative vibrational assignments in the near-threshold TPES spectrum of the monomer have been made with the support of a theoretical approach based on density functional theory.

  16. Broadband Microwave Spectroscopy as a Tool to Study the Structures of Odorant Molecules and Weakly Bound Complexes in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

    2015-06-01

    The rotational spectrum of trans-cinnamaldehyde ((2E)-3-phenylprop-2-enal) has been obtained with chirped-pulse microwave spectroscopy in the frequency range of 2 - 8.5 GHz. The odorant molecule is the essential component in cinnamon oil and causes the characteristic smell. In the measured high-resolution spectrum, we were able to assign the rotational spectra of two conformers of trans-cinnamaldehyde as well as all singly 13C-substituted species of the lowest-energy conformer in natural abundance. Two different methods were used to determine the structure from the rotational constants, which will be compared within this contribution. In addition, the current progress of studying ether-alcohol complexes, aiming at an improved understanding of the interplay between hydrogen bonding and dispersion interaction, will be reported. Here, a special focus is placed on the complexes of diphenylether with small aliphatic alcohols.

  17. Alkali metal mediated resorcarene capsules: an ESI-FTICRMS study on gas-phase structure and cation binding of tetraethyl resorcarene and its per-methylated derivative.

    PubMed

    Mäkinen, Marko; Vainiotalo, Pirjo; Rissanen, Kari

    2002-07-01

    Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) with additional ab initio calculations were used to examine the alkali metal cation binding selectivity (i.e., molecular recognition) and host properties of tetraethyl resorcarene (1) and its per-methylated derivative (2). The significance of intramolecular hydrogen bonding for the crown conformation was demonstrated. The presence of intramolecular flip-flop hydrogen bonding in 1 was confirmed both with calculations and in ND3-exchange experiments. All the alkali metal cations formed host-guest complexes by docking inside the cavity of the host. Complexation with the larger cations, especially Cs+, was favored. All the alkali metal cations also formed dimeric resorcarene capsules with 1. The capsules were directly H-bonded species, with no linking solvent molecules. ND3-exchange experiments and molecular modeling revealed the significance of direct intermolecular H-bonding for the crown conformation of 1 and stability of the capsule structure.

  18. Water in the Gas Phase.

    DTIC Science & Technology

    1998-06-01

    SPECTROSCOPY OF PHENOL(WATER)1.12 CLUSTERS: STRUCTURES AND INTERMOLECULAR VIBRATIONS. » 40 Karl Kleinermanns, Christoph Janzen, Daniel Spangenberg, Wolfgang...Karl Kleinermanns, Christoph Janzen, Daniel Spangenberg, Wolfgang Roth, Michael Schmitt and Markus Gerhards Institut für Physikalische Chemie...Janzen Ch. P7, T19 Coy S. L. P30 Johnson M.A. T31 Crovisier J. T1 Jouvet C. P15 Daniel J. S. P2 Karpov G. V. P9 de Pujo P. P39 Kim J. T31

  19. X-Ray structural and gas phase studies of silver(i) perfluorinated carboxylate complexes with 2,2'-bipyridyl as potential precursors for chemical vapour deposition (CVD).

    PubMed

    Szłyk, Edward; Szczesny, Robert; Wojtczak, Andrzej

    2010-02-21

    [Ag(CF(3)COO)(bpy)] (), [Ag(2)(C(2)F(5)COO)(2)(bpy)] () and [Ag(2)(C(3)F(7)COO)(2)(bpy)] () were prepared and characterized by MS-EI, (1)H, (13)C NMR, variable-temperature IR (VT-IR) spectroscopy (solid sample and evolved volatile species) and thermal analysis. Single-crystal X-ray diffraction data revealed the polymeric structure for [Ag(2)(C(2)F(5)COO)(2)(bpy)] and [Ag(6)(C(3)F(7)COO)(6)(bpy)(4)], with bridging bpy ligand, whereas for [Ag(CF(3)COO)(bpy)] the dimeric system with monodentately linked carboxylate was noted. Mass spectra analysis of () over 30-300 degrees C indicates the presence of binuclear ions [(RCOO)Ag(2)](+) as a main volatile particles, which can be transported in CVD process. VT-IR studies of gases evolved during the thermal decomposition process, demonstrate the presence of fluorocarbon species and CO(2) as the most abundant molecules. Thermal analysis of () revealed a multi-stage decomposition mechanism resulting in Ag(0) formation below 290 degrees C. Compounds were tested for silver metal spray pyrolysis and obtained layers were characterized by scanning electron microscopy (SEM-EDX) and XRD.

  20. QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift.

    PubMed

    Monajjemi, M; Heshmata, M; Haeria, H H

    2006-01-01

    The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.

  1. Substituent effects on the gas-phase acidity of silane

    SciTech Connect

    Gordon, M.S.; Volk, D.E. ); Gano, D.R. )

    1989-12-20

    In a previous paper, the gas-phase acidities of XH{sub n} compounds (X = C, N, O, F, Si, P, S, Cl) were predicted with ab initio wave functions. At the MP4{sup 2} level of theory with extended basis sets acidities for these species were determined to be within 2 kcal/mol of experimental value. In the present work, with 6-31G(d) geometries and full MP4/MC-311++G{sup 6}(3df,2pd) energies, the effects of CH{sub 3}, NH{sub 2}, OH, F, SiH{sub 3}, PH{sub 2}, SH, and Cl on the gas-phase acidity of silane are examined. Only a few related calculations have been carried out. All calculations were performed with Gaussian86, and all structures were verified as minima by diagonalizing the analytically determined hessians. Only the valence electrons were correlated in the perturbation theory calculations.

  2. The physical chemistry of Criegee intermediates in the gas phase

    DOE PAGES

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

  3. The physical chemistry of Criegee intermediates in the gas phase

    SciTech Connect

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular and bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.

  4. Gas-phase nitronium ion affinities.

    PubMed Central

    Cacace, F; de Petris, G; Pepi, F; Angelelli, F

    1995-01-01

    Evaluation of nitronium ion-transfer equilibria, L1NO2+ + L2 = L2NO2+ + L1 (where L1 and L2 are ligands 1 and 2, respectively) by Fourier-transform ion cyclotron resonance mass spectrometry and application of the kinetic method, based on the metastable fragmentation of L1(NO2+)L2 nitronium ion-bound dimers led to a scale of relative gas-phase nitronium ion affinities. This scale, calibrated to a recent literature value for the NO2+ affinity of water, led for 18 ligands, including methanol, ammonia, representative ketones, nitriles, and nitroalkanes, to absolute NO2+ affinities, that fit a reasonably linear general correlation when plotted vs. the corresponding proton affinities (PAs). The slope of the plot depends to a certain extent on the specific nature of the ligands and, hence, the correlations between the NO2+ affinities, and the PAs of a given class of compounds display a better linearity than the general correlation and may afford a useful tool for predicting the NO2+ affinity of a molecule based on its PA. The NO2+ binding energies are considerably lower than the corresponding PAs and well below the binding energies of related polyatomic cations, such as NO+, a trend consistent with the available theoretical results on the structure and the stability of simple NO2+ complexes. The present study reports an example of extension of the kinetic method to dimers, such as L1(NO2+)L2, bound by polyatomic ions, which may considerably widen its scope. Finally, measurement of the NO2+ affinity of ammonia allowed evaluation of the otherwise inaccessible PA of the amino group of nitramide and, hence, direct experimental verification of previous theoretical estimates. PMID:11607578

  5. Gas-Phase Infrared; JCAMP Format

    National Institute of Standards and Technology Data Gateway

    SRD 35 NIST/EPA Gas-Phase Infrared; JCAMP Format (PC database for purchase)   This data collection contains 5,228 infrared spectra in the JCAMP-DX (Joint Committee for Atomic and Molecular Physical Data "Data Exchange") format.

  6. Continuous-Flow Gas-Phase Bioreactors

    NASA Technical Reports Server (NTRS)

    Wise, Donald L.; Trantolo, Debra J.

    1994-01-01

    Continuous-flow gas-phase bioreactors proposed for biochemical, food-processing, and related industries. Reactor contains one or more selected enzymes dehydrated or otherwise immobilized on solid carrier. Selected reactant gases fed into reactor, wherein chemical reactions catalyzed by enzyme(s) yield product biochemicals. Concept based on discovery that enzymes not necessarily placed in traditional aqueous environments to function as biocatalysts.

  7. Continuous-Flow Gas-Phase Bioreactors

    NASA Technical Reports Server (NTRS)

    Wise, Donald L.; Trantolo, Debra J.

    1994-01-01

    Continuous-flow gas-phase bioreactors proposed for biochemical, food-processing, and related industries. Reactor contains one or more selected enzymes dehydrated or otherwise immobilized on solid carrier. Selected reactant gases fed into reactor, wherein chemical reactions catalyzed by enzyme(s) yield product biochemicals. Concept based on discovery that enzymes not necessarily placed in traditional aqueous environments to function as biocatalysts.

  8. EPA GAS PHASE CHEMISTRY CHAMBER STUDIES

    EPA Science Inventory

    Gas-phase smog chamber experiments are being performed at EPA in order to evaluate a number of current chemical mechanisms for inclusion in EPA regulatory and research models. The smog chambers are 9000 L in volume and constructed of 2-mil teflon film. One of the chambers is co...

  9. EPA GAS PHASE CHEMISTRY CHAMBER STUDIES

    EPA Science Inventory

    Gas-phase smog chamber experiments are being performed at EPA in order to evaluate a number of current chemical mechanisms for inclusion in EPA regulatory and research models. The smog chambers are 9000 L in volume and constructed of 2-mil teflon film. One of the chambers is co...

  10. Conformation-resolved UV spectra of Pb(II) complexes: A gas phase study of the sandwich structures [Pb(toluene)2]2+ and [Pb(benzene)2]2+

    NASA Astrophysics Data System (ADS)

    Ma, Lifu; Takashima, Tsukiko; Koka, Joseph; Kimber, Helen J.; Cox, Hazel; Stace, Anthony J.

    2013-04-01

    Toxic heavy metals, such as Pb2+, have become important targets for the development of efficient receptors that are capable of recognizing their presence as environmental and biological pollutants, and an important part of that receptor-metal characterization process is the provision of spectral evidence that identifies the presence of a metal ion. From results reported here on a combined experimental and theoretical study it is shown that, when complexed with aromatic ligands, Pb2+ is capable of yielding structured UV spectra, which: (i) exhibit discrete electronic transitions that include significant contributions from the metal ion; (ii) are very sensitive to the electronic properties of coordinating ligands; and (iii) are sensitive to subtle changes in coordination geometry. Two aromatic sandwich complexes, [Pb(benzene)2]2+ and [Pb(toluene)2]2+ have been prepared in the gas phase and their UV action spectra recorded from ions held and cooled in an ion trap. Whilst [Pb(benzene)2]2+ exhibits a spectrum with very little detail, that recorded for [Pb(toluene)2]2+ reveals a rich structure in the wavelength range 220-280 nm. Theory in the form of density functional theory (DFT) shows that both types of complex take the form of hemidirected structures, and that [Pb(toluene)2]2+ can adopt three distinct conformers depending upon the relative positions of the two methyl groups. Further calculations, using adiabatic time-dependent DFT to assign electronic transitions, provide evidence of individual [Pb(toluene)2]2+ conformers having been resolved in the experimental spectrum. Of particular significance for the development of methods for identifying Pb2+ as an environmental or biological pollutant, is the observation that there are distinct ligand-to-metal charge transfer transitions in the UV that are sensitive to both the geometry and the electronic characteristics of molecules that accommodate the metal ion.

  11. Explaining the structure of the OH stretching band in the IR spectra of strongly hydrogen-bonded dimers of phosphinic acid and their deuterated analogs in the gas phase: a computational study.

    PubMed

    Rekik, Najeh; Ghalla, Houcine; Hanna, Gabriel

    2012-05-10

    We present a simulation of the OH stretching band in the gas-phase IR spectra of strongly hydrogen-bonded dimers of phosphinic acid and their deuterated analogs [(R(2)POOH(D), with R = CH(2)Cl, CH(3)], which is based on a model for a centrosymmetric hydrogen-bonded dimer that treats the high-frequency OH stretches harmonically and the low-frequency intermonomer (i.e., O···O) stretches anharmonically. This model takes into account the following effects: anharmonic coupling between the OH and O···O stretching modes; Davydov coupling between the two hydrogen bonds in the dimer; promotion of symmetry-forbidden OH stretching transitions; Fermi resonances between the fundamental of the OH stretches and the overtones of the in- and out-of-plane bending modes involving the OH groups; direct relaxation of the OH stretches; and indirect relaxation of the OH stretches via the O···O stretches. Using a set of physically sound parameters as input into this model, we have captured the main features in the experimental OH(D) bands of these dimers. The effects of key parameters on the spectra are also elucidated. By increasing the number and strength of the Fermi resonances and by promoting symmetry-forbidden OH stretching transitions in our simulations, we directly see the emergence of the ABC structure, which is a characteristic feature in the spectra of very strongly hydrogen-bonded dimers. However, in the case of the deuterated dimers, which do not exhibit the ABC structure, the Fermi resonances are found to be much weaker. The results of this model therefore shed light on the origin of the ABC structure in the IR spectra of strongly hydrogen-bonded dimers, which has been a subject of debate for decades.

  12. The exocyclic amino group of adenine in Pt(II) and Pd(II) complexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations.

    PubMed

    Silaghi-Dumitrescu, Radu; Mihály, Béla; Mihály, Timea; Attia, Amr A A; Sanz Miguel, Pablo J; Lippert, Bernhard

    2017-03-17

    A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H2, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH(+)) and deprotonated forms (9MeA-H), free and metal-complexed, has been conducted. The metals are Pt(II) and Pd(II), bonded to nitrogen-containing co-ligands (NH3, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp(2)-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H2 acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp(3). Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.

  13. Experimental Thermochemistry of Gas Phase Cytosine Tautomers

    NASA Astrophysics Data System (ADS)

    Morrison, A. M.; Douberly, G. E.

    2011-06-01

    Enthalpies of interconversion are measured for the three lowest energy tautomers of isolated cytosine. The equilibrium distribution of tautomers near 600 K is frozen upon the capture of the gas phase species by low temperature helium nanodroplets. The temperature dependence of the gas phase cytosine tautomer populations is determined with infrared laser spectroscopy of the helium solvated species. The interconverison enthalpies obtained from the van't Hoff relation are 1.14 ± 0.21 and 1.63 ± 0.12 for the C31 rightleftharpoons C32 and C31 rightleftharpoons C1 equilibria, respectively. C31 and C32 are rotamers of an enol tautomer, and C1 is a keto tautomer. The interconversion enthalpies are compared to recent CCSD(T) thermochemistry calculations of cytosine tautomers.

  14. Enzyme-catalyzed, gas-phase reactions.

    PubMed

    Barzana, E; Klibanov, A M; Karel, M

    1987-06-01

    Dehydrated preparations of alcohol oxidase adsorbed on DEAE-cellulose vigorously catalyze a gas-phase oxidation of ethanol vapors with molecular oxygen. The gas-phase reaction is strongly dependent on the water activity of the system. The enzymatic activity is severely inhibited by the product hydrogen peroxide. This inhibition can be alleviated, however, by an addition of catalase or peroxidase to the dry preparation. Such dehydrated, bienzymic catalysts afford a complete and selective conversion of the substrate to acetaldehyde. Dry alcohol oxidase is much more thermostable than in aqueous solution. The results of this work suggest that dehydrated enzymes have potential applications in the analysis of gaseous compounds and in the development of novel gas-solid bioreactors.

  15. Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone.

    PubMed

    Dorofeeva, Olga V; Vogt, Natalja; Vogt, Jürgen; Popik, Mikhail V; Rykov, Anatolii N; Vilkov, Lev V

    2007-07-19

    The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.

  16. Novel Method for Gas Phase Calibrations

    DTIC Science & Technology

    2010-11-01

    Connections 9 4. Control Chart of Repetitive Data Generated by the Ballast Calibrator 11 5. Phosgene Calibration from a GC -TCD/ECD 12 NOVEL METHOD...as phosgene , hydrogen cyanide, cyanogen chloride, and ethylene oxide. In addition, it has been used to successfully calibrate Miran® infrared...spectrometers and Fourier transfer infrared spectrometers with similar gas phase chemicals. For example. Figure 4 shows phosgene data collected over a 3

  17. Laser Studies of Gas Phase Radical Reactions.

    DTIC Science & Technology

    1989-01-01

    Acremonium chrysogenum , was prepared according to the published procedure [6]. This fungal enzyme had a specific activity of 0.023 IUmg1, and was estimated to...Dist-lbitionj Avdielbiity Codes jAvail atidjor Dist 6a A-I . p -1- Laser Studies of Gas Phase Radical Reactions G. Hancock Physical Chemistry...some additional experiments concerning the formation of carbene radicals in liquid phase enzyme cleavage studies are described. Keywords Laser

  18. Bis(trifluoromethyl)phosphinous acid (CF3)2P-O-H: an example of a thermally stable phosphinous acid--synthesis, gas-phase structure, and rotational isomers.

    PubMed

    Hoge, Berthold; Garcia, Placido; Willner, Helge; Oberhammer, Heinz

    2006-04-24

    The bis(trifluoromethyl)phosphinous acid, (CF3)2P-O-H, is the only known example of a thermally stable phosphinous acid. Although this compound has been known since 1960, little is known about the chemistry of this extraordinary compound; this might be due to the tedious, and in some part risky, synthesis that was originally published. An improved, simple, and safe synthesis that is based on the treatment of the easily accessible (CF3)2PNEt2, with at least three equivalents of p-toluene sulfonic acid, is presented. The reaction results in a complete conversion to the phosphinous acid, which is isolated in almost 90 % yield. The compound exists in an equilibrium of two P--OH rotational isomers, a fact which is supported by quantum chemical calculations. The relative enthalpy difference of 6.4 kJ mol(-1), calculated at the B3PW91/6-311G(3d,p) level, is in excellent agreement with the experimental value of 5.9 kJ mol(-1), which was determined from the temperature dependence of the nu(OH) bands of the two rotational isomers. The complete experimental vibrational spectra of both rotamers, their predicted vibrational spectra obtained by using quantum chemical calculations, and an attempt at photoinduced isomerization of matrix-isolated (CF3)2POH is presented. The experimental structure, obtained from an electron-diffraction study in the gas phase, is reproduced very well by ab initio and density functional theory (DFT) methods.

  19. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall,G.E.; Sears, T.J.

    2009-04-03

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

  20. Gas phase laser synthesis and processing of calcium phosphate nanoparticles for biomedical applications

    NASA Astrophysics Data System (ADS)

    Bapat, Parimal V.

    Biochemical processes make pervasive use of calcium and phosphate ions. Calcium phosphate salts that are naturally nontoxic and bioactive have been used for several medical applications in form of coatings and micropowders. Nanoparticle-based calcium phosphates have been shown to be internalized by living cells and be effective in DNA transfection, drug delivery, and transport of fluorophores for imaging of intracellular processes. They are also expected to interact strongly with cell adhesive proteins and are therefore promising elements in approaches to mimic the complex environment of the extra cellular matrix of bone. Harnessing this biomedical potential requires the ability to control the numerous characteristics of nanophase calcium phosphates that affect biological response, including nanoparticle chemical composition, crystal phase, crystallinity, crystallographic orientation of exposed faces, size, shape, surface area, number concentration, and degree of aggregation. This dissertation focuses on the use of laser-induced gas-phase synthesis for creation of calcium phosphate nanoparticles, and corresponding nanoparticle-based substrates that could offer new opportunities for guiding biological responses through well-controlled biochemical and topological cues. Gas-phase synthesis of nanoparticles has several characteristics that could enhance control over particle morphology, crystallinity, and surface area, compared to liquid-phase techniques. Synthesis from gas-phase precursors can be carried out at high temperatures and in high-purity inert or reactive gas backgrounds, enabling good control of chemistry, crystal structure, and purity. Moreover, the particle mean free path and number concentration can be controlled independently. This allows regulation of interparticle collision rates, which can be adjusted to limit aggregation. High-temperature synthesis of well-separated particles is therefore possible. In this work high power lasers are employed to

  1. Observation of exclusively π-stacked heterodimer of indole and hexafluorobenzene in the gas phase

    NASA Astrophysics Data System (ADS)

    Kumar, Sumit; Das, Aloke

    2013-09-01

    In this study, the structure of the indole . . . hexafluorobenzene dimer has been investigated in the gas phase by using resonant two photon ionzation (R2PI) and IR-UV double resonance spectroscopy combined with quantum chemistry calculations. We have confirmed the presence of exclusively π-stacked structure of the dimer from both experimental and theoretical IR spectra in the N-H stretching region. Observation of a single stable structure of the dimer has also been verified through 3D potential energy surface scan of the π-stacked dimer by varying the parallel displacement of the hexafluorobenzene unit simultaneously along the major and minor axes of the indole moiety. π-stacking interaction is present very often between the tryptophan and phenylalanine residues in proteins. But this interaction has not been observed earlier in the gas phase experiment by studying indole . . . benzene dimer because the N-H group of indole predominately directs towards the N-H . . . π hydrogen bonded T-shaped structure. The chosen molecular systems in this study not only rule out the possibility of the formation of the N-H . . . π bound T-shaped dimer but also enable the determination of the structure by probing the N-H group. The π-stacked indole . . . hexafluorobenzene dimer has a unique structure where the center of the hexafluorobenznene ring is aligned with the center of the shared bond of the indole ring. Our work provides useful insight in designing unnatural proteins having strong π-stacking interaction between the tryptophan and phenylalanine residues.

  2. Fluorescence resonance energy transfer of gas-phase ions under ultra high vacuum and ambient conditions.

    PubMed

    Frankevich, Vladimir; Chagovets, Vitaliy; Widjaja, Fanny; Barylyuk, Konstantin; Yang, Zhiyi; Zenobi, Renato

    2014-05-21

    We report evidence for fluorescence resonance energy transfer (FRET) of gas-phase ions under ultra high vacuum conditions (10(-9) mbar) inside a mass spectrometer as well as under ambient conditions inside an electrospray plume. Two different FRET pairs based on carboxyrhodamine 6G (donor) and ATTO590 or Bodipy TR (acceptor) dyes were examined and their gas-phase optical properties were studied. Our measurements indicate a different behavior for the two FRET pairs, which can be attributed to their different conformations in the gas phase. Upon desolvation via electrospray ionization, one of the FRET pairs undergoes a conformational change that leads to disappearance of FRET. This study shows the promise of FRET to obtain a direct correlation between solution and gas-phase structures.

  3. Star formation and gas phase history of the cosmic web

    NASA Astrophysics Data System (ADS)

    Snedden, Ali; Coughlin, Jared; Phillips, Lara Arielle; Mathews, Grant; Suh, In-Saeng

    2016-01-01

    We present a new method of tracking and characterizing the environment in which galaxies and their associated circumgalactic medium evolve. We have developed a structure finding algorithm that uses the rate of change of the density gradient to self-consistently parse and follow the evolution of groups/clusters, filaments and voids in large-scale structure simulations. We use this to trace the complete evolution of the baryons in the gas phase and the star formation history within each structure in our simulated volume. We vary the structure measure threshold to probe the complex inner structure of star-forming regions in poor clusters, filaments and voids. We find that the majority of star formation occurs in cold, condensed gas in filaments at intermediate redshifts (z ˜ 3). We also show that much of the star formation above a redshift z = 3 occurs in low-contrast regions of filaments, but as the density contrast increases at lower redshift, star formation switches to the high-contrast regions, or inner parts, of filaments. Since filaments bridge the void and cluster regions, it suggests that the majority of star formation occurs in galaxies in intermediate density regions prior to the accretion on to groups/clusters. We find that both filaments and poor clusters are multiphase environments distinguishing themselves by different distributions of gas phases.

  4. Retention of Native Protein Structures in the Absence of Solvent: A Coupled Ion Mobility and Spectroscopic Study

    PubMed Central

    Seo, Jongcheol; Hoffmann, Waldemar; Warnke, Stephan; Bowers, Michael T.; Pagel, Kevin

    2016-01-01

    Abstract Can the structures of small to medium‐sized proteins be conserved after transfer from the solution phase to the gas phase? A large number of studies have been devoted to this topic, however the answer has not been unambiguously determined to date. A clarification of this problem is important since it would allow very sensitive native mass spectrometry techniques to be used to address problems relevant to structural biology. A combination of ion‐mobility mass spectrometry with infrared spectroscopy was used to investigate the secondary and tertiary structure of proteins carefully transferred from solution to the gas phase. The two proteins investigated are myoglobin and β‐lactoglobulin, which are prototypical examples of helical and β‐sheet proteins, respectively. The results show that for low charge states under gentle conditions, aspects of the native secondary and tertiary structure can be conserved. PMID:27545682

  5. Theoretical calculations of EPR parameters of gas phase hydracrylonitrile radical

    NASA Astrophysics Data System (ADS)

    Sarikaya, Ebru Karakaş; Dereli, Ömer

    2017-02-01

    As a result of detailed conformational search of the hydracrylonitrile, four different conformers of molecule have been obtained. For these conformations, eleven possible radicals were modelled by using density functional theory (DFT) computations with respect to molecular structure. Electron Paramagnetic Resonance parameters of these model radicals were calculated and then they were compared with the experimental ones. Geometry optimizations of the molecule and modeled radicals were calculated by B3LYP method using 6-311++G(d,p) basis sets in gas phase.

  6. Gas-phase energetics of thorium fluorides and their ions.

    PubMed

    Irikura, Karl K

    2013-02-14

    Gas-phase thermochemistry for neutral ThF(n) and cations ThF(n)(+) (n = 1-4) is obtained from large-basis CCSD(T) calculations, with a small-core pseudopotential on thorium. Electronic partition functions are computed with the help of relativistic MRCI calculations. Geometries, vibrational spectra, electronic fine structure, and ion appearance energies are tabulated. These results support the experimental results by Lau, Brittain, and Hildenbrand for the neutral species, except for ThF. The ion thermochemistry is presented here for the first time.

  7. The study of large biopolymer complexes in solution and the gas phase using electrospray ionization-FTICR mass spectrometry

    SciTech Connect

    Smith, R.D.; Lei, Q.P.; Wu, Qinyuan; Hofstadler, A.

    1997-12-31

    Electrospray ionization (ESI) can transfer large biopolymers and many noncovalently bound complexes into the gas phase and to preserve specific noncovalent biomolecular associations for subsequent mass spectrometric analysis. Although a number of details of the ESI process remain a subject of debate, it is now incontestable that many weak associations can survive transfer to the gas phase and are stable for periods of at least seconds. In this presentation, the application of ESI-Fourier transform ion cyclotron resonance (FTICR) mass spectrometry methods for the study of large biopolymers and their noncovalent complexes will be described. It will also be shown that competitive binding studies can be used to quickly establish relative binding affinities in solution, allowing combinatorial libraries to be rapidly screened. After measurements of the intact complex, dissociation studies can be conducted to probe the structure of the individual constituents of complexes. Studies comparing the relative stabilities of protein-ligand complexes in solution and desolvated in the gas phase will also be presented, and discussed from both fundamental and analytical perspectives.

  8. Junin virus structural proteins.

    PubMed Central

    De Martínez Segovia, Z M; De Mitri, M I

    1977-01-01

    Polyacrylamide gel electrophoresis of purified Junin virus revealed six distinct structural polypeptides, two major and four minor ones. Four of these polypeptides appeared to be covalently linked with carbohydrate. The molecular weights of the six proteins, estimated by coelectrophoresis with marker proteins, ranged from 25,000 to 91,000. One of the two major components (number 3) was identified as a nucleoprotein and had a molecular weight of 64,000. It was the most prominent protein and was nonglycosylated. The other major protein (number 5), with a molecular weight of 38,000, was a glucoprotein and a component of the viral envelope. The location on the virion of three additional glycopeptides with molecular weights of 91,000, 72,000, and 52,000, together with a protein with a molecular weight of 25,000, was not well defined. PMID:189088

  9. Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

    PubMed

    Fleischer, Holger; Wann, Derek A; Hinchley, Sarah L; Borisenko, Konstantin B; Lewis, James R; Mawhorter, Richard J; Robertson, Heather E; Rankin, David W H

    2005-10-07

    The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

  10. Gas phase thermochemistry of organogermanium compounds

    SciTech Connect

    Engel, J.P.

    1993-12-07

    A variety of silyl- and alkyl-germylene precursors have been synthesized and subsequently pyrolyzed in the gas phase. Arrhenius parameters were obtained employing a pulsed-stirred flow reactor for these unimolecular decompositions. These precursors are divided into two major categories by mechanism of germylene extrusion: {alpha}-elimination precursors and germylacetylenes. The extrusion of germylenes from germylacetylene precursors is of primary interest. A mechanism is proposed employing a germacyclopropene intermediate. Evidence supporting this mechanism is presented. In the process of exploring germylacetylenes as germylene precursors, an apparent dyatropic rearrangement between germanium and silicon was observed. This rearrangement was subsequently explored.

  11. Gas-phase photolysis of tungsten hexachloride

    NASA Astrophysics Data System (ADS)

    Kullmer, R.

    1994-07-01

    The laser-induced decomposition of WCl6 in the gas-phase is investigated by means of absorption, Raman and laser-induced fluorescence spectroscopy. With visible Ar+-laser radiation dissociation of WCl6 into WCl4 and Cl2 has been observed. Further decomposition can be achieved in the presence of H2 employing ultraviolet Ar+-laser radiation at 360 nm. A complete reduction to W requires even shorter wavelengths. The experimental results are analyzed on the basis of model calculations. Implications on the Laser-induced Chemical Vapor Deposition (LCVD) of W are discussed.

  12. Receptors useful for gas phase chemical sensing

    DOEpatents

    Jaworski, Justyn W; Lee, Seung-Wuk; Majumdar, Arunava; Raorane, Digvijay A

    2015-02-17

    The invention provides for a receptor, capable of binding to a target molecule, linked to a hygroscopic polymer or hydrogel; and the use of this receptor in a device for detecting the target molecule in a gaseous and/or liquid phase. The invention also provides for a method for detecting the presence of a target molecule in the gas phase using the device. In particular, the receptor can be a peptide capable of binding a 2,4,6-trinitrotoluene (TNT) or 2,4,-dinitrotoluene (DNT).

  13. Synthesis, structural characterization, and gas-phase unimolecular reactivity of the silver hydride nanocluster [Ag3((PPh2)2CH2)3(μ3-H)](BF4)2.

    PubMed

    Zavras, Athanasios; Khairallah, George N; Connell, Timothy U; White, Jonathan M; Edwards, Alison J; Mulder, Roger J; Donnelly, Paul S; O'Hair, Richard A J

    2014-07-21

    A bis(diphenylphosphino)methane-ligated trinuclear silver hydride nanocluster, [Ag3((Ph2P)2CH2)3(μ3-H)](BF4)2, featuring three silver(I) ions coordinated to a μ3-hydride, and its deuteride analogue, [Ag3((Ph2P)2CH2)3(μ3-D)](BF4)2, have been isolated and structurally characterized using electrospray ionization mass spectrometry (ESI-MS), X-ray crystallography, NMR and IR spectroscopy. The position of the deuteride in [Ag3((Ph2P)2CH2)3(μ3-D)](BF4)2 was determined by neutron diffraction. ESI-MS of [Ag3L3(μ3-H/D)](BF4)2 [L = ((Ph2P)2CH2)2] produces [Ag3L3(μ3-H/D)](2+) and [Ag3L3(μ3-H/D)(BF4)](+). A rich gas-phase ion chemistry of [Ag3L3(μ3-H/D)](2+) is observed under conditions of collision-induced dissociation (CID) and electron-capture dissociation (ECD). CID gives rise to the following complementary ion pairs: [Ag3L2](+) and [L+(H/D)](+); [Ag2(H/D)L2](+) and [AgL](+); [Ag2(H/D)L](+) and [AgL2](+). ECD gives rise to a number of dissociation channels including loss of the bis(phosphine) ligand, fragmentation of a coordinated bis(phosphine) ligand via C-P bond activation, and loss of a hydrogen (deuterium) atom with concomitant formation of [Ag3L3](+). Under CID conditions, [Ag3L3(μ3-H/D)(BF4)](+) fragments via ligand loss, the combined loss of a ligand and [H,B,F4], and cluster fragmentation to give [Ag2(BF4)L2](+) and [Ag2(L-H)L](+) [where (L-H) = (Ph2P)2CH(-)].

  14. Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies.

    PubMed

    Strenalyuk, Tatyana; Samdal, Svein; Volden, Hans Vidar

    2008-05-29

    The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are

  15. Multiple protein structure alignment.

    PubMed Central

    Taylor, W. R.; Flores, T. P.; Orengo, C. A.

    1994-01-01

    A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core. PMID:7849601

  16. Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations.

    PubMed

    Vogt, Natalja; Khaikin, Leonid S; Grikina, Olga E; Rykov, Anatolii N; Vogt, Jürgen

    2008-08-21

    Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1

  17. Gas-Phase Fragmentation Analysis of Nitro-Fatty Acids

    PubMed Central

    Bonacci, Gustavo; Asciutto, Eliana K.; Woodcock, Steven R.; Salvatore, Sonia R.; Freeman, Bruce A.; Schopfer, Francisco J.

    2012-01-01

    Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO2− anion or neutral loss of HNO2. The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO2− rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of 13C and 15N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples. PMID:21953257

  18. Conformations of gas-phase ions of ubiquitin, cytochrome c, apomyoglobin, and beta-lactoglobulin produced from two different solution conformations.

    PubMed

    Wright, P John; Zhang, Jianmin; Douglas, D J

    2008-12-01

    At low pH in solutions of 50% methanol, proteins form expanded denatured states (the "H" state). In 90% methanol, proteins form expanded helical denatured states with artificial alpha-helices (the "H(c)" state). Gas-phase ions of ubiquitin, cytochrome c, apomyoglobin, and native and disulfide-reduced beta-lactoglobulin were formed by electrospray ionization (ESI) of the proteins from the H and H(c) states in solution. Both states in solution produce the same charge states in ESI. The conformations of the ions were studied with cross section measurements and gas-phase H/D exchange experiments. The cross sections show that the ions retain considerable folded structure. For a given protein and given charge state, ions produced from the H and H(c) states showed the same cross sections (within approximately 1%). Ions of cytochrome c, apomyoglobin, and native and reduced beta-lactoglobulin of a given charge state showed no differences in H/D exchange level when produced from the H or H(c) state. However, ubiquitin ions produced from the H(c) state consistently exchange fewer ( approximately 13%) hydrogens than ions produced from the H state, suggesting that in this case the gas-phase protein ions retain some memory of their solution conformations.

  19. Gas-phase folding and unfolding of cytochrome c cations.

    PubMed Central

    Wood, T D; Chorush, R A; Wampler, F M; Little, D P; O'Connor, P B; McLafferty, F W

    1995-01-01

    Water is thought to play a dominant role in protein folding, yet gaseous multiply protonated proteins from which the water has been completely removed show hydrogen/deuterium (H/D) exchange behavior similar to that used to identify conformations in solution. Indicative of the gas-phase accessibility to D2O, multiply-charged (6+ to 17+) cytochrome c cations exchange at six (or more) distinct levels of 64 to 173 out of 198 exchangeable H atoms, with the 132 H level found at charge values 8+ to 17+. Infrared laser heating and fast collisions can apparently induce ions to unfold to exchange at a higher distinct level, while charge-stripping ions to lower charge values yields apparent folding as well as unfolding. PMID:7708663

  20. Classical Dynamics Simulations of Dissociation of Protonated Tryptophan in the Gas Phase.

    PubMed

    Krishnan, Yogeshwaran; Sharma, Nishant; Lourderaj, Upakarasamy; Paranjothy, Manikandan

    2017-06-15

    Gas phase decomposition of protonated amino acids are of great interest due to their role in understanding protein and peptide chemistry. Several experimental and theoretical studies have been reported in the literature on this subject. In the present work, decomposition of the aromatic amino acid protonated tryptophan was studied by on-the-fly classical chemical dynamics simulations using density functional theory. Mass spectrometry and electronic structure theory studies have shown multiple dissociation pathways for this biologically relevant molecule. Unlike aliphatic amino acids, protonated tryptophan dissociates via NH3 elimination rather than the usual iminium ion formation by combined removal of H2O and CO molecules. Also, a major fragmentation pathway in the present work involves Cα-Cβ bond fission. Results of the chemical dynamics simulations reported here are in overall agreement with experiments, and detailed atomic level mechanisms are presented.

  1. Effect of additives on gas-phase catalysis with immobilised Thermoanaerobacter species alcohol dehydrogenase (ADH T).

    PubMed

    Trivedi, A H; Spiess, A C; Daussmann, T; Büchs, J

    2006-07-01

    This paper presents a strategy for preparing an efficient immobilised alcohol dehydrogenase preparation for a gas-phase reaction. The effects of additives such as buffers and sucrose on the immobilisation efficiency (residual activity and protein loading) and on the gas-phase reaction efficiency (initial reaction rate and half-life) of Thermoanaerobacter sp. alcohol dehydrogenase were studied. The reduction of acetophenone to 1-phenylethanol under in situ cofactor regeneration using isopropanol as co-substrate was used as a model reaction at fixed reaction conditions (temperature and thermodynamic activities). A strongly enhanced thermostability of the enzyme in the gas-phase reaction was achieved when the enzyme was immobilised with 50 mM phosphate buffer (pH 7) containing sucrose five times the protein amount (on weight/weight basis). This resulted in a remarkable productivity of 200 g L(-1) day(-1) even at non-optimised reaction conditions. The interaction of additives with the enzyme and water affects the immobilisation and gas-phase efficiencies of the enzyme. However, it was not possible to predict the effect of additives on the gas-phase reaction efficiency even after knowing their effect on the immobilisation efficiency.

  2. Stabilized enzymes in continuous gas phase reactions

    SciTech Connect

    Yang, Fangxiao; LeJeune, K.; Yang, Zhen

    1995-12-01

    We are assessing the utility of enzymes to catalyze reactions in a continuous gas phase reactor. First, alcohol dehydrogenase has been used to oxidize an unsaturated alcohol, 3-methyl-2-buten-1-ol (UOL), to the corresponding unsaturated aldehyde, 3-methyl-2-butenal (UAL). Cofactor NAD{sup +} was regenerated by concomitant acetone reduction to isopropyl alcohol. Second, organophosphorus hydrolase (OPH) has been used to hydrolyze pesticide vapors. In order to control enzyme hydration level, enzyme water adsorption isotherms at different temperature have been studied. Huttig`s isotherm model has been found suitable to describe adsorption behavior. The influence of enzyme hydration level, enzyme loading on glass beads, reaction temperature and flow rate on enzymatic reaction rate and biocatalyst stability were investigated. Reaction kinetics were studied and a kinetic model was proposed. We will also report our attempts to further stabilize enzymes for use in gas reactions by incorporating them into polymer matrices.

  3. Simplified procedure for encapsulating cytochrome c in silica aerogel nanoarchitectures while retaining gas-phase bioactivity.

    PubMed

    Harper-Leatherman, Amanda S; Iftikhar, Mariam; Ndoi, Adela; Scappaticci, Steven J; Lisi, George P; Buzard, Kaitlyn L; Garvey, Elizabeth M

    2012-10-16

    Cytochrome c (cyt. c) has been encapsulated in silica sol-gels and processed to form bioaerogels with gas-phase activity for nitric oxide through a simplified synthetic procedure. Previous reports demonstrated a need to adsorb cyt. c to metal nanoparticles prior to silica sol-gel encapsulation and processing to form aerogels. We report that cyt. c can be encapsulated in aerogels without added nanoparticles and retain structural stability and gas-phase activity for nitric oxide. While the UV-visible Soret absorbance and nitric oxide response indicate that cyt. c encapsulated with nanoparticles in aerogels remains slightly more stable and functional than cyt. c encapsulated alone, these properties are not very different in the two types of aerogels. From UV-visible and Soret circular dichroism results, we infer that cyt. c encapsulated alone self-organizes to reduce contact with the silica gel in a way that may bear at least some resemblance to the way cyt. c self-organizes into superstructures of protein within aerogels when nanoparticles are present. Both the buffer concentration and the cyt. c concentration of solutions used to synthesize the bioaerogels affect the structural integrity of the protein encapsulated alone within the dried aerogels. Optimized bioaerogels are formed when cyt. c is encapsulated from 40 mM phosphate buffered solutions, and when the loaded cyt. c concentration in the aerogel is in the range of 5 to 15 μM. Increased viability of cyt. c in aerogels is also observed when supercritical fluid used to produce aerogels is vented over relatively long times.

  4. Gas-phase Dissociation of homo-DNA Oligonucleotides

    NASA Astrophysics Data System (ADS)

    Stucki, Silvan R.; Désiron, Camille; Nyakas, Adrien; Marti, Simon; Leumann, Christian J.; Schürch, Stefan

    2013-12-01

    Synthetic modified oligonucleotides are of interest for diagnostic and therapeutic applications, as their biological stability, pairing selectivity, and binding strength can be considerably increased by the incorporation of unnatural structural elements. Homo-DNA is an oligonucleotide homologue based on dideoxy-hexopyranosyl sugar moieties, which follows the Watson-Crick A-T and G-C base pairing system, but does not hybridize with complementary natural DNA and RNA. Homo-DNA has found application as a bioorthogonal element in templated chemistry applications. The gas-phase dissociation of homo-DNA has been investigated by ESI-MS/MS and MALDI-MS/MS, and mechanistic aspects of its gas-phase dissociation are discussed. Experiments revealed a charge state dependent preference for the loss of nucleobases, which are released either as neutrals or as anions. In contrast to DNA, nucleobase loss from homo-DNA was found to be decoupled from backbone cleavage, thus resulting in stable products. This renders an additional stage of ion activation necessary in order to generate sequence-defining fragment ions. Upon MS3 of the primary base-loss ion, homo-DNA was found to exhibit unspecific backbone dissociation resulting in a balanced distribution of all fragment ion series.

  5. Thermochemical aspects of proton transfer in the gas phase.

    PubMed

    Gal, J F; Maria, P C; Raczyńska, E D

    2001-07-01

    The beginning of the twentieth century saw the development of new theories of acidity and basicity, which are currently well accepted. The thermochemistry of proton transfer in the absence of solvent attracted much interest during this period, because of the fundamental importance of the process. Nevertheless, before the 1950s, few data were available, either from lattice energy evaluations or from calculations using the emerging molecular orbital theory. Advances in mass spectrometry during the last 40 years allowed studies of numerous systems with better accuracy. Thousands of accurate gas-phase acidities or basicities are now available, for simple atomic and molecular systems and for large biomolecules. The intrinsic effect of structure on the Brønsted basic or acidic properties of molecules and the influence of solvents have been unravelled. In this tutorial, the basics of the thermodynamic principles involved are given, and the mass spectrometric techniques are briefly reviewed. Advances in the design and measurements of gas-phase superacids and superbases are described. Recent studies concerning biomolecules are also evoked. Copyright 2001 John Wiley & Sons, Ltd.

  6. Analysis of gas-phase condensation of nickel nanoparticles

    NASA Astrophysics Data System (ADS)

    Gafner, S. L.; Gafner, Yu. Ya.

    2008-10-01

    Gas-phase condensation of 8000 nickel atoms is examined by molecular dynamics simulation with a tight-binding potential. A detailed study of the evolution of the system cooled at a constant rate from 1000 K to 77 K is presented. The results are used to identify four distinct stages of the evolution from a hot atomic gas to a few synthesized particles. An analysis of possible nanoparticle formation mechanisms suggests that cluster-cluster aggregation is the dominant one. The simulation shows that there two stages of cluster formation are of primary importance with regard to aggregation. At the first stage, spherical liquid clusters nucleate with uniform size distribution. The second stage is characterized by a distinct transition from uniform to bimodal size distribution due to aggregation of relatively large clusters. The particles obtained by gas-phase synthesis are analyzed by the CNA method [25]. It is found that most nanoparticles produced in the simulation have either icosahedral or mixed FCC/HCP structure.

  7. Nahoon: Time-dependent gas-phase chemical model

    NASA Astrophysics Data System (ADS)

    Wakelam, V.

    2014-09-01

    Nahoon is a gas-phase chemical model that computes the chemical evolution in a 1D temperature and density structure. It uses chemical networks downloaded from the KInetic Database for Astrochemistry (KIDA) but the model can be adapted to any network. The program is written in Fortran 90 and uses the DLSODES (double precision) solver from the ODEPACK package to solve the coupled stiff differential equations. The solver computes the chemical evolution of gas-phase species at a fixed temperature and density and can be used in one dimension (1D) if a grid of temperature, density, and visual extinction is provided. Grains, both neutral and negatively charged, and electrons are considered as chemical species and their concentrations are computed at the same time as those of the other species. Nahoon contains a test to check the temperature range of the validity of the rate coefficients and avoid extrapolations outside this range. A test is also included to check for duplication of chemical reactions, defined over complementary ranges of temperature.

  8. Structural and relative energy assessments of DFT functionals and the MP2 method to describe the gas phase methylation of nitronates: [R(1)R(2)CNO2](-) + CH3I.

    PubMed

    Mahmood, Ayyaz; Longo, Ricardo L

    2016-06-22

    The performances of 26 combinations of density-functional theory (DFT) functionals or second-order Møller-Plesset (MP2) methods and basis sets were evaluated for the calculation of the activation energy (Δ(‡)E), the energy available (ΔRCE) to the reactant complex, the energy of reaction (ΔrE), and rotational constants of the main structures involved in the methylation reactions of nitronates, [R(1)R(2)CNO2](-) + CH3I, in the gas phase, where R(1) = R(2) = H, R(1) = H and R(2) = CH3, R(1) = R(2) = CH3, and R(1) + R(2) = c-(CH2)2. The separated reactants and products, the reactant and product complexes, and the transition states were considered, leading to 43 data points for the statistical analysis for each method under assessment. Five statistical quantifiers: the mean signed error (MSE), the mean unsigned error (MUE), the percent mean relative error (% MRE), best and worse (BW), and the confidence interval (CI) were used to assess the performance of methods relative to the CCSD(T)/CBS//MP2/aug-cc-pVTZ reference method. The DFT functionals included the widely applied B3LYP and M06-2X global-hybrids and the recently available DSD-PBEP86, DSD-PBEP86-D3BJ and PWPB95 double-hybrids. The basis sets involved an effective core potential (ECP) for describing the inner electrons of iodine such as LANL2DZdp and aug-cc-pVXZ-PP (X = D, T, and Q), and all-electron basis sets for the remaining atoms. The energy available to the reactant complex is described quite well by all methods, however, only the MP2/aug-cc-pVTZ-PP method provided values within 2 kcal mol(-1) (8.4 kJ mol(-1)) from the reference method for Δ(‡)E and ΔrE. Amongst the DFT methods, the global-hybrid M06-2X functional produced the best overall results including BW and CI. Notice that all methods yielded the smallest Δ(‡)E for the C-methylation pathway. The rotational constants of the reactant complexes and the transition state structures were compared, for which the MP2 method and the M06-2X

  9. Protein Structure Prediction by Protein Threading

    NASA Astrophysics Data System (ADS)

    Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

    The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

  10. Fundamentals of gas phase plasmas for treatment of human tissue.

    PubMed

    Kushner, Mark J; Babaeva, Natalia Yu

    2011-01-01

    The use of gas phase plasmas for treating human tissue is at the intersection of two disciplines - plasma physics and engineering, and medicine. In this paper, a primer will be provided for the medical practitioner on the fundamentals of generating gas phase plasmas at atmospheric pressure in air for the treatment of human tissue. The mechanisms for gas phase plasmas interacting with tissue and biological fluids will also be discussed using results from computer modeling.

  11. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry.

    PubMed

    Li, Huilin; Sheng, Yuewei; McGee, William; Cammarata, Michael; Holden, Dustin; Loo, Joseph A

    2017-03-07

    Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and intermolecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with preactivation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.

  12. Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase

    NASA Astrophysics Data System (ADS)

    MacLeod, N. A.; Simons, J. P.

    2007-03-01

    Protonated neurotransmitters have been produced in the gas phase via a novel photochemical scheme: complexes of the species of interest, 1-phenylethylamine, 2-amino-1-phenylethanol and the diastereo-isomers, ephedrine and pseudoephedrine, with a suitable proton donor, phenol (or indole), are produced in a supersonic expansion and ionized by resonant two photon ionization of the donor. Efficient proton transfer generates the protonated neurotransmitters, complexed to a phenoxy radical. Absorption of infrared radiation, and subsequent evaporation of the phenoxy tag, coupled with time of flight mass spectrometry, provides vibrational spectra of the protonated (and also hydrated) complexes for comparison with the results of quantum chemical computation. Comparison with the conformational structures of the neutral neurotransmitters (established previously) reveals the effect of protonation on their structure. The photochemical proton transfer strategy allows spectra to be recorded from individual laser shots and their quality compares favourably with that obtained using electro-spray or matrix assisted laser desorption ion sources.

  13. Efficient and directed peptide bond formation in the gas phase via ion/ion reactions.

    PubMed

    McGee, William M; McLuckey, Scott A

    2014-01-28

    Amide linkages are among the most important chemical bonds in living systems, constituting the connections between amino acids in peptides and proteins. We demonstrate the controlled formation of amide bonds between amino acids or peptides in the gas phase using ion/ion reactions in a mass spectrometer. Individual amino acids or peptides can be prepared as reagents by (i) incorporating gas phase-labile protecting groups to silence otherwise reactive functional groups, such as the N terminus; (ii) converting the carboxyl groups to the active ester of N-hydroxysuccinimide; and (iii) incorporating a charge site. Protonation renders basic sites (nucleophiles) unreactive toward the N-hydroxysuccinimide ester reagents, resulting in sites with the greatest gas phase basicities being, in large part, unreactive. The N-terminal amines of most naturally occurring amino acids have lower gas phase basicities than the side chains of the basic amino acids (i.e., those of histidine, lysine, or arginine). Therefore, reagents may be directed to the N terminus of an existing "anchor" peptide to form an amide bond by protonating the anchor peptide's basic residues, while leaving the N-terminal amine unprotonated and therefore reactive. Reaction efficiencies of greater than 30% have been observed. We propose this method as a step toward the controlled synthesis of peptides in the gas phase.

  14. Oxidation of formic acid on the Pt(111) surface in the gas phase.

    PubMed

    Gao, Wang; Keith, John A; Anton, Josef; Jacob, Timo

    2010-09-28

    Formic acid (HCOOH) oxidation on Pt(111) under gas-phase conditions is a benchmark heterogeneous catalysis reaction used to probe electro-catalytic HCOOH conversion in fuel cells, itself an important reaction in energy conversion. We used density functional theory (DFT) calculations to elucidate the fundamental oxidation mechanisms of HCOOH in the gas phase, determining the relative strengths of chemical interactions between HCOOH oxidation intermediates and the Pt(111) surface. We focused on investigating how water and adsorption coverage affects reaction intermediate structures and transition states. Our results show that adsorbed HCOO is a reactive intermediate in gas phase, and co-adsorbed water plays a key role in HCOOH oxidation influencing the structure of reaction intermediates and reaction barriers on Pt(111). The simulations show the preferred catalytic pathway is qualitatively dependent on surface coverage. These results provide a conceptual basis to better interpret its complicated experimental reaction kinetics.

  15. Comparing the gas-phase fragmentation reactions of protonated and radical cations of the tripeptides GXR

    NASA Astrophysics Data System (ADS)

    Wee, Sheena; O'Hair, Richard A. J.; McFadyen, W. David

    2004-05-01

    Electrospray ionization (ESI) mass spectrometry of methanolic solutions of mixtures of the copper salt (2,2':6',2''-terpyridine)copper(II) nitrate monohydrate ([Cu(II)(tpy)(NO3)2].H2O) and a tripeptide GXR (where X = 1 of the 20 naturally occurring amino acids) yielded [Cu(II)(tpy)(GXR)][radical sign]2+ ions, which were then subjected to collision induced dissociation (CID). In all but one case (GRR), these [Cu(II)(tpy)(GXR)][radical sign]2+ ions fragment to form odd electron GXR[radical sign]+ radical cations with sufficient abundance to examine their gas-phase fragmentation reactions. The GXR[radical sign]+ radical cations undergo a diverse range of fragmentation reactions which depend on the nature of the side chain of X. Many of these reactions can be rationalized as arising from the intermediacy of isomeric distonic ions in which the charge (i.e. proton) is sequestered by the highly basic arginine side chain and the radical site is located at various positions on the tripeptide including the peptide back bone and side chains. The radical sites in these distonic ions often direct the fragmentation reactions via the expulsion of small radicals (to yield even electron ions) or small neutrals (to form radical cations). Both classes of reaction can yield useful structural information, allowing for example, distinction between leucine and isoleucine residues. The gas-phase fragmentation reactions of the GXR[radical sign]+ radical cations are also compared to their even electron [GXR+H]+ and [GXR+2H]2+ counterparts. The [GXR+H]+ ions give fewer sequence ions and more small molecule losses while the [GXR+2H]2+ ions yield more sequence information, consistent with the [`]mobile proton model' described in previous studies. In general, all three classes of ions give complementary structural information, but the GXR[radical sign]+ radical cations exhibit a more diverse loss of small species (radicals and neutrals). Finally, links between these gas-phase results and key

  16. Instabilities in Lean Gas-Phase Combustion

    NASA Astrophysics Data System (ADS)

    Schneider, K.; Bockhorn, H.; Eigenbrod, Ch.; Emerson, D.; Haldenwang, P.; Hoffmann, F.; Roekaerts, D.; Ronney, P.; Triebel, W.; Tummers, M.

    2005-06-01

    Lean burning is the burning of fuel-air mixtures with less than the chemically- balanced (stoichiometric) mixture. It produces a significant increase in fuel efficiency and reduction in pollution. However, the limits and control of lean burning are still not well understood.This is the motivation behind the study of instabilities in lean gas-phase combustion under microgravity conditions via direct numerical simulations and comparison of the results with experimental data.The goal is to gain fundamental insights in order to identify and understand the intrinsic chemical and fluid dynamical mechanisms responsible for these instabilities.The potential of this microgravity combustion research includes the development of technology that would reduce pollution and fire and explosion hazards, improve hazardous waste incineration and increase efficiency of the conversion of chemical energy to electric power or motive force.The results from this fundamental research will thus benefit chemical engineering and power generation. Its wide range of applications in industry includes lean-burning car engines.

  17. Transferring pharmaceuticals into the gas phase

    NASA Astrophysics Data System (ADS)

    Christen, Wolfgang; Krause, Tim; Rademann, Klaus

    2008-11-01

    The dissolution of molecules of biological interest in supercritical carbon dioxide is investigated using pulsed molecular beam mass spectrometry. Due to the mild processing temperatures of most supercritical fluids, their adiabatic expansion into vacuum permits to transfer even thermally very sensitive substances into the gas phase, which is particularly attractive for pharmaceutical and biomedical applications. In addition, supercritical CO2constitutes a chemically inert solvent that is compatible with hydrocarbon-free ultrahigh vacuum conditions. Here, we report on the dissolution and pulsed supersonic jet expansion of caffeine (C8H10N4O2), the provitamin menadione (C11H8O2), and the amino acid derivative l-phenylalanine tert-butyl ester hydrochloride (C6H5CH2CH(NH2)COOC(CH3)3[dot operator]HCl), into vacuum. An on-axis residual gas analyzer is used to monitor the relative amounts of solute and solvent in the molecular beam as a function of solvent densityE The excellent selectivity and sensitivity provided by mass spectrometry permits to probe even trace amounts of solutes. The strong density variation of CO2 close to the critical point results in a pronounced pressure dependence of the relative ion currents of solute and solvent molecules, reflecting a substantial change in solubility.

  18. Resolving Gas-Phase Metallicity In Galaxies

    NASA Astrophysics Data System (ADS)

    Carton, David

    2017-06-01

    Chapter 2: As part of the Bluedisk survey we analyse the radial gas-phase metallicity profiles of 50 late-type galaxies. We compare the metallicity profiles of a sample of HI-rich galaxies against a control sample of HI-'normal' galaxies. We find the metallicity gradient of a galaxy to be strongly correlated with its HI mass fraction {M}{HI}) / {M}_{\\ast}). We note that some galaxies exhibit a steeper metallicity profile in the outer disc than in the inner disc. These galaxies are found in both the HI-rich and control samples. This contradicts a previous indication that these outer drops are exclusive to HI-rich galaxies. These effects are not driven by bars, although we do find some indication that barred galaxies have flatter metallicity profiles. By applying a simple analytical model we are able to account for the variety of metallicity profiles that the two samples present. The success of this model implies that the metallicity in these isolated galaxies may be in a local equilibrium, regulated by star formation. This insight could provide an explanation of the observed local mass-metallicity relation. Chapter 3 We present a method to recover the gas-phase metallicity gradients from integral field spectroscopic (IFS) observations of barely resolved galaxies. We take a forward modelling approach and compare our models to the observed spatial distribution of emission line fluxes, accounting for the degrading effects of seeing and spatial binning. The method is flexible and is not limited to particular emission lines or instruments. We test the model through comparison to synthetic observations and use downgraded observations of nearby galaxies to validate this work. As a proof of concept we also apply the model to real IFS observations of high-redshift galaxies. From our testing we show that the inferred metallicity gradients and central metallicities are fairly insensitive to the assumptions made in the model and that they are reliably recovered for galaxies

  19. Selective transport of amino acids into the gas phase: driving forces for amino acid solubilization in gas-phase reverse micelles.

    PubMed

    Fang, Yigang; Bennett, Andrew; Liu, Jianbo

    2011-01-28

    We report a study on encapsulation of various amino acids into gas-phase sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) reverse micelles, using electrospray ionization guided-ion-beam tandem mass spectrometry. Collision-induced dissociation of mass-selected reverse micellar ions with Xe was performed to probe structures of gas-phase micellar assemblies, identify solute-surfactant interactions, and determine preferential incorporation sites of amino acids. Integration into gas-phase reverse micelles depends upon amino acid hydrophobicity and charge state. For examples, glycine and protonated amino acids (such as protonated tryptophan) are encapsulated within the micellar core via electrostatic interactions; while neutral tryptophan is adsorbed in the surfactant layer. As verified using model polar hydrophobic compounds, the hydrophobic effect and solute-interface hydrogen-bonding do not provide sufficient driving force needed for interfacial solubilization of neutral tryptophan. Neutral tryptophan, with a zwitterionic structure, is intercalated at the micellar interface between surfactant molecules through complementary effects of electrostatic interactions between tryptophan backbone and AOT polar heads, and hydrophobic interactions between tryptophan side chain and AOT alkyl tails. Protonation of tryptophan could significantly improve its incorporation capacity into gas-phase reverse micelles, and displace its incorporation site from the micellar interfacial zone to the core; protonation of glycine, on the other hand, has little effect on its encapsulation capacity. Another interesting observation is that amino acids of different isoelectric points could be selectively encapsulated into, and transported by, reverse micelles from solution to the gas phase, based upon their competition for protonation and subsequent encapsulation within the micellar core.

  20. Pressure Dependence of Gas-Phase Reaction Rates

    ERIC Educational Resources Information Center

    De Persis, Stephanie; Dollet, Alain; Teyssandier, Francis

    2004-01-01

    It is presented that only simple concepts, mainly taken from activated-complex or transition-state theory, are required to explain and analytically describe the influence of pressure on gas-phase reaction kinetics. The simplest kind of elementary gas-phase reaction is a unimolecular decomposition reaction.

  1. Hydrocarbon radical thermochemistry: Gas-phase ion chemistry techniques

    SciTech Connect

    Ervin, Kent M.

    2014-03-21

    Final Scientific/Technical Report for the project "Hydrocarbon Radical Thermochemistry: Gas-Phase Ion Chemistry Techniques." The objective of this project is to exploit gas-phase ion chemistry techniques for determination of thermochemical values for neutral hydrocarbon radicals of importance in combustion kinetics.

  2. Pressure Dependence of Gas-Phase Reaction Rates

    ERIC Educational Resources Information Center

    De Persis, Stephanie; Dollet, Alain; Teyssandier, Francis

    2004-01-01

    It is presented that only simple concepts, mainly taken from activated-complex or transition-state theory, are required to explain and analytically describe the influence of pressure on gas-phase reaction kinetics. The simplest kind of elementary gas-phase reaction is a unimolecular decomposition reaction.

  3. OMVPE growth and gas-phase reactions of AlGaN for UV emitters

    SciTech Connect

    Han, J.; Figiel, J.J.; Crawford, M.H.; Banas, M.A.; Bartram, M.E.; Biefeld, R.M.; Song, Y.K.; Nurmikko, A.V.

    1998-06-01

    Gas-phase parasitic reactions among TMG, TMA, and NH3, are investigated by monitoring of the growth rate/incorporation efficiency of GaN and AlN using an in-situ optical reflectometer. It is suggested that gas phase adduct (TMA: NH{sub 3}) reactions not only reduce the incorporation efficiency of TMA but also affect the incorporation behavior of TMGa. The observed phenomena can be explained by either a synergistic gas-phase scavenging effect or a surface site-blocking effect. Relatively low reactor pressures (30--50 Torr) are employed to grow an AlGaN/GaN QW p-n diode structure. The UV emission at 354 nm (FWHM {approximately} 6 nm) represents the first report of LED operation from an indium-free GaN QW diode.

  4. A protocol for detecting and scavenging gas-phase free radicals in mainstream cigarette smoke.

    PubMed

    Yu, Long-Xi; Dzikovski, Boris G; Freed, Jack H

    2012-01-02

    Cigarette smoking is associated with human cancers. It has been reported that most of the lung cancer deaths are caused by cigarette smoking (5,6,7,12). Although tobacco tars and related products in the particle phase of cigarette smoke are major causes of carcinogenic and mutagenic related diseases, cigarette smoke contains significant amounts of free radicals that are also considered as an important group of carcinogens(9,10). Free radicals attack cell constituents by damaging protein structure, lipids and DNA sequences and increase the risks of developing various types of cancers. Inhaled radicals produce adducts that contribute to many of the negative health effects of tobacco smoke in the lung(3). Studies have been conducted to reduce free radicals in cigarette smoke to decrease risks of the smoking-induced damage. It has been reported that haemoglobin and heme-containing compounds could partially scavenge nitric oxide, reactive oxidants and carcinogenic volatile nitrosocompounds of cigarette smoke(4). A 'bio-filter' consisted of haemoglobin and activated carbon was used to scavenge the free radicals and to remove up to 90% of the free radicals from cigarette smoke(14). However, due to the cost-ineffectiveness, it has not been successfully commercialized. Another study showed good scavenging efficiency of shikonin, a component of Chinese herbal medicine(8). In the present study, we report a protocol for introducing common natural antioxidant extracts into the cigarette filter for scavenging gas phase free radicals in cigarette smoke and measurement of the scavenge effect on gas phase free radicals in mainstream cigarette smoke (MCS) using spin-trapping Electron Spin Resonance (ESR) Spectroscopy(1,2,14). We showed high scavenging capacity of lycopene and grape seed extract which could point to their future application in cigarette filters. An important advantage of these prospective scavengers is that they can be obtained in large quantities from byproducts of

  5. Femtosecond gas phase electron diffraction with MeV electrons.

    PubMed

    Yang, Jie; Guehr, Markus; Vecchione, Theodore; Robinson, Matthew S; Li, Renkai; Hartmann, Nick; Shen, Xiaozhe; Coffee, Ryan; Corbett, Jeff; Fry, Alan; Gaffney, Kelly; Gorkhover, Tais; Hast, Carsten; Jobe, Keith; Makasyuk, Igor; Reid, Alexander; Robinson, Joseph; Vetter, Sharon; Wang, Fenglin; Weathersby, Stephen; Yoneda, Charles; Wang, Xijie; Centurion, Martin

    2016-12-16

    We present results on ultrafast gas electron diffraction (UGED) experiments with femtosecond resolution using the MeV electron gun at SLAC National Accelerator Laboratory. UGED is a promising method to investigate molecular dynamics in the gas phase because electron pulses can probe the structure with a high spatial resolution. Until recently, however, it was not possible for UGED to reach the relevant timescale for the motion of the nuclei during a molecular reaction. Using MeV electron pulses has allowed us to overcome the main challenges in reaching femtosecond resolution, namely delivering short electron pulses on a gas target, overcoming the effect of velocity mismatch between pump laser pulses and the probe electron pulses, and maintaining a low timing jitter. At electron kinetic energies above 3 MeV, the velocity mismatch between laser and electron pulses becomes negligible. The relativistic electrons are also less susceptible to temporal broadening due to the Coulomb force. One of the challenges of diffraction with relativistic electrons is that the small de Broglie wavelength results in very small diffraction angles. In this paper we describe the new setup and its characterization, including capturing static diffraction patterns of molecules in the gas phase, finding time-zero with sub-picosecond accuracy and first time-resolved diffraction experiments. The new device can achieve a temporal resolution of 100 fs root-mean-square, and sub-angstrom spatial resolution. The collimation of the beam is sufficient to measure the diffraction pattern, and the transverse coherence is on the order of 2 nm. Currently, the temporal resolution is limited both by the pulse duration of the electron pulse on target and by the timing jitter, while the spatial resolution is limited by the average electron beam current and the signal-to-noise ratio of the detection system. We also discuss plans for improving both the temporal resolution and the spatial resolution.

  6. Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis.

    PubMed

    Guttman, Miklos; Wales, Thomas E; Whittington, Dale; Engen, John R; Brown, Jeffery M; Lee, Kelly K

    2016-04-01

    Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra. Graphical Abstract ᅟ.

  7. Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis

    NASA Astrophysics Data System (ADS)

    Guttman, Miklos; Wales, Thomas E.; Whittington, Dale; Engen, John R.; Brown, Jeffery M.; Lee, Kelly K.

    2016-04-01

    Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra.

  8. Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

    PubMed Central

    Li, Jinyu; Rossetti, Giulia; Dreyer, Jens; Raugei, Simone; Ippoliti, Emiliano; Lüscher, Bernhard; Carloni, Paolo

    2014-01-01

    Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information. PMID:25210764

  9. The nature of ionic liquids in the gas phase.

    PubMed

    Leal, João P; Esperança, José M S S; da Piedade, Manuel E Minas; Lopes, José N Canongia; Rebelo, Luís P N; Seddon, Kenneth R

    2007-07-19

    Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) experiments showed that when aprotic ionic liquids vaporize under pressure and temperature conditions similar to those of a reduced-pressure distillation, the gas phase is composed of discrete anion-cation pairs. The evolution of the mass spectrometric signals recorded during fractional distillations of binary ionic liquid mixtures allowed us to monitor the changes of the gas-phase composition and the relative volatility of the components. In addition, we have studied a protic ionic liquid, and demonstrated that it exists as separated neutral molecules in the gas phase.

  10. Structural Genomics of Protein Phosphatases

    SciTech Connect

    Almo,S.; Bonanno, J.; Sauder, J.; Emtage, S.; Dilorenzo, T.; Malashkevich, V.; Wasserman, S.; Swaminathan, S.; Eswaramoorthy, S.; et al

    2007-01-01

    The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.

  11. VPDB: Viral Protein Structural Database

    PubMed Central

    Sharma, Om Prakash; Jadhav, Ankush; Hussain, Afzal; Kumar, Muthuvel Suresh

    2011-01-01

    Viral Protein Database is an interactive database for three dimensional viral proteins. Our aim is to provide a comprehensive resource to the community of structural virology, with an emphasis on the description of derived data from structural biology. Currently, VPDB includes ˜1,670 viral protein structures from >277 viruses with more than 465 virus strains. The whole database can be easily accessed through the user convenience text search. Interactivity has been enhanced by using Jmol, WebMol and Strap to visualize the viral protein molecular structure. Availability The database is available for free at http://www.vpdb.bicpu.edu.in PMID:21769196

  12. Gas-phase clusterization of zinc during magnetron sputtering

    NASA Astrophysics Data System (ADS)

    Abduev, A. Kh.; Akhmedov, A. K.; Asvarov, A. Sh.; Alikhanov, N. M.-R.; Emirov, R. M.; Muslimov, A. E.; Belyaev, V. V.

    2017-01-01

    The processes of gas-phase clusterization of zinc during dc magnetron sputtering of a zinc target in an argon atmosphere have been investigated. The influence of the working gas pressure and magnetron discharge current on the morphology and structure of the precipitates formed on substrates previously cooled to-50°C is studied. It is shown that dense textured (002)Zn layers with a columnar structure are formed at relatively low argon pressures in the chamber ( P = 0.5 Pa) and low discharge currents (100 mA). X-ray amorphous deposits with a fractal coral-like structure arise on substrates at an extremely high argon pressure in the chamber ( P = 5 Pa). An increase in the magnetron discharge current at an operating gas pressure of 5 Pa leads to the formation of polycrystalline layers on substrates; the intensity of the XRD peaks related to crystalline zinc increases with an increase in the discharge current. Possible mechanisms of the structural transformation of Zn deposits are considered.

  13. Multiple Multidentate Halogen Bonding in Solution, in the Solid State, and in the (Calculated) Gas Phase.

    PubMed

    Jungbauer, Stefan H; Schindler, Severin; Herdtweck, Eberhardt; Keller, Sandro; Huber, Stefan M

    2015-09-21

    The binding properties of neutral halogen-bond donors (XB donors) bearing two multidentate Lewis acidic motifs toward halides were investigated. Employing polyfluorinated and polyiodinated terphenyl and quaterphenyl derivatives as anion receptors, we obtained X-ray crystallographic data of the adducts of three structurally related XB donors with tetraalkylammonium chloride, bromide, and iodide. The stability of these XB complexes in solution was determined by isothermal titration calorimetry (ITC), and the results were compared to X-ray analyses as well as to calculated binding patterns in the gas phase. Density functional theory (DFT) calculations on the gas-phase complexes indicated that the experimentally observed distortion of the XB donors during multiple multidentate binding can be reproduced in 1:1 complexes with halides, whereas adducts with two halides show a symmetric binding pattern in the gas phase that is markedly different from the solid state structures. Overall, this study demonstrates the limitations in the transferability of binding data between solid state, solution, and gas phase in the study of complex multidentate XB donors.

  14. Noncovalent Halogen Bonding as a Mechanism for Gas-Phase Clustering

    NASA Astrophysics Data System (ADS)

    Wegeberg, Christina; Donald, William A.; McKenzie, Christine J.

    2017-07-01

    Gas-phase clustering of nonionizable iodylbenzene (PhIO2) is attributed to supramolecular halogen bonding. Electrospray ionization results in the formation of ions of proton-charged and preferably sodium-charged clusters assignable to [H(PhIO2) n ]+, n = 1-7; [Na(PhIO2) n ]+, n = 1-6; [Na2(PhIO2) n ]2+, n = 7-20; [HNa(PhIO2) n ]2+, n = 6-19; [HNa2(PhIO2) n ]3+, n = 15-30; and [Na3(PhIO2) n ]3+, n = 14-30. The largest cluster detected has a supramolecular mass of 7147 Da. Electronic structure calculations using the M06-2X functional with the 6-311++G(d,p) basis set for C, H, and O, and LANL2DZ basis set for I and Na predict 298 K binding enthalpies for the protonated and sodiated iodylbenzene dimers and trimers are greater than 180 kJ/mol. This is exceptionally high in comparison with other protonated and sodiated clusters with well-established binding enthalpies. Strongly halogen-bonded motifs found in the crystalline phases of PhIO2 and its derivatives serve as models for the structures of larger gas-phase clusters, and calculations on simple model gas-phase dimer and trimer clusters result in similar motifs. This is the first account of halogen bonding playing an extensive role in gas-phase associations.

  15. Gas-phase reactions of methyl thiocyanate with aliphatic carbanions - A mass spectrometry and computational study.

    PubMed

    Repeć, Barbara; Błaziak, Kacper; Danikiewicz, Witold

    2016-02-15

    Methyl thiocyanate, like other organic thiocyanates, is a molecule with many electrophilic reactive sites and it has many synthetic applications. For better understanding of the intrinsic reactivity of alkyl thiocyanates against nucleophiles it was important to study gas-phase reactions of methyl thiocyanate with carbanions differing by structure and proton affinity values. All experiments were performed using a modified API 365 triple quadrupole mass spectrometer equipped with a TurboIonSpray electrospray ionization (ESI) source. Carbanions were generated in the ESI source by decarboxylation of the respective carboxylic acid anions. Methyl thiocyanate was delivered as a vapor with nitrogen used as a collision gas to the collision cell where the reactions take place. Mass spectra recorded for the gas-phase reactions of five aliphatic carbanions with methyl thiocyanate showed a variety of product ions formed via different reaction mechanisms, depending on the structure and proton affinity of the carbanion. The pathways considered are: SN 2 nucleophilic substitution, cyanophilic reaction, thiophilic reaction and proton transfer, followed in some instances by subsequent transformations. The proposed reaction pathways are supported by density functional theory (DFT) calculations. Our preliminary experiments showed that mass spectrometry together with quantum chemical calculations is a good tool for studying gas-phase reactions of alkyl thiocyanates with carbanions. In the gas phase all four theoretically possible products can be observed and their formation can be rationalized by the results of the modelling of the reaction energy profiles. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  16. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation.

    PubMed

    Hamuro, Yoshitomo

    2017-05-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation. Graphical Abstract ᅟ.

  17. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-05-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

  18. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-02-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

  19. Structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry and molecular dynamics simulations.

    PubMed

    Borysik, Antoni J

    2015-09-01

    The structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry (IMS) and vacuum molecular dynamics (MD) simulations is reported. Direct evidence is provided for the ability of the surfactant dodecyl-β-D-maltoside (DDM) to prevent charge-induced unfolding of the membrane protein (PagP) in the gas-phase. Restraints obtained by IMS are used to map the surfactant positions onto the protein surface. Surfactants occupying more exposed positions at the apexes of the β-barrel structure are most in-line with the experimental observations. MD simulations provide additional evidence for this assembly organization through surfactant inversion and migration on the protein structure in the absence of solvent. Surfactant migration entails a net shift from apolar membrane spanning regions to more polar regions of the protein structure with the DDM molecule remaining attached to the protein via headgroup interactions. These data provide evidence for the role of protein-DDM headgroup interactions in stabilizing membrane protein structure from gas-phase unfolding.

  20. Time Dependent Studies of Reactive Shocks in the Gas Phase

    DTIC Science & Technology

    1978-11-16

    1 LEVEL NRL Memorandum Report 3W tO Time Dependent Studies of Reactive Shocks in the Gas Phase E.S. ORAN, ’T.R. YOUNG and J.P. BORIS Laboratory for...34-• TIME DEPENDENT STUDIES OF REACTIVE SHOCKS IN THE GAS PHASE I. Introduction This paper presents results obtained from a detailed numerical...chemical kinetics, reaction products, and intermediates produced in reactive gas mixtures ignited by the propagation of a shock front. The model is based

  1. Detecting internally symmetric protein structures.

    PubMed

    Kim, Changhoon; Basner, Jodi; Lee, Byungkook

    2010-06-03

    Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information. We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure. SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe.

  2. Detecting internally symmetric protein structures

    PubMed Central

    2010-01-01

    Background Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information. Results We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure. Conclusions SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe. PMID:20525292

  3. Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide

    NASA Astrophysics Data System (ADS)

    Leavitt, Christopher; Raston, Paul; Moody, Grant; Shirley, Caitlyne; Douberly, Gary

    2014-06-01

    The structure-function relationship in proteins is widely recognized, motivating numerous investigations of isolated neutral and ionic polypeptides that generally employ conformation specific, multidimensional UV and IR spectroscopies. This data taken in conjunction with computed harmonic frequencies has provided a snapshot of the underlying molecular physics at play in many polypeptides, but few experiments have been able to probe the energetics of these systems. In this study, we use vibrational spectroscopy to measure the gas-phase enthalpy change for isomerization between two conformations of the dipeptide N-acetyl glycine methyl amide (NAGMA). A two-stage oven source is implemented producing a gas-phase equilibrium distribution of NAGMA molecules that is flash frozen upon pickup by He nanodroplets. Using polarization spectroscopy, the IR spectrum is assigned to a mixture of two conformers having intramolecular hydrogen bonds made up of either five- or seven-membered rings, C5 and C7, respectively. The interconversion enthalpy, obtained from the van't Hoff relation, is 4.52{±}0.12 kJ/mol for isomerization from the C7 to the C5-conformer. This experimental measurement is compared to computations employing a broad range of theoretical methods.

  4. Conformation of Macromolecules in the Gas Phase: Use of Matrix-Assisted Laser Desorption Methods in Ion Chromatography

    NASA Astrophysics Data System (ADS)

    von Helden, Gert; Wyttenbach, Thomas; Bowers, Michael T.

    1995-03-01

    Conformational data for macromolecules in the gas phase have been obtained by the coupling of a matrix-assisted laser desorption ion source to an ion chromatograph. A series of polyethylene glycol (PEG) polymers "cationized" (converted to a cation) by sodium ions (Na^+PEG9 to Na^+PEG19) and a protonated neurotransmitter protein, bradykinin, were studied. Mobilities of Na^+PEG9 to Na^+PEG19 are reported. Detailed modeling of Na^+PEG9 with molecular mechanics methods indicates that the lowest energy structure has the Na^+ ion "solvated" by the polymer chain with seven oxygen atoms as nearest neighbors. The agreement between the model and experiment is within 1 percent for Na^+PEG9, Na^+PEG13, and Na^+PEG17, giving strong support to both the method and the deduced structures. Similar agreement was obtained in initial studies that modeled experimental data for arginine-protonated bradykinin.

  5. Substrate-free gas-phase synthesis of graphene

    NASA Astrophysics Data System (ADS)

    Dato, Albert Manglallan

    Graphene is a single atomic layer of sp2-bonded carbon atoms tightly packed in a two-dimensional honeycomb lattice. The material possesses remarkable properties and has been envisioned for use in numerous applications. Contemporary graphene production techniques require substrates or graphite crystals to create graphene. Furthermore, these approaches involve multiple steps, and sometimes non-ambient conditions, to produce atomically-thin sheets. This dissertation presents the first substrate-free gas-phase graphene synthesis method. The technique can synthesize graphene in a single step at atmospheric pressure, without the use of graphite or substrates. The novel synthesis method was discovered through experiments that tested the hypothesis that graphene could be synthesized through the delivery of alcohols into argon plasmas. The experiments presented in this dissertation were conducted in an atmospheric-pressure microwave plasma reactor. Solid carbon materials were produced by delivering liquid ethanol droplets directly into argon plasmas. Numerous characterization techniques were used to unambiguously prove that the synthesized materials were clean and highly ordered graphene sheets. Additional studies investigated the effects of variable experimental parameters on the graphene synthesis process. The applied microwave power did not significantly affect the types of structures produced in the reactor. Lowering the volumetric flow rate of the plasma gas resulted in the synthesis of graphitic particles. The composition of the precursors delivered into the reactor also affected graphene synthesis. Graphene was not produced through the delivery of methanol or isopropyl alcohol droplets. However, graphene was obtained through dimethyl ether, which is an organic compound with the same atomic composition as ethanol. Thus, the flow rate and precursor composition significantly affected the nucleation, growth, and residence time of the materials created during experiments

  6. Structure of giant muscle proteins

    PubMed Central

    Meyer, Logan C.; Wright, Nathan T.

    2013-01-01

    Giant muscle proteins (e.g., titin, nebulin, and obscurin) play a seminal role in muscle elasticity, stretch response, and sarcomeric organization. Each giant protein consists of multiple tandem structural domains, usually arranged in a modular fashion spanning 500 kDa to 4 MDa. Although many of the domains are similar in structure, subtle differences create a unique function of each domain. Recent high and low resolution structural and dynamic studies now suggest more nuanced overall protein structures than previously realized. These findings show that atomic structure, interactions between tandem domains, and intrasarcomeric environment all influence the shape, motion, and therefore function of giant proteins. In this article we will review the current understanding of titin, obscurin, and nebulin structure, from the atomic level through the molecular level. PMID:24376425

  7. ENGINE EXHAUST PARTICULATE AND GAS PHASE CONTRIBUTIONS TO VASCULAR TOXICITY

    PubMed Central

    Campen, Matthew; Robertson, Sarah; Lund, Amie; Lucero, Joann; McDonald, Jacob

    2014-01-01

    Cardiovascular health effects of near-roadway pollution appear more substantial than other sources of air pollution. The underlying cause of this phenomenon may simply be concentration-related, but the possibility remains that gases and particulate matter (PM) may physically interact and further enhance systemic vascular toxicity. To test this, we utilized a common hypercholesterolemic mouse model (Apolipoprotein E-null) exposed to mixed vehicular emissions (MVE; combined gasoline and diesel exhausts) for 6 h/d × 50 days, with additional permutations of removing PM by filtration and also removing gaseous species from PM by denudation. Several vascular bioassays, including matrix metalloproteinase 9 (MMP9) protein, 3-nitrotyrosine, and plasma-induced vasodilatory impairments, highlighted that the whole emissions, containing both particulate and gaseous components, was collectively more potent than MVE-derived PM or gas mixtures, alone. Thus, we conclude that inhalation of fresh whole emissions induce greater systemic vascular toxicity than either the particulate or gas phase alone. These findings lend credence to the hypothesis that the near-roadway environment may have a more focused public health impact due to gas-particle interactions. PMID:24730681

  8. Compact Structure Patterns in Proteins.

    PubMed

    Chitturi, Bhadrachalam; Shi, Shuoyong; Kinch, Lisa N; Grishin, Nick V

    2016-10-23

    Globular proteins typically fold into tightly packed arrays of regular secondary structures. We developed a model to approximate the compact parallel and antiparallel arrangement of α-helices and β-strands, enumerated all possible topologies formed by up to five secondary structural elements (SSEs), searched for their occurrence in spatial structures of proteins, and documented their frequencies of occurrence in the PDB. The enumeration model grows larger super-secondary structure patterns (SSPs) by combining pairs of smaller patterns, a process that approximates a potential path of protein fold evolution. The most prevalent SSPs are typically present in superfolds such as the Rossmann-like fold, the ferredoxin-like fold, and the Greek key motif, whereas the less frequent SSPs often possess uncommon structure features such as split β-sheets, left-handed connections, and crossing loops. This complete SSP enumeration model, for the first time, allows us to investigate which theoretically possible SSPs are not observed in available protein structures. All SSPs with up to four SSEs occurred in proteins. However, among the SSPs with five SSEs, approximately 20% (218) are absent from existing folds. Of these unobserved SSPs, 80% contain two or more uncommon structure features. To facilitate future efforts in protein structure classification, engineering, and design, we provide the resulting patterns and their frequency of occurrence in proteins at: http://prodata.swmed.edu/ssps/. Copyright © 2016. Published by Elsevier Ltd.

  9. BAYESIAN PROTEIN STRUCTURE ALIGNMENT1

    PubMed Central

    RODRIGUEZ, ABEL; SCHMIDLER, SCOTT C.

    2015-01-01

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key “gap” parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence–structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples. PMID:26925188

  10. Gas-phase synthesis of semiconductor nanocrystals and its applications

    NASA Astrophysics Data System (ADS)

    Mandal, Rajib

    Luminescent nanomaterials is a newly emerging field that provides challenges not only to fundamental research but also to innovative technology in several areas such as electronics, photonics, nanotechnology, display, lighting, biomedical engineering and environmental control. These nanomaterials come in various forms, shapes and comprises of semiconductors, metals, oxides, and inorganic and organic polymers. Most importantly, these luminescent nanomaterials can have different properties owing to their size as compared to their bulk counterparts. Here we describe the use of plasmas in synthesis, modification, and deposition of semiconductor nanomaterials for luminescence applications. Nanocrystalline silicon is widely known as an efficient and tunable optical emitter and is attracting great interest for applications in several areas. To date, however, luminescent silicon nanocrystals (NCs) have been used exclusively in traditional rigid devices. For the field to advance towards new and versatile applications for nanocrystal-based devices, there is a need to investigate whether these NCs can be used in flexible and stretchable devices. We show how the optical and structural/morphological properties of plasma-synthesized silicon nanocrystals (Si NCs) change when they are deposited on stretchable substrates made of polydimethylsiloxane (PDMS). Synthesis of these NCs was performed in a nonthermal, low-pressure gas phase plasma reactor. To our knowledge, this is the first demonstration of direct deposition of NCs onto stretchable substrates. Additionally, in order to prevent oxidation and enhance the luminescence properties, a silicon nitride shell was grown around Si NCs. We have demonstrated surface nitridation of Si NCs in a single step process using non?thermal plasma in several schemes including a novel dual-plasma synthesis/shell growth process. These coated NCs exhibit SiNx shells with composition depending on process parameters. While measurements including

  11. [Protein phosphatases: structure and function].

    PubMed

    Bulanova, E G; Budagian, V M

    1994-01-01

    The process of protein and enzyme systems phosphorylation is necessary for cell growth, differentiation and preparation for division and mitosis. The conformation changes of protein as a result of phosphorylation lead to increased enzyme activity and enhanced affinity to substrates. A large group of enzymes--protein kinases--is responsible for phosphorylation process in cell, which are divided into tyrosine- and serine-threonine-kinases depending on their ability to phosphorylate appropriate amino acid residues. In this review has been considered the functional importance and structure of protein phosphatases--enzymes, which are functional antagonists of protein kinases.

  12. Histidine-Aromatic Interactions in Proteins and Protein-Ligand Complexes:  Quantum Chemical Study of X-ray and Model Structures.

    PubMed

    Cauët, Emilie; Rooman, Marianne; Wintjens, René; Liévin, Jacques; Biot, Christophe

    2005-05-01

    His-aromatic complexes, with the His located above the aromatic plane, are stabilized by π-π, δ(+)-π and/or cation-π interactions according to whether the His is neutral or protonated and the partners are in stacked or T-shape conformations. Here we attempt to probe the relative strength of these interactions as a function of the geometry and protonation state, in gas phase, in water and protein-like environments (acetone, THF and CCl4), by means of quantum chemistry calculations performed up to second order of the Møller-Plesset pertubation theory. Two sets of conformations are considered for that purpose. The first set contains 89 interactions between His and Phe, Tyr, Trp, or Ade, observed in X-ray structures of proteins and protein-ligand complexes. The second set contains model structures obtained by moving an imidazolium/imidazole moiety above a benzene ring or an adenine moiety. We found that the protonated complexes are much more stable than the neutral ones in gas phase. This higher stability is due to the electrostatic contributions, the electron correlation contributions being equally important in the two forms. Thus, π-π and δ(+)-π interactions present essentially favorable electron correlation energy terms, whereas cation-π interactions feature in addition favorable electrostatic energies. The protonated complexes remain more stable than the neutral ones in protein-like environments, but the difference is drastically reduced. Furthermore, the T-shape conformation is undoubtedly more favorable than the stacked one in gas phase. This advantage decreases in the solvents, and the stacked conformation becomes even slightly more favorable in water. The frequent occurrence of His-aromatic interactions in catalytic sites, at protein-DNA or protein-ligand interfaces and in 3D domain swapping proteins emphasize their importance in biological processes.

  13. Gas phase synthesis of two ensembles of silicon nanoparticles

    NASA Astrophysics Data System (ADS)

    Mohan, A.; de Jong, M. M.; Poulios, I.; Schropp, R. E. I.; Rath, J. K.

    2015-09-01

    Dusty plasmas provide a very favorable environment for the growth of silicon nanocrystals. For application of silicon nanocrystals in a solar cell, the fabrication of monodisperse silicon quantum dots has been challenging. We report a single step method to synthesize silicon (Si) nanoparticles in a custom designed dedicated plasma reactor. The nanoparticles produced in the gas phase belong to two different phases exhibiting different structural and optical properties. Particles made in the bulk of the plasma are aggregates of crystalline particles with a mean size of 100 nm. Particles made in locally enhanced plasma regions produced at holes present in the grounded electrode contain free-standing quantum sized particles with crystallites (with mean size of 2.95 nm) embedded within an amorphous matrix. We provide insight on different plasma processes leading to the formation of aggregates and free-standing particles. We hypothesize that the free standing particles are formed due to the excess energetic electrons present in locally enhanced discharges.

  14. Distinct Fragmentation Pathways of Anticancer Drugs Induced by Charge-Carrying Cations in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Hong, Areum; Lee, Hong Hee; Heo, Chae Eun; Cho, Yunju; Kim, Sunghwan; Kang, Dukjin; Kim, Hugh I.

    2017-04-01

    With the growth of the pharmaceutical industry, structural elucidation of drugs and derivatives using tandem mass spectrometry (MS2) has become essential for drug development and pharmacokinetics studies because of its high sensitivity and low sample requirement. Thus, research seeking to understand fundamental relationships between fragmentation patterns and precursor ion structures in the gas phase has gained attention. In this study, we investigate the fragmentation of the widely used anticancer drugs, doxorubicin (DOX), vinblastine (VBL), and vinorelbine (VRL), complexed by a singly charged proton or alkali metal ion (Li+, Na+, K+) in the gas phase. The drug-cation complexes exhibit distinct fragmentation patterns in tandem mass spectra as a function of cation size. The trends in fragmentation patterns are explicable in terms of structures derived from ion mobility mass spectrometry (IM-MS) and theoretical calculations.

  15. Distinct Fragmentation Pathways of Anticancer Drugs Induced by Charge-Carrying Cations in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Hong, Areum; Lee, Hong Hee; Heo, Chae Eun; Cho, Yunju; Kim, Sunghwan; Kang, Dukjin; Kim, Hugh I.

    2016-12-01

    With the growth of the pharmaceutical industry, structural elucidation of drugs and derivatives using tandem mass spectrometry (MS2) has become essential for drug development and pharmacokinetics studies because of its high sensitivity and low sample requirement. Thus, research seeking to understand fundamental relationships between fragmentation patterns and precursor ion structures in the gas phase has gained attention. In this study, we investigate the fragmentation of the widely used anticancer drugs, doxorubicin (DOX), vinblastine (VBL), and vinorelbine (VRL), complexed by a singly charged proton or alkali metal ion (Li+, Na+, K+) in the gas phase. The drug-cation complexes exhibit distinct fragmentation patterns in tandem mass spectra as a function of cation size. The trends in fragmentation patterns are explicable in terms of structures derived from ion mobility mass spectrometry (IM-MS) and theoretical calculations.

  16. The Gas-Phase Deuterium Fractionation of Formaldehyde

    NASA Astrophysics Data System (ADS)

    Osamura, Yoshihiro; Roberts, Helen; Herbst, Eric

    2005-03-01

    The dominant mechanism for the deuteration of formaldehyde in the gas phase of low-temperature interstellar cloud cores occurs via reaction with the deuterating ions H2D+, HD+2, and D+3. Until now, it has been assumed that deuteration leads to an ion that, on recombination with electrons, can produce a deuterated neutral species with a statistical branching fraction. Quantum chemical calculations reported here, however, show an entirely different picture, in which the deuteration of formaldehyde leads to the molecular ion H2COD+, where the deuterium binds only on the oxygen side of the molecule. The structure is quite stable, while an alternative structure, H2DCO+, cannot be produced in a straightforward manner. Dissociative recombination of H2COD+ to reproduce a formaldehyde structure then removes the deuteration if the dissociation is direct, i.e., it occurs without change of structure. There are several possible indirect mechanisms by which dissociative recombination can lead to HDCO, however. For example, if the direct products are HCOD+H, it is possible that subsequent isomerization to HDCO can occur, although this involved process is unlikely. Another possibility is isomerization during the actual dissociation of the H2COD intermediate. Models of deuterium fractionation in which dissociative recombination is predominantly direct are presented, and it is found that the deuterium fractionation of formaldehyde to form both HDCO and D2CO can still occur via other mechanisms, although with less efficiency than previously obtained. If the dissociative recombination is half indirect, however, then we can recover the previously calculated efficiency.

  17. Instrumental parameters in the MALDI-TOF mass spectrometric analysis of quaternary protein structures.

    PubMed

    Zehl, Martin; Allmaier, Günter

    2005-01-01

    Several former studies have shown that MALDI-TOF-MS can be applied successfully to investigate the quaternary structure of proteins. Whereas most of these reports were focused on MALDI sample preparation, there is little information about the influence of instrumental parameters on the desorption/ionization and gas-phase behavior of protein subunit assemblies. Therefore, in addition of giving short examples of the quaternary structure analysis of a microheterogeneous glycoprotein, a metalloenzyme, and a heme-binding enzyme by MALDI-TOF-MS, we report a systematic study of the effect of some instrumental parameters on the analysis of chicken egg white avidin. From these tested parameters, only the laser pulse energy was found to influence the relative abundance of the intact assembly as well as the formation of nonspecific cluster ions significantly. This finding suggests that the disruption of the noncovalent interactions during the desorption/ionization process takes place at a very short time interval after the laser ablation, whereas those assemblies that survive this step are rather stable afterward in the gas phase. In addition, we present clear evidence that protein cluster ions are not preformed during sample preparation but originate from nonspecific assemblage during desorption/ionization.

  18. Oscillatory burning of solid propellants including gas phase time lag.

    NASA Technical Reports Server (NTRS)

    T'Ien, J. S.

    1972-01-01

    An analysis has been performed for oscillatory burning of solid propellants including gas phase time lag. The gaseous flame is assumed to be premixed and laminar with a one-step overall chemical reaction. The propellant is assumed to decompose according to the Arrenhius Law, with no condensed phase reaction. With this model, strong gas phase resonance has been found in certain cases at the characteristic gas-phase frequencies, but the peaking of the acoustic admittance is in the direction favoring the damping of pressure waves. At still higher frequencies, moderate wave-amplifying ability was found. The limit of low frequency response obtained previously by Denison and Baum was recovered, and the limitations of the quasi-steady theory were investigated.

  19. Gas phase metal cluster model systems for heterogeneous catalysis.

    PubMed

    Lang, Sandra M; Bernhardt, Thorsten M

    2012-07-14

    Since the advent of intense cluster sources, physical and chemical properties of isolated metal clusters are an active field of research. In particular, gas phase metal clusters represent ideal model systems to gain molecular level insight into the energetics and kinetics of metal-mediated catalytic reactions. Here we summarize experimental reactivity studies as well as investigations of thermal catalytic reaction cycles on small gas phase metal clusters, mostly in relation to the surprising catalytic activity of nanoscale gold particles. A particular emphasis is put on the importance of conceptual insights gained through the study of gas phase model systems. Based on these concepts future perspectives are formulated in terms of variation and optimization of catalytic materials e.g. by utilization of bimetals and metal oxides. Furthermore, the future potential of bio-inspired catalytic material systems are highlighted and technical developments are discussed.

  20. Oscillatory burning of solid propellants including gas phase time lag.

    NASA Technical Reports Server (NTRS)

    T'Ien, J. S.

    1972-01-01

    An analysis has been performed for oscillatory burning of solid propellants including gas phase time lag. The gaseous flame is assumed to be premixed and laminar with a one-step overall chemical reaction. The propellant is assumed to decompose according to the Arrenhius Law, with no condensed phase reaction. With this model, strong gas phase resonance has been found in certain cases at the characteristic gas-phase frequencies, but the peaking of the acoustic admittance is in the direction favoring the damping of pressure waves. At still higher frequencies, moderate wave-amplifying ability was found. The limit of low frequency response obtained previously by Denison and Baum was recovered, and the limitations of the quasi-steady theory were investigated.

  1. Counting basic sites in oligopeptides via gas-phase ion chemistry

    SciTech Connect

    Stephenson, J.L. Jr.; McLuckey, S.A.

    1997-02-01

    Cations derived from oligopeptides ranging from laminin fragment (5 residues) to {beta}-lactoglobulin (162 residues) have been subjected to gas-phase ion/molecule reactions with hydroiodic acid. The sum of the ion charge state and the maximum number of molecules of hydroiodic acid that attach to the ion is equal to the total number of lysines, arginines, histidines, and N-termini consisting of a primary amine for ions derived from all 21 oligopeptides studied. These results suggest that ion/molecule reactions can provide useful information regarding oligopeptide basic site number, which might be used as a criterion for searching protein data bases instead of, or in conjunction with, use of proteolytic digestion or gas-phase ion dissociation procedures. 31 refs., 3 figs., 1 tab.

  2. Structural Symmetry in Membrane Proteins.

    PubMed

    Forrest, Lucy R

    2015-01-01

    Symmetry is a common feature among natural systems, including protein structures. A strong propensity toward symmetric architectures has long been recognized for water-soluble proteins, and this propensity has been rationalized from an evolutionary standpoint. Proteins residing in cellular membranes, however, have traditionally been less amenable to structural studies, and thus the prevalence and significance of symmetry in this important class of molecules is not as well understood. In the past two decades, researchers have made great strides in this area, and these advances have provided exciting insights into the range of architectures adopted by membrane proteins. These structural studies have revealed a similarly strong bias toward symmetric arrangements, which were often unexpected and which occurred despite the restrictions imposed by the membrane environment on the possible symmetry groups. Moreover, membrane proteins disproportionately contain internal structural repeats resulting from duplication and fusion of smaller segments. This article discusses the types and origins of symmetry in membrane proteins and the implications of symmetry for protein function.

  3. Water in protein structure prediction

    PubMed Central

    Papoian, Garegin A.; Ulander, Johan; Eastwood, Michael P.; Luthey-Schulten, Zaida; Wolynes, Peter G.

    2004-01-01

    Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins. Free energy profile analysis suggests that long-range water-mediated potentials guide folding and smooth the underlying folding funnel. Analyzing simulation trajectories gives direct evidence that water-mediated interactions facilitate native-like packing of supersecondary structural elements. Long-range pairing of hydrophilic groups is an integral part of protein architecture. Specific water-mediated interactions are a universal feature of biomolecular recognition landscapes in both folding and binding. PMID:14988499

  4. Evidence for a Quasi-Equilibrium Distribution of States for Bradykinin [M+3H]3+ Ions in the Gas Phase

    PubMed Central

    Pierson, Nicholas A.; Valentine, Stephen J.; Clemmer, David E.

    2010-01-01

    Multidimensional ion mobility spectrometry coupled with mass spectrometry (IMS–IMS-MS) techniques are used to select and activate six different gas-phase conformations of bradykinin [M+3H]3+ ions. Drift time distributions as a function of activation voltage show that at low voltages selected structures undergo conformational transitions in what appears to be a pathway dependent fashion. Over a relatively wide range of intermediate activation voltages a distribution of states that is independent of the initial conformation selected for activation (as well as the activation voltage in this intermediate region) is established. This distribution appears to represent an equilibrium distribution of gas-phase structures that is reached prior to the energy required for dissociation. Establishment of a quasi-equilibrium prior to dissociation results in identical dissociation patterns for different selected conformations. A discussion of the transition from solution-like to gas-phase structures is provided. PMID:20469905

  5. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

    NASA Astrophysics Data System (ADS)

    Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

    2016-11-01

    We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.

  6. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry.

    PubMed

    Bythell, Benjamin J; Abutokaikah, Maha T; Wagoner, Ashley R; Guan, Shanshan; Rabus, Jordan M

    2016-11-28

    We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the (0,2) A 2 ion from the sodiated forms. Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies. Graphical Abstract ᅟ.

  7. Cationized Carbohydrate Gas-Phase Fragmentation Chemistry

    NASA Astrophysics Data System (ADS)

    Bythell, Benjamin J.; Abutokaikah, Maha T.; Wagoner, Ashley R.; Guan, Shanshan; Rabus, Jordan M.

    2017-04-01

    We investigate the fragmentation chemistry of cationized carbohydrates using a combination of tandem mass spectrometry, regioselective labeling, and computational methods. Our model system is D-lactose. Barriers to the fundamental glyosidic bond cleavage reactions, neutral loss pathways, and structurally informative cross-ring cleavages are investigated. The most energetically favorable conformations of cationized D-lactose were found to be similar. In agreement with the literature, larger group I cations result in structures with increased cation coordination number which require greater collision energy to dissociate. In contrast with earlier proposals, the B n -Y m fragmentation pathways of both protonated and sodium-cationized analytes proceed via protonation of the glycosidic oxygen with concerted glycosidic bond cleavage. Additionally, for the sodiated congeners our calculations support sodiated 1,6-anhydrogalactose B n ion structures, unlike the preceding literature. This affects the subsequent propensity of formation and prediction of B n /Y m branching ratio. The nature of the anomeric center (α/β) affects the relative energies of these processes, but not the overall ranking. Low-energy cross-ring cleavages are observed for the metal-cationized analytes with a retro-aldol mechanism producing the 0,2 A 2 ion from the sodiated forms . Theory and experiment support the importance of consecutive fragmentation processes, particularly for the protonated congeners at higher collision energies.

  8. Gas Phase Hydration of Methyl Glyoxal to Form the Gemdiol

    NASA Astrophysics Data System (ADS)

    Kroll, Jay A.; Axson, Jessica L.; Vaida, Veronica

    2016-06-01

    Methylglyoxal is a known oxidation product of volatile organic compounds (VOCs) in Earth's atmosphere. While the gas phase chemistry of methylglyoxal is fairly well understood, its modeled concentration and role in the formation of secondary organic aerosol (SOA) continues to be controversial. The gas phase hydration of methylglyoxal to form a gemdiol has not been widely considered for water-restricted environments such as the atmosphere. However, this process may have important consequences for the atmospheric processing of VOCs. We will report on spectroscopic work done in the Vaida laboratory studying the hydration of methylglyoxal and discuss the implications for understanding the atmospheric processing and fate of methylglyoxal and similar molecules.

  9. Membrane proteins bind lipids selectively to modulate their structure and function

    PubMed Central

    Allison, Timothy M.; Ulmschneider, Martin B.; Degiacomi, Matteo T.; Baldwin, Andrew J.; Robinson, Carol V.

    2014-01-01

    Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments1-7 and that lipids can bind to specific sites, for example in potassium channels8. Fundamental questions remain however regarding the extent of membrane protein selectivity toward lipids. Here we report a mass spectrometry (MS) approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL), aquaporin Z (AqpZ), and the ammonia channel (AmtB) using ion mobility MS (IM-MS), which reports gas-phase collision cross sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas-phase. By resolving lipid-bound states we then rank bound lipids based on their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Results show that lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability, the highest-ranking lipid however is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation9. AqpZ is also stabilized by many lipids with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays, we discover that cardiolipin modulates AqpZ function. Analogous experiments identify AmtB as being highly selective for phosphatidylglycerol prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that reposition AmtB residues to interact with the lipid bilayer. Overall our results demonstrate that resistance to unfolding correlates with specific lipid-binding events enabling distinction of lipids that merely bind from those that modulate membrane protein structure and/or function. We anticipate that these

  10. Photoelectron Velocity Map Imaging of Vibrationally Excited, Gas-Phase Biomolecules and Their Anions

    NASA Astrophysics Data System (ADS)

    Bakker, Daniël; Bakels, Sjors; van der Made, Rutger; Peters, Atze; Rijs, Anouk

    2016-06-01

    A powerful method in spectroscopy to characterize the structure of large, gas phase molecules is to probe the ionization yield upon irradiating the molecules with infrared (IR) and/or ultraviolet (UV) radiation. When this spectroscopic technique is employed, the photodetached electrons are usually ignored, although they contain information on, for example, the ionization threshold of the molecule and the excited states of the formed ions. Here, the novel combination of a molecular beam mass spectrometer equipped with a laser desorption source, the free electron laser FELIX and the powerful velocity map imaging (VMI) technique is presented. With this extended set of tools we can bring large molecules intact into the gas phase and prepare them in specific vibrationally excited states. UV or VUV radiation can subsequently be used to ionize the molecules. The kinetic energy and the radial distribution of the photoelectrons can be measured using VMI combined with ion detection using a time-of-flight mass spectrometer.

  11. Taming molecular beams; towards a gas-phase molecular laboratory on a chip

    NASA Astrophysics Data System (ADS)

    Meek, Samuel A.; Santambrogio, Gabriele; Conrad, Horst; Meijer, Gerard

    2009-11-01

    The manipulation of gas-phase molecules with electric and magnetic fields above a chip is an emerging field of research. Miniaturization of the electric and magnetic field structures allows for the creation of large field gradients and tight traps above the chip. Present-day microelectronics technology enables the integration of complicated tools and devices on a compact surface area. The molecules can be positioned extremely accurately and reproducibly above the chip where they can be held isolated from their environment and where there is excellent access to them. It is expected that several of the gas-phase molecular beam experiments that are currently being done in machines that are up to several meters in length can in the future be performed on a surface area of a few cm2 and that many new experiments will become possible.

  12. Protein interfacial structure and nanotoxicology

    NASA Astrophysics Data System (ADS)

    White, John W.; Perriman, Adam W.; McGillivray, Duncan J.; Lin, Jhih-Min

    2009-02-01

    Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between β-casein and κ-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a β-casein monolayer is attacked by a κ-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a β-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle "corona" thought to be important for nanoparticle-cell wall penetration.

  13. Ion-Molecule Reactions in Gas Phase Radiation Chemistry.

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

    Discusses some aspects of the radiation chemistry of gases, focusing on the ion-molecule and charge neutralization reactions which set study of the gas phase apart. Uses three examples that illustrate radiolysis, describing the radiolysis of (1) oxygen, (2) carbon dioxide, and (3) acetylene. (CS)

  14. Ion-Molecule Reactions in Gas Phase Radiation Chemistry.

    ERIC Educational Resources Information Center

    Willis, Clive

    1981-01-01

    Discusses some aspects of the radiation chemistry of gases, focusing on the ion-molecule and charge neutralization reactions which set study of the gas phase apart. Uses three examples that illustrate radiolysis, describing the radiolysis of (1) oxygen, (2) carbon dioxide, and (3) acetylene. (CS)

  15. CHEMKIN2. General Gas-Phase Chemical Kinetics

    SciTech Connect

    Rupley, F.M.

    1992-01-24

    CHEMKIN is a high-level tool for chemists to use to describe arbitrary gas-phase chemical reaction mechanisms and systems of governing equations. It remains, however, for the user to select and implement a solution method; this is not provided. It consists of two major components: the Interpreter and the Gas-phase Subroutine Library. The Interpreter reads a symbolic description of an arbitrary, user-specified chemical reaction mechanism. A data file is generated which forms a link to the Gas-phase Subroutine Library, a collection of about 200 modular subroutines which may be called to return thermodynamic properties, chemical production rates, derivatives of thermodynamic properties, derivatives of chemical production rates, or sensitivity parameters. Both single and double precision versions of CHEMKIN are included. Also provided is a set of FORTRAN subroutines for evaluating gas-phase transport properties such as thermal conductivities, viscosities, and diffusion coefficients. These properties are an important part of any computational simulation of a chemically reacting flow. The transport properties subroutines are designed to be used in conjunction with the CHEMKIN Subroutine Library. The transport properties depend on the state of the gas and on certain molecular parameters. The parameters considered are the Lennard-Jones potential well depth and collision diameter, the dipole moment, the polarizability, and the rotational relaxation collision number.

  16. INVESTIGATION OF GAS-PHASE OZONE AS A POTENTIAL BIOCIDE

    EPA Science Inventory

    The paper presents data on the effect of ozone on both vegetative and spore-forming fungi as well as on spore-forming bacteria. (NOTE: Despite the wide use of ozone generators in indoor air cleaning, there is little research data on ozone's biocidal activity in the gas phase.) Dr...

  17. INVESTIGATION OF GAS-PHASE OZONE AS A POTENTIAL BIOCIDE

    EPA Science Inventory

    The paper presents data on the effect of ozone on both vegetative and spore-forming fungi as well as on spore-forming bacteria. (NOTE: Despite the wide use of ozone generators in indoor air cleaning, there is little research data on ozone's biocidal activity in the gas phase.) Dr...

  18. Structural reconstruction of protein ancestry.

    PubMed

    Rouet, Romain; Langley, David B; Schofield, Peter; Christie, Mary; Roome, Brendan; Porebski, Benjamin T; Buckle, Ashley M; Clifton, Ben E; Jackson, Colin J; Stock, Daniela; Christ, Daniel

    2017-03-29

    Ancestral protein reconstruction allows the resurrection and characterization of ancient proteins based on computational analyses of sequences of modern-day proteins. Unfortunately, many protein families are highly divergent and not suitable for sequence-based reconstruction approaches. This limitation is exemplified by the antigen receptors of jawed vertebrates (B- and T-cell receptors), heterodimers formed by pairs of Ig domains. These receptors are believed to have evolved from an extinct homodimeric ancestor through a process of gene duplication and diversification; however molecular evidence has so far remained elusive. Here, we use a structural approach and laboratory evolution to reconstruct such molecules and characterize their interaction with antigen. High-resolution crystal structures of reconstructed homodimeric receptors in complex with hen-egg white lysozyme demonstrate how nanomolar affinity binding of asymmetrical antigen is enabled through selective recruitment and structural plasticity within the receptor-binding site. Our results provide structural evidence in support of long-held theories concerning the evolution of antigen receptors, and provide a blueprint for the experimental reconstruction of protein ancestry in the absence of phylogenetic evidence.

  19. Improved machine learning method for analysis of gas phase chemistry of peptides.

    PubMed

    Gehrke, Allison; Sun, Shaojun; Kurgan, Lukasz; Ahn, Natalie; Resing, Katheryn; Kafadar, Karen; Cios, Krzysztof

    2008-12-03

    Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS) of peptides from complex digests with theoretically derived spectra from a database of protein sequences. Improved discrimination is achieved with theoretical spectra that are based on simulating gas phase chemistry of the peptides, but the limited understanding of those processes affects the accuracy of predictions from theoretical spectra. We employed a robust data mining strategy using new feature annotation functions of MAE software, which revealed under-prediction of the frequency of occurrence in fragmentation of the second peptide bond. We applied methods of exploratory data analysis to pre-process the information in the MS/MS spectra, including data normalization and attribute selection, to reduce the attributes to a smaller, less correlated set for machine learning studies. We then compared our rule building machine learning program, DataSqueezer, with commonly used association rules and decision tree algorithms. All used machine learning algorithms produced similar results that were consistent with expected properties for a second gas phase mechanism at the second peptide bond. The results provide compelling evidence that we have identified underlying chemical properties in the data that suggest the existence of an additional gas phase mechanism for the second peptide bond. Thus, the methods described in this study provide a valuable approach for analyses of this kind in the future.

  20. Improved machine learning method for analysis of gas phase chemistry of peptides

    PubMed Central

    Gehrke, Allison; Sun, Shaojun; Kurgan, Lukasz; Ahn, Natalie; Resing, Katheryn; Kafadar, Karen; Cios, Krzysztof

    2008-01-01

    Background Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS) of peptides from complex digests with theoretically derived spectra from a database of protein sequences. Improved discrimination is achieved with theoretical spectra that are based on simulating gas phase chemistry of the peptides, but the limited understanding of those processes affects the accuracy of predictions from theoretical spectra. Results We employed a robust data mining strategy using new feature annotation functions of MAE software, which revealed under-prediction of the frequency of occurrence in fragmentation of the second peptide bond. We applied methods of exploratory data analysis to pre-process the information in the MS/MS spectra, including data normalization and attribute selection, to reduce the attributes to a smaller, less correlated set for machine learning studies. We then compared our rule building machine learning program, DataSqueezer, with commonly used association rules and decision tree algorithms. All used machine learning algorithms produced similar results that were consistent with expected properties for a second gas phase mechanism at the second peptide bond. Conclusion The results provide compelling evidence that we have identified underlying chemical properties in the data that suggest the existence of an additional gas phase mechanism for the second peptide bond. Thus, the methods described in this study provide a valuable approach for analyses of this kind in the future. PMID:19055745

  1. Method for protein structure alignment

    DOEpatents

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  2. Conformational Study of DNA Sugars: from the Gas Phase to Solution

    NASA Astrophysics Data System (ADS)

    Uriarte, Iciar; Vallejo-López, Montserrat; Cocinero, Emilio J.; Corzana, Francisco; Davis, Benjamin G.

    2017-06-01

    Sugars are versatile molecules that play a variety of roles in the organism. For example, they are important in energy storage processes or as structural scaffolds. Here, we focus on the monosaccharide present in DNA by addressing the conformational and puckering properties in the gas phase of α- and β-methyl-2-deoxy-ribofuranoside and α- and β-methyl-2-deoxy-ribopiranoside. Other sugars have been previously studied in the gas phase The work presented here stems from a combination of chemical synthesis, ultrafast vaporization methods, supersonic expansions, microwave spectroscopy (both chirped-pulsed and Balle-Flygare cavity-based spectrometers) and NMR spectroscopy. Previous studies in the gas phase had been performed on 2-deoxyribose, but only piranose forms were detected. However, thanks to the combination of these techniques, we have isolated and characterized for the first time the conformational landscape of the sugar present in DNA in its biologically relevant furanose form. Our gas phase study serves as a probe of the conformational preferences of these biomolecules under isolation conditions. Thanks to the NMR experiments, we can characterize the favored conformations in solution and extract the role of the solvent in the structure and puckering of the monosaccharides. E. J. Cocinero, A. Lesarri, P. Écija, F. J. Basterretxea, J.-U. Grabow, J. A. Fernández, F. Castaño, Angew. Chem. Int. Edit. 2012, 51, 3119. P. Écija, I. Uriarte, L. Spada, B. G. Davis, W. Caminati, F. J. Basterretxea, A. Lesarri, E. J. Cocinero, Chem. Commun. 2016, 52, 6241. I. Peña, E. J. Cocinero, C. Cabezas, A. Lesarri, S. Mata, P. Écija, A. M. Daly, Á. Cimas, C. Bermúdez, F. J. Basterretxea, S. Blanco, J. A. Fernández, J. C. López, F. Castaño, J. L. Alonso, Angew. Chem. Int. Edit. 2013, 52, 11840.

  3. Noncovalent Halogen Bonding as a Mechanism for Gas-Phase Clustering

    NASA Astrophysics Data System (ADS)

    Wegeberg, Christina; Donald, William A.; McKenzie, Christine J.

    2017-10-01

    Gas-phase clustering of nonionizable iodylbenzene (PhIO2) is attributed to supramolecular halogen bonding. Electrospray ionization results in the formation of ions of proton-charged and preferably sodium-charged clusters assignable to [H(PhIO2) n ]+, n = 1-7; [Na(PhIO2) n ]+, n = 1-6; [Na2(PhIO2) n ]2+, n = 7-20; [HNa(PhIO2) n ]2+, n = 6-19; [HNa2(PhIO2) n ]3+, n = 15-30; and [Na3(PhIO2) n ]3+, n = 14-30. The largest cluster detected has a supramolecular mass of 7147 Da. Electronic structure calculations using the M06-2X functional with the 6-311++G(d,p) basis set for C, H, and O, and LANL2DZ basis set for I and Na predict 298 K binding enthalpies for the protonated and sodiated iodylbenzene dimers and trimers are greater than 180 kJ/mol. This is exceptionally high in comparison with other protonated and sodiated clusters with well-established binding enthalpies. Strongly halogen-bonded motifs found in the crystalline phases of PhIO2 and its derivatives serve as models for the structures of larger gas-phase clusters, and calculations on simple model gas-phase dimer and trimer clusters result in similar motifs. This is the first account of halogen bonding playing an extensive role in gas-phase associations. [Figure not available: see fulltext.

  4. Protein structure refinement by optimization.

    PubMed

    Carlsen, Martin; Røgen, Peter

    2015-09-01

    Knowledge-based protein potentials are simplified potentials designed to improve the quality of protein models, which is important as more accurate models are more useful for biological and pharmaceutical studies. Consequently, knowledge-based potentials often are designed to be efficient in ordering a given set of deformed structures denoted decoys according to how close they are to the relevant native protein structure. This, however, does not necessarily imply that energy minimization of this potential will bring the decoys closer to the native structure. In this study, we introduce an iterative strategy to improve the convergence of decoy structures. It works by adding energy optimized decoys to the pool of decoys used to construct the next and improved knowledge-based potential. We demonstrate that this strategy results in significantly improved decoy convergence on Titan high resolution decoys and refinement targets from Critical Assessment of protein Structure Prediction competitions. Our potential is formulated in Cartesian coordinates and has a fixed backbone potential to restricts motions to be close to those of a dihedral model, a fixed hydrogen-bonding potential and a variable coarse grained carbon alpha potential consisting of a pair potential and a novel solvent potential that are b-spline based as we use explicit gradient and Hessian for efficient energy optimization. © 2015 Wiley Periodicals, Inc.

  5. Insights into the structures of the gas-phase hydrated cations M⁺(H₂O)(n)Ar (M = Li, Na, K, Rb, and Cs; n = 3-5) using infrared photodissociation spectroscopy and thermodynamic analysis.

    PubMed

    Ke, Haochen; van der Linde, Christian; Lisy, James M

    2015-03-12

    The hydration of alkali cations yields a variety of structural conformers with varying numbers of water molecules in the first solvation shell. How these ions move from the aqueous phase into biological systems, such as at the entrance of an ion channel, depends on the interplay between competing intermolecular forces, which first must involve ion-water and water-water interactions. New infrared action spectra, using argon as a messenger or "spy", for Li(+), Na(+), and K(+), with up to five water molecules are reported, and new structural conformers determined from ab initio calculations, combined with previous results on Rb(+) and Cs(+), have identified structural transitions at each hydration level. These transitions are a result of the delicate balance between competing noncovalent interactions and represent a quantitative microscopic view of the macroscopic enthalpy-entropy competition between energy and structural variety. Smaller cations (Li(+) and Na(+)), with higher charge density, yield structural configurations with extended linear networks of hydrogen bonds. Larger cations (Rb(+) and Cs(+)), with lower charge density, generate configurations with cyclic hydrogen-bonded water subunits. It appears that K(+) is somewhat unique, with very simple (and predominantly) single structural conformers. This has led to the suggestion that K(+) can "move" easily in or through biological systems, concealing its identity as an ion, under the "appearance" or disguise of a water molecule.

  6. Secondary structure determines protein topology

    PubMed Central

    Fleming, Patrick J.; Gong, Haipeng; Rose, George D.

    2006-01-01

    Using a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long-range interactions. It has been a long-standing open question whether such information is sufficient to determine a protein's fold. Indeed, even the far simpler problem of reconstructing the three-dimensional structure of a protein from its exact backbone torsion angles has remained a difficult challenge owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, cause large errors in structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm; the longer the arm, the larger the displacement. Here, correct secondary structure assignments (α-helix, β-strand, β-turn, polyproline II, coil) were used to constrain polypeptide backbone chains devoid of side chains, and the most stable folded conformations were determined, using Monte Carlo simulation. Just three terms were used to assess stability: molecular compaction, steric exclusion, and hydrogen bonding. For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them. PMID:16823044

  7. Structural entanglements in protein complexes

    NASA Astrophysics Data System (ADS)

    Zhao, Yani; Chwastyk, Mateusz; Cieplak, Marek

    2017-06-01

    We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both termini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK, and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.

  8. Seleniranium Ions Undergo π-Ligand Exchange via an Associative Mechanism in the Gas Phase.

    PubMed

    Lim, S Fern; Harris, Benjamin L; Khairallah, George N; Bieske, E J; Maître, Philippe; da Silva, Gabriel; Adamson, Brian D; Scholz, Michael S; Coughlan, Neville J A; O'Hair, Richard A J; Rathjen, Michael; Stares, Daniel; White, Jonathan M

    2017-06-16

    Collision-induced dissociation mass spectrometry of the ammonium ions 4a and 4b results in the formation of the seleniranium ion 5, the structure and purity of which were verified using gas-phase infrared spectroscopy coupled to mass spectrometry and gas-phase ion-mobility measurements. Ion-molecule reactions between the ion 5 (m/z = 261) and cyclopentene, cyclohexene, cycloheptene, and cyclooctene resulted in the formation of the seleniranium ions 7 (m/z = 225), 6 (m/z = 239), 8 (m/z = 253), and 9 (m/z = 267), respectively. Further reaction of seleniranium 6 with cyclopentene resulted in further π-ligand exchange giving seleniranium ion 7, confirming that direct π-ligand exchange between seleniranium ion 5 and cycloalkenes occurs in the gas phase. Pseudo-first-order kinetics established relative reaction efficiencies for π-ligand exchange for cyclopentene, cyclohexene, cycloheptene. and cyclooctene as 0.20, 0.07, 0.43, and 4.32. respectively. DFT calculations at the M06/6-31+G(d) level of theory provide the following insights into the mechanism of the π-ligand exchange reactions; the cycloalkene forms a complex with the seleniranium ion 5 with binding energies of 57 and 62 kJ/mol for cyclopentene and cyclohexene, respectively, with transition states for π-ligand exchange having barriers of 17.8 and 19.3 kJ/mol for cyclopentene and cyclohexene, respectively.

  9. Statistical parameter characteristics of gas-phase fluctuations for gas-liquid intermittent flow

    SciTech Connect

    Matsui, G.; Monji, H.; Takaguchi, M.

    1995-09-01

    This study deals with theoretical analysis on the general behaviour of statistical parameters of gas-phase fluctuations and comparison of statistical parameter characteristics for the real void fraction fluctuations measured with those for the wave form modified the real fluctuations. In order to investigate the details of the relation between the behavior of the statistical parameters in real intermittent flow and analytical results obtained from information on the real flow, the distributions of statistical parameters for general fundamental wave form of gas-phase fluctuations are discussed in detail. By modifying the real gas-phase fluctuations to a trapezoidaly wave, the experimental results can be directly compared with the analytical results. The analytical results for intermittent flow show that the wave form parameter, and the total amplitude of void fraction fluctuations, affects strongly on the statistical parameter characteristics. The comparison with experiment using nitrogen gas-water intermittent flow suggests that the parameters of skewness and excess may be better as indicators of flow pattern. That is, the macroscopic nature of intermittent flow can be grasped by the skewness and the excess, and the detailed flow structure may be described by the mean and the standard deviation.

  10. The Decomposition of Hydrazine in the Gas Phase and over an Iridium Catalyst

    SciTech Connect

    Schmidt, Michael W.; Gordon, Mark S.

    2013-09-30

    Hydrazine is an important rocket fuel, used as both a monopropellant and a bipropellant. This paper presents theoretical results to complement the extensive experimental studies of the gas phase and Ir catalyzed decompositions involved in the monopropellant applications of hydrazine. Gas phase electronic structure theory calculations that include electron correlation predict that numerous molecular and free radical reactions occur within the same energy range as the basic free radical pathways: NN bond breaking around 65 kcal/mol and NH bond breaking around 81 kcal/mol. The data suggest that a revision to existing kinetics modeling is desirable, based on the energetics and the new elementary steps reported herein. A supported Ir-6 octahedron model for the Shell 405 Iridium catalyst used in thrusters was developed. Self-Consistent Field and electron correlation calculations (with core potentials and associated basis sets) find a rich chemistry for hydrazine on this catalyst model. The model catalyst provides dramatically lower NN and NH bond cleavage energies and an even smaller barrier to breaking the NH bond by NH2 abstractions. Thus, the low temperature decomposition over the catalyst is interpreted in terms of consecutive NH2 abstractions to produce ammonia and nitrogen. The higher temperature channel, which has hydrogen and nitrogen products, may be due to a mixture of two mechanisms. These two mechanisms are successive NH cleavages with surface H + H recombinations, and the same type of assisted H-2 eliminations found to occur in the gas phase part of this study.

  11. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

    PubMed Central

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-01-01

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic–inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios. PMID:27876797

  12. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-11-01

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

  13. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition.

    PubMed

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-11-23

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

  14. Enantiomer-Selective Photo-Induced Reaction of Protonated Tryptophan with Disaccharides in the Gas Phase.

    PubMed

    Doan, Thuc N; Fujihara, Akimasa

    2017-07-08

    In order to investigate chemical evolution in interstellar molecular clouds, enantiomer-selective photo-induced chemical reactions between an amino acid and disaccharides in the gas phase were examined using a tandem mass spectrometer containing an electrospray ionization source and a cold ion trap. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of protonated tryptophan (Trp) enantiomers with disaccharides consisting of two D-glucose units, such as D-maltose or D-cellobiose, were obtained by photoexcitation of the indole ring of Trp. NH2CHCOOH loss via cleavage of the Cα-Cβ bond in Trp induced by hydrogen atom transfer from the NH3(+) group of a protonated Trp was observed in a noncovalent heterochiral H(+)(L-Trp)(D-maltose) complex. In contrast, a photo-induced chemical reaction forming the product ion with m/z 282 occurs in homochiral H(+)(D-Trp)(D-maltose). For D-cellobiose, both NH2CHCOOH elimination and the m/z 282 product ion were observed, and no enantiomer-selective phenomena occurred. The m/z 282 product ion indicates that the photo-induced C-glycosylation, which links D-glucose residues to the indole moiety of Trp via a C-C bond, can occur in cold gas-phase noncovalent complexes, and its enantiomer-selectivity depends on the structure of the disaccharide.

  15. Enantiomer-Selective Photo-Induced Reaction of Protonated Tryptophan with Disaccharides in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Doan, Thuc N.; Fujihara, Akimasa

    2017-07-01

    In order to investigate chemical evolution in interstellar molecular clouds, enantiomer-selective photo-induced chemical reactions between an amino acid and disaccharides in the gas phase were examined using a tandem mass spectrometer containing an electrospray ionization source and a cold ion trap. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of protonated tryptophan (Trp) enantiomers with disaccharides consisting of two uc(d)-glucose units, such as uc(d)-maltose or uc(d)-cellobiose, were obtained by photoexcitation of the indole ring of Trp. NH2CHCOOH loss via cleavage of the Cα-Cβ bond in Trp induced by hydrogen atom transfer from the NH3 + group of a protonated Trp was observed in a noncovalent heterochiral H+(uc(l)-Trp)(uc(d)-maltose) complex. In contrast, a photo-induced chemical reaction forming the product ion with m/z 282 occurs in homochiral H+(uc(d)-Trp)(uc(d)-maltose). For uc(d)-cellobiose, both NH2CHCOOH elimination and the m/z 282 product ion were observed, and no enantiomer-selective phenomena occurred. The m/z 282 product ion indicates that the photo-induced C-glycosylation, which links uc(d)-glucose residues to the indole moiety of Trp via a C-C bond, can occur in cold gas-phase noncovalent complexes, and its enantiomer-selectivity depends on the structure of the disaccharide.

  16. Protein Structure Comparison and Classification

    NASA Astrophysics Data System (ADS)

    Çamoǧlu, Orhan; Singh, Ambuj K.

    The success of genome projects has generated an enormous amount of sequence data. In order to realize the full value of the data, we need to understand its functional role and its evolutionary origin. Sequence comparison methods are incredibly valuable for this task. However, for sequences falling in the twilight zone (usually between 20 and 35% sequence similarity), we need to resort to structural alignment and comparison for a meaningful analysis. Such a structural approach can be used for classification of proteins, isolation of structural motifs, and discovery of drug targets.

  17. Servers for protein structure prediction.

    PubMed

    Fischer, Daniel

    2006-04-01

    The 1990s cultivated a generation of protein structure human predictors. As a result of structural genomics and genome sequencing projects, and significant improvements in the performance of protein structure prediction methods, a generation of automated servers has evolved in the past few years. Servers for close and distant homology modeling are now routinely used by many biologists, and have already been applied to the experimental structure determination process itself, and to the interpretation and annotation of genome sequences. Because dozens of servers are currently available, it is hard for a biologist to know which server(s) to use; however, the state of the art of these methods is now assessed through the LiveBench and CAFASP experiments. Meta-servers--servers that use the results of other autonomous servers to produce a consensus prediction--have proven to be the best performers, and are already challenging all but a handful of expert human predictors. The difference in performance of the top ten autonomous (non-meta) servers is small and hard to assess using relatively small test sets. Recent experiments suggest that servers will soon free humans from most of the burden of protein structure prediction.

  18. Cation-ether complexes in the gas phase: Bond dissociation energies and equilibrium structures of Li{sup +}[O(CH{sub 3}){sub 2}]{sub x}, x=1-4

    SciTech Connect

    More, M.B.; Armentrout, P.B.; Glendening, E.D.; Ray, D.; Feller, D.

    1996-02-01

    Bond dissociation energies, equilibrium structures, and harmonic vibrational frequencies of Li{sup +}[O(CH{sub 3}){sub 2}]{sub x}, x=1-4, are reported. The bond dissociation energies are determined experimentally by analysis of the thresholds for collision-induced dissociation of the cation-ether complexes by xenon (measured using guided ion beam mass spectrometry) and computationally by ab initio electronic structure calculation at the RHF and MP2 levels of theory. In all cases, the primary and lowest energy dissociation channel observed experimentally is endothermic loss of one ether molecule. The cross-section thresholds are interpreted to yield 0 and 298 K bond energies after accounting for the effects of multiple ion-molecule collisions, internal energy of the complexes, and unimolecular decay rates. The experimental and theoretical bond energies are in good agreement with previous experimental results. Some of the discrepancies disappear at the complete basis set limit. The equilibrium structures are determined primarily by strong electrostatic and polarization interactions. Charge transfer interactions are also important, as indicated by natural energy decomposition analysis of the calculated wave functions. 59 refs., 6 figs., 5 tabs.

  19. Solid- and gas-phase structures and spectroscopic and chemical properties of tris(pentafluorosulfanyl)amine, N(SF5)3, and bis(pentafluorosufanyl)aminyl radical, rad N(SF5)2

    NASA Astrophysics Data System (ADS)

    Nielsen, Jon B.; Zylka, Petra; Kronberg, Marc; Zeng, Xiaoqing; Robinson, Kerry D.; Bott, Simon G.; Zhang, Hongming; Atwood, Jerry L.; Oberhammer, Heinz; Willner, Helge; Thrasher, Joseph S.

    2017-03-01

    Tris(pentafluorosulfanyl)amine, N(SF5)3, and the bis(pentafluorosulfanyl)aminyl radical, rad N(SF5)2, have been synthesized and characterized by gas electron diffraction, single crystal XRD, NMR, EPR, FT-IR, Raman, and UV-vis spectroscopy, and by their thermal decompositions. The amine possesses a planar molecular structure of D3 symmetry with an unusually long Nsbnd S bond of 1.829(6) Å. The long Nsbnd S bonds are in accordance with the small Arrhenius activation barrier for the decay into rad N(SF5)2 and rad SF5 radicals of 6.9 kcal mol-1, and its half-life at room temperature is only 50 min. The aminyl radical possesses C2 symmetry with Nsbnd S = 1.692(4) Å and Ssbnd Nsbnd S = 135.1(5)°, and its structure is similar to that of FN(SF5)2. This radical is much more stable than the amine (half-life at room temperature is 130 min). Dimerization and formation of the corresponding hydrazine, (SF5)2NN(SF5)2, was not observed, nor was the nitrene:NSF5 or its isomer FNdbnd SF4.

  20. Insights into gas-phase structural conformers of hydrated rubidium and cesium cations, M(+)(H2O)(n)Ar (M = Rb, Cs; n = 3-5), using infrared photodissociation spectroscopy.

    PubMed

    Ke, Haochen; van der Linde, Christian; Lisy, James M

    2014-02-27

    Infrared photodissociation (IRPD) spectra of M(+)(H2O)nAr (M = Rb, Cs; n = 3-5) with simultaneous monitoring of [Ar] and [Ar+H2O] fragmentation channels are reported. The comparison between the spectral features in the two channels and corresponding energy analysis provide spectral assignments of the stable structural conformers and insight into the competition between ion-water electrostatic and water-water hydrogen bonding interactions. Results show that as the level of hydration increases, the water-water interaction exhibits the tendency to dominate over the ion-water interaction. Cyclic water tetramer and water pentamer substructures appear in Cs(+)(H2O)4Ar and Cs(+)(H2O)5Ar systems, respectively. However, cyclic water tetramer and pentamer structures were not observed for Rb(+)(H2O)4Ar and Rb(+)(H2O)5Ar systems, respectively, due to the stronger influence of the rubidium ion-water electrostatic interaction. The energy analysis, including the available internal energy and the IR photon energy, helped provide an experimental estimate of water binding energies.

  1. Gas Phase Chiral Separations By Ion Mobility Spectrometry

    PubMed Central

    Dwivedi, Prabha; Wu, Ching; Hill, Herbert H.

    2013-01-01

    This manuscript introduces the concept of Chiral Ion Mobility Spectrometry (CIMS) and presents examples demonstrating the gas phase separation of enantiomers of a wide range of racemates including pharmaceuticals, amino acids and carbohydrates. CIMS is similar to traditional ion mobility spectrometry (IMS), where gas phase ions, when subjected to a potential gradient are separated at atmospheric pressure due to differences in their shapes and sizes. In addition to size and shape, CIMS separates ions based on their stereospecific interaction with a chiral gas. In order to achieve chiral discrimination by CIMS, an asymmetric environment was provided by doping the drift gas with a volatile chiral reagent. In this study S-(+)-2-butanol was used as a chiral modifier to demonstrate enantiomeric separations of atenolol, serine, methionine, threonine, methyl-α-glucopyranoside, glucose, penicillamine, valinol, phenylalanine, and tryptophan from their respective racemic mixtures. PMID:17165808

  2. Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; McGee, William M.; Bu, Jiexun; Barefoot, Nathan Z.; McLuckey, Scott A.

    2015-01-01

    N-hydroxysuccinimide (NHS) esters have been used for gas-phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ɛ-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O18 were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas phase, where they are shown to be reactive, and the solution phase, where they are not regarded as reactive with NHS esters.

  3. Gas phase dynamics of triplet formation in benzophenone.

    PubMed

    Spighi, Gloria; Gaveau, Marc-André; Mestdagh, Jean-Michel; Poisson, Lionel; Soep, Benoît

    2014-05-28

    Benzophenone is a prototype molecule for photochemistry in the triplet state through its high triplet yield and reactivity. We have investigated its dynamics of triplet formation under the isolated gas phase conditions via femtosecond and nanosecond time resolved photoelectron spectroscopy. This represents the complete evolution from the excitation in S2 to the final decay of T1 to the ground state S0. We have found that the triplet formation can be described almost as a direct process in preparing T1, the lowest reacting triplet state, from the S1 state after S2 → S1 internal conversion. The molecule was also deposited by a pick-up technique on cold argon clusters providing a soft relaxation medium without evaporation of the molecule and the mechanism was identical. This cluster technique is a model for medium influenced electronic relaxation and provides a continuous transition from the isolated gas phase to the relaxation dynamics in solution.

  4. Gas-phase diffusion in porous media: Comparison of models

    SciTech Connect

    Webb, S.W.

    1998-09-01

    Two models are commonly used to analyze gas-phase diffusion in porous media in the presence of advection, the Advective-Dispersive Model (ADM) and the Dusty-gas Model (DGM). The ADM, which is used in TOUGH2, is based on a simple linear addition of advection calculated by Darcy`s law and ordinary diffusion using Fick`s law with a porosity-tortuosity-gas saturation multiplier to account for the porous medium. Another approach for gas-phase transport in porous media is the Dusty-Gas Model. This model applies the kinetic theory of gases to the gaseous components and the porous media (or dust) to combine transport due to diffusion and advection that includes porous medium effects. The two approaches are compared in this paper.

  5. Model of boron diffusion from gas phase in silicon carbide

    SciTech Connect

    Aleksandrov, O. V.; Mokhov, E. N.

    2011-06-15

    Boron diffusion from the gas phase in silicon carbide is described on the basis of a two-component model. 'Shallow' boron, i.e., boron at silicon sites, is a slow component with a high surface concentration. Its diffusivity is proportional to the concentration of positively charged intrinsic point defects, which are presumably interstitial silicon atoms. 'Deep' boron, i.e., impurity-defect pairs of boron-carbon vacancy, is a fast component with lower surface concentration. The ratio between the surface concentrations of the components depends on the pressure of silicon or carbon vapors in the gas phase. The diffusion and interaction of components are described by the set of diffusion-reaction equations. The diffusion retardation observed on the concentration-profile tail is related to the capture of impurity-defect pairs and excess vacancies by traps of background impurities and defects.

  6. Gas-Phase Studies of Formamidopyrimidine Glycosylase (Fpg) Substrates.

    PubMed

    Kiruba, G S M; Xu, Jiahui; Zelikson, Victoria; Lee, Jeehiun K

    2016-03-07

    Gas-phase thermochemical properties (tautomerism, acidity, and proton affinity) have been measured and calculated for a series of nucleobase derivatives that have not heretofore been examined under vacuum. The studied species are substrates for the enzyme formamidopyrimidine glycosylase (Fpg), which cleaves damaged nucleobases from DNA. The gas-phase results are compared and contrasted to solution-phase data, to afford insight into the Fpg mechanism. Calculations are also used to probe the energetics of various possible mechanisms and to predict isotope effects that could potentially allow for discrimination between different mechanisms. Specifically, (18) O substitution at the ribose O4' is predicted to result in a normal kinetic isotope effect (KIE) for a ring-opening "endocyclic" mechanism and an inverse KIE for a direct base excision "exocyclic" pathway.

  7. Spectroscopic studies of cold, gas-phase biomolecular ions

    NASA Astrophysics Data System (ADS)

    Rizzo, Thomas R.; Stearns, Jaime A.; Boyarkin, Oleg V.

    While the marriage of mass spectrometry and laser spectroscopy is not new, developments over the last few years in this relationship have opened up new horizons for the spectroscopic study of biological molecules. The combination of electrospray ionisation for producing large biological molecules in the gas phase together with cooled ion traps and multiple-resonance laser schemes are allowing spectroscopic investigation of individual conformations of peptides with more than a dozen amino acids. Highly resolved infrared spectra of single conformations of such species provide important benchmarks for testing the accuracy of theoretical calculations. This review presents a number of techniques employed in our laboratory and in others for measuring the spectroscopy of cold, gas-phase protonated peptides. We show examples that demonstrate the power of these techniques and evaluate their extension to still larger biological molecules.

  8. Para-Hydrogen-Enhanced Gas-Phase Magnetic Resonance Imaging

    SciTech Connect

    Bouchard, Louis-S.; Kovtunov, Kirill V.; Burt, Scott R.; Anwar,M. Sabieh; Koptyug, Igor V.; Sagdeev, Renad Z.; Pines, Alexander

    2007-02-23

    Herein, we demonstrate magnetic resonance imaging (MRI) inthe gas phase using para-hydrogen (p-H2)-induced polarization. A reactantmixture of H2 enriched in the paraspin state and propylene gas is flowedthrough a reactor cell containing a heterogenized catalyst, Wilkinson'scatalyst immobilized on modified silica gel. The hydrogenation product,propane gas, is transferred to the NMR magnet and is spin-polarized as aresult of the ALTADENA (adiabatic longitudinal transport and dissociationengenders net alignment) effect. A polarization enhancement factor of 300relative to thermally polarized gas was observed in 1D1H NMR spectra.Enhancement was also evident in the magnetic resonance images. This isthe first demonstration of imaging a hyperpolarized gaseous productformed in a hydrogenation reaction catalyzed by a supported catalyst.This result may lead to several important applications, includingflow-through porous materials, gas-phase reaction kinetics and adsorptionstudies, and MRI in low fields, all using catalyst-free polarizedfluids.

  9. Gas Phase Reactivity of Carboxylates with N-Hydroxysuccinimide Esters

    PubMed Central

    Peng, Zhou; McGee, William M.; Bu, Jiexun; Barefoot, Nathan Z.; McLuckey, Scott A.

    2015-01-01

    N-hydroxysuccinimide (NHS) esters have been used for gas phase conjugation reactions with peptides at nucleophilic sites, such as primary amines (N-terminus, ε-amine of lysine) or guanidines, by forming amide bonds through a nucleophilic attack on the carbonyl carbon. The carboxylate has recently been found to also be a reactive nucleophile capable of initiating a similar nucleophilic attack to form a labile anhydride bond. The fragile bond is easily cleaved, resulting in an oxygen transfer from the carboxylate-containing species to the reagent, nominally observed as a water transfer. This reactivity is shown for both peptides and non-peptidic species. Reagents isotopically labeled with O18 were used to confirm reactivity. This constitutes an example of distinct differences in reactivity of carboxylates between the gas-phase, where they are shown to be reactive, and the solution-phase, where they are not regarded as reactive with NHS esters. PMID:25338221

  10. Stabilizing factors of the molecular structure in silicon-based peptidomimetics in gas-phase and water solution. Assessment of the correlation between different descriptors of hydrogen bond strength.

    PubMed

    Rodríguez Ortega, María Pilar Gema; Montejo, Manuel; López González, Juan Jesús

    2013-10-01

    The use of DFT (B3LYP and M06L) and ab initio (MP2) computational methods allowed us to perform a thorough conformational study of N-[dihydroxy (methyl)silyl]methylformamide (DHSF) and 3-[dihydroxy (methyl) silyl] propanamide (DHSP), that could be considered simplified models of the environment of the silanediol group in silicon gem-diols that have proven efficiency as protease inhibitors. We have found a total of 13 molecular conformations that represent minima in the potential energy surfaces of DHSF (six conformers) and DHSP (seven conformers). The key feature in their molecular structure is the occurrence of intramolecular hydrogen bonding between the hydroxyl and aminocarbonyl groups. We have estimated the strength of each individual hydrogen bond in the mentioned species using the descriptors proposed by three different methodologies, i.e., the quantum theory of atoms in molecules (QTAIM), the natural bond orbitals population analysis (NBO), and the so-called empirical Rozenberg's enthalpy-distance relationship. We have found a good correlation among the calculated values for the different descriptors within the whole set of conformers in the molecular systems in this study. We have also discussed the predicted order of stabilities of the different conformers of each species in terms of the so-called ring anomeric effect (RAE) and generalized anomeric effect (GAE). Finally, we also analyzed the discrepancies found in the order of stability when going from the isolated molecule approximation to water solution (PCM).

  11. Gas-phase rate coefficients for reactions of NO 3, OH, O 3 and O( 3P) with unsaturated alcohols and ethers: Correlations and structure-activity relations (SARs)

    NASA Astrophysics Data System (ADS)

    Pfrang, Christian; King, Martin D.; Braeckevelt, Mareike; Canosa-Mas, Carlos E.; Wayne, Richard P.

    Experimental difficulties sometimes force modellers to use predicted rate coefficients for reactions of oxygenated volatile organic compounds (oVOCs). We examine here methods for making the predictions for reactions of atmospheric initiators of oxidation, NO 3, OH, O 3 and O( 3P), with unsaturated alcohols and ethers. Logarithmic correlations are found between measured rate coefficients and calculated orbital energies, and these correlations may be used directly to estimate rate coefficients for compounds where measurements have not been performed. To provide a shortcut that obviates the need to calculate orbital energies, structure-activity relations (SARs) are developed. Our SARs are tested for predictive power against compounds for which experimental rate coefficients exist, and their accuracy is discussed. Estimated atmospheric lifetimes for oVOCs are presented. The SARs for alkenols successfully predict key rate coefficients, and thus can be used to enhance the scope of atmospheric models incorporating detailed chemistry. SARs for the ethers have more limited applicability, but can still be useful in improving tropospheric models.

  12. The nucleoside uridine isolated in the gas phase.

    PubMed

    Peña, Isabel; Cabezas, Carlos; Alonso, José L

    2015-03-02

    Herein we present the first experimental observation of the isolated nucleoside uridine, placed in the gas phase by laser ablation and characterized by Fourier transform (FT) microwave techniques. Free from the bulk effects of their native environments, anti/C2'-endo-g+ conformation has been revealed as the most stable form of uridine. Intramolecular hydrogen bonds involving uracil and ribose moieties have been found to play an important role in the stabilization of the nucleoside.

  13. Modeling gas phase nitric oxide release in lung epithelial cells

    PubMed Central

    Jiang, Jingjing; George, Steven C.

    2012-01-01

    Nitric oxide (NO) is present in exhaled breath and is generally considered to be a noninvasive marker of airway inflammation, and is thus of particular relevance to monitoring asthma. NO is produced when l-arginine is converted to l-citrulline by NO synthase (NOS); however, l-arginine is also the substrate for arginase and both enzymes are upregulated in asthma. Recent reports have speculated that enhanced expression of one or both enzymes could lead to a limitation in substrate availability, and hence impact downstream targets or markers such as exhaled NO. The non-linear nature and vastly different kinetics of the enzymes make predictions difficult, particularly over the wide range of enzyme activity between baseline and inflammation. In this study, we developed a steady state model of l-arginine transmembrane transport, NO production, diffusion, and gas phase NO release from lung epithelial cells. We validated our model with experimental results of gas phase NO release and intracellular l-arginine concentration in A549 cells, and then performed a sensitivity analysis to determine relative impact of each enzyme on NO production. Our model predicts intracellular l-arginine and gas phase NO release over a wide range of initial extracellular l-arginine concentrations following stimulation with cytomix (10 ng/ml TNF-α, IL-1β, and INF-γ). Relative sensitivity analysis demonstrates that enhanced arginase activity has little impact on l-arginine bioavailability for NOS. In addition, NOS activity is the dominant parameter which impacts gas phase NO release. PMID:21550413

  14. The Kinetics and Dynamics of Elementary Gas-Phase Reactions

    DTIC Science & Technology

    2002-09-01

    Hawthorne Jati Salh Paul Sharkey Rowland Spencer-Smith Lee Herbert Meez Islam Chris Moore David Stewart Gary Ward Michael Osborne Sarah Henton...energy. The Kinetics and Dynamics of Elementary Gas Phase Reactions, 2002 23 REMPI-LIF Studies of Ion-Molecule Reactions Michael J. Frost...for the Study of Collisional Energy Transfer Hilary Crichton School of Engineering and Physical Sciences, Heriot-Watt University. Previous

  15. Laboratory Studies of Solvated Gas-Phase Anions.

    DTIC Science & Technology

    1982-02-01

    The Journal of Chemical Physics . 2. John F. Paulson, Michael J. Henchman, and Peter M. Hierl, "Effect of Reactant Ion Solvation on Gas-Phase SN2 Reactions," manuscript in final stages of preparation for submission to The Journal of Chemical Physics . D. PROFESSIONAL PERSONNEL Calvin Cole, Ph.D. Candidate, Department of Chemistry, University of Kansas, Lawrence, KS 66045 E. INTERACTIONS i. Oral Presentations P.M. Hierl, M.J. Henchman, and J; I Paulson,

  16. Gas phase fractionation method using porous ceramic membrane

    DOEpatents

    Peterson, Reid A.; Hill, Jr., Charles G.; Anderson, Marc A.

    1996-01-01

    Flaw-free porous ceramic membranes fabricated from metal sols and coated onto a porous support are advantageously used in gas phase fractionation methods. Mean pore diameters of less than 40 .ANG., preferably 5-20 .ANG. and most preferably about 15 .ANG., are permeable at lower pressures than existing membranes. Condensation of gases in small pores and non-Knudsen membrane transport mechanisms are employed to facilitate and increase membrane permeability and permselectivity.

  17. The Nucleoside Uridine Isolated in the Gas Phase**

    PubMed Central

    Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2016-01-01

    Herein we present the first experimental observation of the isolated nucleoside uridine, placed in the gas phase by laser ablation and characterized by Fourier transform microwave techniques. Free from the bulk effects of their native environments, anti/C2’-endo-g+ conformation has been revealed as the most stable form of uridine. Intramolecular hydrogen bonds involving uracil and ribose moieties have been found to play an important role in the stabilization of the nucleoside. PMID:25683559

  18. Gas phase chemical detection with an integrated chemical analysis system

    SciTech Connect

    CASALNUOVO,STEPHEN A.; FRYE-MASON,GREGORY CHARLES; KOTTENSTETTE,RICHARD; HELLER,EDWIN J.; MATZKE,CAROLYN M.; LEWIS,PATRICK R.; MANGINELL,RONALD P.; BACA,ALBERT G.; HIETALA,VINCENT M.

    2000-04-12

    Microfabrication technology has been applied to the development of a miniature, multi-channel gas phase chemical laboratory that provides fast response, small size, and enhanced versatility and chemical discrimination. Each analysis channel includes a sample preconcentrator followed by a gas chromatographic separator and a chemically selective surface acoustic wave detector array to achieve high sensitivity and selectivity. The performance of the components, individually and collectively, is described.

  19. Optically-Based Diagnostics for Gas-Phase Laser Development

    DTIC Science & Technology

    2010-08-01

    Phase Laser Development Acknowledgement of Support and Disclaimer This material is based upon work supported by Air Force Office of Scientific...00-2010 4. TITLE AND SUBTITLE Optically-Based Diagnostics for Gas-Phase Laser Development 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...Sciences Inc. Role of Optical Diagnostics in High Energy Gas Laser Development  Chemically rich, energetic, reacting flow with competing phenomena

  20. Gas Phase Synthesis of Nanostructured Films and Coatings

    DTIC Science & Technology

    2000-01-01

    observed and conditions for stable growth are given. In the plateau regime additional formation of nanoparticles occurs in the gas phase and...suppressed and most of the precursor is transformed into nanoparticles because fewer precursor molecules reach the substrate surface. While this regime...is not desirable in conventional film growth because of the incorporation of the nanoparticles into the films, this regime is used for the formation

  1. Understanding Gas-Phase Ammonia Chemistry in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Chambers, Lauren; Oberg, Karin I.; Cleeves, Lauren Ilsedore

    2017-01-01

    Protoplanetary disks are dynamic regions of gas and dust around young stars, the remnants of star formation, that evolve and coagulate over millions of years in order to ultimately form planets. The chemical composition of protoplanetary disks is affected by both the chemical and physical conditions in which they develop, including the initial molecular abundances in the birth cloud, the spectrum and intensity of radiation from the host star and nearby systems, and mixing and turbulence within the disk. A more complete understanding of the chemical evolution of disks enables a more complete understanding of the chemical composition of planets that may form within them, and of their capability to support life. One element known to be essential for life on Earth is nitrogen, which often is present in the form of ammonia (NH3). Recent observations by Salinas et al. (2016) reveal a theoretical discrepancy in the gas-phase and ice-phase ammonia abundances in protoplanetary disks; while observations of comets and protostars estimate the ice-phase NH3/H2O ratio in disks to be 5%, Salinas reports a gas-phase NH3/H2O ratio of ~7-84% in the disk surrounding TW Hydra, a young nearby star. Through computational chemical modeling of the TW Hydra disk using a reaction network of over 5000 chemical reactions, I am investigating the possible sources of excess gas-phase NH3 by determining the primary reaction pathways of NH3 production; the downstream chemical effects of ionization by ultraviolet photons, X-rays, and cosmic rays; and the effects of altering the initial abundances of key molecules such as N and N2. Beyond providing a theoretical explanation for the NH3 ice/gas discrepancy, this new model may lead to fuller understanding of the gas-phase formation processes of all nitrogen hydrides (NHx), and thus fuller understanding of the nitrogen-bearing molecules that are fundamental for life as we know it.

  2. Sucralose Destabilization of Protein Structure.

    PubMed

    Chen, Lee; Shukla, Nimesh; Cho, Inha; Cohn, Erin; Taylor, Erika A; Othon, Christina M

    2015-04-16

    Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion.

  3. Measuring Uptake Coefficients and Henry's Law Constants of Gas-Phase Species with Models for Secondary Organic Aerosol

    NASA Astrophysics Data System (ADS)

    Fairhurst, M. C.; Waring-Kidd, C.; Ezell, M. J.; Finlayson-Pitts, B. J.

    2014-12-01

    Volatile organic compounds (VOC) are oxidized in the atmosphere and their products contribute to secondary organic aerosol (SOA) formation. These particles have been shown to have effects on visibility, climate, and human health. Current models typically under-predict SOA concentrations from field measurements. Underestimation of these concentrations could be a result of how models treat particle growth. It is often assumed that particles grow via instantaneous thermal equilibrium partitioning between liquid particles and gas-phase species. Recent work has shown that growth may be better represented by irreversible, kinetically limited uptake of gas-phase species onto more viscous, tar-like SOA. However, uptake coefficients for these processes are not known. The goal of this project is to measure uptake coefficients and solubilities for different gases onto models serving as proxies for SOA and determine how they vary based on the chemical composition of the gas and the condensed phase. Experiments were conducted using two approaches: attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and a flow system coupled to a mass spectrometer. The ATR crystal was coated with the SOA proxy and the gas-phase species introduced via a custom flow system. Uptake of the gas-phase species was characterized by measuring the intensity of characteristic IR bands as a function of time, from which a Henry's law constant and initial estimate of uptake coefficients could be obtained. Uptake coefficients were also measured in a flow system where the walls of the flow tube were coated with the SOA proxy and gas-phase species introduced via a moveable inlet. Uptake coefficients were derived from the decay in gas-phase species measured by mass spectrometry. The results of this work will establish a structure-interaction relationship for uptake of gases into SOA that can be implemented into regional and global models.

  4. Peptide bond formation via glycine condensation in the gas phase.

    PubMed

    Van Dornshuld, Eric; Vergenz, Robert A; Tschumper, Gregory S

    2014-07-24

    Four unique gas phase mechanisms for peptide bond formation between two glycine molecules have been mapped out with quantum mechanical electronic structure methods. Both concerted and stepwise mechanisms, each leading to a cis and trans glycylglycine product (four mechanisms total), were examined with the B3LYP and MP2 methods and Gaussian atomic orbital basis sets as large as aug-cc-pVTZ. Electronic energies of the stationary points along the reaction pathways were also computed with explicitly correlated MP2-F12 and CCSD(T)-F12 methods. The CCSD(T)-F12 computations indicate that the electronic barriers to peptide bond formation are similar for all four mechanisms (ca. 32-39 kcal mol(-1) relative to two isolated glycine fragments). The smallest barrier (32 kcal mol(-1)) is associated with the lone transition state for the concerted mechanism leading to the formation of a trans peptide bond, whereas the largest barrier (39 kcal mol(-1)) was encountered along the concerted pathway leading to the cis configuration of the glycylglycine dipeptide. Two significant barriers are encountered for the stepwise mechanisms. For both the cis and trans pathways, the early electronic barrier is 36 kcal mol(-1) and the subsequent barrier is approximately 1 kcal mol(-1) lower. A host of intermediates and transition states lie between these two barriers, but they all have very small relative electronic energies (ca. ± 4 kcal mol(-1)). The isolated cis products (glycylglycine + H2O) are virtually isoenergetic with the isolated reactants (within -1 kcal mol(-1)), whereas the trans products are about 5 kcal mol(-1) lower in energy. In both products, however, the water can hydrogen bond to the dipeptide and lower the energy by roughly 5-9 kcal mol(-1). This study indicates that the concerted process leading to a trans configuration about the peptide bond is marginally favored both thermodynamically (exothermic by ca. 5 kcal mol(-1)) and kinetically (barrier height ≈ 32 kcal mol(-1

  5. Calcium-containing diatomic dications in the gas phase.

    PubMed

    Alves, Tiago Vinicius; Hermoso, Willian; Franzreb, Klaus; Ornellas, Fernando R

    2011-11-07

    Sputtering (ion surface bombardment) of various calcium-containing powder samples with an energetic (17 keV), high-current (16)O(-) beam has produced the diatomic dications of CaSi(2+), CaP(2+), CaF(2+), CaH(2+), CaCl(2+), CaBr(2+) and CaI(2+). These molecular gas-phase species have been identified in positive ion mass spectra at half-integer m/z values; their ion flight times through a magnetic-sector mass spectrometer were roughly 10(-5) s. Most of them appear to be novel molecular ions; the stability of the latter four (CaH(2+), CaCl(2+), CaBr(2+) and CaI(2+)) had been demonstrated in previous theoretical studies, whereas only CaF(2+) and CaBr(2+) had been observed before. Here we combine the results of our experimental search with a detailed theoretical study of the remaining three systems CaSi(2+), CaP(2+) and CaF(2+). All electronic states correlating with the first dissociation channel are characterized using high level ab initio electronic structure calculations. In their ground states, we find CaSi(2+) to be a long-lived metastable molecule, whereas CaF(2+) and CaP(2+) are thermodynamically stable, with respective equilibrium internuclear distances of 6.253, 4.740, and 5.731 a(0). CaSi(2+) has a well depth of 7116 (0.88) cm(-1) (eV) and a dissociation asymptote 7956 (0.99) cm(-1) (eV) below the ground state minimum. The dissociation energy of CaF(2+) is estimated to be 3404 (0.42) cm(-1) (eV), whereas for CaP(2+) we found 2547 (0.32) cm(-1) (eV), and a barrier height of 8118 (1.01) cm(-1) (eV). Their adiabatic double ionisation energies are 22.87, 16.91, and 17.32 eV, respectively, for the F, Si, and P containing dications. This journal is © the Owner Societies 2011

  6. Ab initio studies of aspartic acid conformers in gas phase and in solution

    NASA Astrophysics Data System (ADS)

    Chen, Mingliang; Lin, Zijing

    2007-10-01

    Systematic and extensive conformational searches of aspartic acid in gas phase and in solution have been performed. For the gaseous aspartic acid, a total of 1296 trial canonical structures and 216 trial zwitterionic structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were optimized at the B3LYP /6-311G* level and then subjected to further optimization at the B3LYP /6-311++G** level. A total of 139 canonical conformers were found, but no stable zwitterionic structure was found. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, and vertical ionization energies of the canonical conformers were determined. Single-point energies were also calculated at the MP2/6-311++G** and CCSD /6-311++G** levels. The equilibrium distributions of the gaseous conformers at various temperatures were calculated. The proton affinity and gas phase basicity were calculated and the results are in excellent agreement with the experiments. The conformations in the solution were studied with different solvation models. The 216 trial zwitterionic structures were first optimized at the B3LYP /6-311G* level using the Onsager self-consistent reaction field model (SCRF) and then optimized at the B3LYP /6-311++G** level using the conductorlike polarized continuum model (CPCM) SCRF theory. A total of 22 zwitterions conformers were found. The gaseous canonical conformers were combined with the CPCM model and optimized at the B3LYP /6-311++G** level. The solvated zwitterionic and canonical structures were further examined by the discrete/SCRF model with one and two water molecules. The incremental solvation of the canonical and zwitterionic structures with up to six water molecules in gas phase was systematically examined. The studies show that combining aspartic acid with at least six water molecules in the gas phase or two water molecules and a SCRF solution model is required to provide

  7. A gas-phase amplified quartz crystal microbalance immunosensor based on catalase modified immunoparticles.

    PubMed

    Liu, Wei; Huang, Renliang; Qi, Wei; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2015-02-21

    A novel signal amplification strategy for quartz crystal microbalance (QCM) based on catalytic gas generation was developed to construct an ultrasensitive immunosensor for the detection of proteins (immunoglobulin G, IgG, used as a model). A catalase modified immunoparticle was prepared to form a sandwich-type immunocomplex with the IgG and anti-IgG antibodies that were immobilized on the QCM sensor. The amount of immunoparticles on the sensor surface was thus controlled by the IgG concentration. Then H2O2 was added and catalyzed by catalase for oxygen generation. The generated oxygen replaced some of the liquid on the sensor surface, leading to the change in the shear modulus of the immunocomplex layer and the apparent viscosity and density of the liquid layer. Due to the ultrasensitive response of QCM to these changes, a significant frequency shift related to the IgG concentration was achieved. Different parameters, including the flow cell structure, operation temperature, immunoparticle concentration, and H2O2 concentration were optimized to achieve steady and efficient frequency shifts. Under the optimal conditions, the proposed gas-phase amplified QCM sensor could achieve up to 72 times improvement of detection sensitivity compared to the label-free sensor as a control, in the concentration range of 0.1-3.0 μg mL(-1). The detection limit was also reduced from 236 ng mL(-1) to 51.0 ng mL(-1) at the 3Sblank level.

  8. Encapsulating Cytochrome c in Silica Aerogel Nanoarchitectures without Metal Nanoparticles while Retaining Gas-phase Bioactivity

    PubMed Central

    Harper-Leatherman, Amanda S.; Pacer, Elizabeth R.; Kosciuszek, Nina D.

    2016-01-01

    Applications such as sensors, batteries, and fuel cells have been improved through the use of highly porous aerogels when functional compounds are encapsulated within the aerogels. However, few reports on encapsulating proteins within sol–gels that are processed to form aerogels exist. A procedure for encapsulating cytochrome c (cyt. c) in silica (SiO2) sol-gels that are supercritically processed to form bioaerogels with gas-phase activity for nitric oxide (NO) is presented. Cyt. c is added to a mixed silica sol under controlled protein concentration and buffer strength conditions. The sol mixture is then gelled and the liquid filling the gel pores is replaced through a series of solvent exchanges with liquid carbon dioxide. The carbon dioxide is brought to its critical point and vented off to form dry aerogels with cyt. c encapsulated inside. These bioaerogels are characterized with UV-visible spectroscopy and circular dichroism spectroscopy and can be used to detect the presence of gas-phase nitric oxide. The success of this procedure depends on regulating the cyt. c concentration and the buffer concentration and does not require other components such as metal nanoparticles. It may be possible to encapsulate other proteins using a similar approach making this procedure important for potential future bioanalytical device development. PMID:26967257

  9. A protein structure data and analysis system.

    PubMed

    Tian, Hao; Sunderraman, Rajshekhar; Weber, Irene; Wang, Haibin; Yang, Hong

    2005-01-01

    In this paper, we present the design and implementation of a protein structure data and analysis system that is only used in the lab for analyzing the proprietary data. It is capable of storing public protein data, such as the data in Protein Data Bank (PDB) [1], and life scientists' proprietary data. This toolkit is targeted at life scientists who want to maintain proprietary protein structure data (may be incomplete), to search and query publicly known protein structures and to compare their structure data with others. The comparison functions can be used to find structure differences between two proteins at atom level, especially in mutant versions of proteins. The system can also be used as a tool of choosing better protein structure template in new protein's tertiary structure prediction. The system is developed in Java and the protein data is stored in a relational database (Oracle 9i).

  10. Effects of donor-acceptor electronic interactions on the rates of gas-phase metallocene electron-exchange reactions

    SciTech Connect

    Phelps, D.K.; Gord, J.R.; Freiser, B.S.; Weaver, M.J. )

    1991-05-30

    Rate constants for electron self-exchange, k{sub ex}, of five cobaltocenium-cobaltocene and ferrocenium-ferrocene couples in the gas phase have been measured by means of Fourier transform ion cyclotron resonance mass spectrometry in order to explore the possible effects of donor-acceptor electronic coupling on gas-phase redox reactivity. The systems studied, Cp{sub 2}Co{sup +/0}, Cp{sub 2}Fe{sup +/0} (Cp = cyclopentadienyl), the decamethyl derivative Cp{prime}{sub 2}Fe{sup +/0}, carboxymethyl(cobaltocenium-cobaltocene) (Cp{sub 2}{sup e}Co{sup +/0}), and hydroxymethyl(ferrocenium-ferrocene) (HMFc{sup +/0}), were selected in view of the substantial variations in electronic coupling inferred on the basis of their solvent-dependent reactivities and theoretical grounds. The sequence of k{sub ex} values determined in the gas phase, Cp{sub 2}{sup e}Co{sup +/0} {approx} Cp{sub 2}Co{sup +/0} > Cp{prime}{sub 2}Fe{sup +/0} > HMFc{sup +/0} > Cp{sub 2}Fe{sup +/0}, is roughly similar to that observed in solution, although the magnitude (up to 5-fold) of the k{sub ex} variations is smaller in the former case. The likely origins of these differences in gas-phase reactivity are discussed in light of the known variations in the electronic coupling matrix element H{sub 12}, inner-shell reorganization energy {Delta}E*, and gas-phase ion-molecule interaction energy {Delta}E{sub w} extracted from solution-phase rates, structural data, and theoretical calculations. It is concluded that the observed variations in gas-phase k{sub ex} values, especially for Cp{sub 2}Fe{sup +/0} versus Cp{sub 2}Co{sup +/0}, arise predominantly from the presence of weaker donor-acceptor orbital overlap for the ferrocene couples, yielding inefficient electron tunneling for a substantial fraction of the gas-phase ion-molecule encounters. The anticipated differences as well as similarities of such nonadiabatic effects for gas-phase and solution electron-transfer processes are briefly outlined.

  11. Native like helices in a specially designed β peptide in the gas phase.

    PubMed

    Schubert, Franziska; Pagel, Kevin; Rossi, Mariana; Warnke, Stephan; Salwiczek, Mario; Koksch, Beate; von Helden, Gert; Blum, Volker; Baldauf, Carsten; Scheffler, Matthias

    2015-02-21

    In the natural peptides, helices are stabilized by hydrogen bonds that point backward along the sequence direction. Until now, there is only little evidence for the existence of analogous structures in oligomers of conformationally unrestricted β amino acids. We specifically designed the β peptide Ac-(β(2)hAla)6-LysH(+) to form native like helical structures in the gas phase. The design follows the known properties of the peptide Ac-Ala6-LysH(+) that forms a α helix in isolation. We perform ion-mobility mass-spectrometry and vibrational spectroscopy in the gas phase, combined with state-of-the-art density-functional theory simulations of these molecular systems in order to characterize their structure. We can show that the straightforward exchange of alanine residues for the homologous β amino acids generates a system that is generally capable of adopting native like helices with backward oriented H-bonds. By pushing the limits of theory and experiments, we show that one cannot assign a single preferred structure type due to the densely populated energy landscape and present an interpretation of the data that suggests an equilibrium of three helical structures.

  12. Ditechnetium heptoxide revisited: Solid-state, gas-phase, and theoretical studies

    DOE PAGES

    Childs, Bradley C.; Braband, Henrik; Lawler, Keith; ...

    2016-10-04

    Here, ditechnetium heptoxide was synthesized from the oxidation of TcO2 with O2 at 450 °C and characterized by single crystal X-ray diffraction (SCXRD), electron impact mass spectrometry (EI-MS) and theoretical methods. Refinement of the structure at 100 K indicates that Tc2O7 crystallizes as a molecular solid in the orthorhombic space group Pbca (a = 7.312(3) Å, b = 5.562(2) Å, c = 13.707(5) Å, V = 557.5(3) Å3). The Tc2O7 molecule can be described as corner-sharing TcO4 tetrahedra (Tc---Tc = 3.698(1) Å and Tc-OBri-Tc = 180.0°). The EI-MS spectrum of Tc2O7 consists of both mononuclear and dinuclear species. The mainmore » dinuclear species in the gas-phase are Tc2O7 (100%) and Tc2O5 (56%), while the main mononuclear species are TcO3 (33.9%) and TcO2 (42.8%). The difference in the relative intensities of the M2O5 (M = Tc, Re) fragments (1.7% for Re) indicate that these Group 7 elements exhibit different gas phase chemistry. The solid-state structure of Tc2O7 was investigated by density functional theory (DFT) methods. The optimized structure of the Tc2O7 molecule is in good agreement with the experimental one. Simulations indicate that the more favorable geometry for the Tc2O7 molecule in the gas-phase is bent (Tc-OBri-Tc = 156.5°), while linear (Tc-OBri-Tc = 180.0°) is favored in the solid state.« less

  13. Ditechnetium Heptoxide Revisited: Solid-State, Gas-Phase, and Theoretical Studies.

    PubMed

    Childs, Bradley C; Braband, Henrik; Lawler, Keith; Mast, Daniel S; Bigler, Laurent; Stalder, Urs; Forster, Paul M; Czerwinski, Kenneth R; Alberto, Roger; Sattelberger, Alfred P; Poineau, Frederic

    2016-10-04

    Ditechnetium heptoxide was synthesized from the oxidation of TcO2 with O2 at 450 °C and characterized by single-crystal X-ray diffraction, electron-impact mass spectrometry (EI-MS), and theoretical methods. Refinement of the structure at 100 K indicates that Tc2O7 crystallizes as a molecular solid in the orthorhombic space group Pbca [a = 7.312(3) Å, b = 5.562(2) Å, c = 13.707(5) Å, and V = 557.5(3) Å(3)]. The Tc2O7 molecule can be described as corner-sharing TcO4 tetrahedron [Tc---Tc = 3.698(1) Å and Tc-OBri-Tc = 180.0°]. The EI-MS spectrum of Tc2O7 consists of both mononuclear and dinuclear species. The main dinuclear species in the gas-phase are Tc2O7 (100%) and Tc2O5 (56%), while the main mononuclear species are TcO3 (33.9%) and TcO2 (42.8%). The difference in the relative intensities of the M2O5 (M = Tc, Re) fragments (1.7% for Re) indicates that these group 7 elements exhibit different gas-phase chemistry. The solid-state structure of Tc2O7 was investigated by density functional theory methods. The optimized structure of the Tc2O7 molecule is in good agreement with the experimental one. Simulations indicate that the more favorable geometry for the Tc2O7 molecule in the gas-phase is bent (Tc-OBri-Tc = 156.5°), while a linear geometry (Tc-OBri-Tc = 180.0°) is favored in the solid-state.

  14. MOLECULAR SPECTROSCPY AND REACTIONS OF ACTINIDES IN THE GAS PHASE AND CRYOGENIC MATRICES

    SciTech Connect

    Heaven, Michael C.; Gibson, John K.; Marcalo, Joaquim

    2009-02-01

    temperature or below. For many spectroscopic measurements, low temperatures have been achieved by co-condensing the actinide vapor in rare gas or inert molecule host matrices. Spectra recorded in matrices are usually considered to be minimally perturbed. Trapping the products from gas-phase reactions that occur when trace quantities of reactants are added to the inert host gas has resulted in the discovery of many new actinide species. Selected aspects of the matrix isolation data were discussed in chapter 17. In the present chapter we review the spectroscopic matrix data in terms of its relationship to gas-phase measurements, and update the description of the new reaction products found in matrices to reflect the developments that have occurred during the past two years. Spectra recorded in matrix environments are usually considered to be minimally perturbed, and this expectation is borne out for many closed shell actinide molecules. However, there is growing evidence that significant perturbations can occur for open shell molecules, resulting in geometric distortions and/or electronic state reordering. Studies of actinide reactions in the gas phase provide an opportunity to probe the relationship between electronic structure and reactivity. Much of this work has focused on the reactions of ionic species, as these may be selected and controlled using various forms of mass spectrometry. As an example of the type of insight derived from reaction studies, it has been established that the reaction barriers for An+ ions are determined by the promotion energies required to achieve the 5fn6d7s configuration. Gas-phase reaction studies also provide fundamental thermodynamic properties such as bond dissociation and ionization energies. In recent years, an increased number of gas-phase ion chemistry studies of bare (atomic) and ligated (molecular) actinide ions have appeared, in which relevant contributions to fundamental actinide chemistry have been made. These studies were initiated

  15. A mathematical framework for protein structure comparison.

    PubMed

    Liu, Wei; Srivastava, Anuj; Zhang, Jinfeng

    2011-02-03

    Comparison of protein structures is important for revealing the evolutionary relationship among proteins, predicting protein functions and predicting protein structures. Many methods have been developed in the past to align two or multiple protein structures. Despite the importance of this problem, rigorous mathematical or statistical frameworks have seldom been pursued for general protein structure comparison. One notable issue in this field is that with many different distances used to measure the similarity between protein structures, none of them are proper distances when protein structures of different sequences are compared. Statistical approaches based on those non-proper distances or similarity scores as random variables are thus not mathematically rigorous. In this work, we develop a mathematical framework for protein structure comparison by treating protein structures as three-dimensional curves. Using an elastic Riemannian metric on spaces of curves, geodesic distance, a proper distance on spaces of curves, can be computed for any two protein structures. In this framework, protein structures can be treated as random variables on the shape manifold, and means and covariance can be computed for populations of protein structures. Furthermore, these moments can be used to build Gaussian-type probability distributions of protein structures for use in hypothesis testing. The covariance of a population of protein structures can reveal the population-specific variations and be helpful in improving structure classification. With curves representing protein structures, the matching is performed using elastic shape analysis of curves, which can effectively model conformational changes and insertions/deletions. We show that our method performs comparably with commonly used methods in protein structure classification on a large manually annotated data set.

  16. Adsorption of CO on gas phase and zeolite supported gold monomers: A computational study

    NASA Astrophysics Data System (ADS)

    Deka, Ajanta; Deka, Ramesh Chandra; Choudhury, Amarjyoti

    2010-04-01

    We report for the first time the interaction of carbon monoxide with gold monomer in three oxidation states 0, +1 and +3 on FAU zeolite support using density functional theory. The gas phase structures of the gold carbonyls are retained on the zeolite support with only a slight change in the O-C-Au bond angle. For the supported cluster the CO vibrational frequency shows a blue shift on going to higher oxidation states. The CO binding energies on the supported gold monomers are 1.01, 1.15 and 1.12 eV in the oxidation states 0, +1 and +3, respectively.

  17. Nonresonant femtosecond laser vaporization of aqueous protein preserves folded structure

    PubMed Central

    Brady, John J.; Judge, Elizabeth J.; Levis, Robert J.

    2011-01-01

    Femtosecond laser vaporization-based mass spectrometry can be used to measure protein conformation in vitro at atmospheric pressure. Cytochrome c and lysozyme are vaporized from the condensed phase into the gas phase intact when exposed to an intense (1013 W/cm2), nonresonant (800 nm), ultrafast (75 fs) laser pulse. Electrospray postionization time-of-flight mass spectrometry reveals that the vaporized protein maintains the solution-phase conformation through measurement of the charge-state distribution and the collision-induced dissociation channels. PMID:21746908

  18. Introduction to Protein Structure through Genetic Diseases

    ERIC Educational Resources Information Center

    Schneider, Tanya L.; Linton, Brian R.

    2008-01-01

    An illuminating way to learn about protein function is to explore high-resolution protein structures. Analysis of the proteins involved in genetic diseases has been used to introduce students to protein structure and the role that individual mutations can play in the onset of disease. Known mutations can be correlated to changes in protein…

  19. Introduction to Protein Structure through Genetic Diseases

    ERIC Educational Resources Information Center

    Schneider, Tanya L.; Linton, Brian R.

    2008-01-01

    An illuminating way to learn about protein function is to explore high-resolution protein structures. Analysis of the proteins involved in genetic diseases has been used to introduce students to protein structure and the role that individual mutations can play in the onset of disease. Known mutations can be correlated to changes in protein…

  20. The nature of selenium hydrogen bonding: gas phase spectroscopy and quantum chemistry calculations.

    PubMed

    Mishra, Kamal K; Singh, Santosh K; Ghosh, Paulami; Ghosh, Debashree; Das, Aloke

    2017-08-25

    Subsequent to the recent re-definition of hydrogen bonding by the IUPAC committee, there has been a growing search for finding the presence of this ever interesting non-covalent interaction between a hydrogen atom in an X-H group and any other atom in the periodic table. In recent gas phase experiments, it has been observed that hydrogen bonding interactions involving S and Se are of similar strength to those with an O atom. However, there is no clear explanation for the unusual strength of this interaction in the case of hydrogen bond acceptors which are not conventional electronegative atoms. In this work, we have explored the nature of Se hydrogen bonding by studying indoledimethyl selenide (indmse) and phenoldimethyl selenide (phdmse) complexes using gas phase IR spectroscopy and quantum chemistry calculations. We have found through various energy decomposition analysis (EDA) methods and natural bond orbital (NBO) calculations that, along with electrostatics and polarization, charge transfer interactions are important to understand Se/S hydrogen bonding and there is a delicate balance between the various interactions that plays the crucial role rather than a single component of the interaction energy. An in-depth understanding of this type of non-covalent interaction has immense significance in biology as amino acids containing S and Se are widely present in proteins and hence hydrogen bonding interactions involving S and Se atoms contribute to the folding of proteins.

  1. Protein structure alignment beyond spatial proximity.

    PubMed

    Wang, Sheng; Ma, Jianzhu; Peng, Jian; Xu, Jinbo

    2013-01-01

    Protein structure alignment is a fundamental problem in computational structure biology. Many programs have been developed for automatic protein structure alignment, but most of them align two protein structures purely based upon geometric similarity without considering evolutionary and functional relationship. As such, these programs may generate structure alignments which are not very biologically meaningful from the evolutionary perspective. This paper presents a novel method DeepAlign for automatic pairwise protein structure alignment. DeepAlign aligns two protein structures using not only spatial proximity of equivalent residues (after rigid-body superposition), but also evolutionary relationship and hydrogen-bonding similarity. Experimental results show that DeepAlign can generate structure alignments much more consistent with manually-curated alignments than other automatic tools especially when proteins under consideration are remote homologs. These results imply that in addition to geometric similarity, evolutionary information and hydrogen-bonding similarity are essential to aligning two protein structures.

  2. Fluorescence Spectroscopy of Gas-phase Polycyclic Aromatic Hydrocarbons

    NASA Technical Reports Server (NTRS)

    Thomas, J. D.; Witt, A. N.

    2006-01-01

    The purpose of this investigation was to produce fluorescence spectra of polycyclic aromatic hydrocarbon (PAH) molecules in the gas-phase for comparison with blue luminescence (BL) emission observed in astrophysical sources Vijh et al. (2004, 2005a,b). The BL occurs roughly from 350 to 450 nm, with a sharp peak near 380 nm. PAHs with three to four rings, e.g. anthracene and pyrene, were found to produce luminescence in the appropriate spectral region, based on existing studies. Relatively few studies of the gas-phase fluorescence of PAHs exist; those that do exist have dealt primarily with the same samples commonly available for purchase such as pyrene and anthracene. In an attempt to understand the chemistry of the nebular environment we also obtained several nitrogen substituted PAHs from our colleagues at NASA Ames. In order to simulate the astrophysical environment we also took spectra by heating the PAHs in a flame. The flame environment counteracts the formation of eximers and permits the spectroscopy of free-flying neutral molecules. Experiments with coal tar demonstrate that fluorescence spectroscopy reveals primarily the presence of the smallest molecules, which are most abundant and which possess the highest fluorescence efficiencies. One gas-phase PAH that seems to fit the BL spectrum most closely is phenanthridine. In view of the results from the spectroscopy of coal tar, a compound containing a mixture of PAHs ranging from small to very large PAH molecules, we can not preclude the presence of larger PAHs in interstellar sources exhibiting BL.

  3. Gas-phase chemistry of ruthenium and rhodium carbonyl complexes.

    PubMed

    Cao, Shiwei; Wang, Yang; Qin, Zhi; Fan, Fangli; Haba, Hiromitsu; Komori, Yukiko; Wu, Xiaolei; Tan, Cunmin; Zhang, Xin

    2016-01-07

    Short-lived ruthenium and rhodium isotopes were produced from a (252)Cf spontaneous fission (SF) source. Their volatile carbonyl complexes were formed in gas-phase reactions in situ with the carbon-monoxide containing gas. A gas-jet system was employed to transport the volatile carbonyls from the recoil chamber to the chemical separation apparatus. The gas-phase chemical behaviors of these carbonyl complexes were studied using an online low temperature isothermal chromatography (IC) technique. Long IC columns made up of FEP Teflon were used to obtain the chemical information of the high-volatile Ru and Rh carbonyls. By excluding the influence of precursor effects, short-lived isotopes of (109-110)Ru and (111-112)Rh were used to represent the chemical behaviours of Ru and Rh carbonyls. Relative chemical yields of about 75% and 20% were measured for Ru(CO)5 and Rh(CO)4, respectively, relative to the yields of KCl aerosols transported in Ar gas. The adsorption enthalpies of ruthenium and rhodium carbonyl complexes on a Teflon surface were determined to be around ΔHads = -33(+1)(-2) kJ mol(-1) and -36(+2)(-1) kJ mol(-1), respectively, by fitting the breakthrough curves of the corresponding carbonyl complexes with a Monte Carlo simulation program. Different from Mo and Tc carbonyls, a small amount of oxygen gas was found to be not effective for the chemical yields of ruthenium and rhodium carbonyl complexes. The general chemical behaviors of short-lived carbonyl complexes of group VI-IX elements were discussed, which can be used in the future study on the gas-phase chemistry of superheavy elements - Bh, Hs, and Mt carbonyls.

  4. Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization

    NASA Astrophysics Data System (ADS)

    Li, Jun; Richards, Michele R.; Kitova, Elena N.; Klassen, John S.

    2017-07-01

    The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase.

  5. Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization

    NASA Astrophysics Data System (ADS)

    Li, Jun; Richards, Michele R.; Kitova, Elena N.; Klassen, John S.

    2017-10-01

    The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase. [Figure not available: see fulltext.

  6. Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis

    PubMed Central

    Buesser, B.; Gröhn, A.J.

    2013-01-01

    Aerosol reactors are utilized to manufacture nanoparticles in industrially relevant quantities. The development, understanding and scale-up of aerosol reactors can be facilitated with models and computer simulations. This review aims to provide an overview of recent developments of models and simulations and discuss their interconnection in a multiscale approach. A short introduction of the various aerosol reactor types and gas-phase particle dynamics is presented as a background for the later discussion of the models and simulations. Models are presented with decreasing time and length scales in sections on continuum, mesoscale, molecular dynamics and quantum mechanics models. PMID:23729992

  7. Femtosecond analysis of free molecular rotation in the gas phase

    NASA Astrophysics Data System (ADS)

    Borisevich, N. A.; Khoroshilov, E. V.; Kryukov, I. V.; Kryukov, P. G.; Sharkov, A. V.; Blokhin, A. P.; Tolstorozhev, G. B.

    1992-04-01

    The time-resolved S 1→S *n absorption anisotropy decay resulting from rotation of free gas phase POPOP molecules at 593 K and PPO molecules at 483 K was studied after S 0→S *1 excitation by femtosecond linearly polarized pulses at 308 nm. The time evolution of the anisotropy measured through a few picoseconds after excitation is in agreement with the results of calculations made for POPOP and PPO using orientational correlation functions developed for rigid asymmetric top molecules.

  8. Gas Phase Model of Surface Reactions for N{2} Afterglows

    NASA Astrophysics Data System (ADS)

    Marković, V. Lj.; Petrović, Z. Lj.; Pejović, M. M.

    1996-07-01

    The adequacy of the homogeneous gas phase model as a representation of the surface losses of diffusing active particles in gas phase is studied. As an example the recent data obtained for the surface recombination coefficients are reanalyzed. The data were obtained by the application of the breakdown delay times which consists of the measurements of the breakdown delay times t_d as a function of the afterglow period tau. It was found that for the conditions of our experiment, the diffusion should not be neglected as the final results are significantly different when obtained by approximate gas phase representation and by exact numerical solution to the diffusion equation. While application of the gas phase effective coefficients to represent surface losses gives an error in the value of the recombination coefficient, it reproduces correctly other characteristics such as order of the process which can be obtained from simple fits to the experimental data. Dans cet article, nous étudions la validité du modèle approximatif représentant les pertes superficielles des particules actives qui diffusent de la phase gazeuse comme pertes dans la phase homogène du gaz. Les données actuelles du coefficient de recombination en surface sont utilisées par cette vérification . Les données experimentales sont obtenues en utilisant la technique qui consiste en la mesure du temps de retard du début de la décharge en fonction de la période de relaxation. Nous avons trouvé que, pour nos conditions expérimentales, la diffusion ne peut être négligée. Aussi, les résultats finals sont considérablement différents quand ils sont obtenus en utilisant le modèle approximatif par comparaison aves les résultats obtenus par la solution numérique exacte de l'équation de la diffusion. L'application des coefficients effectifs dans la phase gaseuse pour la présentation des pertes superficielles donne, pour les coefficients de la recombinaison, des valeurs qui diffèrent en

  9. Neurotransmitters in the Gas Phase: La-Mb Studies

    NASA Astrophysics Data System (ADS)

    Cabezas, C.; Mata, S.; López, J. C.; Alonso, J. L.

    2011-06-01

    LA-MB-FTMW spectroscopy combines laser ablation with Fourier transform microwave spectroscopy in supersonic jets overcoming the problems of thermal decomposition associated with conventional heating methods. We present here the results on LA-MB-FTMW studies of some neurotransmitters. Six conformers of dopamine, four of adrenaline, five of noradrenaline and three conformers of serotonin have been characterized in the gas phase. The rotational and nuclear quadrupole coupling constants extracted from the analysis of the rotational spectrum are directly compared with those predicted by ab initio methods to achieve the conclusive identification of different conformers and the experimental characterization of the intramolecular forces at play which control conformational preferences.

  10. Hydration of monomeric metaphosphate anion in the gas phase

    SciTech Connect

    Keesee, R.G.; Castleman, A.W. Jr. )

    1989-12-06

    Thermochemical data for the clustering of water molecules onto the monomeric metaphosphate anion PO{sub 3}{sup {minus}} in the gas phase are derived from a study by high-pressure mass spectrometry. Experimental details are described, and the enthalpy and entropy changes for the successive addition of the first four water (D{sub 2}O) molecules are reported. The results indicate that PO{sub 3}{sup {minus}} undergoes simple adduct formation up to the second hydration step, but the third hydration step involves an isomerization of the ion-water cluster into the dihydrate of the dihydrogen orthophosphate anion.

  11. Gas Phase Chemical Detection with an Integrated Chemical Analysis System

    SciTech Connect

    Baca, Albert G.; Casalnuovo, Stephen A.; Frye-Mason, Gregory C.; Heller, Edwin J.; Hietala, Susan L.; Hietala, Vincent M.; Kottenstette, Richard J.; Lewis, Patrick R.; Manginell, Ronald P.; Matzke, Carloyn M.; Reno, John L.; Sasaki, Darryl Y.; Schubert, W. Kent

    1999-07-08

    Microfabrication technology has been applied to the development of a miniature, multi-channel gas phase chemical laboratory that provides fast response, small size, and enhanced versatility and chemical discrimination. Each analysis channel includes a sample concentrator followed by a gas chromatographic separator and a chemically selective surface acoustic wave detector array to achieve high sensitivity and selectivity. The performance of the components, individually and collectively, is described. The design and performance of novel micromachined acoustic wave devices, with the potential for improved chemical sensitivity, are also described.

  12. The solar system/interstellar medium connection - Gas phase abundances

    NASA Technical Reports Server (NTRS)

    Lutz, Barry L.

    1987-01-01

    Gas-phase abundances in the outer solar system are presented as diagnostics of the interstellar medium at the time of the solar system formation, some 4.55 billion years ago. Possible influences of the thermal and chemical histories of the primitive solar nebula and of the processes which led to the formation and evolution of the outer planets and comets on the elemental and molecular composition of the primordial matter are outlined. The major components of the atmospheres of the outer planets and of the comae of comets are identified, and the cosmogonical and cosmological implications are discussed.

  13. An Interactive Introduction to Protein Structure

    ERIC Educational Resources Information Center

    Lee, W. Theodore

    2004-01-01

    To improve student understanding of protein structure and the significance of noncovalent interactions in protein structure and function, students are assigned a project to write a paper complemented with computer-generated images. The assignment provides an opportunity for students to select a protein structure that is of interest and detail…

  14. An Interactive Introduction to Protein Structure

    ERIC Educational Resources Information Center

    Lee, W. Theodore

    2004-01-01

    To improve student understanding of protein structure and the significance of noncovalent interactions in protein structure and function, students are assigned a project to write a paper complemented with computer-generated images. The assignment provides an opportunity for students to select a protein structure that is of interest and detail…

  15. PRISM: protein interactions by structural matching.

    PubMed

    Ogmen, Utkan; Keskin, Ozlem; Aytuna, A Selim; Nussinov, Ruth; Gursoy, Attila

    2005-07-01

    Prism (http://gordion.hpc.eng.ku.edu.tr/prism) is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution (January 2004). Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.

  16. Protein structure determination using metagenome sequence data.

    PubMed

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A; Kim, David E; Kamisetty, Hetunandan; Kyrpides, Nikos C; Baker, David

    2017-01-20

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost. Copyright © 2017, American Association for the Advancement of Science.

  17. Gas-phase peptide fragmentation: how understanding the fundamentals provides a springboard to developing new chemistry and novel proteomic tools.

    PubMed

    Barlow, Christopher K; O'Hair, Richard A J

    2008-10-01

    This tutorial provides an overview of the evolution of some of the key concepts in the gas-phase fragmentation of different classes of peptide ions under various conditions [e.g. collision-induced dissociation (CID) and electron transfer dissociation (ETD)], and then demonstrates how these concepts can be used to develop new methods. For example, an understanding of the role of the mobile proton and neighboring group interactions in the fragmentation reactions of protonated peptides has led to the design of the 'SELECT' method. For ETD, a model based on the Landau-Zener theory reveals the role of both thermodynamic and geometric effects in the electron transfer from polyatomic reagent anions to multiply protonated peptides, and this predictive model has facilitated the design of a new strategy to form ETD reagent anions from precursors generated via ESI. Finally, two promising, emerging areas of gas-phase ion chemistry of peptides are also described: (1) the design of new gas-phase radical chemistry to probe peptide structure, and (2) selective cleavage of disulfide bonds of peptides in the gas phase via various physicochemical approaches.

  18. TRANSITION STATE FOR THE GAS-PHASE REACTION OF URANIUM HEXAFLUORIDE WITH WATER

    SciTech Connect

    Garrison, S; James Becnel, J

    2008-03-18

    Density Functional Theory and small-core, relativistic pseudopotentials were used to look for symmetric and asymmetric transitions states of the gas-phase hydrolysis reaction of uranium hexafluoride, UF{sub 6}, with water. At the B3LYP/6-31G(d,p)/SDD level, an asymmetric transition state leading to the formation of a uranium hydroxyl fluoride, U(OH)F{sub 5}, and hydrogen fluoride was found with an energy barrier of +77.3 kJ/mol and an enthalpy of reaction of +63.0 kJ/mol (both including zero-point energy corrections). Addition of diffuse functions to all atoms except uranium led to only minor changes in the structure and relative energies of the reacting complex and transition state. However, a significant change in the product complex structure was found, significantly reducing the enthalpy of reaction to +31.9 kJ/mol. Similar structures and values were found for PBE0 and MP2 calculations with this larger basis set, supporting the B3LYP results. No symmetric transition state leading to the direct formation of uranium oxide tetrafluoride, UOF{sub 4}, was found, indicating that the reaction under ambient conditions likely includes several more steps than the mechanisms commonly mentioned. The transition state presented here appears to be the first published transition state for the important gas-phase reaction of UF{sub 6} with water.

  19. Transition state for the gas-phase reaction of uranium hexafluoride with water.

    PubMed

    Garrison, Stephen L; Becnel, James M

    2008-06-19

    Density functional theory and small-core, relativistic pseudopotentials were used to look for symmetric and asymmetric transition states of the gas-phase hydrolysis reaction of uranium hexafluoride, UF 6, with water. At the B3LYP/6-31G(d,p)/SDD level, an asymmetric transition state leading to the formation of a uranium hydroxyl fluoride, U(OH)F 5, and hydrogen fluoride was found with an energy barrier of +77.3 kJ/mol and an enthalpy of reaction of +63.0 kJ/mol (both including zero-point energy corrections). Addition of diffuse functions to all atoms except uranium led to only minor changes in the structures and relative energies of the reacting complex and transition state. However, a significant change in the structure of the product complex was found, significantly reducing the enthalpy of reaction to +31.9 kJ/mol. Similar structures and values were found for PBE0 and MP2 calculations with this larger basis set, supporting the B3LYP results. No symmetric transition state leading to the direct formation of uranium oxide tetrafluoride, UOF 4, was found, indicating that the reaction under ambient conditions likely includes several more steps than the mechanisms commonly mentioned. The transition state presented here appears to be the first published transition state for the important gas-phase reaction of UF 6 with water.

  20. Mass Spectrometry of Protein Complexes: From Origins to Applications

    NASA Astrophysics Data System (ADS)

    Mehmood, Shahid; Allison, Timothy M.; Robinson, Carol V.

    2015-04-01

    Now routine is the ability to investigate soluble and membrane protein complexes in the gas phase of a mass spectrometer while preserving folded structure and ligand-binding properties. Several recent transformative developments have occurred to arrive at this point. These include advances in mass spectrometry instrumentation, particularly with respect to resolution; the ability to study intact membrane protein complexes released from detergent micelles; and the use of protein unfolding in the gas phase to obtain stability parameters. Together, these discoveries are providing unprecedented information on the compositional heterogeneity of biomacromolecules, the unfolding trajectories of multidomain proteins, and the stability imparted by ligand binding to both soluble and membrane-embedded protein complexes. We review these recent breakthroughs, highlighting the challenges that had to be overcome and the physicochemical insight that can now be gained from studying proteins and their assemblies in the gas phase.

  1. Spectroscopy of PAH species in the gas phase

    NASA Astrophysics Data System (ADS)

    Robinson, Michael S.; Beegle, Luther W.; Wdowiak, Thomas J.

    1995-02-01

    At elevated temperatures, the structured CH stretch absorption occurring at room temperature of polycyclic aromatic hydrocarbon (PAH) molecules encapsulated in KBr coalesces to a single peak whose wavelength is a very close match for that of the observed 3.3 μm unidentified infrared band (UIR) emission feature (Flickinger and Wdowiak. Astrophys. J.362, L71-L74. 1990). The temperature of approximately 800 K is significant because a PAH molecule in the interstellar radiation field, upon absorption of an ultraviolet photon, is expected to be excited to an energy equivalent to temperatures of this order (Sellgren, Astrophys. J.277, 623 1984). Our previous study of PAH molecules in the vapor phase at 600-800 K showed that the C-H stretch PAH feature near 3.3 μm is at a shorter wavelength than in the condensed state (Flickinger et al., Astrophys. J.380, L43-L46, 1991). Recent work by Joblin et al. ( 1st Symp. on the Infrared Cirrus and Diffuse Interstellar Clouds. 1994) in a short path length diamond cell indicates the gas phase wavelength of the 3.3 μm region C-H stretch feature of naphthalene is directly proportional to temperature over a large temperature range. Laser-excited IR fluorescence studies have also suggested that the wavelength is sensitive to laser photon energy in a direct relationship (Williams and Leone, The Diffuse Interstellar Bands Conf., 1994). Comprehensive studies of PAHs thermally excited up to the decomposition temperature are therefore important to carry out. We have utilized a long-path-length optical heat pipe to confirm that the wavelength of the peak of the C-H stretch band of naphthalene vapor obeys a direct relationship with temperature as reported by Joblin, and to demonstrate that this feature undergoes a strengthening with respect to the longer wavelength band due to an out-of-plane deformation (782 cm -1) as temperature increases. The shift from 3067.6 to 3063.7 cm -1 over the temperature range of 316-996 K seems to be linear

  2. Gas Phase Chromatography of some Group 4, 5, and 6 Halides

    SciTech Connect

    Sylwester, Eric Robert

    1998-10-01

    Gas phase chromatography using The Heavy Element Volatility Instrument (HEVI) and the On Line Gas Apparatus (OLGA III) was used to determine volatilities of ZrBr4, HfBr4, RfBr4, NbBr5, TaOBr3, HaCl5, WBr6, FrBr, and BiBr3. Short-lived isotopes of Zr, Hf, Rf, Nb, Ta, Ha, W, and Bi were produced via compound nucleus reactions at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory and transported to the experimental apparatus using a He gas transport system. The isotopes were halogenated, separated from the other reaction products, and their volatilities determined by isothermal gas phase chromatography. Adsorption Enthalpy (ΔHa) values for these compounds were calculated using a Monte Carlo simulation program modeling the gas phase chromatography column. All bromides showed lower volatility than molecules of similar molecular structures formed as chlorides, but followed similar trends by central element. Tantalum was observed to form the oxybromide, analogous to the formation of the oxychloride under the same conditions. For the group 4 elements, the following order in volatility and ΔHa was observed: RfBr4 > ZrBr4 > HfBr4. The ΔHa values determined for the group 4, 5, and 6 halides are in general agreement with other experimental data and theoretical predictions. Preliminary experiments were performed on Me-bromides. A new measurement of the half-life of 261Rf was performed. 261Rf was produced via the 248Cm(18O, 5n) reaction and observed with a half-life of 74-6+7 seconds, in excellent agreement with the previous measurement of 78-6+11 seconds. We recommend a new half-life of 75±7 seconds for 261Rf based on these two measurements. Preliminary studies in transforming HEVI from an isothermal (constant

  3. Cool Mist Scavenging of Gas-Phase Molecules.

    PubMed

    Wu, Pei-Chi; Dutkiewicz, Ewelina P; Urban, Pawel L

    2017-01-01

    The purpose of analytical extractions is to simplify sample matrix without losing analyte molecules. Here we present a technique of extracting volatile compounds by scavenging gas-phase molecules with tiny liquid droplets (<10 μm). A cool mist of the extracting solvent is generated by an ultrasonic transducer, transferred to the headspace of the sample chamber under atmospheric conditions, and pushed by a small pressure difference toward a condenser. By slowly passing over the sample, the microdroplets extract volatile species present in the sample headspace, and they coalesce in a cooled zone. The condensed liquid is collected for analysis by direct infusion mass spectrometry or chromatography coupled with mass spectrometry. Due to the high surface-to-volume ratio of the microdroplets, the mist depletes a great share of the volatile organics present in the headspace. Other advantages of cool mist scavenging include: selective extraction of gas-phase molecules, the extracting solvent can be miscible with the sample solvent, simplicity, high speed, and no requirement for heating that could potentially decompose the sample. In this study, cool mist scavenging was first tested on artificial samples containing esters. The relationship between the sample concentration and the extract concentration was verified theoretically and experimentally. Some of the possible confounding effects were tested and discussed. The technique was subsequently applied to qualitative analysis of selected complex samples in liquid and solid phase as well as an esterification reaction.

  4. Gas-phase reactions of cyclopropenylidene with protonated alkyl amines.

    PubMed

    Lin, Ziqing; Tan, Lei; Yang, Yang; Dai, Mingji; Tureček, František; Ouyang, Zheng; Xia, Yu

    2016-04-21

    Vinylidene carbenes (C3H2) are of high interest to interstellar, combustion, and organic chemistry. Due to their high instability, the direct experimental investigation of their chemical reactivity has rarely been achieved. Herein, we report a first study on the reactions of cyclopropenylidene (c-C3H2) with protonated alkyl amines in the gas phase using a home-built ion trap mass spectrometer. The high gas-phase basicity (GB) of ((1)A1) c-C3H2 (calculated as 920 kJ mol(-1)) facilitates the formation of a proton-bound dimer with protonated amines as the first step in the reaction. The dimer can stay as it is or rearrange to a covalent product. The formation of the covalent complex is highly exothermic and its yield is affected by the GB of alkyl amines. The highest yield (82%) was achieved when the GB of the amine was slightly lower but comparable to that of c-C3H2. Our results demonstrate a new reaction pathway of c-C3H2, which has long been considered as a "dead end" in interstellar carbon chemistry.

  5. Gas phase oxidation downstream of a catalytic combustor

    NASA Technical Reports Server (NTRS)

    Tien, J. S.; Anderson, D. N.

    1979-01-01

    Effect of the length available for gas-phase reactions downstream of the catalytic reactor on the emission of CO and unburned hydrocarbons was investigated. A premixed, prevaporized propane/air feed to a 12/cm/diameter catalytic/reactor test section was used. The catalytic reactor was made of four 2.5 cm long monolithic catalyst elements. Four water cooled gas sampling probes were located at positions between 0 and 22 cm downstream of the catalytic reactor. Measurements of unburned hydrocarbon, CO, and CO2 were made. Tests were performed with an inlet air temperature of 800 K, a reference velocity of 10 m/s, pressures of 3 and 600,000 Pa, and fuel air equivalence ratios of 0.14 to 0.24. For very lean mixtures, hydrocarbon emissions were high and CO continued to be formed downstream of the catalytic reactor. At the highest equivalence ratios tested, hydrocarbon levels were much lower and CO was oxidized to CO2 in the gas phase downstream. To achieve acceptable emissions, a downstream region several times longer than the catalytic reactor could be required.

  6. Gas phase reaction of sulfur trioxide with water vapor

    SciTech Connect

    Kolb, C.E.; Molina, M.J.; Jayne, J.T.; Meads, R.F.; Worsnop, D.R.

    1994-12-31

    Sulfur trioxide (SO3) has long been known to react with water to produce sulfuric acid (H2S04). It has been commonly assumed that the gas phase reaction in the Earth`s atmosphere between SO3 and water vapor to produce sulfuric acid vapor is an important step in the production of sulfuric acid aerosol particles. The kinetics of the gas phase reaction of SO3 with water vapor have previously been studied by Castleman and co-workers, Wang et al and Reiner and Arnold. Each of these studies was carried out in a flow reactor, with the first two studies performed at low pressure (1-10 Torr) and the latter from approx. 30 to 260 Torr. Each of these studies measured SO3 decays over a range of H2O vapor levels, obtaining data consistent with interpreting the reaction of gaseous SO3 and H2O as a bimolecular process. It is not clear why previous experimental studies failed to observe a nonlinear dependence of SO3 consumption on water vapor concentration. It is probable that sufficient water dimer exists in much of the Earth`s atmosphere to allow dimer reactions to participate in sulfuric acid vapor formation.

  7. Preconceptual design of the gas-phase decontamination demonstration cart

    SciTech Connect

    Munday, E.B.

    1993-12-01

    Removal of uranium deposits from the interior surfaces of gaseous diffusion equipment will be a major portion of the overall multibillion dollar effort to decontaminate and decommission the gaseous diffusion plants. Long-term low-temperature (LTLT) gas-phase decontamination is being developed at the K-25 Site as an in situ decontamination process that is expected to significantly lower the decontamination costs, reduce worker exposure to radioactive materials, and reduce safeguard concerns. This report documents the preconceptual design of the process equipment that is necessary to conduct a full-scale demonstration of the LTLT method in accordance with the process steps listed above. The process equipment and method proposed in this report are not intended to represent a full-scale production campaign design and operation, since the gas evacuation, gas charging, and off-gas handling systems that would be cost effective in a production campaign are not cost effective for a first-time demonstration. However, the design presented here is expected to be applicable to special decontamination projects beyond the demonstration, which could include the Deposit Recovery Program. The equipment will therefore be sized to a 200 ft size 1 converter (plus a substantial conservative design margin), which is the largest item of interest for gas phase decontamination in the Deposit Recovery Program. The decontamination equipment will allow recovery of the UF{sub 6}, which is generated from the reaction of ClF{sub 3} with the uranium deposits, by use of NaF traps.

  8. High resolution dissociative electron attachment to gas phase adenine

    SciTech Connect

    Huber, D.; Beikircher, M.; Denifl, S.; Zappa, F.; Matejcik, S.; Bacher, A.; Grill, V.; Maerk, T. D.; Scheier, P.

    2006-08-28

    The dissociative electron attachment to the gas phase nucleobase adenine is studied using two different experiments. A double focusing sector field mass spectrometer is utilized for measurements requiring high mass resolution, high sensitivity, and relative ion yields for all the fragment anions and a hemispherical electron monochromator instrument for high electron energy resolution. The negative ion mass spectra are discussed at two different electron energies of 2 and 6 eV. In contrast to previous gas phase studies a number of new negative ions are discovered in the mass spectra. The ion efficiency curves for the negative ions of adenine are measured for the electron energy range from about 0 to 15 eV with an electron energy resolution of about 100 meV. The total anion yield derived via the summation of all measured fragment anions is compared with the total cross section for negative ion formation measured recently without mass spectrometry. For adenine the shape of the two cross section curves agrees well, taking into account the different electron energy resolutions; however, for thymine some peculiar differences are observed.

  9. Multiple gas-phase conformations of proline-containing peptides: Is it always cis/trans isomerization?

    PubMed Central

    Lietz, Christopher B.; Chen, Zhengwei; Son, Chang Yun; Pang, Xueqin; Cui, Qiang; Li, Lingjun

    2016-01-01

    Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structure of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental “signature” has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra are observed. Despite high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y’s wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross sections of [M+4H]4+ ions yield the cis/trans “signature”, molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross section arise with equal frequency. We believe this work further underscores the importance of theoretical calculations in IM-MS structural assignments. PMID:27434776

  10. Multiple gas-phase conformations of proline-containing peptides: is it always cis/trans isomerization?

    PubMed

    Lietz, Christopher B; Chen, Zhengwei; Yun Son, Chang; Pang, Xueqin; Cui, Qiang; Li, Lingjun

    2016-08-02

    Ion mobility-mass spectrometry (IM-MS) is often employed to look at the secondary, tertiary, and quaternary structures of naked peptides and proteins in the gas-phase. Recently, it has offered a unique glimpse into proline-containing peptides and their cis/trans Xxx-Pro isomers. An experimental "signature" has been identified wherein a proline-containing peptide has its Pro residues substituted with another amino acid and the presence or absence of conformations in the IM-MS spectra is observed. Despite the high probability that one could attribute these conformations to cis/trans isomers, it is also possible that cis/trans isomers are not the cause of the additional conformations in proline-containing peptides. However, the experimental evidence of such a system has not been demonstrated or reported. Herein, we present the IM-MS analysis of Neuropeptide Y's wild-type (WT) signal sequence and Leu7Pro (L7P) mutant. Although comparison of arrival times and collision cross-sections of [M + 4H](4+) ions yields the cis/trans "signature", molecular dynamics indicates that a cis-Pro7 is not very stable and that trans-Pro7 conformations of the same cross-section arise with equal frequency. We believe that this work further underscores the importance of theoretical calculations in IM-MS structural assignments.

  11. Protein Structure Determination using Metagenome sequence data

    PubMed Central

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

    2017-01-01

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

  12. Modularity in protein structures: study on all-alpha proteins.

    PubMed

    Khan, Taushif; Ghosh, Indira

    2015-01-01

    Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

  13. Sucralose Destabilization of Protein Structure

    NASA Astrophysics Data System (ADS)

    Cho, Inha; Chen, Lee; Shukla, Nimesh; Othon, Christina

    2015-03-01

    Sucralose is a commonly employed artificial sweetener. Sucralose behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of the globular protein Bovine Serum Albumin (BSA). The melting temperature decreases as a linear function of sucralose concentration. We correlate this destabilization with the increased polarity of the sucralose molecule as compared to sucrose. The strongly polar nature is observed as a large dielectric friction exerted on the excited state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein diffusional model. For sucralose solutions however, the diffusion is linearly dependent with the concentration, strongly diverging from the viscosity predictions. The polar nature of sucralose causes a dramatically different interaction with biomolecules than natural disaccharide molecules. Connecticut Space Grant Consortium.

  14. Towards structure-based protein drug design.

    PubMed

    Zhang, Changsheng; Lai, Luhua

    2011-10-01

    Structure-based drug design for chemical molecules has been widely used in drug discovery in the last 30 years. Many successful applications have been reported, especially in the field of virtual screening based on molecular docking. Recently, there has been much progress in fragment-based as well as de novo drug discovery. As many protein-protein interactions can be used as key targets for drug design, one of the solutions is to design protein drugs based directly on the protein complexes or the target structure. Compared with protein-ligand interactions, protein-protein interactions are more complicated and present more challenges for design. Over the last decade, both sampling efficiency and scoring accuracy of protein-protein docking have increased significantly. We have developed several strategies for structure-based protein drug design. A grafting strategy for key interaction residues has been developed and successfully applied in designing erythropoietin receptor-binding proteins. Similarly to small-molecule design, we also tested de novo protein-binder design and a virtual screen of protein binders using protein-protein docking calculations. In comparison with the development of structure-based small-molecule drug design, we believe that structure-based protein drug design has come of age.

  15. The Conformation of Pentanoates in the Solid and in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Merkens, Carina; Stadtmüller, Tom; Englert, Ulli; Mouhib, Halima; Stahl, Wolfgang

    2014-07-01

    Suitable derivatives of the four isomeric pentanoates have been structurally characterized in the solid and the gas phase. For the latter, the volatile ethyl esters of valeric, isovaleric, methylbutyric, and pivalic acid were investigated by a combination of molecular beam Fourier transform microwave (MB-FTMW) spectroscopy and theoretical calculations. Crystalline salts rather than esters were formed by reaction between the carboxylic acids and trans-1,2-diaminocyclohexane. For both gaseous and crystalline methylbutyrates, an essentially perpendicular arrangement of carboxylate and methyl group was observed; earlier structure determinations documented in the data base agree with this result. Two competing conformers of favourable energy were relevant for the corresponding isovalerates: They were associated with torsion angles around 20° and 50° between the carboxylate and the alkyl chain. Good agreements in conformation have also been achieved for our experimentally observed unbranched valerate derivatives and fully branched pivalates in solid and gas phase. Despite the apparent simplicity of the pentanoates, the identification of their lowest energy conformers represents a challenge for different methods and levels of theory.

  16. On chip steady liquid-gas phase separation for flexible generation of dissolved gas concentration gradient.

    PubMed

    Xu, Bi-Yi; Hu, Shan-Wen; Yan, Xiao-Na; Xia, Xing-Hua; Xu, Jing-Juan; Chen, Hong-Yuan

    2012-04-07

    In this study, steady liquid-gas phase separation is realized by applying a hydrophobic small microchannel array (SMA) to bridge two large microchannels, one for liquid phase and one for gas phase. In this structure, a capillary pressure difference between that in the SMA and the larger channel results in a steady liquid-gas interface. The generated liquid-gas interface allows for fast gas dissolving speed. By coupling the liquid-gas interface with a one directional fluidic field, a steady dissolved gas concentration gradient (DgCG) is generated. The DgCG distribution is easily designable for linear or exponential modes, providing improved flexibility for gas participated processes on chip. To demonstrate its applicability, a CO(2) DgCG chip is fabricated and applied for screening CaCO(3) crystal growth conditions in the DgCG chip. Crystals with transitional structures are successfully fabricated, which is consistent with the CO(2) DgCG distribution. This journal is © The Royal Society of Chemistry 2012

  17. Bacteria and fungi inactivation by photocatalysis under UVA irradiation: liquid and gas phase.

    PubMed

    Rodrigues-Silva, Caio; Miranda, Sandra M; Lopes, Filipe V S; Silva, Mário; Dezotti, Márcia; Silva, Adrián M T; Faria, Joaquim L; Boaventura, Rui A R; Vilar, Vítor J P; Pinto, Eugénia

    2016-06-29

    In the last decade, environmental risks associated with wastewater treatment plants (WWTPs) have become a concern in the scientific community due to the absence of specific legislation governing the occupational exposure limits (OEL) for microorganisms present in indoor air. Thus, it is necessary to develop techniques to effectively inactivate microorganisms present in the air of WWTPs facilities. In the present work, ultraviolet light A radiation was used as inactivation tool. The microbial population was not visibly reduced in the bioaerosol by ultraviolet light A (UVA) photolysis. The UVA photocatalytic process for the inactivation of microorganisms (bacteria and fungi, ATCC strains and isolates from indoor air samples of a WWTP) using titanium dioxide (TiO2 P25) and zinc oxide (ZnO) was tested in both liquid-phase and airborne conditions. In the slurry conditions at liquid phase, P25 showed a better performance in inactivation. For this reason, gas-phase assays were performed in a tubular photoreactor packed with cellulose acetate monolithic structures coated with P25. The survival rate of microorganisms under study decreased with the catalyst load and the UVA exposure time. Inactivation of fungi was slower than resistant bacteria, followed by Gram-positive bacteria and Gram-negative bacteria. Graphical abstract Inactivation of fungi and bacteria in gas phase by photocatalitic process performed in a tubular photoreactor packed with cellulose acetate monolith structures coated with TiO2.

  18. Gas-Phase Oxidation of Neutral Basic Residues in Polypeptide Cations by Periodate.

    PubMed

    Pilo, Alice L; Bu, Jiexun; McLuckey, Scott A

    2016-12-01

    The gas-phase oxidation of doubly protonated peptides containing neutral basic residues to various products, including [M + H + O](+), [M - H](+), and [M - H - NH3](+), is demonstrated here via ion/ion reactions with periodate. It was previously demonstrated that periodate anions are capable of oxidizing disulfide bonds and methionine, tryptophan, and S-alkyl cysteine residues. However, in the absence of these easily oxidized sites, we show here that systems containing neutral basic residues can undergo oxidation. Furthermore, we show that these neutral basic residues primarily undergo different types of oxidation (e.g., hydrogen abstraction) reactions than those observed previously (i.e., oxygen transfer to yield the [M + H + O](+) species) upon gas-phase ion/ion reactions with periodate anions. This chemistry is illustrated with a variety of systems, including a series of model peptides, a cell-penetrating peptide containing a large number of unprotonated basic sites, and ubiquitin, a roughly 8.6 kDa protein. Graphical Abstract ᅟ.

  19. Complex Organic Molecules Formation in Space Through Gas Phase Reactions: A Theoretical Approach

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2017-02-01

    Chemistry in the interstellar medium (ISM) is capable of producing complex organic molecules (COMs) of great importance to astrobiology. Gas phase and grain surface chemistry almost certainly both contribute to COM formation. Amino acids as building blocks of proteins are some of the most interesting COMs. The simplest one, glycine, has been characterized in meteorites and comets and, its conclusive detection in the ISM seems to be highly plausible. In this work, we analyze the gas phase reaction of glycine and {{{CH}}5}+ to establish the role of this process in the formation of alanine or other COMs in the ISM. Formation of protonated α- and β-alanine in spite of being exothermic processes is not viable under interstellar conditions because the different paths leading to these isomers present net activation energies. Nevertheless, glycine can evolve to protonated 1-imide-2, 2-propanediol, protonated amino acetone, protonated hydroxyacetone, and protonated propionic acid. However, formation of acetic acid and protonated methylamine is also a favorable process and therefore will be a competitive channel with the evolution of glycine to COMs.

  20. Carbonyl Compounds in the Gas Phase of Cigarette Mainstream Smoke and Their Pharmacological Properties.

    PubMed

    Horinouchi, Takahiro; Higashi, Tsunehito; Mazaki, Yuichi; Miwa, Soichi

    2016-01-01

    Cigarette mainstream smoke is composed of gas and tar phases and contains >4000 chemical constituents, including nicotine and tar. The substances in the gas phase but not in the tar phase can pass through the airway epithelial barrier, enter the systemic circulation via the pulmonary circulation, and increase systemic oxidative damage, leading to the development of cigarette smoking-related diseases such as atherosclerosis. Recently, we identified some stable carbonyl compounds, including acrolein (ACR) and methyl vinyl ketone (MVK), as major cytotoxic factors in nicotine- and tar-free cigarette smoke extract (CSE) of the gas phase. CSE, ACR, and MVK induce protein kinase C (PKC)-dependent activation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (NOX) and subsequent generation of reactive oxygen species (ROS) via NOX, causing plasma membrane damage and cell apoptosis. CSE, ACR, and MVK also trigger carbonylation of PKC, which is an irreversible oxidative modification. Cell damage and PKC carbonylation in response to treatment with CSE, ACR, or MVK are abolished by thiol-containing antioxidants such as N-acetyl-L-cysteine and reduced glutathione. Thus pharmacological modulation of PKC and NOX activities and the trapping of ROS are potential strategies for the prevention of diseases related to cigarette smoking.

  1. Two-Dimensional Gas-Phase Separations Coupled to Mass Spectrometry for Analysis of Complex Mixtures

    PubMed Central

    Tang, Keqi; Li, Fumin; Shvartsburg, Alexandre A.; Strittmatter, Eric F.; Smith*, Richard D.

    2007-01-01

    Ion mobility spectrometry (IMS) has been explored for decades, and its versatility in separation and identification of gas-phase ions is well established. Recently, field asymmetric waveform IMS (FAIMS) has been gaining acceptance in similar applications. Coupled to mass spectrometry (MS), both IMS and FAIMS have shown the potential for broad utility in proteomics and other biological analyses. A major attraction of these separations is extremely high speed, exceeding that of condensed-phase alternatives by orders of magnitude. However, modest separation peak capacities have limited the utility of FAIMS and IMS for analyses of complex mixtures. We report 2-D gas-phase separations that join FAIMS to IMS, in conjunction with high-resolution and accuracy time-of-flight MS. Implementation of FAIMS/IMS and IMS/MS interfaces using electrodynamic ion funnels greatly improves sensitivity. Evaluation of FAIMS/IMS/TOF performance for a protein mixture tryptic digest reveals high orthogonality between FAIMS and IMS dimensions, and hence the benefit of FAIMS filtering prior to IMS/MS. The effective peak capacities in analyses of tryptic peptides are ~500 for FAIMS/IMS separations and ~106 for 3-D FAIMS/IMS/MS, providing a potential platform for ultrahigh-throughput analyses of complex mixtures. PMID:16194103

  2. Gas-Phase Oxidation of Neutral Basic Residues in Polypeptide Cations by Periodate

    NASA Astrophysics Data System (ADS)

    Pilo, Alice L.; Bu, Jiexun; McLuckey, Scott A.

    2016-12-01

    The gas-phase oxidation of doubly protonated peptides containing neutral basic residues to various products, including [M + H + O]+, [M - H]+, and [M - H - NH3]+, is demonstrated here via ion/ion reactions with periodate. It was previously demonstrated that periodate anions are capable of oxidizing disulfide bonds and methionine, tryptophan, and S-alkyl cysteine residues. However, in the absence of these easily oxidized sites, we show here that systems containing neutral basic residues can undergo oxidation. Furthermore, we show that these neutral basic residues primarily undergo different types of oxidation (e.g., hydrogen abstraction) reactions than those observed previously (i.e., oxygen transfer to yield the [M + H + O]+ species) upon gas-phase ion/ion reactions with periodate anions. This chemistry is illustrated with a variety of systems, including a series of model peptides, a cell-penetrating peptide containing a large number of unprotonated basic sites, and ubiquitin, a roughly 8.6 kDa protein.

  3. PSS-SQL: protein secondary structure - structured query language.

    PubMed

    Mrozek, Dariusz; Wieczorek, Dominika; Malysiak-Mrozek, Bozena; Kozielski, Stanislaw

    2010-01-01

    Secondary structure representation of proteins provides important information regarding protein general construction and shape. This representation is often used in protein similarity searching. Since existing commercial database management systems do not offer integrated exploration methods for biological data e.g. at the level of the SQL language, the structural similarity searching is usually performed by external tools. In the paper, we present our newly developed PSS-SQL language, which allows searching a database in order to identify proteins having secondary structure similar to the structure specified by the user in a PSS-SQL query. Therefore, we provide a simple and declarative language for protein structure similarity searching.

  4. Infrared Structural Biology: Detect Functionally Important Structural Motions of Proteins

    NASA Astrophysics Data System (ADS)

    Xie, Aihua

    Proteins are dynamic. Lack of dynamic structures of proteins hampers our understanding of protein functions. Infrared structural biology (IRSB) is an emerging technology. There are several advantages of IRSB for mechanistic studies of proteins: (1) its excellent dynamic range (detecting structural motions from picoseconds to >= seconds); (2) its high structural sensitivity (detect tiny but functionally important structural motions such as proton transfer and changes in hydrogen bonding interaction); (3) its ability to detect different structural motions simultaneously. Successful development of infrared structural biology demands not only new experimental techniques (from infrared technologies to chemical synthesis and cell biology), but also new data processing (how to translate infrared signals into quantitative structural information of proteins). These topics will be discussed as well as examples of how to use IRSB to study structure-function relationship of proteins. This work was supported by NSF DBI1338097 and OCAST HR10-078.

  5. Protein structural motifs in prediction and design.

    PubMed

    Mackenzie, Craig O; Grigoryan, Gevorg

    2017-06-01

    The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information from the PDB has been used to generate models ranging from specific structural mechanisms to general statistical potentials. With accumulating structural data, it has become possible to mine for more complete and complex structural observations, deducing more accurate generalizations. Motif libraries, which capture recurring structural features along with their sequence preferences, have exposed modularity in the structural universe and found successful application in various problems of structural biology. Here we summarize recent achievements in this arena, focusing on subdomain level structural patterns and their applications to protein design and structure prediction, and suggest promising future directions as the structural database continues to grow. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Gas-phase reactions of halogen species of atmospheric importance

    NASA Astrophysics Data System (ADS)

    Heard, Anne C.

    A low-pressure discharge-flow technique, with various optical detection methods, has been used to determine bimolecular rate coefficients for a number of reactions in the gas-phase between OH radicals and organic halogen-containing molecules and between NO3 radicals and the iodine species I2 and I. These experiments have shown that: (1) the reaction of methyl iodide with OH accounts for approximately 2 percent of the removal of CH3I from the troposphere as compared with photolysis; (2) abstraction of I-atoms from a C-I bond by OH is probable in the gas-phase; (3) the halogen-containing anaesthetic substances halothane CF3CClBrH, enflurane CF2HOCF2CFClH, isoflurane CF2HOCClHCF3 and sevoflurane (CF3)2CHOCFH2 have significantly shorter tropospheric lifetimes than the fully halogenated CFCs and halons because of reaction with the OH radical and are thus unlikely to be transported up to the stratosphere where they could contribute to the depletion of ozone. Data obtained for reactions between OH and some 'CFC alternatives' along with measurements of the integrated absorption cross-sections of the compounds in the spectral region 800-1200 cm(exp -1) were used to calculate ozone depletion potentials (ODP) and greenhouse warming potentials relative to CFCl3 for each compound. The study of the reactions between OH and CF3CFBrH and CF2BrH was used to provide a useful first estimate of the environmental acceptability of these compounds in the context of their possible use as replacements for the conventional CFCs. A method was developed to provide a first estimate of the ODP of a halogenated alkane without use of a complicated (and expensive) computer modeling scheme. A reaction between molecular iodine and the nitrate radical in the gas-phase was discovered and the kinetics of this reaction have been studied. No temperature or pressure dependence was observed for the rate of reaction, the rate constant of which was found to be (1.5 +/- 0.5) x 10(exp -12)/cu cm

  7. Constrained Peptides as Miniature Protein Structures

    PubMed Central

    Yin, Hang

    2012-01-01

    This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions. PMID:25969758

  8. Practical lessons from protein structure prediction

    PubMed Central

    Ginalski, Krzysztof; Grishin, Nick V.; Godzik, Adam; Rychlewski, Leszek

    2005-01-01

    Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins. The development of high-quality prediction methods has been boosted in the last years by objective community-wide assessment experiments. This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed. PMID:15805122

  9. Imprint of evolution on protein structures

    NASA Astrophysics Data System (ADS)

    Tiana, Guido; Shakhnovich, Boris E.; Dokholyan, Nikolay V.; Shakhnovich, Eugene I.

    2004-03-01

    We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from an initial seed lattice structure, evolution of model proteins progresses by sequence duplication and subsequent point mutations. A new gene's ability to fold into a stable and unique structure is tested each time through direct kinetic folding simulations. Where possible, the algorithm accepts the new sequence and structure and thus a "new protein structure" is born. During the course of each run, this model evolutionary algorithm provides several thousand new proteins with diverse structures. Analysis of evolved structures shows that later evolved structures are more designable than seed structures as judged by recently developed structural determinant of protein designability, as well as direct estimate of designability for selected structures by thermodynamic sampling of their sequence space. We test the significance of this trend predicted on lattice models on real proteins and show that protein domains that are found in eukaryotic organisms only feature statistically significant higher designability than their prokaryotic counterparts. These results present a fundamental view on protein evolution highlighting the relative roles of structural selection and evolutionary dynamics on genesis of modern proteins.

  10. Silicon Nanowire-Based Devices for Gas-Phase Sensing

    PubMed Central

    Cao, Anping; Sudhölter, Ernst J.R.; de Smet, Louis C.P.M.

    2014-01-01

    Since their introduction in 2001, SiNW-based sensor devices have attracted considerable interest as a general platform for ultra-sensitive, electrical detection of biological and chemical species. Most studies focus on detecting, sensing and monitoring analytes in aqueous solution, but the number of studies on sensing gases and vapors using SiNW-based devices is increasing. This review gives an overview of selected research papers related to the application of electrical SiNW-based devices in the gas phase that have been reported over the past 10 years. Special attention is given to surface modification strategies and the sensing principles involved. In addition, future steps and technological challenges in this field are addressed. PMID:24368699

  11. Conformational Study of Taurine in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Cortijo, Vanessa; Sanz, M. Eugenia; López, Juan C.; Alonso, José L.

    2009-08-01

    The conformational preferences of the amino sulfonic acid taurine (NH2-CH2-CH2-SO3H) have been investigated in the gas phase by laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) in the 6-14 GHz frequency range. One conformer has been observed, and its rotational, centrifugal distortion, and hyperfine quadrupole coupling constants have been determined from the analysis of its rotational spectrum. Comparison of the experimental constants with those calculated theoretically identifies the detected conformer unambiguously. The observed conformer of taurine is stabilized by an intramolecular hydrogen bond O-H···N between the hydrogen of the sulfonic acid group and the nitrogen atom of the amino group.

  12. Regenerable Air Purification System for Gas-Phase Contaminant Control

    NASA Technical Reports Server (NTRS)

    Constantinescu, Ileana C.; Finn, John E.; LeVan, M. Douglas; Lung, Bernadette (Technical Monitor)

    2000-01-01

    Tests of a pre-prototype regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an adsorbent column have been performed at NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. During the normal operation mode, contaminants are removed from the air on the column. Regeneration of the column is performed on-line. During regeneration, contaminants are displaced and destroyed inside the closed oxidation loop. In this presentation we discuss initial experimental results for the performance of RAPS in the removal and treatment of several important spacecraft contaminant species from air.

  13. Regenerable Air Purification System for Gas-Phase Contaminant Control

    NASA Technical Reports Server (NTRS)

    Constantinescu, Ileana C.; Qi, Nan; LeVan, M. Douglas; Finn, Cory K.; Finn, John E.; Luna, Bernadette (Technical Monitor)

    2000-01-01

    A regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an. adsorbent column into a closed oxidation loop is under development through cooperative R&D between Vanderbilt University and NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. Recent work has focused on fabrication and operation of a RAPS breadboard at NASA Ames, and on measurement of adsorption isotherm data for several important organic compounds at Vanderbilt. These activities support the use and validation of RAPS modeling software also under development at Vanderbilt, which will in turn be used to construct a prototype system later in the project.

  14. Gas-phase synthesis of magnetic metal/polymer nanocomposites.

    PubMed

    Starsich, Fabian H L; Hirt, Ann M; Stark, Wendelin J; Grass, Robert N

    2014-12-19

    Highly magnetic metal Co nanoparticles were produced via reducing flame spray pyrolysis, and directly coated with an epoxy polymer in flight. The polymer content in the samples varied between 14 and 56 wt% of nominal content. A homogenous dispersion of Co nanoparticles in the resulting nanocomposites was visualized by electron microscopy. The size and crystallinity of the metallic fillers was not affected by the polymer, as shown by XRD and magnetic hysteresis measurements. The good control of the polymer content in the product nanocomposite was shown by elemental analysis. Further, the successful polymerization in the gas phase was demonstrated by electron microscopy and size measurements. The presented effective, dry and scalable one-step synthesis method for highly magnetic metal nanoparticle/polymer composites presented here may drastically decrease production costs and increase industrial yields.

  15. Gas-phase synthesis of magnetic metal/polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Starsich, Fabian H. L.; Hirt, Ann M.; Stark, Wendelin J.; Grass, Robert N.

    2014-12-01

    Highly magnetic metal Co nanoparticles were produced via reducing flame spray pyrolysis, and directly coated with an epoxy polymer in flight. The polymer content in the samples varied between 14 and 56 wt% of nominal content. A homogenous dispersion of Co nanoparticles in the resulting nanocomposites was visualized by electron microscopy. The size and crystallinity of the metallic fillers was not affected by the polymer, as shown by XRD and magnetic hysteresis measurements. The good control of the polymer content in the product nanocomposite was shown by elemental analysis. Further, the successful polymerization in the gas phase was demonstrated by electron microscopy and size measurements. The presented effective, dry and scalable one-step synthesis method for highly magnetic metal nanoparticle/polymer composites presented here may drastically decrease production costs and increase industrial yields.

  16. Dissociative attachment reactions of electrons with gas phase superacids

    SciTech Connect

    Liu, X.

    1992-01-01

    Using the flowing afterglow Langmuir probe (FALP) technique, dissociative attachment coefficients [beta] for reactions of electrons with gas phase superacids HCo(PF[sub 3])[sub 4], HRh(PF[sub 3])[sub 4] and carbonyl hydride complexes HMn(CO)[sub 5], HRe(CO)[sub 5] have been determined under thermal conditions over the approximate temperature range 300[approximately]550 K. The superacids react relatively slowly (<1/20 of [beta][sub max]) with free electrons in a thermal plasma, and the values of [beta] obtained this far do not show a correlation between acidity and [beta]. The pioneer researchers in this field had speculated that any superacid would be a rapid attacher of electrons; it was found that this speculation is not true in general. The product distribution of electron attachment reaction to HCo(PF[sub 3])[sub 4] was found to be independent of temperature even though the [beta][HCo(PF[sub 3])[sub 4

  17. Laser-induced chemical deposition from the gas phase

    NASA Astrophysics Data System (ADS)

    Teslenko, V. V.

    1990-02-01

    The results of the study of the chemical reactions involved in the deposition of various substances from the gas phase using the pulsed, quasi-continuous, and continuous laser radiation in the wavelength range 0.193-10.6 μm have been summarised. Particular attention has been paid to the deposition of inorganic substances, including non-metals (C, Si, Ge, etc.), metals (Cu, Au, Zn, Cd, Al, Cr, Mo, W, Ni), and a number of simple compounds. Detailed experimental data are given on the influence of the radiation parameters (wavelength, duration and spacing of the pulses, intensity of radiation, shape and position of the laser beam) and the nature of the reagents (hydrides, halides, carbonyls, alkyl organometallic compounds, etc.) on the rate of deposition and the composition of the deposit. The characteristics of photolytic deposition reactions and their possible applications have been examined. The bibliography contains 202 references.

  18. Regenerable Air Purification System for Gas-Phase Contaminant Control

    NASA Technical Reports Server (NTRS)

    Constantinescu, Ileana C.; Finn, John E.; LeVan, M. Douglas; Lung, Bernadette (Technical Monitor)

    2000-01-01

    Tests of a pre-prototype regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an adsorbent column have been performed at NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. During the normal operation mode, contaminants are removed from the air on the column. Regeneration of the column is performed on-line. During regeneration, contaminants are displaced and destroyed inside the closed oxidation loop. In this presentation we discuss initial experimental results for the performance of RAPS in the removal and treatment of several important spacecraft contaminant species from air.

  19. Enhancement of gas phase heat transfer by acoustic field application.

    PubMed

    Komarov, Sergey; Hirasawa, Masahiro

    2003-06-01

    This study discusses a possibility for enhancement of heat transfer between solids and ambient gas by application of powerful acoustic fields. Experiments are carried out by using preheated Pt wires (length 0.1-0.15 m, diameter 50 and 100 micro m) positioned at the velocity antinode of a standing wave (frequency range 216-1031 Hz) or in the path of a travelling wave (frequency range 6.9-17.2 kHz). A number of experiments were conducted under conditions of gas flowing across the wire surface. Effects of sound frequency, sound strength, gas flow velocity and wire preheating temperature on the Nusselt number are examined with and without sound application. The gas phase heat transfer rate is enhanced with acoustic field strength. Higher temperatures result in a vigorous radiation from the wire surface and attenuate the effect of sound. The larger the gas flow velocity, the smaller is the effect of sound wave on heat transfer enhancement.

  20. Regenerable Air Purification System for Gas-Phase Contaminant Control

    NASA Technical Reports Server (NTRS)

    Constantinescu, Ileana C.; Qi, Nan; LeVan, M. Douglas; Finn, Cory K.; Finn, John E.; Luna, Bernadette (Technical Monitor)

    2000-01-01

    A regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an. adsorbent column into a closed oxidation loop is under development through cooperative R&D between Vanderbilt University and NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. Recent work has focused on fabrication and operation of a RAPS breadboard at NASA Ames, and on measurement of adsorption isotherm data for several important organic compounds at Vanderbilt. These activities support the use and validation of RAPS modeling software also under development at Vanderbilt, which will in turn be used to construct a prototype system later in the project.

  1. The intrinsic (gas-phase) acidities of bridgehead alcohols

    NASA Astrophysics Data System (ADS)

    Herrero, Rebeca; Dávalos, Juan Z.; Abboud, José-Luis M.; Alkorta, I.; Koppel, I.; Koppel, I. A.; Sonoda, T.; Mishima, M.

    2007-11-01

    The gas-phase acidities of 1-adamantanol and perfluoro1-adamantanol were determined by means of Fourier transform ion cyclotron resonance spectrometry (FT-ICR). The acidity of perfluoro1-adamantanol seems to be the highest ever reported for an alcohol. A computational study of these species and their anions at both the MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) levels was performed. Also studied were the tertiary alcohols (including their perfluorinated forms) derived from norbornane, bicyclo[2.2E2]octane and cubane. It was found that: (i) the intrinsic acidity of non-fluorinated bridgehead alcohols increases with the strain of the hydrocarbon framework and, (ii) perfluorination of these compounds strongly increases their acidity and, likely, significantly modifies their internal strain.

  2. Ceramic microreactors for heterogeneously catalysed gas-phase reactions.

    PubMed

    Knitter, Regina; Liauw, Marcel A

    2004-08-01

    The high surface to volume ratio of microchannel components offers many advantages in micro chemical engineering. It is obvious, however, that the reactor material and corrosion phenomena play an important role when applying these components. For chemical reactions at very high temperatures or/and with corrosive reactants involved, microchannel components made of metals or polymers are not suited. Hence, a modular microreactor system made of alumina was developed and fabricated using a rapid prototyping process chain. With exchangeable inserts the system can be adapted to the requirements of various reactions. Two heterogeneously catalysed gas-phase reactions (oxidative coupling of methane, isoprene selective oxidation to citraconic anhydride) were investigated to check the suitability of the system at temperatures of up to 1000 degrees C. Apart from the high thermal and chemical resistance, the lack of any blind activity was found to be another advantage of ceramic components.

  3. Synthesis and Gas Phase Thermochemistry of Germanium-Containing Compounds

    SciTech Connect

    Classen, Nathan Robert

    2002-01-01

    The driving force behind much of the work in this dissertation was to gain further understanding of the unique olefin to carbene isomerization observed in the thermolysis of 1,1-dimethyl-2-methylenesilacyclobutane by finding new examples of it in other silicon and germanium compounds. This lead to the examination of a novel phenylmethylenesilacyclobut-2-ene, which did not undergo olefin to carbene rearrangement. A synthetic route to methylenegermacyclobutanes was developed, but the methylenegermacyclobutane system exhibited kinetic instability, making the study of the system difficult. In any case the germanium system decomposed through a complex mechanism which may not include olefin to carbene isomerization. However, this work lead to the study of the gas phase thermochemistry of a series of dialkylgermylene precursors in order to better understand the mechanism of the thermal decomposition of dialkylgermylenes. The resulting dialkylgermylenes were found to undergo a reversible intramolecular β C-H insertion mechanism.

  4. Photodissociation and spectroscopy of gas phase bimetallic clusters

    SciTech Connect

    Duncan, M.A.

    1992-05-01

    Focus of the research program is the study of gas phase metal clusters for modeling fundamental interactions on metal surfaces. We characterize the chemical bonding between component atoms in clusters as well as the bonding in adsorption on cluster surfaces. Electronic spectra, vibrational frequencies and bond dissociation energies are measured for both neutral and ionized clusters with laser/mass spectrometry techniques. Small bimetallic cluster cations containing Bi/Cr, Bi/Fe, Sn/Bi, and Pb/Sb were photodissociated at various uv wavelengths. Silver dimer van der Waals complexes were produced with a series of rare gas atoms (Ar, Kr, Xe), and their vibrational frequencies and dissociation energies were obtained. (DLC)

  5. Infrared and Ultraviolet Spectroscopy of Gas-Phase Imidazolium and Pyridinium Ionic Liquids.

    NASA Astrophysics Data System (ADS)

    Young, Justin W.; Booth, Ryan S.; Annesley, Christopher; Stearns, Jaime A.

    2015-06-01

    Ionic liquids (ILs) are a highly variable and potentially game-changing class of molecules for a number of Air Force applications such as satellite propulsion, but the complex nature of IL structure and intermolecular interactions makes it difficult to adequately predict structure-property relationships in order to make new IL-based technology a reality. For example, methylation of imidazolium ionic liquids leads to a substantial increase in viscosity but the underlying physical mechanism is not understood. In addition, the role of hydrogen bonding in ILs, and especially its relationship to macroscopic properties, is a matter of ongoing research. Here we describe the gas-phase spectroscopy of a series of imidazolium- and pyridinium-based ILs, using a combination of infrared spectroscopy and density functional theory to establish the intermolecular interactions present in various ILs, to assess how well they are described by theory, and to relate microscopic structure to macroscopic properties.

  6. Gas-Phase Amidation of Carboxylic Acids with Woodward's Reagent K Ions

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; Pilo, Alice L.; Luongo, Carl A.; McLuckey, Scott A.

    2015-06-01

    Gas-phase amidation of carboxylic acids in multiply-charged peptides is demonstrated via ion/ion reactions with Woodward's reagent K (wrk) in both positive and negative mode. Woodward's reagent K, N-ethyl-3-phenylisoxazolium-3'-sulfonate, is a commonly used reagent that activates carboxylates to form amide bonds with amines in solution. Here, we demonstrate that the analogous gas-phase chemistry occurs upon reaction of the wrk ions and doubly protonated (or doubly deprotonated) peptide ions containing the carboxylic acid functionality. The reaction involves the formation of the enol ester intermediate in the electrostatic complex. Upon collisional activation, the ethyl amine on the reagent is transferred to the activated carbonyl carbon on the peptide, resulting in the formation of an ethyl amide (addition of 27 Da to the peptide) with loss of a neutral ketene derivative. Further collision-induced dissoci