Glycine In Gas Phase Research Articles

Polypeptide Chain Growth Mechanisms and Secondary Structure Formation in Glycine Gas-Phase Deposition on Silica Surfaces.

Peptide formation by amino acids condensation represents a crucial reaction in the quest of the origins of life as well as in synthetic chemistry. However, it is still poorly understood in terms of efficiency and reaction mechanism. In the present work, peptide formation has been investigated through thermal condensation of gas-phase glycine in fluctuating silica environments as a model of prebiotic environments. In-situ IR spectroscopy measurements under a controlled atmosphere reveal that a humidity fluctuating system subjected to both temperature and water activity variations results in the formation of more abundant peptides compared to a dehydrated system subjected only to temperature fluctuations cycles. A model is proposed in which hydration steps result in the hydrolysis and redistribution of the oligomers formed during previous deposition in dry conditions. This results in the formation of self-assembled aggregates with well-defined secondary structures (especially β-sheets). Upon further monomers feeding, structural elements are conserved in newly growing chains, with indications of templated polymerization. The structural dynamics of peptides were also evaluated. Rigid self-assembled structures with a high resistance to further wetting/drying cycles and inaccessibility to isotopic exchange were present in the humidity fluctuating system compared to more flexible structures in the dehydrated system. The resistance and growth of self-assembled structures were also investigated for an extended duration of Gly deposition using isotope labeling.

Amino acid gas phase circular dichroism and implications for the origin of biomolecular asymmetry

Life on Earth employs chiral amino acids in stereochemical l-form, but the cause of molecular symmetry breaking remains unknown. Chiroptical properties of amino acids – expressed in circular dichroism (CD) – have been previously investigated in solid and solution phase. However, both environments distort the intrinsic charge distribution associated with CD transitions. Here we report on CD and anisotropy spectra of amino acids recorded in the gas phase, where any asymmetry is solely determined by the genuine electromagnetic transition moments. Using a pressure- and temperature-controlled gas cell coupled to a synchrotron radiation CD spectropolarimeter, we found CD active transitions and anisotropies in the 130–280 nm range, which are rationalized by ab initio calculation. As gas phase glycine was found in a cometary coma, our data may provide insights into gas phase asymmetric photochemical reactions in the life cycle of interstellar gas and dust, at the origin of the enantiomeric selection of life’s l-amino acids.

Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy.

The native-like structures of protonated glycine and peptide Gly3H+ were elucidated using cold ion IR spectroscopy of these biomolecules hydrated by a controlled number of water molecules. The complexes were generated directly from an aqueous solution using gentle electrospray ionization. Already with a single retained water molecule, GlyH+ exhibits the native-like structure characterized by a lack of intramolecular hydrogen bonds. We use our spectra to calibrate the available data for the same complexes, which are produced by cryogenic condensation of water onto the gas-phase glycine. In some conformers of these complexes, GlyH+ adopts the native-like structure, while in the others, it remains "kinetically" trapped in the intrinsic state. Upon condensation of 4-5 water molecules, the embedded amino acid fully adopts its native-like structure. Similarly, condensation of one water molecule onto the tripeptide is insufficient to fully eliminate its kinetically trapped intrinsic states.

An Expanded Gas-grain Model for Interstellar Glycine

The study of the chemical evolution of glycine in the interstellar medium is one of challenging topics in astrochemistry. Here, we present the chemical modeling of glycine in hot cores using the state-of-the-art three-phase chemical model NAUTILUS, which is focused on the latest glycine chemistry. For the formation process of glycine on the grain surface, we obtained consistent results with previous studies that glycine would be formed via the reactions of COOH with CH$_2$NH$_2$. However, we will report three important findings regarding the chemical evolution and the detectability of interstellar glycine. First, with the experimentally obtained binding energy from the temperature programmed thermal desorption (TPD) experiment, a large proportion of glycine was destroyed through the grain surface reactions with NH or CH$_3$O radicals before it fully evaporates. As a result, the formation process in the gas phase is more important than thermal evaporation from grains. If this is the case, NH$_2$OH and CH$_3$COOH rather than CH$_3$NH$_2$ and CH$_2$NH would be the essential precursors to the gas phase glycine. Secondly, since the gas phase glycine will be quickly destroyed by positive ions or radicals, early evolutionary phase of the hot cores would be the preferable target for the future glycine surveys. Thirdly, we suggest the possibility that the suprathermal hydrogen atoms can strongly accelerate the formation of COOH radicals from CO$_2$, resulting in the dramatic increase of formation rate of glycine on grains. The efficiency of this process should be investigated in detail by theoretical and experimental studies in the future.

A New Energy Ordering and the Dipole Moment of Gas Phase Glycine via Plane-Wave Density Functional Theory Calculations

The abundance of glycine (Gly), the simplest amino acid, in meteorites leads us to the next question about its extraterrestrial origin. However, astronomers have not yet found glycine signature in interstellar medium. Laboratory microwave spectroscopy experiments report the most stable Gly conformer has a dipole moment of 4.5 - 5.45 Debye. Theoretical calculations, so far performed only with Gaussian basis functions, has predicted a dipole moment of about 1 Debye. This discrepancy has baffled astronomers. We study the energetics of glycine and its isomers and conformers via plane-wave density functional theory calculations. The geometric structures of the isomers and their conformers are identified, along with their relative stability and their dipole moment. In the case of glycine, we obtain the most stable conformer with a dipole moment of 5.76 Debye, close to the microwave spectroscopy experiments. If the plane wave energy cutoff is reduced to a lower value (~ 400 eV) on purpose, the energy ordering reverses to the case with Gaussian basis calculations.

Fast heavy-ion radiation damage of glycine in aqueous solution

Fast heavy-ion radiolysis of biomolecules in aqueous solution is investigated for an atomistic understanding of radiation damage to normal cells during heavy-particle beam therapy. The smallest amino acid glycine was used as a model biomaterial. Microjets of aqueous glycine solutions under vacuum were irradiated with 4.0-MeV carbon ions corresponding to energies in the Bragg peak region. To understand the effects of the water environment on molecular damage, the yield of glycine dissociation was measured by secondary ion mass spectroscopy. The yield was significantly reduced relative to gas-phase glycine targets. This implies that the numerous water molecules surrounding a single glycine molecule act as a buffer that suppresses dissociation. This is an environmental effect similar to that observed for other biomolecular cluster targets.

A THREE-PHASE CHEMICAL MODEL OF HOT CORES: THE FORMATION OF GLYCINE

A new chemical model is presented that simulates fully-coupled gas-phase, grain-surface and bulk-ice chemistry in hot cores. Glycine (NH2CH2COOH), the simplest amino acid, and related molecules such as glycinal, propionic acid and propanal, are included in the chemical network. Glycine is found to form in moderate abundance within and upon dust-grain ices via three radical-addition mechanisms, with no single mechanism strongly dominant. Glycine production in the ice occurs over temperatures ~40-120 K. Peak gas-phase glycine fractional abundances lie in the range 8 x 10^{-11} - 8 x 10^{-9}, occuring at ~200 K, the evaporation temperature of glycine. A gas-phase mechanism for glycine production is tested and found insignificant, even under optimal conditions. A new spectroscopic radiative-transfer model is used, allowing the translation and comparison of the chemical-model results with observations of specific sources. Comparison with the nearby hot-core source NGC 6334 IRS1 shows excellent agreement with integrated line intensities of observed species, including methyl formate. The results for glycine are consistent with the current lack of a detection of this molecule toward other sources; the high evaporation temperature of glycine renders the emission region extremely compact. Glycine detection with ALMA is predicted to be highly plausible, for bright, nearby sources with narrow emission lines. Photodissociation of water and subsequent hydrogen-abstraction from organic molecules by OH, and NH2, are crucial to the build-up of complex organic species in the ice. The inclusion of alternative branches within the network of radical-addition reactions appears important to the abundances of hot-core molecules; less favorable branching ratios may remedy the anomalously high abundance of glycolaldehyde predicted by this and previous models.

Low-energy electron collisions with glycine

We report cross sections for elastic electron scattering by gas phase glycine (neutral form), obtained with the Schwinger multichannel method. The present results are the first obtained with a new implementation that combines parallelization with OpenMP directives and pseudopotentials. The position of the well known π* shape resonance ranged from 2.3 eV to 2.8 eV depending on the polarization model and conformer. For the most stable isomer, the present result (2.4 eV) is in fair agreement with electron transmission spectroscopy assignments (1.93 ± 0.05 eV) and available calculations. Our results also point out a shape resonance around 9.5 eV in the A' symmetry that would be weakly coupled to vibrations of the hydroxyl group. Since electron attachment to a broad and lower lying σ* orbital located on the OH bond has been suggested the underlying mechanism leading to dissociative electron attachment at low energies, we sought for a shape resonance around ~4 eV. Though we obtained cross sections with the target molecule at the equilibrium geometry and with stretched OH bond lengths, least-squares fits to the calculated eigenphase sums did not point out signatures of this anion state (though, in principle, it could be hidden in the large background). The low energy (~1 eV) integral cross section strongly scales as the bond length is stretched, and this could indicate a virtual state pole, since dipole supported bound states are not expected at the geometries addressed here.

Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF → ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.

Structure of the gas-phase glycine tripeptide

The structural preferences of the neutral gas-phase glycine tripeptide have been investigated using a variety of strategies including a hierarchy of electronic structure theory (encompassing HF/3-21G single-point energy calculation and geometry optimisation, B3LYP/6-31G(d) geometry optimisation and MP2/6-31+G(d) single-point energy calculation and/or geometry optimisation). The structures and relative stabilities of the 20 most stable conformers identified were verified by M05-2X and mPW2-PLYP-D calculations. The most stable conformer located has a folded gamma-turn structure, with an NH...N interaction between the N-terminal nitrogen and the amide hydrogen of glycine (2) and an NH...O interaction between the amide hydrogen of glycine (3) and the carboxyl oxygen of glycine (1). The results show a clear preference for folded over extended structures.

Formation of Gas-Phase Glycine and Cyanoacetylene via Associative Detachment Reactions

The recent discovery of molecular negative ions in the interstellar medium suggests that these species may be reactive intermediates in astrochemical processes. Our recent studies indicate that these anions, despite their high electron binding energies, are reactive with atomic reagents. In this work, we report that two species of interstellar interest, glycine (NH(2)CH(2)COOH) and cyanoacetylene (HC(3)N), can be readily formed by associative detachment of their corresponding deprotonated anions with hydrogen atoms. The reaction rate constants for glycine anion (NH(2)CH(2)CO(2)(-)) and cyanoacetylene anion (C(3)N(-)) with H atom have been measured to be 2.0 +/- 0.5 x10(-10) cm(3) s(-1) and 5.4 +/- 0.2 x 10(-10) cm(3) s(-1), respectively, where the error bars represent one standard deviation of the mean; the estimated total error is +/- 50%. A possible reaction mechanism for chemical conversion of species observed in the interstellar medium is also described.

First-principle conformational analysis of glycine residues in the αβ-tubulin dimer

Amino acids, especially glycine, have been extensively studied whereas their conformational behaviors in proteins are rather limited. In this work, all the polypeptides containing glycine residues are truncated from the alphabeta-tubulin dimer and refined with the partial optimization technique, where the backbone atoms of the previous and posterior residues to the glycine residues are fixed at the experimental Cartesian positions whereas the others fully relaxed. The combination of the polypeptide models and partial optimization technique is validated by twolayer ONIOM calculations, being effective to retain the local structures of proteins and meanwhile optimizing the concerned glycine residues towards energy minima. Owing to the lack of side chains, various types of hydrogen bonding interactions are detected in the glycine residues. The conformational analyses of proteins are mainly based on the dihedrals. Theta(1)( angleH(5)C(2)C(3)O(4)), Theta(2)( angleH(6)C(2)C(3)O(4)) and Theta(3)( angleN(1)C(2)C(3)O(4)) are the three key dihedrals to determine the glycine conformations, which were found to change synchronously and correlate with each other by four linear equations. It thus provided the first evidence of the correlation of intra-dihedrals for the amino acid residues in proteins. In addition, the three dihedrals of the gas-phase glycine conformations were also found to suit well with these linear equations, elucidating the rationality of using amino acids as the computational models of proteins.

Neutral vs Zwitterionic Glycine Forms at the Water/Silica Interface: Structure, Energies, and Vibrational Features from B3LYP Periodic Simulations

B3LYP periodic calculations with a triple-xi-polarized Gaussian basis set have been used to study adsorption of glycine on a hydroxylated silica surface (2.2 OH/nm2) model derived from the (001) surface of edingtonite. The simulation envisages glycine adsorbed either as a gas-phase molecule or when microsolvated by up to five H20 molecules. Both neutral and zwitterionic forms of glycine have been considered and their structural, energetic, and spectroscopic vibrational features compared internally and with experiments. As a gas phase glycine sticks in its neutral form at the silica surface, the zwitterion being highly unstable and with transition-state character. When glycine is microsolvated at the silica interface, two H20 molecules render the zwitterion population comparable to that of the neutral form whereas with four H2O molecules the neutral glycine population is wiped out in favor of the zwitterion. With four H20 molecules the most stable structure shows no direct contact between glycine and the silica surface, H20 acting as a mediator via H-bond interactions. The B3LYP energies and structural data were also supported by comparing the scaled harmonic vibrational features with literature FTIR data of glycine adsorbed on an amorphous silica surface either from the gas phase or in water solution.

Electron scattering from gas-phase glycine molecules

Low-energy electron collisions with gas-phase glycine molecules have been studied using the fixed-nuclei R-matrix method based on state-averaged complete-active-space self-consistent-field orbitals. A total of 40 electronic states of neutral glycine, including 3s and 3p Rydberg excited states, are included in the R-matrix model. A large peak is observed in the A(") partial elastic cross section around 3.4 eV, which originates from the pi( *) shape resonance. In addition, many sharp narrow peaks coming from core excited resonances are seen in the elastic and inelastic cross sections at energies above 5 eV. Although the effect of the Rydberg orbitals on the elastic cross section is insignificant, these orbitals are crucial to represent core excited resonances in the inelastic cross sections. In previous experiments on dissociative electron attachment to gas-phase glycine, noticeable product ion peaks have been observed at electron collision energies around 1-2 and 5-10 eV. The resonance positions obtained in our calculations are generally close to these experimental results.

Low energy electron impact in gas phase glycine, alanine and propanoic acid: Electronic, vibrational excitations and negative ions

Excitation of electronic states below 10 eV and resonant vibrational excitation around 2 eV are investigated in gas phase glycine and d-alanine by electron energy loss spectroscopy. Location of singlet states observed between 5 eV and 10 eV is in good agreement with recent calculations. Vibrational excitation concerns mainly the COOH group and CH stretch modes. Structures in (M–H) − cross-sections between 1 eV and 2 eV have been revisited. Dips are clearly observed revealing OH stretch excitation, interpreted as cusps due to competition between decay channels of the resonant state. (M–H) − anions and vibrational excitation have also been investigated in propanoic acid for comparison.

Dissociative electron attachment to gas phase glycine: Exploring the decomposition pathways by mass separation of isobaric fragment anions

Dissociative electron attachment to gas phase glycine generates a number of fragment ions, among them ions observed at the mass numbers 15, 16 and 26 amu. From stoichiometry they can be assigned to the chemically rather different species NH(-)/CH(3)(-)(15 amu), O(-)/NH(2)(-)(16 amu) and CN(-)/C(2)H(2)(-)(26 amu). Here we use a high resolution double focusing two sector mass spectrometer to separate these isobaric ions. It is thereby possible to unravel the decomposition reactions of the different transient negative ions formed upon resonant electron attachment to neutral glycine in the energy range 0-15 eV. We find that within the isobaric ion pairs, the individual components generally arise from resonances located at substantial different energies. The corresponding unimolecular decompositions involve complex reaction sequences including multiple bond cleavages and substantial rearrangement in the precursor ion. To support the interpretation and assignments we also use (13)C labelling of glycine at the carboxylic group.

Vibrational spectrum of glycine molecule

The infrared and Raman spectra of glycine molecule has been studied in spectral region 400–4000 cm −1 in solid form as well as in water. The vibrational frequencies for the fundamental modes of the glycine in neutral and its zwitterionic form have also been calculated using AM1 semiempirical method as well as ab initio method with minimal basis set. The reliability of the minimal basis set and AM1 method with higher basis sets, for IR spectra of the neutral glycine conformers were examined. We find that the 6–21G basis set calculation yields structural parameters, rotational constant and dipole moment of glycine conformers, which are very similar to those obtained from extended basis set calculation as well as experimental values. IR frequencies for glycine conformer I are also calculated in water using SCRF = PCM model and compared with experimental values. A comparison between calculated frequencies for neutral glycine, and its zwitterionic form with observed IR and Raman bands have been made. The total energies for gas phase glycine and its zwitterionic form along with those of hydrated forms were also calculated. It is found from the calculations that in the gas phase neutral glycine is more stable as compared to its zwitterionic form.

Resonant Capture of Low-Energy Electrons by Gas-Phase Glycine: A Quantum Dynamics Calculation

We present quantum calculations for the low-energy dynamics of electrons interacting with glycine molecules in the gas phase. The scattering equations are formulated within a symmetry-adapted, single-center expansion of both continuum and bound electrons, and the interaction forces are obtained from a combination of ab initio calculations and a nonempirical modeling of exchange plus correlation effects. Several open-channel (shape) resonances are obtained, and the features of the excess electron resonant wave functions are related to the experimental findings about the dissociative electron attachment (DEA) processes that follow the initial formation of those transient negative ions.

Dissociative electron attachment to gas-phase glycine.

By using a high-resolution electron energy monochromator low-energy electron attachment to gas-phase glycine (H2NCH2COOH, or G) has been studied by means of mass spectrometric detection of the product anions. In the same way as for several other biologically relevant molecules no stable parent anion was formed by free electron attachment. The largest dissociative electron attachment (DEA) cross-section, approximately 5x10(-20) m2, was observed for (G-H)-+H at an electron energy of 1.25 eV. Glycine and formic acid (HCOOH) have several common features, because a precursor ion can be characterized by electron attachment to the unoccupied pi* orbital of the -COOH group. At higher incident electron energies several smaller fragment anions are formed. Except for H-, which could not be observed in this study, there was good agreement with an earlier investigation by Gohlke et al.

Inner-Shell Excitation Spectroscopy of the Peptide Bond: Comparison of the C 1s, N 1s, and O 1s Spectra of Glycine, Glycyl-Glycine, and Glycyl-Glycyl-Glycine

Oscillator strengths for C 1s, N 1s, and O 1s excitation spectra of gaseous glycine and the dipeptide, glycyl−glycine, have been derived from inner-shell electron energy-loss spectroscopy recorded under scattering conditions where electric dipole transitions dominate (2.5 keV residual energy, θ ≈ 2°). X-ray absorption spectra of solid glycine, glycyl−glycine, glycyl−glycyl−glycine, and a large protein, fibrinogen, were recorded in a scanning transmission X-ray microscope. The experimental spectra are assigned through interspecies comparisons and by comparison to ab initio computed spectra of various conformations of glycine and glycyl−glycine. Inner-shell excitation spectral features characteristic of the peptide bond are readily identified by comparison of the spectra of gas-phase glycine and glycyl−glycine. They include a clear broadening and a ∼0.3 eV shift of the C 1s → π*CO peak and introduction of a new pre-edge feature in the N 1s spectrum. These effects are due to 1s → π*amide transitions introduc...