Glycine Molecules Research Articles

Stability of the glycine cation in the gas phase after interaction with multiply charged ions

This study presents a coupled experimental and theoretical work on the stability of singly charged glycine molecules (NH2CH2COOH+, the simplest amino acid) produced in the collision of neutral glycine with low-energy multiply charged ions in the gas phase. The main fragments observed experimentally result from Cα-Ccarboxyl bond cleavage. Additionally, some fragments are produced after an intramolecular rearrangement of the glycine cation, in particular the loss of a neutral water molecule following a H-migration. Moreover, this work discusses qualitatively the energy transferred to the molecule in the collision with a comparative study of the fragmentation patterns for different projectile ion charge states.

Radiolysis of amino acids by heavy and energetic cosmic ray analogues in simulated space environments: α-glycine zwitterion form

In this work, we studied the stability of the glycine molecule in the crystalline zwitterion form, known as {\alpha}-glycine ($^{+}$NH$_{3}$CH$_{2}$COO$^{-}$) under action of heavy cosmic ray analogs. The experiments were conducted in a high vacuum chamber at heavy ions accelerator GANIL, in Caen, France. The samples were bombarded at two temperatures (14 K and 300 K) by $^{58}$Ni$^{11+}$ ions of 46 MeV until the final fluence of $10^{13}$ ions cm$^{-2}$. The chemical evolution of the sample was evaluated in-situ using Fourrier Transformed Infrared (FTIR) spectrometer. The bombardment at 14 K produced several daughter species such as OCN$^-$, CO, CO$_2$, and CN$^-$. The results also suggest the appearing of peptide bonds during irradiation but this must be confirmed by further experiments. The halflives of glycine in Interstellar Medium were estimated to be 7.8 $\times 10^3$ years (300 K) and 2.8 $\times 10^3$ years (14 K). In the Solar System the values were 8.4 $\times 10^2$ years (300 K) and 3.6 $\times 10^3$ years (14 K). It is believed that glycine could be present in space environments that suffered aqueous changes such as the interior of comets, meteorites and planetesimals. This molecule is present in proteins of all alive beings. So, studying its stability in these environments provides further understanding about the role of this specie in the prebiotic chemistry on Earth.

Communication: oscillating charge migration between lone pairs persists without significant interaction with nuclear motion in the glycine and Gly-Gly-NH-CH3 radical cations.

Coupled electron-nuclear dynamics has been studied, using the Ehrenfest method, for four conformations of the glycine molecule and a single conformation of Gly-Gly-NH-CH3. The initial electronic wavepacket was a superposition of eigenstates corresponding to ionization from the σ lone pairs associated with the carbonyl oxygens and the amine nitrogen. For glycine, oscillating charge migration (when the nuclei were frozen) was observed for the 4 conformers studied with periods ranging from 2 to 5 fs, depending on the energy gap between the lone pair cationic states. When coupled nuclear motion was allowed (which was mainly NH2 partial inversion), the oscillations hardly changed. For Gly-Gly-NH-CH3, charge migration between the carbonyl oxygens and the NH2 lone pair can be observed with a period similar to glycine itself, also without interaction with nuclear motion. These simulations suggest that charge migration between lone pairs can occur independently of the nuclear motion.

The temperature effect on the glycine decomposition induced by 2 keV electron bombardment in space analog conditions

Glycine is the simplest proteinaceous amino acid that has been extensively detected in carbonaceous meteorites and was recently observed in the cometary samples returned to Earth by NASA’s Stardust spacecraft. In space, such species is exposed to several radiation fields at different temperatures. In aqueous solutions, this species appears mainly as zwitterionic glycine (+NH3CH2COO−) however, in solid phase, it may be found in amorphous or crystalline forms. Here, we present an experimental study on the destruction of two zwitterionic glycine crystals (α- and β-form) at two different temperatures (300 K and 14 K) by 2 keV electrons in an attempt to test the behavior and stability of this molecular species in different space environments. The samples were analyzed in situ by Fourier transform infrared spectrometry at electron fluences. The experiments were carried out under ultra-high vacuum conditions at the Molecular Physics Laboratory at the Open University at Milton Keynes, UK. The dissociation cross section of glycine is approximately 5 times higher for the 14 K samples when compared to the 300 K samples. In contrast, no significant differences emerged between the dissociation cross sections of α- and β-forms of glycine for fixed temperature experiments. We therefore conclude that the destruction cross section is more heavily dependent on temperature than the phase of the condensed glycine material. This may be associated with the opening of additional reaction routes in the frozen samples involving the trapped daughter species (e.g. CO2 and CO). The half-life of studied samples extrapolated to space conditions shows that glycine molecules on the surface of interstellar grains has less survivability and they are highly sensitive to ambient radiations, however, they can survive extended period of time in the solar system like environments. Survivability increases by a factor of 5 if the samples are at 300 K when compared to low temperature experiments at 14 K and is independent of the crystalline structure. In addition, this survival would increase if the molecular species were protected by several layers of other molecular species as trapped in comet mantles or embedded within regolith in asteroids/lunar surfaces. The understanding of the excitation and dissociation processes of organic compounds in space simulation is highly required to put constrains in the puzzle over the origin of life in the primitive Earth.

Formation of Stacked Disc-shaped Layered Double Hydroxides by Homogeneous Precipitation Method

Abstract Effect of glycine addition in reaction systems on the morphology of layered double hydroxides (LDHs) was investigated. The morphology of LDH crystals synthesized by homogeneous precipitation changed from hexagonal plate to stacked disc on increasing the glycine concentration. The morphological changes most likely occurred because of the interaction of glycine molecules with the LDH crystal surfaces. These findings may be applicable to the development of highly functional LDH materials through the control of crystal morphology.

The formation of glycine and other complex organic molecules in exploding ice mantles.

Complex Organic Molecules (COMs), such as propylene (CH3CHCH2) and the isomers of C2H4O2 are detected in cold molecular clouds (such as TMC-1) with high fractional abundances (Marcelino et al., Astrophys. J., 2007, 665, L127). The formation mechanism for these species is the subject of intense speculation, as is the possibility of the formation of simple amino acids such as glycine (NH2CH2COOH). At typical dark cloud densities, normal interstellar gas-phase chemistries are inefficient, whilst surface chemistry is at best ill defined and does not easily reproduce the abundance ratios observed in the gas phase. Whatever mechanism(s) is/are operating, it/they must be both efficient at converting a significant fraction of the available carbon budget into COMs, and capable of efficiently returning the COMs to the gas phase. In our previous studies we proposed a complementary, alternative mechanism, in which medium- and large-sized molecules are formed by three-body gas kinetic reactions in the warm high density gas phase. This environment exists, for a very short period of time, after the total sublimation of grain ice mantles in transient co-desorption events. In order to drive the process, rapid and efficient mantle sublimation is required and we have proposed that ice mantle 'explosions' can be driven by the catastrophic recombination of trapped hydrogen atoms, and other radicals, in the ice. Repeated cycles of freeze-out and explosion can thus lead to a cumulative molecular enrichment of the interstellar medium. Using existing studies we based our chemical network on simple radical addition, subject to enthalpy and valency restrictions. In this work we have extended the chemistry to include the formation pathways of glycine and other large molecular species that are detected in molecular clouds. We find that the mechanism is capable of explaining the observed molecular abundances and complexity in these sources. We find that the proposed mechanism is easily capable of explaining the large abundances of all three isomers of C2H4O2 that are observationally inferred for star-forming regions. However, the model currently does not provide an obvious explanation for the predominance of methyl formate, suggesting that some refinement to our (very simplistic) chemistry is necessary. The model also predicts the production of glycine at a (lower) abundance level, that is consistent with its marginal detection in astrophysical sources.

A DFT study on the interaction between glycine molecules/radicals and the (8, 0) SiCNT

The geometrical structures, energetics and electronic properties of glycine molecules as well as dehydrogenated radical interaction with silicon carbide nanotubes (SiCNTs) are investigated based on density functional theory (DFT) for the first time. Different from the weak adsorption on CNTs, it is shown that glycine molecules tend to be chemisorbed onto SiCNTs. There are three patterns of the individual glycine molecule adsorbed on the (8, 0) SiCNT, including monodentate, cycloaddition and dissociative ones, with the latter two patterns (Eads ranges from -22.08 to -34.99 kcal mol(-1)) more stable than the monodentate one (Eads ranges from -8.16 to -21.14 kcal mol(-1)). In addition, we also investigated the adsorption of multiple glycine molecules on various zigzag (n, 0) (n = 7, 8, 9 and 10) SiCNTs. It is shown that totally n (n = 7, 8, 9 and 10) molecules can be chemisorbed on one circle of the wall of the SiCNT at most. And the Eads per glycine decreases gradually with the increasing tube diameter due to the curvature effects. For the adsorption of dehydrogenated glycine radicals, it is found that both the N-centered and C-centered ones can form stable complexes by attacking the (8, 0) SiCNT. Totally one monodentate and two bidentate adsorption configurations of the N-centered radical and three monodentate configurations of the C-centered one can be found. Note that the important half-metals can be obtained for the bidentate configurations from the N-centered radical due to the hybridization state of the radical and the tube in one spin channel crossing the Fermi level, while the p-type semiconductor can be produced for the monodentate configurations from the C-centered radical because the impurity state derived from the radical itself is closer to the edge of the valence band above the Fermi level, which may be applied in building electronic devices and metal-free catalysis. Finally, we found that the encapsulation of the glycine molecule is exothermic and thus energetically favourable in the SiCNTs with the diameter larger than the (9, 0) SiCNT. The present study is expected to create promising applications in nano-device building and biotechnology.

Sustainable removal of Cu2+, Ni2+ and Zn2+ ions from severe contaminated water using kaolin/poly(glycine) composites, characterization and uptake studies

Kaolinite clay of Saint Catharine, Sinai, was treated by glycine molecules and then modified by various diamino-compounds like ethylenediamine, phenyl hydrazine and polyoxypropylenediamine. The native and modified clays were structurally and texturally characterized by XRD, FTIR, XRF, BET, pore size distribution and SEM in addition to exchange capacity parameters. Phenyl hydrazine and polyoxypropylenediamine organo-modifiers proved superior in function compared to ethylenediamine with regard to in situ glycine polymerization forming large fragments of ordered polypeptides which acted as super clay sheet binders. Adsorption of Cu(II), Ni(II) and Zn(II) ions by the modified kaolinite under variable concentrations of metal ions and interacting time were studied. Adsorption isotherm investigation indicated that Freundlich equation was a better fit than Langmuir model reflecting surfaces of various accommodated active sites with analogue sites distribution. The adsorption rate constants sequence for all modified kaolinite derivatives proved to be Zn2+##xgt;Ni2+##xgt;Cu2+. Near 100% removal for Cu2+, Ni2+ and Zn2+ ions from contaminated water were performed via phenyl hydrazine and polyoxypropylenediamine modified kaolin/poly(glycine) composites due to the expected feature of layers expansion and ultimate exposure of hidden adsorption sites buried deeply in kaolinite interlayers.

Towards a better understanding of the nucleation behavior of α and γ polymorphs of glycine from aqueous solution in the presence of selective additives by charge compensation mechanism

The type of polymorphic nucleation of glycine observed at any instant of time mainly depends on the charge environment of the experimental solution and this is discussed based on the perspective of charge compensation mechanism among the molecular species. The nucleation of α takes place due to self-charge compensation by glycine molecules whereas, γ nucleation occurs by overcoming of self-charge compensation by induced charge compensation in smaller proportions through the charged ions of the externally added induced charge compensators sodium nitrate (ICCNaNO3) and sodium hydroxide (ICCNaOH). The overcoming of self-charge compensation occurs at the critical concentration of the induced charge compensators. Nucleation behaviour of the glycine polymorphs obtained in the present work has been compared with that obtained in our previous work with sodium acetate as ICC. Influence of these ICC charged ions on the solubility, pH, supersaturation, induction time, nucleation and growth of the nucleated polymorphs were studied. Structural conformation and probability nucleation ratio of the nucleated polymorphs were confirmed by powder x-ray diffraction.

Interaction of Glycine with Common Atmospheric Nucleation Precursors

The interaction between the simplest amino acid glycine in three different protonation states and common atmospheric nucleation precursors (H2O, NH3, and H2SO4) has been investigated using computational methods. Each nucleation step has been thoroughly sampled, and statistical Gibbs free energies of formation have been calculated using M06-2X/6-311++G(3df,3pd). From the stepwise ΔG values, the stabilities of the molecular clusters have been evaluated. Glycine in all three protonation states is found to have a favorable interaction with sulfuric acid with a higher cluster stabilizing effect than ammonia. The deprotonated glycine molecule is found to yield the highest stabilizing effect on the sulfuric acid clusters through the interaction of both the amino and carboxylic moieties, while the protonated glycine molecule is found to have a high stabilizing effect on the addition of water and ammonia. Furthermore, we find that a single sulfuric acid molecule is capable of stabilizing the glycine zwitterion. Sulfuric acid is found to be able to catalyze the spontaneous formation of the zwitterion and subsequently stabilize the formed ion. The formation of the glycine zwitterion occurs with a low Gibbs free energy barrier of 2.10 kcal/mol, indicating that this formation could occur rapidly in the atmosphere.

Dynamics of Glycine Dications in the Gas Phase: Ultrafast Intramolecular Hydrogen Migration versus Coulomb Repulsion

We present a combined experimental and theoretical study of the complex dynamics of excited doubly ionized glycine molecules in the gas phase. Multicoincidence mass spectroscopic techniques together with ab initio molecular dynamics simulations and density functional theory calculations allow us to show that an ultrafast intramolecular hydrogen migration (∼30 fs) appears in competiton with the expected Coulomb repulsion.

Thickness-dependent effects in H2O desorption from glycine/amorphous solid water films

The desorption characteristics of H2O from glycine-on-amorphous solid water (ASW) ultrathin films have been systematically investigated as a function of underlying ASW thickness and the amount of top-deposited glycine using TPD. At the early stages of deposition, substantial amounts of glycine molecules penetrate into the water multilayers and, therefore, thermal destabilization of water layers is detected. Glycine diffusion is governed by the thickness-dependent structure of the ASW as revealed by work function measurements and XPS. For higher glycine coverages, a kinetic restriction of water desorption by the continuous amino acid overlayers is observed independent of the ASW substrate thickness.

Crystal Structure and Physicochemical Properties of Two Supramolecular Compounds: (C4H8NH2)4[Mo8O26] and (NH4)Na2[AsIIIMo6O21(O2CCH2NH3)3]·8H2O

Two inorganic–organic hybrid supramolecular compounds based on polyoxometalates formulated as (C4H8NH2)4[Mo8O26] (1) and (NH4)Na2[AsIIIMo6O21(O2CCH2NH3)3]·8H2O (2) have been synthesized by conventional solution method and characterized by infrared, UV–Vis and single-crystal X-ray diffraction analyses. Thermal analysis was performed to study their thermal stability. The atomic arrangement in compound (1) can be described as inorganic layers built by [Mo8O26]4−, pyrrolidinium cations are embedded into layers. The fascinating structural feature of compound (2) is that the glycine molecules are bounded to two edge-sharing Mo centers via their carboxylate functionality leading to functionalized heteropolymolybdate [AsIIIMo6O21(O2CCH2NH3)3]3−, extensive net hydrogen bonds between cations and anions contribute to the crystal packing. The electrochemical behavior of compound (2) has been studied.

Effect of Hydrogen Bond Formation on the NMR Properties of Glycine–HCN Complexes

The influence of the hydrogen bond formation on the nuclear magnetic resonance parameters has been investigated for the binary (1:1) and ternary (1:2) glycine-HCN complexes in the gas phase using high-level density functional theory with the B3LYP/6-31++G(2d,2p)//B3LYP/6-31++G(d,p) model of quantum chemistry. The calculated isotropic/anisotropic shielding parameters of the isolated glycine and HCN molecules are reported and compared with other theoretical results and experimental measurements. Six different conformations of hydrogen-bonded clusters have considered for both 1:1 and 1:2 glycine-HCN complexes. The isotropic and anisotropic chemical shifts for all the constituent atoms of the complexes have been calculated. The spin-spin coupling constants and the Fermi contact terms have also been analyzed in the context of hydrogen-bond formation.

ELECTRON IMPACT FRAGMENTATION OF THE GLYCINE AND METHIONINE MOLECULES

Fragmentation of the glycine (C2H5NO2) and methionine (C5H11NO2S) molecules by low-energy electron impact has been studied both experimentally and theoretically. The main emphasis has been given to the mechanisms of production of positive ionic fragments of both molecules with the same chemical composition. A special attention has been paid to the energy characteristics of the ionic fragment yield. The geometrical parameters of the initial molecule rearrangement have also been analyzed. Keywords: glycine; methionine; mass spectrum; appearance potential; binding energy.

Thermodynamic hydration shell behavior of glycine

Glycine aqueous solutions have been studied as a function of temperature and concentration by means of UV Brillouin and Raman spectroscopes. Brillouin spectra provided information on the average relaxation time τα related to the mechanisms of hydrogen bonds (HBs) formation and breaking. The concentration-temperature behavior of τ has been compared to the vibrational dephasing lifetime of atoms involved in HBs, as derived by a lineshape analysis of Raman spectra. We point out how it is possible to trace the thermodynamic behavior of a selected HB from Raman data. In particular, our results confirm the predominant role played in the hydration process by the water molecules surrounding the hydrophobic groups and, furthermore, evidence how at low temperature the HB strength between these molecules is greater than those found in bulk water and between glycine and water molecules.

Diffuse scattering and the mechanism for the phase transition in triglycine sulphate

Despite the order/disorder nature of its ferroelectric phase transition, and evidence for the evolution of local order as being important for understanding the transition, no comprehensive diffuse scattering study of the short-range order in triglycine sulphate, (TGS), (NH2CH2COOH)3H2SO4 has been undertaken. Diffuse scattering from single crystals is sensitive to two-body correlations, and can act as a probe of local structure, which in a second order phase transition acts as a precursor to the low temperature phase. The role of hydrogen bonding and dipolar interactions in the ferroelectric phase transition in TGS has been a long matter of conjecture. Using neutron and X-ray single crystal diffuse scattering this study shows that hydrogen bond mediated interactions between polarising glycine molecules cause local one-dimensional polarised domains to develop, oriented parallel to the b axis. These domains interact via dipolar interactions, and the three-dimensional ferroelectric order arises. This provides a real-space, interaction-based model for the phase transition in TGS, showing in detail how the local chemistry and physics give rise to the polarised state.

Thermodynamics of Micellization of Triton X-100 in Aqueous Glycine: Tensiometric and Ultrasonic Studies

Abstract Surface tension and compressibility behavior of p-(1,1,3,3-tetramethylbutyl) phenoxypoly(oxyethylene glycol) (Triton X-100, TX-100) in aqueous mixture of glycine (Gly) have been studied at 298.15, 303.15, 308.15, and 313.15 K below and above the micellar composition range. Critical micelle concentration, cmc, of the surfactant TX-100 was obtained by surface tension, γ, density, ρ, and ultrasonic velocity, u, measurements at different temperatures. From the surface tension data, the surface excess concentration, Γ max σ , minimum area per molecule, A min , Gibbs free energy, ΔG mic 0, enthalpy, ΔH mic 0, and entropy, ΔS mic 0 of micelle formation have been evaluated. Apparent molar adiabatic compressibility, κ ϕ , was calculated from density and ultrasonic velocity data. The values of κ ϕ and apparent molar adiabatic compressibility at infinite dilution, κ ϕ 0, in the pre-micellar region and apparent molar compressibility upon micellization, Δκ ϕ m , were obtained. The observed cmc of TX-100 in aqueous glycine is found to be smaller than its value in pure water. A comparison of Γ max σ in aqueous glycine with that in pure water suggests higher adsorption of TX-100 molecules at the air–liquid interface in the former solvent than in the latter one. This was attributed to the highly hydrophilic nature of glycine molecules, causing dehydration of the surfactant molecules, thereby, facilitating the adsorption of TX-100 molecules at the air–liquid interface in the presence of glycine than in its absence. The calculated values of the Gordon parameter, G parameter, suggest that aqueous glycine acts as a good solvent for the micellization of TX-100 amphiphiles. Negative values of ΔG mic 0 and ΔH mic 0 indicate that the process of micellization of the surfactant is spontaneous and exothermic. Moreover, higher values of − TΔS mic 0 than those of ΔH mic 0 truly endorse the view that micellization of TX-100 in aqueous glycine is primarily governed by the entropy gain due to the transfer of hydrophobic groups of the surfactant from the solvent environment to the interior of the micelle. The trends in the behavior of the compressibility parameters also endorse the micellization of TX-100 in aqueous glycine.

A neutron diffraction study of the phase transition of fully deuterated triglycine sulphate (ND2CD2COOD)3.D2SO4

AbstractUsing neutron single crystal and powder diffraction, the first thorough investigation of the structure of fully deuterated triglycine sulphate, (ND2CD2COOD)3.D2SO4 is presented, including its evolution with T, through its structural phase transition. This includes new precise structural parameters determined at several key temperatures above and below TC using single crystal diffraction, and for the first time a parametric study has been undertaken over a wide temperature range — from 4 to 500 K in 2 K steps. It was found that fully deuterated TGS shows a structure consistent with hydrogenous TGS and partially deuterated TGS. The evolution of several key hydrogen bond lengths suggests that weakening of the H‐bond network with T is crucial in decoupling the polarising glycine molecules from the other glycines and allowing the long‐range ferroelectric order to break down. A new parameterisation of the phase transition is demonstrated. Contrary to results of physical properties measurements, there is no evidence of a second low temperature phase transition in TGS – no low temperature anomalies were observed in the crystal structure.

Selective Glycine Polymorph Crystallization by Using Silver Nanoparticles

In the present study, we demonstrate that silver colloid can serve as additive and induced the γ-form polymorph of glycine crystals in the netural solution. The silver colloid could quickly affect the packing arrangements of glycine molecules in aqueous solution leading to the competitive nucleation of the two polymorphs.