Glycine Molecules Research Articles

Improvement in Cobalt Phosphate Electrocatalyst Activity toward Oxygen Evolution from Water by Glycine Molecule Addition and Functional Details.

Electrochemical water splitting using renewable energy shows promise for the development of sustainable hydrogen production methods. The process requires a highly active electrocatalyst for oxygen evolution to improve the overall water splitting efficiency. The present study showed that oxygen evolution improved dramatically upon the addition of glycine to cobalt phosphate, when the glycine was added to the electrolyte solution during electrodeposition. The functionality of the organic molecules was investigated using in situ UV-vis absorption, in situ X-ray absorption fine structure, and in situ infrared (IR) absorption spectroscopy in the attenuated total reflection mode. The results demonstrated that the glycine molecules assembled cobalt oxide clusters composed of CoO6 (CoOOH) octahedrons a few nanometers in diameter upon the electrodeposition of cobalt catalysts. This suggests that the cobalt-glycine catalyst can decompose water to oxygen gas efficiently, because the number of cobalt oxide clusters increased as active reaction sites upon the addition of glycine molecules.

Rotational and vibrational effects on the energy loss of hydrogen colliding on glycine at low irradiation energies

The implications of the energy deposition of neutral hydrogen irradiation on biomolecules is important to understand cell damage by heavy ions in radiotherapy and dosimetry. In this work, we study the energy loss of hydrogen atoms incidents on the glycine molecules in gas phase at low collision energy, based on the Density-Functional Tight-Binding (DFTB) and the Electron-Nuclear Dynamics (END) theories. DFTB is a quantum-classical molecular dynamics approach on a ground state surface, valid at low collision energy while END is an ab initio quantum chemistry approach that includes electronic excitations at the random phase approximation level and accounts for electron and nuclear couplings. These approaches have an overlap collision energy region from 10 to 100 eV, where our results complement fairly well to each other. We find that the electronic energy loss (stopping cross-section) shows a linear velocity dependence with a threshold at a hydrogen velocity of 0.01414 a. u. Corresponding to around 5 eV and 1 eV for the END and DFTB results, respectively. The ro-vibrational and nuclear energy loss become significant producing the main contributions to the energy loss. Finally, we compare to SRIM results showing that it neglects chemical bonding, as well as the ro-vibrational contributions at low collision energy such that it underestimates the energy loss and does not account for threshold effects. Our results shed light on the importance of ro-vibrational chemical processes at low collision energies when describing the energy loss of heavy ions when interacting with molecules.

Distributed glycine in comet 67P/Churyumov-Gerasimenko

Most of the gaseous molecules that are detected in cometary atmospheres are produced through sublimation of nucleus ices. Distributed sources may also occur, that is, production within the coma, from the solid component of dust particles that are ejected from the nucleus. Glycine, the simplest amino acid, was observed episodically in the atmosphere of comet 67P/Churyumov-Gerasimenko (67P) by the ROSINA mass spectrometer on board the Rosetta probe. A series of measurements on 28 March 2015 revealed a distributed density profile at between 14 and 26 km away from the nucleus. We here present and discuss three study cases: (i) glycine emitted directly and only from the nucleus, (ii) glycine emitted from the sublimation of solid-state glycine on the dust particles that are ejected from the nucleus, and (iii) glycine molecules embedded in water ice that are emitted from the sublimation of this ice from the dust particles that are ejected from the nucleus. A numerical model was developed to calculate the abundance of glycine in the atmosphere of comet 67P as a function of the distance from the nucleus, and to derive its initial abundance in the lifted dust particles. We show that a good fit to the observations corresponds to a distributed source of glycine that is embedded in sublimating water ice from dust particles that are ejected from the nucleus (iii). The few hundred ppb of glycine embedded in water ice on dust particles (nominally 170 ppb by mass) agree well with the observed distribution.

Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations.

Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.

Biomolecular self-assembly under extreme Martian mimetic conditions

The recent discovery of subsurface water on Mars has challenged our understanding of the natural limits of life. The presence of magnesium perchlorate (Mg(ClO4)2) on the Martian surface raises the possibility that it may also be present in this subsurface lake. Given that the subsurface lakes on Earth, such as Lake Vostok and Lake Whillans, are capable of harbouring surprising amounts of life, these new findings raise interesting possibilities for how biomolecules might self-assemble in this environment on Mars. Here we investigate the self-association and hydration of the amino acid glycine in aqueous Mg(ClO4)2 at 25°C and −20°C using neutron diffraction with hydrogen isotope substitution and subsequent analysis with empirical potential structure refinement to yield a simulated box of atoms consistent with the scattering data. We find that although the highly chaotropic properties of Mg(ClO4)2 disrupt the hydration and hydrogen bonding ability of the amino acid, as well as the bulk water structure, glycine molecules are nonetheless still able to self-associate. This occurs more readily at lower temperature, where clusters of up to three molecules are observed, allowing us to speculate that the formation of biological molecules is possible in the Martian environment.

Glycine‐functionalized reduced graphene oxide for methylene blue removal

Glycine‐functionalized reduced graphene oxide (GRGO) was prepared through the reaction of glycine and chlorine‐functionalized reduced graphene oxide. The product was characterized by SEM, HRTEM, IR, Raman, and XPS. The nitrogen content (8.28%) was high in product, peak at 285.8 eV was assigned to the C–N bond, which implied that the chlorine residues in raw material were substituted by amine group of glycine. The intensity ratio of D and G peak was about 1.5, which also implied that more saturated carbon atoms were present in the product. Results of SEM, IR, and XPS confirmed that glycine molecules were attached to graphene sheets. Compared with reduced graphene oxide (61.5 mg/g) and active carbon (45.2 mg/g), GRGO had a good adsorption capacity (98.9 mg/g) for methylene blue. The adsorption process was fitted to three kinetic models and three adsorption isotherm models. The adsorption process complied with pseudo‐second order kinetic model and Langmuir model.

First-Principles Nonequilibrium Green's Function Approach to Ultrafast Charge Migration in Glycine.

We investigate the photoinduced ultrafast charge migration phenomenon in the glycine molecule using a recently proposed nonequilibrium Green's functions (NEGF) approach. We first consider the dynamics resulting from the sudden removal of an electron in the valence shells, finding a satisfactory agreement with available data. Then we explicitly simulate the laser-induced photoionization process and study the evolution of the system after the pulse. We disentangle polarization and correlation effects in the electron dynamics and assign the main frequencies to specific elements of the reduced one-particle density matrix. We show that electronic correlations renormalize the bare frequencies, redistribute the spectral weights, and give rise to new spectral features.

Comparative Study of the Photostability of Two Glycine Molecules in Different Medium

ABSTRACTThe photostability of two glycine molecules has been investigated using quantum mechanical methods i.e. at CASSCF/NEVPT2 level theory. It is found that the molecule in water shows vast photostability as a comparison to vacuum. The energies are calculated around HOMO and LUMO orbital. The NEVPT2 computed energies are reasonably matched with experimental results. The study shows that the molecule returns from higher electronically excited states to ground state through CI and AC crossings and these crossings provide a minimum energy path along derivative coupling and gradient differences vector.

Investigation of the effect of the N-oxidation process on the interaction of selected pyridine compounds with biomacromolecules: structural, spectral, theoretical and docking studies.

Two new N-oxide compounds, namely glycinium 2-carboxy-1-(λ1-oxidaneyl)-1λ4-pyridine-6-carboxylate-glycine-water (1/1/1), C2H6NO2+·C7H4NO5-·C2H5NO2·H2O or [(2,6-HpydcO)(HGLY)(GLY)(H2O)], 1, and methyl 6-carboxy-1-(λ1-oxidaneyl)-1λ4-pyridine-2-carboxylate, C8H7NO5 or 2,6-HMepydcO, 2, were prepared and identified by elemental analysis, FT-IR, Raman spectroscopy and single-crystal X-ray diffraction. The X-ray analysis of 1 revealed an ionic compound containing a 2,6-HpydcO- anion, a glycinium cation, a neutral glycine molecule and a water molecule. Compound 2 is a neutral compound with two independent units in its crystal structure. In addition to the hydrogen bonds, the crystal network is stabilized by π-π stacking interactions of the types pyridine-carboxylate and carboxylate-carboxylate. The thermodynamic stability and charge-distribution patterns for isolated molecules of 2,6-H2pydcO and 2,6-HMepydcO, and their two similar derivatives, pyridine-2,6-dicarboxylic acid (2,6-H2pydc) and dimethyl 1-(λ1-oxidaneyl)-1λ4-pyridine-2,6-dicarboxylate (2,6-Me2pydcO), were studied by density functional theory (DFT) and natural bond orbital (NBO) analysis, respectively. The ability of these compounds and their analogues to interact with nine selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS and Top II) was investigated using docking calculations.

Hydrophilicity of the hydrophobic group: Effect of cosolvents and ions

Classical molecular dynamics simulations were performed to study the effect of cosolvents and ions on the solvation structure of zwitterionic glycine in liquid water. Simulations were carried out for 2 M and 1 M concentration of TMAO, Urea, KCl and LiCl solutions to observe the changes in liquid structure of water near the glycine molecule. Radial distribution functions and spatial distribution functions showed the presence of protective hydration layer near the Cα in presence of TMAO which gets reduced in case of urea, KCl and minimum in case of LiCl. LiCl is found to disrupt severely the solvation structure near the glycine molecule. For LiCl system, a small hydration layer is found near Cα unit at higher distances which is mainly due to the first hydration shell of lithium ion bonded to the carboxylate group. Presence of these hydration layers gives extra stabilization energy to the glycine water system. Stabilizing and destabilizing effect of water near the glycine molecule is calculated in terms of Potential Mean Force. The anomalous behaviour of lithium salts with respect to Group I cation salts in protein stabilization can be explained on the basis of this behaviour. We found maximum hydrogen bond lifetime for water molecules in presence of TMAO followed by LiCl, KCl and least in case of urea. The higher lifetimes in presence of ions are found mainly due to their electrostatic force. The stabilization of the hydrophobic part of the glycine molecule can be correlated with the stabilization of proteins in presence of these cosolvents.

Expanding production regions of α-form and β-form glycine using an antisolvent crystallization method assisted by N2 fine bubbles

To develop a crystallization technique that can enhance the production of metastable α-form and unstable β-form glycine, we studied the antisolvent crystallization of glycine using the gas–liquid interfaces around N2 fine bubbles as novel crystallization fields. In the regions near the gas–liquid interfaces, local supersaturation is generated because of the accumulation of glycine and alcohol as an antisolvent as a result of the negative electric charge on the fine bubble surface. Hence, the produced glycine polymorphs change from the stable γ-form to a α-form or β-form glycine. Additionally, local supersaturation at the gas–liquid interfaces can be expected to change via modification of the accumulation of the glycine and alcohol molecules and the interaction of glycine-water-alcohol with the different alcohol additives. At a solution temperature of 303 K, methanol (MeOH), ethanol (EtOH), or isopropanol (IPA) as an antisolvent were rapidly mixed into the saturated glycine solution. While mixing MeOH, EtOH, or IPA with the saturated glycine solution, N2 fine bubbles with an average size of 10 µm were continuously supplied to the mixed solution using a self-supporting bubble generator and a glycine polymorph was crystallized within 5 min. For comparison, an antisolvent crystallization free of N2 fine bubbles was conducted using a propeller type mixer. During antisolvent crystallization with/without fine bubble injection, the additional alcohol volume was varied to control the generation rate of the supersaturation in the bulk solution (rC/CS). Consequently, the production regions of the α-form and β-form glycine were broadened to lower rC/CS via N2 fine bubble injection. The expansion behavior for α-form or β-form glycine significantly increased because of the enhancement of local supersaturation at the regions near the gas–liquid interfaces of the N2 fine bubbles owing to the decreasing carbon number in the alcohol.

Квантово-химическое моделирование водородных связей в α-глицине

Quantum chemistry was used to simulate a fragment of α-glycine crystal consisting of 5 and 6 glycine molecules. The α-glycine crystal fragment model was constructed using X-ray diffraction data contained in the Cambridge Crystallographic Database (CCDC). Theoretical IR spectra were obtained. It was shown that in a fragment of a crystal, glycine molecules in zwitterionic form form N-H...O hydrogen bonds of different strength, which correspond to different frequencies of stretching vibrations νst (N-H) of the NH3+ group. Full optimization of glycine crystal fragments consisting of a small number of molecules, regardless of the method of calculation, leads to the agglomeration of the structure. The system forms the maximum possible number of the most durable hydrogen bonds, thereby lowering the overall energy of the system, which leads to disruption of the crystal structure of the fragment, distortion of the parameters of hydrogen bonds in the crystal, and, consequently, to an unsystematic shift in the frequencies of N-H vibrations. To avoid this process, further modeling was performed by partially optimizing the geometry of the crystal fragment, with the positions of heavy nitrogen atoms, carbon and oxygen atoms being fixed, and only the positions of hydrogen atoms involved in the formation of hydrogen bonds were varied. Using the DFT/B3LYP/6-311G** method, the energies of donor–acceptor interaction in a fragment of a crystal, as well as its oscillation frequencies, are calculated. The calculated frequencies are consistent with the three experimental frequencies in the indicated X-ray region. A comparison was made between the calculated and experimental frequencies of the stretching vibrations of the N-H group of the NH3+ group. According to the geometric characteristics of the HB and the energy of donor-acceptor interaction between the lone electron pairs of oxygen atoms and the *(N-H) loosening orbitals, it was found that the hydrogen bonds of N-H...O between molecules in one layer are stronger than between molecules in different layers of a crystal.

Crystal structure and Hirshfeld surface analysis of poly[[di-μ3-glycine-lithium] perchlorate

In the title salt, {[Li(C2H5NO2)2]ClO4} n , the Li+ cation is coordinated by four carboxyl-ate oxygen atoms of the glycine mol-ecules with a distorted tetra-hedral geometry. The glycine exists in a zwitterionic form with protonated amino and deprotonated carboxyl-ate groups. In the crystalline state, the title salt is primarily stabilized by inter-molecular N-H⋯O and Cα-H⋯O inter-actions which inter-connect various units. Hirshfeld surface analysis indicates that the inter-molecular H⋯O/O⋯H inter-actions are the most important contributors to the crystal packing.

X-ray-initiated photodissociation of the glycine molecule

We investigated the charge distribution and dissociation dynamics of glycine (${\mathrm{NH}}_{2}{\mathrm{CH}}_{2}\mathrm{COOH}$) molecules irradiated with 310-eV x rays from the Advanced Light Source synchrotron. With simultaneous measurements of the fragment ion yield, dissociation angle, and kinetic energy, we were able to reconstruct a three-dimensional image of the x-ray-initiated molecular dissociation. Using coincidence and correlated analysis and applying a systematic comparison of properties of ion species, we partially disentangled the fragmentation pathways and identified the most probable fragmentation channels that lead to the observed fragment ions. In addition, we showed anisotropic angular distributions of dissociation subsequent to core-level photoionization and Auger decay and found an association between the initial bond-breaking sites and the kinetic energies of the final fragment ions.

The hydration of selected biologically relevant molecules – the temperature effect on apparent molar volume and compression

The densities and sound velocities at T = (288.15, 293.15, 298.15, 303.15 and 308.15) K were measured for aqueous solutions of glycine, trimethylamine-N-oxide, taurine and N-methylacetamide. From these data, the apparent molar volumes, VΦ, the apparent molar isentropic compressions, KS,Φ, and the Passynski hydration numbers of solutes were determined. The concentration dependencies of the calculated quantities, their limiting values and temperature characteristics are discussed in terms of solute-solvent and solute-solute interactions. The obtained data clearly show strong hydration of the molecules of glycine, trimethylamine-N-oxide and taurine. Opposite effect, i.e. weak interactions with water molecules, is found for N-methylacetamide.

Quasi-Equilibria and Polarization Transfer Between Adjacent and Remote Spins: 1H-13C CP MAS Kinetics in Glycine.

The 1H-13C CP MAS kinetic curves were measured in glycine powder sample at the MAS rates of 7, 10, and 12 kHz. Each experimental curve contained up to 1000 equidistant points over the whole contact time range of 10 μs - 10 ms. The CP kinetic data for CH2 group, i.e., for the system containing adjacent 1H-13C spin pairs with a definite dominant dipolar coupling can be described in the frame of the isotropic spin-diffusion approach. The local order parameter ⟨ S⟩ ≈ 1.0, determined as the ratio of the measured dipolar 1H-13C coupling constant and the calculated static dipolar coupling constant, is very close to the values deduced in series of other amino acids. The strong narrow peaks observed in the spin coupling spectrum at multiples of the MAS frequency can be considered as the confirmation that the periodic quasi-equilibrium state can appear also in the powder samples. The anisotropic spin-diffusion approach improved by the introducing of the thermal equilibration in the proton bath is the most proper model to describe the CP kinetics in the system containing remote spins. Very realistic values of the spin-cluster size ( N) have been obtained without any constraint on the flow of the nonlinear curve fitting. The finite values of N ≤ 4 means that CP transfer is located within one glycine molecule.

When the Surface Matters: Prebiotic Peptide‐Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT‐D2 Simulations

The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.

Thermal behavior, structure, dynamic properties of aqueous glycine solutions confined in mesoporous silica MCM-41 investigated by x-ray diffraction and quasi-elastic neutron scattering.

Differential scanning calorimetry, X-ray diffraction, and quasi-elastic neutron scattering (QENS) measurements of aqueous glycine solutions confined in mesoporous silica (MCM-41) were performed at different glycine concentrations, pH, and loading ratio (=mass of glycine solution/mass of dry MCM-41) in the temperature range from 305 to 180 K to discuss the confinement effect on the thermal behavior, the structure, and the dynamic properties of the solutions. The freezing points of the confined glycine solutions decreased, compared with those of the bulk solutions. The corresponding exothermic peak due to ice formation became broader with an increase in the glycine concentration. By subtracting X-ray diffraction patterns of dry MCM-41 from those of glycine solution-loaded MCM-41, information about the structure of the confined glycine solutions was obtained. The radial distribution functions of the confined glycine solutions showed that the peaks assigned to the interaction between glycine molecules and the surface silanol (Si-OH) groups of MCM-41 at pH = 5 were observed, in contrast to the case at pH = 2. The QENS data on H/D substituted aqueous glycine solutions gave the translational diffusion coefficients and the residence time of glycine and water molecules confined in MCM-41 individually. The activation energy of the diffusion coefficient of a glycine molecule at pH = 5 was larger than that at pH = 2. These results imply that glycine molecules locate near the pore surface of MCM-41 due to the formation of hydrogen bonding between glycine molecules and the silanol group of the MCM-41 wall at pH = 5.

Modelling the details: integrating structure with function.

Modelling the details: integrating structure with function.

Reactions of Glycolonitrile with Ammonia and Water: A Free Energy Map.

Glycolonitrile, the product of combining CH2O and HCN, is an intermediate in the Strecker reaction leading to the synthesis of the amino acid glycine. However, besides glycine, a plethora of other compounds are also generated when CH2O and HCN react in the presence of ammonia and water. As a starting point to analyze the possible components of this complex mixture, we have employed density functional theory to construct a free energy map of all two-carbon (C2) species that may be present when glycolonitrile participates in addition or elimination reactions with ammonia and water. By identifying thermodynamic sinks and kinetic barriers, we find that the myriad C2 species can be grouped into three broad regions across the free energy landscape. This allows us to trace possible routes to glycine and other molecules of interest in the reaction mixture. The present map also extends our previous work on one-carbon (C1) species. We had previously found one issue with our computational protocol in the C1 map; however, our present C2 map provides a larger data set that supports using an empirical correction to our original protocol for imidic acid to amide transformations, without increasing the computational cost, while retaining the original protocol for other classes of reactions.