Glycine Molecules Research Articles

Компьютерная резонансная динамика молекулы глицина в электрическом поле инфракрасного диапазона

The supercomputer software-computer complex of molecular dynamics is supplemented with an external alternating electric field. Along with nonresonant influences, the mode of resonant excitation of normal vibration modes in the molecules of the amino acid glycine was studied when an electric field was set in the form of a symmetrical meander in the IR frequency range. The technique expands the possibilities of studying the structure, dynamics, and functions of biomolecules, as well as methods for developing hybrid micro and nanoelectronic devices.

Role of the redox state of cerium oxide on glycine adsorption: an experimental and theoretical study.

The role of the oxidation state of cerium cations in a thin oxide film in the adsorption, geometry, and thermal stability of glycine molecules was studied. The experimental study was performed for a submonolayer molecular coverage deposited in vacuum on CeO2(111)/Cu(111) and Ce2O3(111)/Cu(111) films by photoelectron and soft X-ray absorption spectroscopies and supported by ab initio calculations for prediction of the adsorbate geometries, C 1s and N 1s core binding energies of glycine, and some possible products of the thermal decomposition. The molecules adsorbed on the oxide surfaces at 25 °C in the anionic form via the carboxylate oxygen atoms bound to cerium cations. A third bonding point through the amino group was observed for the glycine adlayers on CeO2. In the course of stepwise annealing of the molecular adlayers on CeO2 and Ce2O3, the surface chemistry and decomposition products were analyzed and found to relate to different reactivities of glycinate on Ce4+ and Ce3+ cations, observed as two dissociation channels via C-N and C-C bond scission, respectively. The oxidation state of cerium cations in the oxide was shown to be an important factor, which defines the properties, electronic structure, and thermal stability of the molecular adlayer.

Interfacial Chemistry Modulation via Amphoteric Glycine for a Highly Reversible Zinc Anode.

Zn metal is thermodynamically unstable in aqueous electrolytes, which induces dendrite growth and ongoing parasitic reactions at the interface during the plating process and even during shelf time, resulting in rapid battery failure and hindering the practical application of aqueous Zn ion batteries. In this work, glycine, a common multifunctional additive, is utilized to modulate the solvation shell structure and enhance the interfacial stability to guard the reversibility and stability of the Zn anode. Apart from partially replacing the original SO42- in the contact ion pair of Zn2+[H2O]5·OSO32- complexes to suppress the formation of Zn4(OH)6SO4·xH2O byproducts at the interface, glycine molecules can also form a water-poor electrical double layer on the zinc metal surface during resting and be further reduced to build in situ a ZnS-rich solid electrolyte interphase (SEI) layer during cycling, which further suppresses side reactions and the random growth of Zn dendrites in the whole process. As expected, the cycle life of the symmetrical cells reaches over 3200 h in glycine-containing electrolytes. In addition, the Zn//NVO full cell shows exceptional cycling stability for 3000 cycles at 5 A g-1. Given the low-cost superiority of glycine, the proposed strategy for interfacial chemistry modulation shows considerable potential in promoting the commercialization progress of aqueous batteries.

Interacting electrons and bosons in the doubly screened GW̃ approximation: A time-linear scaling method for first-principles simulations

We augment the time-linear formulation of the Kadanoff-Baym equations for systems of interacting electrons and quantized phonons or photons with the $G\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{W}$ approximation, the Coulomb interaction $\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{W}$ being dynamically screened by both electron-hole pairs and bosonic particles. We also show how to combine different approximations to include simultaneously multiple correlation effects in the dynamics. The final outcome is a versatile framework comprising ${2}^{12}$ distinct diagrammatic methods, each scaling linearly in time and preserving all fundamental conservation laws. The dramatic improvement over current state-of-the-art approximations brought about by $G\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{W}$ is demonstrated in a study of the correlation-induced charge migration of the glycine molecule in an optical cavity.

Separation of heavy metals by amino acid functionalized polymer: Experimental and theoretical insights

A chloromethylated polystyrene resin was chemically functionalized with glycine molecules to introduce metal ions chelating sites. The functionalized resin (PsGly) was loaded in a glass column and successfully used for the extraction of heavy metal ions. Several experimental parameters like solution pH, sample flow rate, adsorbent dose and breakthrough volume was studied and optimized. The adsorption capacity observed for Ni(II), Cu(II) and Zn(II) were 0.72, 0.68 and 0.60 mmol g−1, respectively. The chelating mechanism for metal ion adsorption was studied by density functional theory. The metal-ligand interaction energy, entropy, and Gibbs energy were estimated by employing the B3LYP basis set of density functional theory and suggest that the studied metal ions form strong complexes with the adsorbent. The column procedure was employed for the extraction of heavy metal ions from wastewater with detection limit of 0.2 μg L−1.

Theoretical Analysis on the Stability of 1-Pyrenebutanoic Acid Succinimidyl Ester Adsorbed on Graphene.

The adsorbed structure of 1-pyrenebutanoic acid succinimidyl ester (PASE) on graphene was investigated based on density functional theory. We found two locally stable structures: a straight structure with the chainlike part of butanoic acid succinimidyl ester (BSE) lying down and a bent structure with the BSE part directed away from graphene, keeping the pyrene (Py) part adsorbed on graphene. Then, to elucidate the adsorption mechanism, we separately estimated the contributions of the Py and BSE parts to the entire PASE adsorption, and the adsorption effect of the BSE part was found to be secondary in comparison to the contribution of the Py. Next, the mobility of the BSE part at room temperature was confirmed by the activation energy barrier between straight and bent structures. To take account of the external environment, we considered the presence of amino acids and the hydration effect by a three-dimensional reference interaction site model. The contributions of glycine molecules and the solvent environment to stabilizing the bent PASE structure relative to the straight PASE structure were found. Therefore, the effect of the external environment around PASE is of importance when the standing-up process of the BSE part from graphene is considered.

Electrode reaction-driven orientation regrowth of Fe2O3 crystals from novel dendritic architecture in anode of lithium-ion batteries

Morphology design is one effective strategy for improving the rate capability and cycling stability of Fe2O3 anode material for lithium-ion batteries. Herein, a kind of dendritic Fe2O3 architecture was prepared through a hydrothermal route in which glycine molecules guide crystal growth and turn into carbon in the final composite. The special coralloid Fe2O3/NC composite integrates the structure advantages of porous and low-dimensional regular electrode materials. The mutually supportive architecture provides more space to exchange ions with electrolyte and accommodate mechanical stress to suppress volume change, and improves better electron conductivity compared to isolated particles. The Fe2O3/NC delivers 837.6 mAh g−1 at 10 A g−1 and maintains 788 mAh g−1 after a long-term life of 1000 cycles. One more discovery is that the dendritic Fe2O3 architecture grows into needle-like crystals driven by electrode reaction revolved to ion migration and crystal regeneration.

Ferroelectricity in glycine: A mini-review

Glycine is the simplest natural amino acid, a basic building block for various biomaterials. Supramolecular packing of glycine molecules into three main crystalline polymorphs allows controlling their functional properties, such as piezoelectricity and ferroelectricity. Though piezoelectricity in glycine is well studied and reviewed, its ferroelectric properties were not summarized and analyzed until now. In this mini-review, we briefly discuss glycine polymorphs, their functional properties, and phase transitions, review recent findings on domain structure and polarization switching in β- and γ-glycine, and consider their possible applications in biocompatible photonic and piezoelectric devices.

Electronic quantum coherence in glycine molecules probed with ultrashort x-ray pulses in real time

Here, we use x-rays to create and probe quantum coherence in the photoionized amino acid glycine. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay and by photoelectron emission from sequential double photoionization. Sinusoidal temporal modulation of the detected signal at early times (0 to 25 fs) is observed in both measurements. Advanced ab initio many-electron simulations allow us to explain the first 25 fs of the detected coherent quantum evolution in terms of the electronic coherence. In the kinematically complete x-ray absorption measurement, we monitor its dynamics for a period of 175 fs and observe an evolving modulation that may implicate the coupling of electronic to vibronic coherence at longer time scales. Our experiment provides a direct support for the existence of long-lived electronic coherence in photoionized biomolecules.

Mixed matrix membrane comprising glycine grafted CuBTC for enhanced CO2 separation performances with excellent stability under humid atmosphere

Benefitting from its remarkable adsorption selectivity, CuBTC has been a prospective filler for mixed matrix membranes (MMMs). However, CuBTC is unstable in humid atmosphere, which hinders its further applications. In this work, CuBTC and glycine grafted CuBTC (named Gly@CuBTC) particles were synthesized and embedded into Pebax MH 1657 to form the corresponding MMMs. CuBTC was grafted with glycine molecules to simultaneously enhance its moisture stability and CO2 adsorption capacity. It could be found that Gly@CuBTC exhibited higher CO2 adsorption capacity than pristine CuBTC. Besides, based on characterization by using SEM, XRD, FT-IR and nanomechanical tests, the as-prepared Pebax/Gly@CuBTC MMMs possessed improved interfacial compatibilities and mechanical strengths. Moreover, the CO2/CH4 separation performance of the MMMs were studied at different filler loadings and feeding pressures. With the addition of 5 wt% Gly@CuBTC, the resultant MMM exhibited the best performance with CO2 permeability of 175 Barrer and CO2/CH4 selectivity of 29. Better yet, Pebax/Gly@CuBTC MMMs showed excellent stability against moisture. This work demonstrated that Gly@CuBTC could be a promising filling material to develop industrial MMMs for separation and purification of natural gas.

Single-crystal structure analysis of non-deuterated triglycine sulfate by neutron diffraction at 20 and 298 K: a new disorder model for the 298 K structure.

Precise single-crystal structure analyses of the title compound, bis-(glycinium) sulfate-glycine (1/1), 2C2H6NO2 +·SO4 2-·C2H5NO2 (or C6H17N3O10S), non-deuterated triglycine sulfate (HTGS) at 20 K and 298 K were undertaken using time-of-flight neutron diffraction data. At 20 K for the O-H⋯O hydrogen bond between the glycinium cation and the zwitterionic, unprotonated glycine mol-ecule that is associated with the ferroelectric behaviour of HTGS, O-H = 1.070 (3), H⋯O = 1.408 (3) [δ = 0.338 (4)], O⋯O = 2.4777 (15) Å and O-H⋯O = 179.0 (4)°, which is in good agreement with previous studies. Two reasonable structures for the same three atoms were refined for the 298 K dataset. One is a single-minimum potential-energy model, with O-H = 1.090 (12), H⋯O = 1.361 (12) [δ = 0.271 (17)], O⋯O = 2.450 (7) Å and O-H⋯O = 179.2 (10)°, having the H atom with a large ellipticity along the bond path between the O atoms. The other is a double-minimum potential-energy model having two H atom sites with occupancies of 0.876 (8) and 0.124 (8): for the major occupancy component, O-H = 1.065 (12), H⋯O = 1.387 (12), O⋯O = 2.451 (7) Å and O-H⋯O = 178.2 (11)° and for the minor component, O-H = 1.06 (4), H⋯O = 1.41 (4), O⋯O = 2.451 (7) Å and O-H⋯O = 166 (2)°. These models did not show any significant differences in R factors. In addition, the unit-cell parameters and other structural parameters of HTGS did not show any major differences compared to those of partially deuterated TGS and fully deuterated TGS for both 20 K and 298 K.

Simulating weak-field attosecond processes with a Lanczos reduced basis approach to time-dependent equation-of-motion coupled-cluster theory

A time-dependent equation of motion coupled cluster singles and doubles (TD-EOM-CCSD) method is implemented, which uses a reduced basis calculated with the asymmetric band Lanczos algorithm. The approach is used to study weak-field processes in small molecules induced by ultrashort valence pump and core probe pulses. We assess the reliability of the procedure by comparing TD-EOM-CCSD absorption spectra to spectra obtained from the time-dependent coupled-cluster singles and doubles (TDCCSD) method and observe that spectral features can be reproduced for several molecules, at much lower computational times. We discuss how multiphoton absorption and symmetry can be handled in the method and general features of the core-valence separation (CVS) projection technique. We also model the transient absorption of an attosecond X-ray probe pulse by the glycine molecule.

Soft X-ray Spectroscopy Simulations with Multiconfigurational Wave Function Theory: Spectrum Completeness, Sub-eV Accuracy, and Quantitative Reproduction of Line Shapes.

Multireference methods are known for their ability to accurately treat states of very different nature in many molecular systems, facilitating high-quality simulations of a large variety of spectroscopic techniques. Here, we couple the multiconfigurational restricted active space self-consistent field RASSCF/RASPT2 method (of the CASSCF/CASPT2 methods family) to the displaced harmonic oscillator (DHO) model, to simulate soft X-ray spectroscopy. We applied such an RASSCF/RASPT2+DHO approach at the K-edges of various second-row elements for a set of small organic molecules that have been recently investigated at other levels of theory. X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) are simulated with a sub-eV accuracy and a correct description of the spectral line shapes. The method is extremely sensitive to the observed spectral shifts on a series of differently fluorinated ethylene systems, provides spectral fingerprints to distinguish between stable conformers of the glycine molecule, and accurately captures the vibrationally resolved carbon K-edge spectrum of formaldehyde. Differences with other theoretical methods are demonstrated, which show the advantages of employing a multireference/multiconfigurational approach. A protocol to systematically increase the number of core-excited states considered while maintaining a contained computational cost is presented. Insight is eventually provided for the effects caused by removing core–electrons from a given atom in terms of bond rearrangement and influence on the resulting spectral shapes within a unitary orbital-based framework for both XPS and XANES spectra.

Interaction of evaporated glycine and dipeptide derivatives of glycine with He2+ ions

In this paper we have studied a mechanism for radiation damage of gas phase molecules of glycine [Gly] and dipeptide derivatives of glycine, such as diglycine [Gly-Gly], cyclo(glycylglycyl) [cyclo(Gly-Gly)] and glycyl-leucine [Gly-Leu] by the impact of He2+ ions with energy Ep = 4 keV/u. Relative cross sections of different elementary processes occurring in single collisions between dipeptide derivatives of glycine and ions have been measured for the first time. The fragmentation channels of both singly and multiply charged molecular ions have been studied experimentally. It has been shown that in the process of Gly-Gly sublimation, cyclization in the crystalline sample takes place, which results in formation of cyclo(Gly-Gly). Using the DFT method, the geometry of molecules and singly charged ions of glycine dipeptide derivatives has been calculated, as well as energies of different experimentally observed fragmentation channels of these ions.

Dehydration rate of the glycine‐MgSO4·5H2O complex and the stability of glycine expelled from the complex by in situ Raman spectroscopy under Mars‐relevant conditions

AbstractIn this work, we studied the dehydration process of the glycine‐MgSO4·5H2O complex under Mars‐relevant conditions (99% CO2 and 0.6% H2O under ultra violet (UV) irradiation exposure at 7‐mbar pressure and high vacuum conditions: 8 × 10−5 and 5 × 10−5 mbar) by in situ Raman spectroscopy inside a planetary atmosphere and surface chamber (PASC). This work provides quality Raman spectra taken under simulated planetary conditions (to be integrated in a database), as Raman spectroscopy forms part of the current and upcoming NASA and ESA Mars planetary missions. The results demonstrate that Raman spectroscopy can be used to calculate rates of dehydration of the glycine‐MgSO4·5H2O compound to study the chemical stability with respect to photodecomposition (1) of metal‐bound glycine molecules forming the complex and (2) glycine expelled from the complex, both under Mars‐simulated conditions; finally, Raman spectroscopy can also be used to quantify intermolecular interactions in terms of local pressures. Importantly, advanced detection of water molecules as part of a complex with astrobiological interest under planetary conditions plays a crucial role in planetary missions.

All-vacuum deposited perovskite solar cells with glycine modified NiOxhole-transport layers

Organic–inorganic hybrid perovskite solar cells (PSCs) have attracted enormous research attention due to their high efficiency and low cost. However, most of the PSCs with high efficiencies still need expensive organic materials as their hole-transport layer (HTL). Obviously, the highly expensive materials go against the low-cost concept of advanced PSCs. In this regard, inorganic NiOx was considered as an idea HTL due to its good transmittance in the visible region and outstanding chemical stability. But for most of the PSCs with a NiOx HTL, the hole-extraction efficiency was limited by the unmatched valence band and too many surface defects of the NiOx layer, especially for the vacuum-deposited NiOx and perovskite. Herein, we developed a facile strategy to overcome this issue by using self-assembled glycine molecules to treat the NiOx surface. With glycine on the surface, the NiOx exhibited a deeper valence band maximum and a faster charge-extraction at the NiOx/perovskite interface. What's more, the vacuum-deposited perovskite showed a better crystallinity on the NiOx + glycine substrate. As a result, the PSCs with a glycine interfacial layer achieved a champion PCE of 17.96% with negligible hysteresis. This facile approach is expected to be further developed for fabricating high-efficiency PSCs on textured silicon solar cells.

Structural insights into the substrate selectivity of α-oxoamine synthases from marine Vibrio sp. QWI-06

Pyridoxal phosphate (PLP)–dependent α-oxoamine synthases are generally believed to be responsible for offloading and elongating polyketides or catalyzing the condensation of amino acids and acyl-CoA thioester substrates, such as serine into sphingolipids and cysteate into sulfonolipids. Previously, we discovered vitroprocines, which are tyrosine- and phenylalanine-polyketide derivatives, as potential new antibiotics from the genus Vibrio. Using bioinformatics analysis, we identified putative genes of PLP-dependent enzyme from marine Vibrio sp. QWI-06, implying a capability to produce amino-polyketide derivatives. One of these genes was cloned, and the recombinant protein, termed Vibrio sp. QWI-06 α-oxoamine synthases-1 (VsAOS1), was overexpressed for structural and biochemical characterization. The crystal structure of the dimeric VsAOS1 was determined at 1.8-Å resolution in the presence of L-glycine. The electron density map indicated a glycine molecule occupying the pyridoxal binding site in one monomer, suggesting a snapshot of the initiation process upon the loading of amino acid substrate. In mass spectrometry analysis, VsAOS1 strictly acted to condense L-glycine with C12 or C16 acyl-CoA, including unsaturated acyl analog. Furthermore, a single residue replacement of VsAOS1 (G243S) allowed the enzyme to generate sphingoid derivative when L-serine and lauroyl-CoA were used as substrates. Our data elucidate the mechanism of substrate binding and selectivity by the VsAOS1 and provide a thorough understanding of the molecular basis for the amino acid preference of AOS members.

Assessment of Electrochemical Activity of some Amino acids on the Modified Carbon Electrode Surface

The present work analyzed the electrochemical activity of certain amino acids on the modified carbon electrode as-prepared, such as glycine, threonine and aspartic acid. The electrochemical methods used to investigate surface electrode behavior through amino acid molecules at a fixed concentration and temperature of 298.15 K in the perchloric acid electrolyte solution. The findings showed that the surface electrode was ideal for the analysis of glycine, threonine, and aspartic acid molecules. Aspartic acid showed electrochemical activity by voltage and polarization resistance to 0.533 mV and 9.557 ohms, respectively. In addition, the FE-SEM images showed the thin film layer on the surface electrode from the amino acid molecules in different shapes and dense aggregations, more with aspartic acid under optimum experimental conditions.

Study on synthesis of rare earth tungsten heteropoly acid glycine composite catalyst and degradation of dyes

Using glycine molecules as the carrier, a 1:11 rare earth tungsten heteropoly acid glycine composite catalyst was prepared by hydrothermal synthesis and characterized by XRD, TG, TEM, XPS and other methods. The effects of catalyst dosage, initial dye concentration, initial pH and other factors on the decolorization rate of Congo red simulated dye wastewater were investigated. The experimental results show that when the initial pH is 4, the amount of catalyst is 10 mg, and the dye concentration is 10 mg/L, the catalyst has good degradation performance on Congo red simulated dye wastewater, and the degradation can reach 90.9%.

Influence of Monovalent Salts on α-Glycine Crystal Growth from Aqueous Solution: Molecular Dynamics Simulations at Constant Supersaturation Conditions.

The growth of α-glycine crystals from aqueous solution is investigated at constant supersaturations by utilizing the constant chemical potential molecular dynamics method. The study considers two faces (010) and (011) that predominantly determine the α-glycine crystal morphology. The general Amber force field (GAFF) with two different charge sets derived from semi-empirical calculations using the complete neglect of differential overlap method (CNDO) and from density functional calculations using the double-numerical plus d- and p-polarization basis set (DNP) is applied to describe α-glycine. The extended simple point charge model is used to simulate water. It is observed that the GAFF/DNP set leads to a much slower integration of glycine molecules into the crystal structure than the GAFF/CNDO set. The GAFF/CNDO set, however, causes the growth even at concentrations well below the experimental solubility. For the GAFF/DNP set, the influence of potassium chloride (KCl) and sodium chloride (NaCl) on the face growth rates is investigated. The parameters recently proposed by Yagasaki et al. [J. Chem. Theory Comput. 2020, 16, 2460-2473] are used to describe salt ions, as standard GAFF parameters lead to the unexpected formation of salt clusters at a concentration lower than the experimental solubility value. According to our simulation results, both salts suppress the growth of the (011) and (010) faces. The inhibiting effect of NaCl is much stronger than that of KCl for the (011) face, while both salts have a similar inhibiting effect on the (010) face. The results are in line with the experimental observations of the impact of salt ions on the α-glycine growth rates for the (011) face reported in literature.