Glycine Isomers Research Articles

Temperature driven transformations of glycine molecules embedded in interstellar ice.

The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.

Laboratory detection and astronomical study of interstellar acetohydroxamic acid, a glycine isomer

Aims. In this work, we aim to achieve the first laboratory detection of acetohydroxamic acid (CH3CONHOH), a relevant glycine isomer, to enable its eventual identification in the ISM. Methods. We employed a battery of state-of-the-art rotational spectroscopic techniques in the time domain to measure the microwave spectrum of acetohydroxamic acid. We then used the spectral GOTHAM survey performed with the Green Bank Telescope (GBT) to search for the lowest-energy Z-conformer toward the cold and quiescent molecular cloud TMC-1. We also employed a sensitive spectral survey of the chemically rich Galactic Center molecular cloud G+0.693-0.027, based on IRAM 30 m and Yebes 40 m observations. Results. We report direct experimental frequencies of the ground state of acetohydroxamic acid (up to 40 GHz). The 14N nuclear quadrupole hyperfine structure and the A-E splittings due to the internal rotation were observed and analyzed. Hence, a precise set of the rotational spectroscopic parameters were determined for the two distinct conformers, Z- and E-acetohydroxamic acid, which is the initial and prerequisite step of their radio astronomical search in the ISM using low-frequency surveys. We report the nondetection of acetohydroxamic acid toward both astronomical sources. We derive an upper limit to the column density of this molecule very similar to that obtained for glycine. Its corresponding molecular abundance with respect to molecular hydrogen is found to be ≤1 × 10−9 and 2 × 10−10 in TMC-1 and G+0.693-0.027, respectively, which further constrain the abundance of this glycine isomer in the ISM.

Constraints of the Formation and Abundances of Methyl Carbamate, a Glycine Isomer, in Hot Corinos

Abstract Methyl carbamate CH3OC(O)NH2 is an isomer of glycine. Quantum chemical analyses show that methyl carbamate is a more stable isomer than glycine. Because of this, there could be a higher chance for methyl carbamate to exist in the interstellar medium (ISM) as compared to glycine. Despite immense searches, until now glycine has not been detected in the ISM; therefore, it is worthwhile to search its isomer methyl carbamate. In this paper, we present the constraints of methyl carbamate formation under the interstellar conditions. Large complex organic molecules are favorably produced in hot-corino environments of low-mass protostars. We for the first time carried out astrochemical modeling focusing on the formation of methyl carbamate in physical conditions similar to hot-corino objects. Consequently, we examined ALMA archival data for existing spectral line observations toward hot corinos NGC 1333 IRAS 4A2 and IRAS 16293B. Within the common spectral range toward these sources, we found three features are possibly related to the spectral transitions of methyl carbamate and consequently estimate the upper limit of column densities. Results of chemical modeling are consistent with the observational upper limit of estimated column density/abundance toward the sources. This may hint the validation of the proposed formation mechanism. Future observations using a telescope like ngVLA may confirm the presence of MC toward the hot corinos.

Adsorption and isomerization of amino acids within zeolites: Impacts of acidity, amine functionalization, pore topology and sidechains

Adsorption and isomerization of amino acids within zeolites are investigated by two-layer ONIOM theoretical methods, focusing on the impacts of acidity, amine functionalization, pore topology and sidechains. Meanwhile, relationships of zwitterionic stabilization and isomerization activities with zeolite acidity and basicity are established. Adsorption structures are strongly perturbed by all factors except acidity. Distribution of different glycine isomers is significantly altered by all zeolites and also depends on zeolite basicity. Zwitterionic isomers, the active form to conduct the biological and pharmaceutical functions, are non-existent in the isolated state while remain stable within all acidic zeolites or not very highly basic zeolites. Zwitterions always show stronger interactions with zeolites than canonical isomers and zeolites with moderate acidities or basicities are the most effective for zwitterionic stabilization. Larger porous zeolites favor zwitterionic stabilization, and distinct from the isolated state, sidechains disfavor zwitterionic stabilization within zeolites while degree of influences depends on identity of sidechains, causing relative stabilities with canonical isomers to rank as proline (Pro) > glycine (Gly) > valine (Val) > protonated arginine (ArgH) > arginine (Arg). Zeolites greatly stabilize zwitterions and enable the occurrence of catalytic isomerization reactions. Isomerization to zwitterionic isomers proceeds facilely within all zeolites. Acidity increase of M-ZSM-5 zeolites or basicity decrease of amine-functionalized zeolites facilitates zwitterion formation, and zwitterion formation is the most favorable for Pro while disfavored for Arg. Results also provide insights to other host-guest interactions and catalytic mechanisms.

Interstellar glycolamide: A comprehensive rotational study and an astronomical search in Sgr B2(N).

Glycolamide is a glycine isomer and also one of the simplest derivatives of acetamide (e.g., one hydrogen atom is replaced with a hydroxyl group), which is a known interstellar molecule. In this context, the aim of our work is to provide direct experimental frequencies of the ground vibrational state of glycolamide in the centimeter-, millimeter- and submillimeter-wavelength regions in order to enable its identification in the interstellar medium. We employed a battery of state-of-the-art rotational spectroscopic techniques in the frequency and time domain to measure the frequencies of glycolamide. We used the spectral line survey named Exploring Molecular Complexity with ALMA (EMoCA), which was performed toward the star forming region Sgr B2(N) with ALMA to search for glycolamide in space. We also searched for glycolamide toward Sgr B2(N) with the Effelsberg radio telescope. The astronomical spectra were analyzed under the local thermodynamic equilibrium approximation. We used the gas-grain chemical kinetics model MAGICKAL to interpret the results of the astronomical observations. About 1500 transitions have been newly assigned up to 460 GHz to the most stable conformer, and a precise set of spectroscopic constants was determined. Spectral features of glycolamide were then searched for in the prominent hot molecular core Sgr B2(N2). We report the nondetection of glycolamide toward this source with an abundance at least six and five times lower than that of acetamide and glycolaldehyde, respectively. Our astrochemical model suggests that glycolamide may be present in this source at a level just below the upper limit, which was derived from the EMoCA survey. We could also not detect the molecule in the region's extended molecular envelope, which was probed with the Effelsberg telescope. We find an upper limit to its column density that is similar to the column densities obtained earlier for acetamide and glycolaldehyde with the Green Bank Telescope.

Conformers of dehydrogenated glycine isomers.

We report a comprehensive ab initio investigation of the conformers of dehydrogenated glycine radicals using the STO-3G, 3-21G, and aug-cc-pVDZ (aVDZ) basis sets and the UHF and UMP2 (H2 N-CH-COOH and HN-CH2 -COOH) as well as MCSCF and MRCI (H2 N-CH2 -COO) methods via two different conformational search strategies generating initial structures for optimizations by (a) removing H atoms from glycine conformers and (b) scanning torsional angles describing internal rotation along the CC, CN, and CO (except for H2 N-CH2 -COO) bonds of the radicals. We find four H2 N-CH-COOH {InCH , IInCH , IIInCH , IVnCH } and seven HN-CH2 -COOH {IpNH , IIpNH , IIInNH , IVpNH VnNH , VIpNH , VIIpNH } conformers with classical(adiabatic) relative energies of {0.00(0.00), 1.57(1.55), 5.25(5.03), 9.85(9.72)} and {0.00(0.00), 0.78(1.06), 1.93(2.08), 3.34(3.16), 3.39(3.29), 5.00(4.86), 9.27(8.87)} kcal/mol, respectively, obtained with UCCSD(T)-F12b/aug-cc-pVTZ(+UCCSD(T)-F12b/aVDZ ZPE correction) and four H2 N-CH2 -COO {IpCOO , IInCOO , IIIpCOO , IVnCOO } conformers with MRCI-F12+Q/aVDZ(+MRCI/aVDZ ZPE correction) energies of {0.00(0.00), 1.65(1.64), 1.78(1.75), 2.21(2.21)} kcal/mol, where n and p denote C1 and Cs symmetry. The MRCI-F12+Q[UCCSD(T)-F12b] InCH → IpNH and InCH → IpCOO classical(adiabatic) isomerization energies are 18.51(17.32)[21.20(20.01)] and 31.88(31.66) kcal/mol, respectively.

Toward the origin of life over feldspar surfaces: Adsorption of amino acids and catalysis of conformational interconversions

AbstractFeldspars are a group of tectosilicate minerals terminated with a full layer of hydroxyl groups and have been regarded as “hotbed” for birth of life. In this study, periodic density functional theory calculations are conducted to address two associated issues, as adsorption of amino acids and conformational interconversions over feldspar surfaces. Distribution of glycine isomers depends strongly on the number of interacted surface silanols (n), and canonical isomers exist exclusively for n ≤ 2 while zwitterions predominate for n = 3. Adsorption of amino acids is significantly affected by sidechains, especially those forming H‐bonds with surfaces; however, sidechain contacts with feldspar surfaces disfavor zwitterion stabilization, and zwitterions become preferred without sidechain contacts. For all amino acids, conformational interconversions undergo four elementary steps, and proton transfer between two carboxylic‐O atoms (step 2) is always rate‐decisive. Step 2 is greatly accelerated with catalysis of surface silanols and activation barriers depend significantly on sidechains. All amino acids have moderate activation barriers and conformational interconversions (in both forward and reverse directions) proceed favorably at ambient conditions. Sidechains of amino acids exhibit influences through sidechain contacts with surfaces rather than as substituent effect.

Formation of Protonated Glycine Isomers in the Interstellar Medium

A computational study of protonated glycine isomers with [H6C2O2N]+ molecular formula has been carried out. All of them are possible products of the reaction between protonated hydroxylamine and ac...

Gas Phase Synthesis of Protonated Glycine by Chemical Dynamics Simulations.

In the present work, we investigated the reaction dynamics that will possibly lead to the formation of protonated glycine by an ion-molecule collision. In particular, two analogous reactions were studied: NH3OH+ + CH3COOH and NH2OH2+ + CH3COOH that were suggested by previous experiments to be able to form protonated glycine loosing a neutral water molecule. Chemical dynamics simulations show that both reactants can form a molecule with the mass of the protonated glycine but with different structures, if some translational energy is given to the system. The reaction mechanisms for the most relevant product isomers are discussed as well as the role of collision energy in determining reaction products. Finally, in comparing collision dynamics at room and at very low initial internal temperature of the reactants, the same behavior was obtained for forming the protonated glycine isomers products. This supports the use of standard gas phase ion-chemistry setups to study collision-induced reactivity as a model for astrophysical cold conditions, when some relative translation energy is given to the system.

Complexation of glycine by manganese (II) in the gas phase: A theoretical study

The interaction of Mn 2+, being in three possible spin states, with glycine has been studied using quantum chemical calculations in the gas phase. Seven modes of interaction have been considered in all cases. Investigation of manganese complexes having various possible spin state including high, intermediate and low spins shows that the most stable complexes are high spin (total electron spin S = 5/2). Calculations show that the most stable mode of binding involves the simultaneous interaction of Mn 2+ with two oxygen atoms of the zwitterionic conformers of glycine (η 2-O,O (CO 2 −)), while the second preferred binding site consists of chelation between the carbonyl oxygen and the amino nitrogen (η 2-O,N). These results indicate that the relative affinity of Mn 2+ and the glycine zwitterion makes this isomer of glycine more stable than others, even though it is not stable in its isolated form. The results are in accord with those of previous reports for some doubly charged cations and in some cases with monocations. The nature of the interaction between manganese metal cation and glycine is also discussed employing natural population and molecular orbital analyses. It has been found that electrostatics contribution plays a crucial role in this interaction. Complexation energy ( D 0) of the low lying energy isomer, for the most stable sextet spin state, has been obtained as about 156 kcal/mol. It has also been shown that the computed vibrational frequencies could aid in identification of the most stable Mn 2+–glycine complex.

Glycine Canonical and Zwitterionic Isomers within Zeolites

The glycine zwitterion (GlyA) in the gas phase is not a local energy minimum and transforms to the canonical isomer (GlyB) via a barrierless process. Within ZSM-5 zeolite, it is rendered geometrically stable and even has a lower energy of 7.57 kcal mol(-1) than GlyC, the most stable isomer of glycine in the gas phase; GlyB represents the lowest energy minimum, which is facile to transform into the zwitterion with low-energy barrier (4.46 kcal mol(-1)). In addition, the zwitterion can be efficiently obtained by adsorption of glycine in the deprotonated form at the acidic site of HZSM-5 zeolite. The relative stability of glycine isomers in silicalite-1 increases in the order GlyA<GlyB<GlyC, the same as that in the gas phase. Silicalite-1 stabilizes GlyA somewhat, whereas it destabilizes GlyB greatly. The negative charges of ZSM-5 zeolite created by Al doping are indispensable to the stabilizations of the zwitterion; however, the lattices also play an important role and approximate 74.1% of the contributions of the negative charges.

Synthesis and biological evaluation of (2 S)- and (2 R)-2-(3′-phosphonobicyclo[1.1.1]pentyl)glycines as novel group III selective metabotropic glutamate receptor ligands

The synthesis of (2 S)- and (2 R)-2-(3′-phosphonobicyclo[1.1.1]pentyl)glycine isomers ( 10 and 11), characterized by the bioisosteric replacement of the distal carboxylic group of 2-(3′-carboxybicyclo[1.1.1]pent-1-yl)glycine by the phosphonate moiety, was accomplished by a stereoselective Ugi condensation. The two isomers were tested for their activity against an array of metabotropic glutamate receptors, and the S-isomer ( 10) turned out to be a moderately potent and selective mGluR4 agonist.

A Combined Experimental and Theoretical Study on the Formation of the Amino Acid Glycine (NH2CH2COOH) and Its Isomer (CH3NHCOOH) in Extraterrestrial Ices

We have investigated the synthesis of the simplest aminoacid, glycine, by Galactic cosmic-ray particles in extraterrestrialices.Laboratoryexperimentscombinedwithelectronicstructurecalculationsshowedthatamethylamine molecule [CH3NH2(X 1 A 0 )] can be dissociated through interaction with energetic electrons in the track of a cosmicray particle to form atomic hydrogen and the radicals CH2NH2(X 2 A 0 )a nd CH3NH(X 2 A 0 ). Hydrogen atoms with sufficient kinetic energy could overcome the entrance barrier to add to a carbon dioxide molecule [CO2(X 1 � þ )], yielding a trans-hydroxycarbonyl radical, HOCO(X 2 A 0 ). Neighboring radicals with the correct geometric orientation then recombine to form glycine, NH2CH2COOH(X 1 A), and also its isomer, CH3NHCOOH(X 1 A). These findings expose for the first time detailed reaction mechanisms of how the simplest amino acid glycine and its isomer can be synthesized via nonequilibrium chemistry in interstellar and cometary ices. Our results offer an important alternative to aqueous and photon-induced formation of amino acids in comets and in molecular clouds. These results also predict the existence of a hitherto undetected isomer of glycine in the interstellar medium, suggest that glycine should be observable on Saturn’s moon Titan, and help to account for the synthesis of more complex amino acids in the Murchison and Orgueil meteorites.

Fragmentation and deformation mechanism of glycine isomers in gas phase: Investigations of charge effect.

The structural parameters, relative stability, proton transfer energy barriers of four typical and life related isomers and conformers of different charged (n=0,+/-1,+/-2) glycine species have been investigated using B3LYP, BHLYP, and CCSD(T) methods. Results indicate that those neutral and (+/-1)-charged species are stable. For the (+2)-charged cases, all four triplet-state glycine species and only the singlet-state zwitterionic one are stable. On the other hand, only the singlet-state zwtterionic glycine ((1)GlyZW(-2)) and the corresponding neutral form counterpart ((1)Gly(-2)) are stable for the (-2)-charged cases. Either of the two stable structures holds a proton lying in the position (2-3 A) of being separated from its corresponding parental species. Those unstable divalent glycine species are dissociated into different smaller species spontaneously according to the characters of their different structures and electron spins. The presented fragmentation and deformation mechanisms can effectively predict and satisfactorily explain some experimental phenomena, which had been puzzling the mass spectrometry chemists. Also, the mechanisms should be suitable for any other similar molecule systems. Comparisons of the relative energies of the four (+1)-charged glycine species show that doublet-state glycine III ((2)GlyIII1) is more stable in energy by 12.1 kcal/mol than the (+1)-charged glycine Gly ((2)Gly1). This is consistent with the energy ordering of their corresponding mono-valence metal ion-bound derivatives. In addition, calculations show that an intramolecular proton transfer of (2)Gly(-1) to become its zwitterionic counterpart is preferred due to its least activation energy barrier (5.8 kcal/mol) among four discussed processes.

Rotational Spectrum, Hyperfine Structure, and Internal Rotation of Methyl Carbamate

Methyl carbamate, an isomer of glycine, is a possible candidate for interstellar detection. It might be more abundant than glycine and its dipole moment is much larger. Furthermore, using high-level quantum chemical calculations, it is shown that syn methyl carbamate has a lower energy than glycine. The quadrupole hyperfine structure due to 14N has been measured using microwave Fourier transform spectroscopy. The rotational spectrum of the ground vibrational state has been measured from 8 to 240 GHz and accurate spectroscopic constants have been determined for the A internal rotation components of the rotational lines. Finally, the internal rotation splittings have been analyzed.

Rotational Spectrum, Hyperfine Structure, and Internal Rotation of Methyl Carbamate

Methyl carbamate, an isomer of glycine, is a possible candidate for interstellar detection. It might be more abundant than glycine and its dipole moment is much larger. Furthermore, using high-level quantum chemical calculations, it is shown that syn methyl carbamate has a lower energy than glycine. The quadrupole hyperfine structure due to 14N has been measured using microwave Fourier transform spectroscopy. The rotational spectrum of the ground vibrational state has been measured from 8 to 240 GHz and accurate spectroscopic constants have been determined for the A internal rotation components of the rotational lines. Finally, the internal rotation splittings have been analyzed.

A combined discrete/continuum solvation model: Application to glycine

A new solvation model that combines discrete and continuum descriptions of the solvent has been developed. The discrete solvent molecules are represented by effective fragment potentials (EFP), while the continuum is represented by the Onsager model. This (EFP+Onsager) model has been applied to the relative stabilities of the neutral and zwitterionic forms of glycine. Other supermolecule-continuum calculations were also performed, using quantum mechanical discrete waters and the isodensity polarizable continuum model (IPCM) or solvation model 5.42R (SM5.42R) for the continuum. It is shown that the Onsager model provides a poor description of the solvent in the supermolecule-continuum calculations. On the other hand, more sophisticated models can predict the correct energy order of the glycine isomers. Thus, the development of mixed methods that combine sophisticated continuum models with the discrete EFP model appear to be promising.

Agonist analysis of 2-(carboxycyclopropyl)glycine isomers for cloned metabotropic glutamate receptor subtypes expressed in Chinese hamster ovary cells.

1. 2-(Carboxycyclopropyl)glycines (CCGs) are conformationally restricted glutamate analogues and consist of eight isomers including L- and D-forms. The agonist potencies and selectivities of these compounds for metabotropic glutamate receptors (mGluRs) were studied by examining their effects on the signal transduction of representative mGluR1, mGluR2 and mGluR4 subtypes in Chinese hamster ovary cells expressing the individual cloned receptors. 2. Two extended isomers of L-CCG, L-CCG-I and L-CCG-II, effectively stimulated phosphatidylinositol hydrolysis in mGluR1-expressing cells. The rank order of potencies of these compounds was L-glutamate > L-CCG-I > L-CCG-II. 3. L-CCG-I and L-CCG-II were effective in inhibiting the forskolin-stimulated adenosine 3':5'-cyclic monophosphate (cyclic AMP) accumulation in mGluR2-expressing cells. Particularly, L-CCG-I was a potent agonist for mGluR2 with an EC50 value of 3 x 10(-7) M, which was more than an order of potency greater than that of L-glutamate. 4. L-CCG-I evoked an inhibition of the forskolin-stimulated cyclic AMP production characteristic of mGluR4 with a potency comparable to L-glutamate. 5. In contrast to the above compounds, the other CCG isomers showed no appreciable effects on the signal transduction involved in the three mGluR subtypes. 6. This investigation demonstrates not only the importance of a particular isomeric structure of CCGs in the interaction with the mGluRs but also a clear receptor subtype specificity for the CCG-receptor interaction, and indicates that the CCG isomers would serve as useful agonists for investigation of functions of the mGluR family.

The protective effect of some carbohydrates against the inactivation of complement by heat, together with a note on the effect of glycolamide (an isomer of glycine) on heat-inactivation.

Gordon &amp; Turner (1955) reported that glucose and other sugars intensify the protective action of glycine against the heat-inactivation of complement, so that in their presence the concentration of glycine required to protect complement against inactivation at 55° C. is greatly reduced. Moreover, when high concentrations of glycine (e.g. 10%) were used, higher temperatures were required to inactivate complement if the glycine was dissolved in a high concentration of a sugar. They also showed that although this intensification is a property of a wide range of sugars, it is not shown by the corresponding alcohols, although inositol is exceptional in causing marked intensification. No explanation was offered for these findings and further experiments have been undertaken to throw light on them.