Glycine Dimers: Structure, Stability, and Medium Effects

Computational study of the dimerization of glyphosate: mechanism and effect of solvent

A computational study on the structure and stability of different series of glyphosate (Glyph) dimers comprising nonionized (N) and zwitterionic structures (Z) for neutral monomers, followed by an analysis of energetics of Glyph dimerization process have been performed by means of quantum chemical calculations in different media. Optimized geometries for energy minima, as well as relative potential and free energies of the possible various conformers of each series of Glyph dimer were computed as a function of the medium at B3LYP-D3/6-311++G(2d,2p) level. The solvation model based on density (SMD) is employed for all solution phase computations. Non-ionized dimers (DN), anion-cation (AC) and either zwitterion-zwitterion (DZP and DZC) or non-ionized-phosphonate zwitterion (NZP) ionized neutral forms of Glyph dimer are predicted to exist in the gas phase and in solution in large contrast to Glyph monomers. The DZC dimer form exhibiting a centrosymmetric arrangement of two carboxylate zwitterion units was found to be the most stable dimer structure in all media. In aqueous solution, the DZP and AC dimer type structures are significantly stabilized by hydration. The tautomerisms between DZC, DZP and AC dimer type structures have been investigated in the gas phase and in solution. The DZC type structures are more prone to experience proton transfer in water than in the gas phase and in cyclohexane. The mechanism for the tautomerization process in neutral ionized Glyph dimers proceeds via two direct proton transfer paths: DZP ⇋ AC ⇋ DZC. Results show that solvents play a key role in modulating the energetics of the dimerization process of Glyph. Solvation in cyclohexane, favors the dimerization process however, hydration opposed it. In aqueous solution, the mechanism of the dimerization of Glyph from its phosphonate zwitterionic monomer form (ZP) could be described by a set of equilibria including direct proton transfer paths as follows: 2ZP ⇋ DZP ⇋ AC ⇋ DZC. According to our results, in aqueous solution, DZC Glyph dimers and their corresponding DZP and AC tautomers should be present in higher concentration than phosphonate zwitterionic Glyph monomers for high Glyph concentration, a fact that seems controversial in the literature.

Amino acid chiral amplification using Monte Carlo dynamic

This study investigates the stability of chiral-molecule solution phases, with a specific focus on amino acids. The model framework is based on a two-dimensional square lattice model, where individual sites may be occupied by oriented chiral molecules or structureless solvent particles. Utilizing the Glauber dynamics and statistical mechanical formalism, as previously introduced and examined by Lombardo et al., we explore the influence of temperature, amino acid concentration, enantiomeric excess, and homochiral interaction strength on nucleation mechanisms, equilibrium phase behavior, and crystal composition. Our findings offer thermodynamic insights into the chiral amplification process of amino acids, contributing to a deeper understanding of the underlying processes.

In situ optical spectroscopy of crystallization: One crystal nucleation at a time

While crystallization is a ubiquitous and an important process, the microscopic picture of crystal nucleation is yet to be established. Recent studies suggest that the nucleation process can be more complex than the view offered by the classical nucleation theory. Here, we implement single crystal nucleation spectroscopy (SCNS) by combining Raman microspectroscopy and optical trapping induced crystallization to spectroscopically investigate one crystal nucleation at a time. Raman spectral evolution during a single glycine crystal nucleation from water, measured by SCNS and analyzed by a nonsupervised spectral decomposition technique, uncovered the Raman spectrum of prenucleation aggregates and their critical role as an intermediate species in the dynamics. The agreement between the spectral feature of prenucleation aggregates and our simulation suggests that their structural order emerges through the dynamic formation of linear hydrogen-bonded networks. The present work provides a strong impetus for accelerating the investigation of crystal nucleation by optical spectroscopy.

Volatility Study of Amino Acids by Knudsen Effusion with QCM Mass Loss Detection

This work presents a new Knudsen effusion apparatus employing continuous monitoring of sample deposition using a quartz-crystal microbalance sensor with internal calibration by gravimetric determination of the sample mass loss. The apparatus was tested with anthracene and 1,3,5-triphenylbenzene and subsequently used for the study of sublimation behavior of several proteinogenic amino acids. Their low volatility and thermal instability strongly limit possibilities of studying their sublimation behavior and available literature data. The results presented in this work are unique in their temperature range and low uncertainty required for benchmarking theoretical studies of sublimation behavior of molecular crystals. The possibility of dimerization in the gas phase that would invalidate the effusion experiments is addressed and disproved by theoretical calculations. The enthalpy of sublimation of each amino acid is analyzed based on the contributions in two hypothetical sublimation paths involving the proton transfer in the solid and in the gas phase.

Theoretical study of glycine amino acid adsorption on graphene oxide

The non-dissociative and dissociative adsorptions of zwitterionic Gly on graphene oxide (GO) was studied in the framework of DFT using a cluster model approach. In this work, the interaction with an epoxy group of GO basal plane was mainly considered. As a comparison, the non-dissociative and dissociative adsorptions of neutral Gly were also taken into account. The non-dissociative adsorption modes for zwitterionic and neutral Gly conformers show binding energies of 12.2 and 14.4 kcal mol^-1, respectively. These molecules are thought to remain over the GO surface due to attractive noncovalent interactions. Two dissociative adsorption modes, for Z-Gly and N-Gly, show smaller binding energies of 7.2 and 8.4 kcal mol^-1, where the deprotonated species links strongly through a C-O or C-N covalent bond to the GO surface. The results obtained in the present theoretical approach to the glycine/graphene oxide system support the fact that glycine can be attached to epoxy groups of graphene oxide basal planes in addition to the anchoring on edge oxidation groups. In summary, we conclude that glycine can be used as a reducing agent as well as a functionalizer of GO sheets.

Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine

Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.

Glycine zinc sulfate penta-hydrate: redetermination at 10 K from time-of-flight neutron Laue diffraction

Single crystals of glycine zinc sulfate penta-hydrate [systematic name: hexa-aqua-zinc tetra-aquadiglycinezinc bis-(sulfate)], [Zn(H2O)6][Zn(C2H5NO2)2(H2O)4](SO4)2, have been grown by isothermal evaporation from aqueous solution at room temperature and characterized by single-crystal neutron diffraction. The unit cell contains two unique ZnO6 octa-hedra on sites of symmetry -1 and two SO4 tetra-hedra with site symmetry 1; the octa-hedra comprise one [tetra-aqua-diglycine zinc]2+ ion (centred on one Zn atom) and one [hexa-aqua-zinc]2+ ion (centred on the other Zn atom); the glycine zwitterion, NH3+CH2COO-, adopts a monodentate coordination to the first Zn atom. All other atoms sit on general positions of site symmetry 1. Glycine forms centrosymmetric closed cyclic dimers due to N-H⋯O hydrogen bonds between the amine and carboxyl-ate groups of adjacent zwitterions and exhibits torsion angles varying from ideal planarity by no more than 1.2°, the smallest values for any known glycine zwitterion not otherwise constrained by a mirror plane. This work confirms the H-atom locations estimated in three earlier single-crystal X-ray diffraction studies with the addition of independently refined fractional coordinates and Uij parameters, which provide accurate inter-nuclear X-H (X = N, O) bond lengths and consequently a more accurate and precise depiction of the hydrogen-bond framework.

Solvent Effects on the Monomer/Hydrogen-Bonded Dimer Equilibrium in Carboxylic Acids: (+)-(S)-Ketopinic Acid as a Case Study

The hydrogen-bond-assisted self-association process of a chiral semirigid carboxylic acid, namely, (+)-(S)-ketopinic acid, has been studied. The multiconformational monomer/dimer equilibrium has been evaluated by means of a concentration-dependent FTIR study that enabled the experimental equilibrium constants of the dimer formation reaction (Kdim ) to be determined in two solvents of different polarity. In CDCl3 , dimeric forms predominate, even in diluted solutions (KdimCF =5.074), whereas in CD3 CN the self-association process is hindered and monomers are always the main species, irrespective of solute concentration (KdimAN =0.194). The reliability of the dimerization constants and the derived mono- and dimeric experimental fractions have been proven by means of accurate matching between the experimental vibrational circular dichroism spectra of the species and the theoretical spectra generated by considering the simultaneous weighted contributions of the concomitant monomers and dimers.

Hydrogen bond mediated stabilization of the salt bridge structure for the glycine dimer anion

The formation of a salt bridge in deprotonated glycine dimer anions in a solvent-free environment is investigated using both infrared multiple photon dissociation spectroscopy between 600 and 1800 cm(-1) and theory. The zwitterionic and nonzwitterionic forms of glycine in this complex are computed to be nearly iso-energetic, yet predominantly the zwitterionic form is observed experimentally. The zwitterion stability is attributed to both the Coulombic attraction and the high stabilization from intramolecular hydrogen bonding that drives the energetic cost of proton transfer in a solvent free environment. These results show that there is a fine balance between the stabilities of these two forms of the anion. Elucidating the role of intrinsic factors, such as hydrogen bonding, can lead to a better understanding of the stabilities of salt bridges in the interiors of large proteins or at protein interfaces.

Salt-dependent growth kinetics in glycine polymorphic crystallization

Divalent cation salts inhibit the growth of α-glycine far less severely than that of γ-glycine, causing α-glycine to have a greater competitive advantage over γ-glycine, thus further reinforcing the preferential formation of α-glycine on a relative basis.

Density functional theory study of the oligomerization of carboxylic acids

We present a density functional theory [M06-2X/6-31+G(d,p)] study of the structures and free energies of formation of oligomers of four carboxylic acids (formic acid, acetic acid, tetrolic acid, and benzoic acid) in water, chloroform, and carbon tetrachloride. Solvation effects were treated using the SMD continuum solvation model. The low-lying energy structures of molecular complexes were located by adopting an efficient search procedure to probe the potential energy surfaces of the oligomers of carboxylic acids (CA)n (n = 2-6). The free energies of the isomers of (CA)n in solution were determined as the sum of the electronic energy, vibrational-rotational-translational gas-phase contribution, and solvation free energy. The assessment of the computational protocol adopted in this study with respect to the dimerization of acetic acid, (AA)2, and formic acid, (FA)2, located new isomers of (AA)2 and (FA)2 and gave dimerization constants in good agreement with the experimental values. The calculation of the self-association of acetic acid, tetrolic acid, and benzoic acid shows the following: (i) Classic carboxylic dimers are the most stable isomer of (CA)2 in both the gas phase and solution. (ii) Trimers of carboxylic acid are stable in apolar aprotic solvents. (iii) Molecular clusters consisting of two interacting classic carboxylic dimers (CA)4,(D+D) are the most stable type of tetramers, but their formation from the self-association of classic carboxylic dimers is highly unfavorable. (iv) For acetic acid and tetrolic acid the reactions (CA)2 + 2CA → (CA)4,(D+D) and (CA)3 + CA → (CA)4,(D+D) are exoergonic, but these aggregation pathways go through unstable clusters that could hinder the formation of tetrameric species. (v) For tetrolic acid the prenucleation species that are more likely to form in solution are dimeric and trimeric structures that have encoded structural motifs resembling the α and β solid forms of tetrolic acid. (vi) Stable tetramers of benzoic acid could form in carbon tetrachloride from the aggregation of trimers and monomers. (vii) Higher order clusters such as acetic acid pentamers and tetrolic acid hexamers are highly unstable in all solvation environments.

The molecular structure, geometry, stability, thermal and fundamental modes of vibration of glycine dimer by DFT methods

Glycine is an important amino acid for building up protein synthesis. Single crystal of glycine dimer was grown from aqueous solution by slow evaporation method. Powder X-ray diffraction analysis confirms the crystalline nature of grown crystal. It is interesting to study the molecular structure of a dimer, having well-defined channels formed through amphoterism bonding between CO⋯H bonds with split-valence basis sets, and the conformer is mirror symmetrical, in which the protonated organic cation plays a significant role to have a dimer pattern. Amphiprotic molecules, like dimeric glycine which can either donate or accept a proton (H(+)) from each other. Optical absorption study reveals that the transparency of the crystal in the entire visible region and the cutoff wavelength was found to be 235nm. Powder SHG test and thermogravimetric analysis shows glycine dimer crystal is optically active and thermally stable. The molecular structure, geometry, stability and theoretical vibrational spectra were calculated for glycine as a monomer and as a dimer linked by the amphoterism hydrogen bonding. The theoretical studies were performed using the B3LYP density functional method with the 6-311G (d,p) basis set. The detailed interpretation of the vibrational spectra has been made on the basis of normal coordinate analysis.