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.

A study of the effects of the polarity of the solvents acetone and cyclohexane on the luminescent properties of tryptophan

The luminescent properties of tryptophan in solvents less polar than water, such as acetone, and non-polar ones, such as cyclohexane, are experimentally studied and compared with theoretical calculations using time-dependent density functional theory (TD-DFT) methods. Since tryptophan may present different configurations and charge distributions, the most stable conformer is analyzed for both solvents, including its neutral and zwitterionic forms. To perform the simulation two clusters are proposed with the Zpt conformer in acetone: [Formula: see text] and [Formula: see text] , and four clusters with the Nag⁺ conformer in cyclohexane: (Trp)₁-(C₆H₁₂), (Trp)₂-(C₆H₁₂), (Trp)₃-(C₆H₁₂) and (Trp)₄-(C₆H₁₂), in order to conveniently emulate the concentration in each solvent by reducing the distance between adjacent tryptophan molecules as the concentration increases, since there is no control over the volume parameter. In each case, the UV-vis absorption is computed and compared with the experimental excitation spectra; the results show a good agreement. This calculation allows a more detailed analysis of the experimental results based on the properties of the molecular orbitals involved in electronic transitions. In the present work, a strong effect of the solvent acetone on tryptophan is observed; for this solvent, a charge transfer from the solute to solvent happens. This behavior does not occur with water (polar solvent) or cyclohexane (non-polar solvent). Finally, experimental spectroscopic data of Trp in cyclohexane are explained through the hydrogen bonds between amino acid molecules present in the fluorescent states. In this case, the theoretical and experimental results are compared and also show good agreement.

Stabilization of glyphosate zwitterions and conformational/tautomerism mechanism in aqueous solution: insights from ab initio and density functional theory-continuum model calculations

In this work, a comparative theoretical conformational analysis of the commercially most successful herbicide compound, glyphosate (N-phosphonomethylglycine), has been made at various quantum chemical levels of theory, in the gas phase and aqueous solution, using the integral equation-formalism polarizable continuum model (IEFPCM) and the solvation model density (SMD) approaches. The stable conformers of non-ionized (NE) and ionized or zwitterionic (ZW) neutral forms of glyphosate and the inter-conversions between them are described. Calculations revealed that several NE conformers of glyphosate exist in the gas phase but the zwitterionic form (ZW) is unstable in vacuo at all levels of theory. In aqueous solution, the stabilization of the zwitterion form of glyphosate was unable to be predicted satisfactorily within the equilibrated framework of the IEFPCM polarizable continuum model and using the standard UFF-radii cavity. However, the calculation with the density-based solvation model (SMD) was consistent with the experimental findings and led to the identification of the phosphonate zwitterionic (ZWP) structure as the global minimum energy in aqueous solution. The ZWP ⇋ NE tautomeric equilibrium between the non-ionized and zwitterionic forms of glyphosate was studied in aqueous solution at the SMD-B3LYP-D3/6-311++(2d,2p) level. Zwitterion formation in solution could occur by means of a concerted intramolecular proton transfer from the nitrogen to the oxygen of the phosphonate group. An analysis of the intermolecular mechanism shows that the addition of one water molecule favours the process either thermodynamically or kinetically. The possibility that the tautomerization process of glyphosate via a nonconcerted mechanism with zwitterion carboxylate (ZWC) as the intermediate can be excluded and the ZWP → ZWC proton transfer conversion can be a nearly barrierless process in PES and FES surfaces. comparison with similarly related biologically active systems was made.

Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution

In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.

Abiotic degradation of glyphosate into aminomethylphosphonic acid in the presence of metals

Glyphosate [N-phosphono-methylglycine (PMG)] is the most used herbicide worldwide, particularly since the development of transgenic glyphosate-resistant (GR) crops. Aminomethylphosphonic acid (AMPA) is the main glyphosate metabolite, and it may be responsible for GR crop damage upon PMG application. PMG degradation into AMPA has hitherto been reckoned mainly as a biological process, produced by soil microorganisms (bacteria and fungi) and plants. In this work, we use density functional calculations to identify the vibrational bands of PMG and AMPA in surface-enhanced Raman spectroscopy (SERS) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectra experiments. SERS shows the presence of AMPA after glyphosate is deposited from aqueous solution on different metallic surfaces. AMPA is also detected in ATR-FTIR experiments when PMG interacts with metallic ions in aqueous solution. These results reveal an abiotic degradation process of glyphosate into AMPA, where metals play a crucial role.

Low environmentally relevant levels of bioactive xenobiotics and associated degradation products cause cryptic perturbations of metabolism and molecular stress responses in Arabidopsis thaliana

Anthropic changes and chemical pollution confront wild plant communities with xenobiotic combinations of bioactive molecules, degradation products, and adjuvants that constitute chemical challenges potentially affecting plant growth and fitness. Such complex challenges involving residual contamination and mixtures of pollutants are difficult to assess. The model plant Arabidopsis thaliana was confronted by combinations consisting of the herbicide glyphosate, the fungicide tebuconazole, the glyphosate degradation product aminomethylphosphonic acid (AMPA), and the atrazine degradation product hydroxyatrazine, which had been detected and quantified in soils of field margins in an agriculturally intensive region. Integrative analysis of physiological, metabolic, and gene expression responses was carried out in dose-response experiments and in comparative experiments of varying pesticide combinations. Field margin contamination levels had significant effects on plant growth and metabolism despite low levels of individual components and the presence of pesticide degradation products. Biochemical and molecular analysis demonstrated that these less toxic degradation products, AMPA and hydroxyatrazine, by themselves elicited significant plant responses, thus indicating underlying mechanisms of perception and transduction into metabolic and gene expression changes. These mechanisms may explain observed interactions, whether positive or negative, between the effects of pesticide products (AMPA and hydroxyatrazine) and the effects of bioactive xenobiotics (glyphosate and tebuconazole). Finally, the metabolic and molecular perturbations induced by low levels of xenobiotics and associated degradation products were shown to affect processes (carbon balance, hormone balance, antioxidant defence, and detoxification) that are likely to determine environmental stress sensitivity.