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

Fliss, Outaf; Essalah, Khaled; Fredj, A. Ben

doi:10.1039/d1cp03161a

Cited by 11 publications

(16 citation statements)

References 62 publications

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“…However, this estimate had been based on the energy comparison of single structures and on the use of implicit solvation. Conversely, several literature studies have shown that the computational estimate of the stability of the zwitterion vs nonzwitterion form of either amino acids or peptides was rather challenging and ideally required the employment of high levels of theory, multiconformational representations of the investigated molecules, and explicit solvation. − …”

Section: Resultsmentioning

confidence: 99%

MD-DFT Computational Studies on the Mechanistic and Conformational Parameters for the Chemoselective Tyrosine Residue Reactions of G-Protein-Coupled Receptor Peptides with [CpRh(H₂O)₃](OTf)₂in Water To Form Their [(η⁶-CpRh-Tyr^#)-GPCR peptide]²⁺Complexes: Noncovalent H-Bonding Interactions, Molecular Orbital Analysis, Thermodynamics, and Lowest Energy Conformations

2022

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Bioconjugation of important G-protein-coupled receptor (GPCR) peptides with organometallic aqua complexes has proven to be an exciting new approach for discovering potential drugs acting on their respective GPCR receptors. Thus, in this study, we report on the mechanistic and conformational aspects for the chemoselective reactions of tyrosine-containing GPCR peptides with [Cp*Rh(H 2 O) 3 ](OTf) 2 , in water, at room temperature (J. Am. Chem. Soc. 2012, 134, 10324). We have focused on three critically important GPCR peptides; namely, [Tyr 1 ]-Leu-enkephalin (1), [Tyr 4 ]-neurotensin(8−13) (2), and [Tyr 3 ]-octreotide (3), each having a different position for the tyrosine residue, together with competing functionalities. The edonating effect of the tyrosine phenol OH group was assumed to have provided high chemoselectivity. Therefore, we have concentrated on the important mechanistic and conformational pathways to the chemoselective tyrosine products, the [(η 6 -Cp*Rh-Tyr 1,4,3 )-GPCR peptide](OTf) 2 complexes, utilizing molecular dynamics (MD) and density functional theory (DFT) methods, and have provided a mechanistic rationale for these chemoselective reactions, including noncovalent interactions, molecular orbital analysis, and thermodynamics. Furthermore, the influence of the [Cp*Rh] 2+ group on the lowest energy conformations for the structures of [(η 6 -Cp*Rh-Tyr 1 )-Leu-enkephalin](OTf) 2 , 4, [(η 6 -Cp*Rh-Tyr 4 )neurotensin(8−13)](OTf) 2 , 5, and [(η 6 -Cp*Rh-Tyr 3 )-octreotide](OTf) 2 , 6, were also assessed, including the essential intramolecular, noncovalent interactions that determined the lowest energy conformations of [(η 6 -Cp*Rh-Tyr 1,4,3 ) GPCR peptide] 2+ complexes, 4−6, in comparison to their ligands, GPCR peptides, 1−3. This represented, to our knowledge, the first MD/ DFT study on mechanisms of an organometallic aqua complex reacting in an aqueous media with GPCR peptides, while also determining the critical secondary forces; for example, intramolecular, noncovalent H-bonding interactions that further defined the most stable conformations of the GPCR peptides and those of their [(η 6 -Cp*Rh-Tyr 1,4,3 ) GPCR peptide] 2+ complexes.

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Section: Resultsmentioning

confidence: 99%

MD-DFT Computational Studies on the Mechanistic and Conformational Parameters for the Chemoselective Tyrosine Residue Reactions of G-Protein-Coupled Receptor Peptides with [CpRh(H₂O)₃](OTf)₂in Water To Form Their [(η⁶-CpRh-Tyr^#)-GPCR peptide]²⁺Complexes: Noncovalent H-Bonding Interactions, Molecular Orbital Analysis, Thermodynamics, and Lowest Energy Conformations

2022

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“…FSC can interact with 3D‐POWER via π–π stacking, whereas GLY interacts with the surface chemistry of 3D‐POWER by means of the phosphonate group in P‐O − , P═O − and P‐C‐N‐H bonds, which is stabilized by hydrogen interactions. [ 19 ] However, given the molecular flexibility of GLY (due to its single bonds, see Figure S14 , Supporting Information), a concentration‐dependent SERS fingerprint was observed for this analyte. Hence, the surface coverage of GLY onto 3D‐POWER may modulate the orientation of GLY yielding such a concentration‐dependent spectroscopic behavior, [ 20 ] where the lowest concentrations of GLY allowed for the best observations of a highly detailed Raman signature of GLY by means of 3D‐POWER, see Figures S14 and S15 (Supporting Information), particularly, displaying clearly defined vibrational bands associated to the phosphonate group, see Table S11 (Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

Flexible 3D Plasmonic Web Enables Remote Surface Enhanced Raman Spectroscopy

Rodríguez‐Sevilla,

Álvarez‐Martínez,

Castro‐Beltrán

et al. 2024

Advanced Science

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Nanoplasmonic materials concentrate light in specific regions of dramatic electromagnetic enhancement: hot spots. Such regions can be employed to perform single molecule detection via surface‐enhanced Raman spectroscopy. However, this phenomenon is challenging since hot spots are expected to be highly intense/abundant and positioning of molecules within such hot spots is crucial to manage with ultrasensitive SERS. Herein, it is discovered that a 3D plasmonic web embedded within a biohybrid (3D‐POWER) exhibits plasmonic transmission, spontaneously absorbs the analyte, and meets these so much needed criteria in ultrasensitive SERS. 3D‐POWER is built with nanopaper and self‐assembled layers of graphene oxide and gold nanorods. According to in silico experiments, 3D‐POWER captures light in a small region and performs plasmonic field transmission in a surrounding volume, thereby activating a plasmonic web throughout the simulated volume. The study also provides experimental evidence supporting the plasmonic field transport ability of 3D power, which operates as a SERS signal carrier (even beyond the apparatus field of view), and the ultrasensitive behavior of this ecofriendly and flexible material facilitating yoctomolar limit of detection. Besides, 3D‐POWER is proven useful in food and biofluids analysis. It is foreseen that 3D‐POWER can be employed as a valuable platform in (bio)analytical applications.

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“…34,35 The integral equation formalism polarizable continuum model (IEFPCM) was applied in all the DFT calculations to approximate the solid environment, with the dielectric constant set to 4. 36–41…”

Section: Methodsmentioning

confidence: 99%