Determination of the absolute configuration of conformationally flexible molecules by simulation of chiro-optical spectra: a case study

Mancinelli, Michele; Franzini, Roberta; Renzetti, Andrea; Marotta, Emanuela; Villani, Claudio; Mazzanti, Andrea

doi:10.1039/c9ra03526e

Cited by 11 publications

(6 citation statements)

References 59 publications

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“…Subsequent simulation of electronic circular dichroism of the compounds was carried out using TD-DFT/M062x/6-31G+(d,p)/SMD/water. Selection of these parameters was due the flexibility of the molecules and their side chains, for which the implemented method showed to be suitable for this purpose [24]. As shown in Figure 2 and Figure S6, ECD spectra of all compounds revealed a negative cotton effect (CE) around 225 nm and a positive cotton effect around 200 nm, and all simulated spectra were in good agreement with experimentally recorded ones.…”

Section: Determination Of Absolute Configuration Of Isolated Maas By supporting

confidence: 54%

Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects

et al. 2019

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Mycosporine-like amino acids (MAAs) are water-soluble metabolites, reported to exhibit strong UV-absorbing properties. They have been found in a wide range of marine organisms, especially those that are exposed to extreme levels of sunlight, to protect them against solar radiation. In the present study, the absolute configuration of 14 mycosporine-like-amino acids was determined by combining the results of electronic circular dichroism (ECD) experiments and that of advanced Marfey’s method using LC-MS. The crystal structure of a shinorine hydrate was determined from single crystal X-ray diffraction data and its absolute configuration was established from anomalous-dispersion effects. Furthermore, the anti-aging and wound-healing properties of these metabolites were evaluated in three different assays namely the inhibition of collagenase, inhibition of advanced glycation end products (AGEs) and wound healing assay (scratch assay).

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Section: Determination Of Absolute Configuration Of Isolated Maas By supporting

confidence: 54%

Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects

et al. 2019

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“…The relatively small value of Δ S ‡ indicates a negligible influence of temperature on the values of Δ G ⧧ . The approximate 3:1 ratio after 1 h at 97 °C indicates a t 1/2 for racemization of 1.7 h, which corresponds to a Δ G ⧧ for racemization of ∼28 kcal/mol according to Erying equation . This agrees well with the DFT-computed Δ G ‡ of 26.5 kcal/mol (Figure S1E).…”

Section: Resultsmentioning

confidence: 99%

Stable Axially Chiral Isomers of Arylnaphthalene Lignan Glycosides with Antiviral Potential Discovered from Justicia procumbens

Zhao

et al. 2021

J. Org. Chem.

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Arylnaphthalene lignans (ANLs) were known to have axial chirality due to the biphenyl skeleton with hindered rotation at the single bond. However, the stable ANL atropisomers have not been isolated from nature until the present study. Phytochemical separation of the methanol extract of the stems and barks of Justicia procumbens led to the isolation of 11 ANL glycosides including four pairs of new atropisomers with stable confirmations at room temperature. Their structures were deduced from elucidation of the extensive spectral data, and their absolute configurations were determined by the circular dichroism, electronic circular dichroism, and X-ray methods as well as the total synthesis of one pair of the atropisomers. The ANL compounds were evaluated for their antiviral potential, and it was found that they displayed great antiviral activity discrepancy between a pair of atropisomers due to the geometric orientation. The 1′P-oriented atropisomers showed much more significant antiviral potency than their corresponding 1′M-oriented counterparts. The biological activity discrepancy caused by the axial chirality will not only inspire synthetic design of novel ANL atropisomers to enrich the structural diversity, but also provide important hints to direct the synthetic approaches toward the antiviral drug development of ANL compounds.

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“…DFT with the Minnesota hybrid functional M06-2X , and the triple zeta valence polarized basis set def2-TZVP , are employed throughout. The M06-2X functional has been shown to outperform B3LYP in energy calculations and in the computation of C–NO 2 BDEs for a wide range of organic molecules. − For geometry optimizations, M06-2X seems to yield results of similar accuracy to those obtained using B3LYP. ,, With the additional knowledge that M06-2X is commonly employed in studies on energetic materials, ,,,, applying it for the current work seems appropriate. To produce reliable vibrational frequencies, it proved necessary to employ a larger integration grid than the standard choice in NWChem.…”

Section: Methodsmentioning

confidence: 92%

“… 85 − 88 For geometry optimizations, M06-2X seems to yield results of similar accuracy to those obtained using B3LYP. 57 , 89 , 90 With the additional knowledge that M06-2X is commonly employed in studies on energetic materials, 10 , 28 , 40 , 52 , 91 applying it for the current work seems appropriate. To produce reliable vibrational frequencies, it proved necessary to employ a larger integration grid than the standard choice in NWChem.…”

Section: Methodsmentioning

confidence: 99%

Unimolecular Decomposition Reactions of Picric Acid and Its Methylated Derivatives─A DFT Study

et al. 2022

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To handle energetic materials safely, it is important to have knowledge about their sensitivity. Density functional theory (DFT) has proven a valuable tool in the study of energetic materials, and in the current work, DFT is employed to study the thermal unimolecular decomposition of 2,4,6-trinitrophenol (picric acid, PA), 3-methyl-2,4,6-trinitrophenol (methyl picric acid, mPA), and 3,5-dimethyl-2,4,6-trinitrophenol (dimethyl picric acid, dmPA). These compounds have similar molecular structures, but according to the literature, mPA is far less sensitive to impact than the other two compounds. Three pathways believed important for the initiation reactions are investigated at 0 and 298.15 K. We compare the computed energetics of the reaction pathways with the objective of rationalizing the unexpected sensitivity behavior. Our results reveal a few if any significant differences in the energetics of the three molecules, and thus do not reflect the sensitivity deviations observed in experiments. These findings point toward the potential importance of crystal structure, crystal morphology, bimolecular reactions, or combinations thereof on the impact sensitivity of nitroaromatics.

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Determination of the absolute configuration of conformationally flexible molecules by simulation of chiro-optical spectra: a case study

Abstract: The absolute configuration (AC) assignment of two very flexible organic molecules by TD-DFT simulation of ECD spectra is evaluated by modifying the calculation level in the various steps of the AC assignment process.

Cited by 11 publications

References 59 publications

Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects

Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects

Stable Axially Chiral Isomers of Arylnaphthalene Lignan Glycosides with Antiviral Potential Discovered from Justicia procumbens

Unimolecular Decomposition Reactions of Picric Acid and Its Methylated Derivatives─A DFT Study

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