Vibrational analysis of complexes of urate with IA group metal cations (Li+, Na+ and K+)

Allen, Reeshemah N.; Lipkowski, P.; Shukla, Manoj K.; Leszczyński, Jerzy

doi:10.1016/j.saa.2006.12.040

Cited by 6 publications

(4 citation statements)

References 25 publications

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“…Electronic structure calculations were performed using the Gaussian 03 and 09 software packages. , Structures of the 5-fluorocytosine analogues were optimized using the density functional theory (DFT) method B3LYP, along with the 6-311+G(d,p) basis set. A frequency scaling factor of 0.9679 was used to account for systematic errors arising from the use of calculated harmonic frequencies and also any long-range electron correlation effects. − The B3LYP method in combination with the 6-311+G(d,p) basis set has been shown to be a reliable level of theory with a good compromise between accuracy and cost for smaller systems such as those described here. ,, In addition, this level of theory has previously been shown to produce theoretically generated infrared spectra that approximate IRMPD spectra adequately and has also been shown to outperform other DFT methods, as well as some MP2 calculations. , All geometry optimizations were performed using “tight” force displacement (opt=tight) and energy convergence (scf=tight) specifications. To better approximate electronic energies, single-point calculations were performed at the B2PLYP/aug-cc-pVTZ level of theory on all B3LYP-optimized geometries.…”

Section: Electronic Structure Calculationsmentioning

confidence: 97%

Tridentate Ionic Hydrogen-Bonding Interactions of the 5-Fluorocytosine Cationic Dimer and Other 5-Fluorocytosine Analogues Characterized by IRMPD Spectroscopy and Electronic Structure Calculations

et al. 2011

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Ionic hydrogen-bonding interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, along with the cationic (proton-bound) dimer have been characterized by infrared multiple-photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD action spectra, in combination with calculated spectra and relative energetics, indicate that it is most probable that predominantly a single isomer exists in each experiment. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest-energy isomer convincingly matches the experimental spectrum. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) involving a tridentate ionic hydrogen-bonding interaction. The three sites of intermolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significant calculated binding energy of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, suggests that a tridentate-proton-bound dimer was observed predominantly in the experiments. Comparison of the calculated relative Gibbs free energies (298 K) for this species and several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV.

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Section: Electronic Structure Calculationsmentioning

confidence: 97%

Tridentate Ionic Hydrogen-Bonding Interactions of the 5-Fluorocytosine Cationic Dimer and Other 5-Fluorocytosine Analogues Characterized by IRMPD Spectroscopy and Electronic Structure Calculations

et al. 2011

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“…The analyses are focused on selected vibrational modes: C1 = O1, C4 = O4, C3-O3, and OÀ H bands for all molecules, in addition to C6-H and C3-H for perezone and isoperezone respectively, and C6-S for perezone sulfurs and C3-S for isoperezone sulfurs. The harmonic frequencies, with scaling factor (0.9679) [27,[38][39][40] of the selected modes were compared to the available experimental data. Some selected calculated harmonic frequencies and the descriptions concerning the assignment are listed in Table 5 and were compared with the experimental data.…”

Section: Infrared Spectramentioning

confidence: 99%

Computational Characterization of Perezone, Isoperezone and their Sulfur‐Derivatives: Anti‐inflammatory Activity.

et al. 2019

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Using DFT and in silico methods a theoretical study, to verify the spectroscopically characterization, this in addition to determine the anti‐inflammatory activity of a set of eight sulfur derivatives of perezone and isoperezone was performed. In this sense, conformational studies for the target sulfurs were carried out, in order to obtain the corresponding minimum energy structures. Also, the vibrational frequencies analysis, the magnitude of 1H NMR and 13C NMR spectra for perezone, isoperezone, and its sulfur‐derivatives, obtained by the DFT/B3LYP/6‐311++G(d,p) method correlated satisfactorily with the experimental data. Moreover, the calculation of physicochemical properties, and the prediction of the anti‐inflammatory activity, employing both PASS predictor and docking studies towards COX‐2 for the target compounds, showed that Benzy perezone is a good candidate as a therapeutic agent; finally, the anti‐inflammatory activity of Benzy perezone was evaluated in vivo, showing a similar naproxen activity.

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“…Therefore, the analyses are centered on selected vibrational modes: OÀ H, C1=O1, and C4=O4 for all molecules, in addition to C6À H6, C3À O3 or C3À H3, and C6À O6 for perezone and isoperezone respectively, and C6-S for perezone sulfurs and C3-S for isoperezone sulfurs. The harmonic frequencies, with scaling factor (0.9679) [5,9,[15][16][17] of selected modes were compared to the available experimental data. Some selected calculated harmonic frequencies and the descriptions concerning the assignment are listed in Table 2 and were compared with the experimental and (R)-stereoisomer data.…”

Section: Vibrational Analysismentioning

confidence: 99%

Can (S)‐Stereoisomers of Perezone and Its Derivatives Show Similar Activity to Its (R)‐Stereoisomers? A Computational Characterization and Docking Study

et al. 2021

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Asymmetric synthesis, in particular enantioselectivity, has permitted the assembly of complex molecules; consequently, many clinical trials are going on to compare the efficacy and safety of each pair of enantiomers. In this sense, to envisage the suitability to synthesize the (S)-stereoisomers (hypothetical) of (R)-perezone, (R)-isoperezone and their corresponding sulfurderivatives, in this work, their molecular properties (geometrical, electronic, and spectroscopic) and chemical reactivity descriptors at the theoretical level were compared with the results of the previously studied (R)-stereoisomers, using DFT/ B3LYP/6-311 + + G(d,p), in agreement between both (S/R)enantiomers. Concerning the electronic properties, the 6isopropylsulfanyl-(8S)-perezone (1 a) and 6-benzylsulfanyl-(8R)-perezone (2 c) are hard molecules, in addition (8R)-isoperezone (4), 3-benzylsulfanyl-(8S)-isoperezone (3 c), and 6-benzylsulfanyl-(8S)-perezone (1 c) displayed comparable features to 6benzylsulfanyl-(8R)-perezone (2 c). The docking studies showed that (S)-derivatives exhibited a lower affinity to COX-2 due to steric hindrance. Thus, 2 c showed the highest affinity to COX-2 (ΔG = À 9.53 kcal/mol). The highest differences in ΔG values were shown between 1 c and 2 c, while the lowest differences in ΔG values were displayed by 3 a and 4 a. Finally, the biological activity prediction for the hypothetic (S)-compounds revealed anti-neoplasic activity, consequently their synthesis is recommended.

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Vibrational analysis of complexes of urate with IA group metal cations (Li+, Na+ and K+)

Cited by 6 publications

References 25 publications

Tridentate Ionic Hydrogen-Bonding Interactions of the 5-Fluorocytosine Cationic Dimer and Other 5-Fluorocytosine Analogues Characterized by IRMPD Spectroscopy and Electronic Structure Calculations

Tridentate Ionic Hydrogen-Bonding Interactions of the 5-Fluorocytosine Cationic Dimer and Other 5-Fluorocytosine Analogues Characterized by IRMPD Spectroscopy and Electronic Structure Calculations

Computational Characterization of Perezone, Isoperezone and their Sulfur‐Derivatives: Anti‐inflammatory Activity.

Can (S)‐Stereoisomers of Perezone and Its Derivatives Show Similar Activity to Its (R)‐Stereoisomers? A Computational Characterization and Docking Study

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