Five benzoic acid derivatives: Crystallographic study using X-ray powder diffraction, electronic structure and molecular electrostatic potential calculation

Pramanik, Sourav; Dey, Tanusri; Mukherjee, Alok K.

doi:10.1016/j.molstruc.2018.07.090

Cited by 20 publications

(18 citation statements)

References 59 publications

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“…Reports of theoretical bases of MEP and the development of efficient computational methods state that MEP has become an important reactivity index in studies of a large variety of molecular interactions [1]. The usefulness of this theoretical approach in studies and interpretation of chemical, biochemical, and related phenomena is well documented [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Molecular Electrostatic Potential and Chemometric Techniques as Tools to Design Bioactive Compounds

Santos¹,

Oliveira²,

Figueiredo³

et al. 2020

Cheminformatics and Its Applications

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In this chapter, firstly, we briefly review aspects of the approximation of quantum chemistry, molecular electrostatic potential (MEP), and chemometrics techniques, which are accredited as important tools in the development of chemical science and are frequently used in the study and design of bioactive compounds. Ultimately, we use MEP and pattern recognition (PR) techniques as tools to design nitrofuran compounds with biological activity against Trypanosoma cruzi (T. cruzi). PR models (PCA, HCA, KNN, SDA, and SIMCA) were constructed and demonstrated that 23 nitrofurans can be classified into two classes or groups: more active and less active according to their degrees of activity against T. cruzi. Properties such as charge on the N atom of the nitro group (QN1); the difference between the highest occupied molecular orbital (HOMO) energy and the lowest unoccupied molecular orbital (LUMO) energy (GAP energy); molecular representation of structure based on electron diffraction code of signal 5, unweighted (Mor05u); and Moriguchi water-octanol partition coefficient (MlogP) are responsible for the classification into more active and less active studied nitrofurans. It is interesting to notice that these properties represent three distinct classes of interactions between the nitrofurans and the biological receptor: electronic (QN1 and GAP energy), steric (Mor05u), and hydrophobic (MlogP). The results of the application of PR models on the validation set evidenced two nitrofuran compounds (compounds 25 and 30) as more promising for synthesis and biological assays, which in the future can be used to validate our PR models.

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Section: Introductionmentioning

confidence: 99%

Molecular Electrostatic Potential and Chemometric Techniques as Tools to Design Bioactive Compounds

Santos¹,

Oliveira²,

Figueiredo³

et al. 2020

Cheminformatics and Its Applications

View full text Add to dashboard Cite

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“…The electrostatic potential V(r) of a molecule always confirms a significant role in guiding its reactive behavior. For biological as well as organic molecules, MESP gives significant descriptions for such molecules and considered excellent descriptors for their possible interactions [23][24][25][26][27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Mapping molecular electrostatic potential for heme interacting with nano metal oxides

2020

Biointerface Res Appl Chem

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Interacting various living components with several materials in the gaseous nanoscale form has been of great concern as they are utilized in different life aspects. This work is conducted to assess the impact of interacting heme molecule, the main constituent of blood hemoglobin, with various common and non-common divalent molecules such as O2, CO2, CO, MgO, CoO, NiO, CuO and ZnO. Calculations are calculated at DFT high theoretical level using B3LYP/SDD method. In addition, molecular electrostatic potential (MESP) maps are constructed. Results demonstrate that interacting heme with proposed various structures lowers their energies reflecting more stability. However, the addition of non-familiar species to heme makes it more stable that may affect its transportation function for O2 and CO2 in the presence of these toxic materials in the gaseous state. The calculated TDM of the various proposed structures indicates that they are all more reactive than heme, since TDM of all of them are larger than that of pure heme. MESP maps show that extreme negative electrostatic regions are concentrated around C=O group of terminal carboxyl groups suggesting electrophilic interactions to take place there while positive regions are found around Fe central atom and on the circumference of all the proposed structures that are occupied by H atoms increasing the probability of nucleophilic reactions in these regions. Therefore, presence of such hazardous materials in the gaseous nanoscale may impact negatively the transportation function of heme.

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“…An intrinsic limitation of this approach is, however, the requirement to grow single crystals of appropriate size and quality that make them amenable to structure analysis. With the recent advances in X-ray powder diffraction instrumentation coupled with the developments in direct space approaches for structure solution (Pagola et al ., 2000; Harris and Cheung, 2004; Favre-Nicolin and Cerný, 2004; David and Shankland, 2008), ab-initio crystal structure analysis of molecular compounds using powder X-ray diffraction (PXRD) has become a viable alternative in structural crystallography (Arlin et al ., 2014; Watts et al ., 2016; Chatterjee et al ., 2017; Pramanik et al ., 2019). It should, however, be emphasized that structure analysis from PXRD is significantly more challenging than that of its single-crystal counterpart (Harris et al ., 2001) and the task of ab-initio structure determination via PXRD is far more difficult when the molecule possesses considerable flexibility or the asymmetric unit contains multiple molecules ( Z ′ > 1).…”

Section: Introductionmentioning

confidence: 99%

“…In continuation to our ongoing study of structure analysis of benzoic acid derivatives (Pramanik et al ., 2019) using PXRD and the role of weak intermolecular interactions in building supramolecular assembly, we came across the title compound, 5-(trifluoromethyl)-1-phenyl-1H-pyrazole-4-carboxylic acid ( 1 ), which crystallized with Z ′ = 3. Since there are only two reports of structure analysis of molecular compounds crystallizing with Z ′ = 3, the present work was undertaken.…”

Section: Introductionmentioning

confidence: 99%

“…In continuation to our ongoing study of structure analysis of benzoic acid derivatives (Pramanik et al, 2019) using PXRD and the role of weak intermolecular interactions in building supramolecular assembly, we came across the title compound, a) Author to whom correspondence should be addressed. Electronic mail: akm_ju@rediffmail.com 5-(trifluoromethyl)-1-phenyl-1H-pyrazole-4-carboxylic acid (1), which crystallized with Z ′ = 3.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structure analysis of a phenylpyrazole carboxylic acid derivative crystallizing with three molecules in the asymmetric unit (Z′ = 3) using X-ray powder diffraction

Ghosh¹,

Pramanik

Mukherjee

2019

Powder Diffr.

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Crystal structure analysis of a pyrazole carboxylic acid derivative, 5-(trifluoromethyl)-1-phenyl-1H-pyrazole-4-carboxylic acid (1) has been carried out from laboratory powder X-ray diffraction data. The crystal packing in the pyrazole carboxylic acid derivative exhibits an interplay of strong O–H…O, C–H…N and C–H…F hydrogen bonds to generate a three-dimensional molecular packing via the formation of R22(8) and R22(9) rings. Molecular electrostatic potential calculations indicated that carbonyl oxygen, pyrazole nitrogen and fluorine atoms to be the strongest acceptors. The relative contribution of different interactions to the Hirshfeld surface of pyrazole carboxylic acid and a few related structures retrieved from CSD indicates that H…H, N…H and O…H interactions can account for almost 70% of the Hirsfeld surface area in these compounds.

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Five benzoic acid derivatives: Crystallographic study using X-ray powder diffraction, electronic structure and molecular electrostatic potential calculation

Cited by 20 publications

References 59 publications

Molecular Electrostatic Potential and Chemometric Techniques as Tools to Design Bioactive Compounds

Molecular Electrostatic Potential and Chemometric Techniques as Tools to Design Bioactive Compounds

Mapping molecular electrostatic potential for heme interacting with nano metal oxides

Structure analysis of a phenylpyrazole carboxylic acid derivative crystallizing with three molecules in the asymmetric unit (Z′ = 3) using X-ray powder diffraction

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