scholarly journals Intramolecular Hydrogen Bond, Hirshfeld Analysis, AIM; DFT Studies of Pyran-2,4-dione Derivatives

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 896
Author(s):  
Ahmed T. A. Boraei ◽  
Matti Haukka ◽  
Ahmed A. M. Sarhan ◽  
Saied M. Soliman ◽  
Assem Barakat
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Interactions ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Closed Shell ◽  
Monoclinic Crystal ◽  
Molecular Conformations ◽  
X Ray ◽  
Reactivity Descriptors ◽  
Cell Parameters

Intra and intermolecular interactions found in the developed crystals of the synthesized py-ron-2,4-dione derivatives play crucial rules in the molecular conformations and crystal stabili-ties, respectively. In this regard, Hirshfeld calculations were used to quantitatively analyze the different intermolecular interactions in the crystal structures of some functionalized py-ran-2,4-dione derivatives. The X-ray structure of pyran-2,4-dione derivative namely (3E,3'E)-3,3'-((ethane-1,2-diylbis(azanediyl))bis(phenylmethanylylidene))bis(6-phenyl-2H-pyran-2,4(3H)-dione) was determined. It crystallized in the monoclinic crystal system and C2/c space group with unit cell parameters: a = 14.0869(4) Å, b = 20.9041(5) Å, c = 10.1444(2) Å and β = 99.687(2)°. Generally, the H…H, H…C, O…H and C…C contacts are the most important interactions in the molecular packing of the studied pyran-2,4-diones. The molecular structure of these compounds is stabilized by intramolecular O…H hydrogen bond. The nature and strength of the O…H hy-drogen bonds were analyzed using atoms in molecules calculations. In all compounds, the O…H hydrogen bond belongs to closed-shell interactions where the interaction energies are higher at the optimized geometry than the X-ray one due to the shortening in the A…H distance as a con-sequence of the geometry optimization. These compounds have polar characters with different charged regions which explored using molecular electrostatic potential map. Their natural charges, reactivity descriptors and NMR chemical shifts were computed, discussed and com-pared.

Synthesis, growth, structure and characterization of molybdenum zinc thiourea complex crystals

2015 ◽  
Vol 71 (3) ◽  
pp. 285-292 ◽  
Author(s):  
M. Rajasekar ◽  
K. Muthu ◽  
A. Aditya Prasad ◽  
R. Agilandeshwari ◽  
SP Meenakshisundaram
Keyword(s):  
Single Crystal ◽  
Diffraction Analysis ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Second Harmonic ◽  
Morphological Changes ◽  
Strong Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

Single crystals of molybdenum-incorporated tris(thiourea)zinc(II) sulfate (MoZTS) are grown by the slow evaporation solution growth technique. Crystal composition as determined by single-crystal X-ray diffraction analysis reveals that it belongs to the orthorhombic system with space groupPca21and cell parametersa= 11.153 (2),b= 7.7691 (14),c= 15.408 (3) Å,V= 1335.14 (4) Å3andZ= 4. The surface morphological changes are studied by scanning electron microscopy. The vibrational patterns in FT–IR are used to identify the functional group and TGA/DTA (thermogravimetric analysis/differential thermal analysis) indicates the stability of the material. The structure and the crystallinity of the material were confirmed by powder X-ray diffraction analysis and the simulated X-ray diffraction (XRD) closely matches the experimental one with varied intensity patterns. The band gap energy is estimated using diffuse reflectance data by the application of the Kubelka–Munk algorithm. The relative second harmonic generation (SHG) efficiency measurements reveal that MoZTS has an efficiency comparable to that of tris(thiourea)zinc(II) sulfate (ZTS). Hirshfeld surfaces were derived using single-crystal X-ray diffraction data. Investigation of the intermolecular interactions and crystal packingviaHirshfeld surface analysis reveal that the close contacts are associated with strong interactions. Intermolecular interactions as revealed by the fingerprint plot and close packing could be the possible reasons for facile charge transfer leading to SHG activity.

scholarly journals Synthesis, Characterization, and Crystal Structure of Negundoside (2′-p-Hydroxybenzoyl Mussaenosidic Acid)

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Suresh Sharma ◽  
B. D. Gupta ◽  
Rajni Kant ◽  
Vivek K. Gupta
Keyword(s):  
Crystal Structure ◽  
Room Temperature ◽  
Direct Method ◽  
Monoclinic Crystal System ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Monoclinic Crystal ◽  
Full Matrix ◽  
X Ray ◽  
Cell Parameters

The structure of title compound Negundoside (2′-p-hydroxybenzoyl mussaenosidic acid) was established by spectral and X-ray diffraction studies. The compound crystallizes in the monoclinic crystal system with space group P21 having unit cell parameters: a=11.6201 (5) Å, b=9.2500 (4) Å, c=12.2516 (5) Å, β=97.793 (4)°, and Z=2. The crystal structure was solved by direct method using single crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R value of 0.0520 for 3389 observed reflections.

Correspondence: Hydrogen Bond to Gold? 1H NMR is Not a Proof of Hydrogen Bonds in Transition Metal Complexes

2018 ◽  
Author(s):  
Jan Vícha ◽  
Cina Foroutan-Nejad ◽  
Michal Straka
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
X Ray ◽  
Structure And Dynamics ◽  
Hydrogen Bonding Interactions ◽  
Overall Stability ◽  
Gold Compounds ◽  
C Nmr

Illusive Au<sup>I/III</sup>···H hydrogen bonds and their effect on structure and dynamics of molecules have been a matter of debate. While a number of X-ray studies reported gold compounds with short Au<sup>I/III</sup>···H contacts, a solid spectroscopic evidence for Au<sup>I/III</sup>···H bonding has been missing. Recently<a></a><a>, Bakar <i>et al.</i></a> (NATURE COMMUNICATIONS 8:576) reported compound with four short Au···H contacts (2.61­–2.66 Å; X-ray determined). Assuming the central cluster be [Au<sub>6</sub>]<sup>2+</sup>and observing the <sup>1</sup>H (<sup>13</sup>C) NMR resonances at relevant H(C) nuclei deshielded with respect to precursor compound, the authors concluded with reservations that <i>“the present Au···H–C interaction is a kind of “hydrogen bond”, where the [Au<sub>6</sub>]<sup>2+</sup>serves as an acceptor”</i>. Here, we show that the Au<sub>6</sub>cluster in their compound bears negative charge and the Au···H contacts lead to a weak (~1 kcal/mol) auride···hydrogen bonding interactions, though unimportant for the overall stability of<b></b>the molecule. Additionally, computational analysis of NMR chemical shifts reveals that the deshielding effects at respective hydrogen nuclei are not directly related to Au···H–C hydrogen bonding .

scholarly journals Solvent-Dependent Structures of Natural Products Based on the Combined Use of DFT Calculations and 1H-NMR Chemical Shifts

Molecules ◽  
2019 ◽  
Vol 24 (12) ◽  
pp. 2290 ◽  
Author(s):  
Saima H. Mari ◽  
Panayiotis C. Varras ◽  
Atia-tul-Wahab ◽  
Iqbal M. Choudhary ◽  
Michael G. Siskos ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Natural Products ◽  
Chemical Shift ◽  
Intramolecular Hydrogen Bond ◽  
1H Nmr ◽  
Chemical Shifts ◽  
Oh Groups ◽  
X Ray ◽  
Nmr Chemical Shifts ◽  
Intramolecular Hydrogen

Detailed solvent and temperature effects on the experimental 1H-NMR chemical shifts of the natural products chrysophanol (1), emodin (2), and physcion (3) are reported for the investigation of hydrogen bonding, solvation and conformation effects in solution. Very small chemical shift of │Δδ│ < 0.3 ppm and temperature coefficients │Δδ/ΔΤ│ ≤ 2.1 ppb/K were observed in DMSO-d6, acetone-d6 and CDCl3 for the C(1)–OH and C(8)–OH groups which demonstrate that they are involved in a strong intramolecular hydrogen bond. On the contrary, large chemical shift differences of 5.23 ppm at 298 K and Δδ/ΔΤ values in the range of −5.3 to −19.1 ppb/K between DMSO-d6 and CDCl3 were observed for the C(3)–OH group which demonstrate that the solvation state of the hydroxyl proton is a key factor in determining the value of the chemical shift. DFT calculated 1H-NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model, and discrete solute-solvent hydrogen bond interactions, were found to be in very good agreement with the experimental 1H-NMR chemical shifts even with computationally less demanding level of theory. The 1H-NMR chemical shifts of the OH groups which participate in intramolecular hydrogen bond are dependent on the conformational state of substituents and, thus, can be used as molecular sensors in conformational analysis. When the X-ray structures of chrysophanol (1), emodin (2), and physcion (3) were used as input geometries, the DFT-calculated 1H-NMR chemical shifts were shown to strongly deviate from the experimental chemical shifts and no functional dependence could be obtained. Comparison of the most important intramolecular data of the DFT calculated and the X-ray structures demonstrate significant differences for distances involving hydrogen atoms, most notably the intramolecular hydrogen bond O–H and C–H bond lengths which deviate by 0.152 tο 0.132 Å and 0.133 to 0.100 Å, respectively, in the two structural methods. Further differences were observed in the conformation of –OH, –CH3, and –OCH3 substituents.

Crystallization and preliminary X-ray analysis of recombinant full-length human m-calpain

2000 ◽  
Vol 56 (1) ◽  
pp. 73-75 ◽  
Author(s):  
Hajime Masumoto ◽  
Kazuhiro Nakagawa ◽  
Shota Irie ◽  
Hiroyuki Sorimachi ◽  
Koichi Suzuki ◽  
...  
Keyword(s):  
Full Length ◽  
Data Sets ◽  
Cysteine Proteinases ◽  
Asymmetric Unit ◽  
Unit Cell Parameters ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Parameters ◽  
Cooling Conditions

m-Calpain constitutes the prototype of the superfamily of neutral calcium-activated cysteine proteinases. It is a heterodimer consisting of an 80 and a 30 kDa subunit. Recombinant full-length human m-calpain has been crystallized using macro-seeding techniques and vapour-diffusion methods. Two different monoclinic crystal forms (space group P21) were obtained from a solution containing polyethylene glycol (MW = 10 000) as a pecipitating agent. Complete data sets have been collected to 2.3 and 3.0 Å resolution using cryo-cooling conditions and synchrotron radiation. The unit-cell parameters are a = 64.86, b = 133.97, c = 78.00 Å, β = 102.43° and a = 51.80, b = 171.36, c = 64.66 Å, β = 94.78°, respectively. The Vm values indicate that there is one heterodimer in each asymmetric unit.

scholarly journals New Cocrystals of Antipsychotic Drug Aripiprazole: Decreasing the Dissolution through Cocrystallization

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2414
Author(s):  
Wenwen Liu ◽  
Ru Ma ◽  
Feifei Liang ◽  
Chenxin Duan ◽  
Guisen Zhang ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Single Crystal ◽  
Dissolution Rate ◽  
Intermolecular Interactions ◽  
Antipsychotic Drug ◽  
Phosphate Buffer ◽  
Halogen Bond ◽  
X Ray Diffraction ◽  
Dissolution Experiment ◽  
X Ray

Cocrystallization is an important route to tuning the solubility in drugs development, including improving and reducing. Five cocrystals of aripiprazole (ARI) with resveratrol (RSV) and kaempferol (KAE), ARI-RSV, ARI2-RSV1·MeOH, ARI-KAE, ARI-KAE·EtOH, ARI-KAE·IPA, were synthesized and characterized. The single crystal of ARI2-RSV1·MeOH, ARI-KAE·EtOH, and ARI-KAE·IPA were analyzed by single crystal X-ray diffraction (SCXRD). The SCXRD showed multiple intermolecular interactions between API and the coformers, including hydrogen bond, halogen bond, and π-π interactions. Dissolution rate of the two nonsolvate ARI-RSV and ARI-KAE cocrystals were investigated through powder dissolution experiment in pH = 4.0 acetate buffer and pH = 6.8 phosphate buffer. The result showed that RSV could reduce the dissolution rate and solubility of ARI in both medium through cocrystallization. However, KAE improved the dissolution rate and solubility of ARI in pH = 4.0 medium, on the contrary, the two solubility indicators of ARI were both reduced for ARI-KAE cocrystal.

scholarly journals X-ray structure analysis of 3-chloro-7-hydroxy-4- methyl-chroman-2-one

2011 ◽  
Vol 3 (1) ◽  
pp. 34-37
Author(s):  
Sakshi Sharma ◽  
Sabeta Kohli ◽  
Rajnikant Rajnikant
Keyword(s):  
Hydrogen Bond ◽  
Direct Methods ◽  
Dihedral Angles ◽  
Monoclinic Space Group ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Design And Synthesis ◽  
R Factor ◽  
Trifurcated Hydrogen Bond

The title compound crystallizes in the monoclinic space group P21/c, with unit cell parameters a=7.7203(3), b=14.0481(4), c=8.9066(3) Å, â=112.858(5)º, V= 890.11(5) Å3 and Z = 4. The structure has been solved by direct methods and the final R-factor is 0.0433 for 2832 unique reflections. The molecule, as such, is planar and the planarity is confirmed by the magnitude of dihedral angles between the two rings. Extensive Hydrogen-bonding has been observed and chlorine atom is responsible for the formation of trifurcated hydrogen-bond. Trifurcated hydrogen-bond plays a significant role in the design and synthesis of molecules having drug implications.

Correspondence: Hydrogen Bond to Gold? 1H NMR is Not a Proof of Hydrogen Bonds in Transition Metal Complexes

2018 ◽  
Author(s):  
Jan Vícha ◽  
Cina Foroutan-Nejad ◽  
Michal Straka
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
X Ray ◽  
Structure And Dynamics ◽  
Hydrogen Bonding Interactions ◽  
Overall Stability ◽  
Gold Compounds ◽  
C Nmr

Illusive Au<sup>I/III</sup>···H hydrogen bonds and their effect on structure and dynamics of molecules have been a matter of debate. While a number of X-ray studies reported gold compounds with short Au<sup>I/III</sup>···H contacts, a solid spectroscopic evidence for Au<sup>I/III</sup>···H bonding has been missing. Recently<a></a><a>, Bakar <i>et al.</i></a> (NATURE COMMUNICATIONS 8:576) reported compound with four short Au···H contacts (2.61­–2.66 Å; X-ray determined). Assuming the central cluster be [Au<sub>6</sub>]<sup>2+</sup>and observing the <sup>1</sup>H (<sup>13</sup>C) NMR resonances at relevant H(C) nuclei deshielded with respect to precursor compound, the authors concluded with reservations that <i>“the present Au···H–C interaction is a kind of “hydrogen bond”, where the [Au<sub>6</sub>]<sup>2+</sup>serves as an acceptor”</i>. Here, we show that the Au<sub>6</sub>cluster in their compound bears negative charge and the Au···H contacts lead to a weak (~1 kcal/mol) auride···hydrogen bonding interactions, though unimportant for the overall stability of<b></b>the molecule. Additionally, computational analysis of NMR chemical shifts reveals that the deshielding effects at respective hydrogen nuclei are not directly related to Au···H–C hydrogen bonding .

Synthesis, Characterization, Crystal and Molecular Structure Analysis of 1-(2-Chlorophenyl)-3-methyl-4-(p-tolylthio)-1H-pyrazol-5-ol

2019 ◽  
Vol 4 (4) ◽  
pp. 267-272
Author(s):  
Ronak D. Kamani ◽  
Rahul P. Thummar ◽  
Nirav H. Sapariya ◽  
Beena K. Vaghasiya ◽  
Jemin R. Avalani ◽  
...  
Keyword(s):  
Room Temperature ◽  
Crystal And Molecular Structure ◽  
Spectroscopic Techniques ◽  
X Ray Diffraction ◽  
Monoclinic Crystal ◽  
Methyl Group ◽  
X Ray ◽  
Cell Parameters ◽  
Crystal Class ◽  
Molecular Structure Analysis

The synthesis of a novel tolylthiopyrazol bearing methyl group has been achieved by transition metal free N-chlorosuccinimide mediated direct sulfenylation of 1-aryl pyrazolones at room temperature. The product obtained was characterized by spectroscopic techniques and finally confirmed by X-ray diffraction studies. The compound 1-(2-chlorophenyl)-3-methyl-4-(p-tolylthio)-1H-pyrazol-5-ol (m.f. C17H15N2OSCl) crystallizes in monoclinic crystal class in space group P21/c with cell parameters a = 9.6479(5) Å, b = 15.1233(8) Å, c = 11.4852(6) Å, β = 108.374(2)°, V=1590.4(2) Å3 and Z = 4. The final residual factor R1 = 0.0499.

Three new amidophosphoric acid esters with a P(O)[OCH2C(CH3)2CH2O] segment: X-ray diffraction, DFT, AIM and Hirshfeld surface investigations of bi- and tri-furcated (three and four-center) hydrogen bond interactions

2020 ◽  
Vol 235 (3) ◽  
pp. 69-84 ◽  
Author(s):  
Marjan Sadat Bozorgvar ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Closed Shell ◽  
Hirshfeld Surface ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Amidophosphoric Acid ◽  
Acid Esters

AbstractStructural and packing features of three new amidophosphoric acid esters having a common part XP(O)[OCH2C(CH3)2CH2O], with X = [(CH3)3CNH] (1), [(CH3)2HCNH] (2) and [C6H11(CH3)N] (3), are investigated by single crystal X-ray diffraction. The results illustrate that the compounds 1 and 3 crystallize with one independent molecule in the asymmetric unit; whereas, for 2, the compound crystallizes with three independent molecules in the asymmetric unit. The crystal structures are mostly stabilized via tri-furcated hydrogen bond interactions (C–H · · ·)2(N–H · · ·)O=P in 1 and (C–H · · ·)3O=P in 3, while the stability is given by bi-furcated hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P in 2. For a better understanding of the nature, strength and energetics associated with the formation of the quoted multi-center hydrogen bond interactions, the Natural Bond Order (NBO) method from Density Functional Theory (DFT) and a topological analysis by means of Atoms In Molecules (AIM) and Hirshfeld surface procedures were performed. These studies reveal that the studied multi-center hydrogen bond interactions of the type O · · · H are favoured in the crystal packing displaying enrichment ratios larger than unity. The detailed nature of the different interactions in these multi-center interactions is studied for the first time in such compounds. It is shown that the N–H · · · O interaction is rather non-covalent closed-shell whereas the C–H · · · O interaction is more van der Waals closed-shell. Stronger hydrogen bond interactions are observed for a lower multiple H-atom acceptor oxygen in three-center hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P of 2 than for four-center interactions in 1 [i.e. (C–H · · ·)2(N–H · · ·)O=P] and 3 [i.e. (C–H · · ·)3O=P]. The better H-atom acceptability of the O atom of P=O compared with the esteric O atom is explained by the richer s-character of the hybrid orbital of the O atom acceptor of P=O coupled with enhance of the polarization and charge. The obtained results are also confirmed by Molecular Electrostatic Potential (MEP).

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