DFT Calculation, Hirshfeld Analysis and X-ray Crystal Structure of Some Synthesized N-alkylated(S-alkylated)-[1,2,4]triazolo[1,5-a]quinazolines

The present work aimed to synthesize 2-methylthio-triazoloquinazoline derivatives and study their X-ray, NMR, DFT and Hirshfeld characteristics. The cyclocondensation of dimethyl-N-cyanodithiocarbonate with 2-hydrazinobenzoic acid hydrochloride resulted in an intermediate, 2-methylthio-[1,2,4]triazolo[1,5-a]quinazolin-5-one (A), which upon treatment with phosphorus pentasulfide, transformed into the 2-methylthio-[1,2,4]triazolo[1,5-a]quinazolin-5-thione (B). Reaction of 2-methylthio-triazoloquinazolines (A&B) with alkyl halides (allyl bromide and ethyl iodide) in basic medium afforded 4-allyl-2-methylthio-[1,2,4]triazolo[1,5-a]quinazolin-5-one (1; N-alkylated) and 5-ethylthio-2-methylthio-[1,2,4]triazolo[1,5-a]quinazoline (2; S-alkylated), respectively. Their molecular and supramolecular structures were presented. Unambiguously, the molecular structures of 1 and 2 were confirmed via NMR and single-crystal X-ray diffraction. The resulting findings confirmed the structures of 1 and 2 and determined their crystalized system (monoclinic system; P21/n space group). Hirshfeld analysis of 1 revealed the importance of the significantly short O…H (6.7%), S…S (1.2%) and C…C (2.8%); however, the short H···H (42.6%), S···H (16.3%) and C···C (4.3%) were showed in 2 by intermolecular interactions in the molecular packing. The 1,2,4-triazoloquinzolines (1&2) were anticipated to be relatively polar compounds with net dipole moments of 2.9284 and 4.2127 Debye, respectively. The molecular electrostatic potential, atomic charge distribution maps and reactivity descriptors for 1 and 2 were also determined. The calculated nuclear magnetic resonance spectra of the targets 1 and 2 were well correlated with the experimental data.

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N-Acetyl Indole Linked to a Fused Triazolo/Thiadiazole Scaffold: Synthesis, Single Crystal X-Ray Structure, and Molecular Insight

Crystals ◽

10.3390/cryst10070600 ◽

2020 ◽

Vol 10 (7) ◽

pp. 600

Author(s):

Ahmed T. A. Boraei ◽

Saied M. Soliman ◽

Sammer Yousuf ◽

Memoona Bibi ◽

Assem Barakat

Keyword(s):

Single Crystal ◽

High Resolution Mass Spectrometry ◽

Atomic Charge ◽

Dft Method ◽

Chemical Yield ◽

Structural Features ◽

Strong Interactions ◽

X Ray ◽

Reactivity Descriptors ◽

Hirshfeld Analysis

The designed target compound of N-acetyl indole linked to a fused triazolo/thiadiazole scaffold was synthesized via the reaction of 4-amino-5-(1H-indol-2-yl)-1,2,4-triazol-3(2H)-thione as the starting material with acetic anhydride under reflux conditions for 6 h, resulting in an excellent and pure chemical yield. The structural features of the designed compound were confirmed using spectroscopic tools including single crystal X-ray diffraction analysis along with 1H-NMR, 13C-NMR, 2D-NMR, and high resolution mass spectrometry. Using Hirshfeld analysis, we determined the molecular packing depends on strong interactions (O···H and N···H) along with weak interactions (S···H, C···H and H···H). The shortest contacts corresponding to the N3···H12 (2.490 Å), N2···H5 (2.503 Å), and O1···H2 (2.490 Å) interactions were confirmed based on the Hirshfeld analysis. The calculated dipole moment was 6.6557 Debye. The atomic charge distribution, molecular electrostatic potential map, and reactivity descriptors are also discussed. The computed NMR spectra of the requisite compound correlated well with the results obtained experimentally. The UV-Vis electronic spectra of the requisite compound were simulated using the TD-DFT method and compared with the experimental data. The different σ→σ*, π→π*, n→σ*, and n→π* donor–acceptor interactions and their interaction energies stabilized the studied system to 9.84, 20.65, 29.33, and 45.82 kcal/mol, respectively.

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New Application of 1,2,4-Triazole Derivatives as Antitubercular Agents. Structure, In Vitro Screening and Docking Studies

Molecules ◽

10.3390/molecules25246033 ◽

2020 ◽

Vol 25 (24) ◽

pp. 6033

Author(s):

Zbigniew Karczmarzyk ◽

Marta Swatko-Ossor ◽

Waldemar Wysocki ◽

Monika Drozd ◽

Grazyna Ginalska ◽

...

Keyword(s):

Degrees Of Freedom ◽

Dipole Moments ◽

Triazole Ring ◽

Antimycobacterial Activity ◽

Docking Studies ◽

Molecular Structures ◽

In Vitro Test ◽

X Ray ◽

Triazole Derivatives

A series of 1,2,4-triazole derivatives were synthesized and assigned as potential anti-tuberculosis substances. The molecular and crystal structures for the model compounds C1, C12, and C13 were determined using X-ray analysis. The X-ray investigation confirmed the synthesis pathway and the assumed molecular structures for analyzed 1,2,4-triazol-5-thione derivatives. The conformational preferences resulting from rotational degrees of freedom of the 1,2,4-triazole ring substituents were characterized. The lipophilicity (logP) and electronic parameters as the energy of frontier orbitals, dipole moments, NBO net charge distribution on the atoms, and electrostatic potential distribution for all structures were calculated at AM1 and DFT/B3LYP/6-311++G(d,p) level. The in vitro test was done against M. tuberculosis H37Ra, M. phlei, M. smegmatis, and M. timereck. The obtained results clearly confirmed the antituberculosis potential of compound C4, which turned out to be the most active against Mycobacterium H37Ra (MIC = 0.976 μg/mL), Mycobaterium pheli (MIC = 7.81 μg/mL) and Mycobacerium timereck (62.6 μg/mL). Satisfactory results were obtained with compounds C8, C11, C14 versus Myc. H37Ra, Myc. pheli, Myc. timereck (MIC = 31.25−62.5 μg/mL). The molecular docking studies were carried out for all investigated compounds using the Mycobacterium tuberculosis cytochrome P450 CYP121 enzyme as molecular a target connected with antimycobacterial activity.

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Synthesis and X-ray powder diffraction characterization of tetra- and hexa-imidazole complexes of magnesium(II)

Powder Diffraction ◽

10.1154/1.3005369 ◽

2008 ◽

Vol 23 (4) ◽

pp. 286-291 ◽

Cited By ~ 1

Author(s):

Norberto Masciocchi ◽

Luigi Garlaschelli ◽

Giulia Peli

Keyword(s):

Powder Diffraction ◽

Molecular Structures ◽

Water Molecules ◽

Powder Diffraction Data ◽

Monoclinic System ◽

Space Group ◽

X Ray ◽

Imidazole Complexes ◽

Full Profile

X-ray powder diffraction data for two ionic salts containing imidazole (Him) complexes of the magnesium(II) ion, [Mg(Him)4(H2O)2]Cl2 and [Mg(Him)6](NO3)2, are reported. Their crystal and molecular structures were determined by simulated annealing and full-profile Rietveld refinement methods. [Mg(Him)4(H2O)2]Cl2 was found to crystallize in the monoclinic system with space group C2/c, a=12.3980(3) Å, b=11.0234(2) Å, c=14.4691(3) Å, and β=107.024(1)°. [Mg(Him)6](NO3)2 crystallizes in the trigonal R-3 space group with a=b=12.4631(4) Å and c=14.9449(6) Å. Both species contain centrosymmetric complexes, and Mg is octahedrally coordinated by six imidazoles, as in [Mg(Him)6](NO3)2, or by four imidazoles and two water molecules, as in [Mg(Him)4(H2O)2]Cl2. Additional analytic, thermogravimetric, calorimetric, and spectroscopic characterizations were also performed.

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Kristall- und Molekülstrukturen von zwei trans-1.2.4.5-Tetraza-3.6-diphospha-cyclohexan-3.6-disulfiden / Crystal and Molecular Structures of Two trans- 1,2,4,5-Tetraza-3,6-diphospha-cyclohexane-3,6-disulfides

Zeitschrift für Naturforschung B ◽

10.1515/znb-1984-0301 ◽

1984 ◽

Vol 39 (3) ◽

pp. 269-274 ◽

Cited By ~ 1

Author(s):

Franz Dirschl ◽

Heinrich Nöth

Keyword(s):

Chair Conformation ◽

Molecular Structures ◽

X Ray Diffraction ◽

Monoclinic System ◽

Torsion Angles ◽

Triclinic Space Group ◽

Space Group ◽

X Ray ◽

Crystal And Molecular Structures ◽

Twist Conformation

The crystal and molecular structures of two trans-1,2,4,5-tetraza-diphospha-3,6-cyclohexane- 3,6-disulfides, 2 and 3, have been determined by X-ray diffraction methods. The 3,6-diphenyl- 1,2,4,5-tetramethyl-derivative 2 crystallizes in the monoclinic system, space group C He. Its P2N 4 heterocycle adopts a twist conformation. In contrast, the hexamethyl derivative 3 is triclinic, space group P1̅, and its ring shows chair conformation. Torsion angles in these two compounds and similar ones reveal less interaction between lone pairs of electrons on adjacent N-atoms in the chair conformation but stronger interaction of those bound to phosphorus. It is suggested that the latter interaction is responsible for the larger N -P -N bond angle (107°) as compared to the smaller one (101°) in the P2N4 rings present in twist conformation.

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Synthesis Single Crystal X-ray Structure DFT Studies and Hirshfeld Analysis of New Benzylsulfanyl-Triazolyl-Indole Scaffold

Crystals ◽

10.3390/cryst10080685 ◽

2020 ◽

Vol 10 (8) ◽

pp. 685 ◽

Cited By ~ 2

Author(s):

Ahmed T. A. Boraei ◽

Saied M. Soliman ◽

Sammer Yousuf ◽

Assem Barakat

Keyword(s):

Density Functional Theory ◽

Dft Calculations ◽

Single Crystal ◽

13C Nmr ◽

Density Functional ◽

Chemical Shifts ◽

Functional Theory ◽

X Ray ◽

Reactivity Descriptors ◽

Hirshfeld Analysis

Benzylsulfanyl-triazolyl-indole scaffold was synthesized through coupling of 4-amino-5-(1H-indol-2-yl)-1,2,4-triazol-3(2H)-thione and benzyl bromide in EtOH under basic conditions (K2CO3). The benzylation direction was deduced from the 13C NMR signal found at 35.09 ppm, assigned for the methylene carbon of the benzyl group, this value indicates that the benzyl group attacks sulfur, not nitrogen. 1H NMR, 13C NMR, COSY, HMQC, HRMS and X-ray single crystal diffraction analysis were used for structure assignment. The desired compound accomplished in good yield. Hirshfeld analysis revealed the importance of the short N...H (1.994–2.595 Ǻ), S…H (2.282 Ǻ) and C…H (2.670 Ǻ) contacts as well as the weak π-π stacking interactions in the molecular packing of benzylthio-triazolyl-indole scaffold. Its electronic and structural aspects were predicted using density functional theory (DFT) calculations and the reactivity descriptors as well. The Uv-Vis spectral bands were assigned based on the time-dependant density functional theory TD-DFT calculations, while the gauge-including atomic orbitals (GIAO) method was used to predict the 1H and 13C NMR chemical shifts.

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Design, Construction, and Characterization of a New Regioisomer and Diastereomer Material Based on the Spirooxindole Scaffold Incorporating a Sulphone Function

Symmetry ◽

10.3390/sym12081337 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1337 ◽

Cited By ~ 1

Author(s):

Abdullah Mohammed Al-Majid ◽

Saied M. Soliman ◽

Matti Haukka ◽

M. Ali ◽

Mohammad Shahidul Islam ◽

...

Keyword(s):

Chemical Shifts ◽

Cycloaddition Reaction ◽

X Ray Diffraction ◽

One Pot ◽

Catalyst Synthesis ◽

X Ray ◽

Reactivity Descriptors ◽

Three Component Reaction ◽

Hirshfeld Analysis ◽

Donor Acceptor

The 1,3-dipolar cycloaddition reaction is one of the most rapid, and efficient protocols to access, and construct highly divergent heterocycle chiral auxiliaries. Free catalyst synthesis of spirooxindole scaffold incorporating sulphone moiety via one pot–three component reaction of 6-chloro-isatin, L-proline, and the phenylvinylsulphone as dienophile is presented. The new regioisomer and diastereomer was isolated by precipitation without the tedious purification step, and then characterized via NMR and single crystal X-ray diffraction analysis. Using Hirshfeld analysis, the analysis of molecular packing was performed. It depended mainly on strong O…H and N…H interactions, and weak H…H, C…H, and Cl…H interactions as well. DFT calculations were used to optimize the experimental X-ray structure, which was found well matched with the calculated one. Reactivity descriptors based on the energies of the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals were calculated. Additionally, the donor–acceptor interactions which stabilized the system via σ–σ*, π→π*, n→σ* and n→π* electron delocalization processes were also computed using NBO calculations. The net interaction energies are 49.96, 235.38, 179.66 and 107.06 kJ/mol, respectively. Additionally, the calculated NMR chemical shifts correlated well with the experimental data (R2=0.99).

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Net atomic charges and molecular dipole moments from spherical-atom X-ray refinements, and the relation between atomic charge and shape

Acta Crystallographica Section A ◽

10.1107/s0567739479000127 ◽

1979 ◽

Vol 35 (1) ◽

pp. 63-72 ◽

Cited By ~ 216

Author(s):

P. Coppens ◽

T. N. Guru Row ◽

P. Leung ◽

E. D. Stevens ◽

P. J. Becker ◽

...

Keyword(s):

Dipole Moments ◽

Atomic Charge ◽

Atomic Charges ◽

Molecular Dipole ◽

X Ray

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Structural Study of a new Compound Based on Acid 1,4-Cyclohexanedicarboxylic (1,4-CDC)

JOURNAL OF ADVANCES IN CHEMISTRY ◽

10.24297/jac.v6i1.969 ◽

2010 ◽

Vol 6 (1) ◽

pp. 891-896

Author(s):

Manel Halouani ◽

M. Dammak ◽

N. Audebrand ◽

L. Ktari

Keyword(s):

Aqueous Solution ◽

Water Molecules ◽

Carboxyl Group ◽

X Ray Diffraction ◽

Compound I ◽

Unit Cell Parameters ◽

Monoclinic System ◽

X Ray ◽

Cell Parameters ◽

Cyclohexanedicarboxylic Acid

One nickel 1,4-cyclohexanedicarboxylate coordination polymers, Ni2 [(O10C6H4)(COO)2].2H2O (I), was hydrothermally synthesized from an aqueous solution of Ni (NO3)2.6H2O, (1,4-CDC) (1,4-CDC = 1,4-cyclohexanedicarboxylic acid) and tetramethylammonium nitrate. Compound (I) crystallizes in the monoclinic system with the C2/m space group. The unit cell parameters are a = 20.1160 (16) Å, b = 9.9387 (10) Å, c = 6.3672 (6) Å, β = 97.007 (3) (°), V= 1263.5 (2) (Å3) and Dx= 1.751g/cm3. The refinement converged into R= 0.036 and RW = 0.092. The structure, determined by single crystal X-ray diffraction, consists of two nickel atoms Ni (1) and Ni (2). Lots of ways of which is surrounded by six oxygen atoms, a carboxyl group and two water molecules.

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Crystal structure determination of the conformation of two bicyclo[3.3.1]nonan-ones

Canadian Journal of Chemistry ◽

10.1139/v85-198 ◽

1985 ◽

Vol 63 (6) ◽

pp. 1166-1169 ◽

Cited By ~ 4

Author(s):

John F. Richardson ◽

Ted S. Sorensen

Keyword(s):

Crystal Structure ◽

Direct Methods ◽

Chair Conformation ◽

Molecular Structures ◽

Boat Conformation ◽

X Ray Diffraction ◽

Space Group ◽

X Ray ◽

Final Agreement

The molecular structures of exo-7-methylbicyclo[3.3.1]nonan-3-one, 3, and the endo-7-methyl isomer, 4, have been determined using X-ray-diffraction techniques. Compound 3 crystallizes in the space group [Formula: see text] with a = 15.115(1), c = 7.677(2) Å, and Z = 8 while 4 crystallizes in the space group P21 with a = 6.446(1), b = 7.831(1), c = 8.414(2) Å, β = 94.42(2)°, and Z = 2. The structures were solved by direct methods and refined to final agreement factors of R = 0.041 and R = 0.034 for 3 and 4 respectively. Compound 3 exists in a chair–chair conformation and there is no significant flattening of the chair rings. However, in 4, the non-ketone ring is forced into a boat conformation. These results are significant in interpreting what conformations may be present in the related sp2-hybridized carbocations.

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β-Ketophosphonates with Pentalenofuran Scaffolds Linked to the Ketone Group for the Synthesis of Prostaglandin Analogs

International Journal of Molecular Sciences ◽

10.3390/ijms22136787 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6787

Author(s):

Constantin I. Tănase ◽

Constantin Drăghici ◽

Miron Teodor Căproiu ◽

Anamaria Hanganu ◽

Gheorghe Borodi ◽

...

Keyword(s):

Lithium Salt ◽

Methyl Esters ◽

Secondary Compounds ◽

Molecular Structures ◽

Keto Group ◽

High Yield ◽

Oxidation Reactions ◽

Prostaglandin Analogues ◽

X Ray ◽

Oxidation Of Alcohols

β-Ketophosphonates with pentalenofurane fragments linked to the keto group were synthesized. The bulky pentalenofurane skeleton is expected to introduce more hindrance in the prostaglandin analogues of type III, greater than that obtained with the bicyclo[3.3.0]oct(a)ene fragments of prostaglandin analogues I and II, to slow down (retard) the inactivation of the prostaglandin analogues by oxidation of 15α-OH to the 15-keto group via the 15-PGDH pathway. Their synthesis was performed by a sequence of three high yield reactions, starting from the pentalenofurane alcohols 2, oxidation of alcohols to acids 3, esterification of acids 3 to methyl esters 4 and reaction of the esters 4 with lithium salt of dimethyl methanephosphonate at low temperature. The secondary compounds 6b and 6c were formed in small amounts in the oxidation reactions of 2b and 2c, and the NMR spectroscopy showed that their structure is that of an ester of the acid with the starting alcohol. Their molecular structures were confirmed by single crystal X-ray determination method for 6c and XRPD powder method for 6b.

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