scholarly journals Synthesis, X-Ray Crystallography, Thermal Analysis, and DFT Studies of Ni(II) Complex with 1-Vinylimidazole Ligand

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Fatih Şen ◽  
Ramazan Şahin ◽  
Muharrem Dinçer ◽  
Ömer Andaç ◽  
Murat Taş
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Basis Sets ◽  
Mulliken Charge ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Density Functional Theory

The paper presents a combined experimental and computational study of hexa(1-vinylimidazole)Ni(II) perchlorate complex. The complex was prepared in the laboratory and crystallized in the monoclinic space group P21/n with a=8.442(5), b=13.686(8), c=16.041(9) Å, α=γ=90, β=96.638(5), and Z=1. The complex has been characterized structurally (by single-crystal X-Ray diffraction) and its molecular structure in the ground state has been calculated using the density functional theory (DFT) methods with 6-31G(d) and LanL2DZ basis sets. Thermal behaviour and stability of the complex were studied by TGA/DTA analyses. Besides, the nonlinear optical effects (NLO), molecular electrostatic potential (MEP), frontier molecular orbitals (FMO), and the Mulliken charge distribution were investigated theoretically.

scholarly journals 2-Hetaryl-1,3-tropolones based on five-membered nitrogen heterocycles: synthesis, structure and properties

2015 ◽  
Vol 11 ◽  
pp. 2179-2188 ◽  
Author(s):  
Yury A Sayapin ◽  
Inna O Tupaeva ◽  
Alexandra A Kolodina ◽  
Eugeny A Gusakov ◽  
Vitaly N Komissarov ◽  
...  
Keyword(s):  
Density Functional ◽  
Acetic Acid Solution ◽  
Intramolecular Proton Transfer ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
Derivatives Of

A series of derivatives of 2-hetaryl-1,3-tropolone (β-tropolone) was prepared by the acid-catalyzed reaction of 2-methylbenzoxazoles, 2-methylbenzothiazoles and 2,3,3-trimethylindoline with 3,4,5,6-tetrachloro-1,2-benzoquinone. The molecular structures of the three representative compounds were determined by X-ray crystallography. In crystal and (as shown by the DFT PBE0/6-311+G** calculations) in solution, 2-hetaryl-4,5,6,7-tetrachloro- and 2-hetaryl-5,6,7-trichloro-1,3-tropolones exist in the NH-tautomeric form with a strong resonance-assisted intramolecular N–H···O hydrogen bond. The mechanism of the formation of 1,3-tropolones in the reaction of methylene-active five-membered heterocycles with o-chloranil in acetic acid solution has been studied using density functional theory (DFT) methods. The reaction of 2-(2-benzoxa(thia)zolyl)-5,6,7-trichloro(4,5,6,7-tetrachloro)-1,3-tropolones with alcohols leads to the contraction of the seven-membered tropone ring with the formation of 2-(2-benzoxa(thia)zolyl)-6-alkoxycarbonylphenols. The molecular structure of 2-(2-ethoxycarbonyl-6-hydroxy-3,4,5-trichlorophenyl)benzoxazole has been determined by X-ray diffraction. 2-(2-Benzoxa(thia)zolyl)-6-alkoxycarbonylphenols display intense green fluorescence with anomalous Stokes shifts caused by the excited state intramolecular proton transfer (ESIPT) effects.

Comparison of different theory models and basis sets for the calculation of FbC-M10Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

2013 ◽  
Vol 17 (05) ◽  
pp. 376-383 ◽  
Author(s):  
Jong-Kil Park ◽  
Sang Joon Choe
Keyword(s):  
Density Functional ◽  
Molecular Geometry ◽  
Basis Sets ◽  
Normal Coordinate ◽  
Dft Methods ◽  
Functional Theory ◽  
X Ray ◽  
Bond Lengths ◽  
X Ray Crystallography ◽  
Isomeric Pairs

Various density functional theory (DFT) methods with different basis sets to predict the molecular geometry of FbC-M10Iso-Bn macrocycle, a chlorin-isoimide, are compared in this study. DFT methods, including M06-2X, B3LYP, LSDA, B3PW91, PBEPBE, and BPV86, are examined. Different basis sets, such as 6-31G*, 6-31+G (d, p), 6-311+G (d, p), 6-311++G (d, p), cc-PVDZ, cc-PVTZ, and cc-PVQZ are also considered. The examined hybrid DFT methods are in agreement with the geometry of X-ray crystallography available for comparison. B3LYP/cc-PVDZ level is particularly consistent with available X-ray crystallography in terms of predicting the geometries of FbC-M10Iso-Bn. Geometries of chlorin-imide and chlorin-isoimide isomeric pairs are described through B3LYP/cc-PVDZ method. The bond lengths of chlorin-isoimide, specifically C13–C14, C14–C15, and C2–C3, increase as bond overlap index decreases because of charge transfer. β-β bond lengths (C2–C3 bond lengths) with a three-substituent benzylcarbamoyl group also increase as bond overlap index decreases compared with other molecules. The bond lengths of chlorin-imide are smaller than those of chlorin-isoimide. Angles with β-β bond lengths, specifically C2–C3–C4 in ring A, also decrease with a three-substituent benzylcarbamoyl group; however, the angles in C1–C2–C3 increase. Potential energy on the surfaces of the chlorin-imide and chlorin-isoimide isomeric pairs is optimized by calculating the total and relative energies at B3LYP/cc-PVDZ level. Results indicate that chlorin-imides are more stable than chlorin-isoimides. Normal-coordinate structural decomposition shows that chlorin-imides exhibit greater deformation than chlorin-isoimides except for FbC-M10Iso-Ph.

Synthesis of [Re2Cl4(O)2(µ-O)(3,5-lut)4] and investigation of its structure via X-ray and spectroscopic measurements and DFT calculations

2014 ◽  
Vol 68 (5) ◽  
Author(s):  
Sławomir Michalik ◽  
Jan Małecki ◽  
Natalia Młynarczyk
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Study ◽  
Dft Method ◽  
Time Dependent ◽  
Electronic Transitions ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
The Density Functional Theory

AbstractA combined experimental and computational study of the dinuclear rhenium(V) complex containing (ReO)2(µ-O) core is presented in this article. The solid-state [Re2Cl4(O)2(µ-O)(3,5-lut)4] (3,5-lut = 3,5-dimethylpyridine) complex was characterised structurally (by single crystal X-ray diffraction) and spectroscopically (by IR, NMR, UV-VIS). The electronic structure was examined using the density functional theory (DFT) method. The spin-allowed electronic transitions were calculated using the time-dependent DFT method, and the UV-VIS spectrum was discussed.

A tale of hydrogen abstraction, initially detectedviaX-ray diffraction

2014 ◽  
Vol 70 (3) ◽  
pp. 250-255 ◽  
Author(s):  
Alice K. Hui ◽  
Chun-Hsing Chen ◽  
Adam M. Terwilliger ◽  
Richard L. Lord ◽  
Kenneth G. Caulton
Keyword(s):  
Solid State ◽  
Density Functional ◽  
Computational Study ◽  
Hydrogen Abstraction ◽  
Open Shell ◽  
X Ray Diffraction ◽  
Neutral Radical ◽  
X Ray ◽  
Chloride Ligand ◽  
Synthetic Reaction

Reaction of a bis-tetrazinyl pyridine pincer ligand, btzp, with a vanadium(III) reagent gives not a simple adduct but dichlorido{3-methyl-6-[6-(6-methyl-1,2,4,5-tetrazin-3-yl-κN2)pyridin-2-yl-κN]-1,4-dihydro-1,2,4,5-tetrazin-1-yl-κN1}oxidovanadium(IV) acetonitrile 2.5-solvate, [V(C11H10N9)Cl2O]·2.5CH3CN, a species which X-ray diffraction reveals to have one H atom added to one of the two tetrazinyl rings. This H atom was first revealed by a short intermolecular N...Cl contact in the unit cell and subsequently established, from difference maps, to be associated with a hydrogen bond. One chloride ligand has also been replaced by an oxide ligand in this synthetic reaction. This formula for the complex, [V(Hbtzp)Cl2O], leaves open the question of both ligand oxidation state and spin state. A computational study of all isomeric locations of the H atom shows the similarity of their energies, which is subject to perturbation by intermolecular hydrogen bonding found in X-ray work on the solid state. These density functional calculations reveal that the isomer with the H atom located as found in the solid state contains a neutral radical Hbtzp ligand and tetravalentd1V center, but that these two unpaired electrons are more stable as an open-shell singlet and hence antiferromagnetically coupled.

Powder X-ray diffraction of bendamustine hydrochloride monohydrate, C16H22Cl2N3O2Cl·H2O

2018 ◽  
Vol 34 (1) ◽  
pp. 74-75
Author(s):  
J. A. Kaduk ◽  
K. Zhong ◽  
T. N. Blanton ◽  
S. Gates-Rector ◽  
T. G. Fawcett
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Argonne National Laboratory ◽  
Lymphocytic Leukemia ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrochloride Monohydrate

Bendamustine hydrochloride monohydrate (marketed as Treanda®) is a nitrogen mustard purine analog alkylator used in the treatment of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphomas. Commercial bendamustine hydrochloride monohydrate crystallizes in the monoclinic space group P21/c (14), with a = 4.71348(4) Å, b = 47.5325(3) Å, c = 8.97458 (5) Å, β = 96.6515(8)°, V = 1997.161(23) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database yielded a previously reported crystal structure (Allen, 2002), which did not include hydrogens (Reck, 2006). In this work, the sample was ordered from Santa Cruz Biotechnology, and analyzed as received. The room-temperature crystal structure was refined using synchrotron (λ = 0.413896 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and recalculated during the refinement. The diffraction data were collected on beamline BM-11 at the Advanced Photon Source, Argonne National Laboratory. Figure 1 shows the powder X-ray diffraction pattern of the compound. The pattern is included in the Powder Diffraction File as entry 00-064-1508.

Metal-selenolate chemistry: stereochemistry of adamantane-type clusters of formula [(μ-SePh)6(MSePh)4]2− (M = Zn and Cd)

1992 ◽  
Vol 70 (3) ◽  
pp. 792-801 ◽  
Author(s):  
Jagadese J. Vittal ◽  
Philip A. W. Dean ◽  
Nicholas C. Payne
Keyword(s):  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Bridging Ligands ◽  
Triclinic Space Group ◽  
Space Group ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Minimum Number

The structures of three tetramethylammonium salts containing anions of formula [(μ-SePh)6(MSePh)4]2− (M = Zn and Cd) were determined by single crystal X-ray diffraction techniques. The Zn salt crystallizes in different space groups depending upon the solvent combination used in the synthesis. Thus crystals of (Me4N)2[Zn4(SePh)10], 1, grown from a mixture of methanol, acetonitrile, and acetone are triclinic, space group [Formula: see text] with cell dimensions a = 13.214(2), b = 23.859(2), c = 13.072(1) Å, α = 91.134(8), β = 113.350(8), γ = 79.865(9)°, and Z = 2. In the absence of acetone, a solvated crystal (Me4N)2[Zn4(SePh)10]•CH3CN, 2, is formed, which belongs to the monoclinic space group P21/n with a = 14.248(1), b = 39.722(2), c = 13.408(1) Å, β = 97.132(5)°, and Z = 4. The Cd salt (Me4N)2[Cd4(SePh)10], 3, crystallizes in the monoclinic space group P21/c, with a = 20.830(2), b = 14.282(1), c = 25.872(1) Å, β = 99.626(6)°, and Z = 4. These three salts are the first examples of homoleptic, tetranuclear selenolatometal(II) anions with (μ-Se)6M4 cages of adamantane-type stereochemistry. In each case the phenyl substituents of the bridging ligands adopt the configuration [aae, aae, aee, aee], which has the minimum number of two 1,3-axial–axial non-bonding substituent interactions. Keywords: selenolate complexes, synthesis, X-ray crystallography, isomerism, adamantane stereochemistry.

A complementary experimental and computational study of loxapine succinate and its monohydrate

2013 ◽  
Vol 69 (11) ◽  
pp. 1273-1278 ◽  
Author(s):  
Rajni M. Bhardwaj ◽  
Blair F. Johnston ◽  
Iain D. H. Oswald ◽  
Alastair J. Florence
Keyword(s):  
Succinic Acid ◽  
Powder Diffraction ◽  
Density Functional ◽  
Crystal Packing ◽  
Computational Study ◽  
Geometry Optimization ◽  
Global Optimum ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fixed Cell

The crystal structures of loxapine succinate [systematic name: 4-(2-chlorodibenzo[b,f][1,4]oxazepin-11-yl)-1-methylpiperazin-1-ium 3-carboxypropanoate], C18H19ClN3O+·C4H5O4−, and loxapine succinate monohydrate {systematic name: bis[4-(2-chlorodibenzo[b,f][1,4]oxazepin-11-yl)-1-methylpiperazin-1-ium] succinate succinic acid dihydrate}, 2C18H19ClN3O+·C4H4O42−·C4H6O4·2H2O, have been determined using X-ray powder diffraction and single-crystal X-ray diffraction, respectively. Fixed cell geometry optimization calculations using density functional theory confirmed that the global optimum powder diffraction derived structure also matches an energy minimum structure. The energy calculations proved to be an effective tool in locating the positions of the H atoms reliably and verifying the salt configuration of the structure determined from powder data. Crystal packing analysis of these structures revealed that the loxapine succinate structure is based on chains of protonated loxapine molecules while the monohydrate contains dispersion stabilized centrosymmetric dimers. Incorporation of water molecules within the crystal lattice significantly alters the molecular packing and protonation state of the succinic acid.

scholarly journals Synthesis, crystal and molecular structure, vibrational spectroscopic, DFT study and activity evaluation of 4-(2-chlorobenzyl)-1-(4-hydroxy -3-((4-hydroxypiperidin-1-yl)methyl-5-methoxyphenyl)-[1,2,4] triazolo[4,3-a]quinazolin-5(4H)-one

2021 ◽  
Author(s):  
Qingmei Wu ◽  
Wenjun Ye ◽  
Qian Guo ◽  
Tianhui Liao ◽  
Weike Liao ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Title Compound ◽  
Density Functional ◽  
Frontier Molecular Orbital ◽  
Geometrical Parameters ◽  
X Ray Diffraction ◽  
Mannich Reactions ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ft Ir

In current work, we have firstly synthesized 4-(2-chlorobenzyl)-1-(4-hydroxy-3- ((4-hydroxypiperidin-1-yl)methyl)-5-methoxyphenyl)-[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one (1) by ring-opening, cyclization, substitution, doamine condensation and Mannich reactions. The structural properties of the title compound 1 were explored using spectroscopy (1H NMR, 13C NMR, MS and FT-IR) and X-ray crystallography method. The single-crystal structure confirmed by X-ray diffraction was consistent with the molecular structure optimized by density functional theory (DFT) calculation at B3LYP/6-311G (2d, p) level of theory. The geometrical parameters, molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analysis were performed by DFT using the B3LYP/6-311G (2d, p) method. Molecular docking has shown favorable interaction between the title compound 1 and SHP2 protein. The inhibitory activity of target compound 1 on SHP2 protein at 10 μM is better than the reference compound (SHP244).

scholarly journals Experimental and computational investigations of a cadmium(II) mononuclear complex with 2,6-Bis(3,5-dimethyl-N-pyrazolyl)pyridine (bdmpp) and selenocyanate as ligands

2009 ◽  
Vol 7 (3) ◽  
pp. 402-409 ◽  
Author(s):  
Sinem Odabaşıoğlu ◽  
Raif Kurtaran ◽  
Akin Azizoglu ◽  
Hülya Kara ◽  
Sevi Öz ◽  
...  
Keyword(s):  
Differential Scanning Calorimetry ◽  
Mononuclear Complex ◽  
Monoclinic Space Group ◽  
Ab Initio Method ◽  
Cadmium Atom ◽  
X Ray Diffraction ◽  
Scanning Calorimetry ◽  
Dft Methods ◽  
X Ray ◽  
Distorted Octahedral

AbstractA new cadmium (II) complex, [Cd(bdmpp)(SeCN)2(H2O)] (1) (where bdmpp = 2,6-bis(3,5-dimethyl-N-pyrazolyl)pyridine), has been synthesized and characterized by elemental and spectral (IR, 1H-NMR and 13C-NMR, UV-Vis) analyses, differential scanning calorimetry, and single crystal X-ray diffraction studies. X-ray analysis showed that the structure was crystallized in the monoclinic space group Cc with a = 9.031(2), b = 13.884(3), c = 16.910(3) Å, and Z = 4. The geometry around the cadmium atom is distorted octahedral with a CdN3Se2O setup. The N atoms of the SeCN are engaged in two strong intermolecular H-bonding interactions forming a 3D supramolecular polymeric network. The geometry and vibrational frequencies of complex 1 computed with the DFT methods (BLYP, B3LYP, B3PW91, MPW1PW91) are in better agreement with experiment than those obtained with the ab-initio method except for the bond angles. The molecular orbital diagram has been also calculated and visualized at the B3LYP/LanL2DZ level of theory.

scholarly journals A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

Inorganics ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 119 ◽  
Author(s):  
Hardin ◽  
Ellington ◽  
Nguyen ◽  
Rheingold ◽  
Tschumper ◽  
...  
Keyword(s):  
Self Assembly ◽  
Density Functional ◽  
Computational Study ◽  
Halogen Bond ◽  
Normal Modes ◽  
Halogen Bonding ◽  
Building Blocks ◽  
Molecular Assembly ◽  
X Ray ◽  
X Ray Crystallography

Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C–H···O or C–H···N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly.

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