Crystal Structure Theory and Applications

Journal Information
ISSN / EISSN : 2169-2491 / 2169-2505
Published by: Scientific Research Publishing, Inc. (10.4236)
Total articles ≅ 91
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Dikima D. Bibelayi, Albert S. Lundemba, Philippe V. Tsalu, Pitchouna I. Kilunga, Jules M. Tshishimbi, Zéphirin G. Yav
Crystal Structure Theory and Applications, Volume 11, pp 1-22; https://doi.org/10.4236/csta.2022.111001

Abstract:
Considerable interest in hydrogen bonding involving chalcogen has been growing since the IUPAC committee has redefined hydrogen bonding. Not only the focus is on unconventional acceptors, but also on donors not discussed before. It has been mentioned in previous studies that the proton of the H-C group could be involved in hydrogen bonding, but with conventional acceptors. In this study, we explored the ability of hydrogen bond formation of Se, S and Te acceptors with the H-C donor using Cambridge Structural Database in conjunction with Ab Initio calculations. In the CSD, there are respectively 256, 6249 and 11 R1,R2,-C=Se, R1,R2,-C=S and R1,R2,-C=Te structures that form hydrogen bonds, in which the N,N groups are majority. Except for C=S acceptor which can form a hydrogen bond with its C, C group, both C=Se and C=Te acceptors could form a hydrogen bond only with N,C and N,N groups. CSD analysis shows very similar d (norm) around -0.04 Å, while DFT-calculated interaction for N,C and N,N groups are also similar. Both interaction distances derived from CSD analysis and DFT-calculated interaction energies demonstrate that the acceptors form stable complexes with H-CF3. Besides hydrogen bonds, dispersion interactions are forces stabilizing the complexes since their contribution can reach 50%. Analysis of intra-molecular geometries and Ab Initio partial charges show that this bonding stems from resonance induced Cδ+=Xδ- dipoles. In many respects, both C=Se, C=S and C=Te are similar to C=S, with similar d (norm) and calculated interaction strengths.
Bechir Ouni, Tarek Larbi, Mosbah Amlouk
Crystal Structure Theory and Applications, Volume 11, pp 23-38; https://doi.org/10.4236/csta.2022.112002

Abstract:
Applying the Density Function Theory (DFT) combined with LCAO basis set and employing the B3LYP hybrid functional, the optimized geometrical parameters, electronic properties, as well as the Infrared and Raman spectra for wurtzite-ZnO structure were investigated. Prior to computing, ZnO thin film prepared by the spray pyrolysis method is characterized by X-ray diffraction using Rietveld refinement. This analysis shows that ZnO has hexagonal wurtzite structure (P63mc) with lattice parameters, a = 3.2467 and c = 5.2151 Å in good agreement with our predicted optimized geometry. Atomic force microscopy (AFM), Raman spectroscopy and UV-Vis-NIR spectrophotometry techniques are used to explore morphological, optical and vibrational properties of the sprayed ZnO thin film. The computed band gap is in excellent agreement with that deduced from UV-Vis transmission . The simulated infrared and Raman spectra were also calculated, and a good agreement with the measured spectra is obtained. Finally, a detailed interpretation of the infrared and Raman spectra is reported.
Albert S. Lundemba, Dikima D. Bibelayi, Philippe V. Tsalu, Peter A. Wood, Jason Cole, Jean S. Kayembe, Zephirin G. Yav
Crystal Structure Theory and Applications, Volume 10, pp 57-69; https://doi.org/10.4236/csta.2021.104005

Abstract:
Growing interest in non-covalent interactions involving chalcogen atoms has been ascribed to their importance in crystal engineering, molecular recognition and macromolecular edifices. The present study is dealing with chalcogen bonds involving divalent Sulphur, Selenium and Tellurium atoms, acting as sigma-hole donors, in small-molecule compounds using the Cambridge Structural Database (CSD) in conjunction with ab initio calculations. Results derived from CSD surveys and computational study revealed that nucleophiles formed complexes with the chalcogen-bond donors R1-X-R2 (X = S, Se or Te). The main forces stabilizing the complexes were chalcogen bonds, enhanced by dispersion interactions. Complexation pattern and energetics show that nucleophile bonding at divalent S, Se and Te atoms is a relatively strong and directed interaction. The bond consists of a charge transfer from a nucleophile atom lone pair to an X-R1 or X-R2 antibonding orbital.
Amal Arouri, Rihab Dridi, Riadh Kefi, Mohamed Faouzi Zid
Crystal Structure Theory and Applications, Volume 10, pp 14-26; https://doi.org/10.4236/csta.2021.101002

Abstract:
The title compound, FeCl4(C5N2H6)(C5N2H5) consists of two [(C5N2H6) (C5N2H5)]+ organic cations and [FeCl4]- anion. The geometry of the iron ion is tetrahedral, formed by four chlorine atoms. The complex was characterized by single crystal X-ray diffraction, Fourier Transform Infrared spectroscopy, thermal analysis and UV-Visible spectroscopy. Hirshfeld surface analysis was also used for understanding the intermolecular interactions in the crystal packing. Single-crystal X-ray diffraction analysis indicates that this complex crystallizes in the monoclinic system, P21/c space group with a = 7.598 (3) Å, b = 13.694 (4) Å, c = 17.105 (5) Å, β = 97.203 (6)° V = 1765.7 (10) Å3 and Z = 4. The [FeCl4]- anion and [(C5N2H6)(C5N2H5)]+ cations are linked through three-dimensional hydrogen-bonding network consisting of N-H...Cl and π-π interactions. Hirshfeld surface analysis and the related 2D fingerprint plots reveal that the complex is dominated by N-H...Cl contacts.
Venkat Hariharan, Jignesh Vanjaria, Arul Chakkaravarthi Arjunan, Gary S. Tompa, HongBin Yu
Crystal Structure Theory and Applications, Volume 10, pp 39-56; https://doi.org/10.4236/csta.2021.103004

Abstract:
In the past studies have shown that the addition of Ge and Sn into Si lattice to form SiGeSn enhances its carrier mobility and band-gap properties. Conventionally SiGeSn epitaxial films are grown using Ultra-High Vacuum (UHV) conditions with pressures ranging from 10-8 torr to 10-10 torr which makes high volume manufacturing very expensive. On the contrary, the use of low-pressure CVD processes (vacuum levels of 10-2 torr to 10-4 torr) is economically more viable and yields faster deposition of SiGeSn films. This study outlines the use of a cost-effective Plasma Enhanced Chemical Vapor Deposition (PECVD) reactor to study the impact of substrate temperature and substrate type on the growth and properties of polycrystalline SiGeSn films. The onset of polycrystallinity in the films is attributed to the oxygen-rich PECVD chamber conditions explained using the Volmer-Weber (3D island) mechanism. The properties of the films were characterized using varied techniques to understand the impact of the substrate on film composition, thickness, crystallinity, and strain.
Tetsuji Moriguchi, Hiromasa Kawata, Venkataprasad Jalli
Crystal Structure Theory and Applications, Volume 10, pp 1-13; https://doi.org/10.4236/csta.2021.101001

Abstract:
The strong photoluminescence properties of europium complexes with organic ligands attracted the attention of many researchers and found a wide range of uses in medical, industrial and biological fields. In this article, four new Tetrakis europium complexes 3a, 3b, 3c and 3d have been prepared using 1-phenyl-4,4,4-trifluoro-1,3-butenedionato ligand and pyridinium, bipyridinium, piperazinium and piperidinium counter cations. These complexes have been characterized by negative FAB-mass. The crystal structures of 3a, 3b, 3c and 3d were determined by single crystal X-ray diffraction analysis. The complex 3a crystallized in monoclinic form, space group P21/n with four molecules in the unit cell. The complex 3b crystallized in monoclinic form, space group P2/n with two complex molecules in the unit cell. The complex 3c crystallized in monoclinic form, space group C2/c with sixteen molecules in the unit cell. The complex 3d crystallized in monoclinic form, space group P21/n with four complex molecules in the unit cell. The complex 3a has 1,2-alternative structure, 3b has 1,3-alternative structure, 3c has cone like structure and 3d has partial cone like structure. The photoluminescence properties of these complexes have been evaluated. Strong red emissions were observed in all four complexes due to 5D0 → 7F2 transition of Europium (III) ions under UV excitation. Four β-diketone ligands acted as strong antenna ligands and transferred the absorbed energy to europium (III) ion effectively; consequently strong red luminescence was observed.
Tetsuji Moriguchi, Masataka Okuyama, Venkataprasad Jalli
Crystal Structure Theory and Applications, Volume 10, pp 27-37; https://doi.org/10.4236/csta.2021.102003

Abstract:
Viologens (N,N'-dimethyl-4,4-bipyridinium) are advanced functional materials, found important applications in electrochromic devices, molecular machines, organic batteries, and carbohydrate oxidation catalysts in alkaline fuel. In this article, we investigated the design, synthesis and photophysical properties of N,N'-dimethyl-2,5-Bis(pyridinium)oxadiazole 4 and its precursor 2,5- Bis(pyridine)oxadiazole 2. The crystal structure and photophysical properties of viologen 4 and precursor 2 have been determined. The viologen molecule 4 crystallized in monoclinic form, space group P21/n with four molecules in unit cell. Precursor molecule 2 also crystalized in monoclinic form, space group C2/c with four molecules in unit cell. From X-rd data, we found three cations in the molecular structure of viologen molecule 4, which is unusual in viologens. In the three-dimensional molecular packing diagram of molecule 4, the three cations and iodate anions are stabilized by C···C, C···I, N···I, N···H, H···I, N—H···I and C—H···I. The dihedral angle between planes having oxadiazole and two benzene rings are 5° and 8°, suggesting the molecule 4 is a slightly strained one. The molecular structure of precursor molecule 2 stabilized by C···C and N···H short contacts between the molecules. The molecule 4 displayed strong absorbance at 315 nm and emissions between 390 - 410 nm.
Yingqi Feng, Yongshou Chen, Yixin Ren, Heng Zhang, Shuang Cao
Crystal Structure Theory and Applications, Volume 09, pp 13-21; https://doi.org/10.4236/csta.2020.92002

Abstract:
The absolute configuration of mitomycin C was determined by X-ray single crystal diffraction (CuKα), and a new crystalline dihydrate of mitomycin C had been prepared. The experiment result provides a definitive answer to the real absolute configuration of mitomycin C and may put an end to the dispute that baffles researchers for decades. At the same time, some contentious structures about the mitomycin C in American Pharmacopoeia USP36-NF31, Chinese pharmacopoeia 2015 edtion and numbers of literatures are marked. The absolute configuration is also verified by 1D (1H and 13C) and 2D (HSQC, HMBC, 1H-1H COSY and NOESY) NMR studies indirectly. Powder X-ray diffraction (PXRD) pattern of the mitomycin C dihydrate is similar to that calculated for it, which suggests that the purity of sample is excellent.
Glodi M. Ndefi, Albert S. Lundemba, Dikima D. Bibelayi, Jason T. Kilembe, Eliakim M. Kambale, Céline W. Kadima, Zéphyrin G. Yav
Crystal Structure Theory and Applications, Volume 09, pp 22-35; https://doi.org/10.4236/csta.2020.92003

Abstract:
Inactivation of Glucokinase (GK) is associated with diabetes. Therefore, design of drugs targeting the GK activator site is currently integrated in the strategy of the diabetes treatment. The present work investigated the affinity of 30 ligands to GK based on molecular docking using the Gold 5.6 program. Glucokinase’s structure was derived from the Protein Data Bank (PDB Code 3S41), while the ligands were seleno, sulfo and oxo derivatives of the co-crystallized carboxamide activator (PDB code: S41). The results of the ligand-protein docking revealed that GK formed thermodynamically stable complexes with all ligands. The main forces stabilizing the complexes are lipophilic interactions, enhanced by hydrogen bonds. Ligand molecular areas responsible for lipophilic and hydrogen bonding contacts with amino acid residues in the allosteric site of GK were evidenced by molecular electrostatic potentials (MEPs). Interestingly, twelve of the S41 derivatives interacted with GK more strongly than the co-crystallized activator, while maintaining the lipophilic contacts with key amino acid residues like Arg63, which are catalytically crucial for therapeutic properties of GK activators (GKAs). It is noteworthy that divalent Se and S atoms were also involved in chalcogen bonds in the GKA site. Those bonds were nearly linear like hydrogen bonds. Such bond directionality should guide the design of pharmacophoric ligands containing chalcogen atoms.
Pierre R. Ndong, Martin Signé, Patrice T. Kenfack, Yves A. Mbiangué, Gouet Bebga, Emmanuel Wenger
Crystal Structure Theory and Applications, Volume 09, pp 36-47; https://doi.org/10.4236/csta.2020.92004

Abstract:
A new organic-inorganic hybrid salt pipéridinium trans-diaquabis(oxalato)- chromate(III) tetrahydrate, (C5H10NH2)[Cr(C2O4)2(H2O)2]·4H2O (1), has been synthesized in water and characterized by FTIR and UV-Vis spectroscopies, elemental and thermal analyses and by single-crystal X-ray diffraction. 1 crystallizes in the orthorhombic non-centrosymmetric space group Cmc21 with the unit cell parameters a = 7.4329(3), b = 9.9356(5), c = 23.6756(11) Å, α = β = γ = 90°, V = 1748.45(14) Å3 and Z = 4. The structure of 1 consists of [Cr(C2O4)2(H2O)2]- mononuclear anions, piperidinium cations and uncoordinated water molecules. The CrIII ion in the complex [Cr(C2O4)2(H2O)2]- is coordinated in a slightly distorted octahedral environment by four O atoms from two chelating oxalate dianions in the equatorial plane, and two O atoms from trans-coordinated water molecules occupying the apical positions. In the crystal, N-H···O and O-H···O hydrogen bond interactions connect the components into a 3-D framework. The IR spectrum of 1 is consistent with the presence of the various molecular building constituents, namely oxalato and aqua ligands, piperidinium cations and solvent water molecules. The UV-Vis spectrum shows two absorption bands around 564 and 416 nm which are compatible with an anionic chromium(III) complex in an octahedral environment. Thermal analysis shows a three-step decomposition of 1, leading to formation of a metal oxide residue.
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