Vol 60, No 11 (2019)
- Year: 2019
- Articles: 21
- URL: https://journals.rcsi.science/0022-4766/issue/view/9831
Article
Understanding Hydrogen Bonding in Terms of the Theory of Generalized Charges
Abstract
New expressions for the energy and the length of interatomic bonds depending on atomic number, bond order, and angular momentum are derived within the theory of generalized charges, which is an asymptotic approximation for interatomic forces in the quantum-statistical model of a multicomponent electron gas. In particular, expressions for bond energies and bond lengths in hydrides are derived as functions of atomic numbers. As a consequence of the developed theory, hydrogen bonding is viewed as a one-electron covalent bonding, which is used to derive corresponding quantitative relations. The energy of hydrogen bonding cannot be lower than some specific value determined by the charge of the bonded atom. The region of existence of hydrogen bonding is established. The boundaries of the region are determined by the classes of substances distinguished by their ability to form hydrogen bonding. Quantitative estimations are used to explain the ability or inability of substances containing electronegative atoms to dissolve in water.
A Quantum Chemical Study of Silicon-Substituent Bonds in Three-Coordinated Silicon Compounds
Abstract
Spatial and electronic structures of three-coordinated silicon molecules are calculated within MP2/6-311G(2d,p) and HF/6-311++G(3df,3pd) methods using the PC GAMESS-Firefly software package. AIM and NBO methods are used to determine main characteristics of silicon-substituent bonds in these molecules. Topologically, Si-C, Si-N, Si-Cl, and Si-O bonds may be characterized as “intermediate” bonds, and Si-Si bonds are characterized as covalent bonds.
Re- and Cs-Copromoted Silver Catalysts for Ethylene Epoxidation: A Theoretical Study
Abstract
The effect of Re- and Cs-copromotion of Ag catalysts for ethylene epoxidation is studied computationally using density functional theory approach. The models reflecting Re involvement in the form of oxyanion and as a component of Ag-Re alloys are considered. The synergistic effect of Cs and Re is caused by the formation of the CsReOx species, with Cs stabilizing the Re oxyanion to promote ethylene epoxidation over the Ag catalysts. The role of Re is proposed to be related to altering the electron density distribution, compensating oxygen vacancies, covering non-selective sites, and providing the optimal retention time for initial compounds, products, and oxametallacycles on the catalyst surface.
A New Scale of the Electrophilicity Index Invoking the Force Concept and Its Application in Computing the Internuclear Bond Distance
Abstract
The prediction of the nature of a reactivity descriptor is of paramount importance to theoretical chemists and thus, much work has been carried out in this area. The electrophilicity index (ω), an important theoretical construct of chemistry, is a measure of the electron acceptor affinity to gain an additional electronic charge from the environment. It is quantified in terms of the maximum energy stabilization in species, which arises due to accepting a charge. The electrophilicity concept is being extensively used in modern chemistry, although the finest measurement scale of the electrophilicity index is yet to be designed. In this study, a new scale of the electrophilicity index invoking the force concept based on the effective nuclear charge (Zeff) and absolute atomic radii (r) is proposed for 97 elements of the periodic table, which is determined through the regression analysis. The computed data follows the periodicity very well satisfying the sine qua non of the standard scale of the electrophilicity index. The electrophilicity equalization principle is also established in terms of the computed data. To test the model in the real field, the internuclear bond distance of some molecules is calculated in terms of the computed electrophilicity index. A comparative study of the theoretical vis-à-vis experimental internuclear bond distance reveals the efficacy of the proposed scale.
Theoretical Evaluation of One-Pot Synthesis of Aliphatic PNP Pincer Ligands
Abstract
In this research, one-pot synthesis of aliphatic pincer ligands via SN2 reaction have been studied using theoretical calculations. The kinetics and thermodynamics of the reactions between dialkylhalophosphines and bis(2-haloethyl)amines have been studied and compared with the experimentally successful one-pot synthesis of arene-based PCP/PNP pincer ligands. The effect of the leaving group, hetero atom, solvent, and substitution have been investigated and it has been shown that the synthesis of aliphatic pincer ligands with iodophosphines and bis(2-iodoethyl)amine in the presence of acetonitrile as solvent have the lowest activation free energy (ΔG≠) and highest reaction rate (k). Consequently, the calculations suggest the suitable condition for one-pot synthesis of aliphatic pincer ligands via the proposed SN2 reaction.
Substituent Effect on the Acidity Strength of para-C6H4XB(OH)2 Boronic Acid: A Theoretical Investigation
Abstract
The para-substituent effect on the acidity strength of boronic acid (para-C6H4XB(OH)2; X = NMe2, NH2, OMe, H, F, Cl, CHO, COOH, NO2) is explored at the B3LYP*/6-31+G(d, p) level of theory in an aqueous solution. The conductor-like polarized continuum model (CPCM) is used for the calculation in the aqueous phase. The CPCM calculations are performed with the SMD-Coulomb atomic radii. Then, the pKa values corresponding to these molecules are calculated in an aqueous solution. Atomic charges of the acidic proton are calculated with QTAIM, APT, and Mulliken methods. A linear correlation between the calculated pKa values with the Hammett constant, deprotonating energy, and atomic charges of acidic proton are analyzed.
The Nature of Halogen Dependence of 103Rh NMR Chemical Shift in Complex Anions cis-[X1X2Rh(CO)2]− (X1, X2 = Cl, Br, I)
Abstract
DFT calculations within the two-component quasirelativistic approach and further analysis of 103Rh NMR shielding (including the natural bond orbitals method) in a series of flat-square complex anions cis-[X1X2Rh(CO)2]− (X1, X2 = Cl, Br, I) are used to determine the role of relativistic spin-orbit effects in 103Rh NMR shielding in these systems. Electron delocalization observed in these complexes provides the possibility of relativistic spin-orbit effects but complicates the interpretation of 103Rh NMR shielding in terms of chemically meaningful fragments of electronic system (lone pairs, chemical bonds).
On the Structure of Zinc(II) Coordination Compounds with L-Histidine
Abstract
Spatial and electronic structures of various zinc(II) coordination compounds containing different L-histidine forms are quantum-chemically calculated with the HyperChem 8.0 software taking into account the effect of the solvent (water). Geometry optimization is performed by molecular mechanics, the semiempirical MNDO/d method, and the Polak-Ribière nonlinear conjugate gradient method. Molecular geometry is optimized in the three-dimensional space without symmetry constraints. IR spectroscopy, 13C NMR, and XRD methods are used to determine the composition, structure, and geometry of the coordination site of the zinc(II) complex with L-histidine.
Optical Properties and Defects of Double Doped Crystals LiNbO3:Mg(5.05):Fe(0.009) and LiNbO3:Zn(4.34):Fe(0.02) (mol%)
Abstract
Photoinduced light scattering, laser conoscopy, and IR spectroscopy in the absorption region of OH stretching vibrations are used to study photorefractive properties and compositional homogeneity of double doped (mol%) LiNbO3:Mg(5.05):Fe(0.009) and LiNbO3:Zn(4.34):Fe(0.02) crystals grown from a congruent melt. All frequencies in the IR spectrum of the LiNbO3:Mg(5.05):Fe(0.009) (mol%) crystal in the region of OH stretching vibrations are shifted to the high-frequency region compared with the spectrum of the nominally pure congruent crystal. This is caused by the absence of \(\rm{Nb}_{Li}^{4+}\) point defects and the corresponding (VLi)–OH complex defects in the crystal structure and by the formation of new MgLi–MgNb–OH and MgLi–OH–FeNb complex defects. The LiNbO3:Zn(4.34):Fe(0.02) (mol%) crystal (zinc concentration is between threshold concentrations for ∼3.0 mol% and 7.0 mol% of ZnO) is found to be much more compositionally homogeneous than the LiNbO3:Mg(5.05):Fe(0.009) (mol%) crystal, despite much higher iron content in the former. This is explained by the fact that magnesium content in this crystal is close to the threshold concentration for ∼5.5 mol% of MgO. Neither of the crystals exhibits photoinduced light scattering.
Changes in the Spatial Distribution of Metals Under the Influence of Reaction Medium in the System Formed by a Gold Film Supported on the Surface of a Silver Foil
Abstract
Behavior of gold films supported on the surface of a silver foil is studied using X-ray photoelectron spectroscopy (XPS) when heated in a vacuum or in nitrogen dioxide (under pressure of 10−5 mbar) at 200 °C. The initial gold film is 2–2.7 nm thick. It is shown that the gold film dissolves in the silver foil volume during the heating to form an Ag–Au alloy. The behavior of the ratio of the AgMVV Auger line intensity to the Ag3d photoemission line intensity testifies that the alloy surface is enriched with silver. The enrichment proceeds more efficiently when the system is heated in the presence of NO2.
Crystallographic Analysis of TiO2 Polymorphism (Brookite, Anatase, Rutile)
Abstract
Crystallographic analysis of three TiO2 structures shows that all of them have a rhombohedral anion sublattice close to their cubic closest packing. In brookite it competes with the hexagonal packing, and the packing of TiO6 octahedra is less regular. High symmetry of anatase and rutile is initiated by the local (cubic) symmetry of TiO6 octahedra. Cations occupy most symmetrical special positions and provide a coherent assembly of these “building units” by spreading the local symmetry over the entire structure.
Structural Transformations of [CuEn3]WO4 Complex Salt in the Range 100–390 K and Its Degradation to [CuEn2](WO4)·2H2O
Abstract
The crystal structure of [CuEn3]WO4 (En is ethylenediamine) is studied in the temperature range 100–390 K. Crystallographic data at 100 K are: a = 27.6903(8) Å, c = 9.9405(3) Å, space group P3̄, V = 6600.8(4) Å3, Z = 18. Copper atomic coordination is a distorted square bipyramid. Four short Cu–N distances are within 2.038(5)–2.110(6) Å; two long distances are within 2.374(8)–2.514(7) Å. The lengths of N–H…O interionic contacts lie within 1.96–2.17 Å. A temperature elevation makes the Cu–N distances equal: at 298 K they are within 2.066(2)–2.256(3) Å(a = 16.0391(8) Å, c = 9.9608(6) Å, space group P3̄c1, V = 2219.1(3) Å3, Z = 6), and at 390 K they are 2.151(6) Å(a = 9.2986(10) Å, c = 10.0520(14) Å, P3̄1c, V = 752.7(2) Å3, Z = 2). In the range from 100 K to 390 K the average W–O distances decrease from 1.776 Å to 1.734 Å. Hirshfeld surfaces of complex cations are analyzed. It is shown that with increasing temperature the number of interionic N–H…O contacts decreases. The [CuEn3]WO4 phase is found to be unstable and on storing in air it transforms into [CuEn2](WO4)·2H2O.
Crystal Structures of Bi- and Tetranuclear Halide Complexes of Bi(III) with 2,6-Dimethyl- and 2,4,6-Trimethylpyridine Cations
Abstract
Bi- and tetranuclear complexes (2,6-MePyH)6[Bi4Cl18]·6H2O (1), (2,6-MePyH)4[Bi2Br10]·2H2O (2) and (2,4,6-MePyH)3[Bi2Br9] (3) are obtained by the reactions of [BiX6]3− (X = Cl, Br) solutions with the salts of corresponding substituted pyridines. Compounds 1–3 are characterized by the XRD method.
Synthesis and Structure of Hybrid Compounds Based on Phosphoryl Acetic Acid Hydrazide, Isatin, and Sterically Hindered Phenols
Abstract
In order to obtain novel biologically active substances with various types of activity, hybrid compounds based on 2-(diphenylphosphoryl)acetohydrazide, isatin, and sterically hindered phenols are synthesized. Their molecular and crystal structures are determined by X-ray crystallography.
Structure of Two Complexes of N-Thiophosphorylated Thioamides with a Silver(I) Cation and Triphenylphosphine
Abstract
In order to study the complexation properties of N-thiophosphorylated thioureas, thioamides, and thiosemicarbazides with the general formula RC(S)NHP(S)(OPri)2 (R = AlkNH, Alk2N, ArNH, PyNH, Ph, PhNHNH, NH2(Et)N) towards copper(I) and silver(I) cations, the molecular and crystal structures of silver(I) (triphenylphosphine-P)[N-(diisopropoxythiophosphoryl)thiobenzamide-S,S′] and silver(I) bis-(triphenylphosphine-P)[N-(diisopropoxythiophosphoryl)thiobenzamide-S,S′] are determined.
Structure and Biological Activity of Trichlorophenyl-Thiosemicarbazone and its Complexes with Some Transition Metal Cations
Abstract
The complexes of 4-(2,4,6-trichlorophenyl)-3-thiosemicarbazide (HL1) with transition metal cations VO(II), Co(II), Ni(II), Cu(II), Pd(II), and Pt(II) are prepared and characterized using elemental and thermal analyses, UV-visible spectrophotometry, FTIR, mass, and NMR spectroscopy, X-ray diffraction, and molar conductance and magnetic susceptibility measurements. The results show that the prepared chelates have the following chemical formulae and structures: [(VO)2(L1)(SO4)(C2H5O)·H2O] (square based pyramidal structure), [Co2(HL1)Cl3C2H5OH]·Cl (square planar structure), [Ni(HL1)Cl2]·3H2O (square planar structure), [Cu(L1)2(H2O)2] (octahedral structure), [Pd(HL1)Cl2]·H2O (weakly distorted square planar structure), and [Pt(HL1)Cl2]·1/2H2O (square planar structure). Generally, the complexes exhibit a high thermal stability, however, the Pd(II) and Pt(II) complexes are more stable than the other complexes. The ligand (HL1), and its complexes are screened for their biological activity. Some of the complexes are found more biologically active than the parent ligand.
Studying Dependences Between the Chemotype Structure of Some Natural Compounds and the Spectrum of Their Targeted Activities Correlated with the Hypoglycemic Effect
Abstract
The method of similarity to standards is used to calculate the spectrum of targeted hypoglycemic activities of a series of natural compounds of terpenoid and polyphenol classes. Some compounds are shown to be promising multitargeted hypoglycemic agents. Primary action targets are identified.
Design and Characterization of a Cu(II) Coordination Polymer Based on α-Diimine: Evaluation of the Biomimetic Activity
Abstract
The copper-based polymer is synthesized using a slow evaporation method with an α-diimine chelator (1,10-phenanthroline) as the primary ligand. The synthesized polymer is characterized by various spectroscopic studies (FT-IR, UV-visible, EPR, luminescent), powder XRD and TGA techniques. Single crystal XRD studies reveal the molecular structure as a one-dimensional (1D) coordination polymer (CP) with the composition [Cu(phen)(NO3)2]n. The FT-IR spectrum of CP further ascertains the binding modes of the ligand moiety. The copper ion is present in the +2 oxidation state and the geometry around the central metal ion is distorted square pyramidal. Moreover, CP shows a brilliant catecholase-like activity in methanol, which can easily oxidize the substrate 3,5-di-tert-butylcatechol (3,5-DTBC) to its respective quinone. Kinetic measurements suggest that the catechol oxidation rate follows saturation kinetics with respect to the substrate and first order kinetics with respect to the catalyst. CP shows a very good catalytic activity with Kcat = 8.28 h−1.
Two Novel Ca(II)-Carboxylate Coordination Polymers: Crystal Structures and Antimyeloma Activity Evaluation
Abstract
In this study, two new coordination polymers [Ca3(BTB)2(NMP)2(H2O)2](NMP)(H2O)4 (1, H3BTB = benzene-1,3,5-tribenzoic acid, NMP = N-methyl-pyrrolidone) and [Ca3(NTB)2(DEF)2(H2O)2] (DEF)(H2O)4 (2, H3NTB = 4,4′,4″-nitrilotribenzoic acid, DEF = N,N-diethyl-formamide) based on the alkaline earth metal Ca(II) ion and two rigid C3-symmetric tricarboxylic acid ligands are successfully prepared via the solvothermal reaction. The structural analysis of complexes 1 and 2 demonstrates the existence of different topologies and structures in the as-prepared complexes because of the conformational flexibility of the organic ligands and the diverse geometry of the Ca(II)-based 1D secondary building unit. The particle sizes of these two complexes could be conveniently downsized in nanometer region via a simple treatment. In addition, in vitro anticancer activity of compounds 1 and 2 in nanometer has been studied for inhibition human myeloma cell growth via the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay.
Synthesis, Crystal Structures of Two Novel Metal Coordination Polymers and Study of Their Inhibition of Human Hemangioma Cells
Abstract
In this work, two new InIII-based coordination polymers {(H2NMe2)3[In(TATAB)2](H2O)6}n (1, H3TATAB = 4,4′,4″-s-triazine-1,3,5-triyl-tri-p-aminobenzoic acid) and {(Me2NH2)2[In2(TTA)2(FA)2] (DMF)3}n (2, H3TTA = 4,4′,4″-{[(2,4,6-trimethylbenzene-1,3,5-triyl)tris(methylene)]tris(oxy)}tribenzoic acid, HFA = 2-fluorobenzoic acid, DMF = N,N-dimethylformamide) are successfully prepared under solvothermal conditions and structurally characterized by the single crystal X-ray study (SCXRD) and the powder X-ray analysis (PXRD). In addition, the in vitro anticancer activity of compounds 1 and 2 on three human hemangioma cells (HMEC-1, EAhy926 and SV40) is further investigated.