Journal of Molecular Structure

Published by Elsevier
Online ISSN: 0022-2860
Publications
Article
A novel metal-organic framework, [Zn(2)(OH)(Hcht)(4,4'-bpy)](n).4nH(2)O (1) (H(4)cht = cyclohexane-1,2,4,5-tetracarboxylic acid and 4,4'-bpy = 4,4'-bipyridine), was synthesized by the hydrothermal reaction of Zn(NO(3))(2).6H(2)O, 4,4'-bipyridine, and cyclohexane-1,2,4,5-tetracarboxylic acid in the presence of sodium carbonate. The complex was obtained by controlling the ratio of the starting materials and a reaction temperature at 120 degrees C and was characterized by IR, X-ray powder diffraction, thermogravimetric analysis, fluorescent spectrum, and single crystal X-ray diffraction. Single-crystal X-ray investigation reveals that the structure features a two-dimensional framework with novel coordination mode of Hcht ligand and all Hcht ligands exclusively convert to a sole conformation in the complex. IR spectrum reveals the characteristic absorption peaks of asymmetric stretching vibrations that result from the protonated and deprotonated carboxyl groups,. Thermogravimetric analysis shows four clear courses of weight loss, which corresponds to the decomposition of different ligands. Fluorescent spectrum displays that complex 1 is a potential blue-luminescent material.
 
Article
We have used a novel microwave-assisted method developed in our laboratories to synthesize a series of ruthenium-thiosemicarbazone complexes. The new thiosemicarbazone ligands are derived from benzo[d][1,3]dioxole-5-carbaldehyde (piperonal) and the complexes are formulated as [(diimine)(2)Ru(TSC)](PF(6))(2) (where the TSC is the bidentate thiosemicarbazone ligand). The diimine in the complexes is either 2,2'-bipyridine or 1,10-phenanthroline. The complexes have been characterized by spectroscopic means (NMR, IR and UV-Vis) as well as by elemental analysis. We have studied the biophysical characteristics of the complexes by investigating their anti-oxidant ability as well as their ability to disrupt the function of the human topoisomerase II enzyme. The complexes are moderately strong binders of DNA with binding constants of 10(4) M(-1). They are also strong binders of human serum albumin having binding constants on the order of 10(4) M(-1). The complexes show good in vitro anticancer activity against human colon cancer cells, Caco-2 and HCT-116 and indeed show some cytotoxic selectivity for cancer cells. The IC(50) values range from 7 - 159 μM (after 72 h drug incubation). They also have antibacterial activity against Gram-positive strains of pathogenic bacteria with IC(50) values as low as 10 μM; little activity was seen against Gram-negative strains. It has been established that all the compounds are catalytic inhibitors of human topoisomerase II.
 
Article
The complex of formaldehyde with carbon dioxide has been studied by infrared spectroscopy in argon and nitrogen matrices. The shifts relative to the free species show that the complex is weak and similar in argon and nitrogen. The results give evidence for T-shaped complexes, which are isolated in several configurations. Some evidence is also presented which indicates that, in addition to the two well-known sites in argon, carbon dioxide can be trapped in a third site.
 
Article
The tris(2-mercapto-1-methylbenzimidazolyl)hydroborato cadmium complex, {[Tm(MeBenz)]Cd(μ-Br)}2, may be synthesized via the reaction of [Tm(MeBenz)]K with CdBr2. X-ray diffraction demonstrates that {[Tm(MeBenz)]Cd(μ-Br)}2 exists as a dimer, which is in marked contrast to the monomeric structure of the non-benzannulated counterpart, [Tm(Me)]CdBr, and thereby demonstrates that benzannulation of tris(2-mercapto-1-methylbenzimidazolyl)hydroborato ligands can have a distinct impact on the molecular structure of their metal complexes. In accord with this observation, density functional theory calculations indicate that the benzannulated dimers, {[Tm(MeBenz)]Cd(μ-X)}2 (X = Cl, Br, I), are more stable with respect to dissociation than are their non-benzannulated counterparts, {[Tm(Me)]Cd(μ-X)}2. Furthermore, the calculations also indicate that the stability of the dimer depends on the nature of X, such that the dimer becomes more stable in the sequence I < Br < Cl.
 
Article
A new dinuclear iron nitrosyl complex [Fe(2)(C(14)H(12)N(3)S)(2)(NO)(4)] (1) (C(14)H(12)N(3)S = 2-mercapto-1-[2-(4-pyridyl)-ethyl]-benzimidazolyl) has been obtained by the reaction of Fe(NO)(2)(CO)(2) with 2-mercapto-1-[2-(4-pyridyl)-ethyl]-benzimidazole in CH(3)OH under moderate condition. Complex 1 was characterized by IR, UV-vis, electrochemistry and single crystal X-ray diffraction. IR spectrum displays two strong characteristic NO stretching frequencies (nu(NO)) in solution and in solid state. Cyclic voltammetry shows one irreversible, two quasi-reversible and two reversible one-electron reductions and irreversible oxidizations. This result is consistent with the fact that complex 1 is very unstable and ready to lose NO in the air. As showing in the single crystal X-ray diffraction, complex 1 forms a "chair-shape" structure by the connections of two iron centers and S-C-N frames of benzimidazole. The dihedral angle of benzimidazole ring and 2Fe-2S plane is 73.6 degrees . The crystal data are the following: 1, monoclinic, space group P2(1)/c, a = 10.43940(10) A, b = 16.0900(2) A, c = 10.13240(10) A, alpha = 90 degrees , beta = 111.0940(10) degrees , gamma = 90 degrees , V = 1587.89(3) A(3), Z = 4.
 
Article
Photochromic molecules have the potential to find utility in a wide variety of applications including photoswitchable binding and optical memory. This work explores the relationship between photochromism and structural parameters such as particular bond lengths for this class of compounds for which very few crystal structures have been published. Photochemical kinetics, Density Functional Theory (DFT) and X-ray crystallography were used to study the benzothiazolinic spiropyran 3-methyl-6-nitro-3'-methylspiro-[2H-l-benzopyran-2,2'-benzothiazoline]. A second benzothiazolinic spiropyran 3-methyl-8-methoxy-6-nitro-3'-methylspiro-[2H-l-benzopyran-2,2'-benzothiazoline] was synthesized and subjected to photochemical and computational studies. Selected structural and photochemical data for these, related benzothiazolinic spirooxazines and spiropyrans, and related thiazolidinic spiropyrans are compared. Both benzothiazolinic spiropyrans exhibit photochromic properties that are influenced by substituents, solvent, and temperature. The crystallographic C(spiro)-O bond distance of 3-methyl-6-nitro-3'-methylspiro-[2H-l-benzopyran-2,2'-benzothiazoline] that has been shown to correlate with photochromic properties is 1.458 A. The crystallographic C(spiro)-O bond distance matches that of the structure generated by DFT calculations exactly. The effect of substituents on calculated bond lengths and photochemical parameters was determined. For this class of compounds, both X-ray geometry and DFT optimized geometry may be used to predict photochromism, but not degree of photocolorability.
 
Article
The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard C-C distance representations.
 
Article
The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol-1. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural rigidity is partially responsible for its selectivity.
 
Article
The nature of the bonding in model complexes of di-copper metalloenzymes has been analyzed by means of the electronic localization function (ELF) and by the quantum theory of atoms in molecules (QTAIM). The constrained space orbital variations (CSOV) approach has also been used. Density functional theory (DFT) and CASSCF calculations have been carried out on several models of tyrosinase such as the sole Cu2O22+ central core, the Cu2O2(NH3)62+ complex and the Cu2O2(Imidazol)62+ complex. The influence on the central Cu(2)O(2) moiety of both levels of calculation and ligand environment have been discussed. The distinct bonding modes have been characterized for the two major known structures: [Cu(2)(mu-eta(2): eta(2)-O(2))](2+) and [Cu(2)(mu-O(2))](2+). Particular attention has been given to the analysis of the O-O and Cu-O bonds and the nature of the bonding modes has also been analyzed in terms of mesomeric structures. The ELF topological approach shows a significant conservation of the topology between the DFT and CASSCF approaches. Particularly, three-center Cu-O-Cu bonds are observed when the ligands are attached to the central core. At the DFT level, the importance of self interaction effects are emphasized. Although, the DFT approach does not appear to be suitable for the computation of the electronic structure of the isolated Cu(2)O(2) central core, competitive self interaction mechanisms lead to an imperfect but acceptable model when using imidazol ligands. Our results confirm to a certain extent the observations of [M.F. Rode, H.J. Werner, Theoretical Chemistry Accounts 4-5 (2005) 247.] who found a qualitative agreement between B3LYP and localized MRCI calculations when dealing with the Cu(2)O(2) central core with six ammonia ligands.
 
Article
The synthesis and characterization of diiron(II) complexes supported by 9-triptycenecarboxylate ligands ((-)O(2)CTrp) is described. The interlocking nature of the triptycenecarboxylates facilitates formation of quadruply bridged diiron(II) complexes of the type [Fe(2)(μ-O(2)CTrp)(4)(L)(2)] (L = THF, pyridine or imidazole derivative) with a paddlewheel geometry. A systematic lengthening of the Fe-Fe distance occurs with the increase in steric bulk of the neutral donor L, resulting in values of up to 3 Å without disassembly of the paddlewheel structure. Reactions with an excess of water do not lead to decomposition of the diiron(II) core, indicating that these quadruply bridged complexes are of exceptional stability. The red-colored complexes [Fe(2)(μ-O(2)CTrp)(4)(4-AcPy)(2)] (10) and [Fe(2)(μ-O(2)CTrp)(4)(4-CNPy)(2)] (11) exhibit solvent-dependent thermochromism in coordinating solvents that was studied by variable temperature UV-vis spectroscopy. Reaction of [Fe(2)(μ-O(2)CTrp)(4)(THF)(2)] with N,N,N',N'-tetramethylethylenediamine (TMEDA), tetra-n-butyl ammonium thiocyanate, or excess 2-methylimidazole resulted in the formation of mononuclear complexes [Fe(O(2)CTrp)(2)(TMEDA)] (13), (n-Bu(4)N)(2)[Fe(O(2)CTrp)(2)(SCN)(2)] (14), and [Fe(O(2)CTrp)(2)(2-MeIm)(2)] (15) having an O(4)/N(2) coordination sphere composition.
 
Article
The 2Z-isomer of malyngamide K has been isolated along with the known compounds malyngamide C, deoxy-C and K, and characterized from a Papua New Guinea field collection of the cyanobacterium Lyngbya majuscula. The planar structure was deduced by 1D and 2D NMR spectroscopic and mass spectral data interpretation. The absolute configurations were determined on the basis of spectroscopic techniques, chemical degradation and DFT theoretical calculations.
 
Article
Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.
 
Article
Crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. For the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. This cluster played a dual role in ribosomal crystallography: providing anomalous phasing power and dramatically increased the resolution, by stabilization of a selected functional conformation. Thus, four out of the fourteen clusters that bind to each of the crystallized small subunits are attached to a specific ribosomal protein in a fashion that may control a significant component of the subunit internal flexibility, by "gluing" symmetrical related subunits. Here we highlight basic issues in the relationship between metal ions and macromolecules and present common traits controlling in the interactions between polymetalates and various macromolecules, which may be extended towards the exploitation of polymetalates for therapeutical treatment.
 
Article
Conformational changes are central to the functioning of pore-forming proteins that open and close their molecular gates in response to external stimuli such as pH, ionic strength, membrane voltage or ligand binding. Normal mode analysis (NMA) is used to identify and characterize the slowest motions in the gA, KcsA, ClC-ec1, LacY and LeuT(Aa) proteins at the onset of gating. Global deformation modes of the essentially cylindrical gA, KcsA, LacY and LeuT(Aa) biomolecules are reminiscent of global twisting, transverse and longitudinal motions in a homogeneous elastic rod. The ClC-ec1 protein executes a splaying motion in the plane perpendicular to the lipid bilayer. These global collective deformations are determined by protein shape. New methods, all-atom Monte Carlo Normal Mode Following and its simplification using a rotation-translation of protein blocks (RTB), are described and applied to gain insight into the nature of gating transitions in gA and KcsA. These studies demonstrate the severe limitations of standard NMA in characterizing the structural rearrangements associated with gating transitions. Comparison of all-atom and RTB transition pathways in gA clearly illustrates the impact of the rigid protein block approximation and the need to include all degrees of freedom and their relaxation in computational studies of protein gating. The effects of atomic level structure, pH, hydrogen bonding and charged residues on the large scale conformational changes associated with gating transitions are discussed.
 
Article
The phospholipid and Ca2+ dependent protein kinase (PKC) plays an essential role in a variety of cellular events. Inhibition of PKC was shown to arrest growth in tumor cell cultures making it a target for possible antitumor therapy. Calphostins are potent inhibitors of PKC with high affinity for the enzyme regulatory site. Structural characteristics of calphostins, which confer the inhibitory activity, are investigated by comparing their optimized structures with the existing models for PKC activation. The resulting model of inhibitory activity assumes interaction with two out of the three electrostatic interaction sites postulated for activators. The model shows two sites of hydrophobic interaction and enables the inhibitory activity of gossypol to be accounted for.
 
Article
The application of the matrix isolation technique, which is but one of the experimental techniques pioneered in George Pimentel's laboratories, to interstellar problems is described. Following a brief discussion of the interstellar medium (ISM) three areas are reviewed in which matrix experiments are particularly well-suited to contribute the information which is sorely needed to further our understanding of the ISM. The first involves the measurement of the spectroscopic properties of reactive species. The second is the determination of reaction rates and the elucidation of reaction pathways involving atoms, radicals and ions which are likely to interact on grain surfaces and in grain mantles. The third entails the determination of the spectroscopic, photochemical and photophysical properties of interstellar and cometary ice analogs. Significant, but limited, progress has been made in these three areas and a tremendous amount of work is required to fully address the variety of unique chemical and spectroscopic questions posed by the astronomical observations.
 
Article
The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.
 
Conference Paper
Frequencies of H<sub>2</sub>O pure rotational transitions from 0.5 to 5 THz have been measured with an accuracy of one part in 10<sup>9 </sup> using a tunable far-infrared spectrometer. Measured frequencies of more than a hundred spectral lines provide an excellent wavelength and frequency calibration standard for the far infrared
 
Article
A new binuclear complex NH4(enH2)0.5[Co(en)3][Mo2O7(C2O4)]·H2O was obtained from the hydrothermal reaction of (NH4)6Mo7O24·4H2O, CoC2O4·2H2O, ethylenediamine and H2O at 120 °C, and characterized by single crystal X-ray diffraction and spectroscopic methods. The crystal structure is composed of dimeric [Mo2O7(C2O4)]4− anions, complex [Co(en)3]2+ cations, ethylenediamine cations, ammonium cations and crystallization water molecules, which are held together to an extensive three-dimensional network via hydrogen-bonding interactions. The dimeric structure of [Mo2O7(C2O4)]4− is formed by one MoO4 tetrahedron and one MoO6 octahedron through sharing a bridging oxygen atom, where oxalate acts as a bidentate ligand coordinating to the octahedral molybdenum atom though two deprotonated corboxylate groups. It is shown that the title compound possesses well-separated paramagnetic Co2+ centers.
 
Article
The new mononuclear complexes [Cu(phen)(C5O5)(H2O)]·H2O (1), [Ni(terpy)(C5O5)(H2O)]·H2O (2) and [Ni(terpy)2](NO3)2·0.5H2O (3) [phen=1,10-phenanthroline, =dianion of the 4,5-dihydroxycyclopent-4-ene-1,2,3-trione and terpy=2,2′:6′,2″-terpyridine] have been synthesized and characterized by single-crystal X-ray diffraction. The copper atom of 1 has a distorted square pyramidal environment with two phen-nitrogen and two croconate-oxygen atoms building the equatorial plane and a water molecule in the apical position. The nickel atom of 2 exhibits a distorted NiN3O3 octahedral coordination, which may be described either as tetragonally compressed or as skewed trapezoidal bipyramidal. The nickel atom of 3 is situated on a twofold axis and it has a distorted NiN6 octahedral coordination, with an appreciable tetragonal compression along the N(2)–Ni–N(4) axis [N(2) and N(4) being the central terpy-nitrogens]. The structures of 1 and 2 are compared with related ones from the literature and their potential use as ligands is analyzed.
 
Article
Raman spectroscopy was applied to study nano-scale structure and related phonon anomalies in relaxor-ferroelectric materials of type PbB′0.5B″0.5O3. By comparing the polarized spectra of single crystals, measured at temperature higher than the maximum of the dielectric permittivity, Tm, and by performing normal mode calculations the observed Raman peaks were assigned to definite atomic vibrations. Further, the temperature evolution of the phonon anomalies was investigated on the basis of calculated modes of representative structural units at various atomic positions. It is shown that within a few nm doubling of the unit cell should exist, independently of the degree of B-site ordering. The Raman activity of the silent F2u mode reveals the existence of dynamical off-centred structural fluctuations. The structural perturbation consists of a non-coplanarity of the Pb and O atoms in the planes perpendicular to the cubic body diagonal and non-centre-symmetrical deformations of the BO6 octahedra. On cooling, different structural changes are preferential: for B″=Nb the temperature decrease amplifies the deformation of the individual BO3–Pb species; for B″=Ta the temperature decrease favours the non-coplanarity of Pb and O atoms and enhances the correlation between the stereoactive electron lone pairs of Pb atoms. Besides, within nano-scale spatial regions, PbSc0.5Ta0.5O3 undergoes an additional phase transition near 180 K that involves a reduction of the rotational symmetry. The comparison between the temperature dependence of the inelastic light scattering in stoichiometric and Nb-doped PbSc0.5Ta0.5O3 shows that the presence of Nb even in small concentrations affects the Pb–O sublattice and changes the direction of the local structural transformations.
 
Article
The cw dye laser excitation spectrum of the vibronic transition of the PH2 radical was observed between 18 158 and 18 443 cm−1 at Doppler-limited resolution. The PH2 radical was produced by the reaction of discharged hydrogen with powdered red phosphorus. About 1000 lines were observed for Ka up to 7 and N up to 9. Using the ground-state parameters reported by Endo et al. [Y. Endo, S. Saito and E. Hirota, J. Mol. Spectrosc., 97 (1983) 204–212], upper-state term values were calculated from the observed transition frequencies and were subjected to a least-squares analysis to derive rotational constants, centrifugal distortion constants, and spin-rotation interaction constants in the state. The perturbations observed for the upper state are briefly discussed.
 
Article
The low frequency vibrational spectra of gaseous dimethylselenide and dimethylselenide-d3 have been investigated from 50 to 500 cm−1. A number of torsional transitions have been resolved in the far infrared spectra for both molecules and their analyses have given a torsional potential function based on a semirigid model. For the light molecule the effective barrier to internal rotation was found to be 507 ± 17 cm−1 (1450 cal mol−1) and the cosine-cosine coupling term, V33 was found to be 54 ± 12 cm−1 (154 cal mol−1), whereas the sine-sine coupling term, V33, has a value of 10 10 ± 4 cm−1 (29 cal mol−1). An interaction between the low frequency CSeC bending mode and the (2,0) - (1,0) torsional transition is proposed as a possible explanation for the assignment of the torsional transitions for dimethylselenide-d3. The effective barrier for the -d3 molecule was found to have a value of 520 ± 6 cm−1 (1487 cal mol−1) with a sine-sine coupling term value of −35 ± 7 cm−1 (−100 cal mol−1). A complete vibrational assignment is given for the dimethylselenide-d3 molecule and a normal coordinate calculation has been carried out using a modified valence force field. These results are compared to the similar quantities in some corresponding molecules.
 
Article
The molecular structure of [1,1′-bipyrrolidine]-2,2′-dithione (1) has been determined by single-crystal X-ray crystallography. The compound crystallizes in the orthorhombic system: Pbca, a = 9.314(12), b = 13.213(2), c = 16.321(3) Å, V = 2008.4 Å3, Z = 8, Dc = 1.33 g cm−3, R = 0.042 for 2583 unique reflections and 140 variable parameters. The dihedral angle between the mean planes of the rings is 104.2(7)°. The conformations of the rings themselves are presented in terms of normalized linear combinations of the primitive envelope and twist forms. Certain bond distances are rationalized in terms of the screening of nuclear repulsion. The rorational barrier about the NN bond has been calculated from variable temperature nuclear magnetic resonance (NMR) measurements in deuterated toluene as 73 kJ mol−1. All measured parameters are contrasted with those found in the literature for the 2,2′-dioxo analogue (2), for which the rotational barrier has been determined in this work as 44 kJ mol−1.
 
Article
The structure of 1,1-difluorosilacyclopentane has been studied by gas-phase electron diffraction. The molecule is found to have a barrier of pseudorotion of 2.25(90) kcal mol−1. The potential function has minimum at the twist form (C2) symmetry and maxima at the envelope forms. The major bond distances (itr)g) and valence angles obtained from the least-squares refinements with error estimates are as follow: r(CH) = 1.128(7) A, r(CC)av = 1.553(15) A, r(SiF) = 1.582(6) A, r(SiC) = 1.853(3) A, ∠(CSiF) = 113.4′(3), ∠CCC = 106°(1), and Tau(C1C2C3C4) = 56.0°(32).
 
Article
The crystal structures of N-(2-pyridyl)aminomethane-1,1-diphosphonic acid (1) and N-(4-methyl-2-pyridyl)aminomethane-1,1-diphosphonic acid (2) are determined and discussed with respect to their geometry and solid state organization. Compounds 1 and 2 crystallize as the opposite E and Z isomers. However, in solution both appear as a mixture of the Z and E forms. From the temperature dependence of NMR spectra, the Z/E ratio is assigned to be nearly equal in 1 and 0.69:0.31, respectively, in 2. The role of a substituent position on the pyridyl ring for the Z/E ratio in solution and for solid state conformations of N-(2-pyridyl)aminomethane-1,1-diphosphonic acids is discussed as well.
 
Article
The crystal structures of three new members of the (pyridin-2-yl)aminomethane-1,1-diphosphonic acid (1-a) family are determined by X-ray diffraction and discussed with respect to molecular geometry and solid state organization.The striking structural feature of (3,5-dibromo-6-methylpyridin-2-yl)aminomethane-1,1-diphosphonic acid (2) and (3-chloro-5-trifluoromethylpyridin-2-yl)aminomethane-1,1-diphosphonic acid (3) is that regardless of a multiple substitution on the pyridyl ring the key factor for their conformational stabilization is the intramolecular N–H⋯X (X = Cl, Br) hydrogen bond involving substituent at 3-ring position.In contrast, the solid state conformation of (pyrimidin-2-yl)aminomethane-1,1-diphosphonic acid (4) is stabilized through intermolecular, bifurcated N–H⋯O hydrogen bonds, which is similar to that observed previously in 4- and 5-substituted Z-zwitterionic derivatives of (pyridin-2-yl)aminomethane-1,1-diphosphonic acid. Moreover, the 31P NMR spectra of 4 suggest similar dynamic process in solution, attributable to the rotation around the Cring–Namino bond. However, the rotational barrier in 4 is markedly lower as compared to 4- and 5-substituted (pyridin-2-yl)aminomethane-1,1-diphosphonic acids. This is attributed to low basicity of the nitrogen atom of the 1,3-diazinyl ring, which results in loss of conformational stabilization provided by intermolecular N–H⋯O hydrogen bonds in solution at low pH.
 
Article
Ab initio SCF—MO calculations have been carried out on cyclopropyl chloride and 1,1-dichlorocyclopropane, to illuminate the effect of the substituent upon the cyclopropane ring. For cyclopropyl chloride, reasonable agreement is found with experimental findings. For 1,1-dichlorocyclopropane, excellent agreement is found with the results from a recent NMR study. As a means of studying the effect of a change in basis set, calculations are also carried out on methyl chloride.
 
Article
The absorption and emission properties of benzimidazol-2-yl-quinoline (BIQ) and bis (2-(benzimidazol-2-yl) quinolinato) zinc (ZnBIQ) a new emitter used for organic light emitting device (OLED) were reported. Exciplexes are observed for ZnBIQ with N,N′-bis-(1-naphthyl)-N,N′-diphenyl-1,1′-biphenyl-4,4′-diamine (NPB) system, in both electro- and photoluminescent processes. The identification of exciplex emission in co-evaporated and multi-layer ZnBIQ thin film was reported for the first time. The optical formation of the exciplex involves the excitation of a single molecule, followed by the relaxation of that exciton into a lower energy exciplex state. Both BIQ and ZnBIQ possess very high thermal stabilities and can be purified by subliming under the high vacuum condition. Devices consisting of ZnBIQ as the emitting layer have been fabricated, and the emission spectra of ZnBIQ-base devices gave a voltage-dependent spectrum, with the red emission observed (3–7 V), switching over to strong white emission as the bias was raised.
 
Article
Relative to the sterically hindered model compounds (I) 2,2'-dimethoxy-1,1'-binaphthyl and (II) 3,3'-dimethyl-1,1'-binaphthyl-20-crown-6, the pressure dependence of the fluorescence of racemic crystals of 1,1'-binaphthyl (III) is complex. Compression to 40 kbar at room temperature shifts the 1La fluorescence spectra of all three compounds to longer wavelengths but, for I and II does not change the Intensity profile, except for some 0-0 reabsorption. For III, this red shift characteristic of 1La fluorescence spectra is dominated by growth of new bands about 3.5 to 5.0 × 10 cm−1 to lower energy. Similar new bands are observed when racemic 1,1'-binaphthyl crystals are compressed at 77 K or resolved crystals are compressed at room temperature, but are not found to 50 kbar for dilute solutions of 1,1'-binaphthyl in polyacrylonitrile. Time-resolved fluorescence spectra, excited at 285nm by doubling the 570nm cavity-dumped output of a mode-locked Spectra-Physics 375-01 rhodamin 6G dye laser synchronously pumped by a mode-locked Spectra-Physics 171-05 argon laser, show that the new bands originate from a state with a longer lifetime (τ = 2.0 nsec at 20 kbar) than the 1La state (τ = 1.1 nsec). The planes of adjacent naphthyl residues along →b in the racemic crystal are parallel but offset, the normal distance between planes being 355pm; Raman spectra provide no evidence for a structural phase transformation upon compression. These new bands are assigned as the binaphthyl excimer.
 
Article
1,1′-Trimethylene-bis (5R, 5R′) uracils (R=halogen, R′=halogen or alkyl), 1-methyl-5-chlorouracil, and 1,3-dimethyl-5-chlorouracil in aqueous and acetonitrile-d6 solutions were studied by FTIR and vapour pressure osmometry. FTIR spectra show that with the compounds 5–12 intermolecular NH…OC bonds are formed. The osmometric measurements demonstrate that compounds 5–12 are always dimerized due to hydrogen bonds and dipole—dipole interactions as well as the base—base stacking interactions. Compounds 13 and 14 exist as monomers at low concentration; compound 14 dimerizes with increasing concentration.
 
Article
Racemic forms of 1,1′-bi-(2-naphthol) (BINOL) monopivalate (rac-1) and its 6-nitro substitute (rac-2) were structurally characterized by X-ray crystallography. Molecules of opposite chirality form dimers in the crystalline state of rac-1 through OH⋯O hydrogen-bonds between the free hydroxy and the pivalate carbonyl group. In contrast, polymeric hydrogen-bonded homo chiral chains were encountered for rac-2. In both rac-1 and rac-2, the dihedral angle between the naphthyl systems shows a significant deviation compared to the approximate 90° angle of BINOL. As expected, compound rac-1 exhibits an increased angle (108.80(4)° and 102.09(4)°) as one of the hydroxy groups in BINOL is replaced by the sterically demanding pivaloyl ester. In contrast, the angle is decreased to 72.0(2)° in the nitro derivative rac-2.
 
Article
Gas electron diffraction data are applied to determine the geometrical parameters of the 1,1-dichlorosilacyclobutane molecule using a dynamic model where the ring puckering was treated as a large amplitude motion. The structural parameters and parameters of the potential function were refined taking into account the relaxation of the molecular geometry estimated from ab initio calculations at the Hartree-Fock level of theory using a 6–311 + G∗∗ basis set. The potential function has been described as with the following parameters and ϕe = 25.9 ± 2.6°, where ϕ is the puckering angle of the ring. The classic distribution function used for averaging the local molecular configurations was found to underestimate the value V0 by 8% as compared with the exact quantum mechanical distribution function. The geometric parameters at the minimum V(ϕ) ( in degrees and errors given as three times the standard deviations including a scale error) are: r(Si−Clax) = 2.043(2), r(Si−Cleq) = 2.038(2), r(Si−C) = 1.860(3), r(C−C) = 1.557(4), r(C−H) = 1.091(8), ∠ClSiCl = 105.2(8), ∠CSiC = 81.1(10), ∠SiCHeq = 118.9(54), ∠SiCHax = 109.7(54), ∠CC5Heq = 105.3(63), ∠CC5Hax = 100.9(63), HC3H = 108.0, ∠δ(ClSiCl) = 4.1, ∠δ(HC3H) = 3.0, where the tilt angle δ, and ∠HC3H are estimated from ab initio constraints. The structural parameters are compared with those obtained for related compounds. Distortions of the valence angles at the Si atom in silacyclobutanes are shown to be well explained using the VSEPR model complemented by the concept of bent bonds.
 
Article
C12H21N5S2O2, Mr = 331.46, triclinic, P1̄, a = 7.3645(5), b = 8.8785(9), c = 25.678(4) Å, α = 89.35(1)°, β = 82.49(1)°, γ = 87.46(1)°, V = 1662.9(5) Å3, Z = 4, Dx = 1.324 g cm−3, λ(Cu Kα) = 1.54184 Å, μ = 29.57 cm−1, F(000) = 704.0, T = 293 K, final R = 0.057 for 4830 observed reflections. Nizatidine, Axid®, is a selective H2-receptor antagonist used in the treatment of duodenal ulcers. The pharmaceutical nizatidine crystallizes with two independent molecules in the asymmetric unit. The two molecules have similar conformations, with the exception of the dimethylamino group. The bisalkylamino-2-nitroethene moiety differs from the structurally related hydrogen oxalate salt form of ranitidine in that the nitro group of nizatidine is the cis geometrical isomer with respect to the ethylamino group.
 
Article
The geometric structures of the three title compounds have been determined by gas-phase electron diffraction. In all cases the five-membered rings are strongly puckered and possess half chair conformations with the following geometric parameters (ra values with 3σ error limits). c-C4F8S: (CC)mean=1.548(4), SC=1.822(4) Å, CSC=94.5(3)°, SCC=107.4(3)°, CCC=106.4(4)° and puckering amplitude q=0.411(8) Å. c-C4F8SO: (CC)mean=1.553(5), SC=1.903(4) Å, CSC=89.4(4)°, SCC=110.2(4)°, CCC=106.5(6)°, q=0.403(8) Å. c-C4F8SO2: (CC)mean=1.556(6), SC=1.882(7) Å, CSC=93.2(10)°, SCC=107.7(10)°, CCC=107.9(12)°, q=0.382(10) Å. Comparison with the analogous protonated rings reveals that upon fluorination the degree of puckering decreases slightly in c-C4F8S and c-C4F8SO, whereas it increases strongly in c-C4F8SO2.
 
Article
The infrared spectra of 1,1-dimethyl-1-silacyclobutane in the vapor and solid phases have been recorded from 3300 to 80 cm−1. The Raman spectra of all three phases have been measured and depolarization data have been obtained for the gaseous and liquid states. An assignment of the fundamental vibrations is presented. The methyl torsional frequencies have been assigned to two weak bands appearing in the Raman spectrum of the gas phase at 177 and 172 cm−1. These values result in a barrier to internal rotation of 2.1 kcal mole−1. Evidence is presented for the existence of a quasi-planar conformer in the ambient temperature fluid phases, which obeys Cs selection rules in the low temperature solid state. This structure is compared to those of other silacyclobutanes and possible explanations given for the differences.
 
Article
The IR and Raman spectra of the three substituted germacyclopent-3-enes, CH2CHCHCH2GeR2 for R= Cl, CH3 or OCH3, have been recorded and assigned. The spectra have been found to be consistent with C2v symmetry, corresponding to a planar ring structure for each molecule.
 
Article
The Raman (3500−20 cm−1) and infrared (3500−50 cm−1) spectra of gaseous and solid 1,1-diethynylsilacyclobutane, c-C3H6Si(CCH)2, have been recorded. Additionally, the Raman spectrum of the liquid has been recorded and qualitative depolarization values have been obtained. These spectra have been interpreted on the basis of Cs molecular symmetry where the ring is puckered and the two ethynyl groups are essentially linear. The assignments of the fundamental vibrational frequencies are compared with those obtained from a force field obtained by ab initio calculations employing the RHF/6-31G** basis set. Similar calculations have been carried out for silacyclobutane-d0 and the Si-d2 isotopomer. These results are discussed and compared with those obtained for some related molecules.
 
Article
The electronic structure of organometallic fullerene complex C60Pd(P(C6H5)2)2Fe(C5H4)2 has been investigated using X-ray fluorescent spectroscopy and density functional theory. It was shown that, the electronic state of carbon atoms incorporated into the complex can be related to the electronic state of carbon atoms that constituted the structural units C60, P(C6H5)3, and Fe(C5H5)2. In the studied complex, palladium atom acts as a bridge in the transferring of electronic density from the ligand phosphorus atoms to the fullerene cage.
 
Article
A series of second coordination sphere networks, exhibiting both layered and 3D morphologies, have been structurally characterized by X-ray crystallography. These self-assembled networks are sustained by extended hydrogen bonding interactions between organosulfonate acceptor ligands and metal complexes bearing 1,1,1-tris(aminomethyl)ethane (tame) donor ligands. The rationale behind the choice of the molecular building blocks is explained with respect to the design strategy based on potential N–H⋯O hydrogen bonding synthons. In addition to the metal building blocks: Ni(tame)2Cl2 (1) and Co(tame)2Cl3 (2), the synthesis and characterization of four second sphere networks: [{[Ni(tame)2]1(TS)2(H2O)2}∞] (3, TS=4-toluenesulfonate), [{[Ni(tame)2]1(BDS)1(H2O)4}∞] (4, BPDS=4,4'-biphenyldisulfonate), [{[Co(tame)2]1.5(TS)5(H3O)0.5(H2O)1.2}∞] (5, TS=4-toluenesulfonate), and [{[Co(tame)2]1 (NDS)1(Cl)1(H2O)3}∞] (6, NDS=1,5-naphthalenedisulfonate) are presented in this work. The propensity for tame complexes to participate in reliable supramolecular synthons with the sulfonate functionality is discussed in terms of the observed network structures.
 
Article
The preparation of cyclopropane-1,1,2-tricarboxylic acid from cyanoacetic acid and 2,3-dibropropionic acid has been done in one-step procedure in alkaline medium. The compound has been characterized, by nuclear magnetic resonance, mass spectrometry, and thermal analyses. The mass spectrum showed the molecular ion peak in the negative mode. The thermal analysis results show that the compound decomposes in three steps, and the second step of decomposition was tentatively assigned to the loss of two carboxylic acid groups. Also, theoretical calculations were made in order to assign vibrations and determine the most stable structure for the compound.
 
Article
Charge-transfer (CT) complexes formed in the reactions of 2,9-dimethyl-1,10-phenanthroline (Me2phen) with some acceptors such as chloranil (Chl), picric acid (HPA) and chloranilic acid (H2CA) have been studied in the defined solvent at room temperature. Based on elemental analysis and infrared spectra of the solid CT-complexes along with the photometric titration curves for the reactions, obtained data indicate the formation of 1:1 charge-transfer complexes [(Me2phen)(Chl)] (1), [(Me2phenH)(PA)] (2) and [(Me2phenH)(HCA)] (3), respectively, was proposed. In the three complexes, infrared and 1H NMR spectroscopic data indicate a charge-transfer interaction and as far as complexes 2 and 3 are concerned this interaction is associated with a hydrogen bonding. The formation constants for the complexes (KC) were shown to be dependent upon the nature of the electron acceptors used. The X-ray structure of complex 3 indicate the formation of dimeric units [Me2phenH]2[(HCA)2] in which the two anions (HCA)− are connected by two O–H⋯O hydrogen bonds whereas the cations and anions are joined together by strong three-center (bifurcated) N–H⋯O hydrogen bonds. Furthermore, the cations are arranged in a π–π stacking.
 
Article
Two new chiral ruthenium(II) complexes Δ-[Ru(bpy)2(nfip)]2+ and Λ-[Ru(bpy)2(nfip)]2+ (in which bpy = 2,2′-bipyridine, nfip = 2-(5-nitrofuran-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline) have been synthesized and characterized by elemental analysis, ES-MS, 1H NMR and CD spectra. The binding properties of two chiral complexes with calf thymus DNA have been investigated by different spectrophotometric methods and viscosity measurements. A subtle but detectable difference was observed in the interaction of both enantiomer with CT-DNA, Δ enantiomer binds with DNA more strongly than Λ enantiomer. Viscosity experiments provided evidence that both Δ-[Ru(bpy)2(nfip)]2+ and Λ-[Ru(bpy)2(nfip)]2+ bound to DNA by intercalation.
 
Article
A new copper(II) complex, [Cu(sal-l-val)phen] (sal-l-val = a Schiff base derived from salicylaldehyde and l-valine, phen = 1,10-phenanthroline), has been synthesized and characterized by elemental analysis, IR spectra and X-ray single crystal diffraction. Results show that this crystal structure of the copper(II) complex belongs to triclinic crystal system, P1 space group with crystallographic data: a = 10.3710(16) Å, b = 13.9350(19) Å, c = 16.670(2) Å, α = 79.970(2)°, β = 75.623(2)°, γ = 84.160(3)° and Z = 4. The copper(II) complex has four independent structures in the crystallographic asymmetric unit, three of them show distorted square-pyramidal and the fourth displays distorted trigonal bipyramid CuN3O2 coordination geometry. In the crystal, π–π stacking and the intermolecular hydrogen bonds form two-dimensional network. The interactions between the copper(II) complex and calf thymus DNA(CT-DNA) have been studied by using UV, fluorescence and CD spectra, as well as viscosity and thermal denaturation measurements. Experiment results confirm that the copper(II) complex binds to CT-DNA in an intercalative mode.
 
Article
The reactions of Ga(NO3)3 · 9H2O with 2,2′-bipyridine (bpy), 1,10-phenanthroline (phen) and 2,2′:6′,2″-terpyridine (terpy) in alcohols afford the complexes [Ga2(OH)2(bpy)4](NO3)4 (1), [Ga2(OH)2(phen)4](NO3)4 (2) and [Ga2(OH)2(H2O)2(terpy)2](NO3)4 (3), respectively, in good yields. The crystal structures of 1 · 1.3MeOH · 1.4H2O, 2 · 4.5MeOH and 3 have been solved by single-crystal X-ray crystallography. The three complexes contain the core. Four nitrogen atoms from two chelating bpy (1) or phen (2) complete distorted octahedral coordination at each metal centre. In 3 one tridentate chelating terpy and one aquo ligand complete six coordination at each GaIII atom. The crystal structure of 2 · 4.5MeOH is stabilized by hydrogen bonds and intermolecular π–π stacking interactions, while in 3 hydrogen bonds create a double-chain, ladder-like architecture. Characteristic IR data are discussed in terms of the nature of bonding and the structures of the three complexes. The 1H NMR spectra of complexes 2 and 3 suggest the presence of the free ligand and one solution species containing the coordinated ligand. The structure of the cation [Ca2(OH)2(bpy)4]4+ is retained in D2O as deduced by the 2D homonuclear COSY map.
 
Article
Three novel Cd(II) complexes, formulated as [Cd(3,8-dibromo-1,10-phen-κ2N,N′)(l-tar)]n (1), trans-[Cd(3,8-dibromo-1,10-phen-κ2N,N′)2(NO3-κ2O,O′)2]·(CH3CN) (2) and cis-[Cd(3,6-dibromo-1,10-phen-κ2N,N′)(3-bromo-1,10-phen-κ2N,N′)(NO3-2O,O′)(CH3OH-κO)](NO3) (3) (phen = phenanthroline, l-tarH2 = l-tartaric acid), have been synthesized and characterized in this paper. In coordination polymer 1, the [Cd2(3,8-dibromo-phen)2]4+ cations are bridged by l-tar ligands into an infinite 2D lamellar polymer along the c-axis, and the neighboring 2D polymers are further extended into a 3D supramolecular network by π–π stacking interactions. Complexes 2 and 3 are both mononuclear cadmium complexes but with different conformation (trans or cis). In the crystal packing structures of 2 and 3, molecules are arranged into three-dimensional (3D) frameworks by intermolecular hydrogen bonding and π–π stacking interactions.
 
Article
Proton or charge transfer (CT) complex of donor, 1,10-phenanthroline (Phen) with π-acceptor, p-Nitrophenol (PNP) has been studied spectrophotometrically in methanol at room temperature. The binding of the CT complex with calf thymus (ct) DNA has been investigated by fluorescence spectrum, to establish the ability of the CT complex of its interaction with DNA. Stern–Volmer quenching constant (Ksv) has also been calculated. The formation constant (KCT), molar extinction coefficient (εCT), free energy (ΔGo) and stoichiometric ratio of the CT complex have been determined by Benesi–Hildebrand equation. The stoichiometry was found to be 1:1. The CT complex was screened for its pharmacology as antibacterial and antifungal activity against various bacterial and fungal strains, showing excellent antibacterial and antifungal activity. The newly synthesized CT complex has been characterized by FTIR spectra, elemental analysis, 1H NMR, electronic absorption spectra. TGA–DTA studies were also carried out to check the stability of CT complex.
 
Article
A new cobalt(III) complex salt, [Co(phen)3](dnp)3·4H2O has been synthesized in an effort to utilize [Co(phen)3]3+ cation as a new host for di-substituted phenolate (2,4-dinitrophenolate) anion. This cobalt (III) complex salt has been characterized by elemental analyses and spectroscopic techniques (UV/visible, IR, NMR and conductance measurements). Single crystal X-ray structure determination confirmed the composition [Co(phen)3](dnp)3·4H2O. A strong network of hydrogen bonding interactions C–H...O (phenolate), C–H…O (nitro) involving second sphere coordination and O–H…O hydrogen bonding interactions stabilize the crystal lattice. The formation of a complex salt of definite composition along with solubility product data suggests that [Co(phen)3]3+ present in [Co(phen)3]Cl3 may be used as an anion receptor for 2,4-dinitrophenolate ion.
 
Article
A copper(II) malonate complex with formula [Cu(mal)(phen)(H2O)]2·3H2O (1) [H2mal = malonic acid, phen = 1,10-phenanthroline] has been synthesized and its crystal structure has been re-determined with an improved R value (the compound 1 was originally synthesized and crystallographically characterized by Kwik et al. with R = 0.047, see: J. Chem. Soc. Dalton Trans. (1986) 2529) with the water hydrogen atom positions located. This has led to the revelation that the water molecules organize around the carboxylate group of the malonate ligand forming tetramer, hexamer and octameric water cluster mimics. These cooperative hydrogen-bonding forces and various π-forces (π⋯π, Cu(II)⋯π, carbonyl⋯π) involving 1,10-phenanthroline aromatic rings determine the overall packing of the molecular units in the unit cell. There exists two identical monomers in the asymmetric unit with Z// = 2. TG measurements reveal the loss of water molecules that are all released at 120 °C. The water sorption/desorption process is reversible as supported by FTIR spectroscopic and XRPD studies.
 
Article
The effect of attaching an additional fluorine atom at C-2 in 1-fluoropropane (FP), giving 1,2-difluoropropane (DFP), on its conformational equilibrium, is theoretically evaluated. This substitution causes critical implications on the conformer stabilities of DFP (TG, GT and GG conformations) and the steric and electrostatic interactions should favor the conformer with fluorine atoms trans. However, the gauche effect plays a major role in describing the energies balance in DFP, shifting the equilibrium towards the conformation in which the two fluorine atoms are gauche. The origin of this effect is discussed through an NBO analysis, which allows the evaluation of both classical and non-classical (hyperconjugation and bent bonds) interactions as the prevailing factors governing the conformational equilibrium of molecules containing the 1,2-difluoroethane fragment.
 
Top-cited authors
Jan Baran
  • Polish Academy of Sciences
Zofia Dega-Szafran
  • Adam Mickiewicz University
Heinz Oberhammer
  • University of Tuebingen
Włodzimierz Mozgawa
  • AGH University of Science and Technology in Kraków
Svein Samdal
  • University of Oslo