Showing papers in "Structural Chemistry in 2005"

What Can Tell the Topological Analysis of ELF on Hydrogen Bonding

Abstract: The topological analysis of the electron localization function (ELF) provides a convenient mathematical framework enabling an unambiguous characterization of bonds, and more particularly in terms of bond types In this communication we present an overview of the application of this approach to hydrogen bonding in which we attempt to answer the following questions: 1 What is the ELF based topological definition of the hydrogen bond? 2 Is a hydrogen bonded complex a molecule or an assembly of molecules? 3 Is there a topological descriptor of the hydrogen bond strength? 4 Is it possible to provide a sub-classification of hydrogen bonds? 5 Is the topological approach predictive of the structure of the complex?

Quantum Chemical Calculation Studies on 4-Phenyl-1-(Propan-2-Ylidene)Thiosemicarbazide

Abstract: Ab initio calculations of the structure, atomic charges, natural bond orbital, and thermodynamic functions have been performed at HF/6-311G∗∗ and B3LYP/6-311G∗∗ levels of theory for the title compound of 4-phenyl-1-(propan-2-ylidene)thiosemicarbazide. The calculated results show that the sulfur atom and all of the nitrogen atoms have bigger negative charges and they are the potential sites to react with the metallic ions, which make the title compound become a multidentate ligand. The coordination ability of the sulfur atom and the nitrogen atom of C=N double bond will increase with the increase of the polarity of the solvent. Electronic absorption spectra have been calculated by time-dependent density functional theory (TD-DFT) method. The calculation of the second-order optical nonlinearity also has been carried out, and the molecular hyperpolarizability is 3.068×10−30 esu.

A DFT-Based Study of the Low-Energy Electronic Structures and Properties of Small Gold Clusters

Abstract: Gold clusters Aun of size n = 2–12 atoms were studied by the density-functional theory with an ab-initio pseudopotential and a generalized gradient approximation. Geometry optimizations starting from a number of initial candidate geometries were performed for each cluster size, so as to determine a number of possible low-energy isomers for each size. Along with the lowest-energy structures, metastable structures were obtained for many cluster sizes. Interestingly, a metastable planar zigzag arrangement of Au atoms was obtained for every cluster size n ≥ 5. The stable electronic structure, binding energy, relative stability and HOMO–LUMO gap for the lowest-energy isomer were calculated for each cluster size. Variation of the electronic properties with size is investigated in this paper and compared with experimental results and other calculations.

Theoretical Investigation of Normal to Strong Hydrogen Bonds

Abstract: We review our theoretical work done on a variety of different chemical systems, which show different H-bonding characteristics. The systems include water clusters, its interactions with polar molecules and π-systems, organic nanotubes, enzymes, and ionophores/receptors. Special features of normal, short, short strong, and π-type H-bonding interactions in these systems are discussed in terms of structures, interaction energies, and spectra.

Stacking Interactions in Benzene and Cytosine Dimers: From Molecular Electron Density Perspective

Abstract: The stacking patterns of benzene and cytosine have been compared with the help of Bader’ theory of atoms in molecule using the conventional ab initio method. In addition, the differences in the stacking and hydrogen-bonded interactions in cytosine have also been quantified with the help of various topographical features of molecular electron density. The electron density at the bond critical point does not exhibit linear relationship with the strength of stacking interaction in various twisted cytosine dimers. However, the electron density and Laplacian of electron density at the cage critical point display good linear relationship with the stacking energy. The values of the electron density and Laplacian of electron density derived from AIM theory is highly useful in differentiating stacking and hydrogen-bonded interaction. The aromaticity of cytosine and cytosine stack has been compared with benzene and benzene stack employing NICS criteria.

Two New Octahedral Cd(II) Complexes [Cd(L)2] and {[Cd(LH)2(SCN)2]H2O} [L = C6H5C(OH)NN = C(CH3)C5H4N]: Synthesis and Structural Studies

Abstract: Two new octahedral Cd(II) complexes [Cd(L)2] (1) and {[Cd(LH)2(SCN)2]H2O} (2) [where LH = C14H13N3O] are synthesized using a tridentate hydrazone ligand (LH) and they are characterized by elemental analysis, IR spectra, NMR spectra, thermal studies and finally the structures have been determined by single crystal X-ray diffraction. Complex 1 crystallizes in monoclinic system, space group C2/c with a = 22.565(6) A, b = 10.252(3) A, c = 12.187(4) A, β = 118.851(2)∘, and Z = 4. Complex 2 also crystallizes in the monoclinic system, space group P21/c with a = 9.257(9)A, b = 17.809(2)A, c = 9.548(9)A, β = 107.439(4)∘, and Z = 2. In 1 the ligand binds the Cd(II) ion in tridentate fashion, whereas in 2 it acts as a bidentate ligand.

One Novel Cu(II)–Amino Acid Schiff Base Complex Derived from Salicylaldehyde and L-Serine: Identification of Unusual Monodentate 4,4′-Bipyridine

Abstract: One novel copper(II) complex [Cu(L)(4,4′-bipy)](ClO4) (1), (where L: tridentate Schiff base derived from salicylaldehyde and L-serine) has been synthesised and characterised by spectroscopic and electrochemical studies. The single-crystal structure of the complex was determined. The crystal structure features the presence of [Cu(L)(4,4′-bipy)]+ cations and ClO4− anions aggregated by hydrogen bonding. Here, 4,4′-bipyridine functions as a monodentate ligand, which appears to be an unusual phenomenon.

C≡H ⋅s O Hydrogen Bonds in Small Ring Carbonyl Compounds: Vibrational Spectroscopy and Ab initio Calculations

Abstract: The effect of the molecular structure on the properties of C-H⋅s O bonds was investigated in a set of small cyclic carbonyl compounds, using vibrational spectroscopy and ab initio calculations. Two main effects were studied: the size of the ring and the inclusion of oxygen atoms in the ring. The analysis of the band profile of the carbonyl stretching mode reveals the presence of single dimerization equilibria in the series cyclobutanone-cyclopentanone-cyclohexanone. The smallest cyclobutanone was found to have the lowest dimerization energy, with an experimental ΔH value of 3.7± 0.6 kJ mol−1. The systems with oxygen atoms in the ring, γ-butyrolactone and ethylene carbonate were found to present more complex equilibria. Ab initio calculations suggest that this complexity is due to the presence of additional dimer structures and higher oligomers.

Interplay of Thermochemistry and Structural Chemistry, the Journal (Volume 13, 2002) and the Discipline

Abstract: As practiced disciplines, structural chemistry and thermochemistry need not be related. In the current study they are: the contents of the journal “Structural Chemistry” (Vol. 13) for the year 2002 have been reviewed and then most articles that appeared therein were given a thermochemical commentary, “spin” or “slant.”

Adsorption of 2,4-Dinitrotoluene on Dickite: The Role of H-Bonding

Abstract: The adsorption of 2,4-dinitrotoluene (DNT) on the tetrahedral and octahedral surfaces of dickite (a clay mineral of the kaolinite group with a 1:1 dioctahedral structure characterized by the common chemical formula Al2Si2O5(OH)4) was studied using small representative mineral models. The calculations have been performed at the HF/3-21G level of theory. The orientation of DNT on the tetrahedral surface of dickite was found to be coplanar with the surface plane. In the case of the adsorption on the octahedral surface the DNT molecule is placed with an inclination about 30∘ to the surface plane. This type of adsorption results in an electron density redistribution of DNT on the surface of the mineral that is more significant in the case of the adsorption on the tetrahedral surface. The interaction energies of DNT with the octahedral and tetrahedral surfaces corrected by the BSSE energy were found. The adsorption energy of a DNT-tetrahedral fragment amounts to −6.5 kcal/mol, and the interaction energy of the DNT-octahedral fragment system is −17.7 kcal/mol.

Interplay of Thermochemistry and Structural Chemistry, the Journal (Volume 14, 2003) and the Discipline

Abstract: As practiced disciplines, structural chemistry and thermochemistry need not be related. In the current study, the relation is made more evident from among the contents of the journal “Structural Chemistry” (Vol. 14) for the year 2003. The year's articles have been reviewed, giving to most of those appearing therein a thermochemical commentary, “spin” or “slant.”

Substituent effects on hydrogen bonding in Watson-Crick base pairs. A theoretical study

Abstract: We have theoretically analyzed Watson–Crick AT and GC base pairs in which purine C8 and/or pyrimidine C6 positions carry a substituent X = H, F, Cl or Br, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P. The purpose is to study the effects on structure and hydrogen bond strength if X = H is substituted by a halogen atom. Furthermore, we wish to explore the relative importance of electrostatic attraction versus orbital interaction in the above multiply hydrogen-bonded systems, using a quantitative bond energy decomposition scheme. We find that replacing X = H by a halogen atom has relatively small yet characteristic effects on hydrogen bond lengths, strengths and bonding mechanism. In general, it reduces the hydrogen-bond-accepting- and increases the hydrogen-bond-donating capabilities of a DNA base. The orbital interaction component in these hydrogen bonds is found for all substituents (X = H, F, Cl, and Br) to contribute about 41% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining 59% of the attraction.

Change with the Intermolecular Distance of Electron Properties of Hydrogen Bond Dimers at Equilibrium and Non-equilibrium Geometries

Abstract: The change with the intermolecular distance R of a number of electron properties obtained from the electron density ρ(r) and the electron localization function η(r) along with some selected structural features is investigated for seven dimers linked by conventional hydrogen bonds (HBs). Five non-equilibrium geometries apart from the equilibrium one are optimized in MP2/6-311++G(d,p) ab initio calculations for every dimer. The variation with R of topological descriptors and integrated properties computed from ρ(r) and η (r) reveals that not only features characteristics of hydrogen bonding are still noticed inside the equilibrium distance Req but the sign and magnitude of HB trends are kept at R < Req. Only at the shortest intermolecular distances where dramatic structural changes occur, these trends revert their direction although in most cases HB characteristics are still noticed.

A Theoretical Study on the Tautomerism of C-Carboxylic and Methoxycarbonyl Substituted Azoles

Abstract: DFT calculations (B3LYP/6-31+G**) have been carried out on 106 tautomers and conformers of NH-azoles bearing CO2H and CO2CH3 groups. The following azoles systems have been studied: 2-substituted pyrroles, 2-substituted indoles, 2-substituted imidazoles, 2-substituted benzimidazoles, 4(5)-substituted imidazoles, 3(5)-substituted pyrazoles, 3-substituted indazoles (1H and 2H), 3,4(5)-substituted-1,2,3(5)-triazoles, 2,3(5)-substituted-1,2(3),4-triazoles, 4(5)-1,2,3,4(5)-tetrazoles. In the case of pyrazole, 3,5-disubstituted derivatives have also been computed, including four dimers.

Another Structure Type of Oxotris(oxalato)niobate(V): Molecular and Crystal Structure of Rb3[NbO(C2O4)3]⋅2H2O

Abstract: The compound Rb3[NbO(C2O4)3]⋅2H2O (1) has been synthesized by two different methods and its exact chemical composition established. The niobium atom is heptacoordinated by oxygen atoms forming a distorted pentagonal bipyramid. Inspite of some similarities, the structure of 1 is not isotypic with the structure of (NH4)3[NbO(C2O4)3]⋅H2O.

Synthesis and Characterization of Tetra-μ-phenolatotetrazinc(II) Complex with 1-Phenyl-3-Methyl-4-(salicylidene hydrazone)-Phenylethylene-Pyrazolone-5

Abstract: A new phenoxy-bridged tetranuclear zinc(II) complex with 1-phenyl-3-methyl-4-(salicylidene hydrazone)-phenylethylene-pyrazolone-5 (PMPaP-SAH) has been synthesized and characterized by elemental analysis, IR spectrum, molar conductivity, TG-DTA and single crystal X-ray diffraction. The X-ray diffraction analysis shows that the complex is tetranuclear with a rectangular Zn4 core and metal ions are held together by four μ-phenoxo bridges that lead to the formation of the tetra-μ-phenolatotetrazinc(II) complex. Each Zn(II) ion in the complex is penta-coordinated with a slightly distorted trigonal bipyramid coordination sphere.

A Chiral Coordination Polymer of Silver(I) with Saccharinate and Pyridine: Synthesis, Spectral, Thermal, and Structural Characterization of [Ag(sac)(py)]n

Abstract: The first silver(I) complex of saccharinate (sac) with pyridine (py), [Ag(sac)(py)] n has been synthesized and characterized by elemental analysis, IR spectroscopy and single crystal X-ray diffractometry. The complex crystallizes in chiral, trigonal space group P3121 (No. 152) with unit cell parameters of a = 11.2605(2) A, c = 17.3300(4) A, V = 1903.02(6) A3 and Z = 6. [Ag(sac)(py)] n contains monomeric [Ag(sac)(py)] units linked into infinite helices by way of Ag⋅sAg interactions [d(Ag⋅sAg) = 2.909(2) and 2.985(1) A]. The distorted square-planar environment of Ag is completed by an N-bonded sac [Ag—N = 2.084(2) A] and a py molecule [Ag—N = 2.116(2) A]. The Nsac—Ag—Npy angle is 173.85(10)∘. The one-dimensional chains are crosslinked by C—H⋅sO interactions involving the carbonyl and sulfonyl O atoms of sac and aromatic-ring hydrogen atoms of both sac and py. The thermal stability of the title complex was investigated using thermogravimetry and differential thermal analysis in a static atmosphere of air. The first decomposition stage between 90 and 160∘C corresponds to removal of the py molecule in a single stage, while the degradation of the sac moiety occurs at two stages in the temperature range 370–515∘C, giving an end product of metallic Ag.

High-temperature gas-phase electron diffraction: Unexpected dimer structures among metal halides

Abstract: Gas-phase electron diffraction (GED) studies at high temperatures have several special common features that justify their separate discussion. Due to the difficulties connected with the experiment this technique has developed only in a few laboratories. Most often inorganic systems are studied; lower-valence metal halides and metal oxides. Their low volatility requires high-temperature experimental conditions. Due to the complex vapor composition, other techniques, such as quadrupole mass spectrometry and, to an increasing degree, quantum chemical calculations accompany these GED studies. The analyses often reveal unanticipated structures. In this paper some unexpected and interesting structures of metal halide dimers will be shown, some from GED, others from computations carried out in connection with the high-temperature GED studies of metal halide systems of low volatility.

Hydrogen Bonding Interactions of Radicals

Abstract: Hydrogen bonding interactions of organic radicals are systematically studied using diverse ab initio and density functional theory (DFT) methods. It is found that open-shell hydrogen bonds with radical proton donors are more difficult to model than those with radical proton acceptors. The DFT methods perform significantly worse than the unrestricted second order Moller-Plesset perturbation (UMP2) method in both geometry optimization and interaction energy calculations for the open-shell hydrogen bonds. The UB3LYP method seriously underestimates the donor-acceptor distances and overestimates interaction energies for the open-shell hydrogen bonds with radical proton donors. Nevertheless, use of the UBH&HLYP functional to study the open-shell hydrogen bonds is still acceptable. Furthermore, it is necessary to use sufficiently flexible basis sets, such as 6-311++G(2df,2p), to get reliable interaction energies for the open-shell hydrogen bonds. The open-shell proton donors are stronger Lewis acids than the corresponding closed-shell proton donors. The open-shell proton acceptors are weaker Lewis bases than the corresponding closed-shell proton acceptors.

MH⋅sHX Dihydrogen Bond with M≡Li, Na and X≡F, Cl, Br: A CP-Corrected PES Calculation and an AIM Analysis

Abstract: Dihydrogen-bonded systems MH ⋅s HX (M=Li, Na and X=F, Cl, Br) have been studied at HF, DFT/B3LYP and MP2 level of theory. Some of these complexes are found to be stationary points with two degenerated imaginary frequencies, while the others are considered as minima in the potential energy surface (PES). In order to eliminate the basis set superposition error (BSSE) and have a better description of such stationary points, counterpoise correction (CP) has been applied to the whole surface, obtaining the CP-corrected PES for each system. These BSSE-free PES’ present a new minimum with different topology, i.e. number of imaginary frequencies. Two different groups of complexes can be distinguished, depending on dihydrogen bond strength and electrostatic or covalent contributions. To analyse these interactions, calculations in the framework of atoms in molecules (AIM) theory have been performed, as well as a discussion about charge transfer.

Endohedral Complex of Fullerene C60 with Tetrahedral N4, N4@C60

Abstract: B3LYP/6-31G(d) hybrid HF/DFT and BLYP/6-31G(d, p) DFT calculations were carried out to determine the structural and electronic properties of the endohedral complex of C60 with Tetrahedral N4 (T d N4), N4@C60. It was demonstrated that N4 was seated in the center of the fullerene cage and the tetrahedral structure of N4 is remained in the cage. The formation of this complex is endothermic with inclusion energy of 37.92 kcal/mol. N4 endohedral doping perturbs the molecular orbitals of C60 not so much, the calculated HOMO–LUMO gaps, the electron affinity (EA) and the ionizational potential (IP) of N4@C60 are similar to that of C60.

Polyynes vs. Cumulenes: Their Possible Use as Molecular Wires

Abstract: Polyynes and cumulenes from 2–12 atoms have been calculated at the B3LYP/6-311++G** level and their energies compared using an isodesmic reaction. The chain length has been modeled empirically affording an equation that predicts substantial variation for long chains.

Structure and Vibrational Spectra of 1:1 Chloranilic Acid (CLA)—Tetramethylpyrazine (TMP) Complex

Abstract: A) hydrogen bonds without proton transfer are present. The components of the complex form stacks of parallel arrangement with the distance typical of van der Waals interaction. One can conclude that in packing, interactions via hydrogen bonds play a decisive role. In the IR spectrum one observes a broad, continuous absorption with well resolved trio typical of strong hydrogen bonds. A detailed analysis of IR and Raman spectra in the low frequency region related to deformation vibrations of CH3 groups shows that strong interaction via hydrogen bonding only slightly affects the dynamics of these groups.

Complete NMR Elucidation of Two N-Protected Trishomocubane Hydantoins and the Ethyl Ester of the Corresponding Amino Acid

Abstract: In an attempt to resolve a racemic mixture of a trishomocubane hydantoin, the synthesis of a pair of novel diastereomers was obtained by protecting the racemic hydantoin with chlorocarbonic acid-(−)(R)-sec-butyl ester. An achiral i-propyl ester was first used to establish the procedure. The NMR elucidation of both the chiral and achiral N-protected hydantoins is described. Some proton and carbon NMR shifts on the cage are reversed when relative small changes on the protection group are introduced. The chiral centre on the protective group induced splitting of some carbon signals in the 13C spectrum on the cage skeleton, but effective separation of the diastereomers could not be obtained. In a further attempt to demonstrate the potential use of the trishomocubane amino acid in peptide synthesis, the ethyl ester of the cage amino acid was synthesised. The structures of the amino acid derivatives were elucidated with 2D NMR techniques and the assignment of the NMR data is presented.

Calculations of the Bond Dissociation Energies for NO2 Scission in Some Nitro Compounds

Abstract: The X(C,N,O)—NO2 bond dissociation energy (BDE) for CH3NO2, C2H3NO2, C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2, (CH3)2NNO2 are computed using the DFT (B3LYP, B3PW91), the single and double-coupled cluster excited (CCSD), and the complete basis set (CBS-Q) methods, with the 6-311G** and cc-pVDZ basis sets. By comparing the computed energies and experimental results, we find that the DFT method can not give good results of BDE, but, the BDEs generated by the CCSD/cc-pVDZ, CBS-Q are in good agreement with experimental values.

Porous Solids of Divalent Metal Complexes Assembled Through Hydrogen Bonding and π–π Stacking Interactions

Abstract: The compound N, N′-di(6-methyl-2-pyridyl)formamidine (HDMepyF) has been exploited in preparation of porous materials of divalent metal complexes of the formulae M(HDMepyF)2(NO3)2 (M=Cd, 1; Co, 2; Ni, 3) and M(HDMepyF)2X2 (M=Mn, X=Cl, 4; M=Mn, X=Br, 5; M=Ni, X=Cl, 6; M=Ni, X=Br, 7). Their structures have been determined by X-ray crystallography. Each metal center of these complexes is approximately octahedrally coordinated by four nitrogen and two halogen or oxygen donor atoms. Complexes 1– 5 and 7 self-assemble through similar hydrogen bonding motifs which involve the C–H⋅sX (X=Cl, Br or O) hydrogen bondings and π–π stacking interactions between the HDMepyF ligand and the X atoms to form porous structures.

Syntheses, Crystal Structures, and Magnetic Properties of Carboxylate-Bridged Copper(II) Complexes with Bis(2-Pyridylmethyl)Amino Acids

Abstract: Tetradentate Schiff-base carboxylate-containing ligands, bis(2-pyridylmethyl)amino-5-valeric acid (Hpmva) and bis(2-pyridylmethyl)amino-6-caproic acid (Hpmca), react with copper(II) perchlorate to give rise to the carboxylated bridged chain complexes {[Cu(μ-pmva)(H2O)](ClO4)} n (1) and {[Cu(μ-pmca)(H2O)](ClO4)} n (2). These complexes have been characterized by X-ray crystallography, spectroscopic, and variable-temperature magnetic susceptibility measurements. In 1 and 2, each of the copper(II) ions exhibit CuN3O2 coordination environments with the three nitrogen atoms of the ligand and one oxygen atom belonging to the carboxylate group of an adjacent molecule occupying the basal position and a water molecule coordinated in the axial position. The electronic spectra of the complexes are significantly affected by the coordination geometry. Magnetic susceptibility measurements indicate that complexes exhibit very weak ferromagnetic interactions.

Crystal Structure and Thermal Property of a Binuclear Manganese(II) Sulfate Complex with Carbohydrazide

Abstract: The binuclear manganese(II) complex of formula [Mn2(CHZ)2(H2O)2(SO4)2] (CHZ = carbohydrazide) (1) has synthesized in aqueous solution and characterized by elemental analysis, IR, and single crystal X-ray diffraction. The compound 1 crystallizes in monoclinic system, space group P2(1)/n, a = 7.083(1) A, b = 7.985(1) A, c = 14.045(2) A, β = 90.46(1)∘, V = 794.42(16) A3, Z = 2, R = 0.0308 with 1481 reflections. In the title complex, two Mn(II) cations are bonded via the bridging oxygen atoms into a centrosymmetric dimeric unit. The Mn(II) dimers are further extended into layers by means of the bridging sulfate groups. Each Mn atom in the complex is in bivalent state with a distorted pentagonal bipyramid configuration and has a N2O5 donor set which consists of two nitrogen atoms and five oxygen atoms provided by the ligands of two CHZ molecules, one water molecule, and two sulfate ions. The CHZ tridentate ligands are coordinated with adjacent Mn(II) cation via two terminal N atoms and the carbonyl O atom and sulfate anions act as bidentate bridge ligand. Four kinds of Mn(II) CHZ complex structures are compared. The thermal property of title complex was studied by using DSC and TG-DTG techniques. The results exhibit the title complex is highly stable.

Ab Initio Study and Its Comparison with X-ray Crystal Structure of 4-[1-(4-Chloro-phenylamino)-ethyl] 5-methyl-2- p -tolyl-2,4-dihydro-pyrazol-3-one

Abstract: The ab initio calculation of the title compound was carried out at HF as well as DFT level of theory. The full geometry optimization of the ligand was carried out using 6-31G(d) basis set. The results obtained were correlated with the single crystal X-ray data, also reported in this paper, shows close resemblance between these two. The influence of electron correlation effects also was studied by carrying out geometry optimization at the MP2 level. The attempts were also made to ascertain the most stable tautomer of the said compound.

Ion Selective Electrode Determination of Free Versus Total Fluoride Ion in Simple and Fluoroligand Coordinated Hexafluoropnictate (PnF6−, Pn = P, As, Sb, Bi) Salts

Abstract: Interpretation of the results of determinations of free fluoride (Ff−) and total fluoride (Ft−) obtained with fluoride ISE while conducting elemental chemical analysis of bulk material of newly synthesized inorganic fluoride compounds is of crucial importance for the purpose of determination of purity and stoichiometry of these compounds. Knowledge of the properties and behavior of these compounds in aqueous media is therefore essential. Observations are presented on the determinations of the amounts of Ft− and Ff− in fluorinated compounds, in the particular hexafluoropnictate salts (PnF6−, Pn = P, As, Sb, Bi) as found in aqueous media and in some compounds with XeF2, AsF3 ligands. A critical look at the determined amounts of Ff−, Ft−and calculated amounts of bound fluoride (Fb−) is provided.