Topological Analysis Of Charge Density Research Articles

First-principles calculations of structural and bonding properties of Li-doped tetrahedrite thermoelectrics

Tetrahedrite (copper antimony sulfosalt) is a promising p-type thermoelectric material due to its very low intrinsic thermal conductivity and moderately-high power factor, with one of the limitations being the lack of n-type variant to create a thermoelectric generator. In this paper, DFT calculations have been carried out to study tetrahedrite doped with Li into structural voids, LixCu12Sb4S13 (0≤x≤3). Enthalpies of formation show that the introduction of Li into both 6b and 24 g sites is energetically favorable. Dopants in those positions differently affect the rattling Cu(12e) behavior, as well as vary in the magnitude of induced local disorder. Topological analysis of charge density classifies tetrahedrite as a closed-shell, ionic system of interactions with some degree of covalency. The addition of Li increases bond strain and decreases structural stability. Electronic band structure shows that for x>2.0, material becomes n-type; however, results are not precisely conclusive on whether structure will be synthesizable, which should be determined experimentally.

Palladium and platinum complexes of primary 2-pyridinethioamide

Primary thioamide, 2-pyridinethioamide reacts with palladium and platinum compounds K2PdCl4, K2PtCl4 and Pd(CH3COO)2 to give the products [PdCl2(2-pyridinethioamide)].2DMF (1), [PtCl2(2-pyridinethioamide)] (2a), [Pd(2-pyridinethioamide)2]Cl2 (3), [Pt(2-pyridinethioamide)2]Cl2 (4) and [Pd(2-pyridinethioamidinate)2] (5), respectively. The structures 1, [PtCl(DMSO)(2-pyridinethioamidinate)] (2b), which was obtained from crystallization of 2a in DMSO, 4 and 5 were determined by X-ray crystallography. Compound 3 was spectroscopically analyzed and found to have a structure similar to that of 4. The ligand coordinates in a neutral form in complexes 1, 2a, 3 and 4, but in 2b and 5 it exists in a deprotonated form. Compounds 3 and 4 are cationic complexes with Cl− counterions in the structure. The ligand prefers coordination as the bidentate N(py),S-mode in all the crystallized compounds. In the bis-chelates, the sulfur and the nitrogen atoms are mutually trans-located. Computational DFT calculations and topological charge density analysis were utilized to clarify the coordination modes and to interpret the spectral information.

The effect of halogens in the coordination of 2-pyridinethioamide to gold centers

Primary thioamide, 2-pyridinethioamide reacts with gold compounds Na[AuCl4], [AuCl(tetrahydrothiophene)], AuBr3 and AuI to [AuCl2(2-pyridinecarboxamide)] (1), [AuCl(2-pyridinethioamide)]3 (2), [AuBr(2-pyridinethioamide)]3 (3), and [AuI(2-pyridinethioamide)] (4), respectively. Formation of 1 involves interconversion of thioamide to amide and creation of a N,Ń-auracycle. Compounds 2 and 3 both consist of linear trimeric adducts with aurophilic interactions between the gold atoms. In these compounds, the sulfur donor ligands show monodentate coordination. Similar monomeric unit is present in 4, which in solid state produces dimers via SS chalcogen interactions. The structures were determined by X-ray crystallography. Computational DFT calculations and topological charge density analysis were utilized to clarify interactions, which determine the structures in solid state.

Solvent directs the dimensionality of Cu-dicyanoimidazoles

In this paper, we report one-pot reactions of the same reactants 4,5-dicyanoimidazole and CuI in different solvents. In pure MeCN, the reaction resulted in previously reported MOF structure [Cu(4,5-dicyanoimidazole)]n.(MeCN)0.5n (1). On the other hand, when MeCN/MeOH solvent mixture was used, a new coordination polymer [Cu(4,5-dicyanoimidazole)(MeCN)(CuI)]n (2) was formed. The crystallization yielded very different structures as determined by X-ray crystallography. In 1, the solvent molecule acetonitrile occupies the MOF pores via weak interactions, but in 2 it is coordinated to the metal center. Computational DFT calculations and topological charge density analysis were utilized to explore the different crystal structures with the focus on the role of the methanol solvent.

Benzothiazolethione complexes of coinage metals: from mononuclear complexes to clusters and polymers

The reactions of 2(3H)-benzothiazolethione (Hbtt) with [AuCl(tetrahydrothiophene)] and CuBr2 were studied, and found to yield a tetranuclear cluster compound [Au(btt)]4 [1] and a polymeric structure [CuBr(btt-btt)]n.nTHF (2). Crystallographic and spectroscopic methods were used for the characterization. In 1, the monoanionic ligand acted as a bidentate bridging N,S-donor giving a molecular cluster structure of an asymmetric coordination isomer. In the formation of 2, the ligand was dimerized by forming a S–S bond after deprotonation, and coordination via nitrogen donors to metal atoms took place leading to a polymeric structure. To clarify the diversity of reactions of Hbtt with coinage metals, and to verify the experimental characterization, DFT studies were performed. The nature of the coordination of the Hbtt ligand was further investigated via topological charge density analysis by QTAIM methods.

Impacts of the counter ions on 4,5-dicyano-1-methylimidazole silver coordination

The counter ion regulates the coordination in silver dicyanoimidazole derivatives.

Investigation of Chemical Bonding in In Situ Cryocrystallized Organometallic Liquids.

This Communication presents the crystal structure of the organometallic complexes (η4 -1,3-cyclohexadiene) iron tricarbonyl (I) and (methyl cyclopentadienyl) manganese tricarbonyl (II) which are both liquid at room temperature. The crystal structures were determined using a state-of-the-art in situ cryocrystallization technique. The bonding features were elucidated using topological analysis of charge density in the framework of quantum theory of atoms in molecules (QTAIM) and theoretical charge density analysis (multipolar refinement), to decipher the metal-carbonyl, metal-olefin and metal-carbocyclic ligand interactions in these complexes. Complex I displayed a simultaneous interplay of a "synergic effect" (σ-donation and π-back-bonding in the metal and an end-on coordinated carbonyl interaction) as well as consistency with the Dewar-Chatt-Duncanson (DCD) model (metal and side-on coordinated π-ligand interactions).

On the nature of the coordination bonding of metal–organics for ions with the d10 electronic configuration – Experimental and theoretical analyses

The fundamental goal of this work in applying high resolution crystallographic X-ray measurements of single crystals as well as ab initio and density functional computational methods is to provide a correlation between the experimental electron densities and valence states of atoms with the theoretically predicted ones by methodological approaches of quantum chemistry. In order to test the reliability of the data, we chose to examine statistically the crystallographic datasets of nine metal-organics with Zn2+, Ag+ and Cu2+ ions. There are several premises to the argument for this choice: (i) the different nature of M–L interactions, (ii) various geometries of the chromophores and (iii) distinguishable chemical behavior of the dentate atoms in the inner coordination sphere (L=O, N, Cl). New insights about the nature of the M–L interactions are gained for the following bonding fashions: (a) bonded AgI–X(Y) fragments (X, Y=O and/or N) in tetrahedral (Td) and square planar AgX2Y2 symmetries, (b) bonded ZnII–X(Y) cores (X, Y=O and/or N; or Cl) in Td ZnIIX2Y2 or ZnIIX2 chromophores, (c) ZnII–OH2 interactions in the discrete octahedral {[ZnII(H2O)]2+} charged complex and (d) bonded CuII–X(Y) systems (X, Y=O and/or N) in square planar AgX2Y2 chromophores as comparative examples of complexes with the d9 configurations of the metal ion. The methods of ‘atoms in molecules’ (AIM), ‘natural bond orbital analyses’ (NBO) and electrostatic potentials were employed. The analyses include employment of the bond valence (BV) methodology and non-covalent interaction (NCI) analysis. Quantum chemical prediction of multi-pole moments, orbital population and charge transfer effects (CT), bond covalence, iconicity, different bond order methodologies (BOs); electron density distribution and Laplacian of the total electron density (ED) were carried out. The energetics of the M–L bonds were treated using topological charge density analysis at the bond critical points (bcps). The foci of the presented theoretical and experimental designs allow us to answer our main research questions: Is the nature of the M–L bond with ions having an identical electronic configuration, d10, interacting with one and the same type dentate-ligands the same? and is there a quantitative statistically significant correlation between the theoretically predicted dissociation energetic of the complexes and their experimental topological crystallographic M–L bond energies? The presented comprehensive analyses of this problematic provide crucial new information of both fundamental and applied importance to the field of structural chemistry and the properties of metal–organic molecules. Such results seek to shed light on whether the theoretical models extracting information about the molecular electronic properties of the species in the crystalline state on the base on crystallographic measurements and the corresponding topological, electron density and orbital based methods of computational quantum chemistry are able to enable a common conceptualization about the relationship between ‘crystal structure’–‘molecular structure’–‘electronic structure’–‘M–L bonding type’. The low temperature redetermination of the crystal structure and new description of the structure of the AgI complex of 2-hydroxy-5-sulfo-benzoic acid (1) is reported as well.

Host-guest complex of N-(2-chloroethyl), N-nitroso, N′, N′ -dicyclohexylsulfamid with β-cyclodextrin: Fluorescence, QTAIM analysis and structure-chemical reactivity

In this work, the inclusion complex of DCY/CENS: N-(2-chloroethyl), N-nitroso, N′, N′-dicyclohexylsulfamid and β-cyclodextrin (β-CD) is investigated using the fluorescence spectroscopy, PM3, ONIOM2 and DFT methods. The experimental part reveals that DCY/CENS forms a 1:1 stoichiometric ratio inclusion complex with β-CD. The constant of stability is evaluated using the Benesi-Hildebrand equation. The results of the theoretical optimization showed that the lipophilic fraction of molecule (cyclohexyl group) is inside of β-CD. Accordingly, the Nitroso-Chloroethyl moiety is situated outside the cavity of the macromolecule host. The favorable structure of the optimized complex indicates the existence of weak intermolecular hydrogen bonds and the most important van der Waals (vdW) interactions which are studied on the basis of Natural Bonding Orbital (NBO) analysis. The NBO is employed to compute the electronic donor–acceptor exchanges between drug and β-CD. Furthermore, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), has been accomplished on the most favorable complex using B3LYP/6-31G(d) method. The presence of stabilizing intermolecular hydrogen bonds and van der Waals interactions in the most favorable complex is predicted. Also, the energies of these interactions are estimated with Espinosa's formula. The findings of this investigation reveal that the correlation between the structural parameters and the electronic density is good. Finally, and based on DFT calculations, the reactivity of the interesting molecule in free state was studied and compared with that in the complexed state using chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors.

Persistence of oxidation state III of gold in thione coordination

Ligands N,N'-tetramethylthiourea and 2-mercapto-1-methyl-imidazole form stable Au(III) complexes [AuCl3(N,N'-tetramethylthiourea)] (1) and [AuCl3(2-mercapto-1-methyl-imidazole)] (2) instead of reducing the Au(III) metal center into Au(I), which would be typical for the attachment of sulfur donors. Compounds 1 and 2 were characterized by spectroscopic methods and by X-ray crystallography. The spectroscopic details were explained by simulation of the UV-Vis spectra via the TD-DFT method. Additionally, computational DFT studies were performed in order to find the reason for the unusual oxidation state in the crystalline materials. The preference for Au(III) can be explained via various weak intra- and intermolecular interactions present in the solid state structures. The nature of the interactions was further investigated by topological charge density analysis via the QTAIM method.

Host-guest complex of nabumetone: β-cyclodextrin: quantum chemical study and QTAIM analysis

The aim of the present work is the investigation of the inclusion complex of nabumetone (NAB) and β-cyclodextrin (β-CD) using PM3, DFT, DFT-D and ONIOM2 methods. The results indicate that the most energetically favorable structure predicts a preference of the methoxy group to enter the cavity of β-CD from its wide rim. Consequently, the butanone moiety is positioned outside the cavity on the side of the secondary hydroxyls, with a total insertion of naphthalene group. The semi-empirical PM3 results are in good agreement with those obtained by the DFT optimization (with and without dispersion correction). The donor–acceptor interactions between drug and the cavity wall of the host, studied on the basis of natural bonding orbital (NBO) analysis, show the presence of weak intermolecular hydrogen bonds in addition to the most important van der Waals interactions. Furthermore, it is revealed that among the DFT and DFT-D techniques selected to quantify these interactions, WB97X-D functional provides the greatest values of stabilization energies E(2). Finally, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), developed by Bader and co-workers, has been accomplished using the WB97X-D and B3LYP methods on the most favorable complexes. A good correlation between the structural parameters and the electronic density is found.

Versatile Coordination Modes in Silver-Imidazolecarbaldehyde Oxime Complexes: Structural and Computational Analysis

Silver imidazolecarbaldehyde oxime complexes [Ag(1-methyl-1H-imidazole-2-carbaldehyde oxime)2][NO3] (1), [Ag(1-methyl-1H-imidazole-2-carbaldehyde oxime)2][ClO3] (2), [Ag(1H-5-methylimidazole-4-carbaldehyde oxime)]2[NO3]2 (3), [Ag(1H-imidazole-2-carbaldehyde oxime)]n[NO3]n (4), [Ag(1H-4-methylimidazole-5-carbaldehyde oxime)]n[ClO3]n (5), and [Ag(N-hydroxy-1-methyl-1H-imidazole-2-carboximidamide)2]2[CF3SO3]2 (6) were structurally and computationally analyzed. Weak intramolecular interactions were found to play the main role in determining the most favorable structure of the free ligands, therefore controlling the final coordination mode, and the nuclearity of the complexes. Further information on the nature of the intra- and intermolecular interactions were provided utilizing computational density functional theory calculations and topological charge density analysis according to the Quantum Theory of Atoms in Molecules. The efficient control of the structure of the complexes also results in a better control of the material properties.

Crystal Engineering and Charge Density Study of Pharmaceutical Nonlinear Optical Material: Melamine-Barbital Co-Crystal

This paper presents topological analysis of charge density from multipolar refinement and ab initio calculations for both melamine-barbital co-crystal and isolated molecules. The comparison of electron density properties for the isolated molecules and for the co-crystal allowed one to unravel the factors contributing to the formation of specific hydrogen bond patterns in the co-crystal structure. The inspection of charge density properties revealed that N1A of barbital and N3B of melamine compete for H1A atom in hydrogen bond formation. The hydrogen bond shows an intermediate character between closed and shared shell interaction. The tendency of barbital to adopt tautomeric forms in solution which can be correlated with the shift of electron density (mesomeric effect) was emphasized. Charge density studies confirmed the existence of the mesomeric form B of barbital in the studied co-crystal. The form B was also reported in polar co-crystals comprised of barbital and barbituric acid.

The nature of interactions in nicotinamide crystal

In this study, we analyze the nature of intermolecular interactions in nicotinamide complexes appearing in conformations found in the crystal structure, including many-body effects. In doing so, we employ symmetry-adapted perturbation theory based on density functional theory description of monomers, and we perform the many-body variational–perturbational interaction energy decomposition. The principal finding of this study is that the stability of nicotinamide complexes is a complicated interplay of four (large in magnitude) interaction-energy components, i.e. induction, dispersion, electrostatic and exchange repulsion. However, the last two contributions cancel each other out to a large extent. In the case of considered three-body complexes, the nonadditivity effects are found to be not important. Based on the results of topological analysis of charge densities we characterized also the properties of short H ⋯ H contact and identified it as a weak noncovalent closed shell interaction.

Further orthometalated dinuclear palladium(iii) compounds with bridging N,S-donor ligands

New dinuclear palladium(III) compounds of general formula Pd2[(C6H4)PPh2]2[N-S]2Cl2, N-S being 2-mercaptopyridinate, 3a; 2-mercapto-6-methylpyridinate, 3b; 2-quinolinethiolate, 3c; 2-mercaptopyrimidinate, 3d; 1-methyl-1H-imidazole-2-thiolate, 3e; 1-methyl-1H-benzimidazole-2-thiolate, 3f; 2-mercaptobenzothiazolate, 3g and 5-mercapto-1-methyltetrazolate, 3h have been obtained by oxidation with PhICl2 of the corresponding palladium(II) counterparts. The stability of the new compounds has been studied by (31)P NMR spectroscopy from 200 to 298 K. Compounds 3f-h were relatively stable until room temperature and they have been synthesized and characterized by (31)P, (1)H and (13)C NMR spectroscopy at 223 K. Compound 3h was also structurally characterized by single X-ray diffraction methods at 150 K showing a Pd-Pd distance of 2.6334(6) Å. A topological charge density analysis has also been performed in order to obtain information on the nature of the bonding in these new palladium(II) and (III) compounds. The contribution of the sulphur p orbitals to the HOMO orbitals in the oxidized compounds allows greater stabilization.

New dinuclear copper(I) metallacycles containing bis-Schiff base ligands fused with two 1,2,4-triazole rings: Synthesis, characterization, molecular structures and theoretical calculations

The condensation of 4-amino-3-methyl-1H-1,2,4-triazole-5(4H)-thione (AMTT, L) with 2,2′-[1,2-phenylenebis(methyleneoxy)]dibenzaldehyde in a molar ratio 2:1 in presence of sodium hydroxide in ethanol gave the compound 4,4′-((1Z,1′Z)-((((1,2-phenylenebis(methyl-ene))bis(oxy))bis(2,1-phenylene))bis(methanylylidene))bis(azanylylidene))bis(3-methyl-1H-1,2,4-triazole-5(4H)-thione), H2L1). The reaction of H2L1 with copper(I) chloride in a molar ratio 1:1 in chloroform led to the 42-membered dinuclear metallacycle, [Cu2(H2L1)2(Cl)2]·4CHCl3 (1). The latter underwent halogen exchange reaction with sodium iodide in chloroform forming the complex [Cu2(H2L1)2(I)2]·2CHCl3 (2). All synthesized compounds were characterized by elemental analyses, IR-, 1H NMR-spectroscopy and mass spectrometry as well as X-ray single crystal diffraction analysis. On the basis of determined molecular structures, the complexes 1 and 2 are isostructural and consist of dinuclear metallacyclic units [Cu2(H2L1)2(X)2] (X=Cl (1) and I (2)), in which each ligand acts as bridging agent between two Cu–X units (X=Cl (1) and I (2)) through the sulfur atoms of their five-membered heterocycles. A topological analysis of charge density in the framework of QTAIM shows that there are various noncovalent intramolecular interactions, which control molecular architecture of the complex. The topological and energetic descriptors of the electron density distribution of all BCPs of noncovalent interactions in the complex strongly support the formulation of these interactions as hydrogen bonds and van der Waals interactions, referred to as closed-shell interactions.

Electrochemical potentials of layered oxide and olivine phosphate with aluminum substitution: A first principles study

First-principles prediction of enhancement in the electrochemical potential of LiCoO2 with aluminum substitution has been realized through earlier experiments. For safer and less expensive Li-ion batteries, it is desirable to have a similar enhancement for alternative cathode materials, LiFePO4 and LiCoPO4. Here, we present first-principles density functional theory based analysis of the effects of aluminum substitution on electrochemical potential of LiCoO2, LiFePO4 and LiCoPO4. While Al substitution for transition metal results in increase in electrochemical potential of LiCoO2, it leads to reduction in LiFePO4 and LiCoPO4. Through comparative topological analysis of charge density of these materials, we identify a ratio of Bader charges that correlates with electrochemical potential and determine the chemical origin of these contrasting effects: while electronic charge from lithium is transferred largely to oxygen in LiCoO2, it gets shared by the oxygen and Co/Fe in olivine phosphates due to strong covalency between O and Co/Fe. Our work shows that covalency of transition metal–oxygen bond plays a key role in determining battery potential.

Tuning electrochemical potential of LiCoO2 with cation substitution: first-principles predictions and electronic origin

With a goal to improve the performance of LiCoO2 as a cathode material in Li-ion batteries, we simulate substitution of various elements (X = Be, Mg, Al, Ga, Si and Ti) for Co using first-principles density functional theory and predict changes in its electrochemical potential. While the electrochemical potential of LiCoO2 is enhanced with substitution of Be, Mg, Al and Ga for Co, an opposite effect is predicted of Si and Ti substitution. We determine the electronic origin of these changes in electrochemical potential using (a) Bader method of topological analysis of charge density, (b) partial density of electronic states to estimate oxidation states of metal and oxygen, and charge re-distribution upon lithiation. We find that the distribution of electronic charge donated by Li is influenced by the nature of the X–O bond. A larger electron transfer to O (in XO6 octahedron) upon lithiation leads to stronger Li intercalation and thereby higher electrochemical voltage. Our findings provide a platform for a rational design of cathode materials in Li batteries with enhanced voltage.

Ab initio studies of some hydrogen-bonded complexes of fluoroform – Evidence for blue-shifted behaviour

We have extended a previous study of the complexes of fluoroacetylene with ammonia, water, hydrogen fluoride, phosphine, hydrogen sulphide and hydrogen chloride to the corresponding complexes of fluoroform, as proton donor, with the same series of proton acceptors, in a search for the existence of blue-shifted hydrogen-bonded adducts among these associated species. The complexes with NH3 and PH3 were found to exhibit lengthening of the CH bond of CHF3, but those with H2O, HF, H2S and HCl showed the opposite behaviour. At the harmonic level, with the exception of the NH3 complex, the CH stretching wavenumber of CHF3 was shifted to higher values, while the infrared intensity of this mode decreased uniformly on complexation. At the anharmonic level, on the other hand, all six CH stretching wavenumber shifts were to the blue. In the complexes with NH3, H2O, PH3 and H2S, the CHF3 molecule experienced a net increase of electronic charge but in those with HF and HCl it was found to be the electron donor. A topological charge density analysis showed the presence of bond critical points in the CH⋯X hydrogen-bonded region of all the complexes except CHF3·HF while, in the case of CHF3·HCl, two hydrogen bond critical points and a ring critical point were found. With the exception of the CHF3·NH3 species the remaining complexes successfully meet all the criteria for blue-shifted hydrogen bonding behaviour.

Characterization of Bonding in Cesium Uranyl Chloride: Topological Analysis of the Experimental Charge Density

The topological analysis of the charge density distribution in Cs(2)UO(2)Cl(4) obtained from an accurate X-ray diffraction experiment at 20K is reported. Details of the techniques applied during data collection and data refinement are discussed. A split Hansen-Coppens multipole model for uranium and cesium atoms has been used to describe the charge density features associated with valence electrons and core deformations. The analysis of the deformation density distribution, QTAIM space partitioning, the Laplacian of the electron density, and electron localization function are discussed. Local QTAIM descriptors for bonds to uranium and cesium are reported, as well as integrated properties of each individual atom. U(5f), U(6s), U(6p), U(6d), and U(7s) shells were required to describe the aspherical charge density of the uranium pseudoatom. Observed deformation of the cesium atom core was described by applying the multipole model to Cs(5s) and Cs(5p) shells.