Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes

A set of 44 Zinc‐ligand bond‐lengths and of 60 ligand‐metal‐ligand bond angles from 10 diverse transition‐metal complexes, representative of the coordination spheres of typical biological Zn systems, were used to evaluate the performance of a total of 18 commonly available density functionals in geometry determination. Five different basis sets were considered for each density functional, namely two all‐electron basis sets (a double‐zeta and triple‐zeta formulation) and three basis sets including popular types of effective‐core potentials: Los Alamos, Steven‐Basch‐Krauss, and Stuttgart‐Dresden. The results show that there are presently several better alternatives to the popular B3LYP density functional for the determination of Zn‐ligand bond‐lengths and angles. BB1K, MPWB1K, MPW1K, B97‐2 and TPSS are suggested as the strongest alternatives for this effect presently available in most computational chemistry software packages. In addition, the results show that the use of effective‐core potentials (in particular Stuttgart‐Dresden) has a very limited impact, in terms of accuracy, in the determination of metal‐ligand bond‐lengths and angles in Zinc‐complexes, and is a good and safe alternative to the use of an all‐electron basis set such as 6‐31G(d) or 6‐311G(d,p). © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Chelate ring geometry,and the metal ion selectivity of macrocyclic ligands. Some recent developments

Abstract

The idea (Hancock, 1992) that the dominant architectural feature in controlling metal ion selectivity in both open-chain and macro-cyclic ligands is the size of the chelate ring is pursued further. It is shown that when more than one or two six-membered chelate rings are present in the complex of a nitrogen donor macrocycle, the steric requirements of the six-membered chelate ring of a M-N bond length of 1.6 Å and N-M-N angle of 109.5° become particularly severe, and can only be met by a small tetrahedral metal ion. Thus, the ligand 16-aneN₄ (1,5,9,13-tetraazacyclohexadecane) forms complexes of low stability with all metal ions studied to date, but a conformer of 16-aneN₄ is identified by MM calculation which is predicted to form complexes of high stability with very small tetrahedral metal ions. The question of the M-O bond length and O-M-O angles that will produce minimum strain in chelate rings containing neutral oxygen donor is addressed. The observation (Hay, 1993) that the geometry around an ethereal oxygen coordinated to a metal ion approximates to trigonal planar rather than tetrahedral leads to ideal M-O-C angles of about 126°, which leads to minimum strain energy with much longer M-L lengths in chelate rings containing neutral oxygen donors than neutral nitrogen donors. It is suggested that this fact accounts for the general tendency of crown ethers to form their most stable complexes with potassium out of the alkali metal ions, and also accounts for the very small macrocyclic effect observed in complexes of macrocycles containing mixed nitrogen and oxygen donor groups. The preferred geometry of four-membered chelate rings is discussed, and it is shown that higher coordination numbers of metal ions are associated with four membered chelate rings, and that four membered chelate rings may be used to engineer preference for larger metal ions. Very rigid reinforced chelate rings are discussed, and it is shown that open-chain ligands with reinforced bridges between the donor atoms can display all the thermodynamic and kinetic aspects associated with macrocyclic ligands.     

Structure and bonding in monomeric iron(III) complexes with terminal oxo and hydroxo ligands

We report on the structure and bonding in the title iron(III) complexes, containing the tris[(N'-tert-butylureayl)-N-ethyl]amine ligand, with density functional theory techniques. In agreement with the experimental data, a high-spin electronic state is favored for all of the systems we considered. H bonds between the terminal oxo and hydroxo ligands and NH groups present in the organic ligand coordinated to the metal have a remarkable effect on the overall coordination geometry. In fact, the structure of model complexes without H bonds shows shorter Fe-O bond lengths. This is a consequence of the ability of the H bonds to stabilize a remarkable amount of electron density localized on the terminal oxo and hydroxo ligands. Energy analysis indicates that each H bond stabilizes the nonheme complexes by roughly 35 kJ/mol. Molecular orbital analysis indicates a reduction of two Fe-O bonding electrons on going from a complex with a terminal oxo ligand to a complex with a terminal hydroxo ligand. This reduction in the number of bonding electrons is also supported by frequency analysis.     

Correlation between DFT calculated and X-ray structures from CSD,for Cu(II) and Cu(I) coordination spheres when coordinated to four acyclic amine ligands. A reconsideration of copper(II) planarity

The Cambridge Crystallographic Database (CSD) shows [Cu^IIL₄]²⁺ complexes, L = acyclic amine, fitting well with theoretically calculated structures to describe a planar-to-flat tetrahedral transformation pathway. Statistically, the Cu^II “planar” coordination sphere shows two distinct sets of trans N–Cu–N bond angles, 180° and near 150°, with the latter somewhat energetically favored according to DFT results. The planar structure is not confirmed theoretically when an example of these molecules in the CSD is geometrically minimized, suggesting that crystallographic or packing forces help to generate the planar structure in the crystal. Results of energy calculations from DFT seem to explain this feature. Less planar and more tetrahedral examples in the CSD are also found and compare well with theoretically converged related molecules. Trans N–Cu–N bond angles near 130° seem feasible for both Cu^I and Cu^II coordination spheres. These copper complexes having the copper coordination sphere in a less tetrahedral geometry are suggested as potential alternative models for blue proteins, and they deserve further exploration.     

配位化学中新型金属配合物的电子结构与成键特点

研究配合物的几何电子构型、阐明配位键的本质是配位化学中重要的理论组成部分。本文在回顾配位化学基本的成键理论基础上,介绍几例近年来具有教科书级别的国内高水平原创工作,重点阐述具有独特芳香性、低氧化态、高配位数以及锕系金属的新型金属配合物的电子结构和成键特点,对丰富和拓展配位化学的基本理论具有重要意义。     

First row transition metal complexes of (E)-2-(2-(2-hydroxybenzylidene) hydrazinyl)-2-oxo-N-phenylacetamide complexes

Manganese(II), iron(II), cobalt(II), nickel(II), copper(II), and chromium(III) complexes of (E)-2-(2-(2-hydroxybenzylidene)hydrazinyl)-2-oxo-N-phenylacetamide were synthesized and characterized by elemental and thermal (TG and DTA) analyses, IR, UV-vis and (1)H NMR spectra as well as magnetic moment. Mononuclear complexes are obtained with 1:1 molar ratio except [Mn(HOS)(2)(H(2)O)(2)] and [Co(OS)(2)](H(2)O)(2) complexes which are obtained with 1:2 molar ratios. The IR spectra of ligand and metal complexes reveal various modes of chelation. The ligand behaves as a monobasic bidentate one and coordination occurs via the enolic oxygen atom and azomethine nitrogen atom. The ligand behaves also as a monobasic tridentate one and coordination occurs through the carbonyl oxygen atom, azomethine nitrogen atom and the hydroxyl oxygen. Moreover, the ligand behaves as a dibasic tridentate and coordination occurs via the enolic oxygen, azomethine nitrogen and the hydroxyl oxygen atoms. The electronic spectra and magnetic moment measurements reveal that all complexes possess octahedral geometry except the copper complexes possesses a square planar geometry. From the modeling studies, the bond length, bond angle, HOMO, LUMO and dipole moment had been calculated to confirm the geometry of the ligands and their investigated complexes. The thermal studies showed the type of water molecules involved in metal complexes as well as the thermal decomposition of some metal complexes. The protonation constant of the ligand and the stability constant of metal complexes were determined pH-metrically in 50% (v/v) dioxane-water mixture at 298 K and found to be consistent with Irving-Williams order. Moreover, the minimal inhibitory concentration (MIC) of these compounds against Staphylococcus aureus, Escherechia coli and Candida albicans were determined.     

Metal ion binding modes of hypoxanthine and xanthine versus the versatile behaviour of adenine

The metal coordination patterns of hypoxanthine, xanthine and related oxy-purines have been reviewed on the basis of the structural information available in the Cambridge Structural Database (CSD), including also the most recent reports founded in SciFinder. Attention is paid to the metal ion binding modes and interligand interactions in mixed-ligand metal complexes, as well as the possibilities of metal binding of the exocyclic-O atoms. The information in CSD is also reviewed for the complexes of adenine in cationic, neutral and anionic forms with every metal ion. In contrast to the scarce structural information about hypoxanthine and related complexes, large structural information is available for adenine complexes with a variety of metals that reveals some correlations between the crystal–chemical properties of metal ions. Three aspects are studied in deep: the coordination patterns, the interligand interactions influencing the molecular recognition in mixed-ligand metal complexes and the connectivity between metals for different adenine species, thus supporting its unique versatility as ligand. When possible, the overall behaviour showed by adenine metal complexes is discussed according to the HSAB Pearson criteria and the tautomeric behaviour observed for each protonated species of adenine. The differences between the roles of adenine and the referred oxypurines ligands are underlined.     

Molecular structures of “template” (5555)macrotetracyclic chelates of 3d M(II) ions with 1,4,7,10-tetraaza-1,3,8-dodecatriene-5,6,11,12-tetrathione according to DFT quantum-chemical calculations

The geometric parameters of the molecular structures of M(II) (5555)macrotetracyclic complexes with a tetradentate (NNNN) macrocyclic ligand, formed by template reactions in the systems M(II)-ethanedithioamide-ethanedial-1,2-ethenediol systems, as well as of the molecular structure of the template ligand forming the coordination sphere of these complexes, have been calculated by the OPBE/TZVP density functional theory method. The bond lengths and bond and torsion angles in the complexes, as well as the standard enthalpies, entropies, and Gibbs energies for each of them, are reported.     

The lanthanide contraction revisited

A complete, isostructural series of complexes with La-Lu (except Pm) with the ligand TREN-1,2-HOIQO has been synthesized and structurally characterized by means of single-crystal X-ray analysis. All complexes are 1D-polymeric species in the solid state, with the lanthanide being in an eight-coordinate, distorted trigonal-dodecahedral environment with a donor set of eight unique oxygen atoms. This series constitutes the first complete set of isostructural complexes from La-Lu (without Pm) with a ligand of denticity greater than two. The geometric arrangement of the chelating moieties slightly deviates across the lanthanide series, as analyzed by a shape parameter metric based on the comparison of the dihedral angles along all edges of the coordination polyhedron. The apparent lanthanide contraction in the individual Ln-O bond lengths deviates considerably from the expected quadratic decrease that was found previously in a number of complexes with ligands of low denticity. The sum of all bond lengths around the trivalent metal cation, however, is more regular, showing an almost ideal quadratic behavior across the entire series. The quadratic nature of the lanthanide contraction is derived theoretically from Slater's model for the calculation of ionic radii. In addition, the sum of all distances along the edges of the coordination polyhedron show exactly the same quadratic dependence as the Ln-X bond lengths. The universal validity of this coordination sphere contraction, concomitant with the quadratic decrease in Ln-X bond lengths, was confirmed by reexamination of four other, previously published series of lanthanide complexes. Owing to the importance of multidentate ligands for the chelation of rare-earth metals, this result provides a significant advance for the prediction and rationalization of the geometric features of the corresponding lanthanide complexes, with great potential impact for all aspects of lanthanide coordination.     

A screened hybrid density functional study on energetic complexes: Metal carbohydrazide nitrates

The molecular geometry, electronic structure and thermochemistry of a series of metal carbohydrazide nitrates were investigated using the Heyd–Scuseria–Ernzerhof (HSE) screened hybrid density functional. The results show that Ca, Sr, and Ba complexes have additional coordinated oxygen atoms from the nitrate ion, which differ obviously from Cu, Ni, Co, and Mg complexes in terms of the geometric structure. Detailed NBO analyses clearly indicate that the metal–ligand interactions in Cu, Ni, and Co complexes are covalent, whereas those of Mg, Ca, Sr, and Ba complexes are ionic in nature. Furthermore, the donor–acceptor interactions result in a reduction of occupancies of σ_{C? O} and σ_{N? H} orbitals. Consequently, the bond lengths increase and the bond orders decrease. Finally, the calculated heats of formation predict that the ionic alkaline‐earth metal carbohydrazide nitrates are more stable than the covalent transition metal carbohydrazide nitrates. It agrees well with the available experimental thermal stabilities, indicating that the metal–ligand bonding character plays an important role in the stabilities of these energetic complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A combined experimental and theoretical approach for structural study on a new cinnamoyl derivative of 2-acetyl-1,3-indandione and its metal(II) complexes

The synthesis, structure and spectral properties of a new cinnamoyl derivative of 2-acetyl-1,3-indandione (2AID), p-fluoro-cinnamoyl-1,3-indandione, LH and its metal(II) complexes with Cu(II), Zn(II) and Cd(II), are described. In order to verify the molecular structure of the free ligand and its metal complexes, model geometries based on the spectroscopic data were optimized using quantum chemical methods. The experimental spectroscopic data (IR and NMR) of the ligand, LH, complemented by the calculated ones, show that it exists in the exocyclic enolic form in the gas phase, solution and solid state. Good quality single crystals of Cd(II) complex were obtained from a DMSO solution and were studied by means of single-crystal X-ray diffraction. The data show bidentate coordination of the ligand and two DMSO molecules coordinated to the metal centre, thus forming a complex with octahedral geometry. On the contrary, the spectroscopic data on the amorphous samples indicate a square planar geometry of the Cu(II) complex and distorted octahedral geometry for Zn(II) and Cd(II) complexes with two water molecules coordinated to the metal centre. The used quantum chemical method for structure optimization of the transition metal complexes, B3LYP/LANL2DZ, shows very good agreement with the crystallographic data and, therefore, was also employed for structural determination for the non-crystalline complexes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses

The metal coordination number (CN) is a key determinant of the structure and properties of metal complexes. It also plays an important role in metal selectivity in certain metalloproteins. Despite its central role, the preferred CN for several metal cations remains ambiguous, and the factors determining the metal CN are not fully understood. Here, we evaluate how the CN depends on (1) the metal's size, charge, and charge-accepting ability for a given set of ligands, and (2) the ligand's size, charge, charge-donating ability, and denticity for a given metal by analyzing the Cambridge Structural Database (CSD) structures of metal ions in the periodic table. The results show that for a given ligand type, the metal's size seems to affect its CN more than its charge, especially if the ligand is neutral, whereas, for a given metal type, the ligand's charge and charge-donating ability appear to affect the metal CN more than the ligand's size. Interestingly, all 98 metal cations surveyed could adopt more than than one CN, and most of them show an apparent preference toward even rather than odd CNs. Furthermore, as compared to the preferred metal CNs observed in the CSD, those in protein binding sites generally remain the same. This implies that the protein matrix (excluding amino acid residues in the metal's first and second coordination shell) does not impose severe geometrical restrictions on the bound metal cation.     

Metal-mediated dihydrogen activation. What determines the transition-state geometry?

Density functional theory and absolutely localized molecular orbital energy decomposition analysis calculations were used to calculate and analyze dihydrogen activation transition states and reaction pathways. Analysis of a variety of transition-metal complexes with d(0), d(6), d(8), and d(10) orbital occupation with a diverse range of metal ligands reveals that for transition states, akin to dihydrogen σ complexes, there is a continuum of activated H-H bond lengths that can be classified as "dihydrogen" (0.8-1.0 ?), "stretched or elongated" (1.0-1.2 ?), and "compressed dihydride" (1.2-1.6 ?). These calculations also quantitatively for the first time reveal that the extent to which H(2) is activated in the transition-structure geometry depends on back-bonding orbital interactions and not forward-bonding orbital interactions. This is true regardless of the mechanism or whether the metal ligand complex acts as an electrophile, ambiphile, or nucleophile toward dihydrogen.     

Computational insights into the acceptor chemistry of phosphenium cations

Phosphines are traditionally considered as Lewis bases or ligands in transition metal and main group complexes. Despite their electron-rich (lone pair-bearing) nature, an extensive coordination chemistry for Lewis acidic phosphorus centers is being developed; such chemistry provides a new synthetic approach for phosphorus-element bond formation, leading to new types of structures and modes of bonding. Complexes of Ph2P+ with a variety of donor elements (P, N, C) give experimentally short donor-acceptor bond lengths, when compared to other cationic phosphorus Lewis acid complexes. We have calculated that the energy of the lowest unoccupied molecular orbital (LUMO) in Ph2P+ is lower than that of (Me2N)2P+, which partially explains the greater exothermicity of reactions of donors with the diaryl acceptor. Furthermore, the energies required to distort the diphenylphosphenium cation from its ground-state geometry are significantly smaller than those of the diamido cations and, thus, enhance the exothermicity of donor coordination. These computational data, in conjunction with evidence from experimental solid-state structures, indicate that Ph2P+ is a significantly better Lewis acid relative to the more common diaminophosphenium analogues (R2N)2P+ and are used to elucidate the nature of the bonding in donor-phosphenium complexes.     

Synthesis and spectral characteristics of ruthenium(III), rhodium(III), and palladium(II) complexes with 2-(3-pyridylmethyliminomethyl)phenol

New Ru(III), Rh(III), and Pd(II) complexes with the ambident ligand 2-(3-pyridylmethyliminomethyl)phenol have been synthesized and characterized by electronic absorption and IR spectroscopy, ¹H NMR, and elemental analysis and electrophoresis methods. The synthesis conditions and the nature of the metal turn out to have an effect on the coordination mode of the ligand in the resulting complexes. The existence of the intramolecular hydrogen bond in the ligand molecule is favorable for its coordination in the molecular form to the complex-forming metal.     

The NMR spectra of the porphyrins. 17—Metalloporphyrins as diamagnetic shift reagents,structural and specificity studies

The nature of the metalloporphyrin-ligand complexes produced by zinc, magnesium and cobalt porphyrins with basic ligands has been investigated using the diamagnetic ring current shifts of the porphyrin on the ligand protons. The metal to nitrogen bond lengths in some metallo-meso-tetraphenylporphyrin (pyridine) complexes have been determined and compared with the data of the crystalline complexes. The geometry of the Zn meso-tetraphenylporphyrin complexes with 2-picoline, quinoline and isoquinoline has been investigated. Steric interactions between the ligand and the porphyrin in 2-picoline and quinoline produce a dramatic increase in the Zn? N bond length when compared to the unstrained analogues pyridine and isoquinoline. This large increase is associated with comparatively minor angle distortions in the complex. The specificity of the Zn meso-tetraphenylporphyrin complexation shifts has been determined for a range of benzyl and butyl compounds. The complexation shift is linearly related to the basicity of the ligand for a wide range of basicities.     

Synthesis,spectral, DFT,and antimicrobial studies of tin(II) and lead(II) complexes with semicarbazone and thiosemicarbazones derived from (2-hydroxyphenyl)(pyrrolidin-1-yl)methanone

A new series of metal complexes [M(L)₂] (where M = Sn(II), Pb(II), and HL = semicarbazone, thiosemicarbazone or phenylthiosemicarbazone) have been prepared and characterized by elemental analysis, conductance measurements, molecular weight determinations, UV–visible, infrared, and nuclear magnetic resonance (¹H-, ¹³C-, and ¹¹⁹Sn-NMR) spectral studies. Elemental analysis of the metal complexes suggested 1 : 2 (metal–ligand) stoichiometry. Infrared spectra of the complexes agree with coordination to the metal through the nitrogen of the azomethine (>C=N?) and the oxygen/sulfur of the ketonic/thiolic group. Electronic spectra suggest a distorted tetrahedral geometry for all Schiff base complexes. The bond lengths, bond angles, highest occupied molecular orbital, lowest unoccupied molecular orbital, Mulliken atomic charges, and the lowest energy model structure of the complexes have been determined with DFT calculations. Representative Schiff base and its metal chelates have been screened for their in vitro antibacterial activity against four bacteria, Gram-positive (Bacillus cereus, Staphylococcus aureus) and Gram-negative (Escherichia coli, Klebsiella pneumoniae) and four strains of fungus (Penicillium chrysogenum, Aspergillus niger, Rhizopus nigricans, and Alternaria alternata). The metal chelates possess higher antimicrobial activity than the free ligands.     

Using internal coordinates to describe photoinduced geometry changes in MLCT excited states

A resonance Raman intensity analysis of the metal-to-ligand charge-transfer (MLCT) transition for the rhenium compound Re(2-(2'-pyridyl)quinoxaline)(CO)(3)Cl (RePQX) is presented. Photoinduced geometry changes are calculated, and the results are presented using the vibrational normal modes and the redundant internal coordinates. A density functional theory calculation is used to determine the ground-state nonresonant Raman spectrum and a transformation matrix that transforms the redundant internal coordinates into the normal modes. The normal modes nu(37) (rhenium coordination sphere distortion) and nu(75) (ligand skeletal stretch) show the largest photoinduced geometry change (Delta = 1.0 and 0.7, respectively). A single carbonyl mode is enhanced in the resonance Raman spectra. Time-dependent density functional theory is used to calculate excited-state geometry changes, which are subsequently used to determine the signs of the photoinduced normal mode displacements. Transforming to internal coordinates reveals that all the CO bond lengths are displaced in the excited state. The Re-C and C-C ligand bond lengths are also displaced in the excited state. The results are discussed in terms of a simple one-electron picture for the electronic transition. Many bond angles and torsional coordinates are also displaced by the metal-to-ligand charge transfer, and most of these are associated with the rhenium coordination sphere. It is demonstrated that using internal coordinates presents a clear picture of the geometry changes associated with photoinduced electron transfer in metal polypyridyl systems.