De novo prediction of ground state multiplicity and structural isomerism for transition metal complexes

Prediction of the ground state geometries and multiplicities for 33 transition metal tetrachlorides has been carried out using two different levels of quantum mechanics: semiempirical and density functional theory. All data regarding geometry and spin state provided by both computational methods were compared with experimental data when available. The calculations were performed for all possible spin multiplicities. The most important geometries for coordination number four (tetrahedral, square-planar, dodecahedral, and disphenoidal), as well as less symmetric structural isomers, were evaluated. A match between both computational methods in terms of predicted ground state multiplicity and geometry was found for 26 species, which translated into almost 80% agreement. Even though the PM3(tm) geometry prediction protocol involved more steps for isolating a feasible global minimum, the aggregate of these calculations was still orders of magnitude faster than DFT calculations using extended basis sets. The calculations indicate that caution is needed in the application of the PM3(tm) method to very high-spin transition metal complexes, but point to the suitability of very rapid semiempirical methods for reliable prediction of structural and ‘spin’ isomers, and hence their use in an efficient de novo design protocol for transition metal complexes.     

On the Conformation and Structure of Organometal Complexes in the Solid State: Two Studies Relevant to Chemical Synthesis

Conformational preferences of two classes of organometal complexes have been surveyed by inspecting the Cambridge Structural Database (CSD). Lewis acid carbonyl complexes demonstrate a variety of coordination geometries, depending on the electronic and steric requirements of the carbonyl ligands and the nature of the Lewis acid. Similarly, the solid-state conformation of various π-bonding ligands in metal acyl, metal nitrosyl, metal acetylene, and metal imido complexes is revealed. These insights have stimulated the development of a conformational model that is based on considerations of π-bond hybridization and frontier molecular orbital theory. The analyses are relevant to the mechanism and transition structures of many synthetically important transformations. A deeper understanding of the conformational properties of organometal complexes, based on accurate structural information, will likely expedite the design and improvement of metal-mediated processes.     

Design of molecular ferromagnets

A large variety of molecular ferromagnets have been synthesized since the discovery of the first organic ferromagnets, including pure organic compounds, organometallic charge-transfer complexes, metal complex-organic radical compounds, and transition metal complexes coupled to organic radicals. Besides, there are many reports on the observation of ferromagnetism in polymers and organic matrix composites. Molecular ferromagnets have great potential in different areas of technology such as low frequency magnetic shielding, magnetic imaging, magneto-optics and information storage. We provide a brief review on the current strategies for the design of molecular (organic) ferromagnets. This includes exploiting the inherent advantages of molecular systems, such as the ability to fine-tune the properties at the molecular level, and to control dimensionality, supramolecular structuring and hierarchy of spin interactions etc. for carrying out structural modifications and chemical functionalisations of stable open-shell molecules in order to generate supramolecular structures in which the natural prediction for antiparallel spin alignment (antiferromagnetism) is avoided.     

A conformational analysis method for understanding the energy landscapes of clusters.

A newly developed unbiased structural optimization method, named dynamic lattice searching (DLS), is proposed as an approach for conformational analysis of atomic/molecular clusters and used in understanding the energy landscape of large clusters. The structures of clusters are described in terms of the number of basic tetrahedron (BT) units they contain. We found that the hit numbers of different structural motifs in DLS runs is proportional to the number of BTs. A parameter T(max) is defined to limit the maximal number of atoms moved in a structural transition. Results show that T(max) is a key parameter for modulating the efficiency of the DLS method and has a great influence on the hit number of different motifs in DLS runs. Finally, the effect of potential range on the conformational distribution of the (Morse)(98) cluster is also discussed with different potential-range parameters.     

Structural correlations and conformational preference in edge-sharing binuclear d8 complexes with XR2 bridges. A theoretical study

The binuclear complexes of d8 transition metal ions of the type [M2(mu-XR2)2L4] (where M = RhI, IrI, NiII, PdII, PtII, or AuIII; X = S, N, P, or As) appear in a variety of molecular conformations in which the coordination planes around the two metal atoms are sometimes coplanar, sometimes bent. For the bent compounds with asymmetric bridges, XR1R2, the substituents adopt different orientations relative to the metal framework and to each other. Ab initio theoretical studies on the different conformers of 30 representative complexes, complemented with a structural database analysis, have allowed the establishment of structural correlations in this family of compounds. The conformational choice results from a delicate balance of different interactions which are qualitatively analyzed, such as the changes in bond angles around the bridging atoms, the existence of weak metal...metal bonding in the bent structures, and steric interactions involving the terminal ligands and the substituents at the bridging atoms.     

Transition metal-boron complexes BnM: from bowls (n = 8-14) to tires (n = 14)

Transition metal-boron complexes BnM have been predicted at density functional theory level to be molecular bowls (n = 8-14) hosting a transition metal atom (M) inside or molecular tires (n = 14) centered with a transition metal atom. Small Bn clusters prove to be effective inorganic ligands to all the VB-VIIIB transition metal elements in the periodic table. Density functional evidences obtained in this work strongly suggest that bowl-shaped fullerene analogues of Bn units exist in small BnM complexes and the bowl-to-tire structural transition occur to the first-row transition metal complexes BnM (M = Mn, Fe, Co) at n = 14, a size obviously smaller than n = 20 where the 2D-3D structural transition occurs to bare Bn. The half-sandwich-type B12Cr (C3v), full sandwich-type (B12)2Cr (D3d), bowl-shaped B14Fe (C2), and tire-shaped B14Fe (D7d) and B14Fe- (C7v) are the most interesting prototypes to be targeted in future experiments. These BnM complexes may serve as building blocks to form extended boron-rich BnMm tubes or cages (m > or = 2) or as structural units to be placed inside carbon nanotubes with suitable diameters.     

Influence of electronic effect on catalytic activity of salicylaldiminato nickel(II) complexes

A means of correlation between the activity and the net charge, the metal atom net charge correlation (MANCC), which was successful in the activity prediction of the early‐transition metal catalysts, has been used to study the catalytic activities of salicylaldiminato Ni(II) complexes, the late‐transition metal catalysts, in olefin polymerization or oligomerization. A comparison with the available quantum mechanics/molecular mechanics (QM/MM) calculation data suggests that even without a detailed mechanism, MANCC results mostly agree with QM/MM calculation data regarding insertion barrier data and enthalpy change. Eight experimental complexes were further built up by modeling; their catalytic activities predominantly increased in line with the net charges on the metal atoms. The same results were obtained for the other four complexes synthesized in the present work. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4765–4774, 2004     

TcI(CN)3(CO)3]2- and [ReI(CN)3(CO)3]2- :case studies for the binding properties of CN- and CO

The cyano carbonyl complexes [(99)Tc(CN)(3)(CO)(3)]2- and [Re(CN)(3)(CO)(3)]2- were synthesized and fully characterized. These complexes are additional members of the well-known d(6) transition metal complex series [M(CN)(3)(CO)(3)](n-). The analytical data obtained in this study thus offer a unique opportunity to study similarities and differences of cyanide and carbonyl binding in transition metal complexes.     

Constitutional,configurational and conformational analysis of transition metal coordination complexes

Summary A computational approach to conformational analysis is applied to the study of transition metal coordination complexes. The method provides a means of rapidly exploring conformational space without any inherent reliance on energy calculations and is therefore applicable to a wide variety of systems. It has been incorporated into an algorithm which explores the constitutional, configurational and conformational degrees of freedom for a metal ion and a number of potential ligands. The program determines which of the possible coordination complex products could form stable conformations and can therefore be used to rationalise the products obtained from the mixture. The method is illustrated using two cases: the cobalt(III)-triethylenetetramine-glycine system and complexes of diindolopyridine derivatives.Abbreviations en ethylenediamine - trien triethylenetetramine - gly glycine - RMS root mean square - 3D three dimensional     

Synthesis and characterization of technetiumtetrakis(acetonitrile)bis(triphenylphosphine) cationic complexes

A new route to low-valent technetium complexes containing multiple acetonitrile ligands has been developed. The reduction of TcCl(4)(PPh(3))(2) with zinc metal dust in acetonitrile results in the formation of [Tc(CH(3)CN)(4)(PPh(3))(2)][Zn(2)Cl(6)](1/2). The hexafluorophosphate salt of the analogous Tc(II) cation can be prepared via chemical oxidation of the Tc(I) species, and the Tc(I) cation can be regenerated via chemical reduction. The compounds have been characterized in the solid state via single-crystal X-ray crystallography, and in solution via a combination of spectroscopic techniques and cyclic voltammetry. The structural parameters found in the two complexes are similar to each other; however, the difference in oxidation state is reflected, as expected, in the spectroscopic results. The electrochemical data, obtained from cyclic voltammograms of Tc(CH(3)CN)(4)(PPh(3))(2)](PF(6))(n)() (n = 1,2), mirror the synthetic results in that both compounds possess a reversible redox couple at -0.55 V versus ferrocene, which has been assigned to the Tc(II)/Tc(I) couple.     

The Trigonal Prism in Coordination Chemistry

Herein we analyze the accessibility of the trigonal‐prismatic geometry to metal complexes with different electron configurations, as well as the ability of several hexadentate ligands to favor that coordination polyhedron. Our study combines i) a structural database analysis of the occurrence of the prismatic geometry throughout the transition‐metal series, ii) a qualitative molecular orbital analysis of the distortions expected for a trigonal‐prismatic geometry, and iii) a computational study of complexes of several transition‐metal ions with different hexadentate ligands. Also the tendency of specific electron configurations to present a cis bond‐stretch Jahn–Teller distortion is analyzed.     

The tetracycline: Mg2+ complex: a molecular mechanics force field

Tetracycline (Tc) is an important antibiotic, which binds specifically to the ribosome and several proteins, in the form of a Tc-:Mg2+ complex. To model Tc:protein and Tc:RNA interactions, we have developed a molecular mechanics force field model of Tc, which is consistent with the CHARMM force field for proteins and nucleic acids. We used structures from the Cambridge Crystallographic Data Base to identify the main Tc conformations that are likely to be present in solution and in biomolecular complexes. A conformational search was also done, using the MM3 force field to perform simulated annealing of Tc. Several resulting, low-energy structures were optimized with an ab initio model and used in developing the new Tc force field. Atomic charges and Lennard-Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with Tc at 36 different positions. We considered both a neutral and a zwitterionic Tc form, with and without bound Mg2+. The final rms deviation between the ab initio and force field energies, averaged over all forms, was just 0.35 kcal/mol. The model also reproduces the ab initio geometry and flexibility of Tc. As further tests, we did simulations of a Tc crystal, of Tc:Mg2+ and Tc:Ca2+ complexes in aqueous solution, and of a solvated complex between Tc:Mg2+ and the Tet repressor protein (TetR). With slight, ad hoc adjustments, the model can reproduce the experimental, relative, Tc binding affinities of Mg2+ and Ca2+. It performs well for the structure and fluctuations of the Tc:Mg2+:TetR complex. The model should therefore be suitable to investigate the interactions of Tc with proteins and RNA. It provides a starting point to parameterize other compounds in the large Tc family.     

Low-spin versus high-spin ground state in pseudo-octahedral iron complexes

Pseudo-octahedral complexes of iron find applications as switches in molecular electronic devices, materials for data storage, and, more recently, as candidates for dye-sensitizers in dye-sensitized solar cells. Iron, as a first row transition metal, provides a weak ligand-field splitting in an octahedral environment. This results in the presence of low-lying (5)T excited states that, depending on the identity of iron ligands, can become the ground state of the complex. The small energy difference between the low-spin, (1)A, and high-spin, (5)T, states presents a challenge for accurate prediction of their ground state using density functional theory. In this work, we investigate the applicability of the B3LYP functional to the ground state determination of first row transition metal complexes, focusing mainly on Fe(II) polypyridine complexes with ligands of varying ligand field strength. It has been shown previously that B3LYP artificially favors the (5)T state as the ground state of Fe(II) complexes, and the error in the energy differences between the (1)A and (5)T states is systematic for a set of structurally related complexes. We demonstrate that structurally related complexes can be defined as pseudo-octahedral complexes that undergo similar distortion in the metal-ligand coordination environment between the high-spin and low-spin states. The systematic behavior of complexes with similar distortion can be exploited, and the ground state of an arbitrary Fe(II) complex can be determined by comparing the calculated energy differences between the singlet and quintet electronic states of a complex to the energy differences of structurally related complexes with a known, experimentally determined ground state.     

Comparative investigations of the secondary ion emission of metal complexes under MeV and keV ion bombardment

A series of ionic and neutral Group VIII transition metal complexes with molecular masses up to 2500 u were analysed by time-of-flight secondary ion mass spectrometry (SIMS) and plasma desorption mass spectrometry (PDMS). The secondary ion emission, the secondary ion yields and the yield ratios Y(PDMS)/Y(SIMS) of 20 ionic and neutral metal complexes were determined. Both techniques generally provide both molecular and fragment ion information. Characteristic fragmentation patterns give useful data for structural characterization. Additionally, the stabilities of different secondary ion species were compared by their half-lives. Both PDMS and SIMS are very sensitive, yielding optimum spectra from total sample sizes as low as 5 nmol, and the sample consumption is negligible.     

Density matrix renormalization group calculations on relative energies of transition metal complexes and clusters

The accurate first-principles calculation of relative energies of transition metal complexes and clusters is still one of the great challenges for quantum chemistry. Dense lying electronic states and near degeneracies make accurate predictions difficult, and multireference methods with large active spaces are required. Often density functional theory calculations are employed for feasibility reasons, but their actual accuracy for a given system is usually difficult to assess (also because accurate ab initio reference data are lacking). In this work we study the performance of the density matrix renormalization group algorithm for the prediction of relative energies of transition metal complexes and clusters of different spin and molecular structure. In particular, the focus is on the relative energetical order of electronic states of different spin for mononuclear complexes and on the relative energy of different isomers of dinuclear oxo-bridged copper clusters.     

Structural variation in transition-metal bispidine compounds

The experimentally determined molecular structures of 40 transition metal complexes with the tetradentate bispyridine-substituted bispidone ligand, 2,4-bis(2-pyridine)-3,7-diazabicyclo[3.3.1]nonane-9-one [M(bisp)XYZ]n+; M = CrIII, MnII, FeII, CoII, CuII, CuI, ZnII; X, Y, Z = mono- or bidentate co-ligands; penta-, hexa- or heptacoordinate complexes) are characterized in detail, supported by force-field and DFT calculations. While the bispidine ligand is very rigid (N3...N7 distance = 2.933 +/- 0.025 A), it tolerates a large range of metal-donor bond lengths (2.07 A < sigma(M-N)/4 < 2.35 A). Of particular interest is the ratio of the bond lengths between the metal center and the two tertiary amine donors (0.84 A < M-N3/M-N7 < 1.05 A) and the fact that, in terms of this ratio there seem to be two clusters with M-N3 < M-N7 and M-N3 > or = M-N7. Calculations indicate that the two structural types are close to degenerate, and the structural form therefore depends on the metal ion, the number and type of co-ligands, as well as structural variations of the bispidine ligand backbone. Tuning of the structures is of importance since the structurally differing complexes have very different stabilities and reactivities.     

蛋白质-RNA相互作用界面预测与设计

蛋白质-RNA之间的相互作用是蛋白质在细胞里面行使功能的重要方式之一. 结构生物学家利用实验手段可以得到蛋白质-RNA复合物的三维结构, 通过原子水平的晶体结构来解释蛋白质与RNA的识别过程. 但实验取得蛋白质-RNA的复合物结构非常困难, 耗钱、耗时, 同时受限于其相互作用强度. 因而利用理论的方法对蛋白质-RNA相互作用界面进行预测与设计在生物医学研究中十分重要. 本文主要综述了近期蛋白质-RNA相互作用界面预测与设计方面的进展, 包括以下几个方面: (1) 蛋白质-RNA分子对接算法以及对接前后存在的构象变化的处理; (2) 蛋白质-RNA 识别机制的研究; (3) 基于蛋白质-RNA 相互作用界面的分子设计. 蛋白质-RNA分子对接算法逐步完善将有助于我们对大量未知功能的蛋白质与RNA进行功能注释, 而基于生物大分子相互作用界面的分子设计将在药物设计领域中有广阔的应用前景.     

The Chemistry of Phenylimidotechnetium(V) Complexes with Isocyanides: Steric and Electronic Factors

Organometallic approaches are of ongoing interest for the development of novel functional ^99mTc radiopharmaceuticals, while the basic organotechnetium chemistry seems frequently to be little explored. Thus, structural and reactivity studies with the long-lived isotope ⁹⁹Tc are of permanent interest as the foundation for further progress in the related radiopharmaceutical research with this artificial element. Particularly the knowledge about the organometallic chemistry of high-valent technetium compounds is scarcely developed. Here, phenylimido complexes of technetium(V) with different isocyanides are introduced. They have been synthesized by ligand-exchange procedures starting from [Tc(NPh)Cl₃(PPh₃)₂]. Different reactivity patterns and products have been obtained depending on the steric and electronic properties of the individual ligands. This involves the formation of 1:1 and 1:2 exchange products of Tc(V) with the general formulae [Tc(NPh)Cl₃(PPh₃)(isocyanide)], cis- or trans-[Tc(NPh)Cl₃(isocyanide)₂], but also the reduction in the metal and the formation of cationic technetium(I) complex of the formula [Tc(isocyanide)₆]⁺ when p-fluorophenyl isocyanide is used. The products have been studied by single-crystal X-ray diffraction and spectroscopic methods, including IR and multinuclear NMR spectroscopy. DFT calculations on the different isocyanides allow the prediction of their reactivity towards electron-rich and electron-deficient metal centers by means of the empirical SADAP parameter, which has been derived from the potential energy surface of the electron density on their potentially coordinating carbon atoms.