Sulfur-bridged Research Articles

Spin-adapted density matrix renormalization group algorithms for quantum chemistry

We extend the spin-adapted density matrix renormalization group (DMRG) algorithm of McCulloch and Gulacsi [Europhys. Lett. 57, 852 (2002)] to quantum chemical Hamiltonians. This involves using a quasi-density matrix, to ensure that the renormalized DMRG states are eigenfunctions of Ŝ(2), and the Wigner-Eckart theorem, to reduce overall storage and computational costs. We argue that the spin-adapted DMRG algorithm is most advantageous for low spin states. Consequently, we also implement a singlet-embedding strategy due to Tatsuaki [Phys. Rev. E 61, 3199 (2000)] where we target high spin states as a component of a larger fictitious singlet system. Finally, we present an efficient algorithm to calculate one- and two-body reduced density matrices from the spin-adapted wavefunctions. We evaluate our developments with benchmark calculations on transition metal system active space models. These include the Fe(2)S(2), [Fe(2)S(2)(SCH(3))(4)](2-), and Cr(2) systems. In the case of Fe(2)S(2), the spin-ladder spacing is on the microHartree scale, and here we show that we can target such very closely spaced states. In [Fe(2)S(2)(SCH(3))(4)](2-), we calculate particle and spin correlation functions, to examine the role of sulfur bridging orbitals in the electronic structure. In Cr(2) we demonstrate that spin-adaptation with the Wigner-Eckart theorem and using singlet embedding can yield up to an order of magnitude increase in computational efficiency. Overall, these calculations demonstrate the potential of using spin-adaptation to extend the range of DMRG calculations in complex transition metal problems.

Synthesis and Structure of Binuclear O/S‐Bridged Organobismuth Complexes and Their Cooperative Catalytic Effect on CO2 Fixation

AbstractIn the synthesis of binuclear organobismuth complexes (1–6) through treatment of organobismuth chlorides with NaOH or Na2S⋅9H2O, the two 5,6,7,12‐tetrahydrodibenz [c,f][1,5]azabismocine frameworks are cross‐linked by either a sulfur or an oxygen atom. The complexes (1–6) show high catalytic efficiency in the synthesis of cyclic carbonates from 2‐(chloromethyl)oxirane and CO2. Compared with their precursor chlorides (7–9), methoxide 10 and methanethioate 11 which are mononuclear organobismuth complexes, the binuclear organobismuth complexes show higher cooperative catalytic effect. However, the complexes with an oxygen bridge (1–3) are not stable in air and lose their catalytic efficiency because of hydrolysis or CO2 adsorption (forming organobismuth carbonates in the latter case). Nonetheless, the binuclear organobismuth complexes (4–6) with a sulfur bridge are highly stable in air and can be applied in the synthesis of cyclic carbonates (with the co‐presence of Bu4NI) across various kinds of epoxides, thus exhibiting satisfactory efficiency and selectivity.

Metallothionein Zn2+- and Cu2+-clusters from first-principles calculations

Detailed electronic structures of Zn(II) and Cu(II) clusters from metallothioneins (MT) have been obtained using density functional theory (DFT), in order to investigate how oxidative stress-caused Cu(II) intermediates affect Zn-binding to MT and cooperatively lead to Cu(I)MT. The inferred accuracy is ∼0.02-0.03 Å for metal-thiolate bond lengths for the models that are the most realistic MT models so far studied by DFT. We find terminal Zn-S and Cu-S bond lengths of 2.35-2.38 Å and 2.30-2.34 Å, whereas bridging M-S bonds are 0.05-0.11 Å longer. This electronic effect is also reflected in changes in electron density on bridging sulfurs. Various imposed backbone constraints quantify the sensitivity of cluster electronic structure towards protein conformational changes. The large negative charge densities of the clusters are central to MT function, and the smaller β-clusters are more prone to modification. Oxidative stress-associated Cu(II) binding weakens the Zn-S bonds and is thus likely to impair the Zn(II) transfer function of MTs, providing a mechanism for cooperative Cu(II) binding leading to loss of Zn(II) and dysfunctional Cu(I)MT clusters.

Theoretical study of the bridging effect on the charge carrier transport properties of cyclooctatetrathiophene and its derivatives

The bridging effect on the charge transport properties of cyclooctatetrathiophene and its derivatives (systems 1–4) was investigated at the level of density functional theory (DFT). Insights into their geometries, frontier molecular orbitals, reorganization energies, transfer integrals and band structures were provided in detail. Increasing charge mobilities for both holes and electrons were predicted in cyclooctatetrathiophene derivatives as the number of bridging sulfur atoms increased. The improved charge transport from system 1 to 4 can be interpreted from two contributions: (i) decreased reorganization energy with improved molecular planarity under the consideration of intermolecular interactions; and (ii) enhanced transfer integral derived from the π-stacking arrangement for 2 and 3, and multidimensional S⋯S interactions are found to contribute to charge transport in system 4 besides π⋯π interactions. The charge transport properties were also analyzed with a band-like model and the results were in agreement with those gained from the hopping model in the fact that the paths with large transfer integrals are all along the directions with large dispersions in the valence band or conduction band.

XPS, XES, and quantum chemical investigation of the electronic structure of thiacalix[4]arenes and calix[4]arene thioesters

The X-ray photoelectron and X-ray emission spectra as well as the charge state of thiacalix[4]arenes in the cone and 1,3-alternate conformations and calix[4]arene thioesters were studied. The donor ability of sulfur bridging atoms in the studied compounds was shown to be close to that in dialkyl sulfides. The internal X-ray transitions (Kα and Kβ) were described by the energy of Kohn-Sham orbitals calculated by DFT method with relaxation corrections.

Synthesis and Structure of a Dimeric, Anionic Thioglycolate Derivative of Manganese Carbonyl

The thioglycolate anion reacts with BrMn(CO)5 to form a dimeric complex with bridging sulfur atoms of formula [Mn2(thioglycolate)2(CO)6]2–. This was isolated as the Et3NH+ salt and fully characterized for comparison with the previously reported thiosalicylate analogue.

Influence of conformation on the electronic structure of thiacalixarenes according to DFT calculations and X-ray emission spectroscopy

Abstract The DFT calculations of different thiacalix[4]arenes show that the conformation and geometry of arene core mainly determine the difference in electronic density distribution (frontier occupied MO and ESP charges) between “cone” and “1,3-alternate” conformation. The key factor is orientation of benzene rings relative to average plane through bridging sulfur atoms. Calculated structure of frontier orbitals was verified by experimental sulfur K β spectra, calculated spectra reproducing main features of experimental ones. Difference in HOMO and ESP distribution on carbon atoms in benzene rings for “cone” and “1,3-alternate” conformers correlates with earlier reported data on regioselectivity of electrophilic substitution in these compounds.

Adsorption of n-Butanol from Dilute Aqueous Solution with Grafted Calixarenes

Materials were synthesized for the recovery of n-butanol from dilute aqueous solutions, as may be useful for applications in biofuel-water separations. These materials are composed of hydrophobic, cavity-containing calixarenes covalently bound directly to porous, hydrophilic silica supports through a Si linker atom rather than a flexible organic linker, as is common, at surface coverages of up to ∼0.25 calixarenes/nm(2) (∼250 μmol calix/g matl). The calixarene ring size, upper rim groups, bridging group (calixarene vs thiacalixarene), and surface density were varied. The materials were characterized by NMR, UV-vis, and TGA. The absolute butanol uptake reached ∼0.16 mmol butanol per gram of material at equilibrium concentrations below 0.12 M and increased monotonically with the calixarene surface density. The background adsorption onto the silica surface was small at high calixarene loading. At 298 K, the free energy of adsorption in the calixarene cavities became more favorable by 3 kJ/mol as the surface area of the hydrophobic calixarene upper rim groups increased from H to methyl to tert-butyl, consistent with adsorption driven by van der Waals interactions. A thiacalix[4]arene-SiO(2) material, containing polarizable sulfur bridges and a larger, more conformationally mobile calixarene structure, had slightly stronger adsorption still. All materials except this thiacalixarene exhibited fully reversible adsorption into solution. As a representative material, the adsorption of n-butanol from aqueous solution at a tert-butylcalix[4]arene site was accompanied by a negligible enthalpy change but a small, favorable entropy change of +50 ± 20 J/mol/K, indicating that adsorption is driven by desolvation. Butanol desorbed from tert-butylcalix[4]arene materials at ∼150 °C into the gas phase, well within the range of stability of calixarenes (<300 °C), indicating that these materials have promise as regenerable adsorbents.

Structure and coordination in mono and dinuclear Zn(II)-pyrrolidine dithiocarbamate complexes

The structures of the chelate Zn(PDTC)2 and its dimeric form Zn2(PDTC)4 are investigated theoretically at B3LYP/cc-pVDZ level. The natural bond orbital (NBO) analysis has been performed to explore the metal–ligand coordination of these chelates. In Zn(PDTC)2, the sulfur atoms mainly use 3p sub-shells to coordinate with mixed (4s + 4p x + 4p y + 4p z ) orbital of zinc having sp 3 hybridization. In Zn2(PDTC)4, each zinc atom coordinates with one terminal and two bridging PDTC ligands. The contribution of bridging sulfur atoms in chelation is much more than terminal sulfurs. The bridging sulfur atoms use 3s and 3p sub-shells to coordinate with 4s and 4p sub-shells of metal center zinc. The charge transfer interactions between sulfur and metal center involving 4d, 5s, and 5p sub-shells of zinc are much feeble compared to those involving 4s and 4p sub-shells of zinc.

Mixed-ligand thiosemicarbazone complexes of nickel: Synthesis, structure and catalytic activity

Reaction of thiosemicarbazones of salicylaldehyde, 2-hydroxyacetophenone and 2-hydroxynaphthaldehyde with Ni(ClO 4) 2·6H 2O, using 2,2′-bipyridine as coligand, afforded three dinuclear complexes ( 1a, 1b and 1c). Similar reactions using 2,2′:6′2″-terpyridine as coligand yielded three mononuclear complexes ( 2a, 2b and 2c). Crystal structures of 1b and 2a have been determined. In the dinuclear complexes, one nickel center is surrounded octahedrally by a dianionic O,N,S-donor thiosemicarbazone, a bipyridine and the bridging phenolate oxygen of the other thiosemicarbazone. The second nickel center adopts a square-planar geometry created by the second O,N,S-coordinated thiosemicarbazone and the bridging sulfur of the first thiosemicarbazone. In the mononuclear complexes nickel is complexed by a monoanionic O,N,S-coordinated thiosemicarbazone and a terpyridine, and the cationic species are isolated as perchlorate salts. All these six complexes are paramagnetic ( μ eff = 2.63–2.92 B.M.) and in dimethylsulfoxide solution they show intense absorptions in the visible and ultraviolet region, origin of which has been probed through DFT calculations. Cyclic voltammetry on the complexes shows one irreversible oxidation of coordinated thiosemicarbazone on the positive side of SCE, and one irreversible reduction of the coordinated polypyridine ligand on the negative side. These nickel complexes are found to be efficient catalysts for Suzuki cross-coupling reactions.

Thiacalix[4]arenes: Extraction of palladium and the electronic structure

The extractability of palladium nitro complexes with the charge state of sulfur and oxygen atoms in thiacalix[4]arenas in the cone and 1,3-alternate conformations are compared. The results of X-ray photoelectron and X-ray emission studies indicate the presence of considerable electron density on the bridging sulfur atoms, which is due to the contribution of the sulfur 3p AO to the upper occupied MOs of molecules. A series of changes in the electron density on sulfur atoms in the order calixarene thioethers > thiacalixarenes > dialkylsulfides ((C10H21)2S) > (C6H5)2S not completely coincide with changes in their extrability, which can be caused by different nature and stoichiometry of the formed palladium complexes.

PAs3S3 Cage as a New Building Block in Copper Halide Coordination Polymers

First examples of the coordination chemistry of the PAs(3)S(3) cage were obtained from solutions of PAs(3)S(3)·W(CO)(5) (1) in CH(2)Cl(2) or CH(2)Cl(2)/toluene and CuX (X = Cl, Br, I) in MeCN through interdiffusion techniques. Crystals of [Cu(PAs(3)S(3))(4)]X (2, X = Cl; 3, X = Br) and [(Cu(2)I)(PAs(3)S(3))(3)]I (4) were obtained and characterized by Raman spectroscopy (2) and single-crystal X-ray crystallography. The solid-state structures reveal an unexpected coordination versatility of the PAs(3)S(3) ligand: apical phosphorus and bridging sulfur atoms interact with copper, while As···X interactions determine the dimensionality of the frameworks. The structures of 2 and 3 contain tetrahedral [(PAs(3)S(3))(4)Cu](+) cations as secondary building units (SBUs), which are arranged by interactions with Cl(-) or Br(-) anions into two- and three-dimensional substructures. These interpenetrate into a (2D + 3D) polycatenane. Compound 4 is built up by a one-dimensional [(Cu(2)I)(PAs(3)S(3))(3)](n)(n+) ribbon with PAs(3)S(3) cages as P,S-linkers. The As atoms of the exo PAs(3)S(4) linkers interact with iodide counterions (3.35 < d(As-I) < 3.59 Å). The resulting two-dimensional layer is organized by weak As···I interactions (d(As-I = 3.87 Å) into a 3D network.

S-Alkylation of Thiacalixarenes: A Long-Neglected Possibility in the Calixarene Family

Despite the high nucleophilicity of sulfur atoms, thiacalixarenes have been alkylated only on oxygen atoms thus far. Using strong alkylating agents (triflates, trialkyloxonium salts), the substitution of the sulfur bridges has been successfully accomplished. The corresponding sulfonium salts of thiacalix[4]arene are formed regio- and stereoselectively as a completely new type of substitution pattern in thiacalixarene chemistry. These compounds possess interesting conformational behavior and could be used as unusual alkylating agents with uncommon selectivity.

Conservative Change to the Phosphate Moiety of Cyclic Diguanylic Monophosphate Remarkably Affects Its Polymorphism and Ability To Bind DGC, PDE, and PilZ Proteins

The cyclic dinucleotide c-di-GMP is a master regulator of bacterial virulence and biofilm formation. The activations of c-di-GMP metabolism proteins, diguanylate cyclases (DGCs) and phosophodiesterases (PDEs), usually lead to diametrically opposite phenotypes in bacteria. Analogues of c-di-GMP, which can selectively modulate the activities of c-di-GMP processing proteins, will be useful chemical tools for studying and altering bacterial behavior. Herein we report that a conservative modification of one of the phosphate groups in c-di-GMP with a bridging sulfur in the phosphodiester linkage affords an analogue called endo-S-c-di-GMP. Computational, NMR (including DOSY), and CD experiments all reveal that, unlike c-di-GMP, endo-S-c-di-GMP does not readily form higher aggregates. The lower propensity of endo-S-c-di-GMP to form aggregates (as compared to that of c-di-GMP) is probably due to a higher activation barrier to convert from the "open" conformer (where the two guanines are on opposite faces) to the "closed" conformer (where the two guanines are on the same face). Consequently, endo-S-c-di-GMP has selectivity for proteins that bind monomeric but not dimeric c-di-GMP, which form from the "closed" conformer. For example, endo-S-c-di-GMP can inhibit the hydrolysis of c-di-GMP by RocR (a PDE enzyme that binds monomeric c-di-GMP) but did not bind to Alg44 (a PilZ protein) or regulate WspR (a DGC enzyme that has been shown to bind to dimeric c-di-GMP). This work demonstrates that selective binding to different classes of c-di-GMP binding proteins could be achieved by altering analogue conformer populations (conformational steering). We provide important design principles for the preparation of selective PDE inhibitors and reveal the role played by the c-di-GMP backbone in c-di-GMP polymorphism and binding to processing proteins.

Magnetic and spectral studies on nickel(II) and copper(II) dithiocarbazates derived from isoniazid

Some isonicotinoyldithiocarbazate complexes of nickel(II) and copper(II), of general formulae M(IN-Dtcz)2, [M(IN-DtczH)2]Cl2, and [M(IN-DtczH-Sal)2]Cl2 (M = Ni(II), Cu(II); INDtcz = isonicotinoyldithiocarbazate; IN-DtczH = isonicotinoyldithiocarbazic acid; IN-DtczH-Sal = salicylaldehyde Schiff base of isonicotinoyldithiocarbazic acid), have been synthesized. These complexes have been investigated by elemental analyses, mass, room temperature infrared and electronic spectra, and variable temperature magnetic susceptibility measurements. The three nickel(II) dithiocarbazates and [Cu(IN-DtczH-Sal)2]Cl2 exhibit NS linkage of the ligands, while Cu(IN-Dtcz)2 and [Cu(IN-DtczH)2]Cl2 have ONS binding of the ligands. The nickel(II) dithiocarbazates have [NiN2S2] chromophore. Magnetic and solution electronic absorption spectral data reveal square-planar geometry for Ni(IN-Dtcz)2 and the existence of square-planar–tetrahedral equilibrium for [Ni(IN-DtczH)2]Cl2 and [Ni(IN-DtczH-Sal)2]Cl2. Copper(II) dithiocarbazates, namely Cu(IN-Dtcz)2, [Cu(IN-DtczH)2]Cl2, with ONS ligands having dimeric or polymeric octahedral structures, and [Cu(IN-DtczH-Sal)2]Cl2, with NS binding having dimeric square-planar structure, exhibit antiferromagnetism. Superexchange pathway involving the bridging nitrogen and sulfur of the isonicotinoyldithiocarbazate ligands rather than direct metal–metal exchange is suggested for antiferromagnetic interactions. The spin exchange parameter, −2J = 202.14 and 29.26 cm−1, has been evaluated for [Cu(IN-DtczH)2]Cl2 and [Cu(IN-DtczH-Sal)2]Cl2, respectively, while it could not be evaluated for Cu(IN-Dtcz)2 because the slope was negative due to the non-variation of its magnetic moment with temperature. The difference in antiferromagnetic behavior and inconsistency of 2J for [Cu(IN-DtczH-Sal)2]Cl2 has been attributed to different electronic and steric factors of the three ligands, that is, isonicotinoyldithiocarbazate, its acid, and salicylaldehyde Schiff-base derivative.

Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV

It has long been known that type II topoisomerases require divalent metal ions in order to cleave DNA. Kinetic, mutagenesis and structural studies indicate that the eukaryotic enzymes utilize a novel variant of the canonical two-metal-ion mechanism to promote DNA scission. However, the role of metal ions in the cleavage reaction mediated by bacterial type II enzymes has been controversial. Therefore, to resolve this critical issue, this study characterized the DNA cleavage reaction of Escherichia coli topoisomerase IV. We utilized a series of divalent metal ions with varying thiophilicities in conjunction with oligonucleotides that replaced bridging and non-bridging oxygen atoms at (and near) the scissile bond with sulfur atoms. DNA scission was enhanced when thiophilic metal ions were used with substrates that contained bridging sulfur atoms. In addition, the metal-ion dependence of DNA cleavage was sigmoidal in nature, and rates and levels of DNA cleavage increased when metal ion mixtures were used in reactions. Based on these findings, we propose that topoisomerase IV cleaves DNA using a two-metal-ion mechanism in which one of the metal ions makes a critical interaction with the 3′-bridging atom of the scissile phosphate and facilitates DNA scission by the bacterial type II enzyme.

Structures of the Class D Carbapenemase OXA-24 from Acinetobacter baumannii in Complex with Doripenem

The emergence of class D β-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D β-lactamases with carbapenemase activity are resistant to β-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6α hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.

Complexes of ditopic carbo- and thio-carbohydrazone ligands – mononuclear, 1D chain, dinuclear and tetranuclear examples

Ligands based on carbo- and thio-carbohydrazone cores, modified with pyridine, carboxylate and oxime ends, have been examined. They display a tautomeric versatility based on the flexible nature of the hydrazone linkages, leading to varied coordination motifs. Examples of mononuclear (Co(II), Ni(II)), dinuclear (Co(III)), 1D chain (Cu(II)) and square [2 × 2] grid (Ni(II)) complexes are obtained. Ferromagnetic (Cu(II)) and antiferromagnetic (Ni(II)) exchange is observed, with spin coupling in the Ni(II)(4) square grids propagated through the μ-O and μ-S bridges. Weak antiferromagnetic exchange (J = -6.0 cm(-1)) is observed for the μ-O bridged grid, despite the large Ni-O-Ni angles (137-141°), while for the μ-S bridged grids much stronger exchange is observed (J = -148 cm(-1), -198 cm(-1)). This is much larger than expected based on the Ni-S-Ni bridge angles (151-169°), and is associated with the soft (less polarizing than oxygen) nature of the sulfur bridge, which would allow for much more efficient transmission of spin exchange than observed in the μ-O bridged case. Structures and variable temperature magnetic data are included, and spin exchange is analyzed using normal Heisenberg exchange models. No examples involving oxime (NO) bridging are reported, which reflects the positioning of the N,O and N,S donor combinations in each ligand, and the preferred coordination through these donor atoms.

X-ray photoelectron spectroscopy study of lithium thio-germanate thin films

In this study, the compositions of and chemical speciation in lithium thio-germanate thin films grown by radio frequency (RF) magnetron sputtering were determined by means of X-ray photoelectron spectroscopy (XPS). Three different targets, nLi2S + GeS2 (n = 1, 2, and 3) for RF sputtering were prepared. Thin films of ∼1 μm thickness were grown on single crystal Si [111] substrates using 50 W power and ∼3.3 Pa Ar gas atmospheres. As is commonly observed for RF sputtered non-oxide films, the surfaces of these lithium thio-germanate films were contaminated with both C and O at ∼10 at %. Etching the top surface of the films with Ar removed all of the surface carbon and reduced the oxygen contamination down to an average value of ∼5 at %. After such surface etching, the compositions of the films were found to agree very closely with the nominal composition of the target from which it was made. The Li2GeS3 (n = 1) thin film was found as expected to exhibit a 2 : 1 non-bridging sulfur (Ge–S−Li+, NBS) to bridging sulfur (Ge–S–Ge, BS) ratio. As the Li2S content increased, the Li4GeS4 and Li6GeS5 thin films, n = 2 and 3, exhibited as expected, 100% NBS. For the S2p core peaks, the binding energy of S in GeS2 is the highest due to the nearly covalent bonding in the BS structure, Ge–S–Ge. As the Li2S content increased, the binding energy of S in the thin films progressively decreased due to the progressive increase in the fraction (and number) of NBS (more ionic), Ge–S−Li+, in the films.

Synthesis, Crystal Structure, and Biological Activity of a New Cu(I) Complex of the N-Phenyl-N′-(2-nitrobenzoyl)-thiourea

The complex bis(μ-sulfur)-sulfur-[N-phenyl-N′-(2-nitrobenzoyl)-thiourea]copper (I) was obtained from the reaction between the N-phenyl-N′-(2-nitrobenzoyl)-thiourea(HL) and copper(II). The compound was characterized by IR and 1H NMR, 13C NMR spectroscopy and its structure was determined by single crystal X-ray diffraction. The complex is binuclear with two copper(I) ions coordinated by a terminal sulfur, two bridging sulfurs, and a HL molecule. In addition, the compound is also a considerable plant-growth regulator. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.