Lead(II) thiocyanate complexes with bibracchial lariat ethers: an X-ray and DFT study

Compounds of formula [Pb(L2)(NCS)2] (1) and [Pb(L4)(SCN)2] (2) (where L2 is the lariat crown ether N,N'-bis(3-aminobenzyl)-4,13-diaza-18-crown-6 and L4 is the Schiff-base lariat crown ether N,N'-bis(3-(salicylaldimino)benzyl)-4,13-diaza-18-crown-6) were isolated and structurally characterized by X-ray diffraction analyses. The X-ray crystal structures of both compounds show the metal ion coordinated to the six donor atoms of the crown moiety, leaving the corresponding pendant arms uncoordinated. The coordination sphere of lead(II) is completed by two thiocyanate groups that coordinate either through their nitrogen (1) or sulfur (2) atoms. The organic receptor adopts a syn conformation in 1, while in 2 it shows an anti conformation. To rationalize these unexpected different conformations of the L2 and L4 receptors in compounds 1 and 2, as well as the different binding modes found for the thiocyanate ligands, we have carried out theoretical calculations at the DFT (B3LYP) level. These calculations predict the syn conformation being the most stable in both 1 and 2 complexes. So, the anti conformation found for 2 in the solid state is tentatively attributed to the presence of intermolecular pi-pi interactions between phenol rings, for which the dihedral angle between the least-squares planes of both rings amounts to 2.6 degrees and the distance between the center of both rings is 3.766 A. On the other hand, the analysis of the electronic structure has revealed that the Pb-ligand bonds present highly ionic character in this family of compounds. They also suggest a greater transfer of electron density from the NCS- ligands when they coordinate through the less electronegative S atom. The Pb-SCN covalent bond formation mainly occurs due to an effective overlap of the occupied 3p z orbitals of the S atoms and the unoccupied 6p z AO of the Pb atom, while the Pb-NCS bonding interaction is primarily due to the overlap of the 6s and 7s AO of Pb with sp(1.10) hybrids of the N donor atoms. Our electronic structure calculations can rationalize the different coordination of the thiocyanate groups in compounds 1 and 2: the simultaneous formation of two Pb-SCN bonds is more favorable for S-Pb-S angles close to 180 degrees , for which the overlap between the occupied 3p z orbitals of the S atoms and the unoccupied 6 pz AO of the Pb atom is maximized.     

Azolium-linked cyclophanes: effects of structure, solvent, and counteranions on solution conformation behavior

This paper describes the synthesis, structural characterization, and solution behavior of some xylyl-linked imidazolium and benzimidazolium cyclophanes decorated with alkyl or alkoxy groups. The addition of alkyl/alkoxy chains to the cyclophanes allows for studies in chlorinated solvents, whereas previous solution studies of azolium cyclophanes have generally required highly polar solvents. The azolium cyclophanes may exist in a syn/syn conformation (azolium rings mutually syn, arene rings mutually syn) or a syn/anti conformation (azolium rings mutually syn, arene rings mutually anti). The preferred conformation is significantly affected by (i) binding of bromide (ion pairing) to the protons on the imidazolium or benzimidazolium rings, which occurs in solutions of bromide salts of the cyclophanes in chlorinated solvents, and (ii) the addition of alkoxy groups to the benzimidazolium cyclophanes. These structural modifications have also led to cyclophanes that adopt conformations not previously identified for similar azolium cyclophane analogues. Detailed (1)H NMR studies for one cyclophane identified binding of bromide at two independent sites within the cyclophane.     

Efficient transport of gold atoms with a scanning tunneling microscopy tip and a linker molecule

A thiophene-containing molecule attached to a scanning tunneling microscopy (STM) tip is used to transport gold atoms on a Au(111) surface. The molecule contains eight thiophene rings and therefore has sulfur atoms that are known to bind to gold atoms. Using a gold-coated tip, the molecules previously deposited on the surface bind to the lower-coordination gold atoms of the tip. When that tip is used to scan the surface, the still free thiophene rings (not all of the sulfur atoms bind to the tip) can attach to gold atoms from the surface and drag them along the scanning direction, depositing them either at the position where the tip changes its scanning direction or where the tip encounters an "up step", whichever event occurs first.     

The Intramolecular Interaction of Thiophene and Furan with Aromatic and Fluoroaromatic Systems in Some [3.3]Meta(heterocyclo)paracyclophanes: A Combined Computational and NMR Spectroscopic Study

Four thiophene‐ and furan‐containing [3.3]meta(heterocyclo)paracyclophanes were designed and synthesized to study the intramolecular interaction between standard heteroaromatic rings and tetra‐H‐ or tetra‐F‐substituted benzenes. A complete conformational analysis, carried out by DFT calculations and variable‐temperature NMR techniques, showed that, despite their structural similarity, these adducts have different conformational preferences and undergo different types of isomerizations depending on the nature of the heterocycle. The thiophene‐derived adducts adopted a parallel stacked arrangement of the aromatic systems in the ground‐state conformations. Their isomerization pathways involved a thiophene ring‐flip process passing through an edge‐to‐face arranged transition state in which the heterocycle is perpendicular to the benzene platform and its sulfur atom points toward the center of that ring. The threshold energy barrier to the ring‐flip process was higher by 10 kJ mol^?1 in the case of the adduct featuring the perfluorinated benzene. This difference was rationalized by assuming that the ground‐state conformations of the H‐ and F‐substituted compounds have different stability. On the contrary, the furan‐derived adducts were shown by calculations and NMR spectroscopy to adopt, in their ground‐state conformations, a perpendicular edge‐to‐face disposition of the rings with the oxygen atom pointing toward the benzene platform. The adoption of this arrangement was confirmed by X‐ray crystallography. In the case of these compounds, the isomerization process involved distortion of the CH₂SCH₂ bridges connecting the aromatic systems and the adoption of transition‐state geometries for which the rings were arranged in a parallel‐stacked orientation. Once again a very nice agreement was observed between the predicted and the experimentally determined geometries and pathways. In the case of the furan‐containing compounds, the threshold barriers were found to be much lower in energy that those observed for the thiophene derivatives. Remarkably, they were virtually independent of the presence of fluorine atoms on the platform benzene ring.     

Altering the emission behavior with the turn of a thiophene ring: the photophysics of condensed ring systems of alternating benzenes and thiophenes

Six aromatic compounds with embedded thiophenes differing in the number of rings (2-5) and thiophene orientation along the long axis of the molecule (syn, anti) were investigated. Photophysical properties, steady-state absorption, fluorescence, phosphorescence, lifetimes, quantum yields, and a comprehensive time-resolved spectroscopic analysis (femtosecond and nanosecond transient absorption spectroscopy) have been studied as a function of molecular structure.     

Dinitro and quinodimethane derivatives of terthiophene that can be both oxidized and reduced. Crystal structures,spectra, and a method for analyzing quinoid contributions to structure

Two new oligothiophenes, the dinitro compound 3',4'-dibutyl-5,5' '-dinitro-2,2':5',2' '-terthiophene (1) and the quinodimethane 3',4'-dibutyl-5,5' '-bis(dicyanomethylene)-5,5' '-dihydro-2,2':5',2' '-terthiophene (2), have been synthesized and studied with electrochemistry, UV-vis-NIR-IR spectroscopy, ESR, and X-ray crystallography. These compounds, designed to be both electron and hole carriers, show redox properties that are unusual for oligothiophenes. Cyclic voltammetry and spectroelectrochemistry demonstrated that each compound could be oxidized to a cation radical and reduced to an anion radical and dianion. The spectra of 2 and its three redox partners were analyzed in terms of a limiting structure in which the neutral 2 has orbitals corresponding to those of a substituted-terthiophene dication. Compound 1 crystallizes with the thiophene rings held in an unusual nonplanar, cisoid configuration in face-to-face pi-stacks, with a spacing between molecules of 3.65 A. The C-C bond lengths of the outer nitro-substituted rings have quinoid character. Compound 2 crystallizes with the thiophene rings in a planar, transoid configuration. The molecules are held in pi-stacks formed from pi-dimers with a spacing between molecules of 3.47 and 3.63 A. The C-C bond distances of the thiophene rings of 1 and 2 and other oligomers were analyzed by a principal component analysis. The analysis found that 93% of the structural variance resided in one principal component related to the quinoid structure of the oligothiophene moiety. The analysis reliably demonstrated a quinoid contribution to the structure of 1. This method should be applicable to understanding the structure of other conjugated molecules in which quinoid structures contribute.     

Conformational preferences and internal rotation in alkyl- and phenyl-substituted thiourea derivatives

Potential energy surfaces (PES) for rotation about the N-C(sp(3)) or N-C(aryl) bond and energies of stationary points on PES for rotation about the C(sp(2))-N bond are reported for methylthiourea, ethylthiourea, isopropylthiourea, tert-butylthiourea, and phenylurea, using the MP2/aug-cc-pVDZ method. Analysis of alkylthioureas shows that conformations, with alkyl groups cis to the sulfur atom, are more stable (by 0.4-1.5 kcal/mol) than the trans forms. All minima adopt anti configurations with respect to nitrogen pyramidalization, whereas syn configurations are not stationary points on the MP2 potential surface. In contrast, analysis of phenylthiourea reveals that a trans isomer in a syn geometry is the global minimum, whereas a cis isomer in an anti geometry is a local minimum with a relative energy of 2.7 kcal/mol. Rotation about the C(sp(2))-N bond in alkyl and phenyl thioureas is slightly more hindered (9.1-10.2 kcal/mol) than the analogous motion in the unsubstituted molecule (8.6 kcal/mol). The maximum barriers to rotation for the methyl, ethyl, isopropyl, tert-butyl, and phenyl substituents are predicted to be 1.2, 8.9, 8.6, 5.3, and 0.9 kcal/mol, respectively. Corresponding PESs are consistent with the experimental dihedral angle distribution observed in crystal structures. The results of the electronic structure calculations are used to benchmark the performance of the MMFF94 force field. Systematic discrepancies between MMFF94 and MP2 results were improved by modification of selected torsion parameters and one of the van der Waals parameters for sulfur.     

Structural and spectroscopic properties of trans-dichlorobis(2,2-dimethyl-1,3-diaminopropane)chromium(III) chloride

The structure of trans-[CrCl(2)(Me(2)tn)(2)]Cl (Me(2)tn=2,2-dimethylpropane-1,3-diamine) has been determined by a single-crystal X-ray diffraction study at 150K. The analysis reveals that there are two independent Cr(III) complex cations in the structure, one with crystallographic inversion symmetry and the other with two-fold rotation symmetry, which are conformational isomers of each other. In both conformations, the chromium atom adopts a distorted octahedral structure with the four nitrogen atoms of two Me(2)tn ligands occupying the equatorial plane and two chlorine atoms occupying trans-axial positions. The six-membered chelate rings are in stable chair conformations with N-Cr-N angles of 87.03(8) degrees and 88.99(8) degrees . The two chelate rings in the centrosymmetric complex cation 1 are anti, while those in the rotation-symmetric complex cation 2 are in syn conformations. The mean Cr-N and Cr-Cl bond lengths are 2.0922 and 2.3253 A, respectively. The infrared and UV-visible absorption spectra of trans-[CrCl(2)(Me(2)tn)(2)]Cl have also been measured. The resolved band maxima of the electronic d-d spectrum are fitted with a secular determinant for a quartet energy state of the d(3) configuration in a tetragonal field including configurational but neglecting spin-orbit coupling. It is confirmed that the nitrogen atoms of the Me(2)tn ligand have a strong sigma-donor character, but the chloro ligand has weak sigma- and pi-donor properties toward the chromium(III) ion.     

Long-range sigma-pi interactions in tetrahydro-4H-thiopyran end-capped oligo(cyclohexylidenes). Photo-electron spectroscopy, ab initio SCF MO calculations, and natural bond orbital analyses

Long-range sigma-pi interactions in tetrahydro4H-thiopyran end-capped oligo(cyclohexylidenes) were identified by He(I) photoelectron spectroscopy (PES) and ab initio RHF/6-31G* calculations. The vertical ionization energies Ivj of the highest occupied molecular orbitals (MO's) were assigned using Koopmans' theorem (Iv,j = -epsilonj) and by correlation with the ionizations of related reference compounds. The experimental (PES) and theoretical (RHF/6-31G*) results are in good agreement. For tercyclohexylidene derivatives which contain two nonconjugated pi-bonds splittings deltaIv,j of the pi-bands in the range from approximately 0.5 to 0.7 eV (delta-epsilonj approximately 0.6 to 0.9 eV). For the bi- and tercyclohexylidene compounds containing two sulfur atoms at their alpha- and omega-end positions the pi-type sulfur lone pair bands [Lppi(S)] split significantly by deltaIvj approximately 0.3 to 0.4 eV (delta-epsilonj approximately 0.3 to 0.4 eV), i.e. sigma-pi interactions over distances of ca. 8 and 12 A, respectively, occur. The magnitude of the interactions and the observed splittings are independent of the anti and syn conformations of the oligo(cyclohexylidene) hydrocarbon skeletons. RHF/6-31G* Natural Bond Orbital analyses reveal that the Hax-C-C-Hax precanonical MO's (PCMO's) centered on the cyclohexyl-type rings are paramount for the relay of the through-bond sigma-pi interactions; no through-space sigma-pi interactions were identified.     

Configurational stability of bisindolylmaleimide cyclophanes: from conformers to the first configurationally stable, atropisomeric bisindolylmaleimides

The bisindolylmaleimides are selective protein kinase inhibitors that can adopt two limiting diastereomeric (syn and anti) conformations. The configurational stability of a range of substituted and macrocyclic bisindolylmaleimides was investigated by using appropriate techniques. With unconstrained bisindolylmaleimides, the size of the 2-indolyl substituents was found to affect configurational stability, though not sufficiently to allow atropisomeric bisindolylmaleimides to be obtained. However, with a tether between the two indole nitrogen atoms in place, the steric effect of 2-indolyl substituents was greatly exaggerated, leading to large differences in configurational stability. The rate of interconversion of the syn and anti conformers varied by over twenty orders of magnitude through substitution of a bisindolylmaleimide ring system, which was constrained within a macrocyclic ring. Indeed, the first examples of configurationally stable atropisomeric bisindolylmaleimides are reported; the half-life for epimerisation of these compounds at room temperature was estimated to be >10(7) years.     

Theoretical study of some nitrososulfamide compounds with antitumor activity

The lowest-energy conformations of four 2-chloroethylnitrososulfamides were determined using the MM+ molecular mechanics method as implemented in Hyperchem 6.0. Some of the calculated structural parameters, angles and bonds lengths were compared with the crystal structure data of N-nitroso-N-(2-chloroethyl)-N'-sulfamoyl- proline. Using MM+, AM1 and PM3 the anti conformation was predicted to be more stable than the syn conformation in each of these compounds. With these methods we found that the relative energy of the transition state (TS) was considerably higher, but with the ab initio method using RHF with minimal basic function STO-3G we found that the syn conformation is predicted to be slightly more stable. The determination of some atomic charges of a selection of atoms on the syn, anti and TS structures of the various compounds provided some details about the nature of the transition state.     

Reversible Redox Reaction Between Antiaromatic and Aromatic States of 32π‐Expanded Isophlorins

32π‐antiaromatic expanded isophlorins with a varying number of thiophene and furan rings adopt either planar, ring‐inverted, or twisted conformations depending on the number of furan rings in the macrocycle. However, they exhibit identical reactivity with respect to their oxidation to aromatic 30π‐dicationic species under acidic conditions. These 32π‐antiaromatic macrocycles can also be oxidized with [Et₃O⁺SbCl₆^?]and NOBF₄ to generate dications, thus confirming ring oxidation of macrocycles. Furthermore, they can be reduced back to their parent 32π‐antiaromatic state by triethylamine, Zn, or FeCl₂. Single‐crystal X‐ray diffraction analysis confirmed a figure‐eight conformation for a hexafuran system, which opens to a planar structure upon oxidation.     

Conformations and energetics of sulfur and selenium diimides

The geometries and energetics of different conformations of sulfur and selenium diimides E(NR)(2) (E = S, Se; R = H, Me, (t)Bu, C(6)H(3)Me(2)-2,6, SiMe(3)) have been studied by using various ab initio and DFT molecular orbital techniques. The syn,syn conformation is found to be most stable for parent E(NH)(2), but in general, the preferred molecular conformation for substituted chalcogen diimides is syn,anti. In the case of E(NH)(2) the present calculations further confirm that syn,syn and syn,anti conformations lie energetically close to each other. From the three different theoretical methods used, B3PW91/6-31G proved to be the most suitable method for predicting the geometries of chalcogen diimides. The optimized geometrical parameters are in a good agreement with all available experimental data. While qualitative energy ordering of the different conformations is independent of the level of theory, the quantitative energy differences are dependent on the method used. The performance and reliability of higher level ab initio calculations and DFT methods using large basis sets were tested and compared with experimental information where available. All of the higher level ab inito methods give very similar results, but the use of large basis sets with the B3PW91 method does not increase the reliability of the results. The combination of CCSD(T)/cc-pVDZ with the B3PW91/6-31G-optimized geometries is found to be the method of choice to study energetic properties of chalcogen diimides.     

Dynamics of alkoxy-oligothiophene ground and excited states in nanochannels

Two oligothiophenes, 4,4'-dipentoxy-2,2'-dithiophene and 4,4"-dipentoxy-2,2':5',2":5",2' '-tetrathiophene, have been included in the nanochannels of the autoassembling host TPP (tris-o-phenylenedioxycyclotriphosphazene). The effect of the confinement on the structure and properties of the two dyes, as conformational arrangements, dynamics, and photophysical behavior, was addressed by the combination of high spinning speed solid-state NMR and time-resolved EPR spectroscopy. We compared the conformations of the dyes in their ground and photoexcited triplet states and described in detail the dynamics of the supramolecular adducts from 4 K to room temperature. Above 200 K surprisingly fast spinning rates of the dithiophene core were discovered, while the side chains show far slower reorientation motion, being in bulky gauche-rich conformations. These lateral plugs keep the planar core as appended in the space like a nanoscale gyroscope, allowing a reorientation in the motion regime of liquids and a long triplet lifetime at unusually high temperature. The nuclear magnetic properties of the guest dyes are also largely affected by the aromatic rings of the neighboring host, imparting an impressive magnetic susceptibility effect (2 ppm proton shift). The high mobility is due to the formation of a nanocage in a channel where aliphatic and aromatic functions isolate the thiophene moieties. Instead, two conformers of the tetrathiophene twisted on the central bond are stabilized by interaction with the host. They interconvert fast enough to be averaged in the NMR time scale.     

Addukte schwefelhaltiger Heteroaromaten mit SbCl3 Untersuchungen zur Bildung und Kristallstruktur von 2,2′-Dithienyl · 2 SbCl3 und Benzo[b]thiophen · 2 SbCl3

Adducts of Sulfur-containing Hetero Aromates with SbCl₃: Studies on Formation and Crystal Structure of 2,2′-Dithienyl · 2 SbCl₃ and Benzo[b]thiophene · 2 SbCl₃ Whereas the system 2,2′-dithienyl—SbCl₃ because of irreversible thermal decomposition reactions could not be studied by DTA, this method applied to the system benzo[b]thiophene—SbCl₃ yielded a quasibinary behaviour and the existence of a compound benzo[b]thiophene · 2SbCl_3. melting congruently at 71.2°C. Crystals of this adduct and that of analogue composition 2,2′-dithienyl · 2SbCl₃ were obtained from solution. Their structures were determined by X-ray diffraction as those of bπ-v complexes. They are compared with other Menshutkin complexes. The π…?Sb interactions are indicated by distances between the planes of the planar hetero aromates and the Sb atoms located in a transoid way above both single rings of 316 (dithienyl adduct) and 325 pm (benzothiophene adduct). There is no particular coordinative bond formation by the S atoms. The intermolecular linking in the SbCl₃ partial structures is described.     

Crystal structure of a liquid crystal non‐symmetric dimer: cholesteryl 4‐[4‐(4‐n‐butylphenylethynyl)phenoxy]butanoate

The crystal structure of cholesteryl 4‐[4‐(4‐n‐butylphenylethynyl)phenoxy]butanoate [phase sequence: Cr 155°C (46.1?J?g^?1) SmA 186.8°C (1.5?J?g^?1) TGB‐N* 204.7 (6?J?g^?1) I] has been solved from single crystal X‐ray diffraction data. The compound crystallizes in the monoclinic space group P2₁ with unit cell parameters: a?=?13.129(2), b?=?9.3904(10), c?=?17.4121(8)?Å, β?=?92.790(7)°, Z?=?2. The structure has been solved by direct methods and refined to R?=?0.0606 for 3?250 observed reflections. The bond distances and angles are in good agreement with the corresponding values for compounds containing phenyl and cholesterol moieties. The phenyl rings A and B are planar. The dihedral angle between the least‐squares planes of the two phenyl rings is 28°. The cholesterol moiety has the usual structure: the C and E rings have chair conformations, and the D and F rings adopt half‐chair conformations. The molecules in the unit cell are arranged in an antiparallel manner. The crystal structure is stabilized by an intermolecular C–H…O contact of 2.989(10)?Å.     

New phenylboronic esters derived from inositol [1]

We have prepared two new tetracyclic phenylboronic esters 4 and 5 derived from myo-inositol and from 1,2-O-isopropylidene-myo-inositol, respectively. The structures of these compounds were established from NMR and IR spectra, elemental analyses, and an X-ray diffraction study in the case of 4 . Compound 4 is a tetracyclic derivative of the less stable conformer of inositol (five axial hydroxy groups and one equatorial) with two dioxaboroline rings at opposite faces of the six-membered ring, one formed between the boron atom and the axial hydroxyl groups at C-3 and C-5 and the other between the boron atom and the hydroxyl groups at C-4 and C-6, and a dioxaborolidine ring bridging C-1 and C-2 at axial and equatorial positions. A similar structure was found for 5 with the difference that bridging C-1 and C-2 there is a dioxolane ring. The boron atoms are planar with their attached atoms, stabilized by retrocoordination between the boron and oxygen and carbon atoms, respectively. The two phenyl rings that are in the same face of the molecule are essentially parallel, with a dihedral angle between planes of 28.26 ± 0.79°.     

Synthesis of the anti and syn isomers of thieno[f,f ']bis[1]benzothiophene. Comparison of the optical and electrochemical properties of the anti and syn isomers

We report isomer-pure synthesis of thieno[2,3-f:5,4-f ']bis[1]benzothiophene and thieno[3,2-f:4,5-f ']bis[1]benzothiophene, the anti and syn isomers of a pentacyclic compound consisting of alternating thiophene and benzene rings. The optical and electrochemical properties of both are reported. In the anti isomer, the ribbonlike embedding of three thiophene units leads to a near-planar molecule with favorable pi-pi stacking behavior in the solid state as shown by X-ray crystal structure analysis.     

Syntheses,characterizations of copper compounds containing a series of S-, N-containing aromatic heterocyclic 2,2′:6′,2″-terpyridine derivatives

A series of 2,2′:6′,2″-terpyridine (TPY) based aromatic heterocyclic compounds, extended by thiophene, 4-dibenzothiophene, and thiazole units at the para position of the central pyridine ring in TPY, are described in this paper. A new compound, 4′-(4′-dibenbenzothiophene-5-thiophene-2-yl)-2,2′:6′,2″-terpyridine (L_a), serves as a tridentate ligand to react with Cu(NO₃)₂·3H₂O and CuCl₂·2H₂O, respectively, to produce two different Cu(II) complexes [Cu(L_a)₂](NO₃)₂ and [CuL_aCl₂] with 1?:?2 and 1?:?1 metal/ligand ratios. Dibenzothiophene is first introduced to TPY via the thiophene bridge. The alterations in cis and trans configuration, dihedral angles between adjacent aromatic rings, and photophysical properties have been observed before and after Cu(II) complexation, which has been verified by their crystal structures, UV–vis and fluorescence spectra.     

6‐Amino‐5,5,7‐tri­cyano‐3,3a,4,5‐tetra­hydro‐2H‐indene‐4‐spiro­cyclo­pentane

The positions of the C=C double bonds in the title compound, C₁₆H₁₆N₄, the subject of some dispute in the literature, have been clearly identified. The cyclo­hexene ring has a distorted half‐chair conformation and the cyclo­pentene and cyclo­pentane rings adopt envelope conformations. The dihedral angles between planar fragments of the cyclo­hexene and cyclo­pentene rings and of the cyclo­hexene and cyclo­pentane rings are 7.5 (1) and 86.98 (9)°, respectively. In the crystal, intermolecular N—H?N hydrogen bonds link the mol­ecules into infinite chains running in the [10] direction.