A strategy for the synthesis of metal bis(2,2':6',2' '-terpyridine)-terminated molecular dyads having controlled torsion angles at the central biphenyl linker

The synthesis of a series of binuclear complexes comprising bis(2,2':6',2' '-terpyridine)ruthenium(II) and -osmium(II) centers connected via a geometrically constrained 4,4'-biphenyl bridge is described. These compounds have been prepared by a "synthesis-at-metal" approach as well as by the conventional method of synthesizing the ligand and subsequently attaching the metal center. A computational investigation into the behavior of the biphenyl-based bridges has been used to provide lowest-energy conformations and to estimate the degree of internal fluctuation about the mean torsion angle. It is shown that the length of the constraining strap determines both the torsion angle and the internal flexibility, with longer straps twisting the biphenyl group so as to relax stereochemical interactions between the linking oxygen atoms. Longer straps can be formed from poly(ethylene glycol) residues that provide an additional binding site for small cations. Electrospray mass spectrometry carried out on solutions of these crown ether-like bridges confirmed that Li+, Na+, and K+ ions bind in the form of 1:1 complexes. This range of compounds should permit rational examination of how the torsion angle affects the rate of through-bond electron transfer, electron exchange, and charge shift.     

In situ gap-mode Raman spectroscopy on single-crystal Au(100) electrodes: tuning the torsion angle of 4,4'-biphenyldithiols by an electrochemical gate field

In situ gap-mode Raman spectra were acquired in an electrochemical environment on a single-crystal gold electrode employing a Au(100)|4,4'-biphenyldithiol (BPDT)|Au-NP(55 nm) sandwich assembly. This geometry enabled an investigation of the influence of an applied electrochemical gate field on the conformational changes in nanojunctions, such as the torsion angle (φ) of molecules. A linear correlation between the intensity ratio I(C═C)/I(C(ring)-S) and cos(2) φ in 4,4'-BPDT-type molecular junctions was established and subsequently utilized to estimate the potential dependence of the torsion angle of the "flexible" molecule M1 at different potentials. The latter decreases as the potential (charge) becomes more negative, resulting in better π-π coupling, which correlates with enhanced junction conductance. The demonstrated spectroelectrochemical strategy and the direct correlation of the spectroscopic results with (single) molecular conductance studies may guide the selection and elucidation of functional molecules for potential applications in novel nanodevices.     

Cobalt(II) Tri‐tert‐butoxysilanethiolates with Bidentate Spacer Ligands

A new series of Co^II tri‐tert‐butoxysilanethiolate complexes with bidentate N,N′‐ligands (L) such as pyrazine, quinoxaline and 4,4′‐bipy was obtained: for pyrazine and quinoxaline the complexes are binuclear {[Co{SSi(tBuO)₃}₂]₂(μ‐L)} with metal atoms linked by an adequate heterocyclic base L. The use of 4,4′‐bipy resulted in a coordination polymer [Co{μ‐SSi(tBuO)₃}{SSi(tBuO)₃}(μ‐4,4′‐bipy)]_n and two polymorphic forms of {[Co{SSi(tBuO)₃}₂]₂(μ‐4,4′‐bipy)}. Pyridyl rings in one polymorph form a torsion angle of 0.57°, whereas a rotation about the linking C–C bond of 4,4′‐bipy in second polymorph is significant and results in a torsion angle of 72.4°. Complexes were analysed and characterised using elemental analysis, solid state IR and UV/Vis spectroscopy, and single‐crystal X‐ray analysis.     

Polysulfide anions II: structure and vibrational spectra of the S4(2-) and S5(2-) anions. Influence of the cations on bond length, valence, and torsion angle

The influence of the cations on bond length, valence, and torsion angle of S4(2-) and S5(2-) anions was examined in a series of solid alkali tetra- and pentasulfides by relating their Raman spectra to their known X-ray structures through a force-field analysis. The IR and Raman spectra of BaS4.H2O and the Raman spectra of (NH4)2S4.nNH3, gamma-Na2S4, and delta-Na2S5 are presented. The similarity of spectra of gamma-Na2S4 with those of BaS4.H2O suggests similar structures of the S4(2-) anions in these two compounds with a torsion angle smaller than 90 degrees. The variations of SS bond length, SSS valence angle, and dihedral angle of Sn2- anions are related to the polarization of the lone pair and electronic charge of the anion by the electric field of the cations. A correlation between the torsion angle and the SSS valence angle is shown as that previously reported between the length of the bond around which the torsion takes place and the dihedral angle value. These geometry changes are explained by the hyperconjugation concept and the electron long-pair repulsion.     

Twisting of conjugated oligomers and polymers: case study of oligo- and polythiophene

Interring twisting (change in the dihedral angle between conjugated rings) of polythiophene was studied theoretically using periodic boundary conditions (PBC) at the B3LYP/6-31G(d) level. We find that the band gap of polymers is strongly dependent on the interring twist angle; yet twisting requires very little energy. A twist of 30 degrees increases the band gap by 0.75 eV in polythiophene, while requiring only 0.41 kcal mol(-1) per monomer unit. Such a small energetic value is of the order of crystal packing or van der Waals forces. These results are compared with calculations performed on model oligomers. Sexithiophene, its radical cations, and its dication are optimized at 0-180 degrees end-to-end twist angles (which correspond to 0-36 degrees interring dihedral angles) using the B3LYP/6-31G(d) method. The theoretical results suggest that the HOMO-LUMO gap, ionization potential, and charge distribution of oligomers are strongly dependent on twisting, whereas, similar to the case of polythiophene, twisting of neutral oligothiophenes costs very little energy. In the case of the radical cation, the lowest energy transition is shifted to a longer wavelength region on twisting, while the second-lowest energy transition is shifted to a shorter wavelength region. This implies that twisted, doped conducting polymers (modeled here by an oligomer radical cation), in contrast to planar, doped polymers, should be transparent within a certain optical window (in the far-visible region, at approximately 1.5 eV). This observation is explained on the basis of changes in the shape and overlap of the frontier molecular orbitals.     

New types of the flexible self-assembled metal-organic coordination polymers constructed by aliphatic dicarboxylates and rigid bidentate nitrogen ligands

The reaction of metal ions, flexible aliphatic dicarboxylates and rigid bidentate linear ligands under mild conditions in water afford four novel metal-organic coordination polymers, [Cd(mu-mal)(mu-pyz)(0.5)(H(2)O)](n) 1 (mal = malonate dianion, pyz = pyrazine), [Cd(2)(mu-suc)(2)(mu-pyz)(H(2)O)(2)](n) 2 (suc = succinate dianion), and ([M(mu-bipy)(H(2)O)4][suc].4H(2)O)(n)(M = Co, 3, M = Zn, 4, bipy = 4,4'-bipyridine). The molecular structures of 1-4 have been established by single-crystal X-ray crystallography. 1 is a 3D network being composed of layers of octahedrally coordinated Cd atoms bridged by malonate anions in syn-anti configurations within the layers and pyz molecules between layers. Unlike that in 1, each Cd atom in 2 displays uncommon pentagonal-bipyramidal geometry to form 2D infinite grid sheets with square grid dimensions of ca. 7.936 x 7.936 [Angstrom]. Both 3 and 4 exhibit 1D linear -M-bipy-M-bipy- chain polymers, and these chains were packed as ...ABCABC... layered structures. The bridging succinate ligands in 2 adopt the syn-anti mode with a torsion angle of 60.8(7) degrees, while the solvated succinate ligands in 3 and 4 adopt the anti-anti mode with a torsion angle of 180.0 degrees. To our knowledge, compound 2 represents the first example of flexible self-assembled succinate-pyrazine mixed bridging ligand coordination network. 3 and 4 are the first two cases of succinate-bipy polymers with non-coordinated succinate. The magnetic behavior for 3 was studied in the temperature range of 5-300 K. The result indicates the occurrence of a weak antiferromagnetic coupling between the cobalt(II) ions.     

Chi(1) rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force

The equilibrium angles and distributions of chi(1) rotamers for mobile surface side chains of the small, 63-residue, B1 domain of protein L have been calculated from the static crystal structure by rigid body/torsion angle simulated annealing using a torsion angle database potential of mean force and compared to those deduced by Monte Carlo analysis of side chain residual dipolar couplings measured in solution. Good agreement between theory and experiment is observed, indicating that for side chains undergoing rotamer averaging that is fast on the chemical shift time scale, the equilibrium angles and distribution of chi(1) rotamers are largely determined by the backbone phi/psi torsion angles.     

Quantification of the (anti)aromaticity of fulvalenes subjected to pi-electron cross-delocalization

Fulvalenes 3-12 were theoretically studied at the ab initio level of theory. For the global minima structures, the occupation of the bonding (pi)C=C orbital of the interring C=C double bond obtained by NBO analysis quantitatively proves pi-electron cross-delocalization resulting in, at least partially, 2- or 6pi-electron aromaticity and 8pi-electron antiaromaticity for appropriate moieties. The cross-conjugation was quantified by the corresponding occupation numbers and lengths of the interring C=C double bonds, while the aromaticity or antiaromaticity due to cross-delocalization of the pi-electrons was visualized and quantified by through-space NMR shielding surfaces.     

Application of standard DFT theory for nonbonded interactions in soft matter: prototype study of poly-para-phenylene

We present a detailed analysis of the application of density functional theory (DFT) methods to the study of structural properties of molecular and supramolecular systems, using as a paradigmatic example three para-phenylene-based systems: isolated biphenyl, single chain poly-para-phenylene, and crystalline biphenyl. We use different functionals for the exchange correlation potential, the local density (LDA), and generalized gradient approximations (GGA), and also different basis sets expansions, localized, plane waves (PW), and mixed (localized plus PW), within the reciprocal space formulation for the hamiltonian. We find that regardless of the choice of basis functions, the GGA calculations yield larger interring distances and torsion angles than LDA. For the same XC approximation, the agreement between calculations with different basis functions lies within 1% (LDA) or 0.5% (GGA) for distances, and while PW and mixed basis calculations agree within 1 degrees for torsion angles, the localized basis results show larger angles by approximately 8 degrees and a nonmonotonic dependence on basis size, with differences within 6 degrees. The most prominent features, namely the torsion between rings for isolated molecule and infinite chain, and planarity for the molecule in crystalline environment, are well reproduced by all DFT calculations.     

Localization or delocalization in the electronic structure of Creutz-Taube-type complexes in aqueous solution

Creutz-Taube complex, [(NH3)5Ru-pyrazine-Ru(NH3)5]5+ (1), and its analogues, [(NH3)5Os-pyrazine-Os(NH3)5]5+ (2), [(NH3)5Ru(4,4'-bipyridine)Ru(NH3)5]5+ (3), and [(NH3)5Os(4,4'-bipyridine)Os(NH3)5]5+ (4), were theoretically investigated by the combination of a two-state model and the dielectric continuum model. Their electronic structures are very sensitive to the metal, ligand, and solvent. In the gas phase, the electronic structures of 1-4 would be completely delocalized. In aqueous solution, that of 3 becomes localized because the polar solvent stabilizes the localized electronic structure with the large dipole moment. However, 1 and 2 are still delocalized in aqueous solution. In 4, the electronic structure would be localized when the dihedral angle between two pyridyl rings is 80 degrees , while it would become delocalized when the angle is small. The origins of the difference are the smaller overlap integral and larger energy difference between two diabatic states, of which electronic structure is almost localized on each metal center.     

X–H rotational-echo double-resonance NMR for torsion angle determination of peptides

C–H and N–H rotational-echo double-resonance (REDOR) NMR is developed for determining torsion angles in peptides. The distance between an X spin such as ¹³C or ¹⁵N and a proton is measured by evolving the proton magnetization under REDOR-recoupled X–H dipolar interaction. The proton of interest is selected through its directly bonded heteronuclear spin Y. The sidechain torsion angle χ₁ is extracted from a ¹³Cβ-detected Hβ–N distance, while the backbone torsion angle φ is extracted from an ¹⁵N-detected H^N–C^′ distance. The approach is demonstrated on three model peptides with known crystal structures to illustrate its utility.     

Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.     

Conformationally controlled electron delocalization in n-type rods: synthesis, structure, and optical, electrochemical, and spectroelectrochemical properties of dicyanocyclophanes

A series of dicyanobiphenylcyclophanes 1-6 with various π-backbone conformations and characteristic n-type semiconductor properties is presented. Their synthesis, optical, structural, electrochemical, spectroelectrochemical, and packing properties are investigated. The X-ray crystal structures of all n-type rods allow the systematic correlation of structural features with physical properties. In addition, the results are supported by quantum mechanical calculations based on density functional theory. A two-step reduction process is observed for all n-type rods, in which the first step is reversible. The potential gap between the reduction processes depends linearly on the cos(2) value of the torsion angle φ between the π-systems. Similarly, optical absorption spectroscopy shows that the vertical excitation energy of the conjugation band correlates with the cos(2) value of the torsion angle φ. These correlations demonstrate that the fixed intramolecular torsion angle φ is the dominant factor determining the extent of electron delocalization in these model compounds, and that the angle φ measured in the solid-state structure is a good proxy for the molecular conformation in solution. Spectroelectrochemical investigations demonstrate that conformational rigidity is maintained even in the radical anion form. In particular, the absorption bands corresponding to the SOMO-LUMO+i transitions are shifted bathochromically, whereas the absorption bands corresponding to the HOMO-SOMO transition are shifted hypsochromically with increasing torsion angle φ.     

[Ni(bpy)(mal)(H2O)3]·H2O and [Ni(4,4′-dmbpy)(mal)(H2O)3]·1.5H2O: syntheses,crystal structures,magnetic properties,and computational study of stacking interactions

[Ni(bpy)(mal)(H₂O)₃]·H₂O and [Ni(4,4′-dmbpy)(mal)(H₂O)₃]·1.5H₂O (mal = maleato; bpy = 2,2′-bipyridine; 4,4′-dmbpy = 4,4′-dimethyl-2,2′-bipyridine) exhibit molecular crystal structures. The Ni(II) central ions in both complexes are six-coordinate by one chelate bonded L–L ligand, three aqua ligands, and one position is occupied by a maleato oxygen donor atom. Hydrogen bonded ribbon-like supramolecular structural motifs are present in both studied complexes; these are linked by weaker C–H?O hydrogen bonds in [Ni(bpy)(mal)(H₂O)₃]·H₂O, whereas in [Ni(4,4′-dmbpy)(mal)(H₂O)₃]·1,5H₂O the hydrogen bonded ribbons are linked by O?H-O-H?O hydrogen bonds with the participation of the additional water solvate molecule positioned on the twofold axis. In both structures, π–π stacking interactions with different patterns in respective structures were found. The role of dispersion energy and many-body effects in the stabilization of bpy and 4,4′-dmbpy stacking interactions were investigated using methods of computational chemistry. Those confirm the dispersion-dominated stabilization of the 4,4′-dmbpy supramolecular chain-like structure, with only marginal impact of cooperativity effects. Thermal decompositions of both complexes start with dehydration. Magnetic susceptibility studies performed from 2 to 300 K revealed a dominant effect of the zero-field splitting of the Ni(II) ion, governing the low-temperature magnetic properties of both compounds.     

Improvement of image sticking on liquid crystal displays with polymer layers produced from mixed monomers

As a model of polymer-sustained-alignment liquid crystal display (PSA-LCD), the LC cells having the polymer layers produced from the homopolymers and copolymers of 4,4?-dimethacryloyl-oxy-biphenyl (4,4?-DMABiph) and 2,6-dimethacryloyl-oxy-naphthalene (2,6-DMANaph) were prepared and investigated image sticking phenomenon with evaluations of residual direct current voltage (V_rDC) and difference in pre-tilt angle before and after application of alternate current (AC) voltage (Δtilt). The V_rDC was effectively improved by adding a small amount of 2,6-DMANaph to 4,4?-DMABiph because the concentrations of radicals and ions in the LC layer were decreased due to increase in the rate constant of the polymerisation with the addition of 2,6-DMANaph under UV light exposure. The Δtilt was proportionally increased with increasing the weight ratio of 2,6-DMANaph in the mixed monomers of 4,4?-DMABiph and 2,6-DMANaph. We confirmed that the range of the weight ratio for 2,6-DMANaph in the mixed monomers of 4,4?-DMABiph and 2,6-DMANaph from 10 to 25 wt% was useful for obtaining the small level of image sticking in the PSA-LCD.     

Retrieval of crystallographically-derived molecular geometry information

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.     

紫罗碱衍生物分子结的电学性质理论研究

本文基于密度泛函(DFT)结合非平衡格林函数(NEGF)的方法,以具有氧化还原中心的紫罗碱衍生物(N,N'-bis(4-thioalkyl)-4,4'-bipyridinium,HS-4V4-SH)功能分子构造Au(111)/S-4V4-S/Au(111)分子结,详细分析了分子在三种价态V、V+和V2+下的电学性质与分...     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.