Local C2 Symmetry Research Articles

Structural characterization of a 3-hydroxychromone dye trehalose conjugate for fluorescent labelling of mycobacteria

3-Hydroxychromone (3HC) dye trehalose conjugates have previously been exploited as environment-sensitive fluorescent labels to detect mycobacteria by fluorescence microscopy. We have studied the 3HC dye 2-(6-(diethylamino)benzofuran-2-yl)-3-hydroxy-4H-chromen-4-one (3HC-2) trehalose conjugate 3HC-2-Tre by X-ray crystallography, spectroscopic methods augmented by DFT calculations and conducted preliminary labelling experiments with Mycobacterium abscessus, a non-tuberculous mycobacterium and opportunistic pathogen. In the crystal structure of 3HC-2-Tre ⋅ 3.14 H2O, the 3HC-2-Tre molecules exhibit an intramolecular OH⋅⋅⋅O hydrogen bond between the 5-hydroxy group of trehalose and the chromone carbonyl oxygen atom, and form hydrogen-bonded dimers via the trehalose units with approximate local C2 symmetry. The chromophore adopts an s-cis conformation of the chromone and benzofuran systems about its central CC bond, as previously encountered in the crystal structure of the free dye 3HC-2, and the trehalose moieties approximately retain the shape as found in the crystal structures of anhydrous trehalose and the dihydrate. Absorption spectra of 3HC-2-Tre acquired in four different solvents revealed small positive solvatochromy. Fluorescence microscopy detected M. abscessus cells treated with 3HC-2-Tre in the GFP channel.

Five Step Total Synthesis of Lythranidine

AbstractA concise synthesis of the alkaloid lythranidine is reported. The strategy exploits the target's local C2 symmetry by adopting a two directional synthetic approach, first in an acyclic environment, then in a cyclic system and finally in a bridged macrocyclic domain. The latter phase of the synthesis, which installs all four stereocenters, involves a thermodynamically controlled, twofold intermolecular/transannular aza‐Michael addition and a twofold hydride reduction. The synthesis is one third of the length of the most step‐economic previous approach, providing access to gram quantities of the natural product. The broad‐spectrum nature of the synthesis is demonstrated through the preparation of three diastereomeric analogues of the natural product.

Five Step Total Synthesis of Lythranidine.

A concise synthesis of the alkaloid lythranidine is reported. The strategy exploits the target's local C2 symmetry by adopting a two directional synthetic approach, first in an acyclic environment, then in a cyclic system and finally in a bridged macrocyclic domain. The latter phase of the synthesis, which installs all four stereocenters, involves a thermodynamically controlled, twofold intermolecular/transannular aza-Michael addition and a twofold hydride reduction. The synthesis is one third of the length of the most step-economic previous approach, providing access to gram quantities of the natural product. The broad-spectrum nature of the synthesis is demonstrated through the preparation of three diastereomeric analogues of the natural product.

A Convenient Synthesis of Fused Tetrahydroazocines from Acenaphthylene-1,2-dione, Proline, and Acetylenic Esters

A synthesis of dialkyl (12E,14E)-7-oxo-10,11-dihydro-7H,9H-azocino[2,1-a]benzo[de]isoquinoline-13,14-dicarboxylates through a 1,3-dipolar cycloaddition reaction of azomethine ylides, generated in situ from proline and acenaphthylene-1,2-dione, with dialkyl acetylenedicarboxylates is described. According to the X-ray diffraction data, the tetrahydroazocine ring has a rigid twist-boat form with approximate local C2 symmetry.

Self-assembly of tetracyanonaphtho-quinodimethane (TNAP) based metal–organic networks on Pb(1 1 1): Structural, electronic, and magnetic properties

We use scanning tunneling microscopy and spectroscopy to investigate structural and electronic properties of tetracyanonaphtho-quinodimethane (TNAP) based metal–organic networks on a superconducting Pb(111) surface. At low temperatures, the TNAP molecules form densely packed islands. When deposited at room temperature, Pb adatoms are incorporated into fourfold bonding nodes with the TNAP molecules leading to long-range ordered porous structures. Co-deposition of NaCl with TNAP yields a Na source for an ionically bonded Na-TNAP structure. Fourfold bonding motifs are also created by Fe atoms with the cyano terminations of TNAP. However, the structures are irregular and do not sustain the formation of long-range ordered networks. Some Fe centers with molecules surrounded in a local C2 symmetry exhibit Shiba states as a fingerprint of a magnetic interaction with the superconducting surface.

High-Resolution Scanning Tunneling Spectroscopy of Vortex Cores in Inhomogeneous Electronic States of Bi2Sr2CaCu2Ox

We studied electronic states in vortex cores of slightly overdoped Bi2Sr2CaCu2Ox by scanning tunneling spectroscopy. We have found that they have stripe structures with a 4a0 width extending along the Cu-O bond directions. Vortex core states are observed as two peaks at particle-hole symmetric positions in the energy gap. Along a stripe, the peak positions of vortex core states are constant and not influenced by the spatial variation of the energy gap \Delta. Outer stripes have a larger energy than inner stripes. A mazelike pattern in the electronic states at E = +-\Delta has been observed all over the surface both inside and outside the vortex core. The orientation of stripes of vortex core states was found to be related to the mazelike pattern in the vortex core region. A short-range order of the mazelike pattern spatially coexists with the superconductivity and locally breaks the symmetry of the two Cu-O bond directions. We propose that the vortex core bound states are formed by Bogoliubov quasiparticles owing to the depairing of Cooper pairs and have a local C2 symmetry influenced by the short-range order of the mazelike pattern.

Bimacrocyclic concave N-heterocyclic carbenes (NHCs): Synthesis, structure and application in catalyses

Imidazolinium moieties have been incorporated into bimacrocycles to generate precursors for concave N-heterocyclic carbenes (NHCs). Starting from 2-nitroresorcinol and alkenols, symmetric concave imidazolinium salts 1 were obtained. Bimacrocyclisation was achieved via ring-closing metathesis (RCM). In an analogous fashion, axially chiral concave imidazolinium salts 2 were obtained using a naphthalene bridgehead devoid of local C2-symmetry. The concave NHCs derived from the symmetric precursors 1 were used as nucleophilic catalysts for the synthesis of γ-butyrolactones and as ligands for transition metal catalysts. Copper complex 18 was used as a catalyst for the cyclopropanation of styrene and indene with ethyl diazoacetate (EDA). Palladium complex 24 was used as a catalyst for the Mizoroki–Heck and Suzuki–Miyaura cross-coupling reactions.

M-Phenylenediamine

In the title compound, C6H8N2, there are four mol­ecules in the asymmetric unit, with each mol­ecule, including the H atoms on the N atoms of the amino groups, showing local C2 symmetry. In the crystal structure, all except one of the NH2 groups participate in N—H⋯O hydrogen bonding. The identified hydrogen bonds furnish a three-dimensional network. N—H⋯π contacts are observed with H⋯π distances ranging from 2.516 (17) to 2.815 (16) Å. No π-stacking of the aromatic rings is observed.

Determination of the absolute chirality of adsorbed molecules.

Pasteur's separation of the optical antipodes of ammonium sodium tartrate tetrahydrate in 1848 and the concept of the asymmetrically substituted carbon atom, introduced by van't Hoff and le Bel, marked the birth of stereochemistry. Although the Fischer–Rosanoff convention based on d-(+)glyceraldehyde got general acceptance, it was not possible to link the optical rotary power to the absolute configuration of chiral molecules. In 1951, however, Bijvoet and co-workers determined the absolute configuration of (+)-sodium rubidium tartrate through anomalous X-ray scattering and showed that the arbitrary d-/l-convention matches reality. Increasing computational power and improved quantum mechanical codes nowadays allow to connect chiroptical spectra with absolute configuration, but this approach is still limited to relatively small or rigid molecules. Other methods for determining the absolute configuration, such as wetting or enantioselective adsorption on polar crystals and measurements of the electric polarization in ferroelectric liquid crystals, have been reported. The conformation of chiral molecules adsorbed on a surface plays an important role in biomineralization and in stereoselective heterogeneous catalysis. For example, tartaric acid serves as chiral modifier for the enantioselective hydrogenation of b-ketoesters over supported nickel catalysts. To gain deeper insight into the mechanisms of enantioselective surface chemistry and biomineralization, a detailed analysis of the local adsorbate structure is necessary. The absolute chirality of molecules adsorbed on surfaces has been inferred from scanning tunneling microscopy (STM) images. However, in most cases of molecular adsorption it is very difficult to correlate the observed electron densities with the absolute atomic positions, and modeling of STM images requires extensive theoretical and computational effort. Herein we demonstrate that the absolute configuration of chiral molecules adsorbed on single-crystal surfaces can be determined in a straightforward fashion by means of anglescanned X-ray photoelectron diffraction (XPD), a method delivering direct real-space structural information. For our study we chose the classic tartaric acid molecule adsorbed on the Cu(110) surface. This adsorbate system has been studied in great detail. At low coverages and after activation at 405 K, tartaric acid becomes doubly deprotonated, with the resulting bitartrate species forming long-range ordered chiral structures on the surface. Based on IR spectroscopy results, a local C2 symmetry for the bitartrate adsorbate complex has been proposed. Figure 1 illustrates the basic principles of the XPD experiment for the case of the adsorbed bitartrate species.

Ferromagnetic interactions through control of the bridging geometry

A novel trinuclear Ni(II)Cu(II)Ni(II) complex (3) and three Cu(II)Cu(II) (4), Ni(II)Cu(II) (5), and Mn(II)Cu(II) (6) alternating chain complexes were synthesized using the complexed ligand [Cu(bptap)2] (1) which acts as a bis-mer-tridentate ligand (bptap−=2,4-bis(2-pyridyl)-1,3,5-triazapentanedienate). In all complexes, two adjoining metal ions are connected by bptap− in a κ2N:κ3N bridging fashion with local C2 symmetry. The bridging geometry forces the two dσ orbitals directed towards the ligating atoms to orthogonal to each other. Ferromagnetic interaction occurs between Cu(II)Cu(II), Cu(II)Ni(II), and Cu(II)Mn(II) due to the orthogonality of the magnetic orbitals with the magnitudes of J=1.1 cm−1 for 3 (H=−2J(SNi1·SCu+SCu·SNi2)), J=1.4 cm−1 for 4 (H=−2JΣiSCuiSCui+1), and θ=7.5 K for 5 and 1.1 K for 6 (Curie–Weiss model), respectively.

The O–H(D) stretching potentials of the hydrogen bonded water molecules in MCl2·2H2O (M∈{Mn, Co, Fe}). Ab initio and density functional study

The uncoupled anharmonic O–H(D) stretching vibrations of the hydrogen bonded water molecules with local C2 symmetry in compounds of the type MCl2·2H2O (where M∈{Mn, Co, Fe}) were studied at various levels of theory, within the finite-cluster approach. The studied clusters consisted of one water molecule coordinated to the metal atom and hydrogen bonded to two chloride anions. The vibrational potential energy curves for the uncoupled OH stretching vibrations were obtained from pointwise energy calculations at HF, MP2 and gradient-corrected B3-LYP density functional levels of theory. To solve the HF or the Kohn–Sham equations, the standard 6-311G(d,p) basis set was used on O, H and Cl, while the transition metal atoms were treated within the LANL2DZ basis, employing an effective core potential (ECP) description of the inner shell electrons. From the calculated energies of the vibrational eigenstates, both the fundamental anharmonic and harmonic vibrational frequencies, as well as the anharmonicity constants were computed.

Fac-Tricarbonylchlorobis(pyridine-N)rhenium andfac-Tricarbonylchlorobis(4,4'-bipyridine-N)rhenium

Structural analyses for the title compounds (OC-6–32)-tricarbonylchlorobis(pyridine-N)rhenium(I), [ReCl(C5H5N)2(CO)3] and (OC-6–32)-tricarbonylchlorobis(4,4′-bipyridine-N)rhenium(I), [ReCl(C10H8N2)2(CO)3] show that both complexes have the expected fac-octahedral geometry. The pyridine complex has a local C2 symmetry, with the rotation axis bisecting the N—Re—N' and OC—Re—CO angles. In contrast with closely related tetrameric assemblies which crystallize as porous channel-containing structures, the title compounds form dense crystals which are packed in herring-bone fashion.

Density functional investigation of the geometric and electronic structure of ethylene adsorbed on Si(001)

A detailed first-principles density functional analysis of the geometric and electronic properties of ethylene adsorbed on the dimer reconstructed Si(001)-(2×1) surface is presented. This theoretical study was carried out in close reference to a recent angle-resolved photoemission spectroscopy investigation of the same adsorption system. Adsorbate weighted Kohn-Sham one-particle spectra are calculated and compared to the band structure derived from the angle-resolved photoemission spectra. In addition, the symmetry character of the concomitant Bloch waves is determined to yield information which can directly be related to the results of a dipole selection rule analysis of the corresponding photoemission signals. Total energy minimization of a model slab reveals a distortion of the adsorption complex at saturation coverage to local C2 symmetry involving an 11° rotation of the ethylene molecule around the surface normal and a 27° twist of the methylene groups around the CC axis. This finding is confirmed by a comparison of the calculated band dispersions with those found in the angle-resolved ultraviolet photoelectron spectroscopy (ARUPS) experiments. The driving forces for the distortion of the adsorption complex can be traced to direct Pauli repulsion between the hydrogen atoms of neighboring ethylene molecules and to a bonding overlap contribution from the ethylene 1b2g-derived orbitals of the adlayer.

Dimesityldioxirane

The preparative scale synthesis of dimesityldioxirane (5) via oxidation of dimesitylcarbene (6) is described. The dioxirane was obtained as colorless crystalline material, completely stable at −20 °C and characterized by spectroscopic methods, X-ray crystallography, and DFT calculations (B3LYP/6-31G(d)). The molecule shows approximately local C2 symmetry with the mesityl rings twisted by ca. 60°. The experimental structural parameters, e.g., the O−O distance of 1.503 Å, are in good agreement with the theoretical values. The relief of steric strain caused by the mesityl groups is discussed in terms of the geometric distortion of the three-membered ring and the mesityl groups. Conformational features of 5 in solution are nicely reflected by measured and calculated (SOS-DFPT) NMR chemical shifts.

Atropisomeric Binaphthalene‐Core Phosphacyclic Derivatives in Coordination Chemistry and Homogeneous Catalysis

AbstractBinaphthophospholes and binaphthophosphepines have recently been synthesized. These are the first representatives of a new class of chiral ligands that include within the same structure an endocyclic phosphorus donor, a local C2 symmetry and an axially chiral core. In this review we discuss the synthesis, chemical behaviour and first applications in asymmetric catalysis of these novel derivatives.

A New Zirconocene Complex, [{η5-C5H4-C(CH2)5(CH2)2CH(CH3)2}2ZrCl2

The title compound, dichlorobis­{η5-[1-(3-methylbutyl)cyclohex-1-yl]cyclopentadienyl}zirconium(IV), [ZrCl2(C16H25)2], has a pseudo-tetrahedral bent-metallocene structure in which the substituted cyclopentadienyl rings are asymmetrically bonded to the central Zr atom, due primarily to the interaction between the large substituents and the Cl atoms. The molecule has local C2 symmetry with the substituents positioned in a trans arrangement and directed towards the lateral sector of the bent-metallocene unit.

High-field/high-frequency EPR/ENDOR — A powerful new tool in photosynthesis research

In photosynthesis research the elucidation of the spatial and electronic structures of the electron donor and acceptor ion radicals is very important for an understanding of the light-induced electron transfer process. Recent 3 mm (W-band, 95 GHz) high-field EPR and ENDOR studies on the primary donor cation radicals P+. (bacteriochlorophyll dimer), the acceptor anion radicals Q+. (quinones), and the charge-separated radical pair (P+.Q−.) in photosynthetic bacteria and biomimetic model systems are presented. From single crystals of, for instance,Rb. sphaeroides R-26 reaction centers both the hyperfine tensors of various protons and theg-tensor of P865 +. have been determined and compared with calculated tensor values based on recent X-ray structure data. The results consistently reveal a breaking of the local C2 symmetry of the electronic structure at the primary donor side of the reaction center. This is of particular interest since it might be relevant for the vectorial electron transfer along the protein complex. Among the quinone radical anions studied are frozen solutions of the electron acceptors of bacterial and plant reaction centers (ubiquinone and plastoquinone, respectively). The increased electron Zeeman interaction in high-field EPR leads to almost completely resolvedg-tensor components even in disordered samples. Theg-tensors and component linewidths are sensitive probes for specific anisotropic interactions with the environment. In the case of the transient correlated coupled radical pair P865 +.-QA −. ofRb. sphaeroides (Fe replaced by Zn) the spin-polarized high-field EPR spectra allow an unambiguous determination of the relative orientation of theg-tensors of the donor and acceptor parts. Thereby high-precision structure information is obtained on the electron transfer pigments after light-induced charge separation.

Vibrational spectra of gaseous and liquid tetrakis(dimethylamido)titanium, Ti[N(CH3)2]4, and tetrakis(diethylamido)titanium, Ti[N(C2H5)2

Abstract The IR spectra of gaseous and the Raman spectra of liquid tetrakis(dialkylamido)titanium, Ti(NR2)4 (R = CH3 or C2H5), have been measured and an assignment has been made according to S4 symmetry for the molecule and local C2 symmetry for the -NR2 group. Universal force field calculations have been performed which confirm the local C2 symmetry for the -N(C2H5)2 group.

Synthesis and characterisation of neutral and cationic 2,7-dimethyloctadienediylruthenium(IV) complexes. X-Ray crystal structure of cis-bis(acetonitrile)chloro[(1,2,3,6,7,8-η)-2,7-dimethylocta-2,6-diene-1,8-diyl]ruthenium(IV) tetrafluoroborate

Reactions of [{Ru(η3:η3-C10H16)Cl(µ-Cl)}2]1 with the ligands (L) P(OMe)3, ButNC or PriNC in chloroform solution give the complexes [Ru(η3:η3-C10H16)Cl2L]2–4. Treatment of these complexes with Ag[BF4] and additional free ligand in acetone solution gives the salts [Ru(η3:η3-C10H16)ClL2][BF4]5–7. The reaction of 1 with Ag[BF4] in acetonitrile solution yields [Ru(η3 : η3-C10H16)Cl(NCMe)2][BF4]8 which slowly converts in solution into an alternative stereoisomer 9. The structures proposed for 2–9 all feature an approximate trigonal-bipyramidal co-ordination at ruthenium, occupation of two equatorial sites by the η3 : η3-2,7-dimethyloctadienediyl ligand, and a local C2-symmetry configuration for the octadiendiyl chain. In 2–4 it is the two-electron ligand that occupies the third equatorial site with both chlorides axial. In 5–7 the chloride occupies the third equatorial site and both the two-electron ligands are axial. For the two acetonitrile-containing stereoisomers, the chloride is axial in 8 and equatorial in 9. An equilibrium 8⇌9 exists in acetonitrile solution with K298= 30 ± 5, K298(forward)=(7.6 ± 0.6)× 10–6 s–1, ΔH‡= 123 ± 3 kJ mol–1, ΔS‡= 68 ± 9 J K–1 mol–1, as determined by 1H NMR spectroscopy and sampling techniques. The structure of 8 has been confirmed by X-ray diffraction: space group P with a= 7.80(1), b= 15.69(1), c= 7.63(1)A, α= 96.5(1), β= 87.1(1), γ= 96.9(1)° and Z= 2. The structure was refined to R= 0.082 for 1766 unique reflections.