Self-assembly of the unique heterotrimetallic Cu/Co/M complexes possessing triangular antiferromagnetic {Cu2CoPb}2 and linear ferromagnetic {Cu2CoCd2} cores

Two novel heterotrimetallic octa-[Cu2CoPbCl4(L)4]2 (1) and pentanuclear [Cu2CoCd2Cl6(L)4(HOMe)2] (2) complexes have been prepared in one-pot reactions of zerovalent copper with metal chlorides in a methanol (for 1) or acetonitrile (for 2) solution of 2-(dimethylamino)ethanol (HL) in open air. The crystal structures of both compounds consist of discrete centrosymmetric heterotrimetallic molecules revealing triangular (1) and unique consecutive (2) arrangements of magnetic CuII(2)CoII cores. The complex 1 can be viewed as a dimer made up of tetranuclear Cu2CoPbCl4(L)4 units linked through the two micro(2)-Cl atoms. The molecular structure of 2 is a pentanuclear assembly containing the previously unknown Cu(micro-O)(2)Co(micro-O)(2)Cu core. The magnetic studies of 1 revealed an antiferromagnetic coupling (J(CoCu) = 37 cm(-1) and J(CuCu) = 87 cm(-1)) while 2 exhibits a weak ferromagnetic behavior (J(CoCu) = -3.2 cm(-1) and J(CuCu) = -14.2 cm(-1)). The correlations between magnetic behaviour and structures as well as synthetic features are also discussed.     

Expedient Lewis acid catalyzed synthesis of a 3-substituted 5-arylidene-1-methyl-2-thiohydantoin Library

An efficient and rapid solution phase combinatorial synthesis of a 3-substituted 5-arylidene-1-methyl-2-thiohydantoin library was developed. The salient feature for this library production procedure is the addition of the Lewis acid catalyst, indium(III) trifluoromethanesulfonate, which serves to facilitate the direct condensation of aldehydes with 3-substituted 1-methyl-2-thiohydantoins. Use of this Lewis acid catalyst has resulted in faster reaction times, higher conversions and better purity profiles for these condensation reactions as compared to traditional uncatalyzed reactions. The resulting 315 member library of 3-substituted 5-arylidene-1-methyl-2-thiohydantoin is described.     

2-(4-Tolylsulfonyl)ethoxymethyl (TEM)-a new 2'-OH protecting group for solid-supported RNA synthesis

The 2-(4-tolylsulfonyl)ethoxymethyl (TEM) as a new 2'-OH protecting group is reported for solid-supported RNA synthesis using phosphoramidite chemistry. The usefulness of the 2'-O-TEM group is exemplified by the synthesis of 12 different oligo-RNAs of various sizes (14-38 nucleotides long). The stepwise coupling yield varied from 97-99% with an optimized coupling time of 120 s. The synthesis of all four pure phosphoramidite building blocks is also described. Two new reliable parameters, delta(C2')-delta(C3') and delta(H2')-delta(H3'), have been suggested for the characterization of isomeric 2'-O-TEM and 3'-O-TEM as well as other isomeric mono 2'/3'-protected ribonucleoside derivatives. The most striking feature of this strategy is that the crude RNA prepared using our 2'-O-TEM strategy is sufficiently pure (>90%) for molecular biology research without any additional purification step, thereby making oligo-RNAs easily available at a relatively low cost, saving both time and lab resources.     

Novel,Monomeric Cyanine Dyes as Reporters for DNA Helicase Activity

The dimeric cyanine dyes, YOYO-1 and TOTO-1, are widely used as DNA probes because of their excellent fluorescent properties. They have a higher fluorescence quantum yield than ethidium homodimer, DAPI and Hoechst dyes and bind to double-stranded DNA with high affinity. However, these dyes are limited by heterogeneous staining at high dye loading, photocleavage of DNA under extended illumination, nicking of DNA, and inhibition of the activity of DNA binding enzymes. To overcome these limitations, seven novel cyanine dyes (Cyan-2, DC-21, DM, DM-1, DMB-2OH, SH-0367, SH1015-OH) were synthesized and tested for fluorescence emission, resistance to displacement by Mg²⁺, and the ability to function as reporters for DNA unwinding. Results show that Cyan-2, DM-1, SH-0367 and SH1015-OH formed highly fluorescent complexes with dsDNA. Of these, only Cyan-2 and DM-1 exhibited a large fluorescence enhancement in buffers, and were resistant to displacement by Mg²⁺. The potential of these two dyes to function as reporter molecules was evaluated using continuous fluorescence, DNA helicase assays. The rate of DNA unwinding was not significantly affected by either of these two dyes. Therefore, Cyan-2 and DM-1 form the basis for the synthesis of novel cyanine dyes with the potential to overcome the limitations of YOYO-1 and TOTO-1.     

Solvent effects on the electronic transitions of p-nitroaniline: a QM/EFP study

Solvatochromic shifts of the electronic states of a chromophore can be used as a measure of solute-solvent interactions. The shifts of the electronic states of a model organic chromophore, p-nitroaniline (pNA), embedded in solvents with different polarities (water, 1,4-dioxane, and cyclohexane) are studied using a hybrid quantum mechanics/molecular-mechanics-type technique in which the chromophore is described by the configuration interaction singles with perturbative doubles (CIS(D)) method while the solvent is treated by the effective fragment potential (EFP) method. This newly developed CIS(D)/EFP scheme includes the quantum-mechanical coupling of the Coulomb and polarization terms; however, short-range dispersion and exchange-repulsion terms of EFP are not included in the quantum Hamiltonian. The CIS(D)/EFP model is benchmarked against the more accurate equation of motion coupled cluster with singles and doubles (EOM-CCSD)/EFP method on a set of small pNA-water clusters. CIS(D)/EFP accurately predicts the red solvatochromic shift of the charge-transfer π → π* state of pNA in polar water. The shift is underestimated in less polar dioxane and cyclohexane probably because of the omission of the explicit quantum-mechanical treatment of the short-range terms. Different solvation of singlet and triplet states of pNA results in different probabilities of intersystem crossing (ISC) and internal conversion (IC) pathways of energy relaxation in solvents of different polarity. Computed singlet-triplet splittings in water and dioxane qualitatively explain the active ISC channel in dioxane and predict almost no conversion to the triplet manifold in water, in agreement with experimental findings.     

Synthesis and photoswitching studies of difurylperfluorocyclopentenes with extended π-systems

In an attempt to design molecular optoelectronic switches functioning in molecular junctions between two metal tips, we synthesized a set of photochromic compounds by extending the π-system of 1,2-bis-(2-methyl-5-formylfuran-3-yl)perfluorocyclopentene through suitable coupling reactions involving the formyl functions, thereby also introducing terminal groups with a binding capacity to gold. Avoiding the presence of gold-binding sulphur atoms in the photoreactive centre, as they are present in the frequently used analogous thienyl compounds, the newly synthesized compounds should be more suitable for the purpose indicated. The kinetics of reversible photoswitching of the new compounds by UV and visible light was quantitatively investigated in solution. The role of conformational flexibility of the π-system for the width of the UV/Vis spectra was clarified by using quantum chemical calculations with time-dependent (TD)-DFT. As a preliminary test of the potential of the new compounds to serve as optoelectronic molecular switches, monolayer formation and photochemical switching on gold surfaces was observed by using surface plasmon resonance.     

Probing lipid peroxidation by using linoleic acid and benzophenone

A thorough mechanistic study has been performed on the reaction between benzophenone (BZP) and a series of 1,4-dienes, including 1,4-cyclohexadiene (CHD), 1,4-dihydro-2-methylbenzoic acid (MBA), 1,4-dihydro-1,2-dimethylbenzoic acid (DMBA) and linoleic acid (LA). A combination of steady-state photolysis, laser flash photolysis (LFP), and photochemically induced dynamic nuclear polarization (photo-CIDNP) have been used. Irradiation of BZP and CHD led to a cross-coupled sensitizer-diene product, together with 6, 7, and 8. With MBA and DMBA as hydrogen donors, photoproducts arising from cross-coupling of sensitizer and diene radicals were found; compound 7 was also obtained, but 6 and o-toluic acid were only isolated in the irradiation of BZP with MBA. Triplet lifetimes were determined in the absence and in the presence of several diene concentrations. All three model compounds showed similar reactivity (k(q) ≈10(8) M(-1) s(-1)) towards triplet excited BZP. Partly reversible hydrogen abstraction of the allylic hydrogen atoms of CHD, MBA, and DMBA was also detected by photo-CIDNP on different timescales. Polarizations of the diamagnetic products were in full agreement with the results derived from LFP. Finally, LA also underwent partly reversible hydrogen abstraction during photoreaction with BZP. Subsequent hydrogen transfer between primary radicals led to conjugated derivatives of LA. The unpaired electron spin population in linoleyl radical (LA(.)) was predominantly found on H(1-5) protons. To date, LA-related radicals were only reported upon hydrogen transfer from highly substituted model compounds by steady-state EPR spectroscopy. Herein, we have experimentally established the formation of LA(.) and shown that it converts into two dominating conjugated isomers on the millisecond timescale. Such processes are at the basis of alterations of membrane structures caused by oxidative stress.     

From Hexaoxy‐[6]Pericyclynes to Carbo‐Cyclohexadienes,Carbo‐Benzenes,and Dihydro‐Carbo‐Benzenes: Synthesis,Structure, and Chromophoric and Redox Properties

When targeting the quadrupolar p‐dianisyltetraphenyl‐carbo‐benzene by reductive treatment of a hexaoxy‐[6]pericyclyne precursor 3 with SnCl₂/HCl, a strict control of the conditions allowed for the isolation of three C₁₈‐macrocyclic products: the targeted aromatic carbo‐benzene 1 , a sub‐reduced non‐aromatic carbo‐cyclohexadiene 4 A , and an over‐reduced aromatic dihydro‐carbo‐benzene 5 A . Each of them was fully characterized by its absorption and NMR spectra, which were interpreted by comparison with calculated spectra from static structures optimized at the DFT level. According to the nucleus‐independent chemical shift (NICS) value (NICS≈?13 ppm), the macrocyclic aromaticity of 5 A is indicated to be equivalent to that of 1 . This is confirmed by the strong NMR spectroscopic deshielding of the ortho‐CH protons of the aryl substituents, but also by the strong shielding of the internal proton of the endocyclic trans‐CH?CH double bond that results from the hydrogenation of one of the C?C bonds of 3 . Both the aromatics 1 and 5 A exhibit a high crystallinity, revealed by SEM and TEM images, which allowed for a structural determination by using an X‐ray microsource. A good agreement with calculated molecular structures was found, and columnar assemblies of the C₁₈ macrocycles were evidenced in the crystal packing. The non‐aromatic carbo‐cyclohexadiene 4 A is shown to be an intermediate in the formation of 1 from 3 . It exhibits a remarkable dichromism in solution, which is related to the occurrence of two intense bands in the visible region of its UV/Vis spectrum. These properties could be attributed to the dibutatrienylacetylene (DBA) unit that occurs in the three chromophores, but which is not involved in a macrocyclic π‐delocalization in 4 A only. A versatile redox behavior of the carbo‐chromophores is evidenced by cyclic voltammetry and was analyzed by calculation of the ionization potential, electron affinity, and frontier molecular orbitals.     

A 12-connected metal-organic framework constructed from an unprecedented cyclic dodecanuclear copper cluster

A 12-connected metal-organic framework based on an unprecedented cyclic Cu(12) cluster with a large internal cavity has been prepared, and its cation exchange property was determined.     

Bridging QTAIM with vibrational spectroscopy: the energy of intramolecular hydrogen bonds in DNA-related biomolecules

Physical properties of over 8000 intramolecular hydrogen bonds (iHBs), including 2901 ones of the types OH···O, OH···N, NH···O and OH···C, in 4244 conformers of the DNA-related molecules (four canonical 2'-deoxyribonucleotides, 1,2-dideoxyribose-5-phosphate, and 2-deoxy-D-ribose in its furanose, pyranose and linear forms) have been investigated using quantum theory of atoms in molecules (QTAIM) and vibrational analysis. It has been found that for all iHBs with positive red-shift of the proton donating group stretching frequency the shift value correlates with ρ(cp)-the electron charge density at the (3,-1)-type bond critical point. Combining QTAIM and spectroscopic data new relationships for estimation of OH···O, OH···N, NH···O and OH···C iHB enthalpy of formation (kcal mol(-1)) with RMS error below 0.8 kcal mol(-1) have been established: E(OH···O) = -3.09 + 239·ρ(cp), E(OH···N) = 1.72 + 142·ρ(cp), E(NH···O) = -2.03 + 225·ρ(cp), E(OH···C) = -0.29 + 288·ρ(cp), where ρ(cp) is in e a(0)(-3) (a(0)- the Bohr radius). It has been shown that XHY iHBs with red-shift values over 40 cm(-1) are characterized by the following minimal values of the XHY angle, ρ(cp) and nubla(2)ρ(cp): 112°, 0.005 e a(0)(-3) and 0.016 e a(0)(-5), respectively. New relationships have been used to reveal the strongest iHBs in canonical 2'-deoxy- and ribonucleosides and the O(5')H···N(3) H-bond in ribonucleoside guanosine was found to have the maximum energy (8.1 kcal mol(-1)).