Intramolecular Dimer Research Articles

Mesolysis of Radical Anions of Tetra-, Penta-, and Hexaphenylethanes

A central carbon–carbon (C–C) σ bond dissociation of polyphenylethane radical anions (Ph(n)E•-, n = 3–6), mesolysis, was investigated by the transient absorption measurement during pulse radiolysis of Ph(n)E in 2-methyltetrahydrofuran. The charge resonance (CR) band of 1,1,2,2-tetraphenylethane radical anion (1,1,2,2-Ph4E•-) was observed in the near-infrared region immediately after an electron pulse to be attributed to the intramolecular dimer radical anion. The CR band disappeared with simultaneous formation of two absorption bands at 330 and 460 nm corresponding to diphenylmethyl radical and diphenylmethyl anion, respectively, indicating the occurrence of the mesolysis in 1,1,2,2-Ph4E•-. During pulse radiolysis of 1,1,1,2,2,2-hexaphenylethane (Ph6E), an absorption band of triphenylmethyl radical was observed at 340 nm immediately after an electron pulse. It is suggested that one electron attachment to Ph6E is followed by the subsequent rapid C–C σ bond dissociation. Formation of intramolecular dimer radical anions in Ph(n)E•- such as 1,1,2-triphenylethane (Ph3E), 1,1,1,2-tetraphenylethane (1,1,1,2-Ph4E), and 1,1,1,2,2-pentaphenylethane (Ph5E) was also studied together with the subsequent mesolysis. The mesolysis of Ph(n)E•- is discussed in terms of charge delocalization in the intramolecular dimer radical anions and the central C–C σ bond as well as bond dissociation energy of the central C–C σ bond of Ph(n)E•-.

Computational study of the intramolecular proton transfer reactions of dipicolinic acid (pyridine-2,6-dicarboxylic acid) and its dimers

The intramolecular proton transfer (IPT) reaction and dimerization processes of dipicolinic acid (DPA) have been investigated using density functional theory (DFT) at the B3LYP/6-31G++(d) basis set level. The influence of the solvent on the zwitterion -to- neutral transition of DPA was examined using the continuum model (CPCM) with different dielectric constants (ε=4.9, CHCl3; ε=7.42, THF; ε=32.63, CH3OH; ε=78.39, H2O). The intramolecular proton transfer reaction occurs more readily in the gas phase than solution. Results also show that the stability of DPA dimers in the gas phase is directly affected by the hydrogen bond angle and electrostatic potential (ESP) value in the dimer structure.

Chiral Supramolecular Switches Based on (R)‐Binaphthalene–Bipyridinium Guests and Cucurbituril Hosts

We designed and synthesized the three molecular tweezers 1 a-c(4+) containing an electron acceptor 4,4'-bipyridinium (BPY(2+)) unit in each of the two arms and an (R)-2,2'-dioxy-1,1'-binaphthyl (BIN) unit that plays the role of chiral centre and the hinge of the structure. Each BPY(2+) unit is connected to the BIN hinge by an alkyl chain formed by two- (1 a(4+)), four- (1 b(4+)), or six-CH(2) (1 c(4+)) groups. The behavior of 1 a-c(4+) upon chemical or photochemical reduction in the absence and in the presence of cucurbit[8]uril (CB[8]) or cucurbit[7]uril (CB[7]) as macrocyclic hosts for the bipyridinium units has been studied in aqueous solution. A detailed analysis of the UV/Vis absorption and circular dichroism (CD) spectra shows that the helicity of the BIN unit can be reversibly modulated by reduction of the BPY(2+) units, or by association with cucurbiturils. Upon reduction of 1 a-c(4+) compounds, the formed BPY(+·) units undergo intramolecular dimerization with a concomitant change in the BIN dihedral angle, which depends on the length of the alkyl spacers. The alkyl linkers also play an important role in association to cucurbiturils. Compound 1 a(4+), because of its short carbon chain, associates to the bulky CB[8] in a 1:1 ratio, whereas in the case of the smaller host compound CB[7] a 1:2 complex is obtained. Compounds 1 b(4+) and 1 c(4+), which have longer linkers, associate to two cucurbiturils regardless of their sizes. In all cases, association with CB[8] causes an increase of the BIN dihedral angle, whereas the formation of CB[7] complexes causes an angle decrease. Reduction of the CB[8] complexes results in an enhancement of the BPY(+·) dimerization with respect to free 1 a-c(4+) and causes a noticeable decrease of the BIN dihedral angle, because the BPY(+·) units of the two arms have to enter into the same macrocycle. The dimer formation in the CB[8] complexes characterized by a 1:2 ratio implies the release of one macrocycle showing that the binding stoichiometry of these host-guest complexes can be switched from 1:2 to 1:1 by changing the redox state of the guest. When the reduction is performed on the CB[7] complexes, dimer formation is totally inhibited, as expected because the CB[7] cavity cannot host two BPY(+·) units.

Protonated sugars: vibrational spectroscopy and conformational structure of protonated O-methyl α-D-galactopyranoside

‘Bridging’ protons provide a common structural motif in biological assemblies such as proton wires and proton-bound dimers. Here we present a ‘proof-of-principle’ computational and vibrational spectroscopic investigation of an ‘intra-molecular proton-bound dimer,’ O-methyl α-D-galactopyranoside (αMeGal-H+), generated in the gas phase through photo-ionisation of its complex with phenol in a molecular beam. Its vibrational spectrum corresponds well with a classical molecular dynamics simulation conducted ‘on-the-fly’ and also with the lowest-energy structures predicted by DFT and ab initio calculations. They reveal proton-bound structures that bridge neighbouring pairs of oxygen atoms, preferentially O6 and O4, linked together within the carbohydrate scaffold. Motivated by the possibility of an entry into the microscopic mechanism of its acid (or enzyme)-catalysed hydrolysis, we also report the corresponding predictions for its singly hydrated complex.

Intramolecular Charge Resonance in Dimer Radical Anions of Di-, Tri-, Tetra-, and Pentaphenylalkanes

Intramolecular dimer radical anions of di-, tri-, tetra-, and pentaphenylalkanes were investigated on the basis of absorption spectral measurements during γ-radiolysis in 2-methyltetrahydrofuran (MTHF) glassy matrix at 77 K and theoretical calculations. The absorption spectrum of 1,1,2,2-tetraphenylethane (1,1,2,2-Ph(4)E) radical anion showed two bands in the near-infrared (NIR) region (900-2600 nm). One band observed at shorter wavelength than 2000 nm is assigned to the intramolecular charge resonance (CR) band between two phenyl groups of the 1,1-diphenylmethyl chromophore (1,1-dimer radical anion). The intramolecular CR band of the 1,1-dimer radical anion was observed for various alkanes having 1,1-diphenylmethyl chromophore such as 1,1,1-triphenylmethane (1,1,1-Ph(3)M), 1,1,1,1-tetraphenylmethane (1,1,1,1-Ph(4)M), and so on. The other intramolecular CR band observed at longer wavelength than 2200 nm is assigned to intramolecular dimer radical anion between two phenyl groups of the 1,2-diphenylethyl chromophore (1,2-dimer radical anion). The intramolecular CR band of the 1,2-dimer radical anion was observed for various alkanes having a 1,2-diphenylethyl chromophore, such as 1,1,2-triphenylethane (1,1,2-Ph(3)E), 1,1,2,2-Ph(4)E, and 1,1,1,2,2-pentaphenylethane (1,1,1,2,2-Ph(5)E) and so on. No dimer radical anion was observed for 1,n-diphenylalkanes (n > 2) without 1,1-diphenylmethyl chromophore. The relationship between the structure and negative charge delocalization over two phenyl groups connected by an sp(3) carbon is discussed.

Structure and Molecular Evolution of CDGSH Iron-Sulfur Domains

The recently discovered CDGSH iron-sulfur domains (CISDs) are classified into seven major types with a wide distribution throughout the three domains of life. The type 1 protein mitoNEET has been shown to fold into a dimer with the signature CDGSH motif binding to a [2Fe-2S] cluster. However, the structures of all other types of CISDs were unknown. Here we report the crystal structures of type 3, 4, and 6 CISDs determined at 1.5 Å, 1.8 Å and 1.15 Å resolution, respectively. The type 3 and 4 CISD each contain one CDGSH motif and adopt a dimeric structure. Although similar to each other, the two structures have permutated topologies, and both are distinct from the type 1 structure. The type 6 CISD contains tandem CDGSH motifs and adopts a monomeric structure with an internal pseudo dyad symmetry. All currently known CISD structures share dual iron-sulfur binding modules and a β-sandwich for either intermolecular or intramolecular dimerization. The iron-sulfur binding module, the β-strand N-terminal to the module and a proline motif are conserved among different type structures, but the dimerization module and the interface and orientation between the two iron-sulfur binding modules are divergent. Sequence analysis further shows resemblance between CISD types 4 and 7 and between 1 and 2. Our findings suggest that all CISDs share common ancestry and diverged into three primary folds with a characteristic phylogenetic distribution: a eukaryote-specific fold adopted by types 1 and 2 proteins, a prokaryote-specific fold adopted by types 3, 4 and 7 proteins, and a tandem-motif fold adopted by types 5 and 6 proteins. Our comprehensive structural, sequential and phylogenetic analysis provides significant insight into the assembly principles and evolutionary relationship of CISDs.

Effect of structural features of molecules (Cl3PNZ)2 (Z = CH3 and CH2CH2Cl) on the position exchange of chlorine atoms in the P-Cl fragments

Based on the analysis of structural parameters of molecules (Cl3PNCH3)2 (I) and (Cl3PNCH2CH2Cl)2 (II) by the quantum-chemical nonempirical calculations the following was revealed. The structure of I and II dimers has geometric features, which have a decisive influence on the degree of inhibition of positional exchange of the chlorine atoms in the P-Cl fragments known for the chlorine derivatives of pentacoordinated phosphorus atom. The obstacles to this dynamic process in the mentioned intramolecular dimers is shown to result from the spatial nonvalent interactions due to the short contacts of the chlorine and hydrogen atoms.

Stability of gp41 hairpin and helix bundle assembly probed by combined stacking and circular dichroic approaches

The envelope glycoprotein gp41 of HIV-1 undergoes structural rearrangement to form a helix hairpin during the virus-mediated fusion. Previous studies to investigate the folding and stability of hairpin did not monitor the end-to-end distance of the molecule. To directly probe the distance change, rhodamine dye was conjugated to the gp41 recombinant near the N- and C-terminal regions to detect the UV absorption and fluorescence intensity changes induced by the chemical denaturant guanidinium chloride (GdmCl). Using the singly- and doubly-labeled constructs allowed us to distinguish between the hairpin formation and protein oligomerization. A biphasic transition of helical structure for the wild type protein was revealed by circular dichroism measurements while unfolding of the hairpin occurred at 6M GdmCl. The relevance of our study to the fusion inhibitor for HIV-1 was borne out by results on the mutants at the positions within the N-terminal heptad repeat (NHR) and the C-terminal heptad repeat (CHR) regions. A monophasic transition at lower denaturant concentration was detected for the NHR mutant supporting the concept of differential stability of NHR and CHR helical structure. The conclusion that the observed unstacking of doubly-labeled variant arises principally from the intra-molecular dimers was drawn from the unstacking of the protein labeled in the loop. Remarkably, it is deduced that the hairpin is more stable than the CHR helical structure. A model for denaturation of the helix hairpin bundle was proposed from these results. The biological implications of the findings and further applications of the distance-based approach were discussed.

Mutant cycles at CFTR’s non-canonical ATP-binding site support little interface separation during gating

Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the adenosine triphosphate (ATP)-binding cassette (ABC) superfamily. ABC proteins share a common molecular mechanism that couples ATP binding and hydrolysis at two nucleotide-binding domains (NBDs) to diverse functions. This involves formation of NBD dimers, with ATP bound at two composite interfacial sites. In CFTR, intramolecular NBD dimerization is coupled to channel opening. Channel closing is triggered by hydrolysis of the ATP molecule bound at composite site 2. Site 1, which is non-canonical, binds nucleotide tightly but is not hydrolytic. Recently, based on kinetic arguments, it was suggested that this site remains closed for several gating cycles. To investigate movements at site 1 by an independent technique, we studied changes in thermodynamic coupling between pairs of residues on opposite sides of this site. The chosen targets are likely to interact based on both phylogenetic analysis and closeness on structural models. First, we mutated T460 in NBD1 and L1353 in NBD2 (the corresponding site-2 residues become energetically coupled as channels open). Mutation T460S accelerated closure in hydrolytic conditions and in the nonhydrolytic K1250R background; mutation L1353M did not affect these rates. Analysis of the double mutant showed additive effects of mutations, suggesting that energetic coupling between the two residues remains unchanged during the gating cycle. We next investigated pairs 460–1348 and 460–1375. Although both mutations H1348A and H1375A produced dramatic changes in hydrolytic and nonhydrolytic channel closing rates, in the corresponding double mutants these changes proved mostly additive with those caused by mutation T460S, suggesting little change in energetic coupling between either positions 460–1348 or positions 460–1375 during gating. These results provide independent support for a gating model in which ATP-bound composite site 1 remains closed throughout the gating cycle.

Synthesis and Photopysical Properties of a Polioxo Ethylene Chain Alkaline Earth Metal Fluorescent Sensor with 2-Aminoanthracene As Terminal Group

A new symmetric polioxo ethylene chain fluorescent probe containing 2-aminoanthracene bichromophoric as the terminal group for the alkaline earth metal cation, 2,2'-[oxybis(3-oxapentamethyleneoxy)]-bis[N-(2-anthryl)benzamide)] (1), has been synthesized. The photophysical properties of 1 have been studied by means of absorption, fluorescence spectroscopy, and (1)H NMR. The difference in emission spectra response to concentration of model compound 2-acetamido-anthracene and 1 in acetonitrile implies that intermolecular excited dimers is likely to occur. Fluorescence decay profiles of 2-acetamido-anthracene can be described by a biexponential fit, while three lifetimes, two of which are similar as those of 2-acetamido-anthracene, are found for 1. The third lifetime might be attributed to intramolecular excited dimers. Complex formation with alkaline earth metal ions are investigated in acetonitrile as solvent via fluorimetric titrations. Fluorescence intensity trend of the complex with Mg(2+) differed from those of other alkaline earth metal ions. The compound forms 1:2 (ligand/Mg(2+)) complex with Mg(2+) while formed 1:1 complexes with Ca(2+), Sr(2+), and Ba(2+), producing large hypochromic shifts in the emission spectra and significant cation-induced fluorescence amplifications. On the contrary, the addition of Ca(2+), Sr(2+), or Ba(2+) lead to a decrease in the fluorescence emission first, then an increase and blue shift in emission could be found at the end.

마이코박테리아의 adenylyl cyclase

Adenylyl cyclase (AC) catalyzes the formation of cyclic AMP (cAMP) from ATP. The cAMP produced by AC serves as a secondary messenger in a variety of signal transduction pathways, and controls various cellular functions in many organisms. ACs can be grouped into six classes based on their primary amino acid sequences. Eukaryotes and mycobacteria contain only members of class III AC. The catalytic cyclase domains of class III AC are active as dimers: mammalian ACs, which are composed of a single polypeptide with two catalytic cyclase domains, form the active site as a result of intramolecular dimerization of the catalytic cyclase domains. In contrast, mycobacterial ACs function as homodimers, since their polypeptides contain a single catalytic cyclase domain. Six amino acids are required for the catalytic activity of class III AC - two aspartate residues, a lysine-aspartate pair and an arginine-asparagine pair. 16 ACs belonging to the class III were identified in Mycobacterium tuberculosis H37Rv, and their characteristics are reviewed.

Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions

Stacking interactions between organic fluorophores can cause formation of non-fluorescent H-dimers. Dimer formation and dissociation of two fluorophores site-specifically incorporated in a biomolecule result in fluorescence intermittency that can report on conformational dynamics. We characterize intramolecular dimerization of two oxazine fluorophores MR121 attached to an unstructured polypeptide. Formation of stable non-fluorescent complexes with nano- to microsecond lifetimes is a prerequisite for analysing the intermittent fluorescence emission by fluorescence correlation spectroscopy and extracting relaxation time constants on nano- to millisecond time scales. Destabilization of the generally very stable homodimers by chemical denaturation reduces the lifetime of H-dimers. We demonstrate that H-dimer formation of an oxazine fluorophore reports on end-to-end contact rates in unstructured glycine-serine polypeptides under denaturing conditions.

Distance Measurements within a Concatamer of the Plasma Membrane Cl−/HCO3− Exchanger, AE1

AE1, which exists in the erythrocyte plasma membrane as a noncovalent dimer, facilitates transmembrane Cl⁻/HCO₃⁻ exchange. Here a concatamer of AE1 (two AE1 monomers fused via a two-residue linker to form an intramolecular dimer) was designed to facilitate fluorescence resonance energy transfer (FRET) studies. The concatameric protein (AE1·AE1) was expressed at the plasma membrane at levels similar to that of wild-type AE1 and had Cl⁻/HCO₃⁻ exchange activity indistinguishable from that of wild-type AE1. Nondenaturing gel electrophoresis revealed that AE1·AE1 does not associate into higher-order oligomers when expressed in HEK293 cells and Xenopus laevis oocytes. The cysteine-less concatamer (AE1·AE1-C⁻) enabled introduction of unique cysteine residues into the whole intramolecular dimer. AE1(Q434C)·AE1(Q434C)-C⁻, with a single cysteine residue in each AE1 subunit, was labeled with the donor Alexa Fluor 488 C(5)-maleimide (AF) and the acceptor tetramethylrhodamine methanethiosulfonate (TMR-MTS). Energy transfer efficiency revealed that the distance between these residues in the AE1 dimer is 49 ± 5 Å. The 72% FRET efficiency observed between AE1(Q434C)·AE1-C⁻ labeled with AF and the lipid bilayer labeled with 1,1'-didodecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate indicates that Q434 is less than 33 Å from the lipid bilayer. We thus provide two distance constraints for the position of Q434, which is located in extracellular loop 1, connecting the first two transmembrane segments of AE1.

Dynamics of Radical Cation of Poly(4-hydroxystyrene)-Based Chemically Amplified Resists for Extreme-Ultraviolet and Electron Beam Lithographies

The elucidation of the reaction mechanism after the irradiation of ionizing radiation onto resist polymers is an important issue for extreme-ultraviolet and electron beam chemically amplified resist. The dynamics of radical cations of polymers is essential for elucidating the mechanism of acid formation (deprotonation) in resists. The transient absorption of poly(4-methoxystyrene) (PMOS) was observed in 1,2-dichloroethane and p-dioxane solutions by pulse radiolysis. In the near-infrared region, a characteristic charge resonance band, which represents the π–π interaction between the two benzene rings of the intramolecular PMOS dimer radical cation [(Ph–OCH3)2+·], was observed. In the presence of halogenated hydrocarbon molecules acting as electron scavengers, the yield of (Ph–OCH3)2+· was enhanced by the formation of an ion/charge transfer complex. Density functional theory (DFT) calculations were also performed to investigate the electronic state of (Ph–OCH3)2+·.

On the geometrical structure and spectral properties of pyrene monomer and sterically constrained intramolecular pyrene dimers

The combined theoretical and spectroscopic study of pyrene molecule and its two model sterically constrained dimers ( DPyM: di(1-pyrenylmethyl) ether and DPyS: 2,3-di(4-(1-pyrenemethoxymethyl)-phenyl)butane) is presented. Based on quantum chemical calculations, the origin of the vibronic structure of pyrene fluorescence spectra was analyzed using Franck–Condon analysis. The DPyM linked by a short spacer cannot reach the parallel arrangement of the pyrene chromophores. The elongation of the central part in DPyS increases the distance between the chromophores by about 5 Å and therefore the quasi-parallel arrangement of pyrenes is possible from the structural point of view. The analysis of the selected frontier molecular orbitals and their energy levels with respect to the isolated pyrene molecule indicates that the intramolecular interaction in DPyS plays still non-negligible role for the space orientation of pyrene cores contributing to the excimer formation. The experimental fluorescence energy of DPyS is blue shifted with respect to DPyM.

ChemInform Abstract: Synthesis of Medium- and Large-Size Rings by Intramolecular Nitrile Oxide Dimerization: An Efficient C-C Bond-Forming Ring-Closing Reaction.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

The dimerization domains of MLL are potential therapeutic targets in t(4;11)-leukemias

The human MLL protein – as well as the leukemogenic AF4-MLL fusion protein are specifically hydrolyzed by the endopeptidase Taspase1. The resulting protein fragments are able to form an intramolcular dimer which is necessary for complex formation and stability of both proteins. We have dissected the two dimerization domains, named FYRN and FYRC, by B-2-H experiments, pull-down experiments using recombinant proteins and Co-IP studies in mammalian cells. The minimal interaction domains was experimentally defined as 50 amino acid long peptides that are still able to confer specific binding in vitro and in vivo. Overexpression of these protein fragments affects the MLL wildtype and AF4-MLL fusion protein by competing with the intramolecular dimerization process. This leads to increased levels of apoptosis, prevention of complex fomation and the specific degradation of the leukemogenic AF4-MLL fusion protein. These findings will be quite helpful to design rational therapies for t(4;11) leukemia.

High-Resolution Desorption Electrospray Ionization Mass Spectrometry for Chemical Characterization of Organic Aerosols

Characterization of the chemical composition and chemical transformations of secondary organic aerosol (SOA) is both a major challenge and the area of greatest uncertainty in current aerosol research. This study presents the first application of desorption electrospray ionization combined with high-resolution mass spectrometry (DESI-MS) for detailed chemical characterization and studies of chemical aging of organic aerosol (OA) samples collected on Teflon substrates. DESI-MS offers unique advantages both for detailed characterization of chemically labile components in OA that cannot be detected using traditional electrospray ionization mass spectrometry (ESI-MS) and for studying chemical aging of OA. DESI-MS enables rapid characterization of OA samples collected on substrates by eliminating the sample preparation stage. In addition, it enables detection and structural characterization of chemically labile molecules in OA samples by minimizing the residence time of analyte in the solvent. In this study, DESI-MS and tandem mass spectrometry experiments (MS/MS) were used to examine chemical aging of SOA produced by the ozonolysis of limonene (LSOA) in the presence of gaseous ammonia. Exposure of LSOA to ammonia resulted in measurable changes in the optical properties of the sample observed using ultraviolet (UV)-visible spectroscopy. High-resolution DESI-MS analysis demonstrated that chemical aging results in formation of highly conjugated nitrogen-containing species that are most likely responsible for light-absorbing properties of the aged LSOA. Detailed analysis of the experimental data allowed us to identify several key aging reactions, including the transformation of carbonyls to imines, intramolecular dimerization of imines with other carbonyl compounds in SOA, and intermolecular cyclization of imines. This study presents an important step toward understanding the formation of light-absorbing OA (brown carbon) in the atmosphere.

Excited States of [3.3](4,4′)Biphenylophane: The Role of Charge-Transfer Excitations in Dimers With π−π Interaction

The singlet and triplet electronic excitation manifold of [3.3](4,4')biphenylophane (BPP), an intramolecular dimer, and 4,4'-dimethylbiphenyl (DMBP), the corresponding monomer, has been analyzed by employing the approximate coupled-cluster singles and doubles model (CC2). The calculated triplet-triplet and singlet-singlet transient absorption spectra show good agreement with recent experimental results. The calculations suggest a strong interaction of the two biphenyl moieties of BPP in the first singlet and triplet excited states due to the overlapping pi-electron systems, and Forster-Dexter theory for weak coupling cannot be applied. Both the first excited singlet and triplet states of BPP can be characterized as excimeric states with a strong admixture of charge-transfer contributions.

Near-infrared bis(indolium heptamethine cyanine) dyes with a spacer derived from oligo(ethylene glycol)

Synthesis of a series of near-infrared dimeric dyes is presented. The intramolecular dimers contain two chromophores linked with a conformationally flexible ether or oligoether bridge. Optical properties of the dyes are discussed. J. Heterocyclic Chem., (2009).