Quantum chemical semiempirical approach to the structural and thermodynamic characteristics of fluoroalkanols at the air/water interface

In the framework of quantum chemical PM3 approximation, the geometrical structure and thermodynamic functions characteristics of the formation of monomers (n = 1-14, 34), dimers (n = 1-14, 34), and trimers and tetramers (n = 1-8) of fluoroalkanols with the composition C(n)F(2)(n+1)CH(2)CH(2)OH are calculated. It is shown that, in contrast to the fatty alcohols, which have a flat zigzag structure, the fluoroalkanol monomers are helical with an average backbone torsion angle equal to 162 degrees. For the minimum-energy structure of dimers, the self-organization of the molecules in a dimer was observed; that leads to an opposite alternation of the torsion angles corresponding to the matching atoms in the two molecules that form the dimer. This results in the fact that the most stable conformation of the dimer is the double helix. The lead (39.5 A) and diameter (7.3 A) of the double helix are determined from the calculations of C(34)F(69)CH(2)CH(2)OH dimers. Enthalpy, entropy, and Gibbs energy of the clusterization are shown to be linearly dependent on the length of the fluorinated chain. From the analysis of these thermodynamic quantities, it is concluded that dimerization of fluoroalkanols at the air/water interface takes place if the hydrocarbon link number exceeds 6, whereas for ordinary alcohols this characteristic number is 11. These calculated values agree with experimental data. The additive scheme for the evaluation of the clusterization free energies for arbitrary clusters is developed and applied to obtain the estimate of the Gibbs clusterization energy for infinitely large clusters.     

Synthesis and DNA binding studies of bis-intercalators with a novel spiro-cyclic linker

Threading polyintercalation has been demonstrated as a unique DNA binding mode in which a polyintercalating moiety threads back and forth through the DNA double helix. This binding topology necessitates linkers residing in both the minor and major grooves in an alternating fashion. In the present work, two novel, rigid, cis and trans oriented spiro-cyclic linkers were synthesized as potential groove binding elements in the context of threading bis-intercalation. Analysis of dissociation kinetics indicated that the cis oriented dimer has dramatically slower dissociation from poly(dGdC) and calf thymus (CT) DNA compared to the trans oriented dimer and a linear dimer control.     

Self-assembling of ABC linear triblock copolymers in nanocylindrical tubes

By employing Monte Carlo simulations for various tube diameters and preferences of the tube surface for the A, B, and C segments, the morphologies of A(5)B(5)C(5), A(5)B(10)C(5), and A(5)B(5)C(10) triblock copolymer melts confined in nanocylindrical tubes were examined. The interaction parameters between different segments were considered constant epsilon(AB)=epsilon(AC)=epsilon(BC)=0.3k(B)T, the tube diameter was changed from d=9xlattice parameter to d=33xlattice parameter, and the preferences of the tube surface for the segments A, B, and C (-epsilon(AS),-epsilon(BS), and -epsilon(CS)) were varied between 0.05k(B)T and k(B)T. ABCCBA alternately stacked disks were generated in most tubes when the preference of the tube surface for any of the segments was weak, and the morphologies tended to transform into curved lamellae in tubes with large diameters when the preference for one of the segments was high. Numerous novel morphologies, such as ABC double helixes, AB single helix+C double helixes, AB double helixes+C quadruple helixes, plate morphologies with fins, dendrites, etc., which were located in the phase diagram between the stacked disks and the curved lamellar structures, were identified. Additionally, the orientation parameters indicating the alignments of the polymer chains were calculated and correlated with the morphologies.     

Homo‐double helix formation of an optically active conjugated polymer bearing carboxy groups and amplification of the helicity upon complexation with achiral and chiral amines

An optically active, m‐terphenyl‐based π‐conjugated polymer bearing carboxy groups was synthesized by the copolymerization of the diethynyl monomer bearing a carboxy group with (S,S)‐2,5‐bis(2‐methylbutoxy)‐1,4‐dibromobenzene using Sonogashira reaction. The copolymer showed a weak circular dichroism (CD) in the main‐chain chromophore region due to a homo‐double helix formation with an excess helical handedness biased by the chiral alkoxy substituents through self‐association. However, upon complexation with achiral amines, such as piperidine, the CD intensity of the polymer significantly increased resulting in the formation of a greater excess one‐handed homo‐double helix via hydrogen‐bonded inclusion complexation with the achiral amines between each strand, leading to the amplification of the helicity. A preferred‐handed homo‐double helix was also induced in the polymer in the presence of nonracemic amines. The effect of the achiral and chiral amines on the homo‐double helix formation was investigated by comparing the CD spectra of the polymer to those of its model dimer. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 990–999     

Side chain effect on the double helix formation of ethynylhelicene oligomers

Three series of ethynylhelicene oligomers with different side chains were synthesized: (P)-bD-n (n = 2-6) with branched alkyloxycarbonyl side chains; (P)-S-n (n = 2-7) with decylsulfanyl side chains; and (P)-DF-n (n = 4, 6, 8, 10) with alternating decyloxycarbonyl and perfluorooctyl side chains. The double helix formation of these side chain derivatives was compared to that of (P)-D-n with decyloxycarbonyl side chains. CD, UV-vis, and vapor pressure osmometry (VPO) studies showed that (P)-bD-n formed double helices as well as (P)-D-n. CD studies in trifluoromethylbenzene at different temperatures and concentrations indicated that the stability of the aggregate of (P)-bD-6 was similar to that of (P)-D-6. Bulkiness of side chains had little effect on aggregation, which indicated that π-π interactions of the aromatic moiety were essential for double helix formation. (P)-S-n were random coils in all solvents examined except in trifluoromethylbenzene. Whereas (P)-D-7 formed a double helix at 1 × 10(-3) M in toluene, (P)-S-7 was a random coil. This result indicated that the double helix forming ability of (P)-S-n was substantially lower than that of (P)-D-n. Based on the previous observation that (P)-F-n formed a more stable double helix than (P)-D-n, the order of stability may be summarized as follows: (P)-F-n > (P)-D-n and (P)-bD-n >(P)-S-n. The lower stability of (P)-S-n compared to that of (P)-F-n was ascribed to the softness and/or the electron-rich nature at the m-phenylene moiety. (P)-DF-n did not form a stable double helix. It was speculated that a regular alternating arrangement of soft/hard or electron-rich/deficient moieties is important for stable double helix formation. Side chains of ethynylhelicene oligomers can play significant roles in determining the stability of double helices.     

Equilibrium Shift in Solution: Molecular Shape Recognition and Precipitation of a Synthetic Double Helix Using Helicene‐Grafted Silica Nanoparticles

Chiral silica nanoparticles (70 nm) grafted with (P)‐helicene recognized the molecular shape of double helix and random coil (P)‐ethynylhelicene oligomers in solution. A mixture of the (P)‐nanoparticles and double helix precipitated much faster than a mixture of the (P)‐nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)‐nanoparticles and (P)‐ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)‐nanoparticles, the double helix was precipitated in 53 % yield and was accompanied by equilibrium shift.     

Formation of double helix self-assembled monolayers of ethynylhelicene oligomer disulfides on gold surfaces

Optically active ethynylhelicene pentamers and hexamers linked by disulfide bonds were synthesized. They formed self-assembled monolayers (SAMs) with double helix structure on gold surfaces, which were analyzed by infrared reflection-absorption spectroscopy (IR-RAS), quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and circular dichroism (CD). Double helix SAMs could be formed on gold surfaces either from double helices or random coils in solution. The double helices on the surface were more stable than in solution. This result suggested the presence of strong intercomplex interactions between double helix complexes on the surface.     

Synthesis,characterization, and crystal structure of [Ni(dap(A)<Subscript>2</Subscript>)]<Subscript>2</Subscript> (dap(AH)<Subscript>2</Subscript>: 2,6-diacetylpyridine bis(anthraniloyl hydrazone))—a molecule possessing an infinite double helical chain in the solid state

Anthraniloyl hydrazide (AH) contains two −NH₂ groups, one of them is attached to the aromatic ring and the other is the hydrazinic, −NH₂. It is found that only the later reacts with the carbonyl compounds to form Schiff bases, while the former remains inert. The reasons behind this difference in reactivity are analyzed on the basis of semi-empirical calculations, which show that the lone pair of the ring −NH₂ is considerably delocalized over the ring, resulting in an accumulation of a positive charge on this particular nitrogen. Ni(II) complex of 2,6-diacetylpyridine bis(anthraniloyl hydrazone) has been prepared and characterized by various physico-chemical methods. The structure of the complex was determined by X-ray crystallography. It was found that in the solid state, the compound exist as a dimer, and two coordinated ligand moieties form a double helix around the two metal ions. H-bonding then results in extension of double helix to an infinite chain.     

纳米粒子驱动受限环境下两嵌段共聚物/均聚物混合体系的自组装行为

采用含时金兹堡-朗道理论(time-dependent ginzburg-landau theory,简称TDGL)方法研究了纳米粒子(nanoparticles,简称NPs)掺杂的两嵌段共聚物/均聚物(AB/C)共混体系在球形受限下的自组装行为.在不同球形受限条件下,两嵌段共聚物/均聚物共混体系形成了多种丰富的形貌,如双螺旋结构、单螺旋结构、层状结构和洋葱环状结构等.当在以上前3种体系中掺杂纳米粒子后,体系结构发生了很大的变化.详细研究了纳米粒子的浓度和浸润强度对以上结构的影响.研究结果表明,通过调控纳米粒子的浓度和浸润性质,该共混体系实现了双螺旋结构→层状结构,单螺旋结构→双螺旋结构,层状结构→单螺旋结构等多种取向序的转变.对于洋葱环状结构,纳米粒子的加入对体系这一结构的影响不大.     

Concentration Threshold and Amplification Exhibited by a Helicene Oligomer during Helix‐Dimer Formation: A Proposal on How a Cell Senses Concentration Changes of a Chemical

Sulfonamidohelicene tetramer (M)‐ 1 exhibits a concentration threshold and amplification phenomena in solution during helix‐dimer formation from a random‐coil. The (M)‐tetramer is a random‐coil below a threshold concentration, and the concentration of the helix‐dimer is irreversibly amplified once the threshold concentration is exceeded. For example, a 15 % increase in (M)‐tetramer total concentration from 0.6 to 0.7 mM induces an 8‐fold increase in the concentration of the helix‐dimer, being 8:0.15=53‐fold amplification, under temperature oscillation conditions between 47 and 49 °C. Experiments without oscillation also exhibit concentration amplification. The threshold and amplification phenomenon involves concentration hysteresis, being away from equilibrium, and self‐catalysis. On the basis of this study, a proposal on how a biological cell senses concentration changes of a chemical substance is provided.     

Diastereoselective imine-bond formation through complementary double-helix formation

Optically active amidine dimer strands having a variety of chiral and achiral linkers with different stereostructures are synthesized and used as templates for diastereoselective imine-bond formations between two achiral carboxylic acid monomers bearing a terminal aldehyde group and racemic 1,2-cyclohexanediamine, resulting in a preferred-handed double helix stabilized by complementary salt bridges. The diastereoselectivity of the racemic amine is significantly affected by the chirality of the amidine residues along with the rigidity and/or chirality of the linkers in the templates. NMR and kinetic studies reveal that the present imine-bond formation involves a two-step reversible reaction. The second step involves formation of a preferred-handed complementary double helix assisted by the chiral amidine templates and determines the overall reaction rate and diastereoselectivity of the amine.     

Mode of binding of camptothecins to double helix oligonucleotides

We report an NMR study on the interaction of topotecan (Tpt) and other camptothecins (Cpts) with several double helix and single strand oligonucleotides. The results obtained by (31)P NMR spectroscopy, nuclear Overhauser experiments (NOE) and molecular dynamics (MD) simulations show that Cpt drugs do not intercalate into the double helix, as suggested by many authors. Phosphorus NMR spectra indicated that no deformation occurs at any level of the phosphodiester backbone, while 2D NOESY experiments allowed the detection of several contacts between the aromatic protons of Cpts and those of the double helix. Models of the drug/oligonucleotide complexes, built on the basis of NOE data, show that the drug is located at the end of the double helix, by stacking the A and B rings with the guanine or cytidine of the terminal CG base pairs, with a preference for the 3[prime or minute]-terminal end sites. Cpts interact with double strand, as well as with single strand oligomers, as can be seen from the NMR shift variation observed on the drug protons; but this shielding effect cannot be an evidence of intercalation, as it is largely due to external non-specific interactions of the positively charged drug with the negatively charged ionic surface of the oligonucleotide. The molecular weight of one of the complexes was obtained from the correlation time value. The conformational behaviour of the DNA fragment d(CGTACG)(2) was studied by MD simulations on a ns time scale in the presence of water molecules and Na(+) ions. Different models were examined and the deformations induced on the phosphodiester backbone by molecules that are known to intercalate, were monitored by MD simulations.     

Role of the N-Terminal Transmembrane Helix Contacts in the Activation of FGFR3

Fibroblast growth factor receptor 3 (FGFR3) is a member of receptor tyrosine kinases, which is involved in skeletal cell growth, differentiation, and migration. FGFR3 transduces biochemical signals from the extracellular ligand-binding domain to the intracellular kinase domain through the conformational changes of the transmembrane (TM) helix dimer. Here, we apply generalized replica exchange with solute tempering method to wild type (WT) and G380R mutant (G380R) of FGFR3. The dimer interface in G380R is different from WT and the simulation results are in good agreement with the solid-state nuclear magnetic resonance (NMR) spectroscopy. TM helices in G380R are extended more than WT, and thereby, G375 in G380R contacts near the N-termini of the TM helix dimer. Considering that both G380R and G375C show the constitutive activation, the formation of the N-terminal contacts of the TM helices can be generally important for the activation mechanism. © 2019 Wiley Periodicals, Inc.     

Electrochemical detection of in situ adriamycin oxidative damage to DNA

Adriamycin intercalation and in situ interaction with double helix DNA was investigated using a voltammetric DNA-biosensor. Oxidation and reduction of adriamycin molecules intercalated in double helix DNA were investigated in order to understand the in vivo mechanism of action with this anti-neoplasic drug. The results showed that the interaction of adriamycin with DNA is potential-dependent causing contact between DNA guanine and adenine bases and the electrode surface such that their oxidation is easily detected. A mechanism for adriamycin reduction and oxidation in situ when intercalated in double helix DNA immobilised onto the glassy carbon electrode surface is presented and the formation of the mutagenic 8-oxoguanine explained.     

From helix to macrocycle: anion-driven conformation control of π-conjugated acyclic oligopyrroles

Anion-responsive pyrrole-based linear receptor oligomers were newly synthesized and their anion-driven dynamic conformation changes were investigated. Phenylene-bridged dimers and a tetramer of dipyrrolyldiketone boron complexes as π-conjugated acyclic anion receptors formed anion-driven helical structures in the solid and solution states. In fact, single-crystal X-ray analyses of the receptor-anion complexes exhibited various helical structures, such as [1+1]- and [1+2]-type single helices and a [2+2]-type double helix according to the lengths of oligomers and the existence of terminal aryl substituents. Anion-binding modes and behaviors of the oligomers in solution state were also examined by (1)H NMR and UV/Vis spectra along with ESI-TOF MS. Differences in the binding modes were observed in the solid and solution states. The oligomers showed augmented anion-binding constants and anion-tunable electronic and optical properties in comparison with the monomer receptor. A negative cooperative effect in the tetramer was observed in the second anion binding of the [1+2]-type single helix due to electrostatic repulsion between two anions captured in the helix. Further, an anion-template coupling reaction from the linear dimer provided a receptor macrocycle, which was obtained as a Cl(-) complex with distinct electronic and optical properties. The macrocycle exhibited extremely high anion-binding constants (>10(10) m(-1) in CH(2)Cl(2)) through multiple hydrogen bonding.     

DFT approach to calculate electronic transfer through a segment of DNA double helix

The electronic structures of an entire segment of a DNA molecule were calculated in its single‐strand and double‐helix cases using the DFT method with an overlapping dimer approximation and negative factor counting method. The hopping conductivity of the segment was calculated by the random walk theory from the results of energy levels and wave functions obtained. The results of the single‐strand case show that the DFT method is quantitatively in agreement with that of the HF MP2 method. The results for the double helix are in good agreement with that of the experimental data. Therefore, the long‐range electron transfer through the DNA molecule should be caused by hopping of electronic charge carriers among different energy levels whose corresponding wave functions are localized at different bases of the DNA molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1109–1117, 2000     

Study of 7-azaindole in its first four singlet states

The molecular structure and properties of 7-azaindole in its first four singlet states were studied with a view to improving current understanding of the photophysical behavior of its C(2h) dimer. This dimer, which exhibits a double proton transfer via its two hydrogen bonds upon electronic excitation, has for 35 years been used as a model for the photophysical behavior of DNA base pairs. Electronic excitation of 7-azaindole simultaneously increases its acidity and basicity; these changes facilitate a concerted mechanism for the double proton transfer in the dimer. In this work, we found the acidity and basicity changes to occur only in its first pi,pi(*) excited singlet state.     

Effects of the nature of counterions in solution on interactions of phenoxazones, xanthones, and carbazoles containing benzo-crown groups with DNA

The interactions of DNA with phenoxazones, xanthones, and carbazoles containing the (benzo-18-crown-6)-4′-yl and (benzo-15-crown-5)-4′-yl radicals bonded to the chromophore via spacers of different lengths in the presence of Na⁺ and K⁺ ions were studied by spectrophotometry, circular dichroism, and dynamic birefringence. The thermodynamic parameters of the binding of the compounds with DNA and changes in the macromolecular parameters of the DNA molecule during complexation were determined. Based on the results of these studies, we suggested the models of bonding of these compounds to the double helix of DNA. It is shown that the mode of DNA binding with a phenoxazone derivative containing two (benzo-15-crown-5)-4′-yl radicals bonded via a fragment of glycine to chromophore depends on the type of the counterion in solution. In the presence of Na⁺, the chromophore is intercalated into the double helix of DNA; in the presence of K⁺, it is bound to DNA in the form of a dimer outside the double helix. The type of the counterion does not affect the mode of binding of other crown-containing compounds of actinocin with DNA. For compounds containing the (benzo-18-crown-6)-4′-yl radical, the mode of binding to DNA adepends only on the spacer length.     

Morphology transitions of AB diblock copolymer melts confined in nanocylindrical tubes

By employing Monte Carlo simulations for various values for the interactions energies epsilonAB between the beads A and B, the selectivity of the surface for one of the beads, and the diameter d of the nanotube, the morphology transitions in A5B5 and A7B3 diblock copolymer melts were investigated. In symmetrical systems and for a negligible preference of the surface for A and B and not too large values of d, as epsilonAB increases, increasingly thicker stacked-disk macrodomains normal to the tube surface were formed. When epsilonAB became sufficiently large, a configuration transition to helixes occurred which became deformed at larger values of epsilonAB. The helixes contained an imperfect single helix of A coupled with an imperfect single helix of B or imperfect double helixes of A coupled with imperfect double helixes of B. When at constant and relatively large epsilonAB, the attractive interaction epsilonAS between the A bead and the surface was increased, a transition from a succession consisting of stacked disks and a helix to a helical one occurred, which changed to a circular lamellar structure at a sufficiently large attraction epsilonAS by the surface. When the diameter d was increased, in addition to the helixes already mentioned imperfect triple helixes of A coupled with triple helixes of B were identified. In the asymmetrical case, two kinds of helixes were observed, namely, those identified in the symmetrical case, as well as a helix formed by one kind of beads immersed in the matrix of the other one.     

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC

CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.