Possible incorporation of the purine–purine mispairs in the DNA helix and the interpretation of the transversion-type point mutations

The stereochemical and energetic compatibility of incorporation of the non-Watson–Crick hydrogen bonded purine–purine base pairs of normal tautomers in the helical structure of B-DNA is studied here. The hydrogen bonding positions of the possible “mispairs” of the bases GA, GG, and AA are optimized first in the base plane by translational and rotational movement along the hydrogen bonds and then introduced at an appropriate position in the DNA structure. The optimum backbone geometries which can accommodate the “mispairs” are obtained by force field computations. The stereochemical and energetic aspects of the various mispairs are discussed in light of their possible incorporation in DNA and as mutational intermediates for the “transversion”-type point mutations.     

Anisotropic Conductivity at the Single‐Molecule Scale

In most junctions built by wiring a single molecule between two electrodes, the electrons flow along only one axis: between the two anchoring groups. However, molecules can be anisotropic, and an orientation‐dependent conductance is expected. Here, we fabricated single‐molecule junctions by using the electrode potential to control the molecular orientation and access individual elements of the conductivity tensor. We measured the conductance in two directions, along the molecular plane as the benzene ring bridges two electrodes using anchoring groups (upright) and orthogonal to the molecular plane with the molecule lying flat on the substrate (planar). The perpendicular (planar) conductance is about 400 times higher than that along the molecular plane (upright). This offers a new method for designing a reversible room‐temperature single‐molecule electromechanical switch that controllably employs the electrode potential to orient the molecule in the junction in either “ON” or “OFF” conductance states.     

Silver Makes Better Electrical Contacts to Thiol‐Terminated Silanes than Gold

We report that the single‐molecule junction conductance of thiol‐terminated silanes with Ag electrodes are higher than the conductance of those formed with Au electrodes. These results are in contrast to the trends in the metal work function Φ(Ag)<Φ(Au). As such, a better alignment of the Au Fermi level to the molecular orbital of silane that mediates charge transport would be expected. This conductance trend is reversed when we replace the thiols with amines, highlighting the impact of metal–S covalent and metal–NH₂ dative bonds in controlling the molecular conductance. Density functional theory calculations elucidate the crucial role of the chemical linkers in determining the level alignment when molecules are attached to different metal contacts. We also demonstrate that conductance of thiol‐terminated silanes with Pt electrodes is lower than the ones formed with Au and Ag electrodes, again in contrast to the trends in the metal work‐functions.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.     

Nature of hydrogen interaction and saturation on small titanium clusters

This work explores the nature of interaction and saturation of hydrogen molecules on small titanium clusters using ab initio calculations. Molecular dynamics simulations and ensuing charge density maps were used to gain insight into the key steps involved in dissociation of the hydrogen molecule on the metal clusters. The mechanistic insights gleaned from these simulations were subsequently utilized to obtain realistic models of the hydrogen saturated titanium clusters. It was found that the most stable hydrogen saturated titanium clusters involve hydrogen multicenter bonds. The observed peaks in the experimental mass and photoelectron spectra of hydrogen saturated titanium clusters are attributed to structures possessing hydrogen multicenter bonds. Hydrogen multicenter bonds are also ascribed to the origin of the broad shoulder in the vibrational spectra of hydrogen cycled Ti-doped NaAlH4 reported in a recent study.     

Preferential binding specificity of silver cation to a single nucleobase over base pairs evaluated by abasic site-containing DNA

The binding specificity of silver cations to abasic (AP) site-containing DNA was electrochemically investigated by comparison with the fully matched DNA without the AP site. AP site-containing DNA is designed in a way that only the nucleotide opposite the AP site is variable to allow for coexistence of an unpaired nucleotide and a number of DNA base pairs. The surface of a gold electrode was modified by AP site-containing DNA duplex on which Ag⁺ binding specificity was evaluated. Electrochemical investigations on the AP-DNA-modified electrodes reveal that Ag⁺ preferentially associates to the unpaired nucleotides instead of the coexisted base pairs and shows sequence-dependant binding, especially stronger for purines than for pyrimidines. Additionally, the hydrogen bond pattern moieties of the unpaired nucleotides should be involved in Ag⁺ binding evidenced by a decrease of the redox signal when introducing a ligand with its hydrogen bond moiety complementary to the nucleotide deoxycytidine. This is the first attempt to make a comparison in one DNA molecule for metal ion binding to coexisted unpaired nucleotide and DNA base pairs. The present method demonstrates an easy way for investigating binding specificity of heavy metal ions to AP site in the presence of coexisted DNA base pairs.     

Effect of glucocorticoids and their complexes with apolipoprotein A‐I on the secondary structure of eukaryotic DNA

The tetrahydrocortisol–apolipoprotein A‐I complex specifically interacts with eukaryotic DNA isolated from rat liver. This interaction is highly cooperative and of a saturating nature. One DNA molecule binds about 54 molecules of the complex. Small‐angle X‐ray scattering has shown that hydrogen bonds between nitrous bases are destroyed and that single‐stranded structures are formed at the interaction of the tetrahydrocortisol–apolipoprotein A‐I complex with eukaryotic DNA. The most probable site of binding the tetrahydrocortisol–apolipoprotein A‐I complex with DNA is the sequence of the CC(GCC)_n type entering the structure of many genes, among them the structure of the human apolipoprotein A‐I gene. Oligonucleotide of this type has been synthesized. The association constant (K_ass) of its complexation was shown to be 1.66 · 10⁶ M^?1. Substitution of tetrahydrocortisol for cortisol in the complex results in a considerable decrease of K_ass. IR‐spectroscopy study has shown that the interaction of tetrahydrocortisol with oligonucleotide CC(GCC)_3–5 is accompanied by the formation of hydrogen bonds via the CO‐NH, PO₂, and OH groups of desoxycytidinephosphate. The tetrahydrocortisol–apolipoprotein A‐I complex alters the DNA secondary structure formed at the interaction with the hormone, causing the structural transition “order → tangle.” It is assumed that in the GC‐pairs of the given DNA sequence, tetrahydrocortisol initiates the rupture of hydrogen bonds, while the hydrophobic interactions between nitrous bases and apoA‐I intensify this process. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Highly conducting π-conjugated molecular junctions covalently bonded to gold electrodes

We measure electronic conductance through single conjugated molecules bonded to Au metal electrodes with direct Au-C covalent bonds using the scanning tunneling microscope based break-junction technique. We start with molecules terminated with trimethyltin end groups that cleave off in situ, resulting in formation of a direct covalent σ bond between the carbon backbone and the gold metal electrodes. The molecular carbon backbone used in this study consist of a conjugated π system that has one terminal methylene group on each end, which bonds to the electrodes, achieving large electronic coupling of the electrodes to the π system. The junctions formed with the prototypical example of 1,4-dimethylenebenzene show a conductance approaching one conductance quantum (G(0) = 2e(2)/h). Junctions formed with methylene-terminated oligophenyls with two to four phenyl units show a 100-fold increase in conductance compared with junctions formed with amine-linked oligophenyls. The conduction mechanism for these longer oligophenyls is tunneling, as they exhibit an exponential dependence of conductance on oligomer length. In addition, density functional theory based calculations for the Au-xylylene-Au junction show near-resonant transmission, with a crossover to tunneling for the longer oligomers.     

Modular Construction of Porous Hydrogen-Bonded Molecular Materials from Melams

Ordered materials with predictable structures and properties can be made by a modular approach, using molecules designed to interact with neighbors and hold them in predetermined positions. Incorporating 4,6-diamino-1,3,5-triazin-2-yl (DAT) groups in modules is an effective way to direct assembly because each DAT group can form multiple N−H⋅⋅⋅N hydrogen bonds according to established patterns. We have found that modules with high densities of N(DAT)₂ groups can be made by base-induced double triazinylations of readily available amines. The resulting modules can form structures held together by remarkably large numbers of hydrogen bonds per molecule. Even simple modules with only 1–3 N(DAT)₂ groups and fewer than 70 non-hydrogen atoms can crystallize to form highly open networks in which each molecule engages in over 20 N−H⋅⋅⋅N hydrogen bonds, and more than 70 % of the volume is available for accommodating guests. In favorable cases, guests can be removed to create rigorously porous crystalline solids analogous to zeolites and metal–organic frameworks.     

Analysis of Proton NMR in Hydrogen Bonds in Terms of Lone‐Pair and Bond Orbital Contributions

NMR spectroscopic parameters of the proton involved in hydrogen bonding are studied theoretically. The set of molecules includes systems with internal resonance‐assisted hydrogen bonds, internal hydrogen bonds but no resonance stabilization, the acetic acid dimer (AAD), a DNA base pair, and the hydrogen succinate anion (HSA). Ethanol and guanine represent reference molecules without hydrogen bonding. The calculations are based on zero‐point vibrationally averaged molecular structures in order to include anharmonicity effects in the NMR parameters. An analysis of the calculated NMR shielding and J‐coupling is performed in terms of “chemist’s orbitals”, that is, localized molecular orbitals (LMOs) representing lone‐pairs, atomic cores, and bonds. The LMO analysis associates some of the strong de‐shielding of the protons in resonance‐assisted hydrogen bonds with delocalization involving the π‐backbone. Resonance is also shown to be an important factor causing de‐shielding of the OH protons for AAD and HSA, but not for the DNA base pair. Nitromalonamide (NMA) and HSA have particularly strong hydrogen bonds exhibiting signs of covalency in the associated J‐couplings. The analysis results show how NMR spectroscopic parameters that are characteristic for hydrogen bonded protons are influenced by the geometry and degree of covalency of the hydrogen bond as well as intra‐ and intermolecular resonance.     

Modification of Weld Metal with Tungsten Carbide and Titanium Nitride Nanoparticles in Twin Submerged Arc Welding

The influence of tungsten carbide and titanium nitride nanoparticles on the structure and properties of the weld metal of welded joints made by automatic twin submerged arc welding is considered. The nanoparticles have been introduced into the weld pool as a part of the “master alloy” based on nickel powder (PNE-1 according to GOST 9722). It has been shown that modifying the weld metal with tungsten carbide nanoparticles holds promise for enhancing the impact strength. In addition, it has been found that titanium nitride is prone to dissociation under the same conditions. However, microalloying with titanium, which is due to the release of titanium from the nitride, leads to an increase in the impact strength of the weld metal.     

Conformational Transformations of ε-Caprolactam as an Advantage in the Production of Molecular Complexes Used in Adhesive Technology

The conformations of the ε-caprolactam molecule were calculated using a software package, and three of its conformers were established. It is shown that the conformational change of molecules creates the prerequisites for organizing the nearest contact and strong hydrogen bonds of ε-caprolactam with molecules of other substances. The molecule of ε-caprolactam can be “adapted to a neighbor” to a greater degree, since it can take a different, more advantageous conformation to provide the necessary contact. With the use of ε-caprolactam, molecular complexes have been obtained that have found application in the production of adhesives for rubber–cord systems.     

X-Ray Diffraction Study on Manganese(II) Complexes with Thiophene-2-Carboxylate and Furan-3-Carboxylate Ligands

Abstract

Mn(II) cations in the crystals of trisaquobis(μ-thiophen-2-carboxylato-O,O′)(thiophen-2-carboxylato-O)manganese(II) monohydrate are bridged by oxygen atoms donated by bidentate carboxylic groups of two thiophen-2-carboxylate ligands. In addition, each Mn(II) ion is coordinated by an oxygen atom of a monodentate carboxylic group of this ligand and three oxygen atoms of water molecules. The coordination around the Mn(II) cation is octahedral. The bridging of the ligands results in molecular ribbons propagating in the c-direction of the crystal held together by C?H…O hydrogen bonds. The crystal structure of diaquobis(μ-furan-3-carboxylato-O,O′)di(μ-furan-3-carboxylato-O,O)(μ-aqua-O)manganese(II) consists of dinuclear structural units. In each molecule Mn(II) cations are O,O′ bridged by oxygen atoms of bidentate carboxylic groups of two furan-3-carboxylate ligands and have a water located between the Mn cations. The units are O,O′ bridged to Mn(II) ions located in adjacent units by bidentate oxygen atoms, forming molecular ribbons extending in the c-direction. Octahedral coordination around each Mn(II) ion is completed by two water molecules. The octahedra around two adjacent metal ions in the unit share a common apex - the bridging oxygen atom of the water molecule. The ribbons are held together by C?H…O hydrogen bonds between furan ring oxygen atoms and the carbon atoms of adjacent furan rings.     

Inelastic tunneling spectroscopy of gold-thiol and gold-thiolate interfaces in molecular junctions: The role of hydrogen

It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here, we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances, and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one, or two thiol hydrogen atoms. We find that in most cases, the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum as a gold STM tip approaches the intact S-H group at the end of a molecule bound at its other end to a second electrode. We predict the frequency of a vibrational mode of the thiol H atom to increase by a factor ～2 as the gap between the tip and molecule narrows. Therefore, IETS should be able to track the approach of the tip towards the thiol group of the molecule and detect the detachment of the thiol H atom from the molecule when it occurs.     

cis‐Dichloridobis(1,10‐phenanthroline‐5,6‐diol‐κ2N,N′)manganese(II): a supramolecular chain formed via O—H...Cl bonds and aromatic stacking

The title compound, [MnCl₂(C₁₂H₈N₂O₂)₂], displays a novel supramolecular chain formed by intermolecular O—H...Cl hydrogen bonds and aromatic stacking. The molecule has crystallographically imposed twofold symmetry with the Mn^II atom on the twofold axis. In the 1,10‐phenanthroline‐5,6‐diol ligand, each H atom of the two hydroxy groups is oriented towards the other hydroxy O atom. Both hydroxy groups form intermolecular O—H...Cl hydrogen bonds with a single Cl atom of an adjacent molecule. These hydrogen bonds connect the molecules via operation of the molecular twofold axis and the centre of inversion of the crystal lattice, forming a doubly‐bridged one‐dimensional structure with Mn atoms as the nodes. Strong aromatic π‐stacking between two antiparallel neighbouring 1,10‐phenanthroline‐5,6‐diol ligands also helps to stabilize the chain.     

Hydrogen-bonded supramolecular motifs in crystal structures of trimethoprim barbiturate monohydrate (I) and 2-amino-4,6-dimethylpyrimidinium barbiturate trihydrate (II)

In the present study, we report the crystal structures of two organic salts, namely 2,4-diamino-5-(3′,4′,5′-trimethoxybenzyl)pyrimidinium (TMP) barbiturate monohydrate (TMPBAR) (I), 2-amino-4,6-dimethylpyrimidinium (AMPY) barbiturate trihydrate (AMPYBAR) (II). In both complexes, one ring nitrogen of TMP and AMPY are protonated as a result of proton transfer from the−CH₂ group of barbituric acid. In compound (I), the TMP cation and barbiturate anion are paired through twoN−H···O and one N−H···N hydrogen bonds. This pair further self-organizes through N−H···O hydrogen bonds to generate an array of six hydrogen bonds. These arrays are further cross-linked by N−H···O hydrogen bonds forming a sheet-like structure. The water molecule is also embedded in the sheet via O−H···O and C−H···O hydrogen bonds, forming a rosette-like supramolecular motif. TMP cations are also bridged by alternating water molecules via C−H···O and O−H···N hydrogen bonds. In compound (II), the symmetrical barbiturate anions self-organize on both sides through N−H···O hydrogen bonds generating a supramolecular chain. These chains are cross-linked by the three water molecules. A pair of barbiturate anions and two water molecules constitute an array of four hydrogen bonds (DADA quadruple array). These arrays are cross-linked by another water molecule. 2-Amino-4,6-dimethylpyrimidine cations are paired through N−H···N hydrogen bonds. These pairs are bridged by three water molecules generating a supramolecular ribbon. The barbiturate chains and base pairs are arranged in an alternate manner via N−H···O and O−H···O hydrogen bonds to generate a 3-D network.     

Copper hexacyanoferrate modified electrodes for hydrogen peroxide detection as studied by X-ray absorption spectroscopy

X-ray absorption spectroscopy (XAS) has been used to monitor the local geometry of Fe and Cu sites of copper hexacyanoferrates (CuHCF)-modified electrodes which find application in the electrochemical detection of hydrogen peroxide. The XAS approach has permitted to check the nature of the Cu and Fe sites and to investigate their local structure around about 500 pm from the metal centres. The measurements have been done on electrodes prior and after the addition of known quantities of hydrogen peroxide at two different concentration ranges, following a protocol consisting of H₂O₂ addition, applied potential, and rest period. For the CuHCF-modified electrode, this protocol leads to the increasing conversion to an already present “inactive” component, which limits the usability of the sensor; whereas the electrode modified with the Cu²⁺-loaded CuHCF displays a better resistance to this unavoidable process. In particular, the formation of the “inactive” component takes place more slowly, confirming the capability, at molecular scale, of such Cu-enriched CuHCF used as electrode modifier to detect more efficiently hydrogen peroxide, as recently demonstrated in our previous paper.     

Hydrogen adsorption on carbon-doped boron nitride nanotube

The adsorption of atomic and molecular hydrogen on carbon-doped boron nitride nanotubes is investigated within the ab initio density functional theory. The binding energy of adsorbed hydrogen on carbon-doped boron nitride nanotube is substantially increased when compared with hydrogen on nondoped nanotube. These results are in agreement with experimental results for boron nitride nanotubes (BNNT) where dangling bonds are present. The atomic hydrogen makes a chemical covalent bond with carbon substitution, while a physisorption occurs for the molecular hydrogen. For the H(2) molecule adsorbed on the top of a carbon atom in a boron site (BNNT + C(B)-H(2)), a donor defect level is present, while for the H(2) molecule adsorbed on the top of a carbon atom in a nitrogen site (BNNT + C(N)-H(2)), an acceptor defect level is present. The binding energies of H(2) molecules absorbed on carbon-doped boron nitride nanotubes are in the optimal range to work as a hydrogen storage medium.     

Models of hydration and isomeric transitions of glucose molecules in aqueous solutions

The kinematic viscosity of aqueous glucose solutions is studied. It is found that the hydrodynamic radius of monosaccharide molecule in an aqueous solution depends on temperature in the range of 290–355 K. Using a bimodal model of the energy states of the volume in which the glucose molecule is located and local equilibrium is established, it is shown that the above-mentioned dependence can be attributed to disturbances in the equilibrium of isomeric transitions, induced by variations in temperature. The parameters of isomeric transitions for a glucose molecule in an aqueous solvent, the probability of “chair” and “boat” configurations occurring for glucose molecules, and the number of water molecules in the hydration shells of these configurations are calculated; the strain of the chemical bonds in the chair configuration of a glucose molecule is estimated.     

H2 adsorption by noble gas insertion compounds: A computational study

In order to find a solution of energy-related problems, sophisticated hydrogen storing materials are needed as hydrogen is an abundant and environment friendly fuel. We have investigated the hydrogen storage potential of Ng inserted metal acetylide and metal cyanide compounds (metal ​= ​Cu, Ag and Au) at the ωB97X-D/cc-pVTZ-PP level of theory. Due to the difference in electronegativity and formal charge on metal atoms in the insertion compounds, the interaction with the hydrogen molecule is expected to be different. The adsorption energies, the free energy of adsorption, natural charges on atomic centers/moieties are obtained through the natural population analysis, and energy decomposition analysis has also been carried out for nH₂···MNgCCH and nH₂···MNgCN (n ​= ​1–3). The hydrogen adsorption capacity of the strongest and the weakest cases has also been investigated. Both the insertion compounds, MNgCCH and MNgCN, are found to adsorb a maximum of three hydrogen molecules on the metal site. The single H₂ adsorbed minimum energy structures of studied compounds show a “T-shaped” orientation while double H₂ adsorbed minimum energy structures are of “Y- shaped” geometry and those of tricoordinated structures resemble “T_d-like” shape. The negative value of Gibbs free energy change suggests the thermodynamical spontaneity of the hydrogen adsorption process.