Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA

M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensive ab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only one which preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8 kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model for building an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance with experimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not included the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong electronic correlations.     

Computation of internal coordinates,derivatives, and gradient expressions: torsion and improper torsion

Laplacians and gradient dot products are required for the recently developed internal coordinate quantum Monte Carlo method. New formulas are presented for these quantities for torsion and improper torsion angles. The Laplacians can also be used to economize calculation of sets of second derivatives used in molecular mechanics and other methods. Formulas for torsion angle gradient dot products and Laplacians, and completely new formulas for improper torsion, are presented. In addition, calculations of cos τ and sin τ, some suitable for energy subroutines and others for force subroutines, are shown. Finally, in a related development, several sets of conditions for three atom linearity or four atom planarity involving internal coordinate derivatives are reported. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 553–561, 2000     

On-surface cyclodehydrogenation reaction pathway determined by selective molecular deuterations

Understanding the reaction mechanisms of dehydrogenative C_aryl–C_aryl coupling is the key to directed formation of π-extended polycyclic aromatic hydrocarbons. Here we utilize isotopic labeling to identify the exact pathway of cyclodehydrogenation reaction in the on-surface synthesis of model atomically precise graphene nanoribbons (GNRs). Using selectively deuterated molecular precursors, we grow seven-atom-wide armchair GNRs on a Au(111) surface that display a specific hydrogen/deuterium (H/D) pattern with characteristic Raman modes. A distinct hydrogen shift across the fjord of C_aryl–C_aryl coupling is revealed by monitoring the ratios of gas-phase by-products of H₂, HD, and D₂ with in situ mass spectrometry. The identified reaction pathway consists of a conrotatory electrocyclization and a distinct [1,9]-sigmatropic D shift followed by H/D eliminations, which is further substantiated by nudged elastic band simulations. Our results not only clarify the cyclodehydrogenation process in GNR synthesis but also present a rational strategy for designing on-surface reactions towards nanographene structures with precise hydrogen/deuterium isotope labeling patterns.

Selective deuterations were exploited to synthesize graphene nanoribbons on Au(111) surface with a specific H/D pattern on edges, allowing the determination of cyclodehydrogenation reaction pathway within the framework of pericyclic reactions.     

Cosmological evolution of interacting dark energy in Lorentz violation

The cosmological evolution of an interacting scalar-field model in which the scalar field interacts with dark matter, radiation, and baryons via Lorentz violation is investigated. We propose a model of interaction through the effective coupling, [`(b)]\bar{\beta} . Using dynamical system analysis, we study the linear dynamics of an interacting model and show that the dynamics of critical points are completely controlled by two parameters. Some results can be mentioned as follows. Firstly, the sequence of radiation, the dark matter, and the scalar-field dark energy exist and baryons are subdominant. Secondly, the model also allows for the possibility of having a universe in the phantom phase with constant potential. Thirdly, the effective gravitational constant varies with respect to time through [`(b)]\bar{\beta} . In particular, we consider the simple case where [`(b)]\bar{\beta} has a quadratic form and has a good agreement with the modified ΛCDM and quintessence models. Finally, we also calculate the first post-Newtonian parameters for our model.     

Structure and bonding between an aryl group and metal surfaces

Modifying solid surfaces with aryl groups has many potential applications. Using first principles density functional theory methods, we investigated the trend of the structure and bonding of the phenyl group (C6H5, the simplest aryl group) on selected transition metals across the periodic table. We found that the bond between C6H5 and metal surfaces is chemical in nature. Decreasing bond strength is found from left to right, concurrent with a switching of the preferred orientation for C6H5 from the flat-lying configuration to the upright configuration. This switching is attributed to the increasing of d-electrons; that is, early transition metals, lacking d-electrons, favor the carbon-metal pi-bond and therefore the flat-lying configuration, while late transition metals rich in d-electrons prefer the carbon-metal sigma-bond and thus the upright fashion. C6H5 is also found to undergo beta-dehydrogenation on early transition metals. This work invites further theoretical and experimental research on the aryl-solid interface.     

HERFD XAS/ATR-FTIR batch reactor cell

An autoclave reactor was modified to perform simultaneously high energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy measurements without altering the reactor design. This operando cell allows one to follow changes in the electronic and geometric structure of the catalyst with HERFD XAS and relate them to the simultaneously detected activity and reaction species with ATR-FTIR formed during the reaction in the liquid phase. The capability of the cell is demonstrated by two studies. The first shows the reduction of Au/CeO(2) precursors in different solvents. The second shows that mainly Au(0) is present in the hydrogenation of nitrobenzene over Au/CeO(2).     

Intra‐ and inter‐supramolecular complexation of poly(butyl methacrylate)‐co‐2‐(1,2,3‐triazol‐4‐yl)pyridine copolymers induced by CoII,FeII, and EuIII ions monitored by molecular hydrodynamics methods

Poly(butyl methacrylate) copolymers embedding bidentate 2‐(1,2,3‐triazol‐4‐yl)pyridine (trzpy) chelating units as comonomer in the side chains were synthesized by controlled radical addition‐fragmentation transfer (RAFT) polymerization. Intracomplexation and intercomplexation of the macromolecules of the poly(butyl methacrylate) copolymers containing 20 % mol of trzpy units induced by Co^II, Fe^II, and Eu^III ions were studied in the solutions by macromolecular hydrodynamics methods. The sedimentation velocity of extremely diluted copolymer solutions and the dynamic viscosity of moderately diluted solutions were studied in a wide range of the salts concentrations. Differences were observed with respect to the copolymer behavior in the presence of the Co²⁺, Fe²⁺, Eu³⁺ ions. These differences are namely due to the differences in the number of coordination bonds required for complex formation and not explicitly to the nature of the corresponding anions. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2632–2639     

Amphoteric doping of carbon nanotubes by encapsulation of organic molecules: electronic properties and quantum conductance

In order to investigate and optimize the electronic transport processes in carbon nanotubes doped with organic molecules, we have performed large-scale quantum electronic structure calculations coupled with a Green's function formulation for determining the quantum conductance. Our approach is based on an original scheme where quantum chemistry calculations on finite systems are recast to infinite, non-periodic (i.e., open) systems, therefore mimicking actual working devices. Results from these calculations clearly suggest that the electronic structure of a carbon nanotube can be easily manipulated by encapsulating appropriate organic molecules. Charge transfer processes induced by encapsulated organic molecules lead to efficient n- and p-type doping of the carbon nanotube. Even though a molecule can induce p and n doping, it is shown to have a minor effect on the transport properties of the nanotube as compared to a pristine tube. This type of doping therefore preserves the intrinsic properties of the pristine tube as a ballistic conductor. In addition, the efficient process of charge transfer between the organic molecules and the nanotube is shown to substantially reduce the susceptibility of the pi electrons of the nanotube to modification by oxygen while maintaining stable doping (i.e., no dedoping) at room temperature.     

The determination of sulfide in the aqueous environment

Direct measurements were made by use of a sulfide ion-selective electrode in conjunction with a double-junction reference electrode and an Orion Model 407 A/F specific ion meter. This method enables simple and rapid determinations of the total sulfide ion concentration in water. Total sulfide was determined in samples collected from lakes in Fort Bend County. Texas, which ranged from 4 ppb to 18 ppb and from the Houston Ship Channel which ranged from 13 ppb to 42 ppb.A series of experiments shows that (1) the rate of oxidation of S^2? exposed to air is about three times slower for solutions containing the sulfide antioxidant buffer (SAOB II) and (2) the rate of oxidation of S² in tightly capped containers is about twice as fast for solutions not containing SAOB II than for solutions containing SAOB II.It was concluded that the use of SAOB II almost eliminates the problem of air oxidation of sulfide ions during direct measurements and that sulfide ion concentrations (as low as 4 ppb) can be determined directly in the laboratory and in the field by use ofthis electrode method.