True spin and pseudo spin entanglement around Dirac Points in graphene with Rashba spin–orbit interaction

We analytically obtained the Schmidt decomposition of the entangled state between the pseudo spin and the true spin in graphene with Rashba spin–orbit coupling. The entangled state has the standard form of the Bell state, where the SU(2) spin symmetry is broken. These states can be explicitly expressed as the superposition of two nonorthogonal, but mirror symmetrical spin states entangled with the pseudo spin states. Because of the closely locking between the pseudo spin and the true spin, it is found that the orbit curve in the spin-polarization parameter space for the fixed equi-energy contour around Dirac points has the same shape as the $\delta \overrightarrow{k}$-contour. Due to the spin–orbit coupling that cause the topological transition in the local geometry of the dispersion relation, the new equi-energy contours around the new emergent Dirac Points can be obtained by squeezing the one around the original Dirac point. The spin texture in the momentum space around the Dirac points is analyzed under the Rashba spin–orbit interaction and it is found that the orientation of the spin polarization at each crystal momentum $\overrightarrow{k}$ is independent of the Rashba coupling strength.     

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S⁻)=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G^.+-P(S⁻)=S. The ionization potential of G-P(S⁻)=S was calculated to be slightly lower than that of guanine in 5′-dGMP. Subsequent thermally activated hole transfer from G^.+ to P(S⁻)=S led to dithiyl radical (P-2S^.) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S^. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S⁻)=S concentrations showed a bimolecular conversion of P-2S^. to the σ²-σ*¹-bonded dimer anion radical [-P-2S 2S-P-]⁻ [ΔG (150 K, DFT)=−7.2 kcal mol⁻¹]. However, [-P-2S 2S-P-]⁻ formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=−1.4 kcal mol⁻¹]. Neither P-2S^. nor [-P-2S 2S-P-]⁻ oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.     

Rovibrational and energetic analysis of the hydroxyethynyl anion (CCOH−)

For the first time, high-level structural and rovibrational data are provided for the hyroxyethynyl anion, CCOH^?. CCOH^? is a promising molecule for interstellar detection even though no new anions have been observed in the interstellar medium for the past half-decade. The large dipole moment of the corresponding neutral radical may be key for its creation as has been hypothesised and supported for other anions known to exist in various astronomical environments. Highly accurate quartic force fields are employed where previous benchmarks have produced spectroscopic constants and anharmonic vibrational frequencies within 20 MHz and 1 cm^?1, respectively, of experiment. This same approach is applied here for CCOH^? and its deuterated isotopologue with the goal of assisting laboratory experiments and/or astronomical observers in the potential detection of this anion.     

Small Targeted Cytotoxics: Current State and Promises from DNA‐Encoded Chemical Libraries

The targeted delivery of potent cytotoxic agents has emerged as a promising strategy for the treatment of cancer and other serious conditions. Traditionally, antibodies against markers of disease have been used as drug‐delivery vehicles. More recently, lower molecular weight ligands have been proposed for the generation of a novel class of targeted cytotoxics with improved properties. Advances in this field crucially rely on efficient methods for the identification and optimization of organic molecules capable of high‐affinity binding and selective recognition of target proteins. The advent of DNA‐encoded chemical libraries allows the construction and screening of compound collections of unprecedented size. In this Review, we survey developments in the field of small ligand‐based targeted cytotoxics and show how innovative library technologies will help develop the drugs of the future.     

Use of Mercury Film Glassy Carbon Electrode Modified with Multiwalled Carbon Nanotubes in Electrochemical Analysis of DNA

Mercury film plated on a glassy carbon electrode modified with multiwalled carbon nanotubes (MF/MWNTs/GCE) was used for the analysis of single (ss) and double stranded (ds) DNA, as well as for Jurkat genomic DNAs methylated to different degrees. The results indicated that the DNA molecules adsorbed quite strongly on the MF/MWNTs/GCE surface allowing ex situ adsorption and produce well developed peaks (due to cytosine and adenine) by using adsorptive stripping (Ads, ex situ) square wave voltammetry (SWV). Also, SWV of Jurkat DNA mixtures methylated to different degrees revealed a linear decrease of the peak height with increasing methylation indicating an increase of structural rigidity.     

Theoretical Insights into Intermolecular Hydrogen-Bonding Strengthening in Fluorenone-Methanol Complexes Induced by Electronic Excitation and Bulk Solvent Effect

This work presents a theoretical insight into the variation of the site-specific intermolecular hydrogen-bonding （HB）, formed between C=O group of fluorenone （FN） and O-H groups of methanol （MeOL） molecules, induced by both the electronic excitation and the bulk solvent effect. Through the calculation of molecular ground- and excited-state properties, we not only demonstrate the characters of HB strengthening induced by electronic excitation and the bulk solvent effect but also reveal the underlying physical mechanism which leads to the HB variation. The strengthening of the intermolecular HB in electronically excited states and in liquid solution is characterized by the reduced HB bond-lengths and the red-shift IR spectra accompanied by the increasing intensities of IR absorption corresponding to the characteristic vibrational modes of the O-H and C--O stretching. The HB strengthening in the excited electronic states and in solution mainly arises from the charge redistribution of the FN molecule induced by the electronic excitation and bulk solvent instead of the intermolecular charge transfer. The charge redistribution of the solute molecule increases the partial dipole moment of FN molecule and the FN-MeOL intermolecular interaction, which subsequently leads to the HB strengthening. With the bulk solvent effect getting involved, the theoretical IR spectra of HBed FN-MeOL complexes agree much better with the experiments than those of gas-phase FN-MeOL dimer. All the calculations are carried out based on our developed analytical approaches for the first and second energy derivatives of excited electronic state within the time-dependent density functional theory.     

Error analysis of idealized nanopore sequencing

This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single‐stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K‐12) at least 140 times to achieve 99.99% accuracy (Q40). By exploiting the ability to reread each strand at each pore in an array, arbitrary positioning on an error rate versus throughput tradeoff curve is possible if systematic errors are absent, with throughput governed by the number of pores in the array and the enzyme turnover rate.     

The Effect of Sample Age and Neutron Radiation to Dynamic Nuclear Polarization Parameters in Some Asphaltene Suspensions

Nuclear magnetic resonance and the Overhauser effect type dynamic nuclear polarization experiments were performed to study suspensions of asphaltene in the xylene isomers at a low magnetic field of 1.44 mT at room temperature. Intermolecular spin-spin interactions occur between nuclear spins of hydrogen in the solvent medium and the free electron spins in the asphaltene micelles. The samples were prepared in three different asphaltene concentrations at vacuum. The samples were waited for four years and dynamic nuclear polarization parameters were found via dynamic nuclear polarization experiments performed again. Thus, it was investigated the effect of sample age to dynamic nuclear polarization parameters. In addition, the medium concentrations of each sample were exposed to radiation for 48 hours and neutron radiation effects to the dynamic nuclear polarization parameters were investigated. The results are discussed.     

Synthesis and Properties of Isobicyclo‐DNA

We present the synthesis of the isobicyclo‐DNA building blocks with the nucleobases A, C, G and T, as well as biophysical and biological properties of oligonucleotides derived thereof. The synthesis of the sugar part was achieved in 5 steps starting from a known intermediate of the tricyclo‐DNA synthesis. Dodecamers containing single isobicyclo‐thymidine incorporations, fully modified A‐ and T‐containing sequences, and fully modified oligonucleotides containing all four bases were synthesized and characterized. Isobicyclo‐DNA forms stable duplexes with natural nucleic acids with a pronounced preference for DNA over RNA as complements. The most stable duplexes, however, arise by self‐pairing. Isobicyclo‐DNA forms preferentially B‐DNA‐like duplexes with DNA and A‐like duplexes with complementary RNA as determined by circular dichroism (CD) spectroscopy. Self‐paired duplexes show a yet unknown structure, as judged from CD spectroscopy. Biochemical tests revealed that isobicyclo‐DNA is stable in fetal bovine serum and does not elicit RNaseH activity.