Spectroscopic Analysis of Two Distinct Equilibrium States for the Exchange Reaction of Sodium Cholate and Oligo‐DNA on Single‐Walled Carbon Nanotubes

Understanding the quantitative analysis of the transition adsorption structures of molecules on single‐walled carbon nanotubes (SWNTs) is of importance from the point of view of both fundamental science and applications of nanotubes. Absorption spectroscopy reveals that two different equilibrium states are existent for the exchange reaction of sodium cholate (SC) and oligo‐DNA (single‐stranded 20‐mer cytosine) on SWNTs. This is derived from the transitions of the adsorption structures of different chirality‐types of SWNTs and SC/DNA at certain SC concentrations below the critical micelle concentration of SC.     

Application of XPS imaging analysis in understanding interfacial delamination and X‐ray radiation degradation of PMMA

The recent development of X‐ray Photoelectron Spectroscopy (XPS) instrumentation with spatial resolution down to several microns has advanced the capability of elemental and chemical state imaging. XPS imaging analysis has been applied in understanding the delamination problems of siloxane coatings on polymethyl‐methacrylate (PMMA) polymer. It was found that delamination occurred by interfacial failure, and the coating suffered complete delamination from a PMMA substrate. This example offered an opportunity for the investigation of X‐ray damage on polymers encountered in XPS imaging analysis. This paper also demonstrated how to construct a constrained peak model with the aid of chemical knowledge and supporting evidence of the sample. Monte Carlo error analysis was used to determine the validity of the peak fit models used. Copyright © 2013 John Wiley & Sons, Ltd.     

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala–Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono‐ and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2‐TZVP and CCSD(T)/aug‐cc‐pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI‐)DFT, (RI‐)MP2, and SCS‐MP2, were referenced. It was shown that deviations of 3–5 kcal mol^?1 (translating to 2–3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave‐function methods, both MP2 and SCS‐MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06‐2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave‐function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.     

Multi‐Pathway Excited State Relaxation of Adenine Oligomers in Aqueous Solution: A Joint Theoretical and Experimental Study

The singlet excited states of adenine oligomers, model systems widely used for the understanding of the interaction of ultraviolet radiation with DNA, are investigated by fluorescence spectroscopy and time‐dependent (TD) DFT calculations. Fluorescence decays, fluorescence anisotropy decays, and time‐resolved fluorescence spectra are recorded from the femtosecond to the nanosecond timescales for single strand (dA)₂₀ in aqueous solution. These experimental observations and, in particular, the comparison of the fluorescence behavior upon UVC and UVA excitation allow the identification of various types of electronic transitions with different energy and polarization. Calculations performed for up to five stacked 9‐methyladenines, taking into account the solvent, show that different excited states are responsible for the absorption in the UVC and UVA spectral domains. Independently of the number of bases, bright excitons may evolve toward two types of excited dimers having π–π* or charge‐transfer character, each one distinguished by its own geometry and spectroscopic signature. According to the picture arising from the joint experimental and theoretical investigation, UVC‐induced fluorescence contains contribution from 1) exciton states with a different degree of localization, decaying within a few ps, 2) “neutral” excited dimers decaying on the sub‐nanosecond timescale, being the dominant species, and 3) charge‐transfer states decaying on the nanosecond timescale. The majority of the photons emitted upon UVA excitation are related to charge‐transfer states.     

Adatom Defect Induced Spin Polarization of Asymmetric Structures

The spin polarization of carbon nanomaterials is crucial to design spintronic devices. In this paper, the first-principles is used to study the electronic properties of two defect asymmetric structures, Cap-(9, 0)-Def [6, 6] and Cap-(9, 0)-Def [5, 6]. We found that the ground state of Cap-(9, 0)-Def [6, 6] is sextet and the ground state of Cap-(9, 0)-Def [5, 6] is quartet, and the former has a lower energy. In addition, compared with Cap-(9, 0) CNTs, the C adatom on C₃₀ causes spin polarization phenomenon and Cap-(9, 0)-Def [6, 6] has more spin electrons than Cap-(9, 0)-Def [5, 6] structure. Moreover, different adsorb defects reveal different electron accumulation. This finding shows that spin polarization of the asymmetric structure can be adjusted by introducing adatom defects.     

How to Predict Excited State Geometry by Using Empirical Parameters Obtained from Franck-Condon Analysis of Optical Spectrum

Excited state geometries of molecules can be calculated with highly reliable wavefunction schemes. Most of such schemes, however, are applicable to small molecules and can hardly be viewed as error-free for excited state geometries. In this study, a theoretical approach is presented in which the excited state geometries of molecules can be predicted by using vibrationally resolved experimental absorption spectrum in combination with the theoretical modelling of vibrational pattern based on Franck-Condon approximation. Huang-Rhys factors have been empirically determined and used as input for revealing the structural changes occurring between the ground and the excited state geometries upon photoexcitation. Naphthalene molecule has been chosen as a test case to show the robustness of the proposed theoretical approach. Predicted 1B_2u excited state geometry of the naphthalene has similar but slightly different bond length alternation pattern when compared with the geometries calculated with CIS, B3LYP, and CC2 methods. Excited state geometries of perylene and pyrene molecules are also determined with the presented theoretical approach. This powerful method can be applied to other molecules and specifically to relatively large molecules rather easily as long as vibrationally resolved experimental spectra are available to use.     

Reduction of Dimerization Tendency Due to the Decrease in Hybridization Index by Inclusion of 4s and 4p Semicore States as Valence States in Mon (n=2-18) Clusters: A First-Principles Study

Owing to the unique structural, electronic, and physico-chemical properties, molybdenum clusters are expected to play an important role in future nanotechnologies. However, their ground states are still under debate. In this study, the crystal structure analysis by particle swarm optimization (CALYPSO) approach is used for the global minimum search, which is followed by first-principles calculations, to detect an obvious dimerization tendency in Mo\begin{document}$ _n $\end{document} (\begin{document}$ n $\end{document} = 2\begin{document}$ - $\end{document}18) clusters when the 4s and 4p semicore states are not regarded as the valence states. Further, the clusters with even number of atoms are usually magic clusters with high stability. However, after including the 4s and 4p electrons as valence electrons, the dimerization tendency exhibits a drastic reduction because the average hybridization indices \begin{document}$ H_{ \rm{sp}} $\end{document}, \begin{document}$ H_{ \rm{sd}} $\end{document}, and \begin{document}$ H_{ \rm{pd}} $\end{document} are reduced significantly. Overall, this work reports new ground states of Mo\begin{document}$ _n $\end{document} (\begin{document}$ n $\end{document} = 11, 14, 15) clusters and proves that semicore states are essential for Mo\begin{document}$ _n $\end{document}     

Tuning protonation states of tripelennamine antihistamines by cucurbit[7]uril

The formation of host–guest complexes of cucurbit[7]uril (CB7) with the antihistamine drug tripelennamine (TRP) was studied by optical and NMR spectroscopy. The experimental and computational results are consistent with inclusion of a single TRP molecule in CB7. Addition of CB7 has tuned drug protonation states associated with (de)protonation of the ethyldimethylammonium and exocyclic nitrogens with an increase in the associated pK_a values by 1.5 and 2.5 units, respectively. The incorporation of antihistamines drugs such as TRP in cucurbiturils could be utilized for switching their capability for selective binding to histamine H₁‐receptors, in the future. Copyright © 2015 John Wiley & Sons, Ltd.     

Quantum Zeno dynamics in atoms and cavities

Quantum Zeno Dynamics restricts the evolution of a system in a tailorable subspace of the Hilbert space by repeated measurements of a proper observable. This restricted dynamics can be counterintuitive and lead to the generation of interesting nonclassical states. We describe an experiment implementing the Zeno dynamics in an atomic Rydberg level manifold, and we propose an implementation in the cavity quantum electrodynamics context. Both systems open promising perspectives for quantum-enabled metrology and decoherence studies.     

Topological nature of in‐gap bound states in disordered large‐gap monolayer transition metal dichalcogenides

We propose a physical model based on disordered (a hole punched inside a material) monolayer transition metal dichalcogenides (TMDs) to demonstrate a large‐gap quantum valley Hall insulator. We find an emergence of bound states lying inside the bulk gap of the TMDs. They are strongly affected by spin–valley coupling, rest‐ and kinetic‐mass terms and the hole size. In addition, in the whole range of the hole size, at least two in‐gap bound states with opposite angular momentum, circulating around the edge of the hole, exist.Their topological insulator (TI) feature is analyzed by the Chern number, characterized by spacial distribution of their probabilities and confirmed by energy dispersion curves (energy vs. angular momentum). It not only sheds light on overcoming low‐temperature operating limitation of existing narrow‐gap TIs, but also opens an opportunity to realize valley‐ and spin‐qubits. (© 2016 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)