Ever since the discovery of carbon nanotubes (CNTs), many groups have endeavored to understand the fundamental properties of the CNTs. The redox properties (i.e. electronic densities, the Fermi levels, redox potentials) of single-walled carbon nanotubes (SWNTs) are related to the structures of SWNTs that have a specified diameter and chirality angle uniquely related to a pair of integers (n,m); the so-called chiral indices. [1,2] Many attempts have been made to determine the electronic properties of SWNTs using scanning tunneling spectroscopy, [3] redox titrimetry, [4] photoluminescence (PL) measurements, [5][6][7] and spectroelectrochemistry; [8][9][10][11][12][13] however, the success in the determination of the redox properties as already reported has been low. Recently, Paolucci et al. [12] employed Vis-near-IR absorption spectroelectrochemistry to estimate the redox potentials of the SWNTs dissolved in an ultradry dimethylsulfoxide (DMSO) solution; however, it is not easy to determine the redox potentials of isolated (n,m)SWNTs using this method because SWNTs with several different chiral indices have band gaps in the near-IR region that overlap one another. We now describe a simple method for the determination of the redox potentials of many (in this study, fifteen) individual (n,m)SWNTs using near-IR PL spectroelectrochemistry in an aqueous medium.Strategic approaches toward the solubilization of CNTs are essential for many applications of CNTs [14] and numerous dispersants including carboxymethylcellulose sodium salt (CMC, Figure S1a in the Supporting Information) [15] have been used to individually dissolve SWNTs. In this study, we fabricated a non-fluorescent transparent indium tin oxide (ITO) electrode modified with a cast film of CMC/poly-(diallyldimethylammonium chloride) (PDDA; Figure S1b in the Supporting Information) that contained isolated SWNTs (for details, see Experimental Section in the Supporting Information).We have discovered that we can determine the redox potentials of isolated SWNTs having their own chirality indices by in situ near-IR PL spectroelectrochemistry at the fabricated modified ITO electrode. This modified film retains the isolated SWNTs and the spectroelectrochemical results are analyzed with the Nernst equation.Externally applied potentials were changed in the range of ) and oxidized form (SWNT n+ ) when the external potential was applied to the electrode in arbitrary steps from 0.0 V to À1.0 V and from 0.0 V to + 1.1 V, respectively. After each potential step, the applied potential was returned to 0.0 V and it was confirmed that no significant spectral change in the SWNT had occurred, namely, the SWNTs in the film are stable during these electrochemically driven redox processes. This behavior of the SWNTs is consistent with those in Visnear-IR absorption [8b] and Raman [10b] spectroelectrochemical studies.We carried out in situ near-IR absorption spectroelectrochemistry using the modified electrode. The near-IR absorption spectra of the individually solubilized SWNTs wer...

Ecdysteroids are the principal steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis encoded by Halloween genes were identified and genetically and biochemically characterized. However, the tertiary structures of these proteins have not yet been characterized. Here, we report the results of an integrated series of in silico, in vitro, and in vivo analyses of the Halloween GST protein Noppera-bo (Nobo). We determined crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with GSH and 17β-estradiol, a DmNobo inhibitor. 17β-Estradiol almost fully occupied the putative ligand-binding pocket and a prominent hydrogen bond formed between 17β-estradiol and Asp-113 of DmNobo. We found that Asp-113 is essential for 17β-estradiol–mediated inhibition of DmNobo enzymatic activity, as 17β-estradiol did not inhibit and physically interacted less with the D113A DmNobo variant. Asp-113 is highly conserved among Nobo proteins, but not among other GSTs, implying that this residue is important for endogenous Nobo function. Indeed, a homozygous nobo allele with the D113A substitution exhibited embryonic lethality and an undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue that appears to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. To the best of our knowledge, ours is the first study describing the structural characteristics of insect steroidogenic Halloween proteins. Our findings provide insights relevant for applied entomology to develop insecticides that specifically inhibit ecdysteroid biosynthesis.

COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID: 7BV2 ) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A’ base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.

The isotopologs of liquid water, HO, DO, and TO, are studied systematically by first principles PIMD simulations, in which the whole entity of the electrons and nuclei are treated quantum mechanically. The simulation results are in reasonable agreement with available experimental data on isotope effects, in particular, on the peak shift in the radial distributions of HO and DO and the shift in the evaporation energies. It is found that, due to differences in nuclear quantum effects, the H atoms in the OH bonds more easily access the dissociative region up to the hydrogen bond center than the D (T) atoms in the OD (OT) bonds. The accuracy and limitation in the use of the current density-functional-theory-based first principles PIMD simulations are also discussed. It is argued that the inclusion of the dispersion correction or relevant improvements in the density functionals are required for the quantitative estimation of isotope effects.

Here, we have constructed neural network-based models that predict atomic partial charges with high accuracy at low computational cost. The models were trained using high-quality data acquired from quantum mechanics calculations using the fragment molecular orbital method. We have succeeded in obtaining highly accurate atomic partial charges for three representative molecular systems of proteins, including one large biomolecule (approx. 2000 atoms). The novelty of our approach is the ability to take into account the electronic polarization in the system, which is a system-dependent phenomenon, being important in the field of drug design. Our high-precision models are useful for the prediction of atomic partial charges and expected to be widely applicable in structure-based drug designs such as structural optimization, high-speed and high-precision docking, and molecular dynamics calculations.

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