Houghtonmorsing7412

In this work, we studied, using computational methods, the protonation reactions of telomeric DNA fragments being due to interaction with carboxylated carbon nanotubes. The applied computational methodology is divided into two stages. (i) Using classical molecular dynamics, we generated states in which carboxyl groups are brought to the vicinity of nitrogen atoms within the cytosine rings belonging to the DNA duplex. (ii) From these states, we selected two systems for systematic quantum chemical studies aimed at the analysis of proton-transfer reactions between the carboxyl groups and nitrogen atoms within the cytosine rings. Results of molecular dynamics calculations led to the conclusion that sidewall-functionalized carbon nanotubes deliver carboxyl groups slightly more effectively than the on-tip-functionalized ones. The latter can provide carboxyl groups in various arrangements and more diverse quality of approach of carboxyl groups to the cytosines; however, the differences between various arrangements of carboxyl groups are still not big. It was generally observed that narrow nanotubes can access the cytosine pocket easier than wider ones. Quantum chemical calculations led however to the conclusion that a direct proton transfer from the carboxyl group to the nitrogen atom within the cytosine ring is impossible under normal conditions. Precisely, we detected either very high activation barrier for the proton-transfer reaction or instability of the reaction product, i.e., its spontaneous decomposition toward reaction substrates.In this paper, we report the synthesis of two new derivatives, bis(3-(3-(trifluoromethyl)-1H-1,2,4-triazol-5-yl)-4,4'-azo- and -azoxyfurazans by selective oxidation of 4-(3-(trifluoromethyl)-1H-1,2,4-triazol-5-yl)-1,2,5-oxadiazol-3-amine. Ammonium salts of these derivatives were prepared, and all of them were fully characterized by multinuclear NMR, FTIR spectroscopy, elemental analysis, differential scanning calorimetry (DSC), and single-crystal X-ray diffraction. All of the new compounds have high measured crystal densities, and the energetic properties have been investigated.Nonradiative energy transfer (NRET) under light-matter strong coupling interaction provides an efficient method to achieve the ultralong-distance and ultrafast energy transfer, which is of significance in realizing remote control chemistry and the real-time dynamic research of biological macromolecules interaction and so on. Here we show that not only can the cavity mode first resonate with the donor to form a cascade hybrid light-matter states to drive energy transfer, when the cavity mode first resonates with the acceptor, it also can enhance the nonradiative energy transfer between the donor and the acceptor. Importantly, although these two strong coupling systems can enhance energy transfer, the polariton-mediated energy transfer mechanism behind these processes is different. By employing the quantum Tavis-Cummings theory, we calculate the time evolution of the mean photon number of each polariton state to analyze the energy transfer effect under different strongly coupled states.We have explored the use of range separation as a possible avenue for further improvement on our revDSD minimally empirical double hybrid functionals. Such ωDSD functionals encompass the XYG3 type of double hybrid (i.e., xDSD) as a special case for ω → 0. As in our previous studies, the large and chemically diverse GMTKN55 benchmark suite was used for evaluation. Especially when using the D4 rather than D3BJ dispersion model, xDSD has a slight performance advantage in WTMAD2. As in previous studies, PBEP86 is the winning combination for the semilocal parts. xDSDn-PBEP86-D4 marginally outperforms the previous "best in class" ωB97M(2) Berkeley double hybrid but without range separation and using fewer than half the number of empirical parameters. Range separation turns out to offer only marginal further improvements on GMTKN55 itself. While ωB97M(2) still yields better performance for small-molecule thermochemistry, this is compensated in WTMAD2 by the superior performance of the new functionals for conformer equilibria. Results for two external test sets with pronounced static correlation effects may indicate that range-separated double hybrids are more resilient to such effects.Fourteen new eudesmane sesquiterpenoids (1, 3-5, 7-16) and seven known analogues were isolated from the whole plant of Artemisia hedinii. Their structures were elucidated by spectroscopic data analysis and comparison with published NMR data, and their absolute configurations were confirmed by X-ray diffraction experiments and TDDFT ECD calculation. Compounds 1-15 were identified as eudesmane acids, which represent a kind of lactone ring-opening eudesmane-type sesquiterpenes with an acetoxyl or a hydroxy group attached to C-9. Compounds 1 and 2, 5 and 6, and 7 and 8 are three pairs of epimers isomerized at C-3, C-5, and C-11, respectively. GSK1016790A Compounds 1-9, 11-13, 15-19, and 21 could influence the proinflammatory phenotype of the M1 macrophage. Among them, compounds 5, 8, 9, 12, 16, and 19 consistently exhibited anti-inflammatory effects, as evidenced by downregulating classic pro-inflammatory cytokines TNF-α, IL-12, IL-6, and IFN-γ in LPS-induced primary bone marrow derived M1 macrophages.Nonstandard amino acids are both abundant in nature, where they play a key role in various cellular processes, and can be synthesized in laboratories, for example, for the manufacture of a range of pharmaceutical agents. In this work, we have extended the additive all-atom CHARMM36 and CHARMM General force field (CGenFF) to a large set of 333 nonstandard amino acids. These include both amino acids with nonstandard side chains, such as post-translationally modified and artificial amino acids, as well as amino acids with modified backbone groups, such as chromophores composed of several amino acids. Model compounds representative of the nonstandard amino acids were parametrized for protonation states that are likely at the physiological pH of 7 and, for some more common residues, in both d- and l-stereoisomers. Considering all protonation, tautomeric, and stereoisomeric forms, a total of 406 nonstandard amino acids were parametrized. Emphasis was placed on the quality of both intra- and intermolecular parameters. Partial charges were derived using quantum mechanical (QM) data on model compound dipole moments, electrostatic potentials, and interactions with water. Optimization of all intramolecular parameters, including torsion angle parameters, was performed against information from QM adiabatic potential energy surface (PES) scans. Special emphasis was put on the quality of terms corresponding to PES around rotatable dihedral angles. Validation of the force field was based on molecular dynamics simulations of 20 protein complexes containing different nonstandard amino acids. Overall, the presented parameters will allow for computational studies of a wide range of proteins containing nonstandard amino acids, including natural and artificial residues.Hsp70s are among the most highly conserved proteins in all of biology. Through an iterative binding and release of exposed hydrophobic residues on client proteins, Hsp70s can prevent aggregation and promote folding to the native state of their client proteins. The human proteome contains eight canonical Hsp70s. Because Hsp70s are relatively promiscuous they play a role in folding a large proportion of the proteome. Hsp70s are implicated in disease through their ability to regulate protein homeostasis. In recent years, researchers have attempted to develop selective inhibitors of Hsp70 isoforms to better understand the role of individual isoforms in biology and as potential therapeutics. Selective inhibitors have come from rational design, forced localization, and serendipity, but the development of completely selective inhibitors remains elusive. In the present review, we discuss the Hsp70 structure and function, the known Hsp70 client proteins, the role of Hsp70s in disease, and current efforts to discover Hsp70 modulators.The effects of fatty acid type (myristic, palmitic, stearic, oleic, linoleic, and linolenic acid) on the characteristics of starch-lipid complexes under high temperature were investigated. Fatty acids with a shorter carbon chain or a greater number of double bonds contributed to the formation of V-type starch-lipid complexes. The thermostability of starch-unsaturated fatty acid (UFA) complexes prepared at high temperature was increased compared with those obtained at lower temperature. Resistant starch (RS) contents and melting temperatures had a strong significant positive correlation. Complexes with better thermostability were more resistant to enzymatic hydrolysis. Among them, the starch-stearic acid complexes possessed the highest RS content. The paste of starch-linolenic acid complexes had the lowest internal friction and the strongest thixotropy. The broken of double bonds in UFAs probably accounted for the increased starch-lipid complexes. The crystalline, thermal, rheological, and digestion properties of samples treated at high temperature were significantly affected.The A-type Aurora kinase is upregulated in many human cancers, and it stabilizes MYC-family oncoproteins, which have long been considered an undruggable target. Here, we describe the design and synthesis of a series of pyrimidine-based derivatives able to inhibit Aurora A kinase activity and reduce levels of cMYC and MYCN. Through structure-based drug design of a small molecule that induces the DFG-out conformation of Aurora A kinase, lead compound 13 was identified, which potently (IC50 80% tumor regression of NCI-H446 SCLC xenograft tumors in mice. These results support the potential of 25 for the treatment of MYC-amplified cancers including SCLC.The evolution of local atomic configuration and macroscopic electrical properties of KNbO3 is investigated in detail using ab initio molecular dynamics simulations within the framework of density functional theory. By analyzing the local off-center displacements of K and Nb atoms, the presence of the crossover of displacive and order-disorder mechanisms in the NbO6 octahedron due to orbital hybridization is found, whereas the K is a completely displacive type due to the nonoriented ionic K-O bond. Besides, the order-disorder behavior of Nb atoms is enhanced with the increase in temperature, especially undergoing the phase transition. The predicted high dielectric constant of KNbO3 confirms the key role of the Nb's order-disorder behavior. We discover that the anomalous increase in dielectric constant in the vicinity of the phase boundary is not only from the transformation of the polarized direction but also from the enhancement of order-disorder contribution in the nonpolarized direction. The high dielectric constant with large spontaneous polarization boosts the piezoelectricity at the orthorhombic-tetragonal phase boundary of 500 K, giving rise to the nearly 100% increase than that of 300 K. A rebonding model is developed to illustrate the origin of high piezoelectricity around the tetragonal ferroelectric phase boundary, and the significance of introducing a tetragonal structure is emphasized for developing high piezoelectricity in the inorganic perovskite ferroelectrics.