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https://www.readbyqxmd.com/read/29906110/effect-of-dna-environment-on-electronically-excited-states-of-methylene-blue-evaluated-by-a-three-layered-qm-qm-mm-oniom-scheme
#1
Juan José Nogueira, Sven Rossbach, Christian Ochsenfeld, Leticia Gonzalez
Interactions between chromophores and biological environments may alter the electronic properties of the chromophores. A three-layered QM/QM/MM ONIOM scheme with electrostatic embedding is implemented to investigate the influence of an additional QM layer on excited-state calculations with respect to a standard QM/MM description. The implemented ONIOM scheme is employed to compute the electronic excitations of the photosensitizer methylene blue interacting with a solvated DNA double strand. It is shown that the additional quantum mechanical description of several nucleobases in the vertical energy calculations induces energy shifts in the excited states of methylene blue, compared to the energies of a traditional QM/MM scheme, where the solvated double strand is described fully classically...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29903053/detection-of-cd22-expression-in-living-cancer-cells-by-semiconductor-quantum-dots
#2
Meijiao Zhang, Shizhu Zang, Guangbo Ge, Lingling Jin, Yi Xin, Huizhen Li, Pingkun Liu, Xudong Hou, Dacheng Hao, Lu Chen, Qi Zhou, Jie Hou
CD22 is an important drug target for the treatment of autoimmune diseases and B cell-derived malignancies. In this study, N-acetylneuraminic acid functionalized quantum dots nanoconjugate was synthesized and used for targeting and fluorescence imaging of CD22 on living cells. The nanoprobe was prepared by conjugating N-acetylneuraminic acid (NANA) on the carboxyl groups modified CdSe/ZnS quantum dots (COOH-QDs) via NHS/EDC mediated esterification. The NANA-QDs nanoprobe showed excellent size distribution, very low cytotoxicity and super fluorescent properties for biological imaging applications...
August 1, 2018: Journal of Biomedical Nanotechnology
https://www.readbyqxmd.com/read/29899961/azobenzene-as-a-photoregulator-covalently-attached-to-rna-a-quantum-mechanics-molecular-mechanics-surface-hopping-dynamics-study
#3
Padmabati Mondal, Giovanni Granucci, Dominique Rastädter, Maurizio Persico, Irene Burghardt
The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker...
May 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29896881/polymer-dots-as-effective-phototheranostic-agents
#4
Liang Guo, Jiechao Ge, Pengfei Wang
Conjugated polymer dots (Pdots, also named polymer nanoparticles, PNPs), which consist of π-conjugated organic polymers, are novel organic nanomaterials with size in the range of 1-100 nm. Compared with traditional organic small molecules, semiconductor quantum dots, and inorganic nanomaterials, the Pdots exhibit significant potential applications in biological imaging, sensing and detection, drug delivery, and theranostics, due to their advantages of special optical properties, diverse structure, easy surface modification, and good biocompatibility...
June 13, 2018: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/29895843/terahertz-and-infrared-characteristic-absorption-spectra-of-aqueous-glucose-and-fructose-solutions
#5
Chao Song, Wen-Hui Fan, Ling Ding, Xu Chen, Ze-You Chen, Kai Wang
In this paper, the terahertz (THz) and infrared (IR) characteristic absorption spectra of aqueous glucose solutions and aqueous fructose solutions with different concentrations were measured and studied. The absorption spectra of these two molecules in solid-state and in aqueous solutions were compared and analyzed, the significant effect of molecular adjacent environment on the molecular structure and vibrational mode was revealed. In addition, the THz and IR absorption spectra of these two isomers' aqueous solutions were also compared and explored...
June 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29893898/an-intricate-balance-of-hydrogen-bonding-ion-atmosphere-and-dynamics-facilitates-a-seamless-uracil-to-cytosine-substitution-in-the-u-turn-of-the-neomycin-sensing-riboswitch
#6
Miroslav Krepl, Jennifer Vögele, Holger Kruse, Elke Duchardt-Ferner, Jens Wöhnert, Jiri Sponer
The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop-a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect...
June 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29893479/design-synthesis-and-biological-evaluation-of-tetrahydro-%C3%AE-carboline-derivatives-as-selective-sub-nanomolar-gelatinase-inhibitors
#7
Giuseppe Felice Mangiatordi, Tatiana Guzzo, Eugenio Claudio Rossano, Daniela Trisciuzzi, Domenico Alberga, Giovanni Fasciglione, Massimiliano Coletta, Alessandra Topai, Orazio Nicolotti
Targeting matrix metalloproteinases (MMPs) is a pursued strategy for treating several pathological conditions, such as multiple sclerosis and cancer. Herein, a series of novel tetrahydro-β-carboline derivatives with outstanding inhibitory activity toward MMPs are present. In particular, compounds 9 f, 9 g, 9 h and 9 i show sub-nanomolar IC50 values. Interestingly, compounds 9 g and 9 i also provide remarkable selectivity toward gelatinases; IC50 =0.15 nm for both toward MMP-2 and IC50 =0.63 and 0...
June 12, 2018: ChemMedChem
https://www.readbyqxmd.com/read/29891705/microscale-optoelectronic-infrared-to-visible-upconversion-devices-and-their-use-as-injectable-light-sources
#8
He Ding, Lihui Lu, Zhao Shi, Dan Wang, Lizhu Li, Xichen Li, Yuqi Ren, Changbo Liu, Dali Cheng, Hoyeon Kim, Noel C Giebink, Xiaohui Wang, Lan Yin, Lingyun Zhao, Minmin Luo, Xing Sheng
Optical upconversion that converts infrared light into visible light is of significant interest for broad applications in biomedicine, imaging, and displays. Conventional upconversion materials rely on nonlinear light-matter interactions, exhibit incidence-dependent efficiencies, and require high-power excitation. We report an infrared-to-visible upconversion strategy based on fully integrated microscale optoelectronic devices. These thin-film, ultraminiaturized devices realize near-infrared (∼810 nm) to visible [630 nm (red) or 590 nm (yellow)] upconversion that is linearly dependent on incoherent, low-power excitation, with a quantum yield of ∼1...
June 11, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29883087/the-competition-of-charge-and-energy-transfer-processes-in-donor-acceptor-fluorescence-pairs-calibrating-the-spectroscopic-ruler
#9
Pavel Moroz, Zhicheng Jin, Yuya Sugiyama, D'Andree Lara, Natalia Razgoniaeva, Mingrui Yang, Natalia Kholmicheva, Dmitriy Khon, Hedi Mattoussi, Mikhail Zamkov
Sensing strategies utilizing Fӧrster resonance energy transfer (FRET) are widely used for probing biological phenomena. FRET sensitivity to the donor-acceptor distance makes it ideal for measuring the concentration of a known analyte or determining the spatial separation between fluorescent labels in a macromolecular assembly. The difficulty lies in extracting the FRET efficiency from the acceptor-induced quenching of the donor emission, which may contain a significant non-FRET contribution. Here, we demonstrate a general spectroscopic approach for differentiating between charge transfer (CT) and energy transfer (ET) processes in donor-acceptor assemblies and apply the developed method for unraveling the FRET/non-FRET contributions in cyanine dye-semiconductor quantum dot (QD) constructs...
June 8, 2018: ACS Nano
https://www.readbyqxmd.com/read/29870227/ru-ii-polypyridyl-complexes-derived-from-tetradentate-ancillary-ligands-for-effective-photocaging
#10
Ao Li, Claudia Turro, Jeremy J Kodanko
Metal complexes have many proven applications in the caging and photochemical release of biologically active compounds. Photocaging groups derived from Ru(II) traditionally have been composed of ancillary ligands that are planar and bi- or tridentate, such as 2,2'-bipyridine (bpy), 2,2':6',2″-terpyridine (tpy), and 1,10-phenanthroline (phen). Complexes bearing ancillary ligands with denticities higher than three represent a new class of Ru(II)-based photocaging groups that are grossly underdeveloped. Because high-denticity ancillary ligands provide the ability to increase the structural rigidity and control the stereochemistry, our groups initiated a research program to explore the applications of such ligands in Ru(II)-based photocaging...
June 5, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29869424/recent-progress-in-macromolecule-anchored-hybrid-gold-nanomaterials-for-biomedical-applications
#11
REVIEW
Zheng Luo, Yang Xu, Enyi Ye, Zibiao Li, Yun-Long Wu
Gold nanoparticles (AuNPs), with elegant thermal, optical, or chemical properties due to quantum size effects, may serve as unique species for therapeutic or diagnostic applications. It is worth mentioning that their small size also results in high surface activity, leading to significantly impaired stability, which greatly hinders their biomedical utilizations. To overcome this problem, various types of macromolecular materials are utilized to anchor AuNPs so as to achieve advanced synergistic effect by dispersing, protecting, and stabilizing the AuNPs in polymeric-Au hybrid self-assemblies...
June 4, 2018: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/29852215/mpa-modified-cdte-quantum-dots-increased-interleukin-1beta-secretion-through-myd88-dependent-toll-like-receptor-pathway-and-nlrp3-inflammasome-activation-in-microglia
#12
Tianshu Wu, Xue Liang, Keyu He, Tingting Wei, Yan Wang, Jie Lu, Ying Yao, Ting Zhang, Yuying Xue, Meng Tang
The excellent optical properties of CdTe quantum dots (QDs) make researchers realize their value on the application of biomedicine, especially neuroscience, as an advanced fluorescent probe. Thus, it is important to evaluate the biosafety of CdTe QDs on the central nervous system (CNS). Our previous studies have conducted a systematic biosafety evaluation of CdTe QDs on the CNS and found several toxic endpoints, one of which is the inflammation on the rat hippocampus, but their underlying mechanism remains unclear...
May 28, 2018: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29848976/synthesis-crystal-structure-and-biological-activity-of-ethyl-4-methyl-2-2-dioxo-1-h-2%C3%AE-%C3%A2-1-benzothiazine-3-carboxylate-polymorphic-forms
#13
Igor V Ukrainets, Anna A Burian, Vyacheslav N Baumer, Svitlana V Shishkina, Lyudmila V Sidorenko, Igor A Tugaibei, Natali I Voloshchuk, Pavlo S Bondarenko
Continuing the search for new potential analgesics among the derivatives of 4-methyl-2,2-dioxo-1 H -2λ⁶,1-benzothiazine-3-carboxylic acid, the possibility of obtaining its esters by the alkylation of the corresponding sodium salt with iodoethane in dimethyl sulfoxide (DMSO) at room temperature was studied. It was found that under such conditions, together with the oxygen atom of the carboxyl group, a heteroatom of nitrogen is also alkylated. Therefore, the product of the reaction studied is a mixture of ethyl 4-methyl-2,2-dioxo-1 H -2λ⁶,1-benzothiazine-3-carboxylate (major) and its 1-ethyl-substituted analog (minor)...
May 30, 2018: Scientia Pharmaceutica
https://www.readbyqxmd.com/read/29846758/embryotoxicity-of-quantum-dots-in-rainbow-trout-oncorhynchus-mykiss-during-the-hatching-period
#14
Živilė Jurgelėnė, Nijolė Kazlauskienė, Danguolė Montvydienė, Vytautas Kulvietis, Ričardas Rotomskis, Kęstutis Jokšas
Due to the active development and application of nanotechnology, nanoparticles have emerged as a new class of environmental pollutants. The aim of the study was to investigate quantum dots (QDs) access routes and distribution in embryos and larvae of rainbow trout Oncorhynchus mykiss and to determine the toxicity of QDs to rainbow trout larvae depending on the duration of exposure. CdSe/ZnS-COOH QDs at sublethal concentration was used during the toxicity test (1, 4 and 14 days). The results showed that QDs could get from the solutions into the larvae after hatching...
May 30, 2018: Bulletin of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/29846368/photodynamic-properties-of-aza-analogues-of-phthalocyanines
#15
Miroslav Miletin, Petr Zimcik, Veronika Novakova
The replacement of benzene rings in phthalocyanines with various N-heterocycles produces a number of aza-analogues, azaphthalocyanines. This review summarizes their properties important for photodynamic therapy with a focus on (but not limited to) the most studied derivatives, i.e. tetrapyrazinoporphyrazines, tetra(2,3-pyrido)porphyrazines and tetra(3,4-pyrido)porphyrazines. Specifically, the spectral properties in both organic and aqueous solutions are discussed, with an emphasis on the prevention of undesirable aggregation, which typically leads to a loss of the photodynamic effects...
May 30, 2018: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/29808860/a-photoelectron-imaging-and-quantum-chemistry-study-of-the-deprotonated-indole-anion
#16
Michael A Parkes, Jonathan Crellin, Alice Henley, Helen H Fielding
Indole is an important molecular motif in many biological molecules and exists in its deprotonated anionic form in the cyan fluorescent protein, an analogue of green fluorescent protein. However, the electronic structure of the deprotonated indole anion has been relatively unexplored. Here, we use a combination of anion photoelectron velocity-map imaging measurements and quantum chemistry calculations to probe the electronic structure of the deprotonated indole anion. We report vertical detachment energies (VDEs) of 2...
June 6, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29808823/highly-stable-and-water-soluble-monodisperse-silica-coated-all-inorganic-halide-perovskite-nanocomposites-and-its-applications-in-white-led-and-cells-imaging
#17
Nan Ding, Donglei Zhou, Xueke Sun, Wen Xu, Hongwei Xu, Gencai Pan, Dongyu Li, Shuang Zhang, Biao Dong, Hongwei Song
In spite of the excellent optical properties of all-inorganic halide perovskite quantum dots (PQDs), they still suffer from the inherent poor stability even exposed to atmosphere moisture, restricted their applications, especially in White-LED and cells imaging. Here, we proposed a strategy by encapsulating the CsPbX3 (X=Cl, Br, I) PQDs into silica nanoplates to prepare highly stable and water-soluble CsPbX3/SiO2 nanocomposites. First, the 120 nm monodisperse CsPbX3/SiO2 nanocomposites inlayed with several CsPbX3 PQDs were fabricated via the modified Stöber method...
May 29, 2018: Nanotechnology
https://www.readbyqxmd.com/read/29802794/using-the-relative-energy-gradient-method-with-interacting-quantum-atoms-to-determine-the-reaction-mechanism-and-catalytic-effects-in-the-peptide-hydrolysis-in-hiv-1-protease
#18
Joseph Thacker, Mark Vincent, Paul Popelier
The reaction mechanism in an active site is of the utmost importance when trying to understand the role that an enzyme plays in biological processes. In a recently published paper [Theor.Chem.Acc., 136, 86 (2017)], we formalised the Relative Energy Gradient (REG) method for automating an Interacting Quantum Atoms (IQA) analysis. Here the REG method is utilised to determine the mechanism of peptide hydrolysis in the aspartic active site of the enzyme HIV-1 Protease. Using the REG method along with the IQA approach we determine the mechanism of peptide hydrolysis without employing any arbitrary parameters and with remarkable ease (albeit at large computational cost: the system contains 133 atoms, which means that there are 17,689 individual IQA terms to be calculated)...
May 26, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29802335/sorting-five-human-tumor-types-reveals-specific-biomarkers-and-background-classification-genes
#19
Kimberly E Roche, Marvin Weinstein, Leland J Dunwoodie, William L Poehlman, Frank A Feltus
We applied two state-of-the-art, knowledge independent data-mining methods - Dynamic Quantum Clustering (DQC) and t-Distributed Stochastic Neighbor Embedding (t-SNE) - to data from The Cancer Genome Atlas (TCGA). We showed that the RNA expression patterns for a mixture of 2,016 samples from five tumor types can sort the tumors into groups enriched for relevant annotations including tumor type, gender, tumor stage, and ethnicity. DQC feature selection analysis discovered 48 core biomarker transcripts that clustered tumors by tumor type...
May 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29800890/investigation-of-structural-electronic-properties-and-docking-calculations-of-some-boron-complexes-with-norfloxacin-a-computational-research
#20
Koray Sayin, Duran Karakaş
Quantum chemical calculations are performed over BF2 R (1), B(NO)2 R (2), B(CN)2 R (3) and B(CH3 )2 R (4) [R: 1-ethyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylate]. Mentioned boron complex with fluorine atoms which is BF2 R are optimized at HF/6-31+G(d), B3LYP/6-31+G(d) and M062X/6-31+G(d) level and the best level is determined by comparison of experimental and calculated results. The best calculation level is determined as M06-2X/6-31+G(d) level. The other complexes are optimized at this level...
September 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
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