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Systems chemistry

Rakesh Radhakrishnan, Kumaran G Sreejalekshmi
Probing chemical space of luminescent organic materials built on novel cores is highly imperative for its potential to expand the horizons of advanced functional materials. Small organic fluorophores possessing therapeutic traits can contribute to theranostics. We coupled computational and classical synthetic chemistry strategies for the rational design of 5-(hetero-2-yl)-1,3-thiazoles as colour tunable fluorophore core. With the aid of DFT and TD-DFT, we prove multiheterocyclic system built on thiazole-het core with three inherent tunable sites on thiazole (C2, C4 and C5) capable of accommodating panoply of substituents, as a multifunctional molecular materials' platform...
January 15, 2018: Journal of Organic Chemistry
Emanuele Mauri, Edoardo Micotti, Arianna Rossetti, Lucio Melone, Simonetta Papa, Giulia Azzolini, Stefano Rimondo, Pietro Veglianese, Carlo Punta, Filippo Rossi, Alessandro Sacchetti
Polymer functionalization strategies have recently attracted considerable attention for several applications in biomaterials science. In particular, technological advancements in medical imaging have focused on the design of polymeric matrices to improve non-invasive approaches and diagnostic accuracy. In this scenario, the use of microwave irradiation of aqueous solutions containing appropriate combinations of polymers is gaining increasing interest in the synthesis of sterile hydrogels without using monomers, eliminating the need to remove unreacted species...
January 15, 2018: Soft Matter
Hans Jakob Wörner, Christopher A Arrell, Natalie Banerji, Andrea Cannizzo, Majed Chergui, Akshaya K Das, Peter Hamm, Ursula Keller, Peter M Kraus, Elisa Liberatore, Pablo Lopez-Tarifa, Matteo Lucchini, Markus Meuwly, Chris Milne, Jacques-E Moser, Ursula Rothlisberger, Grigory Smolentsev, Joël Teuscher, Jeroen A van Bokhoven, Oliver Wenger
The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer...
November 2017: Structural Dynamics (Melville, N.Y.)
Ashish Tiwari, S J Dhoble
Chemiluminescence (CL) techniques are extensively utilized for detection of analytes due to their high sensitivity, rapidity and selectivity. With the advent of nanotechnology and incorporation of the nanoparticles in the CL system has revolutionized the assays due to their unique optical and mechanical properties. Several CL-based reactions have been developed where these nanoparticle based CL sensors have evolved as excellent prospects for sensing in various analytical applications. This review article addresses the nanoparticles based CL detection system that are recently developed, the mechanisms has been summarized and the role of luminophors have been discussed...
April 1, 2018: Talanta
Shufang Wang, Yongxin Gao, Shigang Shen, Hui Wen, Huaqing Cui
C5-modified uridines are a valuable class of nucleoside analogues, both as potent chemotherapy agents and through their use as the conjunction site in DNA labeling strategies. As an important C5-modified uridine, BrdU has been used in cell proliferation assays since the 1980s. Currently, the detection of BrdU relies on traditional immunostaining; however, this approach has its limitations. Thus, it is desirable, albeit difficult, to develop chemistry methods to fluorescently label BrdU in a cellular context...
January 12, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Dario Neri, Richard A Lerner
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice...
January 12, 2018: Annual Review of Biochemistry
Robin Shannon, David R Glowacki
The chemical master equation is a powerful theoretical tool for analysing the kinetics of complex multi-well potential energy surfaces in a wide range of different domains of chemical kinetics spanning combustion, atmospheric chemistry, gas-surface chemistry, solution phase chemistry, and biochemistry. There are two well-established methodologies for solving the chemical master equation: a stochastic "kinetic Monte Carlo" approach and a matrix-based approach. In principle, the results yielded by both approaches are identical; the decision of which approach is better suited to a particular study depends on the details of the specific system under investigation...
January 12, 2018: Journal of Physical Chemistry. A
Siddharth Sai Matikonda, Jessica M Fairhall, Franziska Fiedler, Suchaya Sanhajariya, Robert A J Tucker, Sarah Hook, Anna L Garden, Allan B Gamble
Bioorthogonal prodrug activation/decaging strategies need to be selective, rapid and release the drug from the masking group upon activation. The rates of the 1,3-dipolar cycloaddition between a trans-cyclooctene (TCO) and a series of fluorine-substituted azido-PABC self-immolative spacers caging two model drugs, and subsequent release from the 1,2,3-triazoline are reported. As the number of fluorine substituents on the PABC linker increases from one to four, the rate of cycloaddition increases by almost one-order of magnitude...
January 12, 2018: Bioconjugate Chemistry
Tong Li, Jian-Guo Zhang
Metal hydrazineboranes (MHBs), as a kind of new hydrogen storage materials, show the excellent hydrogen storage per-formance and the dehydrogenation property. Herein, we designed multiple dehydrogenation pathways to compare with each other and indicated the metal-controlled effect. Quantum chemistry theory is used to calculate the crystal structure for determining the molecular structure. With the increasing of the metal radius, the energy difference of the isomers also increases. The dehydrogenation pathways of Lithium hydrazineborane (PathA) and Sodium hydrazineborane (PathB) show the totally similar to each other in the dehydrogenation process despite the energy barrier, as well as the comparison Path of A' (for LiHB) and B' (for NaHB)...
January 11, 2018: Journal of Physical Chemistry. A
Stefanie A Mewes, Felix Plasser, Anna Krylov, Andreas Dreuw
Benchmarking is an every-day task in computational chemistry, yet making meaningful comparisons between different methods is non-trivial. Benchmark studies often focus on the most obvious quantities such as energy differences. But to gain insight, it is desirable to explain the discrepancies between theoretical methods in terms of underlying wavefunctions and, consequently, physically relevant quantities. We present a new strategy of benchmarking excited-state calculations, which goes beyond excitation energies and oscillator strengths and involves the analysis of exciton properties based on the one-particle transition density matrix...
January 11, 2018: Journal of Chemical Theory and Computation
Iwona Janica, Violetta Patroniak, Paolo Samorì, Artur Ciesielski
During the last two decades dynamic covalent chemistry (DCC) has emerged as an efficient and versatile strategy for the design and synthesis of complex molecular systems in solution. While early examples of supramolecularly assisted covalent synthesis at surfaces relied strongly on kinetically controlled reactions for post-assembly covalent modification, the DCC method takes advantage of the reversible nature of bond formation and allows the generation of the new covalently bonded structures under thermodynamic control...
January 11, 2018: Chemistry, An Asian Journal
Daniela Espinosa-Hoyos, Anna Jagielska, Kimberly A Homan, Huifeng Du, Travis Busbee, Daniel G Anderson, Nicholas X Fang, Jennifer A Lewis, Krystyn J Van Vliet
Myelination is critical for transduction of neuronal signals, neuron survival and normal function of the nervous system. Myelin disorders account for many debilitating neurological diseases such as multiple sclerosis and leukodystrophies. The lack of experimental models and tools to observe and manipulate this process in vitro has constrained progress in understanding and promoting myelination, and ultimately developing effective remyelination therapies. To address this problem, we developed synthetic mimics of neuronal axons, representing key geometric, mechanical, and surface chemistry components of biological axons...
January 11, 2018: Scientific Reports
(no author information available yet)
The Food and Drug Administration (FDA or we) is classifying the reagents for molecular diagnostic instrument test systems into class I (general controls). We are taking this action because we have determined that classifying the device into class I (general controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.
December 27, 2017: Federal Register
Wolfgang Lefèvre
The Méthode de nomenclature chimique, published by the Académie Royale des Sciences in 1787, is rightly praised as a landmark in the history of early modern chemistry. It is also - though less rightly - considered to be a fruit of Lavoisier's Chemical Revolution. In fact, main features of the Méthode's nomenclatural and classificatory proposal rest on fundamental chemical conceptions that were shared by adherents of the phlogistic chemical system as well. After a short presentation of the Méthode's four authors (Berthollet, Fourcroy, Guyton de Morveau, and Lavoisier) and the circumstances of their collaboration, my paper will focus on those features of the Méthode that illuminate decisive achievements of the entire community of eighteenth-century chemists, as well as those features that reveal an unsettled state of many of its convictions...
January 10, 2018: Ambix
Trevor Croft, Christol James Theoga Raj, Michelle Salemi, Brett S Phinney, Su-Ju Lin
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite participating in cellular redox chemistry and signaling, and the complex regulation of NAD+ metabolism is not yet fully understood. To investigate this, we established a NAD+-intermediate specific reporter system to identify factors required for salvage of metabolically-linked nicotinamide (NAM) and nicotinic acid (NA). Mutants lacking components of the NatB complex, NAT3 and MDM20, appeared as hits in this screen. NatB is an Nα-terminal-acetyltransferase responsible for acetylation of the amino terminus of specific Met-retained peptides...
January 9, 2018: Journal of Biological Chemistry
Philip Serwer
The cause and therapy of neurodegenerative diseases remain unsolved puzzles. These diseases are correlated with presence of beta sheet-rich amyloid assemblies. Here, I derive and assemble puzzle pieces to obtain a loose end-tying hypothesis for cause with direct implications for therapy. I use the following extrapolations to find connectable puzzle pieces: (a) the traditional extrapolation that amyloid/amyloid precursors cause disease, (b) a recent extrapolation that amyloid-forming proteins, some of which are virus protein homologs, are components of an empirically obscure innate immune system that counters insults, including those by both viruses and bacteria, (c) a new extrapolation that various insults produce assemblies with structural features in common and that amyloid-forming, innate immune system proteins recognize these features and, then, counter insults by co-assembly, (d, 1) a second new extrapolation that beta sheet is a common structural feature and is extended during insult-neutralizing co-assembly and (d, 2) an appendix, derived from studies of phages T3 and T4, that most insult-produced assemblies are obscure to current biochemical analysis...
January 2018: Medical Hypotheses
Joaquín Calbo, Juan Carlos Sancho-García, Enrique Ortí, Juan Aragó
Understanding how molecular systems self-assemble to form well-organized superstructures governed by noncovalent interactions is essential in the field of supramolecular chemistry. In the nanoscience context, the self-assembly of different carbon-based nanoforms (fullerenes, carbon nanotubes and graphene) with, in general, electron-donor molecular systems, has received increasing attention as a means of generating potential candidates for technological applications. In these carbon-based systems, a deep characterization of the supramolecular organization is crucial to establish an intimate relation between supramolecular structure and functionality...
January 7, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jiacheng Zhao, Mingxia Lu, Haiwang Lai, Hongxu Lu, Jacques Lalevée, Christopher Barner-Kowollik, Martina H Stenzel, Pu Xiao
Introducing a strategy towards polymer/nanodiamond hybrids with high polymer grafting density and accessible polymer structural characterisation is of critical importance for nanodiamonds surface modification and bioagent attachment for their biomedical application. Here, we report a glycopolymer/nanodiamond hybrid drug delivery system, which was prepared by grafting amonafide-conjugated glycopolymers onto the surface of nanodiamonds via oxime ligation. Poly(1-O-methacryloyl-2,3:4,5-di-O-isopropylidene-β-D-fructopyranose)-b-poly(3-vinylbenzaldehyde-co-methyl methacrylate), featuring pendant aldehyde groups, is prepared via RAFT polymerization...
January 9, 2018: Biomacromolecules
Changmai Chen, Zhenjun Yang, Xinjing Tang
Gene-based therapy is one of essential therapeutic strategies for precision medicine through targeting specific genes in specific cells of target tissues. However, there still exist many problems that need to be solved, such as safety, stability, selectivity, delivery, as well as immunity. Currently, the key challenges of gene-based therapy for clinical potential applications are the safe and effective nucleic acid drugs as well as their safe and efficient gene delivery systems. In this review, we first focus on current nucleic acid drugs and their formulation in clinical trials and on the market, including antisense oligonucleotide, siRNA, aptamer, and plasmid nucleic acid drugs...
January 5, 2018: Medicinal Research Reviews
Min Zheng, Mark P Waller
Herein, we describe the implementation details of our interaction-based partitioning API (application programming interface) called Yoink for QM/MM modeling and fragment-based quantum chemistry studies. Interactions are detected by computing density descriptors such as reduced density gradient, density overlap regions indicator, and single exponential decay detector. Only molecules having an interaction with a user-definable QM core are added to the QM region of a hybrid QM/MM calculation. Moreover, a set of molecule pairs having density-based interactions within a molecular system can be computed in Yoink, and an interaction graph can then be constructed...
January 5, 2018: Journal of Computational Chemistry
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