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https://www.readbyqxmd.com/read/29733591/evidence-that-nucleophile-deprotonation-exceeds-bond-formation-in-the-hdv-ribozyme-transition-state
#1
Jun Lu, Selene C Koo, Benjamin Weissman, Michael E Harris, Nan-Sheng Li, Joseph A Piccirilli
Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5 ́ termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic pKa, consistent with the expected electron-withdrawing effect...
May 7, 2018: Biochemistry
https://www.readbyqxmd.com/read/29732451/gold-i-complexes-of-the-geminal-phosphinoborane-t-bu-2-pch-2-bph-2
#2
Devin H A Boom, Andreas W Ehlers, Martin Nieger, Marc Devillard, Ghenwa Bouhadir, Didier Bourissou, J Chris Slootweg
In this work, we explored the coordination properties of the geminal phosphinoborane t Bu2 PCH2 BPh2 ( 2 ) toward different gold(I) precursors. The reaction of 2 with an equimolar amount of the sulfur-based complex (Me2 S)AuCl resulted in displacement of the SMe2 ligand and formation of linear phosphine gold(I) chloride 3 . Using an excess of ligand 2 , bisligated complex 4 was formed and showed dynamic behavior at room temperature. Changing the gold(I) metal precursor to the phosphorus-based complex, (Ph3 P)AuCl impacted the coordination behavior of ligand 2 ...
April 30, 2018: ACS Omega
https://www.readbyqxmd.com/read/29729071/syntheses-and-evaluation-of-68-ga-and-153-sm-labeled-dota-conjugated-bisphosphonate-ligand-for-potential-use-in-detection-of-skeletal-metastases-and-management-of-pain-arising-from-skeletal-metastases
#3
Sudipta Chakraborty, Dibakar Goswami, Rubel Chakravarty, Shahiralam Khan Mohammed, H D Sarma, Ashutosh Dash
This article reports the syntheses and evaluation of 68 Ga- and 153 Sm-complexes of a new DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid)-conjugated geminal bisphosphonate, DOTA-Bn-SCN-BP, for their potential uses in the early detection of skeletal metastases by imaging and palliation of pain arising from skeketal metastases, respectively. The conjugate was synthesized in high purity following an easily adaptable three step reaction scheme. Gallium-68- and 153 Sm-complexes were prepared in high yield (>98%) and showed excellent in vitro stability in phosphate buffered slaine (PBS) and human serum...
May 5, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29707948/a-modular-approach-to-the-synthesis-of-gem-disubstituted-cyclopropanes
#4
Michael R Harris, Hanna M Wisniewska, Wenhua Jiao, Xiaochun Wang, James N Bradow
A diastereoselective, Pd-catalyzed Suzuki-Miyaura coupling reaction of geminal bis(boryl)cyclopropanes has been developed. The reaction offers a highly modular approach to the synthesis of tertiary cyclopropylboronic esters. The resulting boronic esters may be further functionalized to afford a range of gem-disubstituted cyclopropanes, which represent an important structural motif in the pharmaceutical industry. Sequential Suzuki-Miyaura cross-coupling reactions of gem-bis(boryl)cyclopropanes are also reported...
April 30, 2018: Organic Letters
https://www.readbyqxmd.com/read/29703629/benzofuran-pyran-hybrids-a-new-class-of-potential-bone-anabolic-agents
#5
Sampa Gupta, Sulekha Adhikary, Ram K Modukuri, Dharmendra Choudhary, Ritu Trivedi, Koneni V Sashidhara
Benzofuran moiety is an important pharmacophore showing positive effects on bone health. In the present study, sixteen benzofuran-pyran hybrids were synthesized and were evaluated for their osteogenic effects on primary osteoblast cells isolated from calvaria. Compounds 22 and 24 were found potent in stimulating osteoblast differentiation as assessed by the alkaline phosphatase activity. These compounds were also found to be nontoxic to osteoblast cells as compared to the control cells in MTT assay. Further, Alizarin Red-S staining for visualization of calcium nodules demonstrated compounds 22 and 34 as active in enhancing mineralization in osteoblast cells...
April 21, 2018: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29671744/full-scale-regression-based-injection-coefficients-for-panchromatic-sharpening
#6
Gemine Vivone, Rocco Restaino, Jocelyn Chanussot
Pansharpening is usually related to the fusion of a high spatial resolution but low spectral resolution (panchromatic) image with a high spectral resolution but low spatial resolution (multispectral) image. The calculation of injection coefficients through regression is a very popular and powerful approach. These coefficients are usually estimated at reduced resolution. In this paper, the estimation of the injection coefficients at full resolution for regression-based pansharpening approaches is proposed. To this aim, an iterative algorithm is proposed and studied...
July 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29671457/beyond-geminal-diesters-increasing-the-scope-of-metal-mediated-vinylcyclopropane-annulations-while-decreasing-pre-activation
#7
REVIEW
Duncan K Brownsey, Evgueni Gorobets, Darren J Derksen
The utilization of unactivated substrates in annulation reactions provides access to complex products without the need for subsequent removal of the activating group. Vinylcyclopropanes (VCPs), occurring naturally in several monoterpene natural products, are an important building block for organic chemistry, and can be activated by electron withdrawing substituents directly on the cyclopropane to facilitate ring opening reactions. However, many VCPs that lack these activated groups remain reactive with several group 8, 9 and 10 transition metals, by alternative modes of activation, forming metallacycles...
April 19, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29656475/hydrogenation-of-multiple-bonds-by-geminal-aminoborane-based-frustrated-lewis-pairs
#8
Diana Yepes, Pablo Jaque, Israel Fernandez
By means of Density Functional Theory calculations, the hydrogenation reaction of multiple bonds mediated by geminal aminoborane-based frustrated Lewis pairs (FLPs) has been explored. It is found that the release of the activated dihydrogen occurs in a concerted, yet highly asynchronous, manner. The physical factors controlling the transformation are quantitatively described in detail by means of the Activation Strain Model of reactivity in combination with the Energy Decomposition Analysis method. This approach suggests a cooperative double hydrogen transfer mechanism which is initiated by the migration of the protic (N)H and followed by the nucleophilic attack of the hydride (B)H to the carbon atom of the multiple bond...
April 14, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29626884/fate-of-the-open-shell-singlet-ground-state-in-the-experimentally-accessible-acenes-a-quantum-monte-carlo-study
#9
Nicolas Dupuy, Michele Casula
By means of the Jastrow correlated antisymmetrized geminal power (JAGP) wave function and quantum Monte Carlo (QMC) methods, we study the ground state properties of the oligoacene series, up to the nonacene. The JAGP is the accurate variational realization of the resonating-valence-bond (RVB) ansatz proposed by Pauling and Wheland to describe aromatic compounds. We show that the long-ranged RVB correlations built in the acenes' ground state are detrimental for the occurrence of open-shell diradical or polyradical instabilities, previously found by lower-level theories...
April 7, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29626862/transient-isomers-in-the-photodissociation-of-bromoiodomethane
#10
Moreno Marcellini, Alexandr Nasedkin, Burkhard Zietz, Jonas Petersson, Jonathan Vincent, Federico Palazzetti, Erik Malmerberg, Qingyu Kong, Michael Wulff, David van der Spoel, Richard Neutze, Jan Davidsson
The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2 IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2 I-Br and CH2 Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule...
April 7, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29604496/side-chain-removal-from-corticosteroids-by-unspecific-peroxygenase
#11
René Ullrich, Marzena Poraj-Kobielska, Steffi Scholze, Claire Halbout, Martin Sandvoss, Marek J Pecyna, Katrin Scheibner, Martin Hofrichter
Two unspecific peroxygenases (UPO, EC 1.11.2.1) from the basidiomycetous fungi Marasmius rotula and Marasmius wettsteinii oxidized steroids with hydroxyacetyl and hydroxyl functionalities at C17 - such as cortisone, Reichstein's substance S and prednisone - via stepwise oxygenation and final fission of the side chain. The sequential oxidation started with the hydroxylation of the terminal carbon (C21) leading to a stable geminal alcohol (e.g. cortisone 21-gem-diol) and proceeded via a second oxygenation resulting in the corresponding α-ketocarboxylic acid (e...
March 26, 2018: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29588445/solvent-composition-drives-the-rebinding-kinetics-of-nitric-oxide-to-microperoxidase
#12
Padmabati Mondal, Markus Meuwly
The rebinding kinetics of NO after photodissociation from microperoxidase (Mp-9) is studied in different solvent environments. In mixed glycerol/water (G/W) mixtures the dissociating ligand rebinds with a yield close to 1 due to the cavities formed by the solvent whereas in pure water the ligand can diffuse into the solvent after photodissociation. In the G/W mixture, only geminate rebinding on the sub-picosecond and 5 ps time scales was found and the rebinding fraction is unity which compares well with available experiments...
March 27, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29577126/geminal-cross-coupling-synthesis-ion-induced-emission-and-lysosome-imaging-of-cationic-tetraarylethene-oligoelectrolytes
#13
Qi-Yuan Zhou, Bo Xin, Ya-Long Wang, Chong Li, Ze-Qiang Chen, Qi Yu, Zhen-Li Huang, Ming-Qiang Zhu
Neutral conjugated tetraarylethenes OFn (n = 1-3) and the corresponding cationic conjugated oligoelectrolytes OFn+ (n = 1-3) with aggregation-induced emission activity have been designed and synthesized using geminal cross-coupling. OFn+ (n = 1-3) feature ion-induced emission in aqueous solution. They are used for lysosomal fluorescence imaging and tracing of lysosome events.
March 26, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29566507/photoinduced-transport-in-an-h64q-neuroglobin-antidote-for-carbon-monoxide-poisoning
#14
J Rydzewski, W Nowak
Carbon monoxide (CO) is a leading cause of poisoning deaths worldwide, without available antidotal therapy. Recently, a potential treatment for CO poisoning was introduced, based on binding of CO by neuroglobin (Ngb) with a mutated distal histidine (H64Q). Here, we present an atomistic mechanism of CO trapping by H64Q Ngb revealed by nonadiabatic molecular dynamics. We focused on CO photodissociation and recombination of CO to wild type (WT) and H64Q Ngb. Our results demonstrate that the distribution of CO within the proteins differs substantially due to rearrangement of amino acids surrounding the distal heme pocket...
March 21, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29544266/a-non-jkl-density-matrix-functional-for-intergeminal-correlation-between-closed-shell-geminals-from-analysis-of-natural-orbital-configuration-interaction-expansions
#15
R van Meer, O V Gritsenko, E J Baerends
Almost all functionals that are currently used in density matrix functional theory have been created by some a priori ansatz that generates approximations to the second-order reduced density matrix (2RDM). In this paper, a more consistent approach is used: we analyze the 2RDMs (in the natural orbital basis) of rather accurate multi-reference configuration interaction expansions for several small molecules (CH4 , NH3 , H2 O, FH, and N2 ) and use the knowledge gained to generate new functionals. The analysis shows that a geminal-like structure is present in the 2RDMs, even though no geminal theory has been applied from the onset...
March 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29543985/sulfones-as-synthetic-linchpins-transition-metal-free-sp3-sp2-and-sp2-sp2-cross-couplings-between-geminal-bis-sulfones-and-organolithium-compounds
#16
Barry M Trost, Chris Kalnmals
Herein, we report a valuable umpolung strategy that highlights the ambiphilic nature of the bis(phenylsulfonyl)methyl synthon and demonstrates its utility as a synthetic linchpin. While the bis(phenylsulfonyl)methyl group is typically introduced as an sp3 carbon nucleophile, we demonstrate that it can also function as an effective sp2 carbon electrophile in the presence of organolithium nucleophiles. Akyl- and aryllithiums couple with the central carbon of the bis(phenylsulfonyl)methyl unit to ultimately generate trisubstituted alkenes, comprising a formal sp3-sp2 and sp2-sp2 cross-coupling between organolithiums and bis(sulfones)...
March 15, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29495792/method-for-making-2-electron-response-reduced-density-matrices-approximately-n-representable
#17
Caitlin Lanssens, Paul W Ayers, Dimitri Van Neck, Stijn De Baerdemacker, Klaas Gunst, Patrick Bultinck
In methods like geminal-based approaches or coupled cluster that are solved using the projected Schrödinger equation, direct computation of the 2-electron reduced density matrix (2-RDM) is impractical and one falls back to a 2-RDM based on response theory. However, the 2-RDMs from response theory are not N-representable. That is, the response 2-RDM does not correspond to an actual physical N-electron wave function. We present a new algorithm for making these non-N-representable 2-RDMs approximately N-representable, i...
February 28, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29492893/metagenomic-analyses-of-the-viruses-detected-in-mycorrhizal-fungi-and-their-host-orchid
#18
Hanako Shimura, Chikara Masuta, Yasunori Koda
In nature, mycorrhizal association with soilborne fungi is indispensable for orchid families. Fungal structures from compatible endo-mycorrhizal fungi in orchid cells are digested in cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until shoots develop (leaves) and become photoautotrophic. Seeds of all orchid species surely geminate with the help of their own fungal partners, and this specific partnership has been acquired for a long evolutional history between orchids and fungi...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29491623/fusion-of-maxillary-central-incisors-with-mesiodens
#19
Madhuram Krishnamurthy, V Naveen Kumar, Ashok Leburu, Nadeem Jeddy
Fusion and gemination are developmental anomalies which are quite similar to each other but can be distinguished from each other if properly assessed. Fusion and gemination have been described as a result of developmental anomalies of dental tissues. The exact etiology is still unknown, but a genetic predisposition is suggested. This article highlights the importance of clinical and radiographic correlation in arriving at a definitive diagnosis.
January 2018: Journal of Oral and Maxillofacial Pathology: JOMFP
https://www.readbyqxmd.com/read/29481716/synthesis-of-hebelophyllene-e-an-entry-to-geminal-dimethyl-cyclobutanes-by-2-2-cycloaddition-of-alkenes-and-allenoates
#20
Johannes M Wiest, Michael L Conner, M Kevin Brown
The first synthesis of hebelophyllene E is presented, along with assignment of its previously unknown relative configuration through synthesis of epi-ent-hebelophyllene E. Development of a catalytic enantioselective [2+2] cycloaddition of alkenes and allenoates provides access to the required chiral geminal dimethylcyclobutanes. Key to its success is the identification of a novel oxazaborolidine catalyst which promotes the cycloaddition in high enantioselectivities with good functional-group tolerance (9 examples, up to 97:3 e...
April 16, 2018: Angewandte Chemie
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