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Chemical crystallography

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https://www.readbyqxmd.com/read/27905149/scope-limitations-of-fmoc-chemistry-spps-based-approaches-to-the-total-synthesis-of-insulin-lispro-via-ester-insulin
#1
Stephen Kent, Balamurugan Dhayalan, Kalyaneswar Mandal, Nischay Rege, Michael Weiss, Simon Eitel, Thomas Meier, Ralph Schoenleber
We have systematically explored three approaches based on Fmoc chemistry SPPS for the total chemical synthesis of the key depsipeptide intermediate for the efficient total chemical synthesis of insulin. The approaches used were: stepwise Fmoc chemistry SPPS; the 'hybrid method', in which maximally-protected peptide segments made by Fmoc chemistry SPPS are condensed in solution; and, native chemical ligation using peptide-thioester segments generated by Fmoc chemistry SPPS. A key building block in all three approaches was a Glu[Oβ(Thr)] ester-linked dipeptide equipped with a set of orthogonal protecting groups compatible with Fmoc chemistry SPPS...
November 30, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27897362/unambiguous-determination-of-protein-arginine-ionization-states-in-solution-by-nmr-spectroscopy
#2
Yuichi Yoshimura, Nur Alia Oktaviani, Kento Yonezawa, Hironari Kamikubo, Frans A A Mulder
Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a (13) C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the (15) N(η) and (15) N(ϵ) chemical shifts of an arginine head group are correlated with that of the directly attached (13) C(ζ) ...
November 29, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27891613/a-review-of-spectroscopic-and-biophysical-chemical-studies-of-the-complex-of-cpd-photolyase-and-cryptochrome-dash-with-substrate-dna
#3
Johannes P M Schelvis, Yvonne M Gindt
CPD photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair cyclobutane pyrimidine dimers (CPD) on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, though some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue-light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH...
November 28, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27891541/dft-calculations-in-the-assignment-of-solid-state-nmr-and-crystal-structure-elucidation-of-a-lanthanum-iii-complex-with-dithiocarbamate-and-phenanthroline
#4
Vasantha Gowda, Risto S Laitinen, Ville-Veikko Telkki, Anna-Carin Larsson, Oleg N Antzutkin, Perttu Lantto
The molecular, crystal, and electronic structures as well as spectroscopic properties of a mononuclear heteroleptic lanthanum(iii) complex with diethyldithiocarbamate and 1,10-phenanthroline ligands (3 : 1) were studied by solid-state (13)C and (15)N cross-polarisation (CP) magic-angle-spinning (MAS) NMR, X-ray diffraction (XRD), and first principles density functional theory (DFT) calculations. A substantially different powder XRD pattern and (13)C and (15)N CP-MAS NMR spectra indicated that the title compound is not isostructural to the previously reported analogous rare earth complexes with the space group P21/n...
November 28, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27860401/probing-an-allosteric-pocket-of-cdk2-with-small-molecules
#5
Michael S Christodoulou, Fabiana Caporuscio, Valentina Restelli, Luca Carlino, Giuseppe Cannazza, Elisa Costanzi, Cinzia Citti, Leonardo Lo Presti, Pasquale Pisani, Roberto Battistutta, Massimo Broggini, Daniele Passarella, Giulio Rastelli
The availability of well characterized allosteric modulators is of crucial importance for investigating allosteric regulation of protein function. In a recently identified inactive conformation of CDK2 an open allosteric pocket has been detected and proposed as a site to accommodate allosteric inhibitors. Previous structure-based approaches allowed the identification of a hit compound expected to bind to this pocket. Here, we report the characterization of this compound by X-ray crystallography, which surprisingly provided a chemical structure different from the one previously reported...
November 18, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27827423/radiation-damage-in-xfel-case-study-from-the-oxygen-evolving-complex-of-photosystem-ii
#6
Muhamed Amin, Ashraf Badawi, S S Obayya
Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10-50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II...
November 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27823888/novel-gold-i-complexes-with-5-phenyl-1-3-4-oxadiazole-2-thione-and-phosphine-as-potential-anticancer-and-antileishmanial-agents
#7
Joana Darc S Chaves, Luiza Guimarães Tunes, Chris Hebert de J Franco, Thiago Martins Francisco, Charlane Cimini Corrêa, Silvane M F Murta, Rubens Lima Monte-Neto, Heveline Silva, Ana Paula S Fontes, Mauro V de Almeida
The current anticancer and antileishmanial drug arsenal presents several limitations concerning their specificity, efficacy, costs and the emergence of drug-resistant cells lines, which encourages the urgent need to search for new alternatives. Inspired by the fact that gold(I)-based compounds are promising antitumoral and antileishmanial drug candidates, we synthesized novel gold(I) complexes containing phosphine and 5-phenyl-1,3,4-oxadiazole-2-thione and evaluated their anticancer and antileishmanial activities...
October 24, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27816176/a-grayanotox-9-11-ene-derivative-from-rhododendron-brachycarpum-and-its-structural-assignment-via-a-protocol-combining-nmr-and-dp4-plus-application
#8
Nguyen Quoc Tuan, Joonseok Oh, Hyun Bong Park, Daneel Ferreira, Sanggil Choe, Juseon Lee, MinKyun Na
A growing body of evidence points to the useful roles of computational approaches in the structural characterization of natural products. Rhododendron brachycarpum has been traditionally used for the control of diabetes, hepatitis, hypertension, and rheumatoid arthritis and classified as an endangered species in Korea. A grayanotox-9(11)-ene derivative along with five known diterpenoids, were isolated from the MeOH extract of R. brachycarpum. Extensive 1D and 2D NMR experiments were conducted to establish the 2D structure and relative configuration of the grayanotox-9(11)-ene derivative...
November 2, 2016: Phytochemistry
https://www.readbyqxmd.com/read/27814890/synthesis-characterization-and-binding-affinity-of-hydrosulfide-complexes-of-synthetic-iron-ii-porphyrinates
#9
Daniel J Meininger, Hadi D Arman, Zachary J Tonzetich
The binding and reactivity of the hydrosulfide ion (HS(-)) to iron(II) porphyrinates has been examined for several synthetic meso-tetraphenylporphine (TPP) derivatives. In all cases, HS(-) coordinates to the iron centers in a 1:1 stoichiometry with formation constants (Kf) that reflect the electronic characteristics of the porphyrinate ligands. In the case of the F8TPP ligand (F8TPP=dianion of 5,10,15,20-tetrakis(2,6-difluorophenyl)porphine), an intermediate complex proposed as the hydrosulfide bridged dimer, (Bu4N)[Fe2(μ-SH)(F8TPP)2], was identified by NMR spectroscopy en route to formation of (Bu4N)[Fe(SH)(F8TPP)]...
August 27, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27812562/structural-characterization-and-proton-reduction-electrocatalysis-of-thiolate-bridged-bimetallic-coco-and-cofe-complexes
#10
Peng Tong, Wenjie Xie, Dawei Yang, Baomin Wang, Xiaoxiao Ji, Jianzhe Li, Jingping Qu
Using an assembly method, dinuclear CoCo and CoFe complexes supported by a bdt ligand, [Cp*Co(μ-η(2):η(2)-bdt)(μ-I)CoCp*][PF6] (1[PF6], Cp* = η(5)-C5Me5, bdt = benzene-1,2-dithiolate), and [Cp*Co(μ-η(2):η(4)-bdt)FeCp'][PF6] (3[PF6], Cp' = η(5)-C5Me4H) were synthesized in high yields. Upon chemical reduction with CoCp2, complexes 1[PF6] and 3[PF6] were converted to [Cp*Co(μ-η(2):η(2)-bdt)CoCp*] (2) and [Cp*Co(μ-η(2):η(4)-bdt)FeCp'][PF6] (3), respectively. Treatment of 2 with HBF4 resulted in the protonation of two cobalt centers to generate a hydride bridged complex, [Cp*Co(μ-η(2):η(2)-bdt)(μ-H)CoCp*][BF4] (4[BF4]), which was identified by spectroscopy and X-ray crystallography...
November 4, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27798837/biochemical-and-structural-characterization-of-selective-allosteric-inhibitors-of-the-plasmodium-falciparum-drug-target-prolyl-trna-synthetase
#11
Stephen Nakazawa Hewitt, David M Dranow, Benjamin G Horst, Jan A Abendroth, Barbara Forte, Irene Hallyburton, Chimed Jansen, Beatriz Baragana, Ryan Choi, Kasey L Rivas, Matthew A Hulverson, Mitchell Dumais, Thomas E Edwards, Donald D Lorimer, Alan H Fairlamb, David W Gray, Kevin D Read, Adele M Lehane, Kiaran Kirk, Peter J Myler, Amy Wernimont, Christopher S J Walpole, Robin Stacy, Lynn K Barrett, Ian H Gilbert, Wesley C Van Voorhis
Plasmodium falciparum (Pf) prolyl-tRNA synthetase (ProRS) is one of the few chemical-genetically validated drug targets for malaria, yet highly selective inhibitors have not been described. In this paper, approximately 40,000 compounds were screened to identify compounds that selectively inhibit PfProRS enzyme activity vs. H. sapiens (Hs) ProRS. X-ray crystallography structures were solved for apo, as well as substrate, and inhibitor bound forms of PfProRS. We identified two new inhibitors of PfProRS that bind outside the active site...
October 31, 2016: ACS Infectious Diseases
https://www.readbyqxmd.com/read/27795612/polarized-raman-spectroscopy-for-determining-the-orientation-of-di-d-phenylalanine-molecules-in-a-nanotube
#12
Valentin Sereda, Nicole M Ralbovsky, Milana C Vasudev, Rajesh R Naik, Igor K Lednev
Self-assembly of short peptides into nanostructures has become an important strategy for the bottom-up fabrication of nanomaterials. Significant interest to such peptide-based building blocks is due to the opportunity to control the structure and properties of well-structured nanotubes, nanofibrils, and hydrogels. X-ray crystallography and solution NMR, two major tools of structural biology, have significant limitations when applied to peptide nanotubes because of their non-crystalline structure and large weight...
September 2016: Journal of Raman Spectroscopy: JRS
https://www.readbyqxmd.com/read/27785946/2-2-2-trifluoroethyl-thiadiazines-a-patent-evaluation-of-wo2016023927
#13
Victor V Dotsenko, Elena A Chigorina, Sergey G Krivokolysko
The Alzheimer's disease (AD) is acknowledged as the most common type of dementia in aging adults. It is characterized by the formation of intracellular neurofibrillary tangles and extracellular amyloid plaques. The latter insoluble deposits mainly consist of β-amyloid peptides (Aβ), which are the derivatives of the amyloid precursor protein (APP). The formation of neurotoxic Aβ-peptides involves the cleavage of APP with beta-secretase enzyme (beta-site APP cleaving enzyme 1, BACE1) so the potential of BACE1 inhibitors as therapeutic agents for AD is now drawing much attention...
December 2016: Expert Opinion on Therapeutic Patents
https://www.readbyqxmd.com/read/27779384/nmr-crystallography-of-a-carbanionic-intermediate-in-tryptophan-synthase-chemical-structure-tautomerization-and-reaction-specificity
#14
Bethany G Caulkins, Robert P Young, Ryan A Kudla, Chen Yang, Thomas J Bittbauer, Baback Bastin, Eduardo Hilario, Li Fan, Michael J Marsella, Michael F Dunn, Leonard J Mueller
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography - the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry - to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established...
October 25, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27774349/a-two-metal-ion-mediated-conformational-switching-pathway-for-hdv-ribozyme-activation
#15
Tai-Sung Lee, Brian K Radak, Michael E Harris, Darrin M York
RNA enzymes serve as a potentially powerful platform from which to design catalysts and engineer new biotechnology. A fundamental understanding of these systems provides insight to guide design. The hepatitis delta virus ribozyme (HDVr) is a small, self-cleaving RNA motif widely distributed in nature, that has served as a paradigm for understanding basic principles of RNA catalysis. Nevertheless, questions remain regarding the precise roles of divalent metal ions and key nucleotides in catalysis. In an effort to establish a reaction mechanism model consistent with available experimental data, we utilize molecular dynamics simulations to explore different conformations and metal ion binding modes along the HDVr reaction path...
2016: ACS Catalysis
https://www.readbyqxmd.com/read/27768320/mono-and-dihydroxylated-symmetrical-octamethylcucurbiturils-and-allylated-derivatives
#16
Fang-Fang Shen, Kai Chen, Yun-Qian Zhang, Qian-Jiang Zhu, Zhu Tao, Hang Cong
Mono- and dihydroxylated symmetrical octamethylcucurbit[6]urils {(OH)OMeQ[6] and (OH)2OMeQ[6]} were prepared using a photochemical method to introduce limited alcohol group(s) directly to the parent symmetrical octamethylcucurbit[6]uril (OMeQ[6]), and the resulting compounds were verified by (1)H NMR, Xevo Q-TOF MS, and X-ray crystallography. Further chemical modification of mono- and dihydroxylated OMeQ[6] was also performed.
October 21, 2016: Organic Letters
https://www.readbyqxmd.com/read/27754668/predicting-molecular-crystal-properties-from-first-principles-finite-temperature-thermochemistry-to-nmr-crystallography
#17
Gregory J O Beran, Joshua D Hartman, Yonaton N Heit
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties...
October 18, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27754662/oxidation-of-1-methyl-1-phenylhydrazine-with-oxidovanadium-v-salan-complexes-insight-into-the-pathway-to-the-formation-of-hydrazine-by-vanadium-nitrogenase
#18
Ewa Kober, Zofia Janas, Julia Jezierska
A series of oxidovanadium(V) complexes [VO(L-κ(4)O,N,N,O)(OR)] (1a, R = Et, L = L(1); 1b, R = Me, L = L(1); 2, R = Me, L = L(2); 3, R = Me, L = L(3)) were synthesized by the σ-bond metathesis reaction between [VO(OR)3] and the linear diaminebis(phenol) derivatives H2L (salans) containing different para-substituents on the phenoxo group [CMe3CH2CMe2, L(1); Me, L(2); Cl, L(3)]. As shown by X-ray crystallography complexes 1a, 1b, and 2 exhibit cis-α geometry, do have a stereogenic vanadium center, and exist as a racemic mixture of the Δ cis-α and Λ cis-α enantiomers...
October 18, 2016: Inorganic Chemistry
https://www.readbyqxmd.com/read/27748947/perspectives-on-bioluminescence-mechanisms
#19
REVIEW
John Lee
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria and those utilizing imidazopyrazinone luciferins such as coelenterazine are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography and computational chemistry. The chemical structures of all reactants are well defined, and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high-energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter...
October 17, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27735086/solving-the-hydrogen-and-lithium-substructure-of-poly-triazine-imide-licl-using-nmr-crystallography
#20
Maria B Mesch, Kilian Bärwinkel, Yaşar Krysiak, Charlotte Martineau, Francis Taulelle, Reinhard B Neder, Ute Kolb, Jürgen Senker
Poly(triazine imide) with incorporated lithium chloride has recently attracted substantial attention due to its photocatalytic activity for water splitting. However, an apparent H/Li disorder prevents the delineation of structure-property relationships, for example, with respect to band-gap tuning. Herein, we show that through a combination of one- and two-dimensional, multinuclear solid-state NMR spectroscopy, chemical modelling, automated electron diffraction tomography, and an analysis based on X-ray pair distribution functions, it is finally possible to resolve the H/Li substructure...
November 14, 2016: Chemistry: a European Journal
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