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Amide proton transfer

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https://www.readbyqxmd.com/read/28155086/near-uv-photodissociation-of-tryptic-peptide-cation-radicals-scope-and-effects-of-amino-acid-residues-and-radical-sites
#1
Huong T H Nguyen, František Tureček
Peptide cation-radical fragment ions of the z-type, [(●)AXAR(+)], [(●)AXAK(+)], and [(●)XAR(+)], where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS(3)-near-ultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO─NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [yn](+) type...
February 2, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28154122/measurement-of-lactate-content-and-amide-proton-transfer-values-in-the-basal-ganglia-of-a-neonatal-piglet-hypoxic-ischemic-brain-injury-model-using-mri
#2
Y Zheng, X-M Wang
BACKGROUND AND PURPOSE: As amide proton transfer imaging is sensitive to protein content and intracellular pH, it has been widely used in the nervous system, including brain tumors and stroke. This work aimed to measure the lactate content and amide proton transfer values in the basal ganglia of a neonatal piglet hypoxic-ischemic brain injury model by using MR spectroscopy and amide proton transfer imaging. MATERIALS AND METHODS: From 58 healthy neonatal piglets (3-5 days after birth; weight, 1-1...
February 2, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28145121/redox-driven-conformational-dynamics-in-a-photosystem-ii-inspired-%C3%AE-hairpin-maquette-determined-through-spectroscopy-and-simulation
#3
Hyea Hwang, Tyler G McCaslin, Anthony Hazel, Cynthia V Pagba, Christina M Nevin, Anna Pavlova, Bridgette A Barry, James C Gumbart
Tyrosine-based radical transfer plays an important role in photosynthesis, respiration, and DNA synthesis. Radical transfer can occur either by electron transfer (ET) or proton coupled electron transfer (PCET), depending on the pH. Reversible conformational changes in the surrounding protein matrix may control reactivity of radical intermediates. De novo designed Peptide A is a synthetic 18 amino-acid β-hairpin, which contains a single tyrosine (Y5) and carries out a kinetically significant PCET reaction between Y5 and a cross-strand histidine (H14)...
February 13, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28128026/amide-proton-transfer-weighted-mri-detection-of-traumatic-brain-injury-in-rats
#4
Hong Zhang, Wenzhu Wang, Shanshan Jiang, Yi Zhang, Hye-Young Heo, Xianlong Wang, Yun Peng, Jian Wang, Jinyuan Zhou
The purpose of this study was to explore the capability and uniqueness of amide proton transfer-weighted (APTw) imaging in the detection of primary and secondary injury after controlled cortical impact (CCI)-induced traumatic brain injury (TBI) in rats. Eleven adult rats had craniotomy plus CCI surgery under isoflurane anesthesia. Multi-parameter MRI data were acquired at 4.7 T, at eight time points (1, 6 h, and 1, 2, 3, 7, 14, and 28 days after TBI). At one and six hours post-injury, average APTw signal intensities decreased significantly in the impacted and peri-lesional areas due to tissue acidosis...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28116517/amide-proton-transfer-imaging-to-discriminate-between-low-and-high-grade-gliomas-added-value-to-apparent-diffusion-coefficient-and-relative-cerebral-blood-volume
#5
Yoon Seong Choi, Sung Soo Ahn, Seung-Koo Lee, Jong Hee Chang, Seok-Gu Kang, Se Hoon Kim, Jinyuan Zhou
OBJECTIVES: To evaluate the added value of amide proton transfer (APT) imaging to the apparent diffusion coefficient (ADC) from diffusion tensor imaging (DTI) and the relative cerebral blood volume (rCBV) from perfusion magnetic resonance imaging (MRI) for discriminating between high- and low-grade gliomas. METHODS: Forty-six consecutive adult patients with diffuse gliomas who underwent preoperative APT imaging, DTI and perfusion MRI were enrolled. APT signals were compared according to the World Health Organization grade...
January 23, 2017: European Radiology
https://www.readbyqxmd.com/read/28103693/the-logic-behind-a-physical-organic-chemist-s-research-topics
#6
Charles L Perrin
Although my research has no common theme or defining area, a coherence connects the diverse topics insofar as one project leads logically to another. Thus, studies on mechanisms of hydrogen exchange in amides and amidines led to the influence of hydrogen bonding and to NMR methods for chemical kinetics, including 2D-EXSY spectroscopy. Another connection was the OH(-)-catalyzed NH exchange in amines that had supported the hypothesis of stereoelectronic control. We therefore analyzed that hypothesis critically, tested it, found counterexamples, and proposed an alternative hypothesis...
January 20, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28102675/mechanistic-elucidation-of-zirconium-catalyzed-direct-amidation
#7
Helena Lundberg, Fredrik Tinnis, Jiji Zhang, Andrés G Algarra, Fahmi Himo, Hans Adolfsson
The mechanism of the zirconium-catalyzed condensation of carboxylic acids and amines for direct formation of amides was studied using kinetics, NMR spectroscopy, and DFT calculations. The reaction is found to be first order with respect to the catalyst and has a positive rate dependence on amine concentration. A negative rate dependence on carboxylic acid concentration is observed along with S-shaped kinetic profiles under certain conditions, which is consistent with the formation of reversible off-cycle species...
February 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28096269/differentiation-between-radiation-necrosis-and-tumor-progression-using-chemical-exchange-saturation-transfer
#8
Hatef Mehrabian, Kimberly L Desmond, Hany Soliman, Arjun Sahgal, Gregory J Stanisz
PURPOSE: Stereotactic radiosurgery (SRS) is a common treatment used in patients with brain metastases and is associated with high rates of local control, however, at the risk of radiation necrosis. It is difficult to differentiate radiation necrosis from tumor progression using conventional MRI making it a major diagnostic dilemma for practitioners. This prospective study investigated whether chemical exchange saturation transfer (CEST) was able to differentiate these two conditions. MATERIALS & METHODS: Sixteen patients with brain metastases who had been previously treated with SRS were included...
January 17, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27992380/noninvasive-amide-proton-transfer-magnetic-resonance-imaging-in-evaluating-the-grading-and-cellularity-of-gliomas
#9
Yan Bai, Yusong Lin, Wei Zhang, Lingfei Kong, Lifu Wang, Panli Zuo, Ignacio Vallines, Benjamin Schmitt, Jie Tian, Xiaolei Song, Jinyuan Zhou, Meiyun Wang
Using noninvasive magnetic resonance imaging techniques to accurately evaluate the grading and cellularity of gliomas is beneficial for improving the patient outcomes. Amide proton transfer imaging is a noninvasive molecular magnetic resonance imaging technique based on chemical exchange saturation transfer mechanism that detects endogenous mobile proteins and peptides in biological tissues. Between August 2012 and November 2015, a total number of 44 patients with pathologically proven gliomas were included in this study...
January 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/27988009/nmr-study-of-hydroxy-and-amide-protons-in-hyaluronan-polymers
#10
Gustav Nestor, Corine Sandström
Hyaluronan (HA) is an important and well characterized glycosaminoglycan with high viscosity and water-retaining capacity. Nonetheless, it is not fully understood whether conformational properties of the easily characterized HA oligomers can be transferred to HA polymers. To investigate possible differences in hydration, hydrogen bonding and flexibility between HA polymers and oligomers, hydroxy and amide protons of HA polymers were studied by solution-state and high-resolution magic angle spinning (HR-MAS) NMR spectroscopy...
February 10, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/27918442/some-brief-notes-on-theoretical-and-experimental-investigations-of-intramolecular-hydrogen-bonding
#11
REVIEW
Lucjan Sobczyk, Dorota Chudoba, Peter M Tolstoy, Aleksander Filarowski
A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed...
December 2, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27885356/magnetization-transfer-and-amide-proton-transfer-mri-of-neonatal-brain-development
#12
Yang Zheng, Xiaoming Wang, Xuna Zhao
Purpose. This study aims to evaluate the process of brain development in neonates using combined amide proton transfer (APT) imaging and conventional magnetization transfer (MT) imaging. Materials and Methods. Case data were reviewed for all patients hospitalized in our institution's neonatal ward. Patients underwent APT and MT imaging (a single protocol) immediately following the routine MR examination. Single-slice APT/MT axial imaging was performed at the level of the basal ganglia. APT and MT ratio (MTR) measurements were performed in multiple brain regions of interest (ROIs)...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27883128/modeling-the-archetype-cysteine-protease-reaction-using-dispersion-corrected-density-functional-methods-in-oniom-type-hybrid-qm-mm-calculations-the-proteolytic-reaction-of-papain
#13
Attila Fekete, István Komáromi
A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem...
December 7, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27787988/coordination-chemistry-and-f-element-complexation-by-diethylenetriamine-n-n%C3%A2-bis-acetylglycine-n-n-n%C3%A2-triacetic-acid
#14
Colt R Heathman, Travis S Grimes, Peter R Zalupski
Potentiometric and spectroscopic techniques were used to evaluate the coordination behavior and thermodynamic features of trivalent f-element complexation by diethylenetriamine-N,N″-bis(acetylglycine)-N,N',N″-triacetic acid (DTTA-DAG) and its di(acetylglycine ethyl ester) analogue [diethylenetriamine-N,N″-bis(acetylglycine ethyl ester)-N,N',N″-triacetic acid (DTTA-DAGEE)]. Protonation constants and stability constants of trivalent lanthanide complexes (except Pm(3+)) were determined by potentiometry...
November 7, 2016: Inorganic Chemistry
https://www.readbyqxmd.com/read/27747930/quantitative-analysis-of-the-z-spectrum-using-a-numerically-simulated-look-up-table-application-to-the-healthy-human-brain-at-7t
#15
Nicolas Geades, Benjamin A E Hunt, Simon M Shah, Andrew Peters, Olivier E Mougin, Penny A Gowland
PURPOSE: To develop a method that fits a multipool model to z-spectra acquired from non-steady state sequences, taking into account the effects of variations in T1 or B1 amplitude and the results estimating the parameters for a four-pool model to describe the z-spectrum from the healthy brain. METHODS: We compared measured spectra with a look-up table (LUT) of possible spectra and investigated the potential advantages of simultaneously considering spectra acquired at different saturation powers (coupled spectra) to provide sensitivity to a range of different physicochemical phenomena...
October 17, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/27732585/catalytic-alkylation-of-remote-c-h-bonds-enabled-by-proton-coupled-electron-transfer
#16
Gilbert J Choi, Qilei Zhu, David C Miller, Carol J Gu, Robert R Knowles
Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds...
November 10, 2016: Nature
https://www.readbyqxmd.com/read/27722530/a-comparison-of-the-experimental-and-theoretical-charge-density-distributions-in-two-polymorphic-modifications-of-piroxicam
#17
Felcia Lai, Jonathan J Du, Peter A Williams, Linda Váradi, Daniel Baker, Paul W Groundwater, Jacob Overgaard, James A Platts, David E Hibbs
Experimental charge density distribution studies of two polymorphic forms of piroxicam, β-piroxicam (1) and piroxicam monohydrate (2), were carried out via high-resolution single crystal X-ray diffraction experiments and multipole refinement. The asymmetric unit of (2) consists of two discrete piroxicam molecules, (2a) and (2b), and two water molecules. Geometry differs between (1) and (2) due to the zwitterionic nature of (2) which results in the rotation of the pyridine ring around the C(10)-N(2) bond by approximately 180°...
October 10, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27714249/proton-coupled-electron-transfer-in-the-reduction-of-carbonyls-using-smi2-h2o-implications-for-the-reductive-coupling-of-acyl-type-ketyl-radicals-with-smi2-h2o
#18
Shicheng Shi, Roman Szostak, Michal Szostak
Samarium diiodide-water (SmI2-H2O) reagents have emerged as some of the most practical systems enabling reduction and reductive cyclizations of ketyl radicals. Recently, this reaction manifold has been extended to acyl-type radicals generated from cyclic polar carboxylic acid derivatives. However, the relationship between the fundamental electron- and proton-transfer steps in the generation of ketyl-type radicals with SmI2-H2O remains unclear. An intriguing scenario involves an initial proton-coupled electron transfer (PCET) mechanism from SmI2-H2O to the carbonyl group...
September 26, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27690156/chemical-exchange-saturation-transfer-for-predicting-response-to-stereotactic-radiosurgery-in-human-brain-metastasis
#19
Kimberly L Desmond, Hatef Mehrabian, Sofia Chavez, Arjun Sahgal, Hany Soliman, Radoslaw Rola, Greg J Stanisz
PURPOSE: The purpose of this work was to determine the predictive value of chemical exchange saturation transfer (CEST) metrics in brain metastases treated with stereotactic radiosurgery (SRS). METHODS: CEST spectra at a radiofrequency power of 0.52 µT were collected on a 3 Tesla (T) magnetic resonance imaging from 25 patients at three time points: pretreatment, 1 week, and 1 month post-treatment. Amide proton transfer-weighted images and maps of the amplitude and width of Lorentzian-shaped CEST peaks and the relaxation-compensated AREX metric were constructed at the offset frequencies of amide, amine, and relayed nuclear Overhauser effect (NOE) from aliphatic groups as well as the broad magnetization transfer effect...
September 30, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/27689907/irida-%C3%AE-ketoimines-derived-from-hydrazines-to-afford-metallapyrazoles-or-n-n-bond-cleavage-a-missing-metallacycle-disclosed-by-a-theoretical-and-experimental-study
#20
Itziar Zumeta, Claudio Mendicute-Fierro, Itxaso Bustos, Miguel A Huertos, Antonio Rodríguez-Diéguez, José M Seco, Eider San Sebastian, María A Garralda
Unprecedented metallapyrazoles [IrH2{Ph2P(o-C6H4)CNNHC(o-C6H4)PPh2}] (3) and [IrHCl{Ph2P(o-C6H4)CNNHC(o-C6H4)PPh2}] (4) were obtained by the reaction of the irida-β-ketoimine [IrHCl{(PPh2(o-C6H4CO))(PPh2(o-C6H4CNNH2))H}] (2) in MeOH heated at reflux in the presence and absence of KOH, respectively. In solution, iridapyrazole 3 undergoes a dynamic process due to prototropic tautomerism with an experimental barrier for the exchange of ΔGcoal(⧧) = 53.7 kJ mol(-1). DFT calculations agreed with an intrapyrazole proton transfer process assisted by two water molecules (ΔG = 63...
October 17, 2016: Inorganic Chemistry
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