Crystallographic Structures of Human α-Thrombin Complexed to Peptide Boronic Acids Lacking a Positive Charge at P1. Evidence of Novel Interactions

Two key factors bear on reaction rates for the conjugate addition of alkenyl boronic acids to heteroaryl-appended enones: the proximity of inductively electron-withdrawing heteroatoms to the site of bond formation and the resonance contribution of available heteroatom lone pairs to stabilize the developing positive charge at the enone β-position. For the former, the closer the heteroatom is to the enone β-carbon, the faster the reaction. For the latter, greater resonance stabilization of the benzylic cationic charge accelerates the reaction. Thus, reaction rates are increased by the closer proximity of inductive electron-withdrawing elements, but if resonance effects are involved, then increased rates are observed with electron-donating ability. Evidence for these trends in isomeric substrates is presented, and the application of these insights has allowed for reaction conditions that provide improved reactivity with previously problematic substrates.

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Structure of a new orthorhombic phase in NiTi: Mn shape memory alloys

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100178136 ◽

1990 ◽

Vol 48 (4) ◽

pp. 1000-1001

Author(s):

Jenö Beyer ◽

Lajos Tóth

Keyword(s):

Martensitic Transformation ◽

Structural Changes ◽

High Vacuum ◽

Intermetallic Phase ◽

Orthorhombic Phase ◽

Transformation Process ◽

Analytical Electron ◽

Analytical Electron Microscope ◽

Crystallographic Structures ◽

Ternary Additions

The structural changes during reversible martensitic transformation of near-equiatomic NiTi alloys can best be studied in TEM at around room temperature. Ternary additions like Mn offer this possibility by suppressing the Ms temperature below RT. Besides the stable intermetallic phases (Ti2Ni, TiNi, TiNi3) several metastable phases with various crystallographic structures (rhombohedral, hexagonal, monoclinic, cubic) have also been reported to precipitate due to suitable annealing procedures.TiNi:Mn samples with 0.9 and 1.3 at% Mn were arc melted in argon atmosphere and homogenized at 948 °C for 72 hours in high vacuum in an infrared furnace. After spark cutting slices of 0.2 mm, TEM specimens were prepared by electrochemical polishing with the twin-jet technique in methanol - perchloric acid electrolyte. The TEM study was carried out in a JEOL 200 CX analytical electron microscope.In this paper a new intermetallic phase is reported which has been observed in both samples by TEM during the martensitic transformation process.

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Utilization of electrical charges in the pores of tofu waste for hydrogen production in water

WEENTECH Proceedings in Energy ◽

10.32438/wpe.1720 ◽

2020 ◽

pp. 124-135

Author(s):

I. N. G. Wardana ◽

N. Willy Satrio

Keyword(s):

Magnetic Field ◽

Hydrogen Production ◽

Sodium Bicarbonate ◽

Positive Charge ◽

Electrical Energy ◽

Hydrogen Sensor ◽

Water Molecules ◽

Partial Charge ◽

Delocalized Electron ◽

Water Hydrogen

Tofu is main food in Indonesia and its waste generally pollutes the waters. This study aims to change the waste into energy by utilizing the electric charge in the pores of tofu waste to produce hydrogen in water. The tofu pore is negatively charged and the surface surrounding the pore has a positive charge. The positive and negative electric charges stretch water molecules that have a partial charge. With the addition of a 12V electrical energy during electrolysis, water breaks down into hydrogen. The test was conducted on pre-treated tofu waste suspension using oxalic acid. The hydrogen concentration was measured by a MQ-8 hydrogen sensor. The result shows that the addition of turmeric together with sodium bicarbonate to tofu waste in water, hydrogen production increased more than four times. This is due to the fact that magnetic field generated by delocalized electron in aromatic ring in turmeric energizes all electrons in the pores of tofu waste, in the sodium bicarbonate, and in water that boosts hydrogen production. At the same time the stronger partial charge in natrium bicarbonate shields the hydrogen proton from strong attraction of tofu pores. These two combined effect are very powerful for larger hydrogen production in water by tofu waste.

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THREE-DIMENSIONAL WATER NETWORKS SOLVATING AN EXCESS POSITIVE CHARGE: NEW INSIGHTS INTO THE MOLECULAR PHYSICS OF ION HYDRATION

Proceedings of the 70th International Symposium on Molecular Spectroscopy ◽

10.15278/isms.2015.wj09 ◽

2015 ◽

Author(s):

Conrad Wolke ◽

Mark Johnson ◽

Sotiris Xantheas ◽

Evangelos Miliordos ◽

Gary Weddle ◽

...

Keyword(s):

Positive Charge ◽

Three Dimensional ◽

Water Networks ◽

Molecular Physics ◽

Ion Hydration ◽

Excess Positive Charge

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A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

10.26434/chemrxiv.12278780 ◽

2020 ◽

Author(s):

Egle Maximowitsch ◽

Tatiana Domratcheva

Keyword(s):

Hydrogen Bond ◽

Light Adaptation ◽

Positive Charge ◽

Pyrrole Ring ◽

Md Simulations ◽

Spectral Shift ◽

Specific Domain ◽

Study Guides ◽

Rational Engineering ◽

Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

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A Mild and Simple Method for Making MIDA Boronates

10.26434/chemrxiv.12054036.v1 ◽

2020 ◽

Author(s):

Aidan Kelly ◽

Peng-Jui (Ruby) Chen ◽

Jenna Klubnick ◽

Daniel J. Blair ◽

Martin D. Burke

Keyword(s):

Organic Synthesis ◽

Boronic Acids ◽

Simple Method ◽

Direct Preparation ◽

Synthesis Procedure ◽

Harsh Conditions

<div> <div> <div> <p>Existing methods for making MIDA boronates require harsh conditions and complex procedures to achieve dehydration. Here we disclose that a pre-dried form of MIDA, MIDA anhydride, acts as both a source of the MIDA ligand and an in situ desiccant to enable a mild and simple MIDA boronate synthesis procedure. This method expands the range of sensitive boronic acids that can be converted into their MIDA boronate counterparts. Further utilizing unique properties of MIDA boronates, we have developed a MIDA Boronate Maker Kit which enables the direct preparation and purification of MIDA boronates from boronic acids using only heating and centrifuge equipment that is widely available in labs that do not specialize in organic synthesis. </p> </div> </div> </div>

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The Structural Landscape of SARS-CoV-2 Main Protease: Hints for Inhibitor Search.

10.26434/chemrxiv.12209744.v1 ◽

2020 ◽

Cited By ~ 3

Author(s):

Luigi Leonardo Palese

Keyword(s):

Comparative Analysis ◽

Global Health ◽

Binding Site ◽

Causative Agent ◽

Data Set ◽

Substrate Binding Site ◽

Global Pandemic ◽

Main Protease ◽

Crystallographic Structures ◽

Structural Aspects

In 2019, an outbreak occurred which resulted in a global pandemic. The causative agent of this serious global health threat was a coronavirus similar to the agent of SARS, referred to as SARS-CoV-2. In this work an analysis of the available structures of the SARS-CoV-2 main protease has been performed. From a data set of crystallographic structures the dynamics of the protease has been obtained. Furthermore, a comparative analysis of the structures of SARS-CoV-2 with those of the main protease of the coronavirus responsible of SARS (SARS-CoV) was carried out. The results of these studies suggest that, although main proteases of SARS-CoV and SARS-CoV-2 are similar at the backbone level, some plasticity at the substrate binding site can be observed. The consequences of these structural aspects on the search for effective inhibitors of these enzymes are discussed, with a focus on already known compounds. The results obtained show that compounds containing an oxirane ring could be considered as inhibitors of the main protease of SARS-CoV-2.

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Systematic Engineering of a Protein Nanocage for High-Yield, Site-Specific Modification

10.26434/chemrxiv.7150097 ◽

2018 ◽

Author(s):

Daniel D. Brauer ◽

Emily C. Hartman ◽

Daniel L.V. Bader ◽

Zoe N. Merz ◽

Danielle Tullman-Ercek ◽

...

Keyword(s):

Small Molecules ◽

Protein Modification ◽

Positive Charge ◽

Specific Protein ◽

High Yield ◽

Site Specific ◽

Protein Cage ◽

Protein Carriers ◽

Site Selective ◽

Targeted Library

<div> <p>Site-specific protein modification is a widely-used strategy to attach drugs, imaging agents, or other useful small molecules to protein carriers. N-terminal modification is particularly useful as a high-yielding, site-selective modification strategy that can be compatible with a wide array of proteins. However, this modification strategy is incompatible with proteins with buried or sterically-hindered N termini, such as virus-like particles like the well-studied MS2 bacteriophage coat protein. To assess VLPs with improved compatibility with these techniques, we generated a targeted library based on the MS2-derived protein cage with N-terminal proline residues followed by three variable positions. We subjected the library to assembly, heat, and chemical selections, and we identified variants that were modified in high yield with no reduction in thermostability. Positive charge adjacent to the native N terminus is surprisingly beneficial for successful extension, and over 50% of the highest performing variants contained positive charge at this position. Taken together, these studies described nonintuitive design rules governing N-terminal extensions and identified successful extensions with high modification potential.</p> </div>

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