scholarly journals Evidence for an intrinsic binding force between dodecaborate dianions and receptors with hydrophobic binding pockets

2016 ◽  
Vol 52 (37) ◽  
pp. 6300-6303 ◽  
Author(s):  
Jonas Warneke ◽  
Carsten Jenne ◽  
Johannes Bernarding ◽  
Vladimir A. Azov ◽  
Markus Plaumann
Keyword(s):  
Gas Phase ◽  
Intermolecular Interactions ◽  
Binding Studies ◽  
Binding Force ◽  
Hydrophobic Binding ◽  
Binding Pockets

Gas phase binding studies revealed strong intrinsic intermolecular interactions between dianionic dodecaborates [B12X12]2− and neutral organic hosts.

scholarly journals Molecular Capsule Catalysis: Ready to Address Current Challenges in Synthetic Organic Chemistry?

2020 ◽  
Vol 74 (7) ◽  
pp. 561-568
Author(s):  
Ivana Némethová ◽  
Leonidas-Dimitrios Syntrivanis ◽  
Konrad Tiefenbacher
Keyword(s):  
Organic Chemistry ◽  
Building Blocks ◽  
Short Article ◽  
Molecular Capsules ◽  
Synthetic Organic Chemistry ◽  
Size And Shape ◽  
Molecular Capsule ◽  
Hydrophobic Binding ◽  
Binding Pockets ◽  
Self Assembled

Self-assembled molecular capsules, host structures that form spontaneously when their building blocks are mixed, have been known since the 1990s. They share some basic similarities with enzyme pockets, as they feature defined hydrophobic binding pockets that are able to bind molecules of appropriate size and shape. The potential to utilize such host structures for catalysis has been explored since their discovery; however, applications that solve current challenges in synthetic organic chemistry have remained limited. In this short article, we discuss the challenges associated with the use of molecular capsules as catalysts, and highlight some recent applications of supramolecular capsules to overcome challenges in synthetic organic chemistry.

How carbonyl reductases control stereoselectivity: Approaching the goal of rational design

2010 ◽  
Vol 82 (1) ◽  
pp. 117-128 ◽  
Author(s):  
Dunming Zhu ◽  
Ling Hua
Keyword(s):  
Rational Design ◽  
Reaction Medium ◽  
Site Directed Mutagenesis ◽  
Saturation Mutagenesis ◽  
Rational Approach ◽  
Reaction Conditions ◽  
In Silico Docking ◽  
Enzyme Substrate ◽  
Hydrophobic Binding ◽  
Binding Pockets

Although "Prelog’s rule" and "two hydrophobic binding pockets" model have been used to predict and explain the stereoselectivity of enzymatic ketone reduction, the molecular basis of stereorecognition by carbonyl reductases has not been well understood. The stereoselectivity is not only determined by the structures of enzymes and substrates, but also affected by the reaction conditions such as temperature and reaction medium. Structural analysis coupled with site-directed mutagenesis of stereocomplementary carbonyl reductases readily reveals the key elements of controlling stereoselectivity in these enzymes. In our studies, enzyme-substrate docking and molecular modeling have been engaged to understand the enantioselectivity diversity of the carbonyl reductase from Sporobolomyces salmonicolor (SSCR), and to guide site-saturation mutagenesis for altering the enantioselectivity of this enzyme. These studies provide valuable information for our understanding of how the residues involved in substrate binding affect the orientation of bound substrate, and thus control the reaction stereoselectivity. The in silico docking-guided semi-rational approach should be a useful methodology for discovery of new carbonyl reductases.

scholarly journals Rovibronic Signatures of Molecular Aggregation in the Gas Phase: Subtle Homochirality Trends in the Dimer, Trimer and Tetramer of Benzyl Alcohol

2021 ◽  
Author(s):  
Robert Medel ◽  
Ander Camiruaga ◽  
Rizalina Tama Saragi ◽  
Pablo Pinacho ◽  
Cristóbal Pérez ◽  
...  
Keyword(s):  
Benzyl Alcohol ◽  
Gas Phase ◽  
Intermolecular Interactions ◽  
Chemical Processes ◽  
Molecular Aggregation

Molecular aggregation is of paramount importance in many chemical processes, including those in living beings. Thus, characterization of the intermolecular interactions is an important step on its understanding. We describe...

A Structure-Based Algorithm to Predict Potential Binding Peptides to MHC Molecules with Hydrophobic Binding Pockets

1997 ◽  
Vol 58 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Yael Altuvia ◽  
Alessandro Sette ◽  
John Sidney ◽  
Scott Southwood ◽  
Hanah Margalit
Keyword(s):  
Mhc Molecules ◽  
Potential Binding ◽  
Hydrophobic Binding ◽  
Binding Pockets ◽  
Binding Peptides

Structural insight from intermolecular interactions and energy framework analyses of 2-substituted 6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-ones

2021 ◽  
Vol 77 (3) ◽  
Author(s):  
Akmaljon G. Tojiboev ◽  
Burkhon Zh. Elmuradov ◽  
Halima Mouhib ◽  
Kambarali K. Turgunov ◽  
Askar Sh. Abdurazakov ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Gas Phase ◽  
Intermolecular Interactions ◽  
Correction Term ◽  
Three Dimensional ◽  
Dispersion Interactions ◽  
Additional Information ◽  
Experimental Crystal ◽  
The Impact

The crystal structures of three mackinazolinone derivatives (2-amino-6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one at room temperature, and 2-nitro-6,7,8,9-tetrahydro-11H-pyrido[2,1-b]quinazolin-11-one and N-(11-oxo-6,8,9,11-tetrahydro-7H-pyrido[2,1-b]quinazolin-2-yl)benzamide at 100 K) are explored using X-ray crystallography. To delineate the different intermolecular interactions and the respective interaction energies in the crystal architectures, energy framework analyses were carried out using the CE-B3LYP/6-31G(d,p) method implemented in the CrystalExplorer software. In the structures the different molecules are linked by C—H...O, C—H...N and N—H...O hydrogen bonds. Together with these hydrogen bonds, C—H...π and C—O...π interactions are involved in the formation of a three-dimensional crystal network. A Hirshfeld surface analysis allows the visualization of the two-dimensional fingerprint plots and the quantification of the contributions of H...H, H...C/C...H and H...O/O...H contacts throughout the different crystal structures. To obtain additional information on the intrinsic properties of our targets and to compare the experimental crystal structures with their respective conformations in the gas phase, quantum chemical calculations at the B3LYP-D3BJ/6-311++G(d,p) level of theory, including Grimme's D3 correction term and BJ damping functions, were carried out to account for intramolecular dispersion interactions. The identified energy gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO–LUMO gap) of our targets in the gas phase and in two implicit solvents (methanol and dimethyl sulfoxide) allow us to quantify the impact of different substituents on the reactivity of mackinazolinone derivatives.

scholarly journals Weak intermolecular interactions in gas-phase nuclear magnetic resonance

2011 ◽  
Vol 135 (8) ◽  
pp. 084310 ◽  
Author(s):  
Piotr Garbacz ◽  
Konrad Piszczatowski ◽  
Karol Jackowski ◽  
Robert Moszynski ◽  
Michał Jaszuński
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Gas Phase ◽  
Intermolecular Interactions ◽  
Weak Intermolecular Interactions ◽  
Nuclear Magnetic
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