Heteroditopic Cryptands of Tunable Cavity Size:  Imposition of Distorted Geometry onto Copper(II) and Nickel(II) and Molecular Recognition of Water Molecules

1998 ◽  
Vol 37 (20) ◽  
pp. 5050-5055 ◽  
Author(s):  
Dillip K. Chand ◽  
Parimal K. Bharadwaj
Keyword(s):  
Molecular Recognition ◽  
Water Molecules ◽  
Cavity Size ◽  
Distorted Geometry

Structural and dynamic roles of permanent water molecules in ligand molecular recognition by chicken liver bile acid binding protein

2008 ◽  
Vol 21 (5) ◽  
pp. 348-354 ◽  
Author(s):  
Piero Ricchiuto ◽  
Alessandro Guerini Rocco ◽  
Elisabetta Gianazza ◽  
Dario Corrada ◽  
Tiziana Beringhelli ◽  
...  
Keyword(s):  
Bile Acid ◽  
Molecular Recognition ◽  
Binding Protein ◽  
Chicken Liver ◽  
Water Molecules ◽  
Acid Binding Protein ◽  
Bile Acid Binding

Molecular recognition XI. The synthesis of extensively deoxygenated derivatives of the H-type 2 human blood group determinant and their binding by an anti-H-type 2 monoclonal antibody and the lectin 1 of Ulexeuropaeus

1992 ◽  
Vol 70 (1) ◽  
pp. 254-271 ◽  
Author(s):  
Ulrike Spohr ◽  
Eugenia Paszkiewicz-Hnatiw ◽  
Naohiko Morishima ◽  
Raymond U. Lemieux
Keyword(s):  
Monoclonal Antibody ◽  
Molecular Recognition ◽  
Blood Group ◽  
Human Blood ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Human Blood Group ◽  
Derivatives Of ◽  
Hydrogen Bonded

The relative potencies of a wide variety of deoxygenated derivatives of the methyl glycoside of α-L-Fuc-(1 → 2)-β-D-Gal-(1 → 4)- β-D-GlcNAc (the H-type 2 human blood group related trisaccharide) for the inhibition of the binding of an artificial H-type 2 antigen by the lectin I of Ulexeuropaeus confirmed the previous evidence that the key and productive interaction involves only the three hydroxyl groups of the α-L-fucose unit, the hydroxyl at the 3-position of the β-D-galactose residue, and the nonpolar groups in their immediate environment. Except for the acetamido group and the hydroxymethyl of the β-D-Gal unit, which stay in the aqueous phase, on complex formation the remaining three hydroxyl groups appear to come to reside at or near the periphery of the combining site since their replacement by hydrogen causes relatively small changes (< ± 1 kcal/mol) in the stability of the complex (ΔG0). Relatively much larger but compensating changes occur for the enthalpy and entropy terms, and these may arise primarily from the differences in the water structure about the periphery of the combining site and the oligosaccharide both prior to and after complexation. It is proposed that steric constraints lead to an ordered state of the water molecules hydrogen-bonded to the polar groups within the cleft formed by the key region of the amphiphilic combining site. Their release to form less ordered clusters of more strongly hydrogen-bonded water molecules in bulk solution would contribute importantly to the driving force for complexation. It is demonstrated that the surface used for the binding of H-type 2-OMe by a monoclonal anti-H antibody is virtually identical to that used by the Ulex lectin. Keywords: molecular recognition, H-type 2 blood group determinant and deoxygenated derivatives, lectin I of Ulexeuropaeus, anti-H-type 2 monoclonal antibody, enthalpy–entropy compensation.

Discrete water molecules in the vicinity of two oppositely charged ions

1969 ◽  
Vol 47 (8) ◽  
pp. 873-880 ◽  
Author(s):  
Dieter K. Ross
Keyword(s):  
Water Molecules ◽  
Cavity Size ◽  
Minimum Potential Energy ◽  
Spheroidal Cavity ◽  
Minimum Potential ◽  
Outer Water ◽  
Dielectric Continuum ◽  
Charged Ions ◽  
Oppositely Charged ◽  
Made In

An attempt is made to describe the water molecules in contact with an ion pair in an aqueous solution. One possible arrangement consisting of 10 nonpolarizable water dipoles is considered and a comparison of various energy terms is made in order to decide what factors are most important. The two ions and their attached water dipoles are enclosed in a spheroidal cavity embedded in a dielectric continuum to represent the bulk of the water. It is shown that the energy associated with the water molecules lying in the central region between the two ions is practically unaffected by the cavity size. On the other hand, although the behavior of the "outer" water molecules is extremely sensitive to the cavity size it is a good approximation to the more precise statistical problem to place them in the position of minimum potential energy.

scholarly journals Molecular Recognition of Dye-Modified Cyclodextrins with Different Cavity Size

2005 ◽  
Vol 54 (6) ◽  
pp. 503-508
Author(s):  
Tetsuo KUWABARA ◽  
Kazuya SUZUKI ◽  
Naoya MIYAJIMA ◽  
Yasutada SUZUKI
Keyword(s):  
Molecular Recognition ◽  
Cavity Size ◽  
Modified Cyclodextrins

scholarly journals Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition

2017 ◽  
Author(s):  
Zhiye Tang ◽  
Chia-en A. Chang
Keyword(s):  
Molecular Recognition ◽  
Force Fields ◽  
Md Simulations ◽  
Dissociation Rate ◽  
Water Molecules ◽  
Practical Applications ◽  
Guest Binding ◽  
Hydrogen Bond Networks ◽  
Comprehensive Picture ◽  
Dissociation Rate Constants

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-timescale molecular dynamics (MD) simulations, post-analysis and numerical calculations. We computed association and dissociation rate constants, enthalpy, and solvent and solute entropy of binding. All the computed values of kon, koff, ΔH, ΔS, and ΔG using GAFF-CD and q4MD-CD force fields for β-CD could be compared with experimental data directly and agreed reasonably with experiment findings. Both force fields resulted in similar computed ΔG from independently computed kinetics rates, ΔG=-RTln(kon · C° / k off), and thermodynamics properties, ΔG=ΔH – TΔS. The water entropy calculations show that entropy gain of desolvating water molecules are a major driving force, and both force fields have the same strength of non-polar attractions between solutes and β-CD as well. Water molecules play a crucial role in guest binding to β-CD. However, collective water/β-CD motions could contribute to different computed kon and ΔH values by different force fields, mainly because the parameters of β-CD provide different motions of β-CD, hydrogen-bond networks of water molecules in the cavity of free β-CD and the strength of desolvation penalty. As a result, q4MD-CD suggests that guest binding is mostly driven by enthalpy, while GAFF-CD shows that gaining entropy is the major driven force of binding. The study further interprets experiments, deepens our understanding of ligand binding, and suggests strategies for force field parameterization.

Preparation and molecular recognition of cyclodextrin monolayers with different cavity size on a gold wire electrode

1998 ◽  
Vol 6 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Iwao Suzuki ◽  
Kazufumi Murakami ◽  
Jun-ichi Anzai ◽  
Tetsuo Osa ◽  
Pingang He ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Gold Wire ◽  
Wire Electrode ◽  
Cavity Size

scholarly journals Molecular recognition with cyclodextrin polymer: a novel method for removing sulfides efficiently

RSC Advances ◽  
2017 ◽  
Vol 7 (62) ◽  
pp. 38902-38910 ◽  
Author(s):  
Linlin Li ◽  
Zunbin Duan ◽  
Jinshe Chen ◽  
Yulu Zhou ◽  
Lijun Zhu ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Cavity Size ◽  
Cyclodextrin Polymer ◽  
Novel Method ◽  
Cyclodextrin Polymers

A series of cyclodextrin polymers (CDPs) were synthesized and they were used for removing different sulfides by molecular recognition. It's showed that β-CDP has a more suitable cavity size for removing DBT.

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