Literature DB >> 27432339

Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands.

Matthew R Sullivan1, Punidha Sokkalingam1, Thong Nguyen1, James P Donahue1, Bruce C Gibb2.   

Abstract

In participation of the fifth statistical assessment of modeling of proteins and ligands (SAMPL5), the strength of association of six guests (3-8) to two hosts (1 and 2) were measured by 1H NMR and ITC. Each host possessed a unique and well-defined binding pocket, whilst the wide array of amphiphilic guests possessed binding moieties that included: a terminal alkyne, nitro-arene, alkyl halide and cyano-arene groups. Solubilizing head groups for the guests included both positively charged trimethylammonium and negatively charged carboxylate functionality. Measured association constants (K a ) covered five orders of magnitude, ranging from 56 M-1 for guest 6 binding with host 2 up to 7.43 × 106 M-1 for guest 6 binding to host 1.

Entities:  

Keywords:  Cavitand; Host-guest chemistry; Hydrophobic effect

Mesh:

Substances:

Year:  2016        PMID: 27432339      PMCID: PMC5571645          DOI: 10.1007/s10822-016-9925-0

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  19 in total

1.  On the value of c: can low affinity systems be studied by isothermal titration calorimetry?

Authors:  W Bruce Turnbull; Antonio H Daranas
Journal:  J Am Chem Soc       Date:  2003-12-03       Impact factor: 15.419

2.  Isothermal titration calorimetry at very low c.

Authors:  Joel Tellinghuisen
Journal:  Anal Biochem       Date:  2007-09-02       Impact factor: 3.365

3.  Guest-mediated switching of the assembly state of a water-soluble deep-cavity cavitand.

Authors:  Haiying Gan; Bruce C Gibb
Journal:  Chem Commun (Camb)       Date:  2013-02-18       Impact factor: 6.222

Review 4.  Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.

Authors:  John D Chodera; David L Mobley
Journal:  Annu Rev Biophys       Date:  2013       Impact factor: 12.981

5.  Molecular containers assembled through the hydrophobic effect.

Authors:  Jacobs H Jordan; Bruce C Gibb
Journal:  Chem Soc Rev       Date:  2015-01-21       Impact factor: 54.564

6.  An improved synthesis of 'octa-acid' deep-cavity cavitand.

Authors:  Simin Liu; Sarah E Whisenhunt-Ioup; Corinne L D Gibb; Bruce C Gibb
Journal:  Supramol Chem       Date:  2011-01-01       Impact factor: 1.688

7.  Solvent and guest isotope effects on complexation thermodynamics of alpha-, beta-, and 6-amino-6-deoxy-beta-cyclodextrins.

Authors:  Mikhail V Rekharsky; Yoshihisa Inoue
Journal:  J Am Chem Soc       Date:  2002-10-16       Impact factor: 15.419

8.  Differentiation of small alkane and alkyl halide constitutional isomers via encapsulation.

Authors:  Matthew R Sullivan; Bruce C Gibb
Journal:  Org Biomol Chem       Date:  2015-02-14       Impact factor: 3.876

9.  Anion complexation and the Hofmeister effect.

Authors:  Ryan S Carnegie; Corinne L D Gibb; Bruce C Gibb
Journal:  Angew Chem Int Ed Engl       Date:  2014-09-05       Impact factor: 15.336

10.  Guest binding and orientation within open nanoscale hosts.

Authors:  Zachary R Laughrey; Corinne L D Gibb; Tangi Senechal; Bruce C Gibb
Journal:  Chemistry       Date:  2003-01-03       Impact factor: 5.236

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  14 in total

1.  The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.

Authors:  Jian Yin; Niel M Henriksen; David R Slochower; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2016-09-16       Impact factor: 3.686

2.  The thermodynamics of guest complexation to octa-acid and tetra-endo-methyl octa-acid: reference data for the sixth statistical assessment of modeling of proteins and ligands (SAMPL6).

Authors:  Matthew R Sullivan; Wei Yao; Bruce C Gibb
Journal:  Supramol Chem       Date:  2018-11-18       Impact factor: 1.688

Review 3.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

4.  Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge.

Authors:  Mehtap Işık; Dorothy Levorse; David L Mobley; Timothy Rhodes; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2019-12-19       Impact factor: 3.686

5.  Tuning the Binding Dynamics of a Guest-Octaacid Capsule through Noncovalent Anchoring.

Authors:  Suma S Thomas; Hao Tang; Adam Gaudes; Signe B Baggesen; Corinne L D Gibb; Bruce C Gibb; Cornelia Bohne
Journal:  J Phys Chem Lett       Date:  2017-05-25       Impact factor: 6.475

6.  Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Authors:  Andrea Rizzi; Steven Murkli; John N McNeill; Wei Yao; Matthew Sullivan; Michael K Gilson; Michael W Chiu; Lyle Isaacs; Bruce C Gibb; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2018-11-10       Impact factor: 3.686

7.  Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.

Authors:  Michail Papadourakis; Stefano Bosisio; Julien Michel
Journal:  J Comput Aided Mol Des       Date:  2018-08-29       Impact factor: 3.686

8.  Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data.

Authors:  Jian Yin; Niel M Henriksen; Hari S Muddana; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2018-06-22       Impact factor: 6.006

9.  Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.

Authors:  Naohiro Nishikawa; Kyungreem Han; Xiongwu Wu; Florentina Tofoleanu; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-15       Impact factor: 3.686

Review 10.  Overview of the SAMPL5 host-guest challenge: Are we doing better?

Authors:  Jian Yin; Niel M Henriksen; David R Slochower; Michael R Shirts; Michael W Chiu; David L Mobley; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2016-09-22       Impact factor: 3.686

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