A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions
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Title
A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions
Authors
Keywords
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Journal
MOLECULES
Volume 28, Issue 7, Pages 3124
Publisher
MDPI AG
Online
2023-03-31
DOI
10.3390/molecules28073124
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Note: Only part of the references are listed.- PSMA-Targeted Supramolecular Nanoparticles Prepared From Cucurbit[8]uril-Based Ternary Host–Guest Recognition for Prostate Cancer Therapy
- (2022) Xueyan Zhang et al. Frontiers in Chemistry
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- (2021) Piero Procacci et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
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- (2020) Nasim Ahmadian et al. Journal of Chemical Information and Modeling
- SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations
- (2020) Zhaoxi Sun et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Structural Features of the Inclusion Compound Based on the trans-[Co(en)2Cl2]+ Complex and Cucurbit[8]Uril: A DFT Study
- (2020) T. N. Grishaeva et al. JOURNAL OF STRUCTURAL CHEMISTRY
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- (2018) Xiaohui Wang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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- (2015) D B McClatchy et al. MOLECULAR PSYCHIATRY
- Inclusion compound based on Bis(ethylenediamine)copper(II) complex and cucurbit[8]uril: Quantum chemical prediction for structure and formation thermodynamic parameters
- (2015) T. N. Grishaeva et al. RUSSIAN JOURNAL OF INORGANIC CHEMISTRY
- Density functional investigations on 2-naphthalenecarbonitrile dimerization within cucurbit[8]uril cavitand
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- (2014) Pratyush Tiwary et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Building Water Models: A Different Approach
- (2014) Saeed Izadi et al. Journal of Physical Chemistry Letters
- PLUMED 2: New feathers for an old bird
- (2013) Gareth A. Tribello et al. COMPUTER PHYSICS COMMUNICATIONS
- Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines
- (2013) Pathik S. Brahmkshatriya et al. Current Computer-Aided Drug Design
- Robust and efficient configurational molecular sampling via Langevin dynamics
- (2013) Benedict Leimkuhler et al. JOURNAL OF CHEMICAL PHYSICS
- Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method for Full Quantum Mechanical Calculation of Protein Energy
- (2013) Xianwei Wang et al. JOURNAL OF PHYSICAL CHEMISTRY A
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- (2013) Niels Grønbech-Jensen et al. MOLECULAR PHYSICS
- The critical effect of polarization on the dynamical structure of guanine quadruplex DNA
- (2013) Jianing Song et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
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- (2013) Pratyush Tiwary et al. PHYSICAL REVIEW B
- Involvement of the N-methyl-d-aspartate receptor GluN2D subunit in phencyclidine-induced motor impairment, gene expression, and increased Fos immunoreactivity
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- (2012) Robert B. Best et al. BIOPHYSICAL JOURNAL
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- (2012) Manuel Doemer et al. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
- On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds
- (2012) Michal Kolář et al. Journal of Chemical Theory and Computation
- Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
- (2012) Lee-Ping Wang et al. Journal of Chemical Theory and Computation
- Cucurbituril chemistry: a tale of supramolecular success
- (2011) Eric Masson et al. RSC Advances
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
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- (2011) Frank Neese Wiley Interdisciplinary Reviews-Computational Molecular Science
- GPU-accelerated molecular modeling coming of age
- (2010) John E. Stone et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Umbrella integration in two or more reaction coordinates
- (2009) Johannes Kästner JOURNAL OF CHEMICAL PHYSICS
- A novel 1:2 cucurbit[8]uril inclusion complex with N-phenylpiperazine hydrochloride
- (2009) Xiaojun Wu et al. JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY
- Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters
- (2009) In Suk Joung et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Target Flexibility: An Emerging Consideration in Drug Discovery and Design†
- (2008) Pietro Cozzini et al. JOURNAL OF MEDICINAL CHEMISTRY
- Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
- (2008) In Suk Joung et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Quantum free-energy differences from nonequilibrium path integrals. II. Convergence properties for the harmonic oscillator
- (2008) Ramses van Zon et al. PHYSICAL REVIEW E
- Quantum free-energy differences from nonequilibrium path integrals. I. Methods and numerical application
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- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
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