Host Dynamics under General-Purpose Force Fields

04 May 2023, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Macrocyclic hosts as prototypical receptors to gaseous and drug-like guests are crucial components in pharmaceutical research. The external guests are often coordinated at the center of these macromolecular containers. The formation of host-guest coordination is accompanied by the broken of host-water and host-ion interactions and sometimes also involves some kinds of conformational rearrangements of the host itself. A balanced description of various components of interacting terms is indispensable. However, up to now, the modelling community still lacks a general yet detailed understanding of commonly employed general-purpose force fields and the host dynamics produced by these popular selections. To fill this critical gap, we in this paper profile energetics and dynamics of four types of popular macrocycles, including cucurbiturils, pillararenes, cyclodextrins, and octa acids. The presented investigations of force-field definitions, refitting and evaluations are unprecedently detailed. Based on the valuable observations and insightful explanations, we finally summarize some general guidelines on force-field parametrization and selection in host-guest modelling.

Keywords

Host-guest Binding
Force Field
Fixed-charge Model
RESP
AM1-BCC
HF/6-31G*
B3LYP
BP86
PBE
PW6B95
TPSSh
wB97X-D
def2-QZVPP
ESP
anisotropic distribution
ab initio calculations
Macrocycles
Force Field Development
Conformational Preference
Atomic Charges
electrostatic potential
general AMBER force field
GAFF2
GAFF
Cucurbit[n]urils
pillar[n]arene
cyclodextrin
octa acid
methylation
sulfur substitution
Chemical Modification
RRMSE
Refitting
Regularization
Active Learning
Adaptive Sampling
Ring Size
Torsion
1-4 Interaction
Bond-stretching
Angle-bending
Dihedral-Flipping
Flexibility
general-purpose force fields
Force Error
β-CD
Force-matching
B97-3c
Transferable
Molecule-specific
Host-water interaction
host-ion coordination
radius of gyration
Unbiased Simulation
High-temperature acceleration

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