Towards Automated Design of Mechanically Functional Molecules

2015 ◽  
Author(s):  
Charles A. Manion ◽  
Ryan Arlitt ◽  
Irem Tumer ◽  
Matthew I. Campbell ◽  
P. Alex Greaney
Keyword(s):  
Smart Materials ◽  
De Novo ◽  
Molecular Design ◽  
Metal Organic Framework ◽  
Automated Design ◽  
Computational Approach ◽  
Responsive Materials ◽  
New Class ◽  
De Novo Molecular Design ◽  
Metal Organic

Metal Organic Responsive Frameworks (MORFs) are a proposed new class of smart materials consisting of a Metal Organic Framework (MOF) with photoisomerizing beams (also known as linkers) that fold in response to light. Within a device these new light responsive materials could provide the capabilities such as photo-actuation, photo-tunable rigidity, and photo-tunable porosity. However, conventional MOF architectures are too rigid to allow isomerization of photoactive sub-molecules. We propose a new computational approach for designing MOF linkers to have the required mechanical properties to allow the photoisomer to fold by borrowing concepts from de novo molecular design and graph synthesis. Here we show how this approach can be used to design compliant linkers with the necessary flexibility to be actuated by photoisomerization and used to design MORFs with desired functionality.

scholarly journals Cooperative Light-Induced Breathing of Soft Porous Crystals via Azobenzene Buckling

2020 ◽  
Author(s):  
Simon Krause ◽  
Jack D. Evans ◽  
Volodymyr Bon ◽  
Stefano Crespi ◽  
Wojciech Danowski ◽  
...  
Keyword(s):  
Smart Materials ◽  
Gas Adsorption ◽  
Metal Organic Framework ◽  
Porous Network ◽  
Dynamic Simulations ◽  
Responsive Materials ◽  
Future Design ◽  
Non Invasive ◽  
Metal Organic ◽  
In Situ Diffraction

Although light is a prominent stimulus for smart materials, the application of photoswitches as light-responsive triggers for phase transitions of porous materials remains poorly explored. Here we incorporate an azobenzene photoswitch in the backbone of a metal-organic framework producing light-induced structural contraction of the porous network in parallel to gas adsorption. Light-stimulation enables non-invasive spatiotemporal control over the mechanical properties of the framework, which ultimately leads to pore contraction and subsequent guest release via negative gas adsorption. The complex mechanism of light-gated breathing is established by a series of in situ diffraction and spectroscopic experiments, supported by quantum mechanical and molecular dynamic simulations. Unexpectedly, this study identifies a novel light-induced deformation mechanism of constrained azobenzene photoswitches relevant to the future design of light-responsive materials.

scholarly journals Cooperative Light-Induced Breathing of Soft Porous Crystals via Azobenzene Buckling

2020 ◽  
Author(s):  
Simon Krause ◽  
Jack D. Evans ◽  
Volodymyr Bon ◽  
Stefano Crespi ◽  
Wojciech Danowski ◽  
...  
Keyword(s):  
Smart Materials ◽  
Gas Adsorption ◽  
Metal Organic Framework ◽  
Porous Network ◽  
Dynamic Simulations ◽  
Responsive Materials ◽  
Future Design ◽  
Non Invasive ◽  
Metal Organic ◽  
In Situ Diffraction

Although light is a prominent stimulus for smart materials, the application of photoswitches as light-responsive triggers for phase transitions of porous materials remains poorly explored. Here we incorporate an azobenzene photoswitch in the backbone of a metal-organic framework producing light-induced structural contraction of the porous network in parallel to gas adsorption. Light-stimulation enables non-invasive spatiotemporal control over the mechanical properties of the framework, which ultimately leads to pore contraction and subsequent guest release via negative gas adsorption. The complex mechanism of light-gated breathing is established by a series of in situ diffraction and spectroscopic experiments, supported by quantum mechanical and molecular dynamic simulations. Unexpectedly, this study identifies a novel light-induced deformation mechanism of constrained azobenzene photoswitches relevant to the future design of light-responsive materials.

scholarly journals De novo molecular design and generative models

2021 ◽  
Author(s):  
Joshua Meyers ◽  
Benedek Fabian ◽  
Nathan Brown
Keyword(s):  
De Novo ◽  
Molecular Design ◽  
Generative Models ◽  
De Novo Molecular Design

PRO_LIGAND: An Approach to de Novo Molecular Design. 2. Design of Novel Molecules from Molecular Field Analysis (MFA) Models and Pharmacophores

1994 ◽  
Vol 37 (23) ◽  
pp. 3994-4002 ◽  
Author(s):  
Bohdan Waszkowycz ◽  
David E. Clark ◽  
David Frenkel ◽  
Jin Li ◽  
Christopher W. Murray ◽  
...  
Keyword(s):  
De Novo ◽  
Molecular Design ◽  
Field Analysis ◽  
Molecular Field ◽  
Molecular Field Analysis ◽  
De Novo Molecular Design

scholarly journals Comparison Between SMILES-Based Differential Neural Computer and Recurrent Neural Network Architectures for De Novo Molecule Design

2019 ◽  
Author(s):  
Simon Johansson ◽  
Oleksii Ptykhodko ◽  
Josep Arús-Pous ◽  
Ola Engkvist ◽  
Hongming Chen
Keyword(s):  
De Novo ◽  
Molecular Design ◽  
Research Area ◽  
Computational Time ◽  
Test Cases ◽  
Sequential Data ◽  
Network Architectures ◽  
De Novo Molecular Design ◽  
Molecule Design ◽  
The Cost

In recent years, deep learning for de novo molecular generation has become a rapidly growing research area. Recurrent neural networks (RNN) using the SMILES molecular representation is one of the most common approaches used. Recent study shows that the differentiable neural computer (DNC) can make considerable improvement over the RNN for modeling of sequential data. In the current study, DNC has been implemented as an extension to REINVENT, an RNN-based model that has already been used successfully to make de novo molecular design. The model was benchmarked on its capacity to learn the SMILES language on the GDB-13 and MOSES datasets. The DNC shows improvement on all test cases conducted at the cost of significantly increased computational time and memory consumption.

PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules

1995 ◽  
Vol 9 (1) ◽  
pp. 13-32 ◽  
Author(s):  
David E. Clark ◽  
David Frenkel ◽  
Stephen A. Levy ◽  
Jin Li ◽  
Christopher W. Murray ◽  
...  
Keyword(s):  
Organic Molecules ◽  
De Novo ◽  
Molecular Design ◽  
De Novo Molecular Design
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