Automated design of flexible linkers.

This paper presents a method for the systematic and automated design of flexible organic linkers for construction of metal organic-frameworks (MOFs) in which flexibility, compliance, or other mechanically exotic properties originate at the linker level rather than from the framework kinematics. Our method couples a graph grammar method for systematically generating linker like molecules with molecular dynamics modeling of linkers' mechanical response. Using this approach we have generated a candidate pool of >59,000 hypothetical linkers. We screen linker candidates according to their mechanical behaviors under large deformation, and extract fragments common to the most performant candidate materials. To demonstrate the general approach to MOF design we apply our system to designing linkers for pressure switching MOFs-MOFs that undergo reversible structural collapse after a stress threshold is exceeded.

[1]  Elazer R. Edelman,et al.  Adv. Drug Delivery Rev. , 1997 .

[2]  Peter Willett,et al.  Rapid Quantification of Molecular Diversity for Selective Database Acquisition , 1997, J. Chem. Inf. Comput. Sci..

[3]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[4]  François-Xavier Coudert,et al.  Metal-organic frameworks with wine-rack motif: what determines their flexibility and elastic properties? , 2013, The Journal of chemical physics.

[5]  C. Serre,et al.  Large breathing effects in three-dimensional porous hybrid matter: facts, analyses, rules and consequences. , 2009, Chemical Society reviews.

[6]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[7]  Siegfried Schmauder,et al.  Comput. Mater. Sci. , 1998 .

[8]  G. Vetrovec.  DES , 2021, Encyclopedia of Systems and Control.

[9]  Bart Goethals,et al.  Proceedings of the 1st international workshop on open source data mining: frequent pattern mining implementations , 2005, KDD 2005.

[10]  A. McGaughey,et al.  Thermal conductivity of metal-organic framework 5 (MOF-5): Part I. Molecular dynamics simulations , 2007 .

[11]  David Weininger,et al.  SMILES, 3. DEPICT. Graphical depiction of chemical structures , 1990, J. Chem. Inf. Comput. Sci..

[12]  P. Greaney,et al.  Relationship between thermal conductivity and framework architecture in MOF-5 , 2014 .

[13]  Aamod V. Desai,et al.  Exploiting Framework Flexibility of a Metal-Organic Framework for Selective Adsorption of Styrene over Ethylbenzene. , 2015, Inorganic chemistry.

[14]  Richard L. Martin,et al.  On the flexibility of metal-organic frameworks. , 2014, Journal of the American Chemical Society.

[15]  F. Kapteijn,et al.  Experimental Evidence of Negative Linear Compressibility in the MIL-53 Metal-Organic Framework Family. , 2015, CrystEngComm.

[16]  Zoe A. D. Lethbridge,et al.  Elastic anisotropy and extreme Poisson's ratios in single crystals , 2010 .

[17]  H. B. Mann,et al.  On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other , 1947 .

[18]  Matthew I. Campbell,et al.  Automated synthesis of electromechanical design configurations from empirical analysis of function to form mapping , 2009 .

[19]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[20]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[21]  François-Xavier Coudert,et al.  Anisotropic elastic properties of flexible metal-organic frameworks: how soft are soft porous crystals? , 2012, Physical review letters.

[22]  Maciej Haranczyk,et al.  In Silico Discovery of High Deliverable Capacity Metal–Organic Frameworks , 2015 .

[23]  David Weininger,et al.  SMILES. 2. Algorithm for generation of unique SMILES notation , 1989, J. Chem. Inf. Comput. Sci..

[24]  William A. Goddard,et al.  Metal−Organic Frameworks Provide Large Negative Thermal Expansion Behavior , 2007 .

[25]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..