Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding.

With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments, and quantify inter-fragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems, and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.

[1]  A. Savin,et al.  Classification of chemical bonds based on topological analysis of electron localization functions , 1994, Nature.

[2]  Reinhold Schneider,et al.  Daubechies wavelets as a basis set for density functional pseudopotential calculations. , 2008, The Journal of chemical physics.

[3]  Mikko Kivelä,et al.  Generalizations of the clustering coefficient to weighted complex networks. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[4]  M. Weigt,et al.  On the properties of small-world network models , 1999, cond-mat/9903411.

[5]  I. Mayer,et al.  Bond order and valence indices: A personal account , 2007, J. Comput. Chem..

[6]  M. Pavanello,et al.  Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions , 2015, Journal of physics. Condensed matter : an Institute of Physics journal.

[7]  Ryan P A Bettens,et al.  Energy-Based Molecular Fragmentation Methods. , 2015, Chemical reviews.

[8]  M. Teeter,et al.  Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Adam Wasserman,et al.  On Hardness and Electronegativity Equalization in Chemical Reactivity Theory , 2006 .

[10]  Jean-Philip Piquemal,et al.  NCIPLOT: a program for plotting non-covalent interaction regions. , 2011, Journal of chemical theory and computation.

[11]  S. Goedecker Linear scaling electronic structure methods , 1999 .

[12]  W. Kohn,et al.  Self-Consistent Equations Including Exchange and Correlation Effects , 1965 .

[13]  Travis V. Harris,et al.  The ONIOM Method and Its Applications. , 2015, Chemical reviews.

[14]  Julia Contreras-García,et al.  Revealing noncovalent interactions. , 2010, Journal of the American Chemical Society.

[15]  Christoph R. Jacob,et al.  Subsystem density‐functional theory , 2014 .

[16]  Krzysztof Szalewicz,et al.  Symmetry‐adapted perturbation theory of intermolecular forces , 2012 .

[17]  Kazuo Kitaura,et al.  Modeling and Visualization for the Fragment Molecular Orbital Method with the Graphical User Interface FU, and Analyses of Protein-Ligand Binding , 2017 .

[18]  Stefan Goedecker,et al.  Accurate and efficient linear scaling DFT calculations with universal applicability. , 2015, Physical chemistry chemical physics : PCCP.

[19]  Jiali Gao,et al.  Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations , 1997 .

[20]  S. J. Grabowski Ab Initio Calculations on Conventional and Unconventional Hydrogen BondsStudy of the Hydrogen Bond Strength , 2001 .

[21]  D. Kofke,et al.  Hydrogen fluoride phase behavior and molecular structure: A QM/MM potential model approach , 2003 .

[22]  Krishnan Raghavachari,et al.  Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules. , 2015, Chemical reviews.

[23]  D. Bowler,et al.  O(N) methods in electronic structure calculations. , 2011, Reports on progress in physics. Physical Society.

[24]  István Mayer,et al.  Bond order and valence: Relations to Mulliken's population analysis , 1984 .

[25]  Chris Morley,et al.  Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit , 2008, Chemistry Central journal.

[26]  Laura E Ratcliff,et al.  Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis. , 2016, Journal of chemical theory and computation.

[27]  Álvaro Vázquez-Mayagoitia,et al.  Norm-conserving pseudopotentials with chemical accuracy compared to all-electron calculations. , 2012, The Journal of chemical physics.

[28]  C. Lecomte,et al.  Topological analysis of the electron density in hydrogen bonds. , 1999, Acta crystallographica. Section B, Structural science.

[29]  Wei Li,et al.  Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates. , 2014, Accounts of chemical research.

[30]  M. Reverberi,et al.  Degradation of Aflatoxins by Means of Laccases from Trametes versicolor: An In Silico Insight , 2017, Toxins.

[31]  D. Truhlar,et al.  Multilevel X-Pol: a fragment-based method with mixed quantum mechanical representations of different fragments. , 2012, The journal of physical chemistry. B.

[32]  Donald G Truhlar,et al.  Incorporation of a QM/MM buffer zone in the variational double self-consistent field method. , 2008, The journal of physical chemistry. B.

[33]  Michael A Collins,et al.  Systematic fragmentation of large molecules by annihilation. , 2012, Physical chemistry chemical physics : PCCP.

[34]  P. Willett,et al.  Promoting Access to White Rose Research Papers Similarity-based Virtual Screening Using 2d Fingerprints , 2022 .

[35]  Peter Willett,et al.  Similarity-based virtual screening using 2D fingerprints. , 2006, Drug discovery today.

[36]  John F. Ouyang,et al.  Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules. , 2012, Journal of chemical theory and computation.

[37]  Walter Thiel,et al.  QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.

[38]  Shridhar R. Gadre,et al.  Molecular tailoring approach : towards PC-based ab initio treatment of large molecules , 2006 .

[39]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[40]  Shridhar R Gadre,et al.  Molecular tailoring approach: a route for ab initio treatment of large clusters. , 2014, Accounts of chemical research.

[41]  Spencer R Pruitt,et al.  Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.

[42]  Spencer R Pruitt,et al.  Efficient and accurate fragmentation methods. , 2014, Accounts of chemical research.

[43]  Ernesto Estrada,et al.  The Structure of Complex Networks: Theory and Applications , 2011 .

[44]  Saraswathi Vishveshwara,et al.  Interaction energy based protein structure networks. , 2010, Biophysical journal.

[45]  Robert M Parrish,et al.  Chemical Assignment of Symmetry-Adapted Perturbation Theory Interaction Energy Components: The Functional-Group SAPT Partition. , 2014, Journal of chemical theory and computation.

[46]  Michael A Collins,et al.  Approximate ab initio energies by systematic molecular fragmentation. , 2005, The Journal of chemical physics.

[47]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[48]  Satoru Kawai,et al.  An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..

[49]  Takahito Nakajima,et al.  Massively parallel sparse matrix function calculations with NTPoly , 2017, Comput. Phys. Commun..

[50]  V Ganesh,et al.  Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies. , 2006, The Journal of chemical physics.

[51]  Donald G Truhlar,et al.  The variational explicit polarization potential and analytical first derivative of energy: Towards a next generation force field. , 2008, The Journal of chemical physics.

[52]  W. Thiel,et al.  Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches , 1996 .

[53]  Kazuo Kitaura,et al.  Pair interaction energy decomposition analysis , 2007, J. Comput. Chem..

[54]  Adam Wasserman,et al.  On the foundations of chemical reactivity theory. , 2007, The journal of physical chemistry. A.

[55]  P. Hohenberg,et al.  Inhomogeneous Electron Gas , 1964 .

[56]  Vladimir Sladek,et al.  Protein Residue Networks from Energetic and Geometric Data: Are They Identical? , 2018, Journal of chemical theory and computation.

[57]  François Gygi,et al.  Performance and accuracy of recursive subspace bisection for hybrid DFT calculations in inhomogeneous systems. , 2015, Journal of chemical theory and computation.

[58]  Stefan Goedecker,et al.  Daubechies wavelets for linear scaling density functional theory. , 2014, The Journal of chemical physics.

[59]  James J. P. Stewart,et al.  Bond indices and valency , 1973 .

[60]  Wei Li,et al.  The generalized energy-based fragmentation approach with an improved fragmentation scheme: benchmark results and illustrative applications. , 2013, Chemphyschem : a European journal of chemical physics and physical chemistry.

[61]  R. Adamiak,et al.  The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove. , 2001, Nucleic acids research.

[62]  Richard F. W. Bader A quantum theory of molecular structure and its applications , 1991 .

[63]  Kazuo Kitaura,et al.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. , 2007, The journal of physical chemistry. A.

[64]  S. Hirata,et al.  Ab initio molecular crystal structures, spectra, and phase diagrams. , 2014, Accounts of chemical research.

[65]  Kieron Burke,et al.  Partition Density Functional Theory , 2009, 0901.0942.

[66]  Thierry Deutsch,et al.  Challenges in large scale quantum mechanical calculations , 2016, 1609.00252.

[67]  Jan H. Jensen,et al.  FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations , 2012, PloS one.

[68]  János G. Ángyán,et al.  Approximate electrostatic interaction operator for QM/MM calculations , 2002 .

[69]  Axel D. Becke,et al.  A Simple Measure of Electron Localization in Atomic and Molecular-Systems , 1990 .

[70]  P. Mezey Fuzzy electron density fragments in macromolecular quantum chemistry, combinatorial quantum chemistry, functional group analysis, and shape-activity relations. , 2014, Accounts of chemical research.

[71]  Shridhar R. Gadre,et al.  Molecular Tailoring Approach for Simulation of Electrostatic Properties , 1994 .

[72]  N. Hine,et al.  Applications of large-scale density functional theory in biology , 2016, Journal of physics. Condensed matter : an Institute of Physics journal.

[73]  Ryan P A Bettens,et al.  The combined fragmentation and systematic molecular fragmentation methods. , 2014, Accounts of chemical research.

[74]  S. Goedecker,et al.  Relativistic separable dual-space Gaussian pseudopotentials from H to Rn , 1998, cond-mat/9803286.

[75]  Kenneth B. Wiberg,et al.  Application of the pople-santry-segal CNDO method to the cyclopropylcarbinyl and cyclobutyl cation and to bicyclobutane , 1968 .

[76]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[77]  Shuhua Li,et al.  An efficient implementation of the generalized energy-based fragmentation approach for general large molecules. , 2010, The journal of physical chemistry. A.

[78]  Jiali Gao,et al.  Communication: variational many-body expansion: accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method. , 2012, The Journal of chemical physics.

[79]  D. Truhlar,et al.  QM/MM: what have we learned, where are we, and where do we go from here? , 2007 .

[80]  Xiao He,et al.  Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy. , 2013, The journal of physical chemistry. A.

[81]  J. Recio,et al.  Electron delocalization and bond formation under the ELF framework , 2011 .

[82]  Jiali Gao,et al.  The Design of a Next Generation Force Field: The X-POL Potential. , 2007, Journal of chemical theory and computation.

[83]  John M Herbert,et al.  Fantasy versus reality in fragment-based quantum chemistry. , 2019, The Journal of chemical physics.

[84]  Xiao He,et al.  Fragment quantum mechanical calculation of proteins and its applications. , 2014, Accounts of chemical research.

[85]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[86]  Jiali Gao,et al.  A molecular-orbital derived polarization potential for liquid water , 1998 .

[87]  Luigi Genovese,et al.  Efficient Computation of Sparse Matrix Functions for Large-Scale Electronic Structure Calculations: The CheSS Library. , 2017, Journal of chemical theory and computation.