Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute bond orders

Developing a comprehensive method to compute bond orders is a problem that has eluded chemists since Lewis's pioneering work on chemical bonding a century ago. Here, a computationally efficient method solving this problem is introduced and demonstrated for diverse materials including elements from each chemical group and period. The method is applied to non-magnetic, collinear magnetic, and non-collinear magnetic materials with localized or delocalized bonding electrons. Examples studied include the stretched O2 molecule, 26 diatomic molecules, 3d and 5d transition metal solids, periodic materials with 1 to 8748 atoms per unit cell, a biomolecule, a hypercoordinate molecule, an electron deficient molecule, hydrogen bound systems, transition states, Lewis acid–base complexes, aromatic compounds, magnetic systems, ionic materials, dispersion bound systems, nanostructures, and other materials. From near-zero to high-order bonds were studied. Both the bond orders and the sum of bond orders for each atom are accurate across various bonding types: metallic, covalent, polar-covalent, ionic, aromatic, dative, hypercoordinate, electron deficient multi-centered, agostic, and hydrogen bonding. The method yields similar results for correlated wavefunction and density functional theory inputs and for different SZ values of a spin multiplet. The method requires only the electron and spin magnetization density distributions as input and has a computational cost scaling linearly with increasing number of atoms in the unit cell. No prior approach is as general. The method does not apply to electrides, highly time-dependent states, some extremely high-energy excited states, and nuclear reactions.

[1]  M. Gopinathan,et al.  Valency. I. A quantum chemical definition and properties , 1983 .

[2]  Frank Weinhold,et al.  Natural localized molecular orbitals , 1985 .

[3]  L. Hedin,et al.  A local exchange-correlation potential for the spin polarized case. i , 1972 .

[4]  G. Mazur,et al.  Quantum chemical valence indices from the one-determinantal difference approach , 1996 .

[5]  M. Ozawa,et al.  Experimental demonstration of a universally valid error–disturbance uncertainty relation in spin measurements , 2012, Nature Physics.

[6]  A. Otero-de-la-Roza,et al.  Density-functional description of electrides. , 2014, Physical chemistry chemical physics : PCCP.

[7]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[8]  Kimihiko Hirao,et al.  Cluster expansion of the wavefunction. Symmetry-adapted-cluster expansion, its variational determination, and extension of open-shell orbital theory , 1978 .

[9]  G. Abrams,et al.  The use of intraocular gases. The results of sulfur hexafluoride gas in retinal detachment surgery. , 1981, Ophthalmology.

[10]  B. Lamb,et al.  Measurement of methane emissions from ruminant livestock using a sulfur hexafluoride tracer technique. , 1994, Environmental science & technology.

[11]  P. Schwerdtfeger,et al.  Ground-state properties and static dipole polarizabilities of the alkali dimers from K2 n to Fr2 n(n=0,+1) from scalar relativistic pseudopotential coupled cluster and density functional studies. , 2005, The Journal of chemical physics.

[12]  David Feller The role of databases in support of computational chemistry calculations , 1996 .

[13]  Á. M. Pendás,et al.  A hierarchy of chemical bonding indices in real space from reduced density matrices and cumulants , 2013 .

[14]  P. Ayers,et al.  The conformational sensitivity of iterative stockholder partitioning schemes , 2012 .

[15]  David S. Sholl,et al.  A dimensionless reaction coordinate for quantifying the lateness of transition states , 2009, J. Comput. Chem..

[16]  Adam J. Bridgeman,et al.  The Mayer bond order as a tool in inorganic chemistry , 2001 .

[17]  B. Roos,et al.  Quantum chemical calculations show that the uranium molecule U2 has a quintuple bond , 2005, Nature.

[18]  R. Wheatley,et al.  Redefining the atom: atomic charge densities produced by an iterative stockholder approach. , 2008, Chemical communications.

[19]  Gerald Knizia,et al.  Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts. , 2013, Journal of chemical theory and computation.

[20]  D. L. Cooper,et al.  Chemical Bonding to Hypercoordinate Second-Row Atoms: d Orbital Participation versus Democracy , 1994 .

[21]  Structural characteristics for biological activity of heat-stable enterotoxin produced by enterotoxigenic Escherichia coli: X-ray crystallography of weakly toxic and nontoxic analogs. , 1996 .

[22]  Alexander I Boldyrev,et al.  Developing paradigms of chemical bonding: adaptive natural density partitioning. , 2008, Physical chemistry chemical physics : PCCP.

[23]  R. Kerber If it's resonance, what is resonating? , 2006 .

[24]  Nancy Wilkins-Diehr,et al.  XSEDE: Accelerating Scientific Discovery , 2014, Computing in Science & Engineering.

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

[26]  Hiroshi Nakatsuji,et al.  Cluster expansion of the wavefunction. Calculation of electron correlations in ground and excited states by SAC and SAC CI theories , 1979 .

[27]  Damon Donald Ridley Introduction to Structure Searching with SciFinder Scholar , 2001 .

[28]  M. K. Wilkinson,et al.  NEUTRON DIFFRACTION STUDIES OF VARIOUS TRANSITION ELEMENTS , 1953 .

[29]  A. Becke A multicenter numerical integration scheme for polyatomic molecules , 1988 .

[30]  N. Handy,et al.  Left-right correlation energy , 2001 .

[31]  Chérif F. Matta,et al.  Modeling Biophysical and Biological Properties From the Characteristics of the Molecular Electron Density, Electron Localization and Delocalization Matrices, and the Electrostatic Potential , 2014, J. Comput. Chem..

[32]  R. Ponec Electron pairing and chemical bonds: Chemical bonds from the condition of minimum fluctuation of electron pair , 1998 .

[33]  T Verstraelen,et al.  Hirshfeld-E Partitioning: AIM Charges with an Improved Trade-off between Robustness and Accurate Electrostatics. , 2013, Journal of chemical theory and computation.

[34]  Chemical properties of rutherfordium (Rf) and dubnium (Db) in the aqueous phase , 2016 .

[35]  G. Schaftenaar,et al.  Molden: a pre- and post-processing program for molecular and electronic structures* , 2000, J. Comput. Aided Mol. Des..

[36]  A. Kalemos The nature of the chemical bond in Be2+, Be2, Be2-, and Be3. , 2016, The Journal of chemical physics.

[37]  R. Nalewajski,et al.  Modified valence indices from the two‐particle density matrix , 1994 .

[38]  Robert M. Hanson,et al.  Jmol – a paradigm shift in crystallographic visualization , 2010 .

[39]  J. Ángyán,et al.  COVALENT BOND ORDERS AND ATOMIC VALENCE INDICES IN THE TOPOLOGICAL THEORY OF ATOMS IN MOLECULES , 1994 .

[40]  Kresse,et al.  Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. , 1996, Physical review. B, Condensed matter.

[41]  W. Zurek Decoherence, einselection, and the quantum origins of the classical , 2001, quant-ph/0105127.

[42]  Xavier Fradera,et al.  The calculation of electron localization and delocalization indices at the Hartree–Fock, density functional and post-Hartree–Fock levels of theory , 2002 .

[43]  P. Popelier,et al.  Nature of Chemical Interactions from the Profiles of Electron Delocalization Indices. , 2011, Journal of chemical theory and computation.

[44]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[45]  Tian Lu,et al.  Multiwfn: A multifunctional wavefunction analyzer , 2012, J. Comput. Chem..

[46]  M. Frisch,et al.  Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .

[47]  Jun Li,et al.  Basis Set Exchange: A Community Database for Computational Sciences , 2007, J. Chem. Inf. Model..

[48]  T. Hondoh,et al.  The electron density distribution in ice Ih determined by single‐crystal x‐ray diffractometry , 1990 .

[49]  Artur Michalak,et al.  Natural orbitals for chemical valence as descriptors of chemical bonding in transition metal complexes , 2007, Journal of molecular modeling.

[50]  Damon D. Ridley Strategies for Chemical Reaction Searching in SciFinder , 2000, J. Chem. Inf. Comput. Sci..

[51]  R. Gillespie The octet rule and hypervalence: two misunderstood concepts , 2002 .

[52]  Arshad Mehmood,et al.  The electron delocalization range in stretched bonds , 2016 .

[53]  E. Magnusson Hypercoordinate molecules of second-row elements : d functions or d orbitals ? , 1990 .

[54]  J. Cioslowski,et al.  Rigorous interpretation of electronic wave functions. 2. Electronic structures of selected phosphorus, sulfur, and chlorine fluorides and oxides , 1993 .

[55]  R. Bader,et al.  Spatial localization of the electronic pair and number distributions in molecules , 1975 .

[56]  Alexander I Boldyrev,et al.  Solid state adaptive natural density partitioning: a tool for deciphering multi-center bonding in periodic systems. , 2013, Physical chemistry chemical physics : PCCP.

[57]  A. J. Coleman THE STRUCTURE OF FERMION DENSITY MATRICES , 1963 .

[58]  Jürgen Hafner,et al.  Ab‐initio simulations of materials using VASP: Density‐functional theory and beyond , 2008, J. Comput. Chem..

[59]  A. Szabo,et al.  Modern quantum chemistry , 1982 .

[60]  Clark R. Landis,et al.  NBO 6.0: Natural bond orbital analysis program , 2013, J. Comput. Chem..

[61]  Ernest R. Davidson,et al.  A test of the Hirshfeld definition of atomic charges and moments , 1992 .

[62]  Linus Pauling,et al.  The Nature of the Interatomic Forces in Metals , 1938 .

[63]  L. Curtiss,et al.  Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint , 1988 .

[64]  Jerzy Cioslowski,et al.  Covalent bond orders in the topological theory of atoms in molecules , 1991 .

[65]  Krista A. Novstrup,et al.  Quantitative Effects of Ion Pairing and Sterics on Chain Propagation Kinetics for 1-Hexene Polymerization Catalyzed by Mixed Cp′/ArO Complexes , 2008 .

[66]  R. Ponec,et al.  Chemical Structures from the Analysis of Domain-Averaged Fermi Holes. Hypervalence and the Nature of Bonding in Isocoordinated Molecules SF6 and CLi6 , 2002 .

[67]  J. Simons,et al.  The Dielectric Strength of Gaseous Fluorocarbons , 1950 .

[68]  A. Ravishankara,et al.  Atmospheric Lifetimes of Long-Lived Halogenated Species , 1993, Science.

[69]  Alexey I. Baranov,et al.  Electron localization and delocalization indices for solids , 2011, J. Comput. Chem..

[70]  Gilbert N. Lewis,et al.  The Atom and the Molecule , 1916, Resonance.

[71]  David J. Nesbitt,et al.  Definition of the hydrogen bond (IUPAC Recommendations 2011) , 2011 .

[72]  D. Sholl,et al.  Molecular chemisorption on open metal sites in Cu(3)(benzenetricarboxylate)(2): A spatially periodic density functional theory study. , 2010, The Journal of chemical physics.

[73]  G. Kresse,et al.  From ultrasoft pseudopotentials to the projector augmented-wave method , 1999 .

[74]  Gernot Frenking,et al.  Unicorns in the world of chemical bonding models , 2007, J. Comput. Chem..

[75]  P. Trucano,et al.  Structure of graphite by neutron diffraction , 1975, Nature.

[76]  Linus Pauling,et al.  Atomic Radii and Interatomic Distances in Metals , 1947 .

[77]  Donald W. Brenner,et al.  A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons , 2002 .

[78]  F. L. Hirshfeld Bonded-atom fragments for describing molecular charge densities , 1977 .

[79]  L. Paul Steele,et al.  Sulfur hexafluoride—A powerful new atmospheric tracer , 1996 .

[80]  N. Gidopoulos Potential in spin-density-functional theory of noncollinear magnetism determined by the many-electron ground state , 2007 .

[81]  R. West,et al.  Why Is Methylene a Ground State Triplet while Silylene Is a Ground State Singlet , 2003 .

[82]  Stockholder projector analysis: a Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors. , 2012, The Journal of chemical physics.

[83]  Blöchl,et al.  Projector augmented-wave method. , 1994, Physical review. B, Condensed matter.

[84]  Tian Lu,et al.  Bond order analysis based on the Laplacian of electron density in fuzzy overlap space. , 2013, The journal of physical chemistry. A.

[85]  I. Mayer On bond orders and valences in the Ab initio quantum chemical theory , 1986 .

[86]  Thomas A. Manz,et al.  Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology , 2016 .

[87]  David A Mazziotti,et al.  Towards idempotent reduced density matrices via particle-hole duality: McWeeny's purification and beyond. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[88]  Á. Martín Pendás,et al.  Decay Rate of Correlated Real-Space Delocalization Measures: Insights into Chemical Bonding and Mott Transitions from Hydrogen Chains. , 2016, Journal of chemical theory and computation.

[89]  David S Sholl,et al.  Chemically Meaningful Atomic Charges That Reproduce the Electrostatic Potential in Periodic and Nonperiodic Materials. , 2010, Journal of chemical theory and computation.

[90]  R. Fulton Sharing of electrons in molecules , 1993 .

[91]  J. R. Schmidt,et al.  Generalization of Natural Bond Orbital Analysis to Periodic Systems: Applications to Solids and Surfaces via Plane-Wave Density Functional Theory. , 2012, Journal of chemical theory and computation.

[92]  A. Stone,et al.  Distributed Multipoles from a Robust Basis-Space Implementation of the Iterated Stockholder Atoms Procedure. , 2014, Journal of chemical theory and computation.

[93]  Christian Borgelt,et al.  Mining molecular fragments: finding relevant substructures of molecules , 2002, 2002 IEEE International Conference on Data Mining, 2002. Proceedings..

[94]  D. Sholl,et al.  Methods for Computing Accurate Atomic Spin Moments for Collinear and Noncollinear Magnetism in Periodic and Nonperiodic Materials. , 2011, Journal of chemical theory and computation.

[95]  Pedro Salvador,et al.  Electron sharing indexes at the correlated level. Application to aromaticity calculations. , 2007, Faraday discussions.

[96]  T. Manz,et al.  Introducing DDEC6 atomic population analysis: part 2. Computed results for a wide range of periodic and nonperiodic materials , 2016 .

[97]  James K. Olthoff,et al.  Sulfur hexafluoride and the electric power industry , 1997 .

[98]  J. Gulliver,et al.  Sulfur Hexafluoride Gas Tracer Studies in Streams , 1998 .

[99]  Ian D. Williams,et al.  Cooperative magnetic behavior in the coordination polymers [Cu3(TMA)2L3] (L=H2O, pyridine) , 2000 .

[100]  Á. M. Pendás,et al.  An unexpected bridge between chemical bonding indicators and electrical conductivity through the localization tensor. , 2017, Physical chemistry chemical physics : PCCP.

[101]  Patrick Bultinck,et al.  Critical analysis and extension of the Hirshfeld atoms in molecules. , 2007, The Journal of chemical physics.

[102]  P. Atkins,et al.  Molecular Quantum Mechanics , 1970 .

[103]  H. A. Jahn,et al.  Stability of Polyatomic Molecules in Degenerate Electronic States. I. Orbital Degeneracy , 1937 .

[104]  Ronald J. Gillespie,et al.  Fifty years of the VSEPR model , 2008 .

[105]  D. Truhlar,et al.  A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. , 2006, The Journal of chemical physics.

[106]  I. P. Rothwell,et al.  The nature of aryloxide and arylsulfide ligand bonding in dimethyltitanium complexes containing cyclopentadienyl ligation. , 2005, Dalton transactions.

[107]  Jackson,et al.  Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation. , 1992, Physical review. B, Condensed matter.

[108]  Jeremy M Merritt,et al.  Beryllium Dimer—Caught in the Act of Bonding , 2009, Science.

[109]  J. Cioslowski Isopycnic orbital transformations and localization of natural orbitals , 1990 .

[110]  P. Power π-Bonding and the Lone Pair Effect in Multiple Bonds between Heavier Main Group Elements , 1999 .

[111]  David S Sholl,et al.  Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials. , 2012, Journal of chemical theory and computation.

[112]  Yi-Gui Wang,et al.  Comparison of localization and delocalization indices obtained with Hartree–Fock and conventional correlated methods: Effect of Coulomb correlation , 2003 .

[113]  D. L. Cooper,et al.  Influence of atoms-in-molecules methods on shared-electron distribution indices and domain-averaged Fermi holes. , 2010, The journal of physical chemistry. A.

[114]  J. Pople,et al.  Variational configuration interaction methods and comparison with perturbation theory , 2009 .

[115]  C. Van Alsenoy,et al.  An Extension of the Hirshfeld Method to Open Shell Systems Using Fractional Occupations. , 2011, Journal of chemical theory and computation.

[116]  T. Dunning,et al.  Theory of hypervalency: recoupled pair bonding in SF(n) (n = 1-6). , 2009, The journal of physical chemistry. A.

[117]  Ari P. Seitsonen,et al.  Extracting chemical information from plane wave calculations by a 3D ‘fuzzy atoms’ analysis , 2013 .

[118]  P. Ayers,et al.  Aromaticity of rings-in-molecules (RIMs) from electron localization–delocalization matrices (LDMs) , 2015 .

[119]  Lucas Visscher,et al.  Dirac-Fock atomic electronic structure calculations using different nuclear charge distributions , 1997 .

[120]  George Karypis,et al.  Frequent Substructure-Based Approaches for Classifying Chemical Compounds , 2005, IEEE Trans. Knowl. Data Eng..

[121]  M. Schneider,et al.  SonoVue, a new ultrasound contrast agent , 1999, European Radiology.

[122]  Jürgen Gauss,et al.  Coupled‐cluster methods with noniterative triple excitations for restricted open‐shell Hartree–Fock and other general single determinant reference functions. Energies and analytical gradients , 1993 .

[123]  Thom Vreven,et al.  A direct derivative MC-SCF procedure , 1996 .

[124]  J. Caruthers,et al.  Structure–Activity Correlation for Relative Chain Initiation to Propagation Rates in Single-Site Olefin Polymerization Catalysis , 2012 .

[125]  Xavier Fradera,et al.  The Lewis Model and Beyond , 1999 .

[126]  L. J. Schaad,et al.  Equilibrium Bond Length in H2 , 1970 .

[127]  R. S. Pease An X‐ray study of boron nitride , 1952 .

[128]  J. Hafner,et al.  Understanding the complex metallic element Mn. I. Crystalline and noncollinear magnetic structure of α-Mn , 2003 .

[129]  J. F. Ogilvie,et al.  Potential-energy functions of diatomic molecules of the noble gases I. Like nuclear species , 1992 .

[130]  Covalent bond orders and atomic anisotropies from iterated stockholder atoms. , 2012, Physical chemistry chemical physics : PCCP.

[131]  F. Weinhold,et al.  Natural population analysis , 1985 .

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

[133]  P. Salvador,et al.  Overlap populations, bond orders and valences for fuzzy atoms , 2004 .

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

[135]  P. Ayers,et al.  Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development. , 2016, Journal of chemical theory and computation.

[136]  R. L. Dekock,et al.  Bond multiplicity in transition-metal complexes: applications of two-electron valence indices. , 2008, The journal of physical chemistry. A.