Some References Related to AIMAll

Some References Related to AIMAll (Version 17.01.25)

Citation of AIMAll:

If results from "AIMAll (Version 17.01.25)" are used in publications or for other reasons, please use the following citation:

AIMAll (Version 17.01.25), Todd A. Keith, TK Gristmill Software, Overland Park KS, USA, 2017 (aim.tkgristmill.com)

Some Books About QTAIM:

"Atoms in Molecules: A Quantum Theory", R.F.W. Bader, Oxford University Press, Oxford (1990)
"Atoms in Molecules: An Introduction", Paul L. Popelier, Prentice Hall, London (2000)
"The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design", Edited by C.F. Matta and R.J. Boyd, WILEY-VCH, Weinham, (2007)

Some Review Articles About QTAIM:

"Molecular Fragments or Chemical Bonds?", R.F.W. Bader, Acounts of Chemical Research, 8, 34-40 (1975)
"Quantum Theory of Atoms in Molecules: Dalton Revisited", R.F.W. Bader and T.T. Nguyen-Dang, Advances in Quantum Chemistry, 14, 63-124 (1981)
"A topological theory of molecular structure.", R.F.W. Bader, T.T. Nguyen-Dang and Y. Tal, Reports on Progress in Physics, 44, 893-948 (1981)
"Atoms in Molecules", R.F.W. Bader, Acounts of Chemical Research, 18, 9-15 (1985)
"A Quantum Theory of Molecular Structure and its Applications", R.F.W. Bader, Chemical Reviews, 91, 893-928 (1991)
"Atoms in Molecules", R.F.W. Bader, Encyclopedia of Computational Chemistry, Edited by P.v.R. Schleyer et al, John Wiley and Sons, Chichester, UK, 1, 64-86 (1998)
"Are There Atoms in Molecules?", R.F.W. Bader, Introduction to Advanced Topics of Computational Chemistry, 1-28 (2003)
"Quantum Mechanical Basis for Conceptual Chemistry", R.F.W. Bader, Monatschefte fur Chemie, 136, 819-854 (2005)
"Complementarity of QTAIM and MO Theory in the study of bonding in donor-acceptor complexes", Fernando Cortes-Guzman and Richard F.W. Bader, Coordination Chemistry Reviews, 249, 633-662 (2005)

Atomic Integration Algorithms Used in AIMAll:

Proaim

"Calculation of the Average Properties of Atoms in Molecules. II.", F.W. Biegler-König, R.F.W. Bader and T.H. Tang, Journal of Computational Chemistry, 13, 317-328 (1982)
"Computational Improvements for the Theory of Atoms in Molecules", T.A. Keith, Chapter 4 of Ph.D. Thesis: Molecules in Magnetic Fields, 176-213 (1993)
"Advances in QTAIM Calculations Using AIMAll, T.A. Keith, To be published

Promega

"Computational Improvements for the Theory of Atoms in Molecules", T.A. Keith, Chapter 4 of Ph.D. Thesis: Molecules in Magnetic Fields, 176-213 (1993)
"Advances in QTAIM Calculations Using AIMAll, T.A. Keith, To be published

Sculpt

"Advances in QTAIM Calculations Using AIMAll, T.A. Keith, To be published

Topology of the Electron Density Distribution:

"Definition of bond paths and bond directions in terms of the molecular charge distribution", G.R. Runtz, R.F.W. Bader and R.R. Messer, Canadian Journal of Chemistry, 55, 3040-3045 (1977)
"Orthogonal Trajectories of the Electron Density", Kathleen Collard and George G. Hall, Internation Journal of Quantum Chemistry, 12, 623-627 (1977)
"Quantum Topology of Molecular Charge Distributions. 1", R.F.W. Bader, S.G. Anderson and A.J. Duke, Journal of the American Chemical Society, 101, 1389-1395 (1979)
"Quantum Topology of Molecular Charge Distributions. 2", Richard F.W. Bader, T. Tung Nguyen-Dang, Journal of Chemical Physics, 70, 4316-4329 (1979)
"Quantum Topology: Theory of Molecular Structure and its Change", R.F.W. Bader, Y. Tal, S.G. Anderson and T.T. Nguyen-Dang, Israel Journal of Chemistry, 19, 8-29 (1980)
"Quantum Topology. IV. Relation between the topological and energetic stabilities of molecular structures.", Yoram Tal, Richard F.W. Bader, T. Tung Nguyen-Dang, M. Ojha and Steven G. Anderson, Journal of Chemical Physics, 74, 5162-5167 (1981)
"A topological theory of molecular structure.", R.F.W. Bader, T.T. Nguyen-Dang and Y. Tal, Reports on Progress in Physics, 44, 893-948 (1981)
"The characterization of atomic interactions.", R.F.W. Bader and H. Essen, Journal of Chemical Physics, 80, 1943-1960 (1984)

Atomic Contributions to Molecular Dipole Moments, Polarizabilities and Other Molecular Dipole Moment Derivatives:

"Properties of atoms in molecules: Dipole moments and transferability of properties", R.F.W. Bader, A. Larouche, C. Gatti, M.T. Carroll, P.J. MacDougall and K.B. Wiberg, Journal of Chemical Physics, 87, 1142-1152 (1987)
"Properties of atoms in molecules: Atomic Polarizabilities", Keith E. Laidig and Richard F.W. Bader, Journal of Chemical Physics, 93, 7213-7224 (1990)
"Properties of atoms in molecules: addivity and transferability of group polarizabilities", R.F.W. Bader, T.A. Keith, K.M. Gough and K.E. Laidig, Molecular Physics, 75, 1167-1189 (1992)
"Properties of atoms in molecules: Transition probabilities", R.F.W. Bader, D. Bayles and G.L. Heard, Journal of Chemical Physics, 112, 10095-10105 (2000)
"Properties of atoms in crystals: dielectric polarization", R.F.W. Bader and C.F. Matta, International Journal of Quantum Chemistry, 85, 592-607 (2001)
"Atomic Response Properties.", Todd A. Keith, The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, Chapter 3, 61-95 (2007)
"QTAIM Analysis of Raman Scattering Intensities: Insights into the Relationship Between Molecular Structure and Electronic Charge Flow.", Kathleen M. Gough, Richard Dawes, Jason R. Dwyer and Tammy L. Welshman, The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, Chapter 4, 95-120 (2007)
"Distributed atomic polarizabilities from electron density. 1. Motivations and Theory", Anna Krawczuk-Pantula, Daniel Pérez, Katarzyna Stadnicka, Piero Macchi, http://www.amercrystalassn.org/documents/2011%20Transactions/Macchi.pdf (2011)

Atomic Volumes:

"Properties of Atoms in Molecules: Atomic Volumes.", R.F.W. Bader, M.T. Carroll, J.R. Cheeseman and C. Chang, Journal of the American Chemical Sociery, 109, 7968-7979 (1987)
"Properties of atoms in molecules: addivity and transferability of group polarizabilities", R.F.W. Bader, T.A. Keith, K.M. Gough and K.E. Laidig, Molecular Physics, 75, 1167-1189 (1992)

Virial-Based Atomic Energies:

"Virial Field Relationship for Molecular Charge Distributions and the Spatial Partioning of Molecular Properties.", R.F.W. Bader and P.M. Beddall, Journal of Chemical Physics, 56, 3320-3329 (1972)
"A Theoretical Development of a Virial Relationship for Spatially Defined Fragments of Molecular Systems.", R.F.W. Bader, P.M. Beddall and J. Peslak Jr., Journal of Chemical Physics, 58, 557-566 (1973)
"Virial Partitioning of Charge Distributions and Properties of Diatomic Hydrides.", R.F.W. Bader and P.M. Beddall, Journal of the American Chemical Society, 95, 305-315 (1973)
"Sufficient Conditions for Fragment and Regional Virial Theorems.", S. Srebrenik and R.F.W. Bader, Journal of Chemical Physics, 61, 2536-2539 (1974)
"Towards the Development of the Quantum Mechanics of a Subspace.", S. Srebrenik and R.F.W. Bader, Journal of Chemical Physics, 63, 3945-3961 (1975)
"Subspace quantum mechanics and the variational principle.", Shalom Srebrenik and Richard F.W. Bader and T. Tung Nguyen-Dang Journal of Chemical Physics, 68, 3667-3679 (1978)
"Quantum Topology of Molecular Charge Distributions. 3", R.F.W. Bader, Journal of Chemical Physics, 73, 2871-2883 (1980)

Interacting Quantum Atoms (IQA):

"Atom-atom partitioning of intramolecular and intermolecular Coulomb energy.", P.L.A. Popelier and D.S. Kosov, Journal of Chemical Physics, 114, 6539 (2001)
"One and two-center energy components in the atoms in molecules theory.", P. Salvador, M. Duran and I. Mayer, Journal of Chemical Physics, 115, 1153 (2001)
"Two-electron integrations in the quantum theory of atoms in molecules.", A. Martin Pendas, M.A. Blanco and E. Francisco, Journal of Chemical Physics, 120, 4581-4592 (2004)
"Interacting Quantum Atoms: A Correlated Energy Decomposition Scheme Based on the Quantum Theory of Atoms in Molecules.", M.A. Blanco, A. Martin Pendas and E. Francisco, Journal of Chemical Theory and Computation, 1, 1096-1109 (2005)
"Binding Energies of First Row Diatomics in the Light of the Interacting Quantum Atoms Approach.", A. Martin Pendas, E. Francisco and M.A. Blanco, Journal of Physical Chemistry A, 110, 12864-12869 (2006)
"The nature of the hydrogen bond: A synthesis from the interacting quantum atoms picture", A. Martin Pendas, E. Francisco and M.A. Blanco, Journal of Chemical Physics, 125, 184112 (2006)

Magnetic Response Properties:

"Calculation of magnetic response properties using atoms in molecules.", T.A. Keith and R.F.W. Bader, Chemical Physics Letters, 194, 1-8 (1992)
"Calculation of magnetic response properties using a continuous set of gauge transformations.", T.A. Keith and R.F.W. Bader, Chemical Physics Letters, 210, 223-231 (1993)
"Topological analysis of magnetically induced molecular current distributions", Todd A. Keith and Richard F.W. Bader, Journal of Chemical Physics, 99, 3669-3682 (1993)
"Properties of atoms in molecules: Magnetic susceptibilities", Richard F.W. Bader and Todd A. Keith, Journal of Chemical Physics, 99, 3683-3693 (1993)
"Properties of atoms in molecules: nuclear magnetic shielding", T.A. Keith and R.F.W. Bader, Canadian Journal of Chemistry, 74, 185-200 (1996)
"Calculation of magnetizabilities using GIAO current density distributions", T.A. Keith, Chemical Physics, 213, 123-132 (1996)
"A Comparison of models for calculating nuclear magnetic resonance shielding tensors.", James R. Cheeseman, Gary W. Trucks, Todd A. Keith and Michael J. Frisch, Journal of Chemical Physics, 104, 5497-5509 (1996)
"Atomic Response Properties.", Todd A. Keith, The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, Chapter 3, 61-95 (2007)

Electronic Localization and Delocalization Properties:

"Spatial Localization of the Electronic Pair and Number Distributions in Molecules.", R.F.W. Bader and M.E. Stephens, Journal of the American Chemical Society, 97, 7391-7399 (1975)
"Sharing of Electrons in Molecules.", Robert L. Fulton, Journal of Physical Chemistry, 97, 7516-7529 (1993)
"Electron Delocalization and the Fermi Hole.", Richard F.W. Bader, Andrew Streitwieser, Arnst Neuhaus, Keith E. Laidig and Peter Speers, Journal of the American Chemical Society, 118, 4959-4965 (1996)
"The Electron Pair.", Richard F.W. Bader, S. Johnson, T.H. Tang and P.L.A. Popelier, Journal of Physical Chemistry, 100, 15398-15415 (1996)
"The Lewis Model and Beyond.", Xavier Fradera, Maggie A. Austen and Richard F.W. Bader, Journal of Physical Chemistry A, 103, 304-314 (1999)
"A Practical and Efficient Method to Calculate AIM Localization and Delocalization Indices at Post-HF Levels of Theory.", Yi-Gui Wang and Nick Henry Werstiuk, Journal of Computational Chemistry, 24, 379-385 (2003)
"Comparison of Localization and Delocalization Indices Obtained with Hartree-Fock and Conventional Correlated Methods: Effect of Coulomb Correlation.", Yi-Gui Wang, Cherif Matta and Nick Henry Werstiuk, Journal of Computational Chemistry, 24, 1720-1729 (2003)
"Electron-pairing analysis from localization and delocalization indices in the framework of the atoms-in-molecules theory.", Xavier Fradera, Jordi Poater, Silvia Simon, Miquel Duran and Miquel Sola, Theoretical Chemistry Accounts, 108, 214-224 (2002)
"Bonding in Polycyclic Aromatic Hydrocarbons in Terms of the Electron Density and of Electron Delocalization.", Cherif F. Matta and Jesus Hernandez-Trujillo, Journal of Physical Chemistry A, 107, 7496-7504 (2003)
"Theoretical Evaluation of Electron Delocalization in Aromatic Molecules by Means of Atoms in Molecules (AIM) and Electron Localization Function (ELF) Topological Approaches", Jordi Poater, Miquel Duran, Miquel Sola and Bernard Silvi, Chem . Rev., 105, 3911-3947 (2005)

Approximation (for Electron-Correlated Methods) of Two-Electron Density Matrices in Terms of Natural Orbitals of One-Electron Density Matrices:

"Explicit Approximate Relation Between Reduced Two- and One-Particle Density Matrices.", A.M.K Muller, Physics Letters, 105A, 446-452 (1984)
"Sharing of Electrons in Molecules.", Robert L. Fulton, Journal of Physical Chemistry, 97, 7516-7529 (1993)
"A Practical and Efficient Method to Calculate AIM Localization and Delocalization Indices at Post-HF Levels of Theory.", Yi-Gui Wang and Nick Henry Werstiuk, Journal of Computational Chemistry, 24, 379-385 (2003)
"Theoretical Evaluation of Electron Delocalization in Aromatic Molecules by Means of Atoms in Molecules (AIM) and Electron Localization Function (ELF) Topological Approaches", Jordi Poater, Miquel Duran, Miquel Sola and Bernard Silvi, Chem . Rev., 105, 3911-3947 (2005)

Contour and Isosurface Methods:

"CONREC, A Contouring Subroutine", Paul D. Bourke, http://paulbourke.net/papers/conrec/, June (1987)
"Polygonising a Scalar Field", http://paulbourke.net/geometry/polygonise/, Paul Bourke, May (1994)

Source Function for the Electron Density:

"The Spatial Partitioning and Transferability of Molecular Energies.", R.F.W. Bader and P.M. Beddall, Chem. Phys. Lett., 8, 29-36 (1971)
"The Virial Partitioning Method.", R. F. W. Bader, G. R. Runtz and R. R. Messer, Jerusalem Symposium on Quantum Chemistry and Biochemistry, Israel Academy of Sciences and Humanities, 6, 99-111 (1974)
"A Green's function for the density.", Richard F.W. Bader and Carlo Gatti, Chem. Phys. Lett., 287, 233-238 (1998)

QTAIM Analyses of Effective Core Potential Based Wavefunctions

"Properties of atoms in molecules from valence-electron densities augmented with core-electron contributions", J. Cioslowski, J. and P. Piskorz, Chem. Phys. Lett., 255, 315 (1996)
"Accurate analytical representations of the core-electron densities of the elements 3 through 118", J. Cioslowski, P. Piskorz and P. Rez, J. Chem. Phys., 106, 3607 (1997)
"Core distortions in metal atoms and the use Of effective core potentials", R.F.W. Bader, R. Gillespie and F. Martin, Chem. Phys. Lett., 290, 488 (1998)
"Using Pseudopotentials Within the Interacting Quantum Atoms Approach", D. Tiana, E. Francisco, M.A. Blanco and A.M. Pendas, J. Phys. Chem. A, 113, 7963 (2009)
"Subshell Fitting of Relativistic Atomic Core Electron Densities for Use in QTAIM Analyses of ECP-Based Wave Functions", Todd A. Keith and Michael J. Frisch, J. Phys. Chem. A, 115, 12879?12894 (2011)

Topological Analysis of the Laplacian of the Electron Density

"The Characterization of Atomic Interactions", R.F.W. Bader and H. Essen, J. Chem. Phys., 80, 1943 (1984)
"Bonded and Nonbonded Charge Concentrations and Their Relation to Molecular Geometry and Reactivity", R.F.W. Bader, P.J. MacDougall and C.D.H Lau, J. Am. Chem. Soc., 106, 1594 (1984)
"Structure and Bonding in Sulfur-Nitrogen Compounds", Ting-Hua Tang, R. F. W. Bader and P. J. MacDougall, Inorg. Chem., 24, 207 (1985)
"Toward a Theory of Chemical Reactivity Based on the Charge Density", R.F.W. Bader and P.J. MacDougall, J. Am. Chem. Soc., 107, 6788 (1985)
"Atomic Properties and Reactivity of Carbenes", P.J. MacDougall and R.F.W. Bader, Can. J. Chem., 64, 1496 (1986)
"Prediction of the Structures of Hydrogen-Bonded Complexes Using the Laplacian of the Charge Density", M.T. Carroll, C. Chang and R.F.W. Bader, Mol. Phys., 63, 387 (1988)
"A Physical Basis for the VSEPR Model of Molecular Geometry", R.F.W. Bader, R.J. Gillespie and P.J. MacDougall, J. Am. Chem. Soc., 110, 7329 (1988)

TWOe Program

Pavel M. Polestshuk, J. Comp. Chem., 34, 206 (2013)
Pavel M. Polestshuk, J. Chem. Phys., 139, 054108 (2013)

Non-covalent Interaction (NCI) Plots

"Revealing Noncovalent Interactions", Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc., 132, 6498 (2010)

Test and Example Wavefunction Files Generated Using Gaussian 03, Gaussian 09 and GaussView 5.0.9:

Gaussian 03, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Wallingford CT, 2004

Gaussian 09, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013

GaussView 5.0.9, Roy D. Dennington, Todd A. Keith and John M. Millam, Semichem, Inc., 2009

Other:

"A quadrature formula for the sphere of the 131st algebraic order of accuracy.", V.I. Lebedev and D.N. Laikov, Doklady Mathematics, 59(3), 477-481 (1999)
"Transformation Between Cartesian and Pure Spherical Harmonic Gaussians.", H. Bernard Schlegel and Michael J. Frisch, International Journal of Quantum Chemistry, 54, 83-87 (1995)