JANPA: An open source cross-platform implementation of the Natural Population Analysis on the Java platform

Gonthier, 2012, Quantification of “fuzzy” chemical concepts: a computational perspective, Chem. Soc. Rev., 41, 4671, 10.1039/c2cs35037h McWeeny, 1955, On the basis of orbital theories, Proc. Roy. Soc. Lon. Ser. A, 232, 114, 10.1098/rspa.1955.0205 Mayer, 1986, Bond orders and valences from ab initio wave functions, Int. J. Quantum Chem., 29, 477, 10.1002/qua.560290320 Mayer, 2007, Bond order and valence indices: a personal account, J. Comput. Chem., 28, 204, 10.1002/jcc.20494 Okada, 1975, Electron pair concept and an extension of the Penney-Dirac bond order, Bull. Chem. Soc. Jpn., 48, 2025, 10.1246/bcsj.48.2025 Giambiagi, 1975, Sur la définition d’un indice de liaison (TEV) pour des bases non orthogonales. Propriétés et applications, J. Chim. Phys., 72, 15, 10.1051/jcp/1975720015 Wiberg, 1968, Application of the Pople-Santry-Segal CNDO method to the cyclopropylcarbinyl and cyclobutyl cation and to bicyclobutane, Tetrahedron, 24, 1083, 10.1016/0040-4020(68)88057-3 Johnson, 2010, Revealing noncovalent interactions, J. Am. Chem. Soc., 132, 6498, 10.1021/ja100936w Contreras-Garcia, 2011, NCIPLOT: a program for plotting noncovalent interaction regions, J. Chem. Theor. Comput., 7, 625, 10.1021/ct100641a Savin, 1997, ELF: the electron localization function, Angew. Chem. Int. Ed., 36, 1808, 10.1002/anie.199718081 Bader, 1990 Mayer, 1995, Non-orthogonal localized orbitals and orthogonal atomic hybrids derived from Mulliken’s population analysis, Chem. Phys. Lett., 242, 499, 10.1016/0009-2614(95)00748-S Mayer, 1996, Atomic orbitals from molecular wave functions: the effective minimal basis, J. Phys. Chem., 100, 6249, 10.1021/jp952779i Glendening, 2012, Natural bond orbital methods, WIREs Comput. Mol. Sci., 2, 1, 10.1002/wcms.51 Foster, 1980, Natural hybrid orbitals, J. Am. Chem. Soc., 102, 7211, 10.1021/ja00544a007 Weinhold, 2012, Natural bond orbital analysis: a critical overview of relationships to alternative bonding perspectives, J. Comput. Chem., 33, 2363, 10.1002/jcc.23060 Reed, 1985, Natural population analysis, J. Chem. Phys., 83, 735, 10.1063/1.449486 Reed, 1988, Intermolecular interactions from a natural bond orbital, donor–acceptor viewpoint, Chem. Rev., 88, 899, 10.1021/cr00088a005 Some additional details on NBO transformation can be found at <http://www.chem.wisc.edu/~nbo5/web_nbo.htm> (accessed 27.10.13). Weinhold, 1998, Natural bond orbital methods, vol. 3, 1792 Weinhold, 2005 Weinhold, 2012 Wilkens, 2001, Natural J-coupling analysis: Interpretation of scalar J-couplings in terms of Natural Bond Orbitals, J. Am. Chem. Soc., 123, 12026, 10.1021/ja016284k Weinhold, 1988, Some remarks on nonorthogonal orbitals in quantum chemistry, J. Mol. Struct. Theochem., 165, 189, 10.1016/0166-1280(88)87018-0 Weinhold, 2001, Natural bond orbitals and extensions of localized bonding concepts, Chem. Educ. Res. Pract. Eur., 2, 91, 10.1039/B1RP90011K Weinhold, 2007, Valence and extra-valence orbitals in main group and transition metal bonding, J. Comput. Chem., 28, 198, 10.1002/jcc.20492 F. Weinhold, E.D. Glendening, NBO 6.0 Program Manual: Natural Bond Orbital Analysis Programs, <http://nbo6.chem.wisc.edu/nboman.pdf> (accessed 06.08.14). Dunnington, 2012, Generalization of natural bond orbital analysis to periodic systems: applications to solids and surfaces via plane-wave density functional theory, J. Chem. Theory Comput., 8, 1902, 10.1021/ct300002t Ohwaki, 2014, A method of orbital analysis for large-scale first-principles simulations, J. Chem. Phys., 140, 244105, 10.1063/1.4884119 Ince, 2012, The case for open computer programs, Nature, 482, 485, 10.1038/nature10836 Morin, 2012, Shining light into black boxes, Science, 336, 159, 10.1126/science.1218263 Cardona, 2012, Current challenges in open-source bioimage informatics, Nat. Methods, 9, 661, 10.1038/nmeth.2082 Joppa, 2013, Troubling trends in scientific software use, Science, 340, 814, 10.1126/science.1231535 Shamir, 2013, Practices in source code sharing in astrophysics, Astron. Comput., 1, 54, 10.1016/j.ascom.2013.04.001 Walters, 2013, Modeling, informatics, and the quest for reproducibility, J. Chem. Inf. Model., 53, 1529, 10.1021/ci400197w Pradal, 2013, Publishing scientic software matters, J. Comput. Sci., 4, 311, 10.1016/j.jocs.2013.08.001 Ram, 2013, Git can facilitate greater reproducibility and increased transparency in science, Source Code Biol. Med., 8, 7, 10.1186/1751-0473-8-7 JAMA: A Java Matrix Package <http://math.nist.gov/javanumerics/jama/> (accessed 27.10.13). Schaftenaar, 2000, Molden: a pre-and post-processing program for molecular and electronic structures, J. Comput.-Aided Mol. Des., 14, 123, 10.1023/A:1008193805436 The Molden Format <http://www.cmbi.ru.nl/molden/molden_format.html> (accessed 27.10.13). Jmol: an open-source Java viewer for chemical structures in 3D. <http://www.jmol.org/> (accessed 27.10.13). Jensen, 1999 Löwdin, 1970, On the nonorthogonality problem, Adv. Quantum Chem., 5, 185, 10.1016/S0065-3276(08)60339-1 Löwdin, 1955, Quantum theory of many-particle systems. I. Physical Interpretations by means of density matrices, natural spin-orbitals, and convergence problems in the method of configurational interaction, Phys. Rev., 97, 1474, 10.1103/PhysRev.97.1474 Davidson, 1976, vol. 6 Davidson, 1972, Natural orbitals, Adv. Quantum Chem., 6, 235, 10.1016/S0065-3276(08)60547-X Drake, 2005, Variational methods, 619 Weinberger, 1974 Bruhn, 2006, Löwdin population analysis with and without rotational invariance, Int. J. Quantum Chem., 106, 2065, 10.1002/qua.20981 Harris, 1963, Discussion on natural expansions and properties of the chemical bond, Rev. Mod. Phys., 35, 629, 10.1103/RevModPhys.35.629 Landis, 2007, Valence and extra-valence orbitals in main group and transition metal bonding, J. Comput. Chem., 28, 198, 10.1002/jcc.20492 Miessler, 2003 Reed, 1983, Natural bond orbital analysis of near-Hartree–Fock water dimer, J. Chem. Phys., 78, 4066, 10.1063/1.445134 Carlson, 1957, Orthogonalization procedures and the localization of Wannier functions, Phys. Rev., 105, 102, 10.1103/PhysRev.105.102 Watkins, 2010 Engeln-Müllges, 1996 Accurate matrix multiplication in Matlab, <http://stackoverflow.com/questions/13729613/accurate-matrix-multiplication-in-matlab> (accessed 08.05.14). De Proft, 1996, On the performance of density functional methods for describing atomic populations, dipole moments and infrared intensities, Chem. Phys. Lett., 250, 393, 10.1016/0009-2614(96)00057-7 Szczepanik, 2012, Electron population analysis using a reference minimal set of atomic orbitals, Comp. Theor. Chem., 996, 103, 10.1016/j.comptc.2012.07.021 Krygowski, 2011, Sigma- and pi-electron structure of aza-azoles, J. Mol. Model., 17, 1427, 10.1007/s00894-010-0844-z A.J. Banks, M.S. Bollom, J.L. Holmes, J.J. Jacobsen, J.C. Kotz, J.W. Moore. Lithium-Periodic Table Live!. <http://www.chemeddl.org/resources/ptl/index.html>. Copyright © 1995, 1997, 1999, 2004, 2010 by Division of Chemical Education, Inc. The Chemical Education Digital Library (online): <http://www.chemeddl.org/resources/models360/models.php> (accessed 04.05.14). Turney, 2012, Psi4: an open-source ab initio electronic structure program, WIREs Comput. Mol. Sci., 2, 556, 10.1002/wcms.93 Neese, 2012, The ORCA program system, WIREs Comput. Mol. Sci., 2, 73, 10.1002/wcms.81 Valiev, 2010, NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations, Comput. Phys. Commun., 181, 1477, 10.1016/j.cpc.2010.04.018 Davidson, 1972, Properties and uses of natural orbitals, Rev. Modern Phys., 44, 451, 10.1103/RevModPhys.44.451 McWeeny, 1968, Symmetry properties of natural orbitals and geminals I. Construction of spin-and symmetry-adapted functions, Int. J. Quant. Chem., 2, 187, 10.1002/qua.560020203 Bingel, 1970, The symmetry behaviour of the first-order density matrix and its natural orbitals for linear molecules, Theor. Chim. Acta, 16, 319, 10.1007/BF00527080 Bingel, 1970, Symmetry properties of reduced density matrices and natural p-states, Adv. Quantum Chem., 5, 201, 10.1016/S0065-3276(08)60340-8 Hunter, 1974, Angular momentum adapted wavefunctions and their reduced transition density matrices, J. Chem. Phys., 60, 2670, 10.1063/1.1681425 Larson, 1979, The role of symmetry in representing reduced density operators and reduced transition density operators: general formulation with specific application to atomic systems, Int. J. Quantum Chem., 16, 121, 10.1002/qua.560160815 Kryachko, 1981, Symmetry properties of reduced density matrices, Adv. Quantum Chem., 14, 1, 10.1016/S0065-3276(08)60325-1 Landau, 1977, vol. 3