Subsystem density-functional theory

Wiley Interdisciplinary Reviews: Computational Molecular Science

Volumn 4, Issue 4, 2014, Pages 325-362

  Jacob, Christoph R ^a   Neugebauer, Johannes ^b  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

QUANTUM CHEMISTRY;

DFT CALCULATION; EMBEDDING METHOD; MOLECULAR AGGREGATE; MOLECULAR PROPERTIES; QUANTUM CHEMICAL CALCULATIONS; RECONSTRUCTION TECHNIQUES; TOTAL DENSITY; TOTAL ENERGY;

DENSITY FUNCTIONAL THEORY;

EID: 84902551481     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1175     Document Type: Review

References (238)

1. Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2012, 112:632-672.
2. VandeVondele J, Borštnik U, Hutter J. Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase. J Chem Theory Comput 2012, 8:3563-3573.
3. König C, Neugebauer J. Quantum Chemical Description of Absorption Properties and Excited-State Processes in Photosynthetic Systems. Chem Phys Chem 2012, 13:386-425.
4. Senn H-M, Thiel W. QM/MM Methods for Biological Systems. Top Curr Chem 2007, 268:173-290.
5. Chung LW, Hirao H, Li X, Morokuma K. The ONIOM method: its foundation and applications to metalloenzymes and photobiology. WIREs Comput Mol Sci 2012, 2:327-350.
6. Mennucci B, Cammi R, eds. Continuum Solvation Models in Chemical Physics: From Theory to Applications. New York: Wiley; 2007.
7. Gordon MS, Freitag MA, Bandyopadhyay P, Jensen JH, Kairys V, Stevens WJ. The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry. J Phys Chem A 2001, 105:293-307.
8. Kobayashi M, Nakai H. Extension of linear-scaling divide-and-conquer-based correlation method to coupled cluster theory with singles and doubles excitations. J Chem Phys 2008, 129:044103.
9. Haag MP, Reiher M. Real-Time Quantum Chemistry. Int J Quantum Chem 2013, 113:8-20.
10. Neugebauer J. Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies. Chem Phys Chem 2009, 10:3148-3173.
11. Jensen F. Introduction to Computational Chemistry. 2nd ed. Chichester: Wiley; 2007.
12. Cramer CJ. Essentials of Computational Chemistry. 2nd ed. Chichester: Wiley; 2004.
13. Yang W. Direct Calculation of Electron Density in Density-Functional Theory. Phys Rev Lett 1991, 66:1438-1441.
14. Senatore G, Subbaswamy KR. Density dependence of the dielectric constant of rare-gas crystals. Phys Rev B 1986, 34:5754-5757.
15. Johnson MD, Subbaswamy KR, Senatore G. Hyperpolarizabilities of alkali halide crystals using the local-density approximation. Phys Rev B 1987, 36:9202-9211.
16. Cortona P. Self-consistently determined properties of solids without band-structure calculations. Phys Rev B 1991, 44:8454-8458.
17. Wesolowski TA, Warshel A. Frozen Density Functional Approach for ab Initio Calculations of Solvated Molecules. J Phys Chem 1993, 97:8050-8053.
18. Parr RG, Yang W. Density-Functional Theory of Atoms and Molecules. Oxford: Oxford University Press; 1989.
19. Engel E, Dreizler RM. Density Functional Theory. Heidelberg: Springer; 2011.
20. Levy M. Universal variational functionals of electron densities, first-order density matrices, and natural spin-orbitals and solution of the v-representability problem. Proc Natl Acad Sci USA 1979, 76:6062-6065.
21. Perdew JP, Parr RG, Levy M, Balduz JL Jr. Density-Functional Theory for Fractional Particle Number: Derivative Discontinuities of the Energy. Phys Rev Lett 1982, 49:1691.
22. Wesolowski TA. One-electron equations for embedded electron density: challenge for theory and practical payoffs in multi-level modeling of complex polyatomic systems. In: Leszczynski J, ed. Computational Chemistry: Reviews of Current Trends, vol 10, Singapore: World Scientific; 2006, 1-82.
23. Neugebauer J. Chromophore-specific theoretical spectroscopy: From subsystem density functional theory to mode-specific vibrational spectroscopy. Phys Rep 2010, 489(1-3):1-87.
24. Wesolowski TA, Wang YA, eds. Recent Progress in Orbital-Free Density Functional Theory. Singapore: World Scientific; 2013.
25. Gordon RG, Kim YS. Theory for the Forces between Closed-Shell Atoms and Molecules. J Chem Phys 1972, 56:3122.
26. Kim YS, Gordon RG. Study of the electron gas approximation. J Chem Phys 1974, 60:1842.
27. Gombas P. Die statistische Theorie des Atoms und ihre Anwendungen. Wien: Springer; 1949.
28. Laricchia S, Fabiano E, Della Salla F. Frozen density Embedding with Hybrid Functionals. J Chem Phys 2010, 133:164111.
29. Laricchia S, Fabiano E, Della Salla F. Frozen Density Embedding Calculations with the Orbital-Dependent Localized Hartree-Fock Kohn-Sham Potential. Chem Phys Lett 2011, 518:114-118.
30. Laricchia S, Fabiano E, Della Salla F. On the accuracy of frozen density embedding calculations with hybrid and orbital-dependent functionals for non-bonded interaction energies. J Chem Phys 2012, 137:014102.
31. Kiewisch K, Eickerling G, Reiher M, Neugebauer J. Topological analysis of electron densities from Kohn-Sham and subsystem density functional theory. J Chem Phys 2008, 128:044114.
32. Wesolowski TA, Weber J. Kohn-Sham equations with constrained electron density: an iterative evaluation of the ground-state electron density of interacting molecules. Chem Phys Lett 1996, 248:71-76.
33. Gritsenko OV, Visscher L. Density-orbital embedding theory. Phys Rev A 2010, 82:032519.
34. Gritsenko O. On the principal difference between the exact and approximate frozen-density embedding theory. In: Wesolowski TA, Wang YA, eds. Recent Progress in Orbital-Free Density Functional Theory, Singapore: World Scientific; 2013, 357-370.
35. Wesolowski TA. Embedding a multideterminantal wave function in an orbital-free environement. Phys Rev A 2008, 77:012504.
36. Wesolowski TA, Savin A. Non-additive kinetic energy and potential in analytically solvable systems and their approximated counterparts. In: Wesolowski TA, Wang YA, eds. Recent Progress in Orbital-Free Density Functional Theory. Singapore: World Scientific; 2013, 275-295.
37. See the preface to Ref [24].
38. Pernal K, Wesołowski TA. Orbital-Free Effective Embedding Potential: Density-Matrix Functional Theory Case. Int J Quantum Chem 2009, 109:2520-2525.
39. Kaminski JW, Gusarov S, Wesołowski TA, Kovalenko A. Modeling Solvatochromic Shifts Using the Orbital-Free Embedding Potential at Statistically Mechanically Averaged Solvent Density. J Phys Chem A 2010, 114:6082-6096.
40. Wesolowski TA, Tran F. Gradient-free and gradient-dependent approximations in the total energy bifunctional for weakly overlapping electron densities. J Chem Phys 2003, 118:2072.
41. Huang C, Pavone M, Carter EA. Quantum mechanical embedding theory based on a unique embedding potential. J Chem Phys 2011, 134:154110.
42. Elliot P, Cohen MH, Burke K, Wasserman A. Density Functional Partition Theory with Fractional Occupations. J Chem Theory Comput 2009, 5:827-833.
43. Elliot P, Burke K, Cohen MH, Wasserman A. Partition density-functional theory. Phys Rev A 2010, 82:024501.
44. Cohen MH, Wasserman A. On Hardness and Electronegativity Equalization in Chemical Reactivity Theory. J Stat Phys 2006, 125:1121-1139.
45. Warshel A, Levitt M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 1976, 103:227-249.
46. Senn HM, Thiel W. QM/MM Methods for Biomolecular Systems. Angew Chem, Int Ed 2009, 48:1198-1229.
47. Fradelos G, Wesolowski TA. Importance of the Intermolecular Pauli Repulsion in Embedding Calculations for Molecular Properties: The Case of Excitation Energies for a Chromophore in Hydrogen-Bonded Environments. J Phys Chem A 2011, 115:10018-10026.
48. Jacob Ch R, Reiher M. Spin in density-functional theory. Int J Quantum Chem 2012, 112:3661-3684.
49. Wesołowski TA, Weber J. Spin-densities in charge-transfer complexes derived from DFT calculations using an orbital-free embedding scheme for interacting subsystems. In: Barone V, Bencini A, Fantucci P, eds. Recent Advances in Density Functional Methods Part III. Singapore: World Scientific; 2002, 371-386.
50. Goodpaster JD, Ananth N, Manby FR, Miller TF III. Exact nonadditive kinetic potentials for embedded density functional theory. J Chem Phys 2010, 133:084103.
51. Solovyeva A, Pavanello M, Neugebauer J. Spin Densities from Subsystem Density-Functional Theory: Assessment and Application to a Photosynthetic Reaction Center Complex Model. J Chem Phys 2012, 136:194104.
52. Laio A, VandeVondele J, Rothlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. J Chem Phys 2002, 116:6941-6947.
53. Fradelos G, Lutz JJ, Wesołowski TA, Piecuch P, Włoch M. Embedding vs Supermolecular Strategies in Evaluating the Hydrogen-Bonding-Induced Shifts of Excitation Energies. J Chem Theory Comput 2011, 7:1647-1666.
54. Stefanovich EV, Truong TN. Embedded density functional approach for calculations of adsorption on ionic crystals. J Chem Phys 1996, 104:2946-2955.
55. 2{dot operator}{dot operator}{dot operator}X (X=He, Ne, Ar, Kr, Xe, Hg) van der Waals complexes. J Chem Phys 2005, 123:174104.
56. Dulak M, Wesolowski TA. On the electron leak problem in orbital-free embedding calculations. J Chem Phys 2006, 124:164101.
57. Wesolowski TA. Exact inequality involving the kinetic energy functional Ts[ρ] and pairs of electron densities. J Phys A: Math Gen 2003, 36:10607-10613.
58. Manby FR, Stella M, Goodpaster JD, Miller TF III. A Simple, Exact Density-Functional-Theory Embedding Scheme. J Chem Theory Comput 2012, 8:2564-2568.
59. Fux S, Jacob Ch R, Neugebauer J, Visscher L, Reiher M. Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds. J Chem Phys 2010, 132:164101.
60. Wesolowski TA, Morgantini P-Y, Weber J. Intermolecular interaction energies from the total energy bifunctional: A case study of carbazole complexes. J Chem Phys 2002, 116:6411-6421.
61. Wang YA, Carter EA. Orbital-free kinetic-energy density functional theory. In: Schwartz SD, ed. Theoretical Methods in Condensed Phase Chemistry. Dordrecht: Kluwer; 2000, 117-184.
62. Dreizler RM, Gross EKU. Density Functional Theory - An Approach to the Quantum Many-Body Problem. Berlin: Springer; 1990.
63. Hodges CH. Quantum Corrections to the Thomas-Fermi Approximation - The Kirzhnits Method. Can J Phys 1973, 51:1428-1437.
64. Lee H, Lee C, Parr RG. Conjugate gradient correction to the Hartree-Fock kinetic- and exchange-energy density functionals. Phys Rev A 1991, 44:768-771.
65. March NH, Santamaria R. Non-Local Relation Between Kinetic and Exchange Energy Densities in Hartree-Fock Theory. Int J Quantum Chem 1991, 39:585-592.
66. Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 1988, 38:3098-3100.
67. Perdew JP. Unified Theory of Exchange and Correlation Beyond the Local Density Approximation. In: Ziesche P, Eschrig H, eds. Electronic Structure of Solids '91. Berlin: Akademie Verlag; 1991, 11-20.
68. Lembarki A, Chermette H. Obtaining a gradient-corrected kinetic-energy functional from the Perdew-Wang exchange functional. Phys Rev A 1994, 50:5328.
69. Tran F, Wesolowski TA. Semilocal approximations for the kinetic energy. In: Wesolowski TA, Wang YA, eds. Recent Progress in Orbital-Free Density Functional Theory. Singapore: World Scientific; 2013, 429-442.
70. Thomas LA. The calculation of atomic fields. Proc Camb Phil Soc 1927, 23:542-548.
71. Fermi E. Eine statistische Methode zur Bestimmung einiger Eigenschaften des Atoms und ihre Anwendung auf die Theorie des periodischen Systems der Elemente. Z Phys 1928, 48:73-79.
72. von Weizsäcker CF. Zur Theorie der Kernmassen. Z Phys 1935, 96:431-458.
73. Lee D, Constantin LA, Perdew JP, Burke K. Condition on the Kohn-Sham kinetic energy and modern parametrization of the Thomas-Fermi density. J Chem Phys 2009, 130:034107.
74. Ou-Yang H, Levy M. Approximate Noninteracting Kinetic Energy Functionals from a Nonuniform Scaling Requirement. Int J Quantum Chem 1991, 40:379-388.
75. Lacks DJ, Gordon RG. Tests of nonlocal kinetic energy functionals. J Chem Phys 1994, 100:4446-4452.
76. Tran F, Wesolowski TA. Link between the Kinetic- and Exchange-Energy Functionals in the Generalized Gradient Approximation. Int J Quantum Chem 2002, 89:441-446.
77. Thakkar AJ. Comparison of kinetic-energy density functionals. Phys Rev A 1992, 46:6920-6924.
78. Karasiev VV, Trickey SB, Harris FE. Born-Oppenheimer interatomic forces from simple, local kinetic energy density functionals. J Compu-Aid Mat Des 2006, 13:111-129.
79. Constantin LA, Fabiano E, Laricchia S, Sala FD. Semiclassical Neutral Atom as a Reference System in Density Functional Theory. Phys Rev Lett 2011, 106:186406.
80. Laricchia S, Fabiano E, Constantin L, Sala FD. Generalized Gradient Approximation of the Noninteracting Kinetic Energy from the Semiclassical Atom Theory: Rationalization of the Accuracy of the Frozen Density Embedding Theory for Nonbonded Interactions. J Chem Theory Comput 2011, 7:2439-2451.
81. Wang YA, Govind N, Carter EA. Orbital-free kinetic-energy functionals for the nearly free electron gas [Errata: Phys. Rev. B 60 (1998), 17162; Phys. Rev. B 64 (2001), 129901]. Phys Rev B 1998, 58:13465-13471.
82. Choly N, Kaxiras E. Kinetic energy density functionals for non-periodic systems. Sol State Commun 2002, 121:281-286.
83. García-Aldea D, Alvarellos JE. Fully nonlocal kinetic energy density functionals: A proposal and a general assessment for atomic systems. J Chem Phys 2008, 129:074103.
84. Karasiev VV, Trickey SB. Issues and challenges in orbital-free density functional calculations. Comput Phys Commun 2012, 183:2519-2527.
85. Huang C, Carter EA. Nonlocal orbital-free kinetic energy density functional for semiconductors. Phys Rev B 2010, 81:045206.
86. Xia J, Huang C, Shin I, Carter EA. Can orbital-free density functional theory simulate molecules. J Chem Phys 2012, 136:084102.
87. Oliver GL, Perdew JP. Spin-density gradient expansion for the kinetic energy. Phys Rev A 1979, 20:397-403.
88. Scuseria GE, Staroverov VN. Progress in the development of exchange-correlation functionals. In: Dykstra CE, Frenking G, Kim KS, Scuseria GE, eds. Theory and Applications of Computational Chemistry: The First Forty Years. Amsterdam: Elsevier; 2005, 669-724.
89. Wesolowski TA. Density functional theory with approximate kinetic energy functionals applied to hydrogen bonds. J Chem Phys 1997, 106:8516-8526.
90. Dulak M, Wesolowski TA. The Basis Set Effect on the Results of the Minimization of the Total Energy Bifunctional E[ρA, ρB]. Int J Quantum Chem 2005, 101:543-549.
91. Dułak M, Wesołowski TA. Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory. J Mol Model 2007, 13:631-642.
92. Wesolowski TA, Chermette H, Weber J. Accuracy of approximate kinetic energy functionals in the model of Kohn-Sham equations with constrained electron density: The FH{dot operator}{dot operator}{dot operator}NCH complex as a test case. J Chem Phys 1996, 105:9182.
93. Wesolowski TA, Weber J. Kohn-Sham Equations with Constrained Electron Density: The Effect of Various Kinetic Energy Functional Parametrizations on the Ground-State Molecular Properties. Int J Quantum Chem 1997, 61:303.
94. García-Lastra JM, Kaminski JW, Wesolowski TA. Orbital-free effective embedding potential at nuclear cusps. J Chem Phys 2008, 129:074107.
95. Fux S, Kiewisch K, Jacob Ch R, Neugebauer J, Reiher M. Analysis of electron density distributions from subsystem density functional theory applied to coordination bonds. Chem Phys Lett 2008, 461:353-359.
96. Beyhan SM, Götz AW, Jacob Ch R, Visscher L. The weak covalent bond in NgAuF (Ng=Ar, Kr, Xe): A challenge for subsystem density functional theory. J Chem Phys 2010, 132:044114.
97. Wesolowski T, Warshel A. Ab Initio Free Energy Pertubation Calculations of Solvation Free Energy Using the Frozen Density Functional Approach. J Phys Chem 1994, 98:5183-5187.
98. Jacob Ch R, Jensen L, Neugebauer J, Visscher L. Comparison of frozen-density embedding and discrete reaction field solvent models for molecular properties. Phys Chem Chem Phys 2006, 8:2349-2359.
99. Amsterdam density functional program. Theoretical Chemistry, Vrije Universiteit, Amsterdam. URL: http://www.scm.com. (Accessed January 1, 2013).
100. te Velde G, Bickelhaupt FM, Baerends EJ, van Gisbergen SJA, Fonseca Guerra C, Snijders JG, Ziegler T. Chemistry with ADF. J Comput Chem 2001, 22:931-967.
101. Jacob Ch R, Neugebauer J, Visscher L. A flexible implementation of frozen-density embedding for use in multilevel simulations. J Comput Chem 2008, 29:1011-1018.
102. Jacob Ch R, Beyhan SM, Visscher L. Exact functional derivative of the nonadditive kinetic-energy bifunctional in the long-distance limit. J Chem Phys 2007, 126:234116.
103. Jacob Ch R, Visscher L. Towards the description of covalent bonds in subsystem density-functional theory. In: Wesolowski TA, Wang YA, eds. Recent Progress in Orbital-Free Density Functional Theory. Singapore: World Scientific; 2013, 299-324.
104. Gritsenko OV, Schipper PRT, Baerends EJ. Approximation of the exchange-correlation Kohn-Sham potential with a statistical average of different orbital model potentials. Chem Phys Let 1999, 302:199-207.
105. Gritsenko OV, Schipper PRT, Baerends EJ. Ensuring Proper Short-Range and Asymptotic Behavior of the Exchange-Correlation Kohn-Sham potential by Modeling with a Statistical Average of Different Orbital Model Potentials. Int J Quantum Chem 2000, 76:407-419.
106. Schipper PRT, Gritsenko OV, van Gisbergen SJA, Baerends EJ. Molecular calculations of excitation energies and (hyper)polarizabilities with a statistical average of orbital model exchange-correlation potentials. J Chem Phys 2000, 112:1344-1352.
107. Liu S, Ayers PW. Functional derivative of noninteracting kinetic energy density functional. Phys Rev A 2004, 70:022501.
108. Wesolowski TA. Comment on "Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds" [J. Chem. Phys. 132, 164101 (2010)]. J Chem Phys 2011, 135:027101.
109. Fux S, Jacob Ch R, Neugebauer J, Visscher L, Reiher M. Response to "Comment on: 'Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds' ". J Chem Phys 2011, 135:027102.
110. Savin A, Wesolowski TA. Orbital-free embedding effective potential in analytically solvable cases. In: Piecuch P, Maruani J, Delgado-Barrio G, Wilson S, eds. Advances in the Theory of Atomic and Molecular Systems. Dordrecht: Springer; 2009, 311-326.
111. de Silva P, Wesolowski TA. Exact non-additive kinetic potentials in realistic chemical systems. J Chem Phys 2012, 137:094110.
112. de Silva P, Wesolowski TA. Pure-state noninteracting v-representability of electron densities from Kohn-Sham calculations with finite basis sets. Phys Rev A 2012, 85:032518.
113. Jacob Ch R, Visscher L. Density-functional theory approach for the quantum chemical treatment of proteins. J Chem Phys 2008, 128:155102.
114. Kiewisch K, Jacob Ch R, Visscher L. Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory. J Chem Theory Comput 2013, 9:2425-2440.
115. Zhao Q, Morrison RC, Parr RG. From electron densities to Kohn-Sham kinetic energies, orbital energies, exchange-correlation potentials, and exchange-correlation energies. Phys Rev A 1994, 50:2138-2142.
116. van Leeuwen R, Baerends EJ. An exchange-correlation potential with correct asymptotic behaviour. Phys Rev A 1994, 49:2421-2431.
117. Kadantsev ES, Stott MJ. Variational method for inverting the Kohn-Sham procedure. Phys Rev A 2004, 69:012502.
118. Wang Y, Parr RG. Construction of exact Kohn-Sham orbitals from a given electron density. Phys Rev A 1993, 47:R1591.
119. Colonna F, Savin A. Correlation energies for some two- and four-electron systems along the adiabatic connection in density functional theory. J Chem Phys 1999, 110:2828.
120. Goodpaster JD, Barnes TA, Miller TF. Embedded density functional theory for covalently bonded and strongly interacting subsystems. J Chem Phys 2011, 134:164108.
121. Yang W, Wu Q. Direct Method for Optimized Effective Potentials in Density-Functional Theory. Phys Rev Lett 2002, 89:143002.
122. Wu Q, Yang W. A direct optimization method for calculating density functionals and exchange-correlation potentials from electron densities. J Chem Phys 2003, 118:2498-2509.
123. Hirata S, Ivanov S, Grabowski I, Bartlett RJ, Burke K, Talman JD. Can optimized effective potentials be determined uniquely? J Chem Phys 2001, 115:1635-1649.
124. Staroverov VN, Scuseria GE, Davidson ER. Optimized effective potentials yielding Hartree-Fock energies and densities. J Chem Phys 2006, 124:141103.
125. Görling A, Heßelmann A, Jones M, Levy M. Relation between exchange-only optimized potential and Kohn-Sham methods with finite basis sets, and effect of linearly depe ndent products of orbital basis functions. J Chem Phys 2008, 128:104104.
126. Heßelmann A, Götz AW, Della Sala F, Görling A. Numerically stable optimized effective potential method with balanced Gaussian basis sets. J Chem Phys 2007, 127:054102.
127. Kollmar C, Filatov M. Optimized effective potential method: Is it possible to obtain an accurate representation of the response function for finite orbital basi s sets? J Chem Phys 2007, 127:114104.
128. Heaton-Burgess T, Bulat FA, Yang W. Optimized Effective Potentials in Finite Basis Sets. Phys Rev Lett 2007, 98:256401.
129. Heaton-Burgess T, Yang W. Optimized effective potentials from arbitrary basis sets. J Chem Phys 2008, 129:194102.
130. King RA, Handy NC. Kinetic energy functionals from the Kohn-Sham potential. Phys Chem Chem Phys 2000, 2:5049-5056.
131. Jacob Ch R. Unambiguous optimization of effective potentials in finite basis sets. J Chem Phys 2011, 135:244102.
132. Boguslawski K, Jacob Ch R, Reiher M. Optimized unrestricted Kohn-Sham potentials from ab initio spin densities. J Chem Phys 2013, 138:044111-044111-16.
133. Grimme S. Density functional theory with London dispersion corrections. WIREs Comput Mol Sci 2011, 1:211-228.
134. Beyhan SM, Götz AW, Visscher L. Bond energy decomposition analysis for subsystem density functional theory. J Chem Phys 2013, 138:094113.
135. Wesolowski TA, Ellinger Y, Weber J. Density functional theory with an approximate kinetic energy functional applied to study structure and stability of weak van der Waals complexes. J Chem Phys 1998, 108:6078.
136. Tran F, Weber J, Wesolowski TA. Theoretical Study of the Benzene Dimer by the Density-Functional-Theory Formalism Based on Electron-Density Partitioning. Helv Chim Acta 2001, 84:1489-1503.
137. Tran F, Weber J, Wesolowski TA. Physisorption of Molecular Hydrogen on Polycyclic Aromatic Hydrocarbons: A Theoretical Study. J Phys Chem B 2002, 106:8689-8696.
138. Tran F, Alameddinee B, Jenny TA, Wesolowski TA. π-Stacking Behavior of Selected Nitrogen-Containing PAHs. J Phys Chem A 2004, 108:9155-9160.
139. Leopoldini M, Russo N, Toscano M, Dulak M, Wesolowski TA. Mechanism of Nitrate Reduction by Desulfovibrio desulfuricans Nitrate Reductase-A Theoretical Investigation. Chem Eur J 2006, 12:2532-2541.
140. Zhao Y, Truhlar DG. Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions. J Phys Chem A 2005, 109:5656-5667.
141. Zhao Y, Truhlar DG. How well can new-generation density functional methods describe stacking interactions in biological systems? Phys Chem Chem Phys 2005, 7:2701-2705.
142. Kevorkyants R, Dulak M, Wesolowski TA. Interaction energies in hydrogen-bonded systems: A testing ground for subsystem formulation of density-functional theory. J Chem Phys 2006, 124:024104.
143. Götz AW, Beyhan SM, Visscher L. Performance of Kinetic Energy Functionals for Interaction Energies in a Subsystem Formulation of Density Functional Theory. J Chem Theory Comput 2009, 5:3161-3174.
144. Hong G, Strajbl M, Wesolowski T, Warshel A. Constraining the Electron Densities in DFT Method as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions. J Comput Chem 2000, 21:1554-1561.
145. Štrajbl M, Hong G, Warshel A. Ab Initio QM/MM Simulation with Proper Sampling: "First Principle" Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution. J Phys Chem B 2002, 106:13333-13343.
146. Olsson MHM, Hong G, Warshel A. Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin. J Am Chem Soc 2003, 125:5025-5039.
147. Trail JR, Bird DM. Density-functional embedding using a plane-wave basis. Phys Rev B 2000, 62:16402-16411.
148. Mehl MJ, Stokes HT, Boyer LL. Development of a Kohn-Sham like Potential in the Self-Consistent Atomic Deformation Model. J Phys Chem Solids 1996, 57:1405-1407.
149. Stokes HT, Boyer LL, Mehl MJ. Spherical self-consistent atomic deformation model for first-principles energy calculations in ionic crystalline solids. Phys Rev B 1996, 54:7729-7736.
150. Boyer LL, Stokes HT, Mehl MJ. Application of a Kohn-Sham-like Formulation of the Self-Consistent Atomic Deformation Model. Ferroelectrics 1997, 194:173-186.
151. Boyer LL, Stokes HT, Mehl MJ. Calculation of Polarization Using a Density Functional Method with Localized Charge. Phys Rev Lett 2000, 84:709-712.
152. Ossowski MM, Boyer LL, Mehl MJ, Stokes HT. Lattice dynamics and elastic properties of corundum by the self-consistent atomic deformation method. Phys Rev B 2002, 66:224302.
153. Boyer LL, Stokes HT, Ossowski MM, Mehl MJ. Self-consistent atomic deformation method for application of density functional theory. Phys Rev B 2008, 78:045121.
154. Zhang X, Lu G. Quantum mechanics/molecular mechanics methodology for metals based on orbital-free density functional theory. Phys Rev B 2007, 76:245111.
155. Zhang X, Wang C-Y, Lu G. Electronic structure analysis of self-consistent embedding theory for quantum/molecular mechanics simulations. Phys Rev B 2008, 78:235119.
156. Zhang X, Lu G, Curtin WA. Multiscale quantum/atomistic coupling using constrained density functional theory. Phys Rev B 2013, 87:054113.
157. Hong G, Rosta E, Warshel A. Using the constrained DFT Approach in Generating Diabatic Surfaces and Off Diagonal Empirical Valence Bond Terms for Modeling Reactions in Condensed Phases. J Phys Chem B 2006, 110:19570-19574.
158. Xiang Y, Warshel A. Quantifying Free Energy Profiles of Proton Transfer Reactions in Solution and Proteins by Using a Diabatic FDFT Method. J Phys Chem B 2008, 112:1007-1015.
159. Kamerlin SCL, Warshel A. The empirical valence bond model: theory and applications. WIREs Comp Mol Sci 2011, 1:30-45.
160. Kaduk B, Kowalczyk T, Voorhis TV. Constrained Density Functional Theory. Chem Rev 2012, 112:321-370.
161. Pavanello M, Neugebauer J. Modelling charge transfer reactions with the Frozen Density Embedding formalism. J Chem Phys 2011, 135:234103.
162. Pavanello M, Voorhis TV, Visscher L, Neugebauer J. An accurate and linear-scaling method for calculating charge-transfer energies and diabatic couplings. J Chem Phys 2013, 138:054101.
163. Reichardt C, Welton T. Solvents and Solvent Effects in Organic Chemistry. Weinheim: Wiley-VCH; 2011.
164. Bader R. Atoms in Molecules. Oxford: Clarendon Press; 1990.
165. García-Lastra JM, Wesolowski TA, Barriuso MT, Aramburu JA, Moreno M. Optical and vibrational properties of MnF64- complexes in cubic fluoroperovskites: insight through embedding calculations using Kohn-Sham equations with constrained electron density. J Phys: Condens Matter 2006, 18:1519-1534.
166. Salahub DR, Goursot A, Weber J, Köster AM. Applied density functional theory and the deMon codes 1964-2004. In: Dykstra CE, Frenking G, Kim KS, Scuseria GE, eds. Theory and Applications of Computational Chemistry: The First Forty Years. Amsterdam: Elsevier; 2005, 1079-1097.
167. Wesolowski TA, Goursot A, Weber J. Properties of CO adsorbed in ZSM5 zeolite: Density functional theory study using the embedding scheme based on electron density partitioning. J Chem Phys 2001, 115:4791.
168. Dułak M, Kamiński JW, Wesołowski TA. Equilibrium Geometries of Noncovalently Bound Intermolecular Complexes Derived from Subsystem Formulation of Density Functional Theory. J Chem Theory Comput 2007, 3:735-745.
169. Iannuzzi M, Kirchner B, Hutter J. Density functional embedding for molecular systems. Chem Phys Lett 2006, 421:16-20.
170. Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J Chem Phys 2008, 128:014101.
171. Shimojo F, Kalia RK, Nakano A, Vashishta P. Embedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theory. Comput Phys Commun 2005, 167:151-164.
172. Vashishta P, Kalia RK, Nakano A, Homan BE, McNesby KL. Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials. J Propul Power 2007, 23:688-692.
173. Jacob Ch R, Visscher L. Calculation of nuclear magnetic resonance shieldings using frozen-density embedding. J Chem Phys 2006, 125:194104.
174. Bulo RE, Jacob Ch R, Visscher L. NMR Solvent Shifts of Acetonitrile from Frozen Density Embedding Calculations. J Phys Chem A 2008, 112:2640-2647.
175. + embedded in Ne and Ar matrices. Chem Phys Lett 1999, 311:87-92.
176. Neugebauer J, Louwerse MJ, Belanzoni P, Wesolowski TA, Baerends EJ. Modeling solvent effects on electron spin resonance hyperfine couplings by frozen-density embedding. J Chem Phys 2005, 123:114101.
177. Fradelos G, Wesolowski TA. Importance of Going beyond Coulombic Potential in Embedding Calculations for Molecular Properties: The Case of Iso-G for Biliverdin in Protein-Like Environment. J Chem Theory Comput 2011, 7:213-222.
178. Fleming GR, Martin JL, Breton J. Rates of primary electron transfer in photosynthetic reaction centres and their mechanistic implications. Nature 1988, 333:190.
179. Kirmaier C, Holten D, Parson W. Temperature and detection-wavelength dependence of the picosecond electron-transfer kinetics measured in Rhodopseudomonas sphaeroides reactions centers. Resolution of new spectral and kinetic components in the primary charge-separation process. Biochim Biophys Acta 1985, 810:49-61.
180. Collins AM, Kirmaier C, Holten D, Blankenship RE. Kinetics and energetics of electron transfer in reaction centers of the photosynthetic bacterium Roseiflexus castenholzii. Biochim Biophys Acta 2011, 1807:262.
181. Zbiri M, Atanasov M, Daul C, Garcia-Lastra JM, Wesolowski TA. Application of the density functional theory derived orbital-free embedding potential to calculate the splitting energies of lanthanide cations in chloroelpasolite crystals. Chem Phys Lett 2004, 397:441-446.
182. Zbiri M, Daul C, Wesolowski TA. Effect of the f-Orbital Delocalization on the Ligand-Field Splitting Energies in Lanthanide-Containing Elpasolites. J Chem Theory Comput 2006, 2:1106-1111.
183. Atanasov M, Daul C, Güdel HU, Wesolowski TA, Zbiri M. Ground States, Excited States, and Metal-Ligand Bonding in Rare Earth Hexachloro Complexes: A DFT-Based Ligand Field Study. Inorg Chem 2005, 44:2954-2963.
184. Casida ME, Wesolowski TA. Generalization of the Kohn-Sham Equations with Constrained Electron Density Formalism and Its Time-Dependent Response Theory Formulation. Int J Quantum Chem 2004, 96:577-588.
185. Casida ME. Time-dependent density functional response theory for molecules. In: Chong DP, ed. Recent Advances in Density Functional Methods Part I. Singapore: World Scientific; 1995, 155-192.
186. van Gisbergen SJA, Snijders JG, Baerends EJ. Implementation of time-dependent density functional response equations. Comput Phys Commun 1999, 118:119-138.
187. Marques MAL, Gross EKU. Time-dependent density-functional theory. In: Fiolhais C, Nogueira F, Marques M, eds. A Primer in Density Functional Theory. Berlin: Springer; 2003, 144-184.
188. Rosa A, Ricciardi G, Gritsenko OV, Baerends EJ. Excitation energies of metal complexes with time-dependent density functional theory. Struct Bonding 2004, 112:49-116.
189. Marques MAL, Gross EKU. Time-Dependent Density Functional Theory. Annu Rev Phys Chem 2004, 55:427-455.
190. Dreuw A, Head-Gordon M. Single-Reference ab Initio Methods for the Calculation of Excited States of Large Molecules. Chem Rev 2005, 105:4009-4037.
191. Wesolowski TA. Hydrogen-bonding induced shifts of the excitation energies in nucleic acid bases: an interplay between electrostatic and electron density overlap effects. J Am Chem Soc 2004, 126:11444-11445.
192. Neugebauer J. Couplings between electronic transitions in a subsystem formulation of time-dependent density functional theory. J Chem Phys 2007, 126:134116.
193. Fradelos G, Kaminski JW, Wesołowski TA, Leutwyler S. Cooperative Effect of Hydrogen-Bonded Chains in the Environment of a π→π* Chromophore. J Phys Chem A 2009, 113:9766-9771.
194. Neugebauer J. Photophysical Properties of Natural Light-Harvesting Complexes Studied by Subsystem Density Functional Theory. J Phys Chem B 2008, 112:2207-2217.
195. König C, Schlüter N, Neugebauer J. Direct determination of exciton couplings from subsystem time-dependent density-functional theory within the tamm-dancoff approximation. J Chem Phys 2013, 138:034104.
196. Pavanello M. On the subsystem formulation of linear-response time-dependent DFT. J Chem Phys 2013, 138:204118.
197. Neugebauer J. Orbital-free embedding calculations of electronic spectra. In: Wesolowski TA, Wang YA, eds. Recent Progress in Orbital-Free Density Functional Theory. Singapore: World Scientific; 2013, 325-356.
198. Neugebauer J, Louwerse MJ, Baerends EJ, Wesolowski TA. The merits of the frozen-density embedding scheme to model solvatochromic shifts. J Chem Phys 2005, 122:094115.
199. Neugebauer J, Jacob Ch R, Wesolowski TA, Baerends EJ. An Explicit Quantum Chemical Method for Modeling Large Solvation Shells Applied to Aminocoumarin C151. J Phys Chem A 2005, 109:7805-7814.
200. Zhou X, Wesolowski TA, Tabacchi G, Fois E, Calzaferri G, Devaux A. First-principles simulation of the absorption bands of fluorenone in zeolite L. Phys Chem Chem Phys 2013, 15:159-167.
201. Kovyrshin A, Neugebauer J. Potential-Energy Surfaces of Local Excited States from Subsystem- and Selective Kohn-Sham-TDDFT. Chem Phys 2011, 391:147-156.
202. Neugebauer J, Baerends EJ. Exploring the Ability of Frozen-Density Embedding to Model Induced Circular Dichroism. J Phys Chem A 2006, 110:8786-8796.
203. Tomasi J, Mennucci B, Cammi R. Quantum Mechanical Continuum Solvation Models. Chem Rev 2005, 105:2999-3094.
204. Kovalenko A. Three-dimensional RISM theory for molecular liquids and solid-liquid interfaces. In: Hirata F, ed. Molecular Theory of Solvation: Understanding Chemical Reactivity. Dordrecht, The Netherlands: Kluwer; 2003, 169-275.
205. Klamt A, Schüürmann G. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc, Perkin Trans 1993, 2:799-805.
206. Zhou X, Kaminski JW, Wesołowski TA. Multi-scale modelling of solvatochromic shifts from frozen-density embedding theory with non-uniform continuum model of the solvent: the coumarin 153 case. Phys Chem Chem Phys 2011, 13:10565-10576.
207. Fradelos G, Lutz JJ, Wesołowski TA, Piecuch P, Włoch M. Shifts in excitation energies induced by hydrogen bonding: a comparison of the embedding and supermolecular time-dependent density functional theory calculations with the equation-of-motion coupled-cluster results. In: Hoggan PE, Brändas EJ, Maruani J, Piecuch P, Delgado-Barrio G, eds. Advances in the Theory of Quantum Systems in Chemistry and Physics, vol 22 of Progress in Theoretical Chemistry and Physics. Dordrecht: Springer; 2012, 219-248.
208. König C, Neugebauer J. First-principles calculations of electronic spectra of light-harvesting complex II. Phys Chem Chem Phys 2011, 13:10475-10490.
209. König C, Neugebauer J. Protein effects on the optical spectrum of the fenna-matthews-olson complex from fully quantum chemical calculations. J Chem Theory Comput 2013, 9:1808-1820.
210. Neugebauer J, Veldstra J, Buda F. Theoretical Spectroscopy of Astaxanthin in Crustacyanin Proteins: Absorption, Circular Dichroism, and Nuclear Magnetic Resonance. J Phys Chem B 2011, 115:3216-3225.
211. Neugebauer J, Curutchet C, Munos-Losa A, Mennucci B. A Subsystem TDDFT Approach for Solvent Screening Effects on Excitation Energy Transfer Couplings. J Chem Theory Comput 2010, 6:1843-1851.
212. König C, Neugebauer J. Exciton coupling mechanisms analyzed with subsystem tddft: Direct vs. pseudo exchange effects. J Phys Chem B 2013, 117:3480-3487.
213. Neugebauer J. On the calculation of general response properties in subsystem density functional theory. J Chem Phys 2009, 131:084104.
214. Mukhopadhyay P, Zuber G, Wipf P, Beratan DN. Contribution of a solute's chiral solvent imprint to optical rotation. Angew Chem, Int Ed 2007, 46:6450-6452.
215. Neugebauer J. Induced Chirality in Achiral Media - How Theory Unravels Mysterious Solvent Effects. Angew Chem, Int Ed 2007, 46:7738-7740.
216. Huang P, Carter EA. Advances in Correlated Electronic Structure for Solids, Surfaces, and Nanostructures. Annu Rev Phys Chem 2008, 59:261-290.
217. Gomes ASP, Jacob Ch R. Quantum-chemical embedding methods for treating local electronic excitations in complex chemical systems. Annu Rep Prog Chem C 2012, 108:222.
218. Govind N, Wang YA, da Silva AJR, Carter EA. Accurate ab initio energetics of extended systems via explicit correlation embedded in a density functional environment. Chem Phys Lett 1998, 295:129-134.
219. Govind N, Wang YA, Carter EA. Electronic-structure calculations by first-principles density-based embedding of explicitly correlated systems. J Chem Phys 1999, 110:7677-7688.
220. Aquilante F, Wesolowski TA. Self-consistency in frozen-density embedding theory based calculations. J Chem Phys 2011, 135:084120.
221. Klüner T, Govind N, Wang YA, Carter EA. Prediction of electronic excited states of adsorbates on metal surfaces from first principles. Phys Rev Lett 2001, 86:5954-5957.
222. Klüner T, Govind N, Wang YA, Carter EA. Periodic density functional embedding theory for complete active space self-consistent field and configuration interaction calculations: Ground and excited states. J Chem Phys 2002, 116:42-54.
223. Huang P, Carter EA. Self-consistent embedding theory for locally correlated configuration interaction wave functions in condensed matter. J Chem Phys 2006, 125:084102.
224. Lahav D, Klüner T. A self-consistent density based embedding scheme applied to the adsorption of CO on Pd(111). J Phys: Condens Matter 2007, 19:226001.
225. Huang C, Carter EA. Embedding theory for excited states. J Chem Phys 2011, 135:194104.
226. Khait YG, Hoffmann MR. Embedding theory for excited states. J Chem Phys 2010, 133:044107.
227. Höfener S, Gomes ASP, Visscher L. Molecular properties via a subsystem density functional theory formulation: A common framework for electronic embedding. J Chem Phys 2012, 136:044104.
228. Christiansen O, Jørgensen P, Hättig C. Response functions from Fourier component variational perturbation theory applied to a time-averaged quasienergy. Int J Quantum Chem 1998, 68:1-52.
229. Kanan DK, Sharifzadeh S, Carter EA. Quantum mechanical modeling of electronic excitations in metal oxides: Magnesia as a prototype. Chem Phys Lett 2012, 519-520:18-24.
230. Gomes ASP, Jacob Ch R, Visscher L. Calculation of local excitations in large systems by embedding wave-function theory in density-functional theory. Phys Chem Chem Phys 2008, 10:5353-5362.
231. Daday C, König C, Valsson O, Neugebauer J, Filippi C. State-Specific Embedding Potentials for Excitation-Energy Calculations. J Chem Theory Comput 2013, 9:2355-2367.
232. Höfener S, Visscher L. Calculation of electronic excitations using wave-function in wave-function frozen-density embedding. J Chem Phys 2012, 137:204120.
233. Roncero O, de Lara-Castells MP, Villarreal P, Flores F, Ortega J, Paniagua M, Aguado A. An inversion technique for the calculation of embedding potentials. J Chem Phys 2008, 129:184104.
234. Roncero O, Zanchet A, Villarreal P, Aguado A. A density-division embedding potential inversion technique. J Chem Phys 2009, 131:234110.
235. Goodpaster JD, Barnes TA, Manby FR, Miller TF. Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes. J Chem Phys 2012, 137:224113.
236. 2 Oxidative Addition. J Phys Chem 1996, 100:19357-19363.
237. Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M. Fragment molecular orbital method: an approximate computational method for large molecules. Chem Phys Lett 1999, 313:701-706.
238. Fedorov DG, Kitaura K. Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method. J Phys Chem A 2007, 111:6904-6914.