Jaguar References

The first 18 references listed below provide general information about the algorithms used in Jaguar and some of their applications. Their titles are included in the listings. The other listings in this section are referenced throughout the Jaguar manuals.

1. Friesner, R. A. Solution of Self-Consistent Field Electronic Structure Equations by a Pseudospectral Method. Chem. Phys. Lett. 1985, 116, 39, DOI: 10.1016/0009-2614(85)80121-4
2. Friesner, R. A. Solution of the Hartree-Fock equations by a pseudospectral method: Application to diatomic molecules. J. Chem. Phys. 1986, 85, 1462, DOI: 10.1063/1.451237
3. Friesner, R. A. Solution of the Hartree-Fock equations for polyatomic molecules by a pseudospectral method. J. Chem. Phys. 1987, 86, 3522, DOI: 10.1063/1.451955
4. Friesner, R. A. An Automatic Grid Generation Scheme for Pseudospectral Self-Consistent Field Calculations on Polyatomic Molecules. J. Phys. Chem. 1988, 92, 3091, DOI: 10.1021/j100322a017
5. Ringnalda, M. N.; Won, Y.; Friesner, R. A. Pseudospectral Hartree-Fock calculations on glycine. J. Chem. Phys. 1990, 92, 1163, DOI: 10.1063/1.458178
6. Langlois, J. -M.; Muller, R. P.; Coley, T. R.; Goddard, W. A., III; Ringnalda, M. N.; Won, Y.; Friesner, R. A. Pseudospectral generalized valence-bond calculations: Application to methylene, ethylene, and silylene. J. Chem. Phys. 1990, 92, 7488, DOI: 10.1063/1.458184
7. Ringnalda, M. N.; Belhadj, M.; Friesner, R. A. Pseudospectral Hartree-Fock theory: Applications and algorithmic improvements. J. Chem. Phys. 1990, 93, 3397, DOI: 10.1063/1.458819
8. Won, Y.; Lee, J. -G.; Ringnalda, M. N.; Friesner, R. A. Pseudospectral Hartree-Fock gradient calculations. J. Chem. Phys. 1991, 94, 8152, DOI: 10.1063/1.460097
9. Friesner, R. A. New Methods for Electronic Structure Calculations on Large Molecules. Annu. Rev. Phys. Chem. 1991, 42, 341, DOI: 10.1146/annurev.pc.42.100191.002013
10. Pollard, W. T.; Friesner, R. A. Efficient Fock matrix diagonalization by a Krylov-space method. J. Chem. Phys. 1993, 99, 6742, DOI: 10.1063/1.465817.
11. Muller, R. P.; Langlois, J. -M.; Ringnalda, M. N.; Friesner, R. A.; Goddard, W. A., III. A generalized direct inversion in the iterative subspace approach for generalized valence bond wave functions. J. Chem. Phys. 1994,100, 1226, DOI: 10.1063/1.466653
12. Murphy, R. B.; Friesner, R. A.; Ringnalda, M. N.; Goddard, W. A., III. Pseudospectral Contracted Configuration Interaction From a Generalized Valence Bond Reference. J. Chem. Phys. 1994, 101, 2986, DOI: 10.1063/1.467611
13. Greeley, B. H.; Russo, T. V.; Mainz, D. T.; Friesner, R. A.; Langlois, J. -M.; Goddard, W. A., III; Donnelly, R. E., Jr., Ringnalda, M. N. New Pseudospectral Algorithms for Electronic Structure Calculations: Length Scale Separation and Analytical Two-Electron Integral Corrections. J. Chem. Phys. 1994, 101, 4028, DOI: 10.1063/1.467520
14. Langlois, J. -M.; Yamasaki, T.; Muller, R. P.; Goddard, W. A. Rule Based Trial wave functions for Generalized Valence Bond Theory. J. Phys. Chem. 1994, 98, 13498, DOI: 10.1021/j100102a012
15. Tannor, D. J.; Marten, B.; Murphy, R.; Friesner, R. A.; Sitkoff, D.; Nicholls, A.; Ringnalda, M.; Goddard, W. A., III; Honig, B. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory. J. Am. Chem. Soc. 1994, 116, 11875, DOI: 10.1021/ja00105a030
16. Murphy, R. B.; Beachy, M. D.; Friesner, R. A.; Ringnalda, M. N. Pseudospectral Localized MP2 Methods: Theory and Calculation of Conformational Energies. J. Chem. Phys. 1995, 103, 1481, DOI: 10.1063/1.469769
17. Lu, D.; Marten, B.; Cao, Y.; Ringnalda, M. N.; Friesner, R. A.; Goddard, W. A., III. Ab initio Predictions of Large Hyperpolarizability Push-Pull Polymers: Julolidinyl-n-isoxazolone and Julolidinyl-n-N,N’-diethylthiobarbituric acid. Chem. Phys. Lett. 1995, 242, 543, DOI: 10.1016/0009-2614(95)00793-4
18. Cao, Y.; Friesner, R. A. Molecular (hyper)polarizabilities computed by pseudospectral methods. J. Chem. Phys. 2005, 122, 104102, DOI: 10.1063/1.1855881
19. Cao, Y.; Beachy, M. D.; Braden, D. A.; Morrill, L. A.; Ringnalda, M. N.; Friesner, R. A. Nuclear-magnetic-resonance shielding constants calculated by pseudospectral methods. J. Chem. Phys. 2005, 122, 224116, DOI: 10.1063/1.1924598
20. Murphy, R. B.; Pollard, W. T.; Friesner, R. A. Pseudospectral localized generalized Møller-Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies. J. Chem. Phys. 1997, 106, 5073, DOI: 10.1063/1.473553
21. Vacek, G.; Perry, J. K.; Langlois, J. -M. Advanced initial-guess algorithm for self-consistent-field calculations on organometallic systems. Chem. Phys. Lett. 1999, 310, 189, DOI: 10.1016/S0009-2614(99)00722-8
22. Bobrowicz F. W.; Goddard, W. A., III. Chapter 4. In Modern Theoretical Chemistry: Methods of Electronic Structure Theory; Schaefer, H. F., III, Ed., 3; Plenum: New York, 1977.
23. BIOGRAF manual.
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26. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T; Hutchison G. R. Open Babel: An open chemical toolbox. J. Cheminf. 2011, 3, 33, DOI:  10.1186/1758-2946-3-33
27. Dunietz, B. D.; Murphy, R. B.; Friesner, R. A. Calculation of enthalpies of formation by a multi-configurational localized perturbation theory - application for closed shell cases. J. Chem. Phys. 1999, 110, 1921, DOI: 10.1063/1.477859
28. Kaminski, G. A.; Maple, J. R.; Murphy, R. B.; Braden, D. A.; Friesner, R. A. Pseudospectral Local Second-Order Møller−Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs. J. Chem. Theory Comput. 2005, 1, 248, DOI: 10.1021/ct049880o
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30. Hirata, S.; Head-Gordon, M. Time-dependent density functional theory within the Tamm–Dancoff approximation. Chem. Phys. Lett. 1999, 314, 291, DOI: 10.1016/S0009-2614(99)01149-5
31. Becke, A. D. A new mixing of Hartree–Fock and local density‐functional theories. J. Chem. Phys. 1993, 98, 1372, DOI: 10.1063/1.464304
32. Becke, A. D. Density‐functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648, DOI: 10.1063/1.464913
33. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 1994, 98, 11623, DOI: 10.1021/j100096a001
34. Slater, J. C. Quantum Theory of Molecules and Solids, Vol. 4: The Self-Consistent Field for Molecules and Solids. McGraw-Hill: New York, 1974.
35. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200, DOI: 10.1139/p80-159
(The VWN correlation functional is described in the paragraph below equation [4.4] on p. 1207, while the VWN5 functional is described in the caption of Table 5 and on p. 1209.)
36. Perdew, J. P. In Electronic Structure Theory of Solids; Ziesche, P., Eschrig, H., Eds.; Akademie Verlag: Berlin, 1991. Perdew, J. P.; Chevary, J. A.; Vosko, S. H.; Jackson, K. A.; Pederson, M. R.; Singh, D. J.; Fiolhais, C. Phys. Rev. B 1992, 46, 6671, DOI: 10.1103/PhysRevB.46.6671
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38. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785, DOI: https://doi.org/10.1103/PhysRevB.37.785; implemented as described in Miehlich, B.; Savin, A.; Stoll, H.; Preuss, H. Results obtained with the correlation energy density functionals of Becke and Lee, Yang and Parr. Chem. Phys. Lett. 1989, 157, 200, DOI: 10.1016/0009-2614(89)87234-3
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41. Becke, A. D. Density‐functional thermochemistry. IV. A new dynamical correlation functional and implications for exact‐exchange mixing. J. Chem. Phys. 1996, 104, 1040, DOI: 10.1063/1.470829
42. Becke, A. D. Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J. Chem. Phys. 1997, 107, 8554, DOI: 10.1063/1.475007
43. Becke, A. D. A new inhomogeneity parameter in density-functional theory. J. Chem. Phys. 1998, 109, 2092, DOI: 10.1063/1.476722
44. Schmider, H. L.; Becke, A. Density functionals from the extended G2 test set: Second-order gradient corrections. J. Chem. Phys. 1998, 109, 8188, DOI: https://doi.org/10.1063/1.477481; Schmider, H. L.; Becke, A. Optimized density functionals from the extended G2 test set. J. Chem. Phys. 1998, 108, 9624, DOI: 10.1063/1.476438
45. Hamprecht, F. A.; Cohen, A. J.; Tozer, D. J.; Handy, N. C. Development and assessment of new exchange-correlation functionals. J. Chem. Phys. 1998, 109, 6264, DOI: 10.1063/1.477267
46. Boese, A. D.; Handy, N. C. A new parametrization of exchange–correlation generalized gradient approximation functionals. J. Chem. Phys. 2001, 114, 5497, DOI: 10.1063/1.1347371
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48. Handy, N. C.; Cohen, A. J. Left-right correlation energy. Mol. Phys. 2001, 99, 403, DOI: 10.1080/00268970010018431
49. Grimme, S. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction. J. Comput. Chem. 2006, 27, 1787, DOI: 10.1002/jcc.20495
50. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 154104, DOI: 10.1063/1.3382344
51. Goerigk, L.; Grimme, S. A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions. Phys. Chem. Chem. Phys. 2011, 13, 6670, DOI: 10.1039/C0CP02984J
52. Adamo, C.; Barone, V. Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models. J. Chem. Phys. 1998, 108, 664, DOI: 10.1063/1.475428
53. Adamo, C.; Barone, V. Toward reliable density functional methods without adjustable parameters: The PBE0 model. J. Chem. Phys. 1999, 110, 6158, DOI: 10.1063/1.478522
54. Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D. G. Adiabatic Connection for Kinetics. J. Phys. Chem. A 2000, 104, 4811, DOI: 10.1021/jp000497z
55. Xu, X; Goddard, W. A., III. The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 2673, DOI: 10.1073/pnas.0308730100
56. Zhao, Y.; Lynch, B. J.; Truhlar, D. G. Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics. J. Phys. Chem. A 2004, 108, 2715, DOI: 10.1021/jp049908s
57. Zhao, Y.; Truhlar, D. G. Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions. J. Phys. Chem. A 2005, 109, 5656, DOI: 10.1021/jp050536c
58. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions. J. Chem. Phys. 2005, 123, 161103, DOI: 10.1063/1.2126975
59. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions. J. Chem. Theory Comput. 2006, 2, 364, DOI: 10.1021/ct0502763
60. Zhao, Y.; Truhlar, D. G. A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J. Chem. Phys. 2006, 125, 194101, DOI: 10.1063/1.2370993
61. Zhao, Y.; Truhlar, D. G. Density Functional for Spectroscopy:  No Long-Range Self-Interaction Error, Good Performance for Rydberg and Charge-Transfer States, and Better Performance on Average than B3LYP for Ground States. J. Phys. Chem. A 2006, 110, 13126, DOI: 10.1021/jp066479k
62. Zhao, Y.; Truhlar, D. G. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120, 215, DOI: 10.1007/s00214-007-0310-x
63. Zhao, Y.; Truhlar, D. G. Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions J. Chem. Theory Comput. 2008, 4, 1849, DOI: 10.1021/ct800246v
64. Peverati, R.; Truhlar, D. G. Exchange-Correlation Functional with Good Accuracy for Both Structural and Energetic Properties while Depending Only on the Density and Its Gradient.J. Chem. Theory Comput. 2012, 8, 2310, DOI: 10.1021/ct3002656
65. Peverati, R.; Truhlar, D. G. An improved and broadly accurate local approximation to the exchange–correlation density functional: The MN12-L functional for electronic structure calculations in chemistry and physics. Phys. Chem. Chem. Phys. 2012, 14, 13171, DOI: 10.1039/C2CP42025B
66. Yu, H. S.; He, X; Li, S. L.; Truhlar, D. G. MN15: A Kohn-Sham global-hybrid exchange-correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions. Chem. Sci. 2016, 7, 5032., DOI: 10.1039/C6SC00705H
67. Yu, H. S.; He, X; Truhlar, D. G. MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids. J. Chem. Theory Comput. 2016, 12, 1280, DOI: 10.1021/acs.jctc.5b01082
68. Iikura, H.; Tsuneda, T.; Yanai, T.; Hirao, K. A long-range correction scheme for generalized-gradient-approximation exchange functionals. J. Chem. Phys. 2001, 115, 3540, DOI: 10.1063/1.1383587
69. Yanai, T.; Tew, D. P.; Handy, N. C. A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem. Phys. Lett. 2004, 393, 51, DOI: 10.1016/j.cplett.2004.06.011
70. Henderson, T. M.; Janesko, B. G.; Scuseria, G. E. Generalized gradient approximation model exchange holes for range-separated hybrids. J. Chem. Phys. 2008, 128, 194105, DOI: 10.1063/1.2921797
71. Vydrov O. A.; Scuseria, G. E. Assessment of a long-range corrected hybrid functional. J. Chem. Phys. 2006, 125, 234109, DOI: 10.1063/1.2409292
72. Rohrdanz, M. A.; Martins, K. M.; Herbert, J. M. A long-range-corrected density functional that performs well for both ground-state properties and time-dependent density functional theory excitation energies, including charge-transfer excited states. J. Chem. Phys. 2009, 130, 054112, DOI: 10.1063/1.3073302
73. Heyd, J.; Scuseria, G. E.; Ernzerhof, M. Hybrid functionals based on a screened Coulomb potential. J. Chem. Phys. 2003, 118, 8207, DOI: 10.1063/1.1564060
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75. Krukau, A. V.; Vydrov O. A.; Izmaylov A. F.; Scuseria, G. E. Influence of the exchange screening parameter on the performance of screened hybrid functionals. J. Chem. Phys. 2006, 125, 224106, DOI: 10.1063/1.2404663
76. Peverati, R.; Truhlar, D.G. Improving the Accuracy of Hybrid Meta-GGA Density Functionals by Range Separation. J. Phys. Chem. Lett. 2011, 2, 2810, DOI: 10.1021/jz201170d
77. Peverati, R.; Truhlar, D.G. M11-L: A Local Density Functional That Provides Improved Accuracy for Electronic Structure Calculations in Chemistry and Physics. J. Phys. Chem. Lett. 2012, 3, 117, DOI: 10.1021/jz201525m
78. Chai, J.-D.; Head-Gordon M. Systematic optimization of long-range corrected hybrid density functionals. J. Chem. Phys. 2008, 128, 084106, DOI: 10.1063/1.2834918
79. Chai, J.-D.; Head-Gordon M. Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections. Phys. Chem. Chem. Phys. 2008, 10, 6615, DOI: 10.1039/B810189B
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82. Schneebeli, S. T.; Bochevarov, A. D.; Friesner R. A. Parameterization of a B3LYP Specific Correction for Noncovalent Interactions and Basis Set Superposition Error on a Gigantic Data Set of CCSD(T) Quality Noncovalent Interaction Energies. J. Chem. Theory Comput. 2011, 7 658, DOI: 10.1021/ct100651f
83. Friesner, R. A.; Knoll, E. H.; Cao Y. A localized orbital analysis of the thermochemical errors in hybrid density functional theory: Achieving chemical accuracy via a simple empirical correction scheme. J. Chem. Phys. 2006, 125, 124107, DOI: 10.1063/1.2263795
84. Knoll, E. H.; Friesner, R. A. Localized Orbital Corrections for the Calculation of Ionization Potentials and Electron Affinities in Density Functional Theory. J. Phys. Chem. B2006, 110, 18787, DOI: 10.1021/jp0619888
85. Goldfeld, D. A.; Bochevarov, A. D.; Friesner R. A. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions. J. Chem. Phys. 2008, 129, 214105, DOI: 10.1063/1.3008062
86. Hall, M. L.; Goldfeld, D. A.; Bochevarov, A. D.; Friesner R. A. Localized Orbital Corrections for the Barrier Heights in Density Functional Theory. J. Chem. Theory Comput. 2009, 5, 2996, DOI: 10.1021/ct9003965
87. Hall, M. L.; Zhang, J.; Bochevarov, A. D.; Friesner R. A. Continuous Localized Orbital Corrections to Density Functional Theory: B3LYP-CLOC. J. Chem. Theory Comput. 2010, 6, 3647, DOI: 10.1021/ct100418n
88. Rinaldo, D.; Tian,L.; Harvey, J. H.; Friesner R. A. Density functional localized orbital corrections for transition metals. J. Chem. Phys. 2008, 129, 164108, DOI: 10.1063/1.2974101
89. Hughes, T. F.; Friesner R. A. Correcting Systematic Errors in DFT Spin-Splitting Energetics for Transition Metal Complexes. J. Chem. Theory Comput. 2011, 7, 19, DOI: 10.1021/ct100359x
90. Hughes, T. F.; Friesner R. A. Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450. J. Chem. Theory Comput. 2012, 8, 442, DOI: 10.1021/ct2006693
91. Hughes, T. F.; Harvey, J. H.; Friesner R. A. A B3LYP-DBLOC empirical correction scheme for ligand removal enthalpies of transition metal complexes: parameterization against experimental and CCSD(T)-F12 heats of formation. Phys. Chem. Chem. Phys. 2012, 14, 7724, DOI: 10.1039/C2CP40220C
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