Binding interactions in dimers of phenalenyl and closed-shell analogues

Journal of Physical Chemistry A

Volumn 117, Issue 17, 2013, Pages 3642-3649

  Kolb, Brian ^a   Kertesz, Miklos ^b   Thonhauser, T ^a  

^a WAKE FOREST UNIVERSITY   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX PHYSICAL SYSTEMS; ELECTRICAL AND MAGNETIC PROPERTY; ELECTRONIC KINETIC ENERGY; EQUILIBRIUM DISTANCES; EXCHANGE FUNCTIONAL; SPIN-POLARIZED DENSITY FUNCTIONAL THEORY; STACKED CONFIGURATION; VAN DER WAALS RADIUS;

BINDING ENERGY; BORON; CARBON; DENSITY FUNCTIONAL THEORY; ELECTRIC PROPERTIES; KINETICS; MOLECULAR CRYSTALS; NITROGEN; VAN DER WAALS FORCES;

DIMERS;

FREE RADICAL; POLYCYCLIC HYDROCARBON;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; QUANTUM THEORY;

BINDING SITES; DIMERIZATION; FREE RADICALS; MOLECULAR STRUCTURE; POLYCYCLIC COMPOUNDS; QUANTUM THEORY;

EID: 84877076478     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp3095424     Document Type: Article

References (51)

1. Goto, K.; Kubo, T.; Yamamoto, K.; Nakasuji, K.; Sato, K.; Shiomi, D.; Takui, T.; Kubota, M.; Kobayashi, T.; Yakusi, K. A Stable Neutral Hydrocarbon Radical: Synthesis, Crystal Structure, and PHysical Properties of 2,5,8-Tri-tert-butyl-phenalenyl J. Am. Chem. Soc. 1999, 121, 1619-1620
2. Itkis, M. E.; Chi, X.; Cordes, A. W.; Haddon, R. C. Magneto-Opto- Electronic Bistability in a Phenalenyl-Based Neutral Radical Science 2002, 296, 1443-1445
3. Tagami, K.; Wang, L.; Tsukada, M. Interface Sensitivity in Quantum Transport Through Single Molecules Nano Lett. 2004, 4, 209-212
4. Dutta, P.; Maiti, S. K.; Karmakar, S. Multi-Termial electron Transport Through Single Phenalenyl Molecule: A Theoretical Study Org. Electron. 2010, 11, 1120-1128
5. Fan, Z.-Q.; Zhang, Z.-H.; Ming, Q.; Tang, G.-P.; Chen, K.-Q. First-Principles Study of Repeated Current Switching in a Bimolecular Device Comput. Mater. Sci. 2012, 53, 294-297
6. Tian, Y. H.; Kertesz, M. Is There a Lower Limit to the CC Bonding Distances in Neutral Radical π-Dimers? The Case of Phenalenyl Derivatives J. Am. Chem. Soc. 2010, 132, 10648-10649
7. Chi, X.; Itkis, M. E.; Patrick, B. O.; Barclay, T. M.; Reed, R. W.; Oakley, R. T.; Cordes, A. W.; Haddon, R. C. The First Phenalenyl-Based Neutral Radical Molecular Conductor J. Am. Chem. Soc. 1999, 121, 10395-10402
8. Mandal, S. K.; Samanta, S.; Itkis, M. E.; Jensen, D. W.; Reed, R. W.; Oakley, R. T.; Tham, F. S.; Donnadieu, B.; Haddon, R. C. Resonatng Valence Bond Ground State in Oxygen-Functionalized Phenalenyl-Based Neutral Radical Molecular Conductors J. Am. Chem. Soc. 2006, 128, 1982-1994
9. Sarkar, A.; Itkis, M. E.; Tham, F. S.; Haddon, R. C. Synthesis, Structure, and Physical Properties of a Partial π-Stacked Phenalenyl-Based Neutral Radical Molecular Conductor Chemistry 2011, 17, 11576-11584
10. Beer, L.; Mandal, S. K.; Reed, R. W.; Oakley, R. T.; Tham, F. S.; Donnadieu, B.; Haddon, R. C. The First Electronically Stabilized Phenalenyl Radical: Effects of Substituents on Solution Chemistry and Solid-State Structure Cryst. Growth Des. 2007, 7, 802-809
11. Wan, X.; Lv, X.; He, G.; Yu, A.; Chen, Y. Synthesis of Neutral Stable Polyradicals and Their Application on Phtovoltaic Devices Eur. Polym. J. 2011, 47, 1018-1030
12. Pal, S. K.; Itkis, M. E.; Tham, F. S.; Reed, R. W.; Oakley, R. T.; Donnadieu, B.; Haddon, R. C. Phenalenyl-Based Neutral Radical Molecular Conductors: Substituent Effects on Solid-State Structures and Properties J. Am. Chem. Soc. 2007, 129, 7163-7174
13. Liao, P.; Itkis, M. E.; Oakley, R. T.; Tham, F. S.; Haddon, R. C. Light-Mediated C-C σ-Bond Driven Crystallization of a Phenalenyl Radical Dimer J. Am. Chem. Soc. 2004, 126, 14297-142302
14. Pal, S. K.; Itkis, M. E.; Tham, F. S.; Reed, R. W.; Oakley, R. T.; Haddon, R. C. Trisphenalenyl-Based Neutral Radical Molecular Conductor J. Am. Chem. Soc. 2008, 130, 3942-3951
15. Huang, J.; Kertesz, M. Spin Crossover of Spiro-Biphenalenyl Neutral Radical Molecular Conductors J. Am. Chem. Soc. 2003, 125, 13334-13335
16. Dion, M.; Rydberg, H.; Schröder, E.; Langreth, D.; Lundqvist, B. van der Waals Functional for General Geometries Phys. Rev. Lett. 2004, 92, 22-25
17. Thonhauser, T.; Cooper, V. R.; Li, S.; Puzder, A.; Hyldgaard, P.; Langreth, D. C. van der Waals Density Functional: Self-Consistent Potential and the Nature of the van der Waals Bond Phys. Rev. B 2007, 76, 125112
18. Langreth, D. C.; Lundqvist, B. I.; Chakarova-Käck, S. D.; Cooper, V. R.; Dion, M.; Hyldgaard, P.; Kelkkanen, A.; Kleis, J.; Kong, L.; Li, S. A Density Functional for Sparse Matter J. Phys.: Condens. Matt. 2009, 21, 084203
19. Thonhauser, T.; Puzder, A.; Langreth, D. C. Interaction Energies of Monosubstituted Benzene Dimers via Nonlocal Density Functional Theory J. Chem. Phys. 2006, 124, 164106
20. Li, S.; Cooper, V. R.; Thonhauser, T.; Puzder, A.; Langreth, D. C. A Density Functional Theory Study of the Benzene-Water Complex J. Phys. Chem. A 2008, 112, 9031-9036
21. Björk, J.; Hanke, F.; Palma, C.-A.; Samori, P.; Cecchini, M.; Persson, M. Adsorption of Aromatic and Anti-Aromatic Systems on Graphene through π-π Stacking J. Phys. Chem. Lett. 2010, 1, 3407-3412
22. Mura, M.; Gulans, A.; Thonhauser, T.; Kantorovich, L. Role of van der Waals Interaction in Forming Molecule-Metal Junctions: Flat Organic Molecules on the Au(111) Surface Phys. Chem. Chem. Phys. 2010, 12, 4759-4767
23. Chen, D.-L.; Al-Saidi, W.; Johnson, J. Nobel Gases on Metal Surfaces: INsights on Adsorption Site Preference Phys. Rev. B 2011, 84, 2-5
24. Cooper, V. R.; Thonhauser, T.; Puzder, A.; Schröder, E.; Lundqvist, B. I.; Langreth, D. C. Stacking interactions and the Twist of DNA J. Am. Chem. Soc. 2008, 130, 1304-1308
25. Cooper, V. R.; Thonhauser, T.; Langreth, D. C. An Application of the van der Waals Density Functional: Hydrogen Bonding and Stacking Interactions Between Nucleobases J. Chem. Phys. 2008, 128, 204102
26. h Phys. Rev. B 2011, 84, 045116
27. Lin, Y.; Ma, H.; Matthews, C. W.; Kolb, B.; Sinogeikin, S.; Thonhauser, T.; Mao, W. L. Experimental and Theoretical Studies on a High Pressure Monoclinic Phase of Ammonia Borane J. Phys. Chem. C 2012, 116, 2172-2178
28. 2 from Density Functional Theory Phys. Rev. B 2011, 83, 224103
29. Klimeš, J.; Bowler, D.; Michaelides, A. van der Waals Density Functionals Applied to Solids Phys. Rev. B 2011, 83, 195131
30. 5: First-Principles Density-Functional Calculations Phys. Rev. B 2010, 82, 1-8
31. Hamada, I.; Lee, K.; Morikawa, Y. Interation of Water with a Metal Surface: Importance of van der Waals Forces Phys. Rev. B 2010, 81, 115452
32. Román-Pérez, G.; Soler, J. M. Efficient Implementation of a van der Waals Density Functional: Application to Double-Wall Carbon Nanotubes Phys. Rev. Lett. 2009, 103, 096102
33. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate ab Initio Parameterization of Density functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu J. Chem. Phys. 2010, 132, 154104
34. Zhao, Y.; Truhlar, D. G. Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions J. Phys. Chem. A 2004, 108, 6908-6918
35. 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
36. 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, 51-57
37. Vydrov, O. A.; Heyd, J.; Krukau, A. V.; Scuseria, G. E. Importance of Short-Range Versus Long-Range Hartree-Fock Exchange for the Performance of Hybrid Density Functionals J. Chem. Phys. 2006, 125, 074106-074114
38. Chai, J.-D.; Head-Gordon, M. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections Phys. Chem. Chem. Phys. 2008, 10, 6615-6620
39. Kolb, B.; Thonhauser, T. Molecular Biology at the Quantum Level: Can Modern DFT Forge the Path? Nano LIFE 2012, 02, 1230006
40. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Gaussian 03, Revision D.02; Gaussian, Inc.: Wallingford, CT, 2004.
41. Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G. L.; Cococcioni, M.; Dabo, I. QUANTUM ESPRESSO: A Modular and Open-Source Software Project for Quantum Simulations of Materials J. Phys.: Condens. Matter 2009, 21, 395502 (19pp)
42. Vydrov, O. A.; Van Voorhis, T. Nonlocal van der Waals Density Functional Made Simple Phys. Rev. Lett. 2009, 103, 063004
43. Vydrov, O. A.; Voorhis, T. V. Nonlocal van der Waals Density Functional: The Simpler the Better J. Chem. Phys. 2010, 133, 244103
44. Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L. NWChem: A Comprehensive and Scalable Open-Source Solution for Large Scale Molecular Simulations Comput. Phys. Commun. 2010, 181, 1477-1489
45. Slater, J. C.; Johnson, K. H. Self-Consistent-Field χα Cluster Method for Polyatomic Molecules and Solids Phys. Rev. B 1972, 5, 844-853
46. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
47. Suzuki, S.; Morita, Y.; Fukui, K.; Sato, K.; Shiomi, D.; Takui, T.; Nakasuji, K. Aromaticity on the Pancake-Bonded Dimer of Neutral Phenalenyl Radical as Studied by MS and NMR Spectroscopies and NICS Analysis J. Am. Chem. Soc. 2006, 128, 2530-2531
48. .- and Phenalenyl Radical Dimers: A Unified Description of Multicenter, Long Bonds J. Am. Chem. Soc. 2009, 131, 7699-7707
49. Small, D.; Zaitsev, V.; Jung, Y.; Rosokha, S. V.; Head-Gordon, M.; Kochi, J. K. Intermolecular π-to-π Bonding Between Stacked Aromatic Dyads. Experimental and Theoretical Binding Energies and Near-IR Optical Transitions for Phenalenyl Radical/Radical versus Radical/Cation Dimerizations J. Am. Chem. Soc. 2004, 126, 13850-13858
50. Grimme, S. Accurate Description of van der Waals Complexes by Density Functional Theory Including Empirical Corrections J. Comput. Chem. 2004, 25, 1463-1473
51. Tian, Y.-H.; Huang, J. S.; Kertesz, M. Fluxional σ-Bonds of 2,5,8-Tri-tert-butyl-1,3-diazaphenalenyl Dimers: Stepwise [3,3], [5,5] and [7,7] Sigmatropic Rearrangements via n-Dimer Intermediates Phys. Chem. Chem. Phys. 2010, 12, 5084-5093