MOLECULAR SENSORS FOR ANIONS – A COMPUTATIONAL STUDY XIE HUIFANG NATIONAL UNIVERSITY OF SINGAPORE 2011 MOLECULAR SENSORS FOR ANIONS – A COMPUTATIONAL STUDY XIE HUIFANG (B.Sc.(Hons), NUS) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF CHEMISTRY NATIONAL UNIVERSITY OF SINGAPORE 2011 Acknowledgement First and foremost, I would like to express profound gratitude to my supervisor, Professor Wong Ming Wah, Richard, for his constant guidance and patience throughout the course of this work In addition, I am grateful for the learning opportunities he has given me in broadening my horizons I thank NUS and the Department of Chemistry for giving me the chance to take on this exciting journey of computational chemistry research I thank the seniors in the research group, particularly Dr Wang Li and Dr Adrian Matthew Mak, who have been sources of inspiration in my early days of research I thank my colleagues Yang Hui, Bokun, Cao Ye, Viet Cuong and Soo Tin for the assistance they have given me in one way or another, as well as former group members who have provided me with many learning experiences I thank my parents, sister and friends who have given me tremendous support and encouragement throughout the course of my candidature Last but not least, I give special thanks to my late grandmother who did not always know what I was doing, but rendered generous love and support nonetheless i Thesis Declaration The work in this thesis is the original work of Xie Huifang, performed independently under the supervision of Professor Wong Ming Wah, Richard, Chemistry Department, National University of Singapore, between August 2007 and August 2011 Name Signature Date ii Table of Contents Acknowledgement …… ………………………………………………………….… i Table of Contents ……………………………………………….………… ……… iii Summary ………………………………………………………………………… ix List of Tables …………………………………………………………………… … xi List of Figures ………………………………………………….……………… xiii Chapter Introduction to Anion Sensors ………………………………… - 1.1 General Introduction ……………………… ……………………………… 1.2 The Receptor Moiety ………………………………… …………………… 1.3 The Sensing Moiety ………………………………………………………… 1.4 Anion Sensors: A Computational Approach ………………………………… Chapter Theoretical Methodology ……………………………………… - 48 2.1 Introduction ………………………………………………………………… 2.2 The Schrödinger Equation ……………………………………………….… 2.3 The Hamiltonian Operator ………………………………………………… 10 2.4 Born-Oppenheimer Approximation ……………………………………… 11 2.5 Hartree-Fock Theory ……………………………………………………… 12 2.5.1 Hartree-product Wavefunction …………………….……………… 13 2.5.2 The Wavefunction as a Slater Determinant ……………………… 14 2.5.3 Basis Sets ………………………………………………………… 15 2.5.4 The Variational Principle ………………………………………… 18 2.5.5 The Hartree-Fock Equations ……………………………………… 19 iii 2.5.6 2.5.7 2.6 The Roothaan-Hall Equations …………………………………… 20 Open-shell Hartree-Fock ………………………………………… 22 Electron Correlation Methods ……………………………………… …… 22 2.6.1 2.6.2 2.7 Configuration Interaction (CI) and Coupled Cluster (CC) Theory 23 Møller-Plesset (MP) Perturbation Theory ……………… ……… 24 Density Functional Theory (DFT) ………….………………………… … 26 2.7.1 The Hohenberg-Kohn Theorems ………………………… ……… 26 2.7.2 The Kohn-Sham Theorem ……………………………… ………… 28 2.7.3 The Local Density Approximation (LDA) and Local Spin-Density Approximation (LSDA) …………………… ……………… …… 29 2.7.4 2.7.5 2.8 The Generalized Gradient Approximation (GGA) ……… ……… 30 Hybrid Functionals ………………………………………………… 31 Calculating Electronic Excited States ……………………………… …… 33 2.8.1 CI-Singles (CIS)…………………………………………… ……… 33 2.8.2 Time-Dependent Density Functional Theory (TD-DFT)………….… 34 2.9 Solvation Methods ………………………………………………… …… 37 2.10 Classical Molecular Dynamics (MD) Simulations……………….….…… 40 2.10.1 Setting Up a System ………………………………………………… 41 2.10.2 Initialization……………………………………………… ……… 42 2.10.3 Force Calculation …………………………………………… …… 43 2.10.4 Integrating Newton’s Equations of Motion………………………… 43 2.10.5 Simulated Annealing………………………………………………… 45 2.11 Selected Computational Methodology …………………………………… 46 iv Chapter The Receptor Moiety: Binding Properties of Various Functional Groups Used in Anion Receptors ……………………….… 49 - 71 3.1 Introduction …………………………………………………… ………… 49 3.2 Computational Methodology ……………………………………………… 51 3.3 Results and Discussion ………………………………………………………51 3.3.1 3.3.2 Guanidinium ………………………………………………… …… 61 3.3.3 Urea and Thiourea …………………………………………….…… 61 3.3.4 Amide and Thioamide ………………………………………….…… 63 3.3.5 Pyrrole ……………………………………………………………… 64 3.3.6 Phenol ……………………………………………………………… 65 3.3.7 Aromatic Hydrogens ………………………………………… …… 66 3.3.8 3.4 Ammonium ………………………………………………………… 59 Comparison across the Various Functional Groups … ………… 67 Conclusions ……………………………………………………………… 71 Chapter The Sensing Moiety: Benchmarking of TD-DFT Excitation Energies for Various Chromogenic Molecules ………………72 - 90 4.1 Introduction ………………………………………………………………… 72 4.2 Computational Methodology ……………………………………….……… 75 4.3 Results and Discussion …………………………………………… ……… 77 4.3.1 4.3.2 Performance of Functionals …………………………… ………… 83 4.3.3 4.4 Comparisons between Experiments and Theory ………… ……… 77 Statistical Analysis and Scaling Factors ………………….……… 87 Conclusions ………………………………………………… …………… 90 v Chapter N-amido Thiourea Based Optical Sensor …………… …… 91 - 101 5.1 Introduction …………………………………………………………… … 91 5.2 Computational Methodology ……………………………………….……… 92 5.3 Results and Discussion …………………………………………….……… 92 5.3.1 5.3.2 TD-DFT Prediction of UV Spectra …….……………….… …… 96 5.3.3 5.4 Structural Properties and Binding Energies …….……………… 92 p-NO2 Substituted System ………………….………………….…… 99 Conclusions …………………………………………………… ………… 100 Chapter N-amino Thiourea Based Optical Sensor ………………… 102 - 128 6.1 Introduction ……………………………………………………….……… 102 6.2 Computational Methodology ………………………………… ….……… 103 6.3 Results and Discussion ……………………………………………….…… 104 6.3.1 6.3.2 Binding Energy and Selectivity …………………………………… 110 6.3.3 TD-DFT Study of Excitation Wavelengths ……………………… 111 6.3.4 Molecular Dynamics Simulations ……………………………… 117 6.3.5 Effects of Counter-cation ………………………………………… 119 6.3.6 Substituent Effects on Geometries and Excitation Energies ……… 121 6.3.7 6.4 Geometry Optimization of Complexes …………………………… 104 Study of the N-N Rotation of N-amino Amide ……….……… … 123 Conclusions …………………………………………………………….… 127 Chapter Anion Recognition by Azophenol Thiourea-Based Chromogenic Sensors ……………………………………….………………129 - 148 7.1 Introduction ………………………………………………………….…… 129 vi 7.2 Computational Methodology ………………………………………… … 131 7.3 Results and Discussion ……………………………………………….…… 131 7.3.1 7.3.2 Structures and Interaction Energies of Receptor-Anion Complexes 134 7.3.3 Molecular Dynamics Simulations ………………………………… 140 7.3.4 7.4 Structures of Anion Receptors …………………………………… 132 Calculated NMR and UV-Visible Spectra ………………………… 143 Conclusions ……………………………………………………………… 147 Chapter Amide Based Cyclophane for Nitrate Sensing …… …… 149 - 166 8.1 Introduction ………………………………………………………… …… 149 8.2 Computational Methodology ……………………………………… …… 150 8.3 Results and Discussion …………………………………………………… 151 8.3.1 8.3.2 Complex Formation with Anions ……………………………….… 152 8.3.3 Binding Affinity, Solvent Effects, Charge Distribution …………… 155 8.3.4 Molecular Dynamics Simulations ……….……………… ……… 160 8.3.5 8.4 Structure of Receptor …………………………………… ……… 151 Development as an Optical Sensor ……………………………… 163 Conclusions ……………………………………………………………… 166 Chapter Thiourea Based Cyclophane for Anion Sensing…….…… 167 - 192 9.1 Introduction ……………………………………………………………… 167 9.2 Computational Methodology ……………………………………………… 168 9.3 Results and Discussion ………………………………………… ……… 169 9.3.1 Molecular Structures ………………………………………… … 169 9.3.2 Binding Affinity and Charge Distribution …………………….… 172 vii 9.3.3 9.3.4 Comparing with an Amide Cyclophane ………………………… 181 9.3.5 Molecular Dynamics Simulations ………………………… …… 182 9.3.6 9.4 Hexasulfur Analogue ……………………………………… …… 179 Towards the Development of an Optical Sensor ………………… 185 Conclusions ……………………………………………… ……………… 191 Chapter 10 Conclusion and Future Work ……………………… … 193 - 195 10.1 Final Conclusions ………………………………………………….……… 193 10.2 Future Work ……………………………………………………….……… 194 Chapter 11 References………………………………………………… 196 - 218 11.1 Chapter ………………………………………………… ………… 196 11.2 Chapter …………………………………………………… ……… 199 11.3 Chapter ……………………………………………………… …… 205 11.4 Chapter …………………………………………………… ……… 206 11.5 Chapter ………………………………………………… ………… 210 11.6 Chapter ………………………………………………………………… 211 11.7 Chapter ………………………………………………………………… 213 11.8 Chapter ………………………………………………………………… 215 11.9 Chapter ………………………………………………………………… 217 viii Chapter 11 M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J E.; Hratchian, H P.; Cross, J B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R E.; Yazyev, O.; Austin, A J.; Cammi, R.; Pomelli, C.; Ochterski, J W.; Ayala, P Y.; Morokuma, K.; Voth, G A.; Salvador, P.; Dannenberg, J J.; Zakrzewski, V G.; Dapprich, S.; Daniels, A D.; Strain, M C.; Farkas, O.; Malick, D K.; Rabuck, A D.; Raghavachari, K.; Foresman, J B.; Ortiz, J V.; Cui, Q.; Baboul, A G.; Clifford, S.; Cioslowski, J.; Stefanov, B B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R L.; Fox, D J.; Keith, T.; Al-Laham, M A.; Peng, C Y.; Nanayakkara, A.; Challacombe, M.; Gill, P M W.; Johnson, B.; Chen, W.; Wong, M W.; Gonzalez, C.; and Pople, J A Gaussian 03; Gaussian, Inc., Wallingford CT, 2004 (80) Case, D.A.; Darden, T.A.; Cheatham, T.E III; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Crowley, M.; Walker, Ross C.; Zhang, W.; Merz, K.M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K.F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S.R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D.H.; Seetin, M.G.; Sagui, C.; Babin, V.; and Kollman, P.A.; AMBER 10, University of California, San Francisco, 2008 (81) Wang, J.; Wolf, R M.; Caldwell, J W.; Kollman, P A.; Case, D A J Comput Chem 2004, 25, 1157 (82) Cieplak, P.; Caldwell, J.; Kollman, P J Comput Chem 2001, 22, 1048 (83) Blas, J R.; Márquez, M.; Sessler, J L.; Luque, F J.; Orozco, M J Am Chem Soc 2002, 124, 12796 (84) Loncharich, R J.; Brooks, B R.; Pastor, R W Biopolymers 1992, 32, 523 204 Chapter 11 11.3 Chapter (1) Llinares, J M.; Powell, D.; Bowman-James, K Coord Chem Rev 2003, 240, 57 (2) Blondeau, P.; Segura, M.; Pérez-Fernández, R.; de Mendoza, J Chem Soc Rev 2007, 36, 198 (3) Li, A F.; Wang, J H.; Wang, F.; Jiang, Y B Chem Soc Rev 2010, 39, 3729 (4) Amendola, V.; Fabbrizzi, L.; Mosca, L Chem Soc Rev 2010, 39, 3889 (5) Bondy, C R.; Loeb, S J Coord Chem Rev 2003, 240, 77 (6) Kang, S O.; Begum, R A.; Bowman-James, K Angew Chem Int Ed 2006, 45, 7882 (7) Gale, P A Acc Chem Res 2006, 39, 465 (8) Zieliński, T.; Jurczak, J Tetrahedron 2005, 61, 4081 (9) Gale, P A.; Anzenbacher Jr., P.; Sessler, J L Coord Chem Rev 2001, 222, 57 (10) Anzenbacher, P Top Heterocycl Chem 2010, 24, 205 (11) Smith, D K Org Biomol Chem 2003, 1, 3874 (12) Hua, Y.; Flood, A H Chem Soc Rev 2010, 39, 1262 (13) Li, Y.; Flood, A H Angew Chem Int Ed 2008, 47, 2649 (14) Yoon, D W.; Gross, D E.; Lynch, V M.; Sessler, J L.; Hay, B P.; Lee, C H Angew Chem Int Ed 2008, 47, 5038 (15) Zhu, S S.; Staats, H.; Brandhorst, K.; Grunenberg, J.; Gruppi, F.; Dalcanale, E.; Lützen, A.; Rissanen, K.; Schalley, C A Angew Chem Int Ed 2008, 47, 788 205 Chapter 11 (16) Becke, A D J Chem Phys 1993, 98, 5648 (17) Lee, C.; Yang, W.; Parr, R G Phys Rev B 1988, 37, 785 (18) Cancès, E.; Mennucci, B.; Tomasi, J J Chem Phys 1997, 107, 3032 (19) Mennucci, B.; Cancès, E.; Tomasi, J J Phys Chem B 1997, 101, 10506 (20) Barone, V.; Cossi, M.; Tomasi, J J Chem Phys 1997, 107, 3210 (21) Pashynska, V.; Kosevich, M.; Stepanian, S.; Adamowicz, L J Mol Struct Theochem 2007, 815, 55 (22) Davies, A S.; George, W O.; Howard, S T Phys Chem Chem Phys 2003, 5, 4533 (23) Rozas, I.; Kruger, P E J Chem Theory Comput 2005, 1, 1055 (24) Jose, D A.; Singh, A.; Das, A.; Ganguly, B Tetrahedron Lett 2007, 48, 3695 (25) Hay, B P.; Firman, T K.; Moyer, B A J Am Chem Soc 2005, 127, 1810 (26) Čajan, M.; Stibor, I.; Koča, J J Phys Chem A 1999, 103, 3778 (27) Bandyopadhyay, I.; Raghavachari, K.; Flood, A H ChemPhysChem 2009, 10, 2535 (28) Bryantsev, V S.; Hay, B P J Am Chem Soc 2005, 127, 8282 11.4 Chapter (1) Jacquemin, D.; Perpète, E A.; Ciofini, I.; Adamo, C Acc Chem Res 2009, 42, 326 (2) Bacon, A D.; Zerner, M C Theoret Chim Acta 1979, 53, 21 (3) Foresman, J B.; Head-Gordon, M.; Pople, J A.; Frisch, M J J Phys Chem 1992, 96, 135 (4) Bauernschmitt, R Chem Phys Lett 1996, 256, 454 206 Chapter 11 (5) Casida, M E.; Jamorski, C.; Casida, K C.; Salahub, D R J Chem Phys 1998, 108, 4439 (6) Dreuw, A.; Head-Gordon, M J Am Chem Soc 2004, 126, 4007 (7) Grimme, S.; Parac, M ChemPhysChem 2003, 4, 292 (8) Magyar, R J.; Tretiak, S J Chem Theory Comput 2007, 3, 976 (9) Tozer, D J J Chem Phys 2003, 119, 12697 (10) André, E.; Lapouge, C.; Cornard, J P J Mol Struct Theochem 2007, 806, 131 (11) Jaramillo, J.; Scuseria, G E Theor Chem Acc 2000, 105, 62 (12) Dierksen, M.; Grimme, S J Phys Chem A 2004, 108, 10225 (13) Jacquemin, D.; Wathelet, V.; Perpète, E A.; Adamo, C J Chem Theory Comput 2009, 5, 2420 (14) Jacquemin, D.; Perpète, E A.; Scuseria, G E.; Ciofini, I.; Adamo, C Chem Phys Lett 2008, 465, 226 (15) Cusati, T.; Granucci, G.; Persico, M.; Spighi, G J Chem Phys 2008, 128, 194312 (16) Jacquemin, D.; Preat, J.; Charlot, M.; Wathelet, V.; André, J M.; Perpète, E A J Chem Phys 2004, 121, 1736 (17) Perpète, E A.; Wathelet, V.; Preat, J.; Lambert, C.; Jacquemin, D J Chem Theory Comput 2006, 2, 434 (18) Jacquemin, D.; Perpète, E A.; Scalmani, G.; Frisch, M J.; Kobayashi, R.; Adamo, C J Chem Phys 2007, 126, 144105 (19) Jacquemin, D.; Assfeld, X.; Preat, J.; Perpète, E A Mol Phys 2007, 105, 325 (20) Wong, B M.; Cordaro, J G J Chem Phys 2008, 129, 214703 (21) Bamgbelu, A.; Wang, J.; Leszczynski, J J Phys Chem A 2010, 114, 3551 207 Chapter 11 (22) Miao, L.; Yao, Y.; Yang, F.; Wang, Z.; Li, W.; Hu, J J Mol Struct Theochem 2008, 865, 79 (23) Perpète, E A.; Jacquemin, D J Mol Struct Theochem 2009, 914, 100 (24) Niikura, K.; Bisson, A P.; Anslyn, E V J Chem Soc., Perkin Trans 1999, 1111 (25) Gunnlaugsson, T.; Kruger, P E.; Jensen, P.; Tierney, J.; Ali, H D P.; Hussey, G M J Org Chem 2005, 70, 10875 (26) Frisch, M J.; Trucks, G W.; Schlegel, H B.; Scuseria, G E.; Robb, M A.; Cheeseman, J R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H P.; Izmaylov, A F.; Bloino, J.; Zheng, G.; Sonnenberg, J L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, Jr., J A.; Peralta, J E.; Ogliaro, F.; Bearpark, M.; Heyd, J J.; Brothers, E.; Kudin, K N.; Staroverov, V N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J C.; Iyengar, S S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, N J.; Klene, M.; Knox, J E.; Cross, J B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R E.; Yazyev, O.; Austin, A J.; Cammi, R.; Pomelli, C.; Ochterski, J W.; Martin, R L.; Morokuma, K.; Zakrzewski, V G.; Voth, G A.; Salvador, P.; Dannenberg, J J.; Dapprich, S.; Daniels, A D.; Farkas, Ö.; Foresman, J B.; Ortiz, J V.; Cioslowski, J.; Fox, D J Gaussian 09; Gaussian, Inc., Wallingford CT, 2009 (27) Gore, P H.; Wheeler, O H J Org Chem 1961, 26, 3295 (28) Bell, M G W.; Day, M.; Peters, A T J Soc Dyers Colourist 2008, 82, 410 (29) Perkampus, H H UV-Vis Atlas of Organic Compounds; 2nd ed.; VCH: Weinheim [u.a.], 1992 208 Chapter 11 (30) Wintgens, V.; Valat, P.; Kossanyi, J.; Biczok, L.; Demeter, A.; Bérces, T J Chem Soc Faraday Trans 1994, 90, 411 (31) Jones, L A.; Hancock, C K J Org Chem 1960, 25, 226 (32) Chu, K Y.; Griffiths, J J Chem Research (S) 1978, 180 (33) Thomson, R Naturally Occurring Quinones; 2nd ed.; Academic Press: London; New York, 1971 (34) Monahan, A R.; Kuder, J E J Org Chem 1972, 37, 4182 (35) Vosko, S H.; Wilk, L.; Nusair, M Can J Phys 1980, 58, 1200 (36) Slater, J Phys Rev 1951, 81, 385 (37) Becke, A D Phys Rev A 1988, 38, 3098 (38) Lee, C.; Yang, W.; Parr, R G Phys Rev B 1988, 37, 785 (39) Perdew, J P.; Wang, Y Phys Rev B 1992, 45, 13244 (40) Perdew, J P.; Jackson, K A.; Pederson, M R.; Singh, D J.; Fiolhais, C Phys Rev B 1992, 46, 6671 (41) Perdew, J.; Chevary, J.; Vosko, S.; Jackson, K.; Pederson, M.; Singh, D.; Fiolhais, C Phys Rev B 1993, 48, 4978 (42) Perdew, J.; Burke, K.; Wang, Y Phys Rev B 1996, 54, 16533 (43) Adamo, C.; Barone, V J Chem Phys 1998, 108, 664 (44) Van Voorhis, T.; Scuseria, G E J Chem Phys 1998, 109, 400 (45) Becke, A D J Chem Phys 1993, 98, 5648 (46) Perdew, J Phys Rev B 1986, 33, 8822 (47) Xu, X Proc Natl Acad Sci USA 2004, 101, 2673 (48) Hoe, W Chem Phys Lett 2001, 341, 319 (49) Handy, N.; Cohen, A Mol Phys 2001, 99, 403 (50) Perdew, J P.; Burke, K.; Ernzerhof, M Phys Rev Lett 1996, 77, 3865 209 Chapter 11 (51) Perdew, J P.; Burke, K.; Ernzerhof, M Phys Rev Lett 1997, 78, 1396 (52) Adamo, C.; Barone, V J Chem Phys 1999, 110, 6158 (53) Tao, J.; Perdew, J.; Staroverov, V.; Scuseria, G Phys Rev Lett 2003, 91, 146401 (54) Boese, A D.; Handy, N C J Chem Phys 2002, 116, 9559 (55) Zhao, Y.; Schultz, N E.; Truhlar, D G J Chem Phys 2005, 123, 161103 (56) Zhao, Y.; Truhlar, D G Theor Chem Acc 2007, 120, 215 (57) Yanai, T.; Tew, D.; Handy, N Chem Phys Lett 2004, 393, 51 (58) Vydrov, O A.; Scuseria, G E J Chem Phys 2006, 125, 234109 (59) Tawada, Y.; Tsuneda, T.; Yanagisawa, S.; Yanai, T.; Hirao, K J Chem Phys 2004, 120, 8425 (60) Rohrdanz, M A.; Herbert, J M J Chem Phys 2008, 129, 034107 (61) Jacquemin, D.; Perpète, E A.; Scuseria, G E.; Ciofini, I.; Adamo, C J Chem Theory Comput 2008, 4, 123 11.5 Chapter (1) Boiocchi, M.; Del Boca, L.; Gómez, D E.; Fabbrizzi, L.; Licchelli, M.; Monzani, E J Am Chem Soc 2004, 126, 16507 (2) Esteban-Gómez, D.; Fabbrizzi, L.; Licchelli, M J Org Chem 2005, 70, 5717 (3) Amendola, V.; Esteban-Gómez, D.; Fabbrizzi, L.; Licchelli, M Acc Chem Res 2006, 39, 343 (4) Pérez-Casas, C.; Yatsimirsky, A K J Org Chem 2008, 73, 2275 (5) Nie, L.; Li, Z.; Han, J.; Zhang, X.; Yang, R.; Liu, W X.; Wu, F Y.; Xie, J W.; Zhao, Y F.; Jiang, Y B J Org Chem 2004, 69, 6449 210 Chapter 11 (6) Evans, L S.; Gale, P A.; Light, M E.; Quesada, R Chem Commun 2006, 965 (7) Quinlan, E.; Matthews, S E.; Gunnlaugsson, T Tetrahedron Lett 2006, 47, 9333 (8) Quinlan, E.; Matthews, S E.; Gunnlaugsson, T J Org Chem 2007, 72, 7497 (9) Wu, F Y.; Li, Z.; Wen, Z C.; Zhou, N.; Zhao, Y F.; Jiang, Y B Org Lett 2002, 4, 3203 (10) Wu, F Y.; Li, Z.; Guo, L.; Wang, X.; Lin, M H.; Zhao, Y F.; Jiang, Y B Org Biomol Chem 2006, 4, 624 (11) Koteeswari, R.; Ashokkumar, P.; Ramakrishnan, V T.; Malar, E J P.; Ramamurthy, P Chem Commun 2010, 46, 3268 (12) Liu, W X.; Jiang, Y B J Org Chem 2008, 73, 1124 (13) Duke, R M.; Gunnlaugsson, T Tetrahedron Lett 2010, 51, 5402 11.6 Chapter (1) Gunnlaugsson, T.; Kruger, P E.; Jensen, P.; Tierney, J.; Ali, H D P.; Hussey, G M J Org Chem 2005, 70, 10875 (2) Li, Z.; Wu, F Y.; Guo, L.; Li, A F.; Jiang, Y B J Phys Chem B 2008, 112, 7071 (3) Shao, J.; Lin, H.; Lin, H K Spectrochim Acta A 2008, 70, 682 (4) Ali, H D P.; Kruger, P E.; Gunnlaugsson, T New J Chem 2008, 32, 1153 (5) Becke, A D J Chem Phys 1993, 98, 5648 (6) Lee, C.; Yang, W.; Parr, R G Phys Rev B 1988, 37, 785 (7) Cancès, E.; Mennucci, B.; Tomasi, J J Chem Phys 1997, 107, 3032 211 Chapter 11 (8) Barone, V.; Cossi, M.; Tomasi, J J Chem Phys 1997, 107, 3210 (9) Mennucci, B.; Cancès, E.; Tomasi, J J Phys Chem B 1997, 101, 10506 (10) Slater, J Phys Rev 1951, 81, 385 (11) Vosko, S H.; Wilk, L.; Nusair, M Can J Phys 1980, 58, 1200 (12) Becke, A D Phys Rev A 1988, 38, 3098 (13) Perdew, J P.; Burke, K.; Ernzerhof, M Phys Rev Lett 1996, 77, 3865 (14) Perdew, J P.; Burke, K.; Ernzerhof, M Phys Rev Lett 1997, 78, 1396 (15) Adamo, C.; Barone, V J Chem Phys 1999, 110, 6158 (16) Zhao, Y.; Truhlar, D G Theor Chem Acc 2007, 120, 215 (17) Grimme, S J Comput Chem 2006, 27, 1787 (18) Bauernschmitt, R Chem Phys Lett 1996, 256, 454 (19) Casida, M E.; Jamorski, C.; Casida, K C.; Salahub, D R J Chem Phys 1998, 108, 4439 (20) Yanai, T.; Tew, D.; Handy, N Chem Phys Lett 2004, 393, 51 (21) Tawada, Y.; Tsuneda, T.; Yanagisawa, S.; Yanai, T.; Hirao, K J Chem Phys 2004, 120, 8425 (22) Vydrov, O A.; Heyd, J.; Krukau, A V.; Scuseria, G E J Chem Phys 2006, 125, 074106 (23) Vydrov, O A.; Scuseria, G E J Chem Phys 2006, 125, 234109 (24) Vydrov, O A.; Scuseria, G E.; Perdew, J P J Chem Phys 2007, 126, 154109 (25) Frisch, M J.; Trucks, G W.; Schlegel, H B.; Scuseria, G E.; Robb, M A.; Cheeseman, J R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H P.; Izmaylov, A F.; Bloino, J.; Zheng, G.; Sonnenberg, J L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; 212 Chapter 11 Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, Jr., J A.; Peralta, J E.; Ogliaro, F.; Bearpark, M.; Heyd, J J.; Brothers, E.; Kudin, K N.; Staroverov, V N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J C.; Iyengar, S S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, N J.; Klene, M.; Knox, J E.; Cross, J B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R E.; Yazyev, O.; Austin, A J.; Cammi, R.; Pomelli, C.; Ochterski, J W.; Martin, R L.; Morokuma, K.; Zakrzewski, V G.; Voth, G A.; Salvador, P.; Dannenberg, J J.; Dapprich, S.; Daniels, A D.; Farkas, Ö.; Foresman, J B.; Ortiz, J V.; Cioslowski, J.; Fox, D J Gaussian 09; Gaussian, Inc., Wallingford CT, 2009 (26) Blas, J R.; Márquez, M.; Sessler, J L.; Luque, F J.; Orozco, M J Am Chem Soc 2002, 124, 12796 (27) Reed, A E.; Curtiss, L A.; Weinhold, F Chem Rev 1988, 88, 899 (28) Lee, H J.; Lee, M H.; Choi, Y S.; Park, H M.; Lee, K B J Mol Struct Theochem 2003, 631, 101 (29) Song, L.; Liu, M.; Wu, W.; Zhang, Q.; Mo, Y J Chem Theory Comput 2005, 1, 394 (30) Song, J W.; Lee, H J.; Choi, Y S.; Yoon, C J J Phys Chem A 2006, 110, 2065 11.7 Chapter (1) Li, A F.; Wang, J H.; Wang, F.; Jiang, Y B Chem Soc Rev 2010, 39, 3729 (2) Kato, R.; Nishizawa, S.; Hayashita, T.; Teramae, N Tetrahedron Lett 2001, 42, 5053 213 Chapter 11 (3) Lee, D H.; Lee, K H.; Hong, J I Org Lett 2001, 3, (4) Lee, D H.; Lee, H Y.; Lee, K H.; Hong, J I Chem Commun 2001, 1188 (5) Lee, D H.; Im, J H.; Son, S U.; Chung, Y K.; Hong, J I J Am Chem Soc 2003, 125, 7752 (6) Nayak, M K.; Seo, J.; Park, S.; Park, S Y J Photochem & Photobio A 2007, 191, 228 (7) Chen, Y J.; Chung, W S Eur J Org Chem 2009, 2009, 4770 (8) Becke, A D J Chem Phys 1993, 98, 5648 (9) Lee, C.; Yang, W.; Parr, R G Phys Rev B 1988, 37, 785 (10) Wong, M W Chem Phys Lett 1996, 256, 391 (11) Cossi, M Chem Phys Lett 1996, 255, 327 (12) Barone, V.; Cossi, M.; Tomasi, J J Chem Phys 1997, 107, 3210 (13) Mennucci, B.; Cancès, E.; Tomasi, J J Phys Chem B 1997, 101, 10506 (14) Reed, A E.; Curtiss, L A.; Weinhold, F Chem Rev 1988, 88, 899 (15) Messerschmidt, M.; Wagner, A.; Wong, M W.; Luger, P J Am Chem Soc 2002, 124, 732 (16) Wolinski, K.; Hinton, J F.; Pulay, P J Am Chem Soc 1990, 112, 8251 (17) Cheeseman, J R.; Trucks, G W.; Keith, T A.; Frisch, M J J Chem Phys 1996, 104, 5497 (18) Casida, M E.; Jamorski, C.; Casida, K C.; Salahub, D R J Chem Phys 1998, 108, 4439 (19) Bauernschmitt, R Chem Phys Lett 1996, 256, 454 (20) Bondi, A J Phys Chem 1964, 68, 441 (21) Ran, J.; Wong, M W Aust J Chem 2009, 62, 1062 (22) Desiraju, G R Chem Commun 2005, 2995 214 Chapter 11 (23) Desiraju, G The Weak Hydrogen Bond in Structural Chemistry and Biology; Oxford University Press: Oxford, 1999 (24) Steiner, T Chem Commun 1997, 727 (25) Wenthold, P G.; Squires, R R J Phys Chem 1995, 99, 2002 (26) Ghosh, T.; Maiya, B G.; Wong, M W J Phys Chem A 2004, 108, 11249 (27) Jose, D A.; Singh, A.; Das, A.; Ganguly, B Tetrahedron Lett 2007, 48, 3695 (28) Böes, E S.; Andrade, J de; Stassen, H.; Gonỗalves, P F B Chem Phys Lett 2007, 436, 362 (29) Böes, E S.; Livotto, P R.; Stassen, H Chem Phys 2006, 331, 142 11.8 Chapter (1) Okunola, O.; Santacroce, P.; Davis, J Supramolecular Chem 2008, 20, 169 (2) Herges, R.; Dikmans, A.; Jana, U.; Köhler, F.; Jones, P G.; Dix, I.; Fricke, T.; König, B Eur J Org Chem 2002, 3004 (3) Blondeau, P.; Benet-Buchholz, J.; de Mendoza, J New J Chem 2007, 31, 736 (4) Hay, B P.; Gutowski, M.; Dixon, D A.; Garza, J.; Vargas, R.; Moyer, B A J Am Chem Soc 2004, 126, 7925 (5) Hay, B P.; Dixon, D A.; Bryan, J C.; Moyer, B A J Am Chem Soc 2002, 124, 182 (6) Hay, B P.; Firman, T K.; Moyer, B A J Am Chem Soc 2005, 127, 1810 (7) Mason, S.; Clifford, T.; Seib, L.; Kuczera, K.; Bowman-James, K J Am Chem Soc 1998, 120, 8899 (8) Cronin, L.; McGregor, P A.; Parsons, S.; Teat, S.; Gould, R O.; White, V A.; Long, N J.; Robertson, N Inorg Chem 2004, 43, 8023 215 Chapter 11 (9) Koropatkin, N M.; Pakrasi, H B.; Smith, T J Proc Natl Acad Sci 2006, 103, 9820 (10) Choi, K.; Hamilton, A D J Am Chem Soc 2003, 125, 10241 (11) Bisson, A P.; Lynch, V M.; Monahan, M K C.; Anslyn, E V Angew Chem Int Ed Engl 1997, 36, 2340 (12) Niikura, K.; Bisson, A P.; Anslyn, E V J Chem Soc., Perkin Trans 1999, 1111 (13) Capitán-Vallvey, L F.; Arroyo-Guerrero, E.; Fernández-Ramos, M D.; Santoyo-Gonzalez, F Anal Chem 2005, 77, 4459 (14) Becke, A D J Chem Phys 1993, 98, 5648 (15) Lee, C.; Yang, W.; Parr, R G Phys Rev B 1988, 37, 785 (16) Mennucci, B.; Cancès, E.; Tomasi, J J Phys Chem B 1997, 101, 10506 (17) Barone, V.; Cossi, M.; Tomasi, J J Chem Phys 1997, 107, 3210 (18) Cancès, E.; Mennucci, B.; Tomasi, J J Chem Phys 1997, 107, 3032 (19) Reed, A E.; Curtiss, L A.; Weinhold, F Chem Rev 1988, 88, 899 (20) Bacon, A D.; Zerner, M C Theoret Chim Acta 1979, 53, 21 (21) Casida, M E.; Jamorski, C.; Casida, K C.; Salahub, D R J Chem Phys 1998, 108, 4439 (22) Bauernschmitt, R Chem Phys Lett 1996, 256, 454 (23) Perdew, J P.; Burke, K.; Ernzerhof, M Phys Rev Lett 1996, 77, 3865 (24) Perdew, J P.; Burke, K.; Ernzerhof, M Phys Rev Lett 1997, 78, 1396 (25) Adamo, C.; Barone, V J Chem Phys 1999, 110, 6158 (26) March, J Advanced Organic Chemistry; 4th ed.; John Wiley & Sons, 1992 (27) Atkins, P W.; Shriver, D F Inorganic Chemistry; 3rd ed.; Oxford University Press, 1999 216 Chapter 11 11.9 Chapter (1) Li, A F.; Wang, J H.; Wang, F.; Jiang, Y B Chem Soc Rev 2010, 39, 3729 (2) Ghosh, K.; Adhikari, S Tetrahedron Lett 2006, 47, 8165 (3) Jose, D A.; Kumar, D K.; Ganguly, B.; Das, A Tetrahedron Lett 2005, 46, 5343 (4) Gunnlaugsson, T.; Kruger, P E.; Jensen, P.; Tierney, J.; Ali, H D P.; Hussey, G M J Org Chem 2005, 70, 10875 (5) Lee, K H.; Hong, J I Tetrahedron Lett 2000, 41, 6083 (6) Sasaki, S ; Mizuno, M.; Naemura, K.; Tobe, Y J Org Chem 2000, 65, 275 (7) Jose, D A.; Singh, A.; Das, A.; Ganguly, B Tetrahedron Lett 2007, 48, 3695 (8) Pascal, R.; Spergel, J.; Van Engen, D Tetrahedron Lett 1986, 27, 4099 (9) Heyer, D.; Lehn, J M Tetrahedron Lett 1986, 27, 5869 (10) Mascal, M Angew Chem Int Ed 2006, 45, 2890 (11) Niikura, K.; Bisson, A P.; Anslyn, E V J Chem Soc., Perkin Trans 1999, 1111 (12) Hisaki, I.; Sasaki, S.; Hirose, K.; Tobe, Y Eur J Org Chem 2007, 2007, 607 (13) Gunnlaugsson, T.; Glynn, M.; Toccineehussey, G.; Kruger, P.; Pfeffer, F Coord Chem Rev 2006, 250, 3094 (14) Suksai, C.; Tuntulani, T Chem Soc Rev 2003, 32, 192 (15) Martínez-Máđez, R.; Sancenón, F Chem Rev 2003, 103, 4419 (16) Becke, A D J Chem Phys 1993, 98, 5648 (17) Lee, C.; Yang, W.; Parr, R G Phys Rev B 1988, 37, 785 (18) Cancès, E.; Mennucci, B.; Tomasi, J J Chem Phys 1997, 107, 3032 217 Chapter 11 (19) Barone, V.; Cossi, M.; Tomasi, J J Chem Phys 1997, 107, 3210 (20) Reed, A E.; Curtiss, L A.; Weinhold, F Chem Rev 1988, 88, 899 (21) Bauernschmitt, R Chem Phys Lett 1996, 256, 454 (22) Casida, M E.; Jamorski, C.; Casida, K C.; Salahub, D R J Chem Phys 1998, 108, 4439 (23) Atkins, P W.; Shriver, D F Inorganic Chemistry; 3rd ed.; Oxford University Press, 1999 (24) March, J Advanced Organic Chemistry; 4th ed.; John Wiley & Sons, 1992 (25) Wiskur, S L.; Ait-Haddou, H.; Lavigne, J J.; Anslyn, E V Acc Chem Res 2001, 34, 963 (26) Nguyen, B.; Anslyn, E Coord Chem Rev 2006, 250, 3118 (27) Linn, M M.; Poncio, D C.; Machado, V G Tetrahedron Lett 2007, 48, 4547 (28) Gale, P A.; Gale, P A.; Twyman, L J.; Handlin, C I.; Sessler, J L Chem Commun 1999, 1851 218 ... λmax values calculated from conventional hybrid functionals against experimental values Figure 4.4 Plots of λmax values calculated from long-range corrected functionals against experimental values... substrates and co-factors are anionic; nitrates and phosphates from fertilizers used in agricultural activities are water pollutants; sulfate and nitrate are present in acid rain; and the production... Sensors: A Computational Approach The modeling of anion sensors via computational methods can offer many insights to the binding and sensing properties of the sensors, such as the conformational preferences