References:

(1) Possmayer, F.; Zuo, Y. Y.; Veldhuizen, R. A. W.; Petersen, N. O. Pulmonary Surfactant: A Mighty Thin Film. Chem. Rev. 2023, 123 (23), 13209–13290. https://doi.org/10.1021/acs.chemrev.3c00146.
(2) Myers, D. Surfactant Science and Technology, 3rd ed.; Wiley-Interscience: Hoboken, NJ, USA, 2006.
(3) Swarup, S.; Schoff, C. K. A Survey of Surfactants in Coatings Technology. Prog. Org. Coatings 1993, 23 (1), 1–22. https://doi.org/10.1016/0033-0655(93)80002-R.
(4) Jones, D. S.; McMeel, S.; Adair, C. G.; Gorman, S. P. Characterisation and Evaluation of Novel Surfactant Bacterial Anti-Adherent Coatings for Endotracheal Tubes Designed for the Prevention of Ventilator-Associated Pneumonia. J. Pharm. Pharmacol. 2003, 55 (1), 43–52. https://doi.org/10.1111/j.2042-7158.2003.tb02432.x.
(5) Treter, J.; Bonatto, F.; Krug, C.; Soares, G. V.; Baumvol, I. J. R.; Macedo, A. J. Washing-Resistant Surfactant Coated Surface Is Able to Inhibit Pathogenic Bacteria Adhesion. Appl. Surf. Sci. 2014, 303, 147–154. https://doi.org/10.1016/j.apsusc.2014.02.123.
(6) Dundas, A. A.; Cuzzucoli Crucitti, V.; Haas, S.; Dubern, J. F.; Latif, A.; Romero, M.; Sanni, O.; Ghaemmaghami, A. M.; Williams, P.; Alexander, M. R.; Wildman, R.; Irvine, D. J. Achieving Microparticles with Cell-Instructive Surface Chemistry by Using Tunable Co-Polymer Surfactants. Adv. Funct. Mater. 2020, 30 (36), 2001821. https://doi.org/10.1002/adfm.202001821.
(7) Ariga, K.; Hill, J. P.; Endo, H. Developments in Molecular Recognition and Sensing at Interfaces. Int. J. Mol. Sci. 2007, 8 (8), 864–883. https://doi.org/10.3390/i8080864.
(8) Greene, J. E. Tracing the 4000 Year History of Organic Thin Films: From Monolayers on Liquids to Multilayers on Solids. Appl. Phys. Rev. 2015, 2 (1), 011101. https://doi.org/10.1063/1.4907770.
(9) Strutt, J. W. Measurements of the Amount of Oil Necessary in Order to Check the Motions of Camphor upon Water. Proc. R. Soc. London 1890, 47, 364–367. https://doi.org/10.1017/cbo9780511703980.028.
(10) Strutt, J. W. XXXVI. Investigations in Capillarity:—The Size of Drops.—The Liberation of Gas from Supersaturated Solutions.—Colliding Jets.—The Tension of Contaminated Water-Surfaces. London, Edinburgh, Dublin Philos. Mag. J. Sci. 1899, 48 (293), 321–337. https://doi.org/10.1080/14786449908621342.
(11) Ulman, A. An Introduction to Ultrathin Organic Films: From Langmuir-Blodgett to Self-Assembly; Academic Press: San Diego, CA, USA, 1991.
(12) Pockels, A. Surface Tension. Nature 1891, 43, 437–439.
(13) Langmuir, I. The Constitution and Fundamental Properties of Solids and Liquids. II. Liquids. J. Am. Chem. Soc. 1917, 39 (9), 1848–1906. https://doi.org/10.1021/ja02254a006.
(14) Lyklema, J. Fundamentals of Interface and Colloid Science, Volume III: Liquid-Fluid Interfaces; Lyklema, J., Ed.; Academic Press: San Diego, CA, USA, 2000.
(15) Stefaniu, C.; Brezesinski, G. X-Ray Investigation of Monolayers Formed at the Soft Air/Water Interface. Curr. Opin. Colloid Interface Sci. 2014, 19 (3), 216–227. https://doi.org/10.1016/j.cocis.2014.01.004.
(16) Petty, M. C. Langmuir-Blodgett Films, 1st ed.; Cambridge University Press: Cambridge, England, 1996. https://doi.org/10.1017/CBO9780511622519.
(17) Blodgett, K. B. Monomolecular Films of Fatty Acids on Glass. J. Am. Chem. Soc. 1934, 56 (2), 495. https://doi.org/10.1021/ja01317a513.
(18) Blodgett, K. B. Films Built by Depositing Successive Monomolecular Layers on a Solid Surface. J. Am. Chem. Soc. 1935, 57 (6), 1007–1022. https://doi.org/10.1021/ja01309a011.
(19) Bigelow, W. C.; Pickett, D. L.; Zisman, W. A. Oleophobic Monolayers. I. Films Adsorbed from Solution in Non-Polar Liquids. J. Colloid Sci. 1946, 1 (6), 513–538. https://doi.org/10.1016/0095-8522(46)90059-1.
(20) Rajasingam, A. Design, Synthesis and Fabrication of Phenolic Thin Films. M. Sc. thesis, Concordia University, Montreal, QC, Canada, 2014.
(21) Ulman, A. Formation and Structure of Self-Assembled Monolayers. Chem. Rev. 1996, 96 (4), 1533–1554. https://doi.org/10.1021/cr9502357.
(22) Janasek, D.; Franzke, J.; Manz, A. Scaling and the Design of Miniaturized Chemical-Analysis Systems. Nature 2006, 442 (7101), 374–380. https://doi.org/10.1038/nature05059.
(23) Sinz, D. K. N.; Darhuber, A. A. Self-Propelling Surfactant Droplets in Chemically-Confined Microfluidics - Cargo Transport, Drop-Splitting and Trajectory Control. Lab Chip 2012, 12 (4), 705–707. https://doi.org/10.1039/c2lc21082g.
(24) Rahimnejad, M.; Rabiee, N.; Ahmadi, S.; Jahangiri, S.; Sajadi, S. M.; Akhavan, O.; Saeb, M. R.; Kwon, W.; Kim, M.; Hahn, S. K. Emerging Phospholipid Nanobiomaterials for Biomedical Applications to Lab-on-a-Chip, Drug Delivery, and Cellular Engineering. ACS Appl. Bio Mater. 2021, 4 (12), 8110–8128. https://doi.org/10.1021/acsabm.1c00932.
(25) Cammann, K. Bio-Sensors Based on Ion-Selective Electrodes. Fresenius’ Zeitschrift für Anal. Chemie 1977, 287 (1), 1–9.
(26) Biosensors: Fundamentals and Applications; Turner, A. P. F., Karube, I., Wilson, G. S., Eds.; Oxford Science Publications: Oxford, UK, 1987. https://doi.org/10.1515/9783110641080.
(27) Thévenot, D. R.; Toth, K.; Durst, R. A.; Wilson, G. S. Electrochemical Biosensors: Recommended Definitions and Classification. Biosens. Bioelectron. 2001, 16 (1–2), 121–131. https://doi.org/10.1016/S0956-5663(01)00115-4.
(28) Scheller, F. W.; Wollenberger, U.; Warsinke, A.; Lisdat, F. Research and Development in Biosensors. Curr. Opin. Biotechnol. 2001, 12 (1), 35–40. https://doi.org/10.1016/S0958-1669(00)00169-5.
(29) Nuzzo, R. G.; Allara, D. L. Adsorption of Bifunctional Organic Disulfides on Gold Surfaces. J. Am. Chem. Soc. 1983, 105 (13), 4481–4483. https://doi.org/10.1021/ja00351a063.
(30) Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. Spontaneously Organized Molecular Assemblies. 4. Structural Characterization of n-Alkyl Thiol Monolayers on Gold by Optical Ellipsometry, Infrared Spectroscopy, and Electrochemistry. J. Am. Chem. Soc. 1987, 109 (12), 3559–3568. https://doi.org/10.1021/ja00246a011.
(31) Sagiv, J. Organized Monolayers by Adsorption. 1. Formation and Structure of Oleophobic Mixed Monolayers on Solid Surfaces. J. Am. Chem. Soc. 1980, 102 (1), 92–98.
(32) Horáček, J.; Skládal, P. Improved Direct Piezoelectric Biosensors Operating in Liquid Solution for the Competitive Label-Free Immunoassay of 2,4-Dichlorophenoxyacetic Acid. Anal. Chim. Acta 1997, 347 (1–2), 43–50. https://doi.org/10.1016/S0003-2670(97)00125-6.
(33) Navrátilová, I.; Skládal, P. The Immunosensors for Measurement of 2,4-Dichlorophenoxyacetic Acid Based on Electrochemical Impedance Spectroscopy. Bioelectrochemistry 2004, 62 (1), 11–18. https://doi.org/10.1016/j.bioelechem.2003.10.004.
(34) Gaspar, S.; Zimmermann, H.; Gazaryan, I.; Csöregi, E.; Schuhmann, W. Hydrogen Peroxide Biosensors Based on Direct Electron Transfer from Plant Peroxidases Immobilized on Self-Assembled Thiol-Monolayer Modified Gold Electrodes. Electroanalysis 2001, 13 (4), 284–288. https://doi.org/10.1002/1521-4109(200103)13:4<284::AID-ELAN284>3.0.CO;2-Z.
(35) Willner, I.; Riklin, A.; Shoham, B.; Rivenzon, D.; Katz, E. Development of Novel Biosensor Enzyme Electrodes: Glucose Oxidase Multilayer Arrays Immobilized onto Self‐assembled Monolayers on Electrodes. Adv. Mater. 1993, 5 (12), 912–915. https://doi.org/10.1002/adma.19930051206.
(36) Rodgers, M. A.; Findlay, J. B. C.; Millner, P. A. Lipocalin Based Biosensors for Low Mass Hydrophobic Analytes; Development of a Novel SAM for Polyhistidine Tagged Proteins. Sensors Actuators, B Chem. 2010, 150 (1), 12–18. https://doi.org/10.1016/j.snb.2010.07.053.
(37) Thiel, A. J.; Frutos, A. G.; Jordan, C. E.; Corn, R. M.; Smith, L. M. In Situ Surface Plasmon Resonance Imaging Detection of DNA Hybridization to Oligonucleotide Arrays on Gold Surfaces. Anal. Chem. 1997, 69 (24), 4948–4956. https://doi.org/10.1021/ac9708001.
(38) Berggren, C.; Stålhandske, P.; Brundell, J.; Johansson, G. A Feasibility Study of a Capacitive Biosensor for Direct Detection of DNA Hybridization. Electroanalysis 1999, 11 (3), 156–160. https://doi.org/10.1002/(SICI)1521-4109(199903)11:3<156::AID-ELAN156>3.0.CO;2-O.
(39) Aoki, H.; Bühlmann, P.; Umezawa, Y. Electrochemical Detection of a One-Base Mismatch in an Oligonucleotide Using Ion-Channel Sensors with Self-Assembled PNA Monolayers. Electroanalysis 2000, 12 (16), 1272–1276. https://doi.org/10.1002/1521-4109(200011)12:16<1272::AID-ELAN1272>3.0.CO;2-F.
(40) Berganza, J.; Olabarria, G.; García, R.; Verdoy, D.; Rebollo, A.; Arana, S. DNA Microdevice for Electrochemical Detection of Escherichia Coli 0157:H7 Molecular Markers. Biosens. Bioelectron. 2007, 22 (9–10), 2132–2137. https://doi.org/10.1016/j.bios.2006.09.028.
(41) Prime, K. L.; Whitesides, G. M. Self-Assembled Organic Monolayers: Model Systems for Studying Adsorption of Proteins at Surfaces. Science (80-. ). 1991, 252 (5009), 1164–1166.
(42) Spinke, J.; Liley, M.; Schmitt, F. J.; Guder, H. J.; Angermaier, L.; Knoll, W. Molecular Recognition at Self-Assembled Monolayers: Optimization of Surface Functionalization. J. Chem. Phys. 1993, 99 (9), 7012–7019. https://doi.org/10.1063/1.465447.
(43) Sheller, N. B.; Petrash, S.; Foster, M. D.; Tsukruk, V. V. Atomic Force Microscopy and X-Ray Reflectivity Studies of Albumin Adsorbed onto Self-Assembled Monolayers of Hexadecyltrichlorosilane. Langmuir 1998, 14 (16), 4535–4544. https://doi.org/10.1021/la970916s.
(44) Choi, E. J.; Foster, M. D. The Role of Specific Binding in Human Serum Albumin Adsorption to Self-Assembled Monolayers. Langmuir 2002, 18 (2), 557–561. https://doi.org/10.1021/la010964j.
(45) Petrash, S.; Cregger, T.; Zhao, B.; Pokidysheva, E.; Foster, M. D.; Brittain, W. J.; Sevastianov, V.; Majkrzak, C. F. Changes in Protein Adsorption on Self-Assembled Monolayers with Monolayer Order: Comparison of Human Serum Albumin and Human Gamma Globulin. Langmuir 2001, 17 (24), 7645–7651. https://doi.org/10.1021/la011192u.
(46) Metallo, S. J.; Kane, R. S.; Holmlin, R. E.; Whitesides, G. M. Using Bifunctional Polymers Presenting Vancomycin and Fluorescein Groups to Direct Anti-Fluorescein Antibodies to Self-Assembled Monolayers Presenting D-Alanine-D-Alanine Groups. J. Am. Chem. Soc. 2003, 125 (15), 4534–4540. https://doi.org/10.1021/ja030045a.
(47) Su, X.; Chew, F. T.; Li, S. F. Y. Self-Assembled Monolayer-Based Piezoelectric Crystal Immunosensor for the Quantification of Total Human Immunoglobulin E. Anal. Biochem. 1999, 273 (1), 66–72. https://doi.org/10.1006/abio.1999.4186.
(48) Ameur, S.; Martelet, C.; Jaffrezic-Renault, N.; Chovelon, J. M. Sensitive Immunodetection through Impedance Measurements onto Gold Functionalized Electrodes. Appl. Biochem. Biotechnol. - Part A Enzym. Eng. Biotechnol. 2000, 89 (2–3), 161–170. https://doi.org/10.1385/ABAB:89:2-3:161.
(49) Meskini, O.; Abdelghani, A.; Tlili, A.; Mgaieth, R.; Jaffrezic-Renault, N.; Martelet, C. Porous Silicon as Functionalized Material for Immunosensor Application. Talanta 2007, 71 (3), 1430–1433. https://doi.org/10.1016/j.talanta.2006.05.089.
(50) Revell, D. J.; Knight, J. R.; Blyth, D. J.; Haines, A. H.; Russell, D. A. Self-Assembled Carbohydrate Monolayers: Formation and Surface Selective Molecular Recognition. Langmuir 1998, 14 (16), 4517–4524. https://doi.org/10.1021/la9802466.
(51) Shen, Z.; Huang, M.; Xiao, C.; Zhang, Y.; Zeng, X.; Wang, P. G. Nonlabeled Quartz Crystal Microbalance Biosensor for Bacterial Detection Using Carbohydrate and Lectin Recognitions. Anal. Chem. 2007, 79 (6), 2312–2319. https://doi.org/10.1021/ac061986j.
(52) Min, D. H.; Tang, W. J.; Mrksich, M. Chemical Screening by Mass Spectrometry to Identify Inhibitors of Anthrax Lethal Factor. Nat. Biotechnol. 2004, 22 (6), 717–723. https://doi.org/10.1038/nbt973.
(53) Narayan, T.; Kumar, S.; Kumar, S.; Augustine, S.; Yadav, B. K.; Malhotra, B. D. Protein Functionalised Self Assembled Monolayer Based Biosensor for Colon Cancer Detection. Talanta 2019, 201 (February), 465–473. https://doi.org/10.1016/j.talanta.2019.04.039.
(54) Kato, M.; Mrksich, M. Using Model Substrates to Study the Dependence of Focal Adhesion Formation on the Affinity of Integrin-Ligand Complexes. Biochemistry 2004, 43 (10), 2699–2707. https://doi.org/10.1021/bi0352670.
(55) Caiazzo, M.; Alessandrini, A.; Facci, P. A Highly Selective, Biofunctional Surface for Molecule/Cell Sorting. ACS Appl. Mater. Interfaces 2009, 1 (2), 514–518. https://doi.org/10.1021/am800175h.
(56) Fung, Y. S.; Wong, Y. Y. Self-Assembled Monolayers as the Coating in a Quartz Piezoelectric Crystal Immunosensor to Detect Salmonella in Aqueous Solution. Anal. Chem. 2001, 73 (21), 5302–5309. https://doi.org/10.1021/ac010655y.
(57) Qian, X.; Metallo, S. J.; Choi, I. S.; Wu, H.; Liang, M. N.; Whitesides, G. M. Arrays of Self-Assembled Monolayers for Studying Inhibition of Bacterial Adhesion. Anal. Chem. 2002, 74 (8), 1805–1810. https://doi.org/10.1021/ac011042o.
(58) Mayall, R. M.; Renaud-Young, M.; Gawron, E.; Luong, S.; Creager, S.; Birss, V. I. Enhanced Signal Amplification in a Toll-like Receptor-4 Biosensor Utilizing Ferrocene-Terminated Mixed Monolayers. ACS Sensors 2019, 4 (1), 143–151. https://doi.org/10.1021/acssensors.8b01069.
(59) Haslam, E. Natural Polyphenols (Vegetable Tannins) as Drugs: Possible Modes of Action. J. Nat. Prod. 1996, 59 (2), 205–215. https://doi.org/10.1021/np960040+.
(60) Hagerman, A. E. Fifty Years of Polyphenol – Protein Complexes. In Recent Advances in Polyphenol Research; Cheynier, V., Sarni-Manchado, P., Quideau, S., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2012; Vol. 3, pp 71–97.
(61) Adamczyk, B.; Simon, J.; Kitunen, V.; Adamczyk, S.; Smolander, A. Tannins and Their Complex Interaction with Different Organic Nitrogen Compounds and Enzymes: Old Paradigms versus Recent Advances. ChemistryOpen 2017, 6 (5), 610–614. https://doi.org/10.1002/open.201700113.
(62) Haslam, E. Plant Polyphenols: Vegetable Tannins Revisited; Cambridge University Press: Cambridge, England, 1989.
(63) Haslam, E.; Cai, Y. Plant Polyphenols (Vegetable Tannins): Gallic Acid Metabolism. Nat. Prod. Rep. 1994, 11, 41–66. https://doi.org/10.1039/NP9941100041.
(64) Glabasnia, A.; Hofmann, T. Identification and Sensory Evaluation of Dehydro- and Deoxy-Ellagitannins Formed upon Toasting of Oak Wood (Quercus Alba L.). J. Agric. Food Chem. 2007, 55 (10), 4109–4118. https://doi.org/10.1021/jf070151m.
(65) Weinges, K.; Freudenberg, K. Condensed Proanthocyanidins from Cranberries and Cola Nuts. Chem. Commun. 1965, No. 11, 220–222. https://doi.org/10.1039/C19650000220.
(66) Santos-Buelga, C.; Scalbert, A. Proanthocyanidins and Tannin-like Compounds – Nature, Occurrence, Dietary Intake and Effects on Nutrition and Health. J. Sci. Food Agric. 2000, 80, 1094–1117.
(67) Jöbstl, E.; O’Connell, J.; Fairclough, J. P. A.; Williamson, M. P. Molecular Model for Astringency Produced by Polyphenol/Protein Interactions. Biomacromolecules 2004, 5 (3), 942–949. https://doi.org/10.1021/bm0345110.
(68) Shimada, T. Salivary Proteins as a Defense against Dietary Tannins. J. Chem. Ecol. 2006, 32 (6), 1149–1163. https://doi.org/10.1007/s10886-006-9077-0.
(69) Yan, Q.; Bennick, A. Identification of Histatins as Tannin-Binding Proteins in Human Saliva. Biochem. J. 1995, 311 (1), 341–347. https://doi.org/10.1042/bj3110341.
(70) Carregaro, F.; Stefanini, A. C. B.; Henrique, T.; Tajara, E. H. Study of Small Proline-Rich Proteins (SPRRs) in Health and Disease: A Review of the Literature. Arch. Dermatol. Res. 2013, 305 (10), 857–866. https://doi.org/10.1007/s00403-013-1415-9.
(71) Rahim, M. A.; Kristufek, S. L.; Pan, S.; Richardson, J. J.; Caruso, F. Phenolic Building Blocks for the Assembly of Functional Materials. Angew. Chemie - Int. Ed. 2019, 58 (7), 1904–1927. https://doi.org/10.1002/anie.201807804.
(72) Zhou, J.; Lin, Z.; Ju, Y.; Rahim, M. A.; Richardson, J. J.; Caruso, F. Polyphenol-Mediated Assembly for Particle Engineering. Acc. Chem. Res. 2020, 53 (7), 1269–1278. https://doi.org/10.1021/acs.accounts.0c00150.
(73) Yu, H.; Palazzolo, J. S.; Zhou, J.; Hu, Y.; Niego, B.; Pan, S.; Ju, Y.; Wang, T. Y.; Lin, Z.; Hagemeyer, C. E.; Caruso, F. Bioresponsive Polyphenol-Based Nanoparticles as Thrombolytic Drug Carriers. ACS Appl. Mater. Interfaces 2022, 14 (3), 3740–3751. https://doi.org/10.1021/acsami.1c19820.
(74) Scheiner, S. Hydrogen Bonding: A Theoretical Perspective; Oxford University Press: New York, NY, USA, 1997.
(75) Moore, T. S.; Winmill, T. F. CLXXVII. - The State of Amines in Aqueous Solution. J. Chem. Soc. Trans. 1912, 101, 1635–1676. https://doi.org/10.1039/CT9120101635.
(76) Steiner, T.; Saenger, W. Role of C-H⋯O Hydrogen Bonds in the Coordination of Water Molecules. Analysis of Neutron Diffraction Data. J. Am. Chem. Soc. 1993, 115 (11), 4540–4547. https://doi.org/10.1021/ja00064a016.
(77) Arunan, E.; Desiraju, G. R.; Klein, R. A.; Sadlej, J.; Scheiner, S.; Alkorta, I.; Clary, D. C.; Crabtree, R. H.; Dannenberg, J. J.; Hobza, P.; Kjaergaard, H. G.; Legon, A. C.; Mennucci, B.; Nesbitt, D. J. Defining the Hydrogen Bond: An Account (IUPAC Technical Report). Pure Appl. Chem. 2011, 83 (8), 1619–1636. https://doi.org/10.1351/PAC-REP-10-01-01.
(78) Cubero, E.; Orozco, M.; Luque, F. J. Electron Density Topological Analysis of the C-H...O Anti-Hydrogen Bond in the Fluoroform-Oxirane Complex. Chem. Phys. Lett. 1999, 310 (5–6), 445–450. https://doi.org/10.1016/S0009-2614(99)00831-3.
(79) Brown, T. L.; LeMay, H. E. J.; Bursten, B. E. Chemistry: The Central Science, 9th ed.; Pearson Education: Upper Saddle River, NJ, USA, 2003.
(80) Kotz, J. C.; Treichel, P. M.; Townsend, J. R.; Treichel, D. A. Chemistry and Chemical Reactivity, 11th ed.; Cengage Learning: Boston, MA, USA, 2023.
(81) Karachewski, A. M.; McNiel, M. M.; Eckert, C. A. A Study of Hydrogen Bonding in Alcohol Solutions Using NMR Spectroscopy. Ind. Eng. Chem. Res. 1989, 28 (3), 315–324. https://doi.org/10.1021/ie00087a010.
(82) Pavia, D. L.; Lampman, G. M.; Kriz, G. S.; Vyvyan, J. R. Introduction to Spectroscopy, 5th ed.; Cengage Learning: Stamford, CT, USA, 2015.
(83) Patkar, D.; Bharati Ahirwar, M.; Deshmukh, M. M. A Tug of War between the Self- and Cross-Associating Hydrogen Bonds in Neutral Ammonia-Water Clusters: Energetic Insights by Molecular Tailoring Approach. ChemPhysChem 2022, 23 (24), e202200476. https://doi.org/10.1002/cphc.202200476.
(84) Sarkhel, S.; Desiraju, G. R. N-H…O , O-H…O , and C-H…O Hydrogen Bonds in Protein-Ligand Complexes: Strong and Weak Interactions in Molecular Recognition. Proteins Struct. Funct. Bioinforma. 2004, 54 (2), 247–259.
(85) Desiraju, G.; Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology; Oxford University Press: Oxford, UK, 1999. https://doi.org/10.1093/acprof:oso/9780198509707.001.0001.
(86) Czernek, J.; Brus, J.; Czerneková, V.; Kobera, L. Quantifying the Intrinsic Strength of C-H...O Intermolecular Interactions. Molecules 2023, 28, 4478.
(87) Sutor, D. J. The C-H...O Hydrogen Bond in Crystals. Nature 1962, 195, 68–69.
(88) Sutor, D. J. Evidence for the Existence of C–H...O Hydrogen Bonds in Crystals. J. Chem. Soc. 1963, 1105–1110. https://doi.org/10.1039/jr9630001105.
(89) Donohue, J. The Hydrogen Bond in Organic Crystals. J. Phys. Chem. 1952, 56 (4), 502–510. https://doi.org/10.1021/j150496a023.
(90) Donohue, J. The C-H…O Hydrogen Bond: What Is It? In Structural Chemistry and Molecular Biology; Rich, A., Davidson, N., Eds.; W. H. Freeman: San Francisco, CA, USA, 1968; pp 459–463.
(91) Schwalbe, C. H. June Sutor and the C-H...O Hydrogen Bonding Controversy. Crystallogr. Rev. 2012, 18 (3), 191–206. https://doi.org/10.1080/0889311X.2012.674945.
(92) Extance, A. The forgotten female crystallographer who discovered C-H...O bonds. Chemistry World. https://www.chemistryworld.com/features/the-forgotten-female-crystallographer-who-discovered-c-ho-bonds/3010324.article (accessed 2024-06-12).
(93) Desiraju, G. R. The C-H⋯O Hydrogen Bond: Structural Implications and Supramolecular Design. Acc. Chem. Res. 1996, 29 (9), 441–449. https://doi.org/10.1021/ar950135n.
(94) Taylor, R.; Kennard, O. Crystallographic Evidence for the Existence of C-H⋯O, C-H⋯N, and C-H⋯Cl Hydrogen Bonds. J. Am. Chem. Soc. 1982, 104 (19), 5063–5070. https://doi.org/10.1021/ja00383a012.
(95) Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, 5th ed.; W. H. Freeman: New York, NY, USA, 2008.
(96) Burley, S. K.; Petsko, G. A. Aromatic-Aromatic Interaction: A Mechanism of Protein Structure. Science (80-. ). 1985, 229 (4708), 23–28.
(97) Riley, K. E.; Hobza, P. On the Importance and Origin of Aromatic Interactions in Chemistry and Biodisciplines. Acc. Chem. Res. 2013, 46 (4), 927–936. https://doi.org/10.1021/ar300083h.
(98) Yakovchuk, P.; Protozanova, E.; Frank-Kamenetskii, M. D. Base-Stacking and Base-Pairing Contributions into Thermal Stability of the DNA Double Helix. Nucleic Acids Res. 2006, 34 (2), 564–574. https://doi.org/10.1093/nar/gkj454.
(99) Arunan, E.; Gutowsky, H. S. The Rotational Spectrum, Structure and Dynamics of a Benzene Dimer. J. Chem. Phys. 1993, 98 (5), 4294–4296. https://doi.org/10.1063/1.465035.
(100) Schnell, M.; Erlekam, U.; Bunker, P. R.; Vonhelden, G.; Grabow, J. U.; Meijer, G.; Vanderavoird, A. Structure of the Benzene Dimer - Governed by Dynamics. Angew. Chemie - Int. Ed. 2013, 52 (19), 5180–5183. https://doi.org/10.1002/anie.201300653.
(101) Cox, E. G. The Crystalline Structure of Benzene. Proc. R. Soc. A 1932, 135 (827), 491–497.
(102) Cox, E. G.; Cruickshank, D. W. J.; Smith, J. A. S. The Crystal Structure of Benzene at -3°C. Proc. R. Soc. London. Ser. A. Math. Phys. Sci. 1958, 247 (1248), 1–21. https://doi.org/10.1098/rspa.1958.0167.
(103) Piermarini, G. J.; Mighell, A. D.; Weir, C. E.; Block, S. Crystal Structure of Benzene II at 25 Kilobars. Science (80-. ). 1969, 165 (3899), 1250–1255. https://doi.org/10.1126/science.165.3899.1250.
(104) Janda, K. C.; Hemminger, J. C.; Winn, J. S.; Novick, S. E.; Harris, S. J.; Klemperer, W. Benzene Dimer: A Polar Molecule. J. Chem. Phys. 1975, 63 (4), 1419–1421. https://doi.org/10.1063/1.431502.
(105) Katrusiak, A.; Podsiadło, M.; Budzianowski, A. Association CH⋯π and No van Der Waals Contacts at the Lowest Limits of Crystalline Benzene I and II Stability Regions. Cryst. Growth Des. 2010, 10 (8), 3461–3465. https://doi.org/10.1021/cg1002594.
(106) Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. Estimates of the Ab Initio Limit for π-π Interactions: The Benzene Dimer. J. Am. Chem. Soc. 2002, 124 (36), 10887–10893. https://doi.org/10.1021/ja025896h.
(107) Sinnokrot, M. O.; Sherrill, C. D. Highly Accurate Coupled Cluster Potential Energy Curves for the Benzene Dimer: Sandwich, T-Shaped, and Parallel-Displaced Configurations. J. Phys. Chem. A 2004, 108 (46), 10200–10207. https://doi.org/10.1021/jp0469517.
(108) Sinnokrot, M. O.; Sherrill, C. D. High-Accuracy Quantum Mechanical Studies of π-π Interactions in Benzene Dimers. J. Phys. Chem. A 2006, 110 (37), 10656–10668. https://doi.org/10.1021/jp0610416.
(109) Podeszwa, R.; Bukowski, R.; Szalewicz, K. Potential Energy Surface for the Benzene Dimer and Perturbational Analysis of π-π Interactions. J. Phys. Chem. A 2006, 110 (34), 10345–10354. https://doi.org/10.1021/jp064095o.
(110) Hunter, C. A.; Leighton, P.; Sanders, J. K. M. Allosteric Ligand Binding to Cofacial Metalloporphyrin Dimers: The Mechanism of Porphyrin Disaggregation. J. Chem. Soc. Perkin Trans. 1 1989, No. 3, 547–552. https://doi.org/10.1039/p19890000547.
(111) Hunter, C. A.; Sanders, J. K. M. The Nature of π-π Interactions. J. Am. Chem. Soc. 1990, 112 (14), 5525–5534. https://doi.org/10.1021/ja00170a016.
(112) Sinnokrot, M. O.; Sherrill, C. D. Unexpected Substituent Effects in Face-to-Face π-Stacking Interactions. J. Phys. Chem. A 2003, 107 (41), 8377–8379. https://doi.org/10.1021/jp030880e.
(113) Carter-Fenk, K.; Herbert, J. M. Electrostatics Does Not Dictate the Slip-Stacked Arrangement of Aromatic π-π Interactions. Chem. Sci. 2020, 11 (26), 6758–6765. https://doi.org/10.1039/d0sc02667k.
(114) Carter-Fenk, K.; Liu, M.; Pujal, L.; Loipersberger, M.; Tsanai, M.; Vernon, R. M.; Forman-Kay, J. D.; Head-Gordon, M.; Heidar-Zadeh, F.; Head-Gordon, T. The Energetic Origins of Pi-Pi Contacts in Proteins. J. Am. Chem. Soc. 2023, 145, 24836–24851. https://doi.org/10.1021/jacs.3c09198.
(115) Kamya, P. R. N.; Muchall, H. M. New Insights into the Use of (TD-)DFT for Geometries and Electronic Structures of Constrained π-Stacked Systems: [N.n]Paracyclophanes. J. Phys. Chem. A 2008, 112 (51), 13691–13698. https://doi.org/10.1021/jp808144e.
(116) Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. Estimates of the Ab Initio Limit for π−π Interactions: The Benzene Dimer. J. Am. Chem. Soc. 2002, 124 (19), 10887–10893.
(117) Bader, R. F. W. Atoms in Molecules — a Quantum Theory; Clarendon Press: Oxford, UK, 1994.
(118) Zhikol, O. A.; Shishkin, O. V.; Lyssenko, K. A.; Leszczynski, J. Electron Density Distribution in Stacked Benzene Dimers: A New Approach towards the Estimation of Stacking Interaction Energies. J. Chem. Phys. 2005, 122 (14), 144104. https://doi.org/10.1063/1.1877092.
(119) Rutledge, L. R.; Churchill, C. D. M.; Wetmore, S. D. A Preliminary Investigation of the Additivity of π-π or π+-π Stacking and T-Shaped Interactions between Natural or Damaged DNA Nucleobases and Histidine. J. Phys. Chem. B 2010, 114 (9), 3355–3367. https://doi.org/10.1021/jp911990g.
(120) Churchill, C. D. M.; Rutledge, L. R.; Wetmore, S. D. Effects of the Biological Backbone on Stacking Interactions at DNA-Protein Interfaces: The Interplay between the Backbone⋯π and π⋯π Components. Phys. Chem. Chem. Phys. 2010, 12 (43), 14515–14526. https://doi.org/10.1039/c0cp00550a.
(121) Moa, M. J. G.; Mandado, M.; Mosquera, R. A. A Computational Study on the Stacking Interaction in Quinhydrone. J. Phys. Chem. A 2007, 111 (10), 1998–2001. https://doi.org/10.1021/jp0661701.
(122) Quiñonero, D.; Frontera, A.; Garau, C.; Ballester, P.; Costa, A.; Deyà, P. M. Interplay between Cation-π, Anion-π and π-π Interactions. ChemPhysChem 2006, 7 (12), 2487–2491. https://doi.org/10.1002/cphc.200600343.
(123) Escudero, D.; Frontera, A.; Quiñonero, D.; Deyà, P. M. Interplay between Edge-to-Face Aromatic and Hydrogen-Bonding Interactions. J. Phys. Chem. A 2008, 112 (26), 6017–6022. https://doi.org/10.1021/jp802370s.
(124) Matta, C. F.; Castillo, N.; Boyd, R. J. Extended Weak Bonding Interactions in DNA: π-Stacking (Base-Base), Base-Backbone, and Backbone-Backbone Interactions. J. Phys. Chem. B 2006, 110 (1), 563–578. https://doi.org/10.1021/jp054986g.
(125) Matta, C. F.; Boyd, R. J. The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design; Matta, C. F., Boyd, R. J., Eds.; Wiley-VCH Verlag GmbH & Co KGgA, 2007. https://doi.org/10.1002/9783527610709.
(126) Mosquera, R. A.; González Moa, M. J.; Estévez, L.; Mandado, M.; Gran̂a, A. M. An Electron Density-Based Approach to the Origin of Stacking Interactions. Quantum Biochem. 2010, 365–387. https://doi.org/10.1002/9783527629213.ch11.
(127) Kamya, P. R. N.; Muchall, H. M. Revisiting the Effects of Sequence and Structure on the Hydrogen Bonding and π-Stacking Interactions in Nucleic Acids. J. Phys. Chem. A 2011, 115 (45), 12800–12808. https://doi.org/10.1021/jp203918z.
(128) Nishio, M. The CH/π Hydrogen Bond in Chemistry. Conformation, Supramolecules, Optical Resolution and Interactions Involving Carbohydrates. Phys. Chem. Chem. Phys. 2011, 13 (31), 13873–13900. https://doi.org/10.1039/c1cp20404a.
(129) Kar, K.; Ibrar, S.; Nanda, V.; Getz, T. M.; Kunapuli, S. P.; Brodsky, B. Aromatic Interactions Promote Self-Association of Collagen Triple-Helical Peptides to Higher-Order Structures. Biochemistry 2009, 48 (33), 7959–7968. https://doi.org/10.1021/bi900496m.
(130) Neuheuser, T.; Hess, B. A.; Reutel, C.; Weber, E. Ab Initio Calculations of Supramolecular Recognition Modes. Cyclic versus Noncyclic Hydrogen Bonding in the Formic Acid/Formamide System. J. Phys. Chem. 1994, 98 (26), 6459–6467. https://doi.org/10.1021/j100077a007.
(131) Feyereisen, M. W.; Feller, D.; Dixon, D. A. Hydrogen Bond Energy of the Water Dimer. J. Phys. Chem. 1996, 100 (8), 2993–2997. https://doi.org/10.1021/jp952860l.
(132) Del Bene, J. E. Ab Initio Molecular Orbital Study of the Structures and Energies of Neutral and Charged Bimolecular Complexes of H2O with the Hydrides AHn (A = N , O , F , P , S , and Cl). J. Phys. Chem. 1988, 92 (28), 2874–2880.
(133) Guo, H.; Karplus, M. Ab Initio Studies of Hydrogen Bonding of N-Methylacetamide: Structure, Cooperativity, and Internal Rotational Barriers. J. Phys. Chem. 1992, 96 (18), 7273–7287. https://doi.org/10.1021/j100197a027.
(134) Nishio, M.; Umezawa, Y.; Fantini, J.; Weiss, M. S.; Chakrabarti, P. CH-π Hydrogen Bonds in Biological Macromolecules. Phys. Chem. Chem. Phys. 2014, 16 (25), 12648–12683. https://doi.org/10.1039/c4cp00099d.
(135) Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. The Magnitude of the CH/π Interaction between Benzene and Some Model Hydrocarbons. J. Am. Chem. Soc. 2000, 122 (15), 3746–3753. https://doi.org/10.1021/ja993972j.
(136) Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. Origin of Attraction and Directionality of the π/π Interaction: Model Chemistry Calculations of Benzene Dimer Interaction. J. Am. Chem. Soc. 2002, 124 (1), 104–112. https://doi.org/10.1021/ja0105212.
(137) Newberry, R. W.; Raines, R. T. Secondary Forces in Protein Folding. ACS Chem. Biol. 2019, 14 (8), 1677–1686. https://doi.org/10.1021/acschembio.9b00339.
(138) Newberry, R. W.; Vanveller, B.; Guzei, I. A.; Raines, R. T. N → π* Interactions of Amides and Thioamides: Implications for Protein Stability. J. Am. Chem. Soc. 2013, 135 (21), 7843–7846. https://doi.org/10.1021/ja4033583.
(139) Echeverría, J.; Aullón, G.; Danovich, D.; Shaik, S.; Alvarez, S. Dihydrogen Contacts in Alkanes Are Subtle but Not Faint. Nat. Chem. 2011, 3 (4), 323–330. https://doi.org/10.1038/nchem.1004.
(140) van der Veen, J. N.; Kennelly, J. P.; Wan, S.; Vance, J. E.; Vance, D. E.; Jacobs, R. L. The Critical Role of Phosphatidylcholine and Phosphatidylethanolamine Metabolism in Health and Disease. Biochim. Biophys. Acta - Biomembr. 2017, 1859 (9), 1558–1572. https://doi.org/10.1016/j.bbamem.2017.04.006.
(141) Hauser, H.; Pascher, I.; Pearson, R. H.; Sundell, S. Preferred Conformation and Molecular Packing of Phosphatidylethanolamine and Phosphatidylcholine. BBA - Rev. Biomembr. 1981, 650 (1), 21–51. https://doi.org/10.1016/0304-4157(81)90007-1.
(142) Conti Nibali, V.; Branca, C.; Wanderlingh, U.; D’angelo, G. Intermolecular Hydrogen-Bond Interactions in DPPE and DMPC Phospholipid Membranes Revealed by Far-Infrared Spectroscopy. Appl. Sci. 2021, 11 (21), 10038. https://doi.org/10.3390/app112110038.
(143) Cadenhead, D. A.; Demchak, R. J.; Phillips, M. C. Monolayer Characteristics of 1,2-Dimyristin, 1,2-Dimyristoyl-3-Cephalin and 1,2-Dimyristoyl-3-Lecithin at the Air-Water Interface. Kolloid-Zeitschrift Zeitschrift für Polym. 1967, 220 (1), 59–64. https://doi.org/10.1007/BF02086058.
(144) Keough, K. M. W.; Hawco, M. W.; Parsons, C. S. The Effect of Methylation of Phosphatidylethanolamine on the Behaviour of Lipid Monolayers at the Air-Water Interface. Biochem. Cell Biol. 1988, 66 (5), 405–417. https://doi.org/10.1139/o88-049.
(145) Miller, C. E.; Busath, D. D.; Strongin, B.; Majewski, J. Integration of Ganglioside GT1b Receptor into DPPE and DPPC Phospholipid Monolayers: An X-Ray Reflectivity and Grazing-Incidence Diffraction Study. Biophys. J. 2008, 95 (7), 3278–3286. https://doi.org/10.1529/biophysj.107.128538.
(146) Brezesinski, G.; Dobner, B.; Stefaniu, C.; Vollhardt, D. Monolayer Characteristics of a Long-Chain N,O-Diacyl Substituted Ethanolamine at the Air/Water Interface. Langmuir 2011, 27 (9), 5386–5392. https://doi.org/10.1021/la200243y.
(147) Miclette Lamarche, R. Controlling the Air-Water Behavior of Phenolic Surfactants and Their ω-Thiolated Derivatives Using Subphase Modification: Towards Deposition of Functional Thin Films. Ph. D. thesis, Concordia University, Montreal, QC, Canada, 2019.
(148) Slotte, J. P. The Importance of Hydrogen Bonding in Sphingomyelin’s Membrane Interactions with Co-Lipids. Biochim. Biophys. Acta - Biomembr. 2016, 1858 (2), 304–310. https://doi.org/10.1016/j.bbamem.2015.12.008.
(149) Yamaguchi, T.; Suzuki, T.; Yasuda, T.; Oishi, T.; Matsumori, N.; Murata, M. NMR-Based Conformational Analysis of Sphingomyelin in Bicelles. Bioorganic Med. Chem. 2012, 20 (1), 270–278. https://doi.org/10.1016/j.bmc.2011.11.001.
(150) Adam, N. K. The Structure of Thin Films. Part IV.—Benzene Derivatives. A Condition of Stability in Monomolecular Films. Proc. R. Soc. London. Ser. A, Contain. Pap. a Math. Phys. Character 1923, 103 (723), 676–687. https://doi.org/10.1098/rspa.1923.0087.
(151) Peikert, M.; Chen, X.; Chi, L.; Brezesinski, G.; Janich, S.; Würthwein, E. U.; Schäfer, H. J. Phase Behavior and Molecular Packing of Octadecyl Phenols and Their Methyl Ethers at the Air/Water Interface. Langmuir 2014, 30 (20), 5780–5789. https://doi.org/10.1021/la404340h.
(152) DeWolf, C.; Brezesinski, G.; Weidemann, G.; Möhwald, H.; Kjaer, K.; Howes, P. B. Influence of Temperature on the Phase Behavior of 1,2-Diol Derivatives. J. Phys. Chem. B 1998, 102 (17), 3238–3242. https://doi.org/10.1021/jp9802174.
(153) Vollhardt, D.; Gehlert, U. The Phase Behavior of an Ether Lipid Monolayer Compared with an Ester Lipid Monolayer. Trends Colloid Interface Sci. VIII 2007, 302–306. https://doi.org/10.1007/bfb0115188.
(154) Brezesinski, G.; Dietrich, A.; Struth, B.; Böhm, C.; Bouwman, W. G.; Kjaer, K.; Möhwald, H. Influence of Ether Linkages on the Structure of Double-Chain Phospholipid Monolayers. Chem. Phys. Lipids 1995, 76 (2), 145–157. https://doi.org/10.1016/0009-3084(95)02439-P.
(155) Lewis, R. N. A. H.; Pohle, W.; McElhaney, R. N. The Interfacial Structure of Phospholipid Bilayers: Differential Scanning Calorimetry and Fourier Transform Infrared Spectroscopic Studies of 1,2-Dipalmitoyl-Sn-Glycero-3-Phosphorylcholine and Its Dialkyl and Acyl-Alkyl Analogs. Biophys. J. 1996, 70 (6), 2736–2746. https://doi.org/10.1016/S0006-3495(96)79843-0.
(156) Guler, S. D.; Ghosh, D. D.; Pan, J.; Mathai, J. C.; Zeidel, M. L.; Nagle, J. F.; Tristram-Nagle, S. Effects of Ether vs. Ester Linkage on Lipid Bilayer Structure and Water Permeability. Chem. Phys. Lipids 2009, 160 (1), 33–44. https://doi.org/10.1016/j.chemphyslip.2009.04.003.
(157) Kruczek, J.; Saunders, M.; Khosla, M.; Tu, Y.; Pandit, S. A. Molecular Dynamics Simulations of Ether- and Ester-Linked Phospholipids. Biochim. Biophys. Acta - Biomembr. 2017, 1859 (12), 2297–2307. https://doi.org/10.1016/j.bbamem.2017.08.023.
(158) Rosen, M. J. Surfactants and Interfacial Phenomena, 3rd ed.; Wiley-Interscience: Hoboken, NJ, USA, 2004. https://doi.org/10.1016/0166-6622(89)80030-7.
(159) Andersson, M.; Jackman, J.; Wilson, D.; Jarvoll, P.; Alfredsson, V.; Okeyo, G.; Duran, R. Vesicle and Bilayer Formation of Diphytanoylphosphatidylcholine (DPhPC) and Diphytanoylphosphatidylethanolamine (DPhPE) Mixtures and Their Bilayers’ Electrical Stability. Colloids Surfaces B Biointerfaces 2011, 82 (2), 550–561. https://doi.org/10.1016/j.colsurfb.2010.10.017.
(160) Kara, S.; Afonin, S.; Babii, O.; Tkachenko, A. N.; Komarov, I. V.; Ulrich, A. S. Diphytanoyl Lipids as Model Systems for Studying Membrane-Active Peptides. Biochim. Biophys. Acta - Biomembr. 2017, 1859 (10), 1828–1837. https://doi.org/10.1016/j.bbamem.2017.06.003.
(161) Boese, R.; Weiss, H. C.; Bläser, D. The Melting Point Alternation in the Short-Chain n-Alkanes: Single-Crystal X-Ray Analyses of Propane at 30 K and of n-Butane to n-Nonane at 90 K. Angew. Chemie - Int. Ed. 1999, 38 (7), 988–992. https://doi.org/10.1002/(SICI)1521-3773(19990401)38:7<988::AID-ANIE988>3.0.CO;2-0.
(162) Bond, A. D. On the Crystal Structures and Melting Point Alternation of the N-Alkyl Carboxylic Acids. New J. Chem. 2004, 28 (1), 104–114. https://doi.org/10.1039/b307208h.
(163) Izumi, H.; Yamagami, S.; Futamura, S.; Nafie, L. A.; Dukor, R. K. Direct Observation of Odd-Even Effect for Chiral Alkyl Alcohols in Solution Using Vibrational Circular Dichroism Spectroscopy. J. Am. Chem. Soc. 2004, 126 (1), 194–198. https://doi.org/10.1021/ja037752o.
(164) Varghese, N.; Shetye, G. S.; Yang, S.; Wilkens, S.; Smith, R. P.; Luk, Y. Y. The Ability of Single-Chain Surfactants to Emulsify an Aqueous-Based Liquid Crystal Oscillates with Odd-Even Parity of Alkyl-Chain Length. J. Colloid Interface Sci. 2013, 412, 95–99. https://doi.org/10.1016/j.jcis.2013.08.044.
(165) Wang, Z.; Chen, J.; Oyola-Reynoso, S.; Thuo, M. The Porter-Whitesides Discrepancy: Revisiting Odd-Even Effects in Wetting Properties of n-Alkanethiolate SAMs. Coatings 2015, 5, 1034–1055. https://doi.org/10.3390/coatings5041034.
(166) Folkers, J. P.; Laibinis, P. E.; Whitesides, G. M. Self-Assembled Monolayers of Alkanethiols on Gold: Comparisons of Monolayers Containing Mixtures of Short-and Long-Chain Constituents with CH3 and CH2OH Terminal Groups. Langmuir 1992, 8 (5), 1330–1341. https://doi.org/10.1021/la00041a015.
(167) Mangiarotti, A.; Caruso, B.; Wilke, N. Phase Coexistence in Films Composed of DLPC and DPPC: A Comparison between Different Model Membrane Systems. Biochim. Biophys. Acta - Biomembr. 2014, 1838 (7), 1823–1831. https://doi.org/10.1016/j.bbamem.2014.02.012.
(168) Möhwald, H. Phospholipid Monolayers. In Phospholipids Handbook; Cevc, G., Ed.; Marcel Dekker, Inc.: New York, NY, USA, 1993; pp 579–602. https://doi.org/10.1201/9780203743577-16.
(169) Moraille, P.; Badia, A. Highly Parallel, Nanoscale Stripe Morphology in Mixed Phospholipid Monolayers Formed by Langmuir-Blodgett Transfer. Langmuir 2002, 18 (11), 4414–4419. https://doi.org/10.1021/la020129h.
(170) Fahy, E.; Subramaniam, S.; Brown, H. A.; Glass, C. K.; Merrill, A. H.; Murphy, R. C.; Raetz, C. R. H.; Russell, D. W.; Seyama, Y.; Shaw, W.; Shimizu, T.; Spener, F.; Van Meer, G.; VanNieuwenhze, M. S.; White, S. H.; Witztum, J. L.; Dennis, E. A. A Comprehensive Classification System for Lipids. J. Lipid Res. 2005, 46 (5), 839–861. https://doi.org/10.1194/jlr.E400004-JLR200.
(171) Fahy, E.; Subramaniam, S.; Murphy, R. C.; Nishijima, M.; Raetz, C. R. H.; Shimizu, T.; Spener, F.; Van Meer, G.; Wakelam, M. J. O.; Dennis, E. A. Update of the LIPID MAPS Comprehensive Classification System for Lipids. J. Lipid Res. 2009, 50 (SUPPL.), 9–14. https://doi.org/10.1194/jlr.R800095-JLR200.
(172) Beharry, A. A.; Sadovski, O.; Woolley, G. A. Azobenzene Photoswitching without Ultraviolet Light. J. Am. Chem. Soc. 2011, 133 (49), 19684–19687. https://doi.org/10.1021/ja209239m.
(173) Delamarche, E.; Michel, B.; Biebuyck, H. A.; Gerber, C. Golden Interfaces: The Surface of Self-Assembled Monolayers. Adv. Mater. 1996, 8 (9), 719–729. https://doi.org/10.1002/adma.19960080903.
(174) Rojas-Gutierrez, P. A.; Bhuckory, S.; Mingoes, C.; Hildebrandt, N.; Dewolf, C.; Capobianco, J. A. A Route to Triggered Delivery via Photocontrol of Lipid Bilayer Properties Using Lanthanide Upconversion Nanoparticles. ACS Appl. Nano Mater. 2018, 1 (9), 5345–5354. https://doi.org/10.1021/acsanm.8b01396.
(175) Hopkins Hatzopoulos, M.; Eastoe, J.; Dowding, P. J.; Rogers, S. E.; Heenan, R.; Dyer, R. Are Hydrotropes Distinct from Surfactants? Langmuir 2011, 27 (20), 12346–12353. https://doi.org/10.1021/la2025846.
(176) Hopkins Hatzopoulos, M.; Eastoe, J.; Dowding, P. J.; Grillo, I.; Demé, B.; Rogers, S. E.; Heenan, R.; Dyer, R. Effects of Structure Variation on Solution Properties of Hydrotropes: Phenyl versus Cyclohexyl Chain Tips. Langmuir 2012, 28 (25), 9332–9340. https://doi.org/10.1021/la301222m.
(177) Dou, R. F.; Ma, X. C.; Xi, L.; Yip, H. L.; Wong, K. Y.; Lau, W. M.; Jia, J. F.; Xue, Q. K.; Yang, W. S.; Ma, H.; Jen, A. K. Y. Self-Assembled Monolayers of Aromatic Thiols Stabilized by Parallel-Displaced π-π Stacking Interactions. Langmuir 2006, 22 (7), 3049–3056. https://doi.org/10.1021/la052987u.
(178) Bennett, W. F. D.; Tieleman, D. P. Computer Simulations of Lipid Membrane Domains. Biochim. Biophys. Acta - Biomembr. 2013, 1828 (8), 1765–1776. https://doi.org/10.1016/j.bbamem.2013.03.004.
(179) Brown, F. L. H. Continuum Simulations of Biomembrane Dynamics and the Importance of Hydrodynamic Effects. Q. Rev. Biophys. 2011, 44 (4), 391–432. https://doi.org/10.1017/S0033583511000047.
(180) Walter, J. C.; Barkema, G. T. An Introduction to Monte Carlo Methods. Phys. A Stat. Mech. its Appl. 2015, 418, 78–87. https://doi.org/10.1016/j.physa.2014.06.014.
(181) Swanson, D. R.; Hardy, R. J.; Eckhardt, C. J. Monte Carlo Simulation of the Solid to Super Liquid Phase Transition of Langmuir Monolayers Using Cross-Section Potentials. J. Chem. Phys. 1993, 99 (10), 8194–8199. https://doi.org/10.1063/1.465646.
(182) Düchs, D.; Schmid, F. Phase Behaviour of Amphiphilic Monolayers: Theory and Simulation. J. Phys. Condens. Matter 2001, 13 (21), 4853–4862. https://doi.org/10.1088/0953-8984/13/21/313.
(183) Mao, Q.; Feng, M.; Jiang, X. Z.; Ren, Y.; Luo, K. H.; van Duin, A. C. T. Classical and Reactive Molecular Dynamics: Principles and Applications in Combustion and Energy Systems. Prog. Energy Combust. Sci. 2023, 97 (September 2022), 101084. https://doi.org/10.1016/j.pecs.2023.101084.
(184) Hong, C.; Tieleman, D. P.; Wang, Y. Microsecond Molecular Dynamics Simulations of Lipid Mixing. Langmuir 2014, 30 (40), 11993–12001. https://doi.org/10.1021/la502363b.
(185) Koldsø, H.; Shorthouse, D.; Hélie, J.; Sansom, M. S. P. Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers. PLoS Comput. Biol. 2014, 10 (10), e1003911. https://doi.org/10.1371/journal.pcbi.1003911.
(186) Nencini, R.; Ollila, O. H. S. Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments. J. Phys. Chem. B 2022, 126 (36), 6955–6963. https://doi.org/10.1021/acs.jpcb.2c05024.
(187) Baaden, M.; Sansom, M. S. P. OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme. Biophys. J. 2004, 87 (5), 2942–2953. https://doi.org/10.1529/biophysj.104.046987.
(188) Apajalahti, T.; Niemelä, P.; Govindan, P. N.; Miettinen, M. S.; Salonen, E.; Marrink, S. J.; Vattulainen, I. Concerted Diffusion of Lipids in Raft-like Membranes. Faraday Discuss. 2009, 144, 411–430. https://doi.org/10.1039/b901487j.
(189) Bennett, W. F. D.; MacCallum, J. L.; Hinner, M. J.; Marrink, S. J.; Tieleman, D. P. Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments. J. Am. Chem. Soc. 2009, 131 (35), 12714–12720. https://doi.org/10.1021/ja903529f.
(190) Risselada, H. J.; Marrink, S. J. The Molecular Face of Lipid Rafts in Model Membranes. Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (45), 17367–17372. https://doi.org/10.1073/pnas.0807527105.
(191) Klein, M. L.; Shinoda, W. Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems. Science (80-. ). 2008, 321, 798–800.
(192) Hub, J. S.; Salditt, T.; Rheinstädter, M. C.; De Groot, B. L. Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments. Biophys. J. 2007, 93 (9), 3156–3168. https://doi.org/10.1529/biophysj.107.104885.
(193) Jensen, F. Introduction to Computational Chemistry, 3rd ed.; Wiley: Chichester, England, 2017. https://doi.org/10.1007/s00214-013-1372-6.
(194) Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: A New General Purpose Quantum Mechanical Molecular Model1. J. Am. Chem. Soc. 1985, 107 (13), 3902–3909. https://doi.org/10.1021/ja00299a024.
(195) Jin, A. Y.; Benesch, L. A.; Weaver, D. F. Computational Conformational Analysis of Neural Membrane Lipids:Development of Force Field Parameters for Phospholipids Using Semi-Empirical Molecular Orbital Calculations. Can. J. Chem. 1994, 72 (6), 1596–1604. https://doi.org/10.1139/v94-199.
(196) Urbina-Villalba, G.; Reif, I.; Márquez, M. L.; Rogel, E. Theoretical Study on the Structure and Interfacial Areas of Nonyl Phenol Ethoxylated Surfactants. Colloids Surfaces A Physicochem. Eng. Asp. 1995, 99 (2–3), 207–220. https://doi.org/10.1016/0927-7757(95)03113-R.
(197) Kartashynska, E. S.; Vysotsky, Y. B.; Fainerman, V. B.; Vollhardt, D.; Miller, R. Quantum-Chemical Analysis of Condensed Monolayer Phases of N-Alkanoyl-Substituted Alanine at the Air/Water Interface. Colloids Surfaces A Physicochem. Eng. Asp. 2018, 546 (February), 346–359. https://doi.org/10.1016/j.colsurfa.2018.03.027.
(198) Vysotsky, Y. B.; Kartashynska, E. S.; Belyaeva, E. A.; Vollhardt, D.; Fainerman, V. B.; Miller, R. Analysis of Temperature and Alkyl Chain Length Impacts on the Morphological Peculiarities of Nonionic Surfactant Clusterization. A Quantum Chemical Approach. J. Phys. Chem. C 2015, 119 (32), 18404–18413. https://doi.org/10.1021/acs.jpcc.5b05458.
(199) Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method. J. Comput. Chem. 1989, 10 (2), 209–220.
(200) Csonka, G. I.; Ángyán, J. G. The Origin of the Problems with the PM3 Core Repulsion Function. J. Mol. Struct. THEOCHEM 1997, 393 (1-3 SPEC. ISS.), 31–38. https://doi.org/10.1016/s0166-1280(96)04872-5.
(201) Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements. J. Mol. Model. 2007, 13 (12), 1173–1213. https://doi.org/10.1007/s00894-007-0233-4.
(202) Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods VI: More Modifications to the NDDO Approximations and Re-Optimization of Parameters. J. Mol. Model. 2013, 19 (1), 1–32. https://doi.org/10.1007/s00894-012-1667-x.
(203) Marion, A.; Monard, G.; Ruiz-López, M. F.; Ingrosso, F. Water Interactions with Hydrophobic Groups: Assessment and Recalibration of Semiempirical Molecular Orbital Methods. J. Chem. Phys. 2014, 141 (3). https://doi.org/10.1063/1.4886655.
(204) Kartashynska, E. S.; Vollhardt, D. 2D-Monolayer Formation of 3-Monoacyl-sn-Glycerols at the Air/Water Interface. A Comprehensive Quantum Chemical Approach. Colloids Surfaces A Physicochem. Eng. Asp. 2023, 667 (March), 131400. https://doi.org/10.1016/j.colsurfa.2023.131400.
(205) Soler, J. M.; Artacho, E.; Gale, J. D.; García, A.; Junquera, J.; Ordejón, P.; Sánchez-Portal, D. The SIESTA Method for Ab Initio Order-N Materials Simulation. J. Phys. Condens. Matter 2002, 14 (11), 2745–2779. https://doi.org/10.1088/0953-8984/14/11/302.
(206) García, A.; Papior, N.; Akhtar, A.; Artacho, E.; Blum, V.; Bosoni, E.; Brandimarte, P.; Brandbyge, M.; Cerdá, J. I.; Corsetti, F.; Cuadrado, R.; Dikan, V.; Ferrer, J.; Gale, J.; García-Fernández, P.; García-Suárez, V. M.; García, S.; Huhs, G.; Illera, S.; Korytár, R.; Koval, P.; Lebedeva, I.; Lin, L.; López-Tarifa, P.; Mayo, S. G.; Mohr, S.; Ordejón, P.; Postnikov, A.; Pouillon, Y.; Pruneda, M.; Robles, R.; Sánchez-Portal, D.; Soler, J. M.; Ullah, R.; Yu, V. W. Z.; Junquera, J. Siesta: Recent Developments and Applications. J. Chem. Phys. 2020, 152 (20), 204108. https://doi.org/10.1063/5.0005077.
(207) Toledano, Ó.; Gálvez, Ó. Energetics and Structure of Langmuir Monolayers of Palmitic Acid: A DFT Study. Phys. Chem. Chem. Phys. 2019, 21 (21), 11203–11213. https://doi.org/10.1039/c9cp01563a.
(208) Zhao, Y. Monolayer Behavior of Phenolic Lipids: Experimental and Computational Studies. M. Sc. thesis, Concordia University, Montreal, QC, Canada, 2008.
(209) Erlekam, U.; Frankowski, M.; Meijer, G.; Von Helden, G. An Experimental Value for the B1u C-H Stretch Mode in Benzene. J. Chem. Phys. 2006, 124 (17). https://doi.org/10.1063/1.2198828.
(210) Miyazaki, M.; Fujii, M. Real Time Observation of the Excimer Formation Dynamics of a Gas Phase Benzene Dimer by Picosecond Pump-Probe Spectroscopy. Phys. Chem. Chem. Phys. 2015, 17 (39), 25989–25997. https://doi.org/10.1039/c5cp03010b.
(211) De Meijere, A.; Huisken, F. CO2-Laser Induced Photodissociation Studies of Size-Selected Small Benzene Clusters. J. Chem. Phys. 1990, 92 (10), 5826–5834. https://doi.org/10.1063/1.458403.
(212) Börnsen, K. O.; Lin, S. H.; Selzle, H. L.; Schlag, E. W. Spectra of Isotopically Mixed Benzene Trimers. J. Chem. Phys. 1989, 90 (3), 1299–1306. https://doi.org/10.1063/1.456124.
(213) Seifert, N. A.; Steber, A. L.; Neill, J. L.; Pérez, C.; Zaleski, D. P.; Pate, B. H.; Lesarri, A. The Interplay of Hydrogen Bonding and Dispersion in Phenol Dimer and Trimer: Structures from Broadband Rotational Spectroscopy. Phys. Chem. Chem. Phys. 2013, 15 (27), 11468–11477. https://doi.org/10.1039/c3cp51725j.
(214) Ebata, T.; Watanabe, T.; Mikami, N. Evidence for the Cyclic Form of Phenol Trimer: Vibrational Spectroscopy of the OH Stretching Vibrations of Jet-Cooled Phenol Dimer and Trimer. J. Phys. Chem. 1995, 99 (16), 5761–5764. https://doi.org/10.1021/j100016a006.
(215) Di Palma, T. M.; Bende, A.; Borghese, A. Photoionisation and Structures of Jet-Formed Toluene Clusters. Chem. Phys. Lett. 2010, 495 (1–3), 17–23. https://doi.org/10.1016/j.cplett.2010.06.053.
(216) Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M. Ab Initio Calculations of Structures and Interaction Energies of Toluene Dimers Including CCSD(T) Level Electron Correlation Correction. J. Chem. Phys. 2005, 122 (14). https://doi.org/10.1063/1.1876092.
(217) Rogers, D. M.; Hirst, J. D.; Lee, E. P. F.; Wright, T. G. Ab Initio Study of the Toluene Dimer. Chem. Phys. Lett. 2006, 427 (4–6), 410–413. https://doi.org/10.1016/J.CPLETT.2006.07.022.
(218) Musgrave, A.; Wright, T. G. Electronic Spectroscopy of Small Toluene Clusters. J. Chem. Phys. 2005, 122 (7). https://doi.org/10.1063/1.1850473.
(219) Capello, M. C.; Hernández, F. J.; Broquier, M.; Dedonder-Lardeux, C.; Jouvet, C.; Pino, G. A. Hydrogen Bonds vs. π-Stacking Interactions in the ρ-Aminophenol. . . ρ-Cresol Dimer: An Experimental and Theoretical Study. Phys. Chem. Chem. Phys. 2016, 18 (45), 31260–31267. https://doi.org/10.1039/c6cp06352g.
(220) Saeki, M.; Ishiuchi, S. I.; Sakai, M.; Fujii, M. Structure of the Jet-Cooled 1-Naphthol Dimer Studied by IR Dip Spectroscopy: Cooperation between the π-π Interaction and the Hydrogen Bonding. J. Phys. Chem. A 2007, 111 (6), 1001–1005. https://doi.org/10.1021/jp0668910.
(221) Seifert, N. A.; Hazrah, A. S.; Jäger, W. The 1-Naphthol Dimer and Its Surprising Preference for π-π Stacking over Hydrogen Bonding. J. Phys. Chem. Lett. 2019, 10 (11), 2836–2841. https://doi.org/10.1021/acs.jpclett.9b00646.
(222) Kuzmenko, I.; Kaganer, V. M.; Leiserowitz, L. Packing of Hydrocarbon Chains and Symmetry of Condensed Phases in Langmuir Monolayers. Langmuir 1998, 14 (14), 3882–3888. https://doi.org/10.1021/la970819z.
(223) Miclette Lamarche, R.; DeWolf, C. E. Strong Headgroup Interactions Drive Highly Directional Growth and Unusual Phase Co-Existence in Self-Assembled Phenolic Films. ACS Appl. Mater. Interfaces 2019, 11 (48), 45354–45363. https://doi.org/10.1021/acsami.9b16958.
(224) Pollastri, M. P.; Porter, N. A.; McIntosh, T. J.; Simon, S. A. Synthesis, Structure, and Thermal Properties of 1,2-Dipalmitoylgalloylglycerol (DPGG), a Novel Self-Adhering Lipid. Chem. Phys. Lipids 2000, 104 (1), 67–74. https://doi.org/10.1016/S0009-3084(99)00110-3.
(225) Schmidt, R.; DeWolf, C. E. Monolayer Behavior of 1,2-Dipalmitoylgalloylglycerol, a Synthetic Lipid with Strong Cohesive Properties. Langmuir 2004, 20 (8), 3284–3288.
(226) Schmidt, R.; Carrigan, J. G.; DeWolf, C. E. Synthesis and Characterization of a Series of Novel Phenol- and Polyphenol-Based Glycerolipids. Can. J. Chem. 2006, 84 (10), 1411–1415. https://doi.org/10.1139/V06-102.
(227) Miclette Lamarche, R.; DeWolf, C. E. Unpublished Data.
(228) Boze, H.; Marlin, T.; Durand, D.; Pérez, J.; Vemhet, A.; Canon, F.; Sami-Manchado, P.; Cheynier, V.; Cabane, B. Proline-Rich Salivary Proteins Have Extended Conformations. Biophys. J. 2010, 99 (2), 656–665. https://doi.org/10.1016/j.bpj.2010.04.050.
(229) Theillet, F.-X.; Kalmar, L.; Tompa, P.; Han, K.-H.; Selenko, P.; Dunker, A. K.; Daughdrill, G. W.; Uversky, V. N. The Alphabet of Intrinsic Disorder: Act like a Pro: On the Abundance and Roles of Proline Residues in Intrinsically Disordered Proteins. Intrinsically Disord. Proteins 2014, 1 (1), e24360.
(230) Ruggiero, M. T.; Sibik, J.; Orlando, R.; Zeitler, J. A.; Korter, T. M. Measuring the Elasticity of Poly- l -Proline Helices with Terahertz Spectroscopy. Angew. Chemie - Int. Ed. 2016, 55 (24), 6877–6881. https://doi.org/10.1002/anie.201602268.
(231) Rath, A.; Davidson, A. R.; Deber, C. M. The Structure of “Unstructured” Regions in Peptides and Proteins: Role of the Polyproline II Helix in Protein Folding and Recognition. Biopolym. - Pept. Sci. Sect. 2005, 80 (2–3), 179–185. https://doi.org/10.1002/bip.20227.
(232) Adzhubei, A. A.; Sternberg, M. J. E.; Makarov, A. A. Polyproline-II Helix in Proteins: Structure and Function. J. Mol. Biol. 2013, 425 (12), 2100–2132. https://doi.org/10.1016/j.jmb.2013.03.018.
(233) Bennick, A. Interaction of Plant Polyphenols with Salivary Proteins. Crit. Rev. Oral Biol. Med. 2002, 13 (2), 184–196. https://doi.org/10.1177/154411130201300208.
(234) Baxter, N. J.; Lilley, T. H.; Haslam, E.; Williamson, M. P. Multiple Interactions between Polyphenols and a Salivary Proline-Rich Protein Repeat Result in Complexation and Precipitation. Biochemistry 1997, 36 (18), 5566–5577. https://doi.org/10.1021/bi9700328.
(235) Canon, F.; Ballivian, R.; Chirot, F.; Antoine, R.; Sarni-Manchado, P.; Lemoine, J.; Dugourd, P. Folding of a Salivary Intrinsically Disordered Protein upon Binding to Tannins. J. Am. Chem. Soc. 2011, 133 (20), 7847–7852. https://doi.org/10.1021/ja200534f.
(236) Hagerman, A. E.; Butler, L. G. Protein Precipitation Method for the Quantitative Determination of Tannins. J. Agric. Food Chem. 1978, 26 (4), 809–812. https://doi.org/10.1021/jf60218a027.
(237) Simon, C.; Barathieu, K.; Laguerre, M.; Schmitter, J. M.; Fouquet, E.; Pianet, I.; Dufourc, E. J. Three-Dimensional Structure and Dynamics of Wine Tannin-Saliva Protein Complexes. A Multitechnique Approach. Biochemistry 2003, 42 (35), 10385–10395. https://doi.org/10.1021/bi034354p.
(238) Hagerman, A. E.; Butler, L. G. The Specificity of Proanthocyanidin-Protein Interactions. J. Biol. Chem. 1981, 256 (9), 4494–4497. https://doi.org/10.1016/s0021-9258(19)69462-7.
(239) Wong, R. S.; Bennick, A. The Primary Structure of a Salivary Calcium-Binding Proline-Rich Phosphoprotein (Protein C), a Possible Precursor of a Related Salivary Protein A. J. Biol. Chem. 1980, 255 (12), 5943–5948. https://doi.org/10.1016/s0021-9258(19)70721-2.
(240) Murray, N. J.; Williamson, M. P.; Lilley, T. H.; Haslam, E. Study of the Interaction between Salivary Proline‐rich Proteins and a Polyphenol by 1H‐NMR Spectroscopy. Eur. J. Biochem. 1994, 219 (3), 923–935. https://doi.org/10.1111/j.1432-1033.1994.tb18574.x.
(241) Hatano, T.; Yoshida, T.; Hemingway, R. W. Interaction of Flavanoids with Peptides and Proteins and Conformations of Dimeric Flavanoids in Solution. In Basic Life Sciences: Plant Polyphenols 2; Gross, G. G., Hemingway, R. W., Yoshida, T., Eds.; Kluwer Academic/Plenum Publishers: New York, NY, USA, 1999; Vol. 66, pp 509–526. https://doi.org/10.1007/978-1-4615-4139-4_28.
(242) Cala, O.; Pinaud, N.; Simon, C.; Fouquet, E.; Laguerre, M.; Dufourc, E. J.; Pianet, I. NMR and Molecular Modeling of Wine Tannins Binding to Saliva Proteins: Revisiting Astringency from Molecular and Colloidal Prospects. FASEB J. 2010, 24 (11), 4281–4290. https://doi.org/10.1096/fj.10-158741.
(243) He, H.; Huang, Y.; Zhang, Q.; Wang, J. R.; Mei, X. Zwitterionic Cocrystals of Flavonoids and Proline: Solid-State Characterization, Pharmaceutical Properties, and Pharmacokinetic Performance. Cryst. Growth Des. 2016, 16 (4), 2348–2356. https://doi.org/10.1021/acs.cgd.6b00142.
(244) Zondlo, N. J. Aromatic-Proline Interactions: Electronically Tunable CH/π Interactions. Acc. Chem. Res. 2013, 46 (4), 1039–1049. https://doi.org/10.1021/ar300087y.
(245) Pal, D.; Chakrabarti, P. Cis Peptide Bonds in Proteins: Residues Involved, Their Conformations, Interactions and Locations. J. Mol. Biol. 1999, 294 (1), 271–288. https://doi.org/10.1006/jmbi.1999.3217.
(246) Bhattacharyya, R.; Chakrabarti, P. Stereospecific Interactions of Proline Residues in Protein Structures and Complexes. J. Mol. Biol. 2003, 331 (4), 925–940. https://doi.org/10.1016/S0022-2836(03)00759-9.
(247) Iwasaki, W.; Miyatake, H.; Miki, K. Crystal Structure of the Small Form of Glucose-Inhibited Division Protein A from Thermus Thermophilus HB8. Proteins Struct. Funct. Genet. 2005, 61 (4), 1121–1126. https://doi.org/10.1002/prot.20667.
(248) Persikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. Amino Acid Propensities for the Collagen Triple-Helix. Biochemistry 2000, 39 (48), 14960–14967. https://doi.org/10.1021/bi001560d.
(249) Miclette Lamarche, R.; DeWolf, C. ω-Thiolation of Phenolic Surfactants Enables Controlled Conversion between Extended, Bolaform, and Multilayer Conformations. Langmuir 2020, 36 (11), 2847–2857. https://doi.org/10.1021/acs.langmuir.9b03670.
(250) Foresman, J. B.; Frisch, A. Exploring Chemistry with Electronic Structure Methods, 3rd ed.; Gaussian Inc.: Wallingford, CT, 2015.
(251) Schrödinger, E. An Undulatory Theory of the Mechanics of Atoms and Molecules. Phys. Rev. 1926, 28 (6), 1049–1070.
(252) Born, M.; Oppenheimer, R. Zur Quantentheorie Der Molekeln. Ann. Phys. 1927, 389 (20), 457–484. https://doi.org/10.1002/andp.19273892002.
(253) Hartree, D. R. The Wave Mechanics of an Atom with a Non-Coulomb Central Field, Part II: Some Results and Discussion. Math. Proc. Cambridge Philos. Soc. 1928, 24 (1), 111–132. https://doi.org/10.1017/S0305004100011920.
(254) Gaunt, J. A. A Theory of Hartree’s Atomic Fields. Math. Proc. Cambridge Philos. Soc. 1928, 24 (2), 328–342. https://doi.org/10.1017/S0305004100015851.
(255) Slater, J. C. The Self Consistent Field and the Structure of Atoms. Phys. Rev. 1928, 32 (3), 339–348. https://doi.org/10.1103/PhysRev.32.339.
(256) Slater, J. C. Note on Hartree’s Method. Phys. Rev. 1930, 35 (2), 210–211. https://doi.org/10.1103/PhysRev.35.210.2.
(257) Fock, V. Näherungsmethode Zur Lösung Des Quantenmechanischen Mehrkörperproblems. Zeitschrift für Phys. 1930, 61 (1–2), 126–148. https://doi.org/10.1007/BF01340294.
(258) Fock, V. “Selfconsistent Field” Mit Austausch Für Natrium. Zeitschrift für Phys. 1930, 61 (77), 795–805.
(259) Hartree, D. R.; Hartree, W. Self-Consistent Field, with Exchange, for Beryllium. Proc. R. Soc. London Ser. A - Math. Phys. Sci. 1935, 150 (869), 9–33. https://doi.org/10.1098/rspa.1935.0085.
(260) Lewars, E. G. Computational Chemistry, 3rd ed.; Springer International Publishing: Cham, Switzerland, 2016. https://doi.org/10.1007/978-90-481-3862-3.
(261) Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. 1934, 46 (7), 618–622. https://doi.org/10.1103/PhysRev.46.618.
(262) Head-Gordon, M.; Pople, J. A.; Frisch, M. J. MP2 Energy Evaluation by Direct Methods. Chem. Phys. Lett. 1988, 153 (6), 503–506. https://doi.org/10.1016/0009-2614(88)85250-3.
(263) Pople, J. A.; Binkley, J. S.; Seeger, R. Theoretical Models Incorporating Electron Correlation. Int. J. Quantum Chem. 1976, 10 (10 S), 1–19. https://doi.org/10.1002/qua.560100802.
(264) Krishnan, R.; Pople, J. A. Approximate Fourth‐order Perturbation Theory of the Electron Correlation Energy. Int. J. Quantum Chem. 1978, 14 (1), 91–100. https://doi.org/10.1002/qua.560140109.
(265) Raghavachari, K.; Pople, J. A.; Replogle, E. S.; Head-Gordon, M. Fifth-Order Møller-Plesset Perturbation Theory: Comparison of Existing Correlation Methods and Implementation of New Methods Correct to Fifth Order. J. Phys. Chem. 1990, 94 (14), 5579–5586. https://doi.org/10.1021/j100377a033.
(266) Čížek, J. On the Correlation Problem in Atomic and Molecular Systems. Calculation of Wavefunction Components in Ursell-Type Expansion Using Quantum-Field Theoretical Methods. J. Chem. Phys. 1966, 45 (11), 4256–4266. https://doi.org/10.1063/1.1727484.
(267) Paldus, J.; Čížek, J.; Shavitt, I. Correlation Problems in Atomic and Molecular Systems. IV. Extended Coupled-Pair Many-Electron Theory and Its Application to the BH3 Molecule. Phys. Rev. A 1972, 5 (1), 50–67. https://doi.org/10.1103/PhysRevA.5.50.
(268) Bartlett, R. J. The Coupled-Cluster Revolution. Mol. Phys. 2010, 108 (21–23), 2905–2920. https://doi.org/10.1080/00268976.2010.531773.
(269) Pople, J. A.; Seeger, R.; Krishnan, R. Variational Configuration Interaction Methods and Comparison with Perturbation Theory. Int. J. Quantum Chem. 1977, 12 (11 S), 149–163. https://doi.org/10.1002/qua.560120820.
(270) Krishnan, R.; Schlegel, H. B.; Pople, J. A. Derivative Studies in Configuration-Interaction Theory. J. Chem. Phys. 1979, 72 (8), 4654–4655. https://doi.org/10.1063/1.439708.
(271) Raghavachari, K.; Pople, J. A. Calculation of One‐electron Properties Using Limited Configuration Interaction Techniques. Int. J. Quantum Chem. 1981, 20 (5), 1067–1071. https://doi.org/10.1002/qua.560200503.
(272) Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas. Phys. Rev. 1964, 136 (3B), B864–B871. https://doi.org/10.1103/PhysRev.136.B864.
(273) Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects. Phys. Rev. 1965, 140 (4A), A1133–A1138.
(274) Vikramaditya, T.; Lin, S. Limitations of Global Hybrids in Predicting the Geometries and Torsional Energy Barriers of Dimeric Systems and the Role of Hartree Fock and DFT Exchange. J. Comput. Chem. 2019, 40 (32), 2810–2818. https://doi.org/10.1002/jcc.26056.
(275) Perdew, J. P.; Schmidt, K. Jacob’s Ladder of Density Functional Approximations for the Exchange-Correlation Energy. In AIP Conference Proceedings: Density Functional Theory and its Application to Materials; Van Doren, V., Van Alsenoy, C., Geerlings, P., Eds.; American Institute of Physics: Antwerp, Belgium, 2001; Vol. 577, pp 1–20. https://doi.org/10.1063/1.1390175.
(276) Perdew, J. P.; Ruzsinszky, A.; Tao, J.; Staroverov, V. N.; Scuseria, G. E.; Csonka, G. I. Prescription for the Design and Selection of Density Functional Approximations: More Constraint Satisfaction with Fewer Fits. J. Chem. Phys. 2005, 123 (6), 062201. https://doi.org/10.1063/1.1904565.
(277) Kristyán, S.; Pulay, P. Can (Semi)Local Density Functional Theory Account for the London Dispersion Forces? Chem. Phys. Lett. 1994, 229 (3), 175–180. https://doi.org/10.1016/0009-2614(94)01027-7.
(278) Toulouse, J.; Colonna, F.; Savin, A. Long-Range - Short-Range Separation of the Electron-Electron Interaction in Density-Functional Theory. Phys. Rev. A - At. Mol. Opt. Phys. 2004, 70 (6), 1–16. https://doi.org/10.1103/PhysRevA.70.062505.
(279) Grimme, S. Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction. J. Comput. Chem. 2006, 27 (15), 1787–1799. https://doi.org/10.1002/jcc.
(280) Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the Damping Function in Dispersion Corrected Density Functional Theory. J. Comput. Chem. 2011, 32 (7), 1456–1465. https://doi.org/10.1002/jcc.21759.
(281) Grimme, S. Density Functional Theory with London Dispersion Corrections. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1 (2), 211–228. https://doi.org/10.1002/wcms.30.
(282) Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. General Performance of Density Functionals. J. Phys. Chem. A 2007, 111 (42), 10439–10452. https://doi.org/10.1021/jp0734474.
(283) Chai, J.-D.; Head-Gordon, M. Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections. Phys. Chem. Chem. Phys. 2008, 10 (44), 6615–6620. https://doi.org/10.1039/b810189b.
(284) Mohan, N.; Vijayalakshmi, K. P.; Koga, N.; Suresh, C. H. Comparison of Aromatic NH...Pi, OH...Pi, and CH...Pi Interactions of Alanine Using MP2, CCSD, and DFT Methods. J. Comput. Chem. 2010, 31, 2874–2882. https://doi.org/10.1002/jcc.
(285) Mardirossian, N.; Head-Gordon, M. Thirty Years of Density Functional Theory in Computational Chemistry: An Overview and Extensive Assessment of 200 Density Functionals. Mol. Phys. 2017, 115 (19), 2315–2372. https://doi.org/10.1080/00268976.2017.1333644.
(286) Mardirossian, N.; Head-Gordon, M. ω B97M-V: A Combinatorially Optimized, Range-Separated Hybrid, Meta-GGA Density Functional with VV10 Nonlocal Correlation. J. Chem. Phys. 2016, 144 (21), 214110. https://doi.org/10.1063/1.4952647.
(287) 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 Function. Theor. Chem. Acc. 2008, 120 (1–3), 215–241. https://doi.org/10.1007/s00214-007-0310-x.
(288) Becke, A. D. A New Mixing of Hartree-Fock and Local Density-Functional Theories. J. Chem. Phys. 1993, 98 (2), 1372–1377. https://doi.org/10.1063/1.464304.
(289) Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B 1988, 37 (2), 785–789. https://doi.org/10.1016/0009-2614(89)85118-8.
(290) 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 (45), 11623–11627. https://doi.org/10.1021/j100096a001.
(291) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77 (7), 3865–3868. https://doi.org/10.1103/PhysRevLett.77.3865.
(292) Perdew, J. P.; Burke, K.; Ernzerhof, M. [ERRATA] Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1997, 78 (7), 1396.
(293) Ernzerhof, M.; Perdew, J. P. Generalized Gradient Approximation to the Angle- and System-Averaged Exchange Hole. J. Chem. Phys. 1998, 109 (9), 3313–3320. https://doi.org/10.1063/1.476928.
(294) Adamo, C.; Barone, V. Toward Reliable Density Functional Methods without Adjustable Parameters: The PBE0 Model. J. Chem. Phys. 1999, 110 (13), 6158–6170. https://doi.org/10.1063/1.478522.
(295) Chai, J.-D.; Head-Gordon, M. Systematic Optimization of Long-Range Corrected Hybrid Density Functionals. J. Chem. Phys. 2008, 128 (8). https://doi.org/10.1063/1.2834918.
(296) Becke, A. D. Density-Functional Thermochemistry. V. Systematic Optimization of Exchange-Correlation Functionals. J. Chem. Phys. 1997, 107 (20), 8554–8560. https://doi.org/10.1063/1.475007.
(297) Tao, J.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the Density Functional Ladder: Nonempirical Meta–Generalized Gradient Approximation Designed for Molecules and Solids. Phys. Rev. Lett. 2003, 91 (14), 146401. https://doi.org/10.1103/PhysRevLett.91.146401.
(298) Schmider, H. L.; Becke, A. D. Optimized Density Functionals from the Extended G2 Test Set. J. Chem. Phys. 1998, 108 (23), 9624–9631. https://doi.org/10.1063/1.476438.
(299) Vosko, S. H.; Wilk, L.; Nusair, M. Accurate Spin-Dependent Electron Liquid Correlation Energies for Local Spin Density Calculations: A Critical Analysis. Can. J. Phys. 1980, 58 (8), 1200–1211. https://doi.org/10.1139/p80-159.
(300) Pople, J. A.; Beveridge, D. L. Approximate Molecular Orbital Theory; McGraw-Hill Book Company: New York, NY, USA, 1970.
(301) Grimme, S.; Bannwarth, C.; Shushkov, P. A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All Spd-Block Elements (Z = 1-86). J. Chem. Theory Comput. 2017, 13 (5), 1989–2009. https://doi.org/10.1021/acs.jctc.7b00118.
(302) Elstner, M.; Seifert, G. Density Functional Tight Binding. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 2014, 372 (2011), 20120483. https://doi.org/10.1098/rsta.2012.0483.
(303) Bannwarth, C.; Caldeweyher, E.; Ehlert, S.; Hansen, A.; Pracht, P.; Seibert, J.; Spicher, S.; Grimme, S. Extended Tight-Binding Quantum Chemistry Methods. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2021, 11 (2), 1–49. https://doi.org/10.1002/wcms.1493.
(304) Pollice, R.; Fleckenstein, F.; Shenderovich, I.; Chen, P. Compensation of London Dispersion in the Gas Phase and in Aprotic Solvents. Angew. Chemie - Int. Ed. 2019, 58 (40), 14281–14288. https://doi.org/10.1002/anie.201905436.
(305) Moshniaha, L.; Żyła-Karwowska, M.; Chmielewski, P. J.; Lis, T.; Cybińska, J.; Gońka, E.; Oschwald, J.; Drewello, T.; Rivero, S. M.; Casado, J.; Stȩpień, M. Aromatic Nanosandwich Obtained by σ-Dimerization of a Nanographenoid π-Radical. J. Am. Chem. Soc. 2020, 142 (7), 3626–3635. https://doi.org/10.1021/jacs.9b13942.
(306) Martínez, M. A.; Doncel-Giménez, A.; Cerdá, J.; Calbo, J.; Rodríguez, R.; Aragó, J.; Crassous, J.; Ortí, E.; Sánchez, L. Distance Matters: Biasing Mechanism, Transfer of Asymmetry, and Stereomutation in N-Annulated Perylene Bisimide Supramolecular Polymers. J. Am. Chem. Soc. 2021, 143 (33), 13281–13291. https://doi.org/10.1021/jacs.1c06125.
(307) Zhang, Z.; Kummeth, A. L.; Yang, J. Y.; Alexandrova, A. N. Inverse Molecular Design of Alkoxides and Phenoxides for Aqueous Direct Air Capture of CO2. Proc. Natl. Acad. Sci. U. S. A. 2022, 119 (25), 1–11. https://doi.org/10.1073/pnas.2123496119.
(308) Nagy, B.; Jensen, F. Basis Sets in Quantum Chemistry. In Reviews in Computational Chemistry; Parrill, A. L., Lipkowitz, K. B., Eds.; John Wiley and Sons: Hoboken, NJ, USA, 2017; Vol. 30, pp 93–149. https://doi.org/10.1002/9781119148739.
(309) Tsuzuki, S.; Uchimaru, T.; Mikami, M.; Tanabe, K. Basis Set Effects on the Calculated Bonding Energies of Neutral Benzene Dimers: Importance of Diffuse Polarization Functions. Chem. Phys. Lett. 1996, 252 (3–4), 206–210. https://doi.org/10.1016/0009-2614(96)00173-X.
(310) Waller, M. P.; Robertazzi, A.; Platts, J. A.; Hibbs, D. E.; Williams, P. A. Hybrid Density Functional Theory for Pi-Stacking Interactions: Application to Benzenes, Pyridines, and DNA Bases. J. Comput. Chem. 2006, 27, 491–504. https://doi.org/10.1002/jcc.
(311) Vidal, Á. V.; De Vicente Poutás, L. C.; Faza, O. N.; López, C. S. On the Use of Popular Basis Sets: Impact of the Intramolecular Basis Set Superposition Error. Molecules 2019, 24 (20), 1–11. https://doi.org/10.3390/molecules24203810.
(312) Boys, S. F.; Bernardi, F. The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. Some Procedures with Reduced Errors. Mol. Phys. 1970, 19 (4), 553–566. https://doi.org/10.1080/00268977000101561.
(313) Simon, S.; Duran, M.; Dannenberg, J. J. How Does Basis Set Superposition Error Change the Potential Surfaces for Hydrogen-Bonded Dimers? J. Chem. Phys. 1996, 105 (24), 11024–11031. https://doi.org/10.1063/1.472902.
(314) Vijay, D.; Sakurai, H.; Sastry, G. N. The Impact of Basis Set Superposition Error on the Structure of π...π Dimers. Int. J. Quantum Chem. 2011, 111, 1893–1901.
(315) Schlegel, H. B. Exploring Potential Energy Surfaces for Chemical Reactions: An Overview of Some Practical Methods. J. Comput. Chem. 2003, 24 (12), 1514–1527. https://doi.org/10.1002/jcc.10231.
(316) Dewyer, A. L.; Argüelles, A. J.; Zimmerman, P. M. Methods for Exploring Reaction Space in Molecular Systems. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2018, 8 (2), e1354. https://doi.org/10.1002/wcms.1354.
(317) Metneja, B. S. An Algorithm To Explore Molecular Potential Energy Surfaces. M. Sc. thesis, Concordia University, Montreal, QC, Canada, 2021.
(318) Bachrach, S. M. Computational Organic Chemistry, 2nd ed.; John Wiley and Sons: Hoboken, NJ, USA, 2014.
(319) Cramer, C. J.; Truhlar, D. G. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem. Rev. 1999, 99 (8), 2161–2200. https://doi.org/10.1021/cr960149m.
(320) Cramer, C. J.; Truhlar, D. G. Continuum Solvation Models. In Solvent Effects and Chemical Reactivity; Tapia, O., Bertrán, J., Eds.; Kluwer Academic Publishers: Dordrecht, Netherlands, 1996; pp 1–80. https://doi.org/10.1201/9781420065442.ch26.
(321) Born, M. Volumen Und Hydratationswärme Der Ionen. Zeitschrift für Phys. 1920, 1, 45–48. https://doi.org/10.1007/BF01881023.
(322) Onsager, L. Electric Moments of Molecules in Liquids. J. Am. Chem. Soc. 1936, 58 (8), 1486–1493. https://doi.org/10.1021/ja01299a050.
(323) Barker, J. A.; Watts, R. O. Monte Carlo Studies of the Dielectric Properties of Water-like Models. Mol. Phys. 1973, 26 (3), 789–792. https://doi.org/10.1080/00268977300102101.
(324) Watts, R. O. Monte Carlo Studies of Liquid Water. Mol. Phys. 1974, 28 (4), 1069–1083. https://doi.org/10.1080/00268977400102381.
(325) Westheimer, F. H.; Kirkwood, J. G. The Electrostatic Influence of Substituents on the Dissociation Constants of Organic Acids. II. J. Chem. Phys. 1938, 6 (9), 513–517. https://doi.org/10.1063/1.1750303.
(326) Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112 (16), 6127–6129. https://doi.org/10.1021/ja00172a038.
(327) Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii. J. Phys. Chem. A 1997, 101 (16), 3005–3014. https://doi.org/10.1021/jp961992r.
(328) Reddy, M. R.; Erion, M. D.; Agarwal, A.; Viswanadhan, V. N.; McDonald, D. Q.; Still, W. C. Solvation Free Energies Calculated Using the GB/SA Model: Sensitivity of Results on Charge Sets, Protocols, and Force Fields. J. Comput. Chem. 1998, 19 (7), 769–780. https://doi.org/10.1002/(SICI)1096-987X(199805)19:7<769::AID-JCC7>3.0.CO;2-O.
(329) Onufriev, A. V.; Case, D. A. Generalized Born Implicit Solvent Models for Biomolecules. Annu. Rev. Biophys. 2019, 48, 275–296. https://doi.org/10.1146/annurev-biophys-052118-115325.
(330) Anslyn, E. V.; Dougherty, D. A. Modern Physical Organic Chemistry; University Science Books: Dulles, VA, USA, 2006.
(331) Löwdin, P.-O. Quantum Theory of Many-Particle Systems. I. Physical Interpretations by Means of Density Matrices, Natural Spin-Orbitals, and Convergence Problems in the Method of Configurational Interaction. Phys. Rev. 1955, 97 (6), 1474–1489. https://doi.org/10.1103/PhysRev.97.1474.
(332) Reed, A. E.; Curtiss, L. A.; Weinhold, F. Intermolecular Interactions from a Natural Bond Orbital, Donor—Acceptor Viewpoint. Chem. Rev. 1988, 88, 899–926. https://doi.org/10.1021/cr00088a005.
(333) Weinhold, F.; Landis, C. R. Natural Bond Orbitals and Extensions of Localized Bonding Concepts. Chem. Educ. Res. Pract. 2001, 2 (2), 91–104. https://doi.org/10.1039/b1rp90011k.
(334) Foster, J. P.; Weinhold, F. Natural Hybrid Orbitals. J. Am. Chem. Soc. 1980, 102, 7211–7218.
(335) Reed, A. E.; Weinhold, F. Natural Bond Orbital Analysis of Near-Hartree-Fock Water Dimer. J. Chem. Phys. 1983, 78 (6), 4066–4073. https://doi.org/10.1063/1.445134.
(336) Reed, A. E.; Weinstock, R. B.; Weinhold, F. Natural Population Analysis. J. Chem. Phys. 1985, 83 (2), 735–746. https://doi.org/10.1063/1.449486.
(337) Reed, A. E.; Weinhold, F. Natural Localized Molecular Orbitals. J. Chem. Phys. 1985, 83 (4), 1736–1740. https://doi.org/10.1063/1.449360.
(338) Zhang, L.; Peslherbe, G. H.; Muchall, H. M. A General Measure of Conjugation in Biphenyls and Their Radical Cations. Can. J. Chem. 2010, 88 (11), 1175–1185. https://doi.org/10.1139/V10-126.
(339) Matta, C. F.; Boyd, R. J. An Introduction to the Quantum Theory of Atoms in Molecules. In The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design; Matta, C. F., Boyd, R. J., Eds.; Wiley-VCH Verlag GmbH & Co KGgA: Weinheim, Germany, 2007; pp 1–34. https://doi.org/10.1002/9783527610709.ch1.
(340) Leboeuf, M.; Köster, A. M.; Jug, K.; Salahub, D. R. Topological Analysis of the Molecular Electrostatic Potential. J. Chem. Phys. 1999, 111 (11), 4893–4905. https://doi.org/10.1063/1.479749.
(341) Balanarayan, P.; Gadre, S. R. Topography of Molecular Scalar Fields. I. Algorithm and Poincaré-Hopf Relation. J. Chem. Phys. 2003, 119 (10), 5037–5043. https://doi.org/10.1063/1.1597652.
(342) Bader, R. F. W. Bond Paths Are Not Chemical Bonds. J. Phys. Chem. A 2009, 113 (38), 10391–10396. https://doi.org/10.1021/jp906341r.
(343) Koch, U.; Popelier, P. L. A. Characterization of C-H-O Hydrogen Bonds on the Basis of the Charge Density. J. Phys. Chem. 1995, 99, 9747–9754.
(344) Mallinson, P. R.; Smith, G. T.; Wilson, C. C.; Grech, E.; Wozniak, K. From Weak Interactions to Covalent Bonds: A Continuum in the Complexes of 1,8-Bis(Dimethylamino)Naphthalene. J. Am. Chem. Soc. 2003, 125 (14), 4259–4270. https://doi.org/10.1021/ja029389b.
(345) Parthasarathi, R.; Subramanian, V.; Sathyamurthy, N. Hydrogen Bonding without Borders: An Atoms-in-Molecules Perspective. J. Phys. Chem. A 2006, 110 (10), 3349–3351. https://doi.org/10.1021/jp060571z.
(346) Bankiewicz, B.; Matczak, P.; Palusiak, M. Electron Density Characteristics in Bond Critical Point (QTAIM) versus Interaction Energy Components (SAPT): The Case of Charge-Assisted Hydrogen Bonding. J. Phys. Chem. A 2012, 116 (1), 452–459. https://doi.org/10.1021/jp210940b.
(347) Wick, C. R.; Clark, T. On Bond-Critical Points in QTAIM and Weak Interactions. J. Mol. Model. 2018, 24 (6), 1–9. https://doi.org/10.1007/s00894-018-3684-x.
(348) Hansch, C.; Leo, A.; Taft, R. W. A Survey of Hammett Substituent Constants and Resonance and Field Parameters. Chem. Rev. 1991, 91 (2), 165–195. https://doi.org/10.1021/cr00002a004.
(349) Wheeler, S. E.; Houk, K. N. Substituent Effects in the Benzene Dimer Are Due to Direct Interactions of the Substituents with the Unsubstituted Benzene. J. Am. Chem. Soc. 2008, 130 (33), 10854–10855. https://doi.org/10.1021/ja802849j.
(350) Gillier-Pandraud, H. Structure Cristalline Du Phénol. Bull. Soc. Chim. Fr. 1967, 6, 1988–1995.
(351) Zavodnik, V. E.; Bel’skii, V. K.; Zorkii, P. M. Crystal Structure of Phenol at 123 K. J. Struct. Chem. 1988, 28, 793–795.
(352) Steiner, T. The Hydrogen Bond in the Solid State. Angew. Chemie - Int. Ed. 2002, 41, 48–76.
(353) Akella, J.; Kennedy, G. C. Phase Diagram of Benzene to 35 Kbar. J. Chem. Phys. 1971, 55 (2), 793–796. https://doi.org/10.1063/1.1676145.
(354) Thiéry, M. M.; Léger, J. M. High Pressure Solid Phases of Benzene. I. Raman and x-Ray Studies of C 6H6 at 294 K up to 25 GPa. J. Chem. Phys. 1988, 89 (7), 4255–4271. https://doi.org/10.1063/1.454809.
(355) Cansell, F.; Fabre, D.; Petitet, J. P. Phase Transitions and Chemical Transformations of Benzene up to 550 °C and 30 GPa. J. Chem. Phys. 1993, 99 (10), 7300–7304. https://doi.org/10.1063/1.465711.
(356) Ciabini, L.; Santoro, M.; Bini, R.; Schettino, V. High Pressure Crystal Phases of Benzene Probed by Infrared Spectroscopy. J. Chem. Phys. 2001, 115 (8), 3742–3749. https://doi.org/10.1063/1.1388543.
(357) Raiteri, P.; Martoňák, R.; Parrinello, M. Exploring Polymorphism: The Case of Benzene. Angew. Chemie - Int. Ed. 2005, 44 (24), 3769–3773. https://doi.org/10.1002/anie.200462760.
(358) Nayak, S. K.; Sathishkumar, R.; Row, T. N. G. Directing Role of Functional Groups in Selective Generation of C-H⋯π Interactions: In Situ Cryo-Crystallographic Studies on Benzyl Derivatives. CrystEngComm 2010, 12 (10), 3112–3118. https://doi.org/10.1039/c001190h.
(359) Andre, D.; Fourme, R.; Bruneaux-Poulle, J.; Bosio, L. Crystal Structure of the Metastable β-Phase of Toluene. J. Mol. Struct. 1982, 81 (3–4), 253–259. https://doi.org/10.1016/0022-2860(82)85338-6.
(360) 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, J. A., Jr.; 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, J. M.; 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, Revision B.01. Gaussian, Inc., Wallingford, CT, 2009.
(361) Biegler-Konig, F.; Schonbohm, J.; Derdau, R.; Bayles, D.; Bader, R. F. W. AIM2000. Buro Streibel Biegler-Konig Innovative Software: Bielefeld, Germany 1998.
(362) Keith, T. A. AIMAll. TK Gristmill Software: Overland Park, KS, USA 2019. aim.tkgristmill.com.
(363) Cieplak, P.; Kollman, P. A. Calculation of the Free Energy of Association of Nucleic Acid Bases in Vacuo and Water Solution. J. Am. Chem. Soc. 1988, 110 (12), 3734–3739. https://doi.org/10.1021/ja00220a003.
(364) Kabelac, M.; Ryjacek, F.; Hobza, P. Already Two Water Molecules Change Planar H-Bonded Structures of the Adenine···thymine Base Pair to the Stacked Ones: A Molecular Dynamics Simulations Study. Phys. Chem. Chem. Phys. 2000, 2 (21), 4906–4909. https://doi.org/10.1039/b007167f.
(365) Lo, R.; Manna, D.; Vacek, J.; Bouř, P.; Wu, T.; Osifová, Z.; Socha, O.; Dračínský, M.; Hobza, P. Striking Impact of Solvent Polarity on the Strength of Hydrogen-Bonded Complexes: A Nexus Between Theory and Experiment. Angew. Chemie - Int. Ed. 2025, 64 (12), e202422594. https://doi.org/10.1002/anie.202422594.
(366) Rajasingam, A.; Schmidt, R.; Woo, S.; DeWolf, C. E.; Forgione, P. Efficient Preparation of Novel Phenolic Surfactants for Self-Assembled Monolayers. Synth. Commun. 2014, 44 (8), 1066–1075. https://doi.org/10.1080/00397911.2013.844259.
(367) Azmi, A. A.; Ebralidze, I. I.; Dickson, S. E.; Horton, J. H. Characterization of Hydroxyphenol-Terminated Alkanethiol Self-Assembled Monolayers: Interactions with Phosphates by Chemical Force Spectrometry. J. Colloid Interface Sci. 2013, 393 (1), 352–360. https://doi.org/10.1016/j.jcis.2012.10.026.
(368) Jung, H. H.; Won, Y. Do; Shin, S.; Kim, K. Molecular Dynamics Simulation of Benzenethiolate and Benzyl Mercaptide on Au(111). Langmuir 1999, 15 (4), 1147–1154. https://doi.org/10.1021/la9808667.
(369) Dirama, T. E.; Johnson, J. A. Conformation and Dynamics of Arylthiol Self-Assembled Monolayers on Au(111). Langmuir 2007, 23 (24), 12208–12216. https://doi.org/10.1021/la7015963.
(370) Salzner, U.; Aydin, A. Improved Prediction of Properties of π-Conjugated Oligomers with Range-Separated Hybrid Density Functionals. J. Chem. Theory Comput. 2011, 7 (8), 2568–2583. https://doi.org/10.1021/ct2003447.
(371) Burns, L. A.; Vázquez-Mayagoitia, Á.; Sumpter, B. G.; Sherrill, C. D. Density-Functional Approaches to Noncovalent Interactions: A Comparison of Dispersion Corrections (DFT-D), Exchange-Hole Dipole Moment (XDM) Theory, and Specialized Functionals. J. Chem. Phys. 2011, 134 (8), 084107. https://doi.org/10.1063/1.3545971.
(372) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; Zakrzewski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A. . J.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. Gaussian 16, Revision C.01. Gaussian, Inc., Wallingford, CT, 2016.
(373) Schmidt, J. R.; Polik, W. F. WebMO Pro, Version 21.0.010p. WebMO LLC: Holland, MI, USA August 2021.
(374) Gaba, J. H.; DeWolf, C. E.; Muchall, H. M. Noncovalent Interactions Governing Self-Assembly of Oligomeric Phenolic Surfactant Film Models. Manuscript in revision, J. Phys. Org. Chem. 2025.
(375) Sathyapriya, S.; Bharani, G.; Nangalingam, M.; Jayanthi, M.; Kanagavalli, U. Potential of Salivary Protein as a Biomarker in Prognosis of Diabetes Mellitus. J. Pharm. Res. 2011, 4 (7), 2228–2229.
(376) Grimme, S.; Bannwarth, C.; Caldeweyher, E.; Pisarek, J.; Hansen, A. A General Intermolecular Force Field Based on Tight-Binding Quantum Chemical Calculations. J. Chem. Phys. 2017, 147 (16). https://doi.org/10.1063/1.4991798.
(377) Vuckovic, S.; Burke, K. Quantifying and Understanding Errors in Molecular Geometries. J. Phys. Chem. Lett. 2020, 11 (22), 9957–9964. https://doi.org/10.1021/acs.jpclett.0c03034.
(378) Gaba, J. H.; DeWolf, C. E.; Muchall, H. M. Electronic Effects on the Self-Assembly of Monolayers from Surfactants Possessing Aromatic Headgroups. Manuscript in revision, Langmuir 2025.
(379) Schmitz, S.; Seibert, J.; Ostermeir, K.; Hansen, A.; Göller, A. H.; Grimme, S. Quantum Chemical Calculation of Molecular and Periodic Peptide and Protein Structures. J. Phys. Chem. B 2020, 124 (18), 3636–3646. https://doi.org/10.1021/acs.jpcb.0c00549.
(380) Hollóczki, O. Evidence for Protein Misfolding in the Presence of Nanoplastics. Int. J. Quantum Chem. 2021, 121 (3), 1–15. https://doi.org/10.1002/qua.26372.
(381) Ding, Y.; Krogh-Jespersen, K. The Glycine Zwitterion Does Not Exist in the Gas Phase: Results from a Detailed Ab Initio Electronic Structure Study. Chem. Phys. Lett. 1992, 199 (3–4), 261–266. https://doi.org/10.1016/0009-2614(92)80116-S.
(382) Jensen, J. H.; Gordon, M. S. On the Number of Water Molecules Necessary To Stabilize the Glycine Zwitterion. J. Am. Chem. Soc. 1995, 117 (31), 8159–8170. https://doi.org/10.1021/ja00136a013.
(383) Aikens, C. M.; Gordon, M. S. Incremental Solvation of Nonionized and Zwitterionic Glycine. J. Am. Chem. Soc. 2006, 128 (39), 12835–12850. https://doi.org/10.1021/ja062842p.
(384) Tortonda, F. R.; Pascual-Ahuir, J. L.; Silla, E.; Tuñón, I. Why Is Glycine a Zwitterion in Aqueous Solution? A Theoretical Study of Solvent Stabilising Factors. Chem. Phys. Lett. 1996, 260 (1–2), 21–26. https://doi.org/10.1016/0009-2614(96)00839-1.
(385) Boča, R.; Štofko, J.; Imrich, R. Effect of Solvation on Glycine Molecules: A Theoretical Study. ACS Omega 2023, 8 (31), 28577–28582. https://doi.org/10.1021/acsomega.3c02972.
(386) Szabo, Z. Description of polyproline helices. https://web.archive.org/web/20191019180315/http://www.cryst.bbk.ac.uk/pps97/assignments/projects/szabo/pphelix.htm (accessed 2019-10-03).
(387) McLain, S. E.; Soper, A. K.; Terry, A. E.; Watts, A. Structure and Hydration of L-Proline in Aqueous Solutions. J. Phys. Chem. B 2007, 111 (17), 4568–4580. https://doi.org/10.1021/jp068340f.
(388) Pitzer, J.; Steiner, K.; Schmid, C.; Schein, V. K.; Prause, C.; Kniely, C.; Reif, M.; Geier, M.; Pietrich, E.; Reiter, T.; Selig, P.; Stückler, C.; Pöchlauer, P.; Steinkellner, G.; Gruber, K.; Schwab, H.; Glieder, A.; Kroutil, W. Racemization-Free and Scalable Amidation of l-Proline in Organic Media Using Ammonia and a Biocatalyst Only. Green Chem. 2022, 24 (13), 5171–5180. https://doi.org/10.1039/d2gc00783e.
(389) Zhang, A.; Guo, Y. High Stability of the Polyproline II Helix in Polypeptide Bottlebrushes. Chemistry - A European Journal. 2008, pp 8939–8946. https://doi.org/10.1002/chem.200801191.
(390) Krome, A. J. A Computational Investigation of the Intermolecular Interactions Driving the Dimerization of Stacked Para-Substituted Phenols. B. Sc. Honours thesis, Concordia University, Montreal, QC, Canada, 2024.
(391) Owino, J.; Yu, Z.; Gaba, J. H.; DeWolf, C. E.; Muchall, H. M. Toward Patterning of Phenolic Surfactant Monolayers: A Computational Study. Presented at the 108th Canadian Chemistry Conference and Exhibition, Ottawa, ON, Canada, June 15-19, 2025; abstract 1874.
(392) Roothaan, C. C. J. New Developments in Molecular Orbital Theory. Rev. Mod. Phys. 1951, 23 (2), 69–89.
(393) Hall, G. G. The Molecular Orbital Theory of Chemical Valency. VIII. A Method of Calculating Ionization Potentials. Proc. R. Soc. London. Ser. A. Math. Phys. Sci. 1951, 205 (1083), 541–552. https://doi.org/10.1098/rspa.1952.0113.
(394) Brémond, É.; Tognetti, V.; Chermette, H.; Sancho-García, J. C.; Joubert, L.; Adamo, C. Electronic Energy and Local Property Errors at QTAIM Critical Points While Climbing Perdew’s Ladder of Density-Functional Approximations. J. Chem. Theory Comput. 2022, 18 (1), 293–308. https://doi.org/10.1021/acs.jctc.1c00981.
(395) Su, H.; Wang, H.; Wang, H.; Lu, Y.; Zhu, Z. Description of Noncovalent Interactions Involving π-System with High Precision: An Assessment of RPA, MP2, and DFT-D Methods. J. Comput. Chem. 2019, 40 (17), 1643–1651. https://doi.org/10.1002/jcc.25817.
(396) Marek, P. H.; Szatylowicz, H.; Krygowski, T. M. Stacking of Nucleic Acid Bases: Optimization of the Computational Approach—the Case of Adenine Dimers. Struct. Chem. 2019, 30 (1), 351–359. https://doi.org/10.1007/s11224-018-1253-7.
(397) Popelier, P. L. A. Atoms in Molecules: An Introduction; Pearson Education: Harlow, Essex, England, 2000.