Chemistry Projects

Studies of Halogen Bonding and Electron-Transfer in Halogen Bonded Systems

Figure 1 r1The importance of non-covalent interactions (e.g., van der Waals forces, hydrogen bonding) in chemistry and biochemistry is well established and spans such fundamental and diverse areas as protein–ligand interactions and drug discovery,(1-7) molecular recognition and self-assembly,(8-19) crystal engineering,(20-24) chemical sensing,(10, 25) electron transfer,(26-28) and organic synthesis.(29-31)  Increasingly, non-covalent interactions involving halogen atoms (X; X= F, Cl, Br, I) have been recognized to play a key role in many of these areas, stimulating much recent work in the nature of halogen bonding. By analogy with hydrogen bonding, halogen bonds involve the interaction of a polarizable halogen atom (R–X), acting as an electron acceptor, with an electron donor.  The strength of halogen bonds ranges from ~ 2 kJ/mol to ~ 160 kJ/mol,(12, 32, 33) rivaling or exceeding that of hydrogen bonds.  Recent studies of biological systems using a combination of crystallography and theory found that organic halogen atoms are widely involved in protein–ligand interactions.(1, 4, 6, 7)  Just as our ever-evolving understanding of the hydrogen bond has been aided to a great degree by the study of model systems, the study of halogen bonding also requires fundamental probes of interactions in prototypical systems. In particular, the need exists to systematically correlate properties of the donor/acceptor with structural characteristics of halogen bonding.  This need is being addressed in our group by probing the structure, properties, reactivity and electron transfer dynamics of prototypical halogen bonded systems. Our experiments use both gas-phase methods and matrix isolation techniques at 4 K to interrogate these systems. In recent work, we have examined photoinduced electron transfer in model donor-acceptor halogen bonded complexes, and explored the role of halogen bonding in competition with π-stacking and C-H/π interactions in model haloaromatic clusters using resonantly enhanced multiphoton ionization methods in concert with high level ab initio calculations.

Energy and Electron Transfer in π-stacked Molecular AssemFigure 1 JACS comm newblies

In collaboration with the group of Dr. Rajendra Rathore, we are exploring mechanisms of energy and electron transport in π-stacked molecular assemblies.  We use a variety of methods including two-color resonant ionization and laser induced fluorescence to probe these processes, motivated by potential applications in photovoltaics and molecular electronics.  In our initial studies, we have found, using a novel covalently linked fluorene based biochromophore, that the geometrical requirements for exciton vs hole stabilization are different, with the former more restrictive.  This work was recently published in the Journal of Physical Chemistry Letters.

Reaction Paths at High Energies: Isomerization, Roaming, and Proton-Coupled Electron Transfer

jp-2013-03114s_0009Recent detailed experimental measurements have shed light on new reaction pathways that are testing traditional theoretical approaches to chemical kinetics and reaction dynamics (e.g., transition state theory).  At the forefront of this charge is the “roaming” mechanism that was first evidenced in the photochemistry of formaldehyde, H2CO.  Roaming represents a pathway to molecular (H2 + CO) products, where the initially formed radical pair (here HCO + H) does not completely separate, and the H atom undergoes large amplitude motion in the van der Waals region of the potential, eventually returning to abstract a H atom and form H2.   The prescence of the roaming mechanism alters the product yield in the reaction, and many experimental and theoretical studies over the past 10 years have shown that roaming is an important pathway in many systems.  Our entry into this field began with studies of iso-CF2X2 (X=Br,I), which are weakly bound isomers of atmospherically important halons that are photochemical products in condensed phase environments, and can be stabilized and studied at low temperature .  Our characterization of iso-CF2Br2 revealed that isomerization represents a route to molecular products that can explain the yield of molecular products observed in previous gas-phase experiments, which had been attributed to roaming.  Working with researchers at UW-Madison, we examined the condensed phase isomerization of a related system, CH2ClI, in real time using ultrafast (femtosecond or 10-15 second) laser spectroscopy.  We found that, following photolysis of the parent compound, the isomer was formed within 2 ps (1 ps = 10-12 sec) and vibrationally cooled into its well with a time constant of ~ 50 ps, largely invariant to environment (solution vs. cryogenic matrix). In extending these studies to larger systems, such as the dihaloethanes, we find that the isomer is not trapped in steady state experiments, rather the dihalogen or hydrogen halide elimination products are observed.  Calculations have identified a transition state from the isomer to the dehydrohalogenation products, which represents a sequential electron/proton transfer event.  A lower energy pathway corresponding to a concerted proton coupled electron transfer event was also identified – this then, is an excellent system for exploring the competition between concerted and sequential pathways of proton-coupled electron transfer, and further studies of this and related systems are on-going.

Studies of Chemical Intermediates important in Planetary Atmospheres

Another current focus of study in the Reid group are reactive intermediates that play a role in the chemistry of planetary atmospheres, wherein are targeted the spectroscopy and photochemistry of radicals and radical-molecule complexes of relevance to the chemistry of planetary atmospheres, including haloalkyl, hydroxyalkl, nitroalkyl and cyanoalkyl radicals in addition to peroxy, trioxy and sulfoxy radicals.  Spectroscopic detection and photochemical studies of the initial radicals provide important information for modeling the competition between photodestruction and reaction in the atmosphere.  An example is provided in their recent studies of the hitherto unobserved C2F5Br radical, where both infrared and electronic spectra of the radical were measured.  It was shown that the electronic spectrum of the radical overlapped significantly with the solar actinic spectrum, which had not previously been considered , and the combination of IR and electronic spectra with ab initio calculations afforded quantitative information concerning the UV cross-section of the radical that, in turn, was used to derive a solar photolysis rate.  We use late-mixing techniques, as demonstrated in a recent study of photoinduced electron transfer in the pre-reactive C2H4—Br2 complex, to examine the formation and fate of important radical-molecule adducts.  Radical initiated processes typically proceed via formation of a radical-molecule adduct, and the role of weakly bound radical-molecule complexes in the atmosphere has been the subject of much recent discussion in the literature,(34-44)  and a Solvay Institutes Workshop on this topic was held in April 2010 in Brussels.(45)   In 2006, our group reported the first observation of the gas-phase electronic spectrum of a halocarbenium ion.  Recently, pulsed jet discharge matrix isolation spectroscopy has been used to study the CX2Br+ (X=H,F) ions,(46) in studies that have yielded insights into the effect of halogen substitution on the structure and properties of these ions.   Now we are developing new late mixing strategies for the clean production of ions, and plan to study the spectroscopy and photochemistry of key ions and their adducts.

Studies of Metal–Containing Reactive Intermediates

An emerging focus of study in our group deals with metal-containing reactive intermediates.  Catalytic reactions involving metals are central to an immense array of chemical and biochemical processes; important applications with respect to energy and the environment include C-H and C-C bond activation, olefin metathesis and polymerization, heterogenous Fischer-Tropsch reactions, fuel reforming and methanation, hydrodehalogenation of chlorofluorocarbons (CFCs),and N-H bond activation. These catalytic processes often involve intermediates such as metal (M) alkyls (M-CR3), carbenes (M=CR2) and carbynes (M≡CR), which have proven difficult to characterize experimentally. Although recent progress has been made, both in the characterization of surface-bound species(16) and gas-phase organometallic intermediates, the reactivity of and chemical bonding in these species is far from understood.  To address this gap, we are examining the vibrational and electronic spectroscopy of key organometallic species which are intermediates in catalytic reactions involving metals.  Their specific aims are: 1) to develop spectroscopic signatures for these intermediates, 2) to probe the nature of the metal-ligand bond and its dependence on substituent, metal, and oxidation state, 3) to examine spin-orbit interactions in prototypical systems, and 4) to provide sorely needed benchmark data for ab initio electronic structure theory.


1.     Voth, A. R.; Ho, P. S. The role of halogen bonding in inhibitor recognition and binding by protein kinases. Current Topics in Medicinal Chemistry 2007, 1336-1348.

2.     Zhou, P.; Zou, J.; Tian, F.; Shang, Z. Fluorine Bonding – How Does It Work In Protein-Ligand Interactions? Journal of Chemical Information and Modeling 2009, 2344-2355.

3.     Riley, K. E.; Murray, J. S.; Politzer, P.; Concha, M. C.; Hobza, P. Br…O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone. Journal of Chemical Theory and Computation 2009, 5, 155-163.

4.     Lu, Y.; Shi, T.; Wang, Y.; Yang, H.; Yan, X.; Luo, X.; Jiang, H.; Zhu, W. Halogen Bonding – A Novel Interaction for Rational Drug Design? J. Med. Chem. 2009, 52, 2854-2862.

5.     Kortagere, S.; Ekins, S.; Welsh, W. J. Halogenated ligands and their interactions with amino acids: Implications for structure-activity and structure-toxicity relationships. J. Mol. Graphics Modell. 2008, 27, 170-177.

6.     Auffinger, P.; Hays, F. A.; Westhof, E.; Ho, P. S. Halogen bonds in biological molecules. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 16789-16794.

7.     Lu, Y.; Wang, Y.; Zhu, W. Nonbonding interactions of organic halogens in biological systems:

implications for drug discovery and biomolecular design. Phys. Chem. Chem. Phys. 2010, 12, 4543-4551.

8.     Metrangolo, P.; Carcenac, Y.; Lahtinen, M.; Pilati, T.; Rissanen, K.; Vij, A.; Resnati, G. Nonporous Organic Solids Capable of Dynamically Resolving Mixtures of Diiodoperfluoroalkanes. Science (Washington, DC, United States) 2009, 323, 1461-1464.

9.     Metrangolo, P.; Meyer, F.; Pilati, T.; Resnati, G.; Terraneo, G. Halogen bonding in supramolecular chemistry. Angew. Chem., Int. Ed. 2008, 47, 6114-6127.

10.  Wei, H.-Q.; Jin, W.-J. Applications of halogen bonding in chemical sensing and molecular recognition. Fenxi Huaxue 2007, 35, 1381-1386.

11.  Takeuchi, T.; Minato, Y.; Takase, M.; Shinmori, H. Molecularly imprinted polymers with halogen bonding-based molecular recognition sites. Tetrahedron Lett. 2005, 46, 9025-9027.

12.  Metrangolo, P.; Neukirch, H.; Pilati, T.; Resnati, G. Halogen Bonding Based Recognition Processes: A World Parallel to Hydrogen Bonding. Acc. Chem. Res. 2005, 38, 386-395.

13.  Fox, D. B.; Liantonio, R.; Metrangolo, P.; Pilati, T.; Resnati, G. Perfluorocarbon-hydrocarbons self-assembly: halogen bonding mediated intermolecular recognition. J. Fluorine Chem. 2004, 125, 271-281.

14.  Liantonio, R.; Metrangolo, P.; Pilati, T.; Resnati, G.; Stevenazzi, A. Perfluorocarbon-Hydrocarbon Self-Assembly: First Crystalline Halogen-Bonded Complex Involving Bromoperfluoroalkanes. Cryst. Growth Des. 2003, 3, 799-803.

15.  Burton, D. D.; Fontana, F.; Metrangolo, P.; Pilati, T.; Resnati, G. Halogen bonding driven self-assembly of (E)-1,2-diiodo-1,2-difluoroethene with nitrogen substituted hydrocarbons. Tetrahedron Lett. 2003, 44, 645-648.

16.  Liantonio, R.; Luzzati, S.; Metrangolo, P.; Pilati, T.; Resnati, G. Perfluorocarbon-hydrocarbon self-assembly. Part 16: Anilines as new electron donor modules for halogen bonded infinite chain formation. Tetrahedron 2002, 58, 4023-4029.

17.  Messina, M. T.; Metrangolo, P.; Panzeri, W.; Pilati, T.; Resnati, G. Intermolecular recognition between hydrocarbon oxygen-donors and perfluorocarbon iodine-acceptors: the shortest O…I non-covalent bond. Tetrahedron 2001, 57, 8543-8550.

18.  Navarrini, W.; Metrangolo, P.; Pilati, T.; Resnati, G. Crown ethers as pre-organized exo-receptors in the divergent recognition of alpha ,w-diiodoperfluoroalkanes. New Journal of Chemistry 2000, 24, 777-780.

19.  Sarwar, M. G.; Dragisic, B.; Sagoo, S.; Taylor, M. S. A Tridentate Halogen-Bonding Receptor for Tight Binding of Halide Anions. Angew. Chem., Int. Ed. 2010, 49, 1674-1677, S1674/1-S1674/18.

20.  Saha, B. K.; Nangia, A.; Jaskolski, M. Crystal engineering with hydrogen bonds and halogen bonds. CrystEngComm 2005, 7, 355-358.

21.  Logothetis, T. A.; Meyer, F.; Metrangolo, P.; Pilati, T.; Resnati, G. Crystal engineering of brominated tectons: N-methyl-3,5-dibromo-pyridinium iodide gives particularly short C-Br…I halogen bonding. New Journal of Chemistry 2004, 28, 760-763.

22.  Brammer, L.; Zordan, F.; Espallargas, G. M.; Purver, S. L.; Marin, L. A.; Adams, H.; Sherwood, P. Complementary features of inorganic and organic halogens: application to crystal engineering. ACA Transactions 2004, 39, 114-122.

23.  Guardigli, C.; Liantonio, R.; Lorenza Mele, M.; Metrangolo, P.; Resnati, G.; Pilati, T. Design and Synthesis of New Tectons for Halogen Bonding-driven Crystal Engineering. Supramol. Chem. 2003, 15, 177-188.

24.  Walsh, R. B.; Padgett, C. W.; Metrangolo, P.; Resnati, G.; Hanks, T. W.; Pennington, W. T. Crystal Engineering through Halogen Bonding: Complexes of Nitrogen Heterocycles with Organic Iodides. Cryst. Growth Des. 2001, 1, 165-175.

25.  Mele, A.; Metrangolo, P.; Neukirch, H.; Pilati, T.; Resnati, G. A Halogen-Bonding-Based Heteroditopic Receptor for Alkali Metal Halides. J. Am. Chem. Soc. 2005, 127, 14972-14973.

26.  Wang, Y.-H.; Lu, Y.-X.; Zou, J.-W.; Yu, Q.-S. Theoretical investigation on charge-assisted halogen bonding interactions in the complexes of bromocarbons with some anions. Int. J. Quantum Chem. 2007, 108, 90-99.

27.  Lu, Y.-X.; Zou, J.-W.; Wang, Y.-H.; Jiang, Y.-J.; Yu, Q.-S. Ab Initio Investigation of the Complexes between Bromobenzene and Several Electron Donors: Some Insights into the Magnitude and Nature of Halogen Bonding Interactions. J. Phys. Chem. A 2007, 111, 10781-10788.

28.  Rosokha, S. V.; Neretin, I. S.; Rosokha, T. Y.; Hecht, J.; Kochi, J. K. Charge-transfer character of halogen bonding: molecular structures and electronic spectroscopy of carbon tetrabromide and bromoform complexes with organic s- and pi-donors. Heteroat. Chem. 2006, 17, 449-459.

29.  Tawarada, R.; Seio, K.; Sekine, M. Synthesis and properties of artificial base pairs by use of halogen bonds. Nucleic Acids Symposium Series 2006, 121-122.

30.  Marras, G.; Metrangolo, P.; Meyer, F.; Pilati, T.; Resnati, G.; Vij, A. Solid state synthesis under supramolecular control of a 2D heterotetratopic self-complementary tecton tailored to halogen bonding. New Journal of Chemistry 2006, 30, 1397-1402.

31.  Xu, J.; Liu, X.; Lin, T.; Huang, J.; He, C. Synthesis and Self-Assembly of Difunctional Halogen-Bonding Molecules: A New Family of Supramolecular Liquid-Crystalline Polymers. Macromolecules 2005, 38, 3554-3557.

32.  Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. An overview of halogen bonding. J. Mol. Model. 2007, 13, 305-311.

33.  Martinez Amezaga, N. J.; Pamies, S. C.; Peruchena, N. M.; Sosa, G. L. Halogen Bonding: A Study based on the Electronic Charge Density. J. Phys. Chem. A 2010, 114, 552-562.

34.  Klemperer, W.; Vaida, V. Molecular complexes in close and far away. Proceedings of the National Academy of Sciences of the United States of America 2006, 103, 10584-10588.

35.  Clark, J.; English, A. M.; Hansen, J. C.; Francisco, J. S. Computational study on the existence of organic peroxy radical-water complexes (RO2-H2O). J. Phys. Chem. A 2008, 112, 1587-1595.

36.  Sennikov, P. G.; Ignatov, S. K.; Schrems, O. Complexes and clusters of water relevant to atmospheric chemistry: H2O complexes with oxidants. Chemphyschem 2005, 6, 392-412.

37.  Karakus, N.; Ozkan, R. Ab initio study of atmospheric reactions of the hydroxyl radical-water complex (OH-H2O) with saturated hydrocarbons (methane, ethane and propane). J. Mol. Struct.-THEOCHEM 2005, 724, 39-44.

38.  Du, S. Y.; Francisco, J. S. Spectroscopic properties and stability of the SH-H2O open shell complex. J. Chem. Phys. 2009, 130, 124304/7.

39.  Du, S. Y.; Francisco, J. S. OH-N2 and SH-N2 radical-molecule van der Waals complex. J. Chem. Phys. 2009, 131, 064307/7.

40.  O’donnell, B. A.; Li, E. X. J.; Lester, M. I.; Francisco, J. S. Spectroscopic identification and stability of the intermediate in the OH+HONO2 reaction. Proceedings of the National Academy of Sciences of the United States of America 2008, 105, 12678-12683.

41.  Aloisio, S.; Francisco, J. S. Complexes of hydroperoxyl radical with glyoxal, methylglyoxal, methylvinyl ketone, acrolein, and methacrolein: Possible new sinks for HO2 in the atmosphere? J. Phys. Chem. A 2003, 107, 2492-2496.

42.  Belair, S. D.; Kais, S.; Francisco, J. S. Potential energy surface for the hydroperoxy and water (HO2-H2O) radical complex. Mol. Phys. 2002, 100, 247-253.

43.  Aloisio, S.; Francisco, J. S. Structure and energetics of hydrogen bonded HOx-HNO3 complexes. J. Phys. Chem. A 1999, 103, 6049-6053.

44.  Aloisio, S.; Francisco, J. S. Radical-water complexes in Earth’s atmosphere. Accounts of Chemical Research 2000, 33, 825-830.

45.  In Solvay Institutes, “Molecular Complexes in our Atmosphere and Beyond”, Solvay,  Brussels, Solvay,  Brussels, 2010.

46.  George, L.; Kalume, A.; Reid, S. A. Pulsed jet discharge matrix isolation and computational study of CX2Br+ (X=H,F). Chem. Phys. Lett. 2009.

47.  Wayne, R. P. Chemistry of atmospheres : an introduction to the chemistry of the atmospheres of earth, the planets, and their satellites. 3rd ed.; Oxford University Press: Oxford, 2000; p 775 p.

48.  de Petris, G.; Cartoni, A.; Troiani, A.; Angelini, G.; Ursini, O. Water activation by SO2+ ions: an effective source of OH radicals. Phys. Chem. Chem. Phys. 2009, 11, 9976-9978.

49.  Cacace, F. Discovery and characterization of atmospherically relevant inorganic species by structurally diagnostic mass spectrometric techniques. Int. J. Mass spectrom. 2001, 212, 403-411.