Our research focuses on theoretical and computational studies of different condensed phase and interfacial systems.

Margulis Publications

  1. Structure and Dynamics of an Ionic Liquid Mixture Film Confined by Mica. Waruni V. Karunaratne and Claudio J. Margulis. Submitted to JPC, 2019

  2. Structural Analysis of Ionic Liquids With Symmetric and Asymmetric Fluorinated Anions. Man Zhao, Boning Wu, Sharon Lall-Ramnarine, Jasodra D. Ramdihal, Kristina Papacostas, Eddie D. Fernandez, Rawlric Sumner, Claudio Margulis, James Wishart, and Edward Castner, Jr.. Submitted to JCP, 2019

  3. Ionic Liquid Mixture at the Vacuum Interface and the Peaks and Antipeaks Analysis of X-ray Reflectivity. F Wu, WV Karunaratne, CJ Margulis. The Journal of Physical Chemistry C123 (8),4914, 2019

  4. In an ionic liquid, high local friction is determined by the proximity to the charge network. JC Araque, CJ Margulis. The Journal of chemical physics 149 (14), 144503, 2018

  5. Dynamics of an excess hole in the 1-methyl-1-butyl-pyrrolidinium dicyanamide ionic-liquid. Fei Wu, Changhui Xu and Claudio J. Margulis. J. Chem. Phys. 148, 193831, 2018

  6. Excess Electron and Hole in 1-Benzylpyridinium-Based Ionic Liquids. Kamal B. Dhungana, Fei Wu and Claudio J. Margulis J. Phys. Chem. B. 121(37):8809-8816, 2017

  7. Stiff and Soft Nano-Environments and the "Octopus Effect" Are the Crux of Ionic Liquid Structural and Dynamical Heterogeneity. Ryan P. Daly, Juan Carlos Araque and Claudio J. Margulis. J. Chem. Phys. Communications 147, 061102, 2017

  8. Comparison of the Structural Response to Pressure of Ionic Liquids with Ether and Alkyl Functionalities. Kamal B. Dhungana and Claudio J. Margulis. J. Phys. Chem. B.,121 (28), pp 6890–6897, 2017

  9. Bulk and Vacuum Interfaces of Ionic Liquids with Symmetric Ions. Alkyl vs. Isoelectronic Diether Tails.Jeevapani J. Hettige, Weththasinghage D. Amith, Edward W. Castner Jr., and Claudio J. Margulis. J. Phys. Chem. B, 121 (1), pp 174–179. DOI: 10.1021/acs.jpcb.6b09148, 2017

  10. Structures of Ionic Liquid Having both Anionic and Cationic Octyl Tails: Lamellar Vacuum Interface vs. Sponge-Like Bulk Order. Weththasinghage Don Amith, Jeevapani J. Hettige, Edward W. Castner Jr. and Claudio J. Margulis. J. Phys. Chem. Lett., 2016, 7 (19), pp 3785–3790 DOI: 10.1021/acs.jpclett.6b01763

  11. Rotational Dynamics in Ionic Liquids from NMR Relaxation Experiments and Simulations: Benzene and 1-Ethyl-3-Methylimidazolium. Chris Rumble, Anne Kaintz, Sharad K. Yadav, Brian Conway, Juan C. Araque, Gary Baker, Claudio Margulis, and Mark Maroncelli. J. Phys. Chem. B, 120 (35), pp 9450–9467, 2016

  12. Structure of cyano-anion ionic liquids: X-ray scattering and simulations. Kamal B. Dhungana, Luiz F. O. Faria, Boning Wu, Min Liang, Mauro C. C. Ribeiro, Claudio J. Margulis and Edward W. Castner, Jr., J. Chem. Phys. 145, 024503, 2016

  13. A Link Between Structure, Diffusion and Rotations of Hydrogen Bonding Tracers in Ionic Liquids. Juan Carlos Araque, Ryan P. Daly, and Claudio J. Margulis. J. Chem. Phys. 144, 204504, 2016

  14. Communication: Nanoscale Structure of tetradecyltrihexylphosphonium based Ionic Liquids. Jeevapani J. Hettige, Juan C. Araque, Hemant K. Kashyap and Claudio J. Margulis. J. Chem. Phys. J. Chem. Phys., 2016,144, 121102

  15. A Rigid Hinge Region is Necessary for High Affinity Binding of Dimannose to Cyanovirin and Associated Constructs.Zhen Li, Ashini Bolia, Jason D. Maxwell, Andrey A. Bobkov, Giovanna Ghirlanda, Sefika Banu Ozkan, and Claudio Javier Margulis.
    Biochemistry, 2015, 54 (46), pp 6951–6960  DOI:10.1021/acs.biochem.5b00635

  16. Ionic Liquids--Conventional Solvent Mixtures, Structurally Different but Dynamically Similar . Juan Carlos Araque, Jeevapani Hettige and Claudio J. Margulis.J. Chem. Phys. 143, 134505, 2015.DOI:10.1063/1.4932331

  17. Modern Room Temperature Ionic Liquids, a Simple Guide to Understand Their Structure and How It May Relate to Dynamics. Juan Carlos Araque, Jeevapani Hettige and Claudio J. Margulis. J. Phys. Chem. B, 119 (40), pp 12727–12740, 2015 Invited Feature Article. DOI: 10.1021/acs.jpcb.5b05506 (JOURNAL COVER)

  18. How is Diffusion of Neutral and Charged Tracers Related to the Structure and Dynamics of a Room-Temperature Ionic-Liquid? Large Deviations from Stokes-Einstein Behavior Explained. Juan Carlos Araque, Sharad K Yadav, Michael Shadeck, Mark Maroncelli, and Claudio Javier Margulis. J. Phys. Chem. B., 119 (23), pp 7015–7029, 2015 DOI: 10.1021/acs.jpcb.5b01093 (JOURNAL COVER)

  19. Solvation of an Excess Electron in Pyrrolidinium Dicyanamide Based Ionic Liquids. Changhui Xu and Claudio J. Margulis. DOI: 10.1021/jp5108922. J. Phys. Chem. B., 119, 532−542, 2015

  20. Bicontinuity and Multiple Length Scale Ordering in Triphilic Hydrogen-Bonding Ionic Liquids. Jeevapani J. Hettige, Juan Carlos Araque, Claudio. J. Margulis. J. Phys. Chem. B, 2014, 118 (44), pp 12706–12716 (JOURNAL COVER)

  21. Communication: Anomalous Temperature Dependence of the Intermediate Range Order in Phosphonium Ionic Liquids. Jeevapani Hettige, Hemant K. Kashyap, Claudio Margulis J. Chem. Phys., 140, 111102, 2014

  22. The Role of Glu41 in the Binding of Dimannose to P51G-m4-CVN. Sai Kumar Ramadugu, Zhen Li, Hemant Kashyap, Claudio Margulis. Biochemistry, 53 (9), pp 1477–1484, 2014 DOI: 10.1021/bi4014159

  23. Dynamics of Excess Electronic Charge in Aliphatic Ionic Liquids Containing the Bis(trifluoromethylsulfonyl)amide Anion. Changhui Xu, Aleksander Durumeric, Hemant K. Kashyap, Jorge J. Kohanoff, and Claudio Javier Margulis. J. Am. Chem. Soc., 135 (46), pp 17528–17536, 2013 DOI: 10.1021/ja409338z

  24. Structure of 1-Alkyl-1-methylpyrrolidinium Bis(trifluoromethylsulfonyl)amide Ionic Liquids with Linear, Branched and Cyclic Alkyl Groups. Kashyap, Hemant; Santos, Cherry; Murthy, N. Sanjeeva; Hettige, Jeevapani; Ramati, Sharon; Kerr, Kijana; Gwon, JinHee; Gohdo, Masao; Lall-Ramnarine, Sharon; Wishart, James; Margulis, Claudio; Castner, Edward. J. Phys. Chem. B, 117 (49), pp 15328–15337, 2013 DOI: 10.1021/jp403518j

  25. How does the Ionic Liquid Organizational Landscape Change when Nonpolar Cationic Alkyl Groups Are Replaced by Polar Isoelectronic Diethers? Hemant Kashyap, Cherry Santos, Ryan Daly, Jeevapani Hettige, N. Murthy, Hideaki Shirota, Edward Castner Jr., Claudio J. Margulis. J. Phys. Chem. B, 117 (4), pp 1130–1135, 2013 DOI: 10.1021/jp311032p

  26. Anions, the Reporters of Structure in Ionic Liquids. Jeevapani J. Hettige, Hemant K. Kashyap, Harsha V. R. Annapureddy and Claudio J. Margulis. J. Phys. Chem. Lett., 4 (1), pp 105–110, 2013 DOI: 10.1021/jz301866f

  27. Theoretical Deconstruction of the X-ray Structure Function Exposes Polarity Alternations in Room Temperature Ionic Liquids. H. K. Kashyap and C. J. Margulis. For the 222nd ECS Meeting in Honolulu, Hawaii. ECS Transactions, 50 (11), 301–307, 2012. doi:10.1149/05011.0301ecst

  28. SAXS Anti-Peaks Reveal the Length-Scales of Dual Positive/Negative and Polar/Apolar Ordering in Room-Temperature Ionic Liquids. Hemant K. Kashyap, Jeevapani J. Hettige, Harsha V. R. Annapureddy and Claudio J. Margulis. ChemComm (Special Issue on Ionic Liquids), 48, 5103-5105, 2012 DOI: 10.1039/C2CC30609C

  29. Temperature-dependent structure of ionic liquids : X-ray scattering and simulations. Hemant K. Kashyap, Cherry S. Santos, Harsha V. R. Annapureddy, N. Sanjeeva Murthy, Claudio J. Margulis and Edward W. Castner, Jr. Faraday Discussions, 154, 133,  2012 (Advance Article, Accepted 15 Jun 2011, published on web Jul 19, 2011) DOI: 10.1039/C1FD00059D

  30. Dry Excess Electrons in Room-Temperature Ionic Liquids. Claudio Javier Margulis , Harsha V. R. Annapureddy , Pablo Martin De Biase , David Coker , Jorge Kohanoff, and Mario G. Del Popolo, Journal of the American Chemical Society, 2011, 133 (50),  20186–20193 DOI: 10.1021/ja203412v

  31. Searching and Optimizing Structure Ensembles for Complex Flexible Sugars. Junchao Xia, Claudio J. Margulis, and David A. Case. Journal of the American Chemical Society (Communication), 2011, 133 (39), 15252–15255 DOI: 10.1021/ja205251j

  32. How is Charge Transport Different in Ionic Liquids and Electrolyte Solutions? Hemant K. Kashyap, Harsha V. R. Annapureddy, Fernando O. Raineri and Claudio J. Margulis. J. Phys. Chem. B, 2011, 115 (45),  13212–13221 DOI: 10.1021/jp204182c

  33. Ionic Liquids: Structure and Photochemical Reactions. Edward W. Castner Jr., Claudio J. Margulis, Mark Maroncelli and James F. Wishart. Annual Review of Physical Chemistry, 62, 2011. First Posted Online Nov 22, 2010 DOI: 10.1146/annurev-physchem-032210-103421

  34. Temperature-dependent structure of methyltributylammonium bis(trifuoromethylsulfonyl)amide: X-ray scattering and simulations. Cherry S. Santos, Harsha V. R. Annapureddy, N. Sanjeeva Murthy, Hemant K. Kashyap, Edward W. Castner Jr. and Claudio J. Margulis. J. Chem. Phys. 134, 064501, 2011  (JOURNAL COVER) http://dx.doi.org/10.1063/1.3526958

  35. What is the Origin of the Prepeak in the X-Ray Scattering of Imidazolium Based Room Temperature Ionic Liquids? Harsha V. R. Annapureddy, Hemant K. Kashyap, Pablo M. De Biase, and Claudio J. Margulis. J. Phys. Chem. B, 114 (50), 16838–16846, 2010  (JOURNAL COVER) DOI: 10.1021/jp108545z

  36. In Silico Prediction of the 3D Structure of Trimeric Asialoglycoprotein Receptor Bound to Triantennary Oligosaccharide. Sai Kumar Ramadugu, Ying-Hua Chung, Ernesto J. Fuentes, Kevin G. Rice and Claudio J. Margulis. Journal of the American Chemical Society, 132 (26), 9087–9095, 2010 DOI: 10.1021/ja1021766

  37. Measuring the Magnitude of Internal Motion in a Complex Hexasaccharide. Soumya Ganguly, Junchao Xia, Claudio Margulis, Liz Stanwyck and C. Allen Bush. Biopolymers, 95, 1, 2010 DOI: 10.1002/bip.21532

  38. Computational Study of the Conformational Structures of Saccharides in Solution Based on J couplings and the “Fast Sugar Structure Prediction Software”. Junchao Xia and Claudio J. Margulis. Biomacromolecules, 10, 11, 3081-3088, 2009. DOI: 10.1021/bm900756q

  39. When sugars get wet. A comprehensive study of the behavior of water on the surface of oligosaccharides. Sai Kumar Ramadugu, Ying-Hua Chung and Claudio J. Margulis. J. Phys. Chem. B, 113 (31), 11003–11015, 2009 DOI: 10.1021/jp904981v

  40. Controlling the outcome of Electron Transfer Reactions in Ionic Liquids. Harsha V. R. Annapureddy and Claudio J. Margulis. J. Phys. Chem. B, 113, 35, 12005-12012, 2009  DOI: 10.1021/jp905144n

  41. Rationalization of the Difference in Lifetime of Two Covalent Sialosyl-Enzyme Intermediates of Trypanosoma rangeli Sialidase. Laura L. Parker, Ying-Hua Chung, Claudio J. Margulis and Jan H. Jensen. J. Phys. Chem. B (Letter), 112, 45, 14093-14095, 2008 DOI: 10.1021/jp804314x

  42. A tool for the prediction of structures of complex sugars. Junchao Xia and C. Margulis. JB-NMR, 42,4, 2008 DOI: 10.1007/s10858-008-9279-6

  43.  Molecular dynamics study of the temperature-dependent Optical Kerr effect spectra and intermolecular dynamics of room temperature ionic liquid 1-methoxyethylpyridinium dicyanoamide. Zhonghan Hu, Xuhui Huang, Harsha V. R. Annapureddy and Claudio J. Margulis, J. Phys. Chem. B 112(26); 7837-7849, 2008. DOI: 10.1021/jp800729g

  44. How does water affect the dynamics of the room temperature ionic liquid 1-hexyl-3-methylimidazolium hexafluorophosphate and the fluorescence spectroscopy of Coumarin-153 when dissolved in it? Harsha V. R. Annapureddy, Zhonghan Hu, Junchao Xia and C. J. Margulis, J. Phys. Chem. B, 112 (6), 1770 -1776, 2008 DOI: 10.1021/jp077623k

  45. Dynamics of Water Adsorption on Calcite Surface as a Function of Relative Humidity. Asif Rahaman, Vicki Grassian and Claudio J. Margulis, J. Phys. Chem. C, 112 (6), 2109 -2115, 2008 DOI: 10.1021/jp077594d

  46. The Diffusion and Residence Time of Hydrogen Peroxide and Water in Crowded Protein Environments. Ying-Hua Chung, Junchao Xia and Claudio J. Margulis.  Journal of Physical Chemistry B, 111(46), 1336-13344, 2007  DOI: 10.1021/jp075251+

  47.  Room-Temperature Ionic Liquids: Slow Dynamics, Viscosity and the Red Edge Effect. Zhonghan Hu and C. J. Margulis. Accounts of Chemical Research, 40 (11), 1097–1105, 2007 DOI: 10.1021/ar700046m

  48. Sugar Folding: A novel structural prediction tool for oligosaccharides and polysaccharides I. J. Xia, R. P. Daly, F-C Chuang, L. Parker, J. H. Jensen and C. J. Margulis. Journal of Chemical Theory and Computation, 3, 1620-1629, 2007  DOI: 10.1021/ct700033y

  49. Sugar Folding: A novel structural prediction tool for oligosaccharides and polysaccharides II. J. Xia, R. P. Daly, F-C Chuang, L. Parker, J. H. Jensen and C. J. Margulis. Journal of Chemical Theory and Computation, 3, 1629-1643, 2007  DOI: 10.1021/ct700034q

  50. On the Response of an Ionic Liquid to External Perturbations and the Calculation of Shear Viscosity. Z. Hu and C. J. Margulis. Journal of Physical Chemistry B, 111(18); 4705-4714, 2007  DOI: 10.1021/jp067076n

  51. Heterogeneity in a Room Temperature Ionic Liquid. Persistent Local Environments and the Red Edge Effect. Z. Hu and C. J. Margulis. Proceedings of the National Academy of Sciences, 103(4), 831-836, 2006 DOI: 10.1073/pnas.0507364103

  52. A Study of the Time-Resolved Fluorescence Spectrum and Red Edge Effect of ANF in a Room-Temperature Ionic Liquid. Z. Hu and C. J. Margulis. Journal of Physical Chemistry B, 110(23), 11025-11028, 2006 (Letters) DOI: 10.1021/jp061652y

  53. Computational Study of the Dynamics of Mannose Disaccharides Free in Solution and Bound to the Potent Anti-HIV Virucidal Protein Cyanovirin. C. J. Margulis. J. Phys. Chem. B., 109(8), 2005  DOI: 10.1021/jp0406971

  54. Conformational dynamics of Sialyl LewisX in aqueous solution and its interaction with SelectinE. A study by Molecular Dynamics. K. Veluraja and C. J. Margulis. J. of Biomolecular Structure & Dynamics., 23(1), 2005 DOI:10.1080/07391102.2005.10507051

  55. Why is the partial molar volume of CO2 so small when dissolved in a room temperature ionic liquid? A study of the dynamics and structure of CO2 dissolved in [BMIM+][PF6-]?. X. Huang, C. J. Margulis and B. J. Berne. Journal of the American Chemical Society, 127 (50), 17842-17851, 2005 DOI: 10.1021/ja055315z

  56. Computational Study of Imidazolium Based Ionic Solvents with Alkyl Substituents of Different Lengths. C. J. Margulis.  Molecular Physics, 102 (9-10), 2004  DOI:10.1080/00268970410001683843

  57. Ultrafast Non-Adiabatic Dynamics: Quasiclassical calculation of the transient photoelectron spectrum of I2-(CO2)8. N. Yu, C. J. Margulis and D. F. Coker. J. Chem. Phys., 120(8), 2004 http://dx.doi.org/10.1063/1.1642584

  58.  Hydrophobic collapse in multidomain protein folding. R. H. Zhou, X. Huang, C. J. Margulis and B. J. Berne. Science, 305 (5690), 2004 DOI: 10.1126/science.1101176

  59. Comment: Reply to the Comment on “Do Molecules as Small as Neopentane Induce a Hydrophobic Response Similar to that of Large Hydrophobic Surfaces?” X. Huang, C. J. Margulis and B. J. Berne. J. Phys. Chem. B. 108 (26), 9373-9374, 2004

  60. Dewetting and collapse of nano-size hydrophobic systems. X. Huang, C. J. Margulis and B. J. Berne. Proc. Natl. Acad. Sci. USA, 100 (21), 2003                              DOI: 10.1073/pnas.193483710

  61.  Do molecules as small as neopentane induce a hydrophobic response similar to that of large hydrophobic surfaces? X. Huang, C. J. Margulis and B. J. Berne. J. Phys. Chem. B, 107 (42), 2003 DOI: 10.1021/jp030652k

  62.  Helix unfolding and intramolecular hydrogen bond dynamics in small alpha-helices in explicit solvent. C. J. Margulis, H. A. Stern and B. J. Berne. J. Phys. Chem. B, 106, 2002 DOI: 10.1021/jp0205158

  63.  A new semi-empirical approach to study ground and excited states of transition metal complexes in biological systems. C. J. Margulis, V. Guallar, E. Sim, R. A. Friesner and B. J. Berne. J. Phys. Chem. B, 106 (33), 2002 DOI: 10.1021/jp020705i

  64.  Solvation effects on equilibria: triazoles and N-methyl piperdinol. Stuart E. Murdock, R. M. Lynden-Bell, J. Kohanoff, C. J. Margulis and Graham J. Sexton. Phys. Chem. Chem. Phys., 4, 2002 DOI: 10.1039/B203429H

  65.  Computer simulation of a “green chemistry” room-temperature ionic solvent. C. J. Margulis, H. A. Stern and B. J. Berne. J. Phys. Chem. B, 106 (46), 2002 DOI: 10.1021/jp021392u

  66.  Influence of solvation environment on excited state avoided crossings and photodissociation dynamics. N. Yu, C. J. Margulis and D. F. Coker. J. Phys. Chem. B, 105 (28), 2001 DOI: 10.1021/jp0108925

  67.  Symmetry breaking of the triiodide ion in acetonitrile solution. C. J. Margulis, D. F. Coker and R. M. Lynden-Bell. Chem. Phys. Lett., 341 (5-6), 2001 http://dx.doi.org/10.1016/S0009-2614(01)00548-6

  68.  Modeling solvation of excited electronic states of flexible polyatomic molecules: Diatomics in molecules for I3 in argon clusters. C. J. Margulis and D. F. Coker. J. Chem. Phys., 114 (15), 2001 http://dx.doi.org/10.1063/1.1357799

  69.  A Monte Carlo study of symmetry breaking of I−3 in aqueous solution using a multistate diabatic Hamiltonian. C. J. Margulis, D. F. Coker and R. M. Lynden-Bell. J. Chem. Phys., 114 (1), 2001 http://dx.doi.org/10.1063/1.1328757

  70.  Applying DIM in excited electronic state calculations for flexible polyatomic molecules: The I3 molecule. C. J. Margulis and D. F. Coker. J. Chem. Phys., 113 (15), 2000 http://dx.doi.org/10.1063/1.1308548

  71.  Vibrational dynamics of the I3 radical: A semiempirical potential surface, and semiclassical calculation of the anion photo-electron spectrum. C. J. Margulis, D. A. Horner, S. Bonella, and D. F. Coker. J. Phys. Chem. A, 103 (47), 1999 DOI: 10.1021/jp992596m

  72.  Nonadiabatic molecular dynamics simulations of the photofragmentation and geminate recombination dynamics in size-selected I2-(CO2)n cluster ions. C. J. Margulis and D. F. Coker. J. Chem. Phys. 110 (12), 1999 http://dx.doi.org/10.1063/1.478466

  73.  Ionic aggregates in steam. Part 1.-Equilibrium configurations. Claudio Margulis, Daniel Laria and Roberto Fernandez-Prini. J. Chem. Soc. Faraday T., 92 (15), 1996 DOI: 10.1039/FT9969202703