Dr. George Barnes
Chemistry Department Chair & Professor
Office
JH Julian Hall 214
Office Hours
By appointment
Office Phone
Email
- About
- Education
- Selected Research
Current Courses
CHE 299.002 Independent Honor Study In Chemistry
CHE 499.002 Independent Research For The Master's Thesis
CHE 290.002 Research in Chemistry
CHE 490.002 Research In Chemistry
Research Interests & Areas
My research focuses on modeling chemical reactions that occur in experimental tandem mass spectrometry, with a particular emphasis on elucidating the dissociation mechanisms of polypeptides. Molecular dynamics simulations reveal atomistic details concerning the reaction mechanism for peptide fragmentation in these high-energy collision systems. Graph theory is then employed to elucidate reaction mechanisms. In particular, the Barnes group has shown that proton motion and non-covalent complexes play a crucial role in the dynamics and the overall products formed during dissociation events.
PhD Chemistry
University of Wisconsin, Madison
Madison, WI
BS Chemistry
University of Nevada, Reno
Reno, NV
Journal Article
Automatic Identification and Visualization of Reaction Mechanisms Contained within Direct Dynamics Simulations
T Kobulnicky, Emmanuel Boafo, George Barnes.
ACS OMEGA, (2025), 10.1021/acsomega.5c04493
A computational and experimental examination of the CID of phosphorylated serine-H
George Barnes, KJ Kolonko, K Lucas, KA Poplawski.
CHEMICAL PHYSICS LETTERS, 819, (2023), 10.1016/j.cplett.2023.140442
Comparing the collision-induced dissociation of trimethyl lysine plus and acetyl lysine-H
George Barnes, KJ Kolonko, K Lucas, AMY Chen, M Schubmehl.
CHEMICAL PHYSICS LETTERS, 833, (2023), 10.1016/j.cplett.2023.140907
AutoMeKin2021: An open-source program for automated reaction discovery
George Barnes.
(2021)
Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach
Kenneth Lucas, Amy Chen, Megan Schubmehl, Kristopher J. Kolonko, George Barnes.
Journal of the American Society for Mass Spectrometry, 32 (11), 2675--2684, (2021), 10.1021/jasms.1c00225
Editorial - William L. Hase memorial issue
George Barnes.
(2020)
Fast Fragmentation During Surface-Induced Dissociation: An Examination of Peptide Size and Structure
George Barnes, Amanda Shlaferman, Monica Strain.
Chemical Physics Letters, (2020), 10.26434/chemrxiv.12148431.v2
Memorial Viewpoint for William L. Hase
Hans Lischka, John Tully, Haobin Wang, George Barnes.
The Journal of Physical Chemistry A, 124 (21), 4183-4184, (2020), 10.1021/acs.jpca.0c03827
Modeling the Effects of O-Sulfonation on the CID of Serine
Kenneth Lucas, George Barnes.
Journal of the American Society for Mass Spectrometry, 31 (5), 1114--1122, (2020), 10.1021/jasms.0c00037
Modeling the Effects of O-sulfonation on the CID of Serine
George Barnes.
(2020)
Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces
Ana Martin Somer, Veronica Macaluso, George Barnes, Li Yang, Subha Pratihar, Kihyung Song, William L. Hase, Riccardo Spezia.
Journal of the American Society for Mass Spectrometry, 31 (1), 2-24, (2020), 10.1021/jasms.9b00062
Role of chemical dynamics simulations in mass spectrometry studies of collision-induced dissociation and collisions of biological ions with organic surfaces
George Barnes.
(2020)
Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces
Ana Martin Somer, Veronica Macaluso, George Barnes, Li Yang, Subha Pratihar, Kihyung Song, William L. Hase, Riccardo Spezia.
Journal of the American Society for Mass Spectrometry, 31 (1), 2--24, (2019), 10.1021/jasms.9b00062
A Computational Comparison of Soft Landing of α-Helical vs Globular Peptides
Danielle Frederickson, Meghan McDonough, George Barnes.
The Journal of Physical Chemistry B, 122 (41), 9549-9554, (2018), 10.1021/acs.jpcb.8b06232
tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics
Aurelio Rodr\'\iguez, Roberto Rodr\'\iguez-Fern\'andez, Saulo A. V\'azquez, George Barnes, James J. P. Stewart, Emilio Mart\'\inez-N\'u\~nez.
Journal of Computational Chemistry, 39 (23), 1922--1930, (2018), 10.1002/jcc.25370
Direct Chemical Dynamics Simulations
Subha Pratihar, Xinyou Ma, Zahra Homayoon, George Barnes, William L. Hase.
Journal of the American Chemical Society, 139 (10), 3570--3590, (2017), 10.1021/jacs.6b12017
Simulating the Effect of Charge State on Reactive Landing of a Cyclic Tetrapeptide on Chemically Modified Alkylthiolate Self-Assembled Monolayer Surfaces
George Barnes, Amanda Podczerwinski.
The Journal of Physical Chemistry C, 121 (27), 14628-14635, (2017), 10.1021/acs.jpcc.7b03478
Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces
Subha Pratihar, George Barnes, William L. Hase.
Chemical Society Reviews, 45 (13), 3595--3608, (2016), 10.1039/c5cs00482a
Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters
Zahra Homayoon, Subha Pratihar, Edward Dratz, Ross Snider, Riccardo Spezia, George Barnes, Veronica Macaluso, Ana Martin Somer, William L. Hase.
The Journal of Physical Chemistry A, 120 (42), 8211--8227, (2016), 10.1021/acs.jpca.6b05884
Energy and temperature dependent dissociation of the Na+(benzene)1,2 clusters: Importance of anharmonicity
Sujitha Kolakkandy, Amit K. Paul, Subha Pratihar, Swapnil C. Kohale, George Barnes, Hai Wang, William L. Hase.
The Journal of Chemical Physics, 142 (4), 044306, (2015), 10.1063/1.4906232
The effect of protonation site and conformation on surface-induced dissociation in a small, lysine containing peptide
Kulsum Shaikh, Jacob Blackwood, George Barnes.
Chemical Physics Letters, 637, 83--87, (2015), 10.1016/j.cplett.2015.07.062
The Role of Proton Transfer in Surface-Induced Dissociation
Zackary Gregg, Waleed Ijaz, Stephen Jannetti, George Barnes.
The Journal of Physical Chemistry C, 118 (38), 22149--22155, (2014), 10.1021/jp507069x
The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory
Upakarasamy Lourderaj, Rui Sun, Swapnil C. Kohale, George Barnes, Wibe A. de Jong, Theresa L. Windus, William L. Hase.
Computer Physics Communications, 185 (3), 1074--1080, (2014), 10.1016/j.cpc.2013.11.011
Complex Formation during SID and Its Effect on Proton Mobility
Waleed Ijaz, Zackary Gregg, George Barnes.
The Journal of Physical Chemistry Letters, 4 (22), 3935--3939, (2013), 10.1021/jz402093q
Surface Deposition Resulting from Collisions between Diglycine and Chemically Modified Alkylthiolate Self-Assembled Monolayer Surfaces
Andrew Geragotelis, George Barnes.
The Journal of Physical Chemistry C, 117 (25), 13087--13093, (2013), 10.1021/jp402424z
Time dependent quantum thermodynamics of a coupled quantum oscillator system in a small thermal environment
George Barnes, Michael E. Kellman.
The Journal of Chemical Physics, 139 (21), 214108, (2013), 10.1063/1.4833566
Visualizing the zero order basis of the spectroscopic Hamiltonian
George Barnes, Michael E. Kellman.
The Journal of Chemical Physics, 136 (2), 024114, (2012), 10.1063/1.3674994
Detailed analysis of polyad-breaking spectroscopic Hamiltonians for multiple minima with above barrier motion: Isomerization in HO2
George Barnes, Michael E. Kellman.
The Journal of Chemical Physics, 134 (7), 074108, (2011), 10.1063/1.3552086
Communication: Effective spectroscopic Hamiltonian for multiple minima with above barrier motion: Isomerization in HO2
George Barnes, Michael E. Kellman.
The Journal of Chemical Physics, 133 (10), 101105, (2010), 10.1063/1.3480017
Model non-equilibrium molecular dynamics simulations of heat transfer from a hot gold surface to an alkylthiolate self-assembled monolayer
Yue Zhang, George Barnes, Tianying Yan, William L. Hase.
Physical Chemistry Chemical Physics, 12 (17), 4435, (2010), 10.1039/b923858c
Energy Transfer, Unfolding, and Fragmentation Dynamics in Collisions of N-Protonated Octaglycine with an H-SAM Surface
George Barnes, William L. Hase.
Journal of the American Chemical Society, 131 (47), 17185--17193, (2009), 10.1021/ja904925p
NH4+ + CH4 Gas Phase Collisions as a Possible Analogue to Protonated Peptide/Surface Induced Dissociation
George Barnes, William L. Hase.
The Journal of Physical Chemistry A, 113 (26), 7543--7547, (2009), 10.1021/jp900919s
An equilibrium focused approach to calculating the Raman spectrum of the symmetric OH stretch in formic acid dimer
George Barnes, Edwin L. Sibert.
Journal of Molecular Spectroscopy, 249 (2), 78--85, (2008), 10.1016/j.jms.2008.02.008
Symmetric Double Proton Tunneling in Formic Acid Dimer:\hspace0.167em A Diabatic Basis Approach
George Barnes, Shane M. Squires, Edwin L. Sibert.
The Journal of Physical Chemistry B, 112 (2), 595--603, (2007), 10.1021/jp075376e
Ion imaging studies of product rotational alignment in collisions of NO with Ar
Elisabeth A. Wade, K. Thomas Lorenz, David W. Chandler, James W. Barr, George Barnes, Joseph I. Cline.
Chemical Physics, 301 (2-3), 261--272, (2004), 10.1016/j.chemphys.2004.02.014
Recombination and Reaction Dynamics Following Photodissociation of CH3OCl in Solution
Christopher G. Elles, M. Jocelyn Cox, George Barnes, F. Fleming Crim.
The Journal of Physical Chemistry A, 108 (50), 10973--10979, (2004), 10.1021/jp046627b
Direct Measurement of the Preferred Sense of NO Rotation After Collision with Argon
K. Thomas Lorenz, David W. Chandler, James W. Barr, Wenwu Chen, George Barnes, Joseph I. Cline.
Science, 293 (5537), 2063--2066, (2001), 10.1126/science.1062754