RESEARCH
PROTEIN DYNAMICS AND FUNCTION
CHARACTERIZATION OF STRUCTURAL AND FUNCTIONAL WATER
POLYSACCHARIDES IN SOLUTION
POLYMER DESIGN FOR METAL CHELATION
Molecular dynamics, polarizable force fields, electrostatic interactions.
PUBLICATIONS
* denotes corresponding author
** denotes equal contribution
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43. "The need to implement FAIR principles in biomolecular simulations."
R. Amaro et al.
Nat. Methods, 2025, 22, 641-645
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42. "Gelation During Ring-Opening Reactions of Cellulosics with Cyclic Anhydrides: Phenomena and Mechanisms."
S. Petrova, Z. Zheng, D. Heinze, V. Vaissier Welborn, M. Bortner, K. Schmidt-Rohr and K. Edgar*
Biomacromolecules, 2024, 25, 7777-7787
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41. "Polarizable AMOEBA force field predicts thin and dense hydration layer around monosaccharides for accurate simulations of carbohydrates in solution."
L. Newman, M. Patton, B. Rodriguez, E. Sumner, V. Vaissier Welborn
Chem. Commun. 2024, 60, 14431-14434​
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40. "Electric fields in polymeric systems."
M. Rothermund**, S. Koehler** and V. Vaissier Welborn*
Chem. Rev. 2024, 124, 13331-13369 (Front cover)
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39. "Kinetics of calcite nucleation onto sulfated chitosan derivatives and implications for water-polysaccharide interactions during crystallization of sparingly soluble salts."
B. Knight, R. Mondal, N. Han, N. Pietra, B. Hall, K. Edgar, V. Vaissier Welborn, L. Madsen, J. De Yoreo, and P. Dove*
Cryst. Growth Des. 2024, 24, 6338-6353
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38. "Preorganized electric fields facilitate ion binding and permeation in voltage-gated sodium channels"
Y. Zheng, T. Chen and V. Vaissier Welborn*
ChemRxiv, 2024, 10.26434/chemrxiv-2024-cm35v-v2
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37. "Dynamics accelerate the kinetics of ion diffusion through channels: Continuous-time random walk models beyond the mean field approximation."
R. Mondal and V. Vaissier Welborn*
J. Chem. Phys. 2024, 160, 144109 (2024)
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36. "Understanding cysteine reactivity in protein environments with electric fields."
V. Vaissier Welborn*
J. Phys. Chem. B 2023, 127, 9936-9942
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35. "Polymer tacticity effects in polymer-lanthanides chelation thermodynamics."
W. R. Archer, T. Chen, V. Vaissier Welborn and M. D. Schulz*
Macromolecules, 2023, 56, 9062-9069
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34. "Characterizing ion-polymer interactions in aqueous environment with electric fields."
V. Vaissier Welborn*, W. R. Archer and M. D. Schulz
J. Chem. Inf. Model, 2022, 63, 2030-2036
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33. "Tuning the catalytic activity of synthetic enzyme KE15 with DNA."
Y. Zheng and V. Vaissier Welborn*
J. Phys. Chem. B, 2022, 126, 3407-3413
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32. "Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase."
M. M. Lawal and V. Vaissier Welborn*
ChemBioChem, 2022, DOI:10.1002/cbic.202200097
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31. "Exploring the role of polymer hydrophobicity in polymer-metal binding thermodynamics."
W. R. Archer, C. M. B. Gallagher, V. Vaissier Welborn and M. D. Schulz*
Phys. Chem. Chem. Phys., 2022, 24, 3579-3585
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30. "Beyond structural analysis of molecular enzyme-inhibitor interactions."
V. Vaissier Welborn*
Electron. Struct., 2022, 4, 014006
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29. "The role of water dynamics in age-related bone weakening."
V. Vaissier Welborn*
Research Outreach, 2021, 127, DOI:10.32907/RO-127-1960557845
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28. "Structural Dynamics and Computational Design of Synthetic Enzymes."
V. Vaissier Welborn*
Chem. Catalysis, 2021, 2, 19-28
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27. "Organocatalytic trans Semireduction of Primary and Secondary Propiolamides: Substrate Scope and Mechanistic Studies."
R. J. Grams, M. M. Lawal, C. Szwetkowski, D. Foster, C. A. Rosenblum, C. Slebodnick, V. Vaissier Welborn and W. L. Santos
Adv. Synth. Catal., 2021, 364, 172-178
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26. "Critical Role of Thermal Fluctuations for CO Binding on Electrocatalytic Metal Surfaces."
W-L. Li, C. Lininger, K. Chen, V. Vaissier Welborn, E. Rossomme, A. Bell, M. Head-Gordon and T. Head-Gordon
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25. "Environment-controlled water adsorption at hydroxyapatite/collagen interfaces."
V. Vaissier Welborn* - Selected "Hot article 2021" - Front cover article
Phys. Chem. Chem. Phys., 2021, 23, 13789-13796
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24. "Challenges for density functional theory: calculation of CO adsorption on electrocatalytically relevant metals."
C. Lininger, J. Gauthier, W-L. Li, E. Rossomme, V. Vaissier Welborn, Z. Lin, T. Head-Gordon, M. head-Gordon and A. Bell
Phys. Chem. Chem. Phys., 2021, 23, 9394-9406
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23. "ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code."
J. Nash, T. Barnes, V. Vaissier Welborn*
J. Open Source Softw., 2020, 5, 2576
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22. "The effect of inner-sphere reorganization on charge separated state lifetimes at sensitized TiO2 interfaces."
M. C. Kessinger, C. Brillhart, V. Vaissier Welborn and A. J. Morris*
J. Chem. Phys., 2020, 153, 124711
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21. "Enamel synthesis explained."
V. Vaissier Welborn*
Proc. Natl. Acad. Sci. USA, 2020, 117, 21847-21848
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20. "Investigation of external quantum efficiency roll-off in OLEDs using the mean field steady state kinetic model."
A. R. McIsaac, V. Vaissier Welborn, M. Einzinger, N. Geva, H. Weir, M. A. Baldo and T. Van Voorhis
J. Phys. Chem. C, 2020, 124, 14424-14431
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19. "Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold"
V. Vaissier Welborn, W-L Li and T. Head-Gordon*
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18. "Fluctuations of electric fields in the active site of the enzyme ketosteroid isomerase"
V. Vaissier Welborn and T. Head-Gordon*
J. Am. Chem. Soc., 2019, 141, 12487-12492
17. "Computational design of synthetic enzymes"
V. Vaissier Welborn and T. Head-Gordon*
Chem. Rev., 2019, 119, 6613-6630
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16. "Electrostatics Generated by a Supramolecular Capsule Stabilizes the Transition State for Carbon-Carbon Reductive Elimination from Gold(III) Complex"
V. Vaissier Welborn and T. Head-Gordon*
J. Phys. Chem. Lett., 2018, 9, 3814-3818
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15. "Computational optimization of electric fields for better catalysis design"
V. Vaissier Welborn, L. R. Pestana and T. Head-Gordon*
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14. "Computational optimization of electric fields for improving catalysis of a designed Kemp eliminase"
V. Vaissier**, S. Sharma**, A. Bowhmick, K. Schaettle, T. Zhang and T. Head-Gordon*
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13. "Non-radiative deactivation of cytosine derivatives at elevated temperatures"
V. Vaissier Welborn and T. Van Voorhis*
Mol. Phys. Michael Baer Festschrift, 2018, 116, 2591-2598
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12. "Geometry of molecular motions in dye monolayers at various coverages"
V. Vaissier and T. Van Voorhis*
J. Chem. Phys. C, 2017, 121, 12562-12568
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11. "Mean field treatment of heterogeneous steady state kinetics"
V. Vaissier**, N. Geva**, J. Sheperd and T. Van Voorhis*
Chem. Phys. Lett., 2017, 685, 185-190
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10. "Quantum chemical approaches to [NiFe] hydrogenase"
V. Vaissier and T. Van Voorhis*
Essays Biochem., 2017, 61, 293-303
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9. "The adiabatic approximation in explicit solvent models of redox chemistry"
V. Vaissier and T. Van Voorhis*
J. Chem. Theory Comput., 2016, 12, 5111-5116
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8. "Inter-dye hole transport accelerates electron to oxidized dye recombination in dye sensitized nanocrystals"
D. Moia, A. Szumska, V. Vaissier, M. Plannels, N. Robertson, B. O'Regan et al.
J. Am. Chem. Soc., 2016, 138, 13197-13206
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7. "How mobile are dye adsorbates and acetonitrile molecules on the surface of TiO2 nanoparticles?
A quasi-elastic neutron scattering study"
V. Vaissier, V. Garcia-Sakai, X. Li, G. Sakai, J. Cabral, J. Nelson and P. Barnes
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6. "Evidence for photo-induced charge separation between dye molecules adsorbed to aluminum oxide surfaces"
U. Cappel, D. Moia, A. Bruno, V. Vaissier, S. Haque and P. Barnes
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5. "Influence of intermolecular interactions on the reorganization energy of charge transfer between surface attached dye molecules"
V. Vaissier, J. Frost, P. Barnes and J. Nelson
J. Phys. Chem. C, 2015, 119, 24337-24341
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4. "The influence of a nearby substrate on the outer sphere polarization energy and reorganization energy of charged molecules"
F. Manke, J. Frost, V. Vaissier and P. Barnes
Phys. Chem. Chem. Phys. 2015, 17, 7345-7354
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3. "Effect of molecular fluctuations on hole diffusion within dye monolayers"
V. Vaissier, E. Mosconi, D. Moia, M. Pastore, J. Frost, F. De Angelis, P. Barnes and J. Nelson
Chem. Mater. 2014, 26, 4731-4740
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2. "The reorganization energy of intermolecular hole hopping between dyes anchored to surfaces"
D. Moia, V. Vaissier, I. Lopez-Duarte, T. Torres, M. Nazeeruddin, B. O'Regan et al.
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1. "Influence of polar medium on the reorganization energy of charge transfer between dyes in dye sensitized film"
V. Vaissier, P. Barnes, J. Kirkpatrick and J. Nelson
PEOPLE
Valerie Welborn
2017-2019 Postdoc UC Berkeley
(advisor: Teresa Head-Gordon)
2015-2017 Postdoc MIT
(advisor: Troy Van Voorhis)
2011-2014 PhD Imperial College London, CDT TSM
(advisors: Jenny Nelson, Piers Barnes)
Postdocs
Stephen Koehler (skoehler@vt.edu)
Stephen obtained a BS in Chemistry from Duquesne University in 2017. He investigated gas phase reactions of group II metal-carbanion complexes using mass spectrometry under the supervision of Prof. Michael Van Stipdonk.
He completed his PhD in Chemistry at Penn State in 2023 working for Prof. Beth Elacqua. He used organic synthesis and density functional theory to investigate conjugated polymers toward high efficiency solar cells. Stephen is currently a postdoc in the Welborn and Figg labs where he is working to understand how α-synuclein fibrilizes using both molecular dynamics and experimental biochemistry.
Mawuli Deegbey (mdeegbe@vt.edu)
Mawuli has a BSc in Chemistry from Kwame Nkrumah University of Science & Technology in Ghana, and then moved to Starkville to obtain a Masters in physical chemistry at Mississippi State University under the direction of Prof Steven R Gwaltney.
He completed his PhD in Chemistry at North Carolina State University in 2024 under the direction of Prof Elena Jakubikova. His PhD research focused on electronic structure and photochemistry of transition metal complexes, as well as the electrocatalytic reduction of CO/CO2. As a postdoc in the Welborn group, he will utilize ab initio modeling and molecular dynamic simulations to gain chemical insights into the reactivity of proteins and carbohydrates.
Graduate students
Taoyi Chen (tychen@vt.edu)
Taoyi Chen obtained his Bachelor’s degree in Chemical Engineering from both New Mexico State University and East China University of Science and Technology, China in 2016.
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He graduated from New Mexico State University in 2018 and 2020 with Masters and PhD degrees in Chemical Engineering under the supervision of Dr. Thomas A. Manz.
His MS project focuses on developing and utilizing atomic population analysis methods to describe interactions of atoms in materials for quantum chemistry calculations.
Ronnie Mondal (mondal@vt.edu)
Ronnie Mondal graduated from the Indian Institute of Technology, Bombay in 2020 with a BS in Chemistry.
His undergraduate research in Dr. Pradeepkumar’s group focused on prediction algorithms and Machine Learning-assisted ligand design for stabilisation of G-Quadruplexes and I-Motifs. After completion of his degree he worked with Swiggy, a food delivery app, where he campaign benchmarking and customer engagement. He is currently a graduate student in the Welboorn group and his work focuses on facilitating molecular dynamics simulations of polymer-based materials.
Junbao Liang (junbaol@vt.edu)
Junbao Liang got his bachelor’s degree from China Univ. of Mining & Tech. in 2019 and Master’s degree from Univ. of Oregon in 2020.
His undergrad research in Prof. Lang Xu’s lab focuses on the synthesis of carbon-based material, trying to make some environment-friendly material with high performance in energy storage. His research at Univ. of Oregon followed the instruction of Dr. Chris Hendon. He tried to figure out how the functional groups tune the property of MOFs...
Luke graduated from Liberty University in 2022, with a major in Chemistry and a minor in Biology.
His undergraduate research, directed by Dr. Matthew Brynteson, studied the binding affinities of BPA derivatives to the human estrogen receptor. Protein-ligand docking software, AutoDock, was utilized to study the binding orientations and obtain simulated energies. This research introduced Luke to molecular modeling as a tool for chemical research.
Mark Rothermund (markr96@vt.edu)
Mark earned his BSc in Chemistry from Western Carolina University in 2019, followed by a MSc in Chemistry in 2022.
During his master's program, his research focused on the application of chemometric analysis of infrared spectra to determine mosquito gonotrophic life stages. Now as a Ph.D. student, Mark is focused on modeling aggregates of the protein alpha-synuclein, which has been implicated as the main constituent of Lewy bodies involved in Parkinson's disease, Alzheimer's disease, and other Lewy body diseases.
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Ashini de Silva (ashinids@vt.edu)
Ashini graduated from the University of Colombo in 2023 with a BSc (Honors) in Computational Chemistry.
Her undergraduate research, under the supervision of Dr. W. M. C. Sameera and Dr. Gayathri N. Silva, focused on small molecule blockers for bacterial fluoride ion channels. Her work combined computational and experimental techniques. On the computational side, she performed molecular docking and molecular dynamics simulations to equilibrate protein-ligand complexes.
Undergraduate students
Ethan Sumner
Ethan is currently pursuing his undergraduate degree in Medicinal Chemistry and Biological Sciences from Virginia Tech.
During the summer, Ethan does undergraduate research at Fox Chase Cancer Center, working in an epigenetics lab focusing on DNA amplifications as a result of histone methylation. He is currently an Undergraduate student in the Welborn lab focusing on utilizing the Poltype2/AMOEBA+ force field to analyze carbohydrates.
Alumni
Monsurat M. Lawal
(Postdoc)
Chengen Li
(UG)
Zachary Hoyer
(UG)
Sarasi Banerjee
(MS)
Yi Zheng
(PhD)
CONTACT
Luke Newman
Luke graduated from Liberty University in 2022, with a major in Chemistry and a minor in Biology.
His undergraduate research, directed by Dr. Matthew Brynteson, studied the binding affinities of BPA derivatives to the human estrogen receptor. Protein-ligand docking software, AutoDock, was utilized to study the binding orientations and obtain simulated energies. This research introduced Luke to molecular modeling as a tool for chemical research.