Selected publications

ARTICLES AND BOOK CHAPTERS (*=undergraduate coauthor, **=high school student coauthor)

U.S. Hassan*, M.A. Amat, R.Q. Topper, Decomposition and growth pathways for ammonium nitrate clusters and nanoparticles, Journal of Physical Chemistry A 128(42), 9184-9194 (2024). Invited article for the Mark A. Johnson Festschrift. DOI: 10.1021/acs.jpca.4c04630.
R.Q. Topper, S.L. Topper, S. Lee*, TransRot: A portable software package for simulated annealing Monte Carlo geometry optimization of atomic and molecular clusters, in Physical Chemistry Research at Undergraduate Institutions: Innovative and Impactful Approaches, Vol.1, T. Hopkins and C.A. Parish, Eds., Chapter 2, pp, 19-38, ACS Symposium Series Vol. 1428 (2022). eISBN: 9780841297425
A.J.V. Lomboy*, R.Q. Topper, Nonuniform proton transfer and strong hydrogen bonding within cation, anion, and neutral clusters of ammonia and hydrogen fluoride, Journal of Physical Chemistry A, 125(12), pp. 2546-2557 (2021). DOI: 10.1021/acs.jpca.1c00732.
J.R. Cendagorta, J. Tolpin*, E. Schneider, R.Q. Topper, M.E. Tuckerman, Comparison of the performance of machine learning models in representing high-dimensional free energy surfaces and generating observables, Journal of Physical Chemistry B,124(18), pp.3647-3660(2020). DOI: 10.1021/acs.jpcb.0c01218
E. Schneider, L. Dai**, R.Q. Topper, C. Drechsel-Grau, M.E. Tuckerman, Stochastic neural network approach for learning high-dimensional free energy surfaces, Physical Review Letters, 119, p.150601(2017). DOI: 10.1103/PhysRevLett.119.150601
J.J. Biswakarma*, V. Ciocoi*, R.Q. Topper, Energetics, thermodynamics, and hydrogen bonding diversity in ammonium halide clusters, Journal of Physical Chemistry A, 120(40), pp. 7924-7934 (2016). DOI: 10.1021/acs.jpca.6b06788
R.Q. Topper, W. V. Feldmann*, I. Markus*, D. Bergin*, P.R. Sweeney*, Simulated annealing and density functional theory calculations of structural and energetic properties of the ammonium chloride clusters (NH4Cl)n, (NH4+)(NH4Cl)n, and (Cl–)(NH4Cl)n, n = 1–13, Journal of Physical Chemistry A, 115(38), pp. 10423-10432 (2011). DOI: 10.1021/jp2069732
T.A. Isgro, N. Mathew**, R.Q. Topper, Structural characterization of N-acetyl-2-aminofluorene adducts to guanine and deoxyguanosine via a molecular mechanics, semi-empirical and density-functional theory cascade method,Journal of Molecular Structure (THEOCHEM)710, pp.31-43 (2004). DOI: 10.1016/j.theochem.2004.08.005
S. Ling, R.Q. Topper, On the zero point energy difficulty of quasiclassical trajectory simulations, in Handbook of Computational Chemistry Research, C. T. Collett and C. D. Robson, Eds., Nova Science Publishers, Hauppauge, NY, pp. 467-476 (2010). ISBN: 978-1-60741-047-8
R.Q. Topper, D.L. Freeman, D. Bergin, K. LaMarche*, Computational techniques and strategies for Monte Carlo thermodynamic calculations with applications to nanoclusters, in Reviews in Computational Chemistry, Vol. 19, Chapter 1, pp. 1-41, K.B. Lipkowitz, R. Larter and T.R. Cundari, Eds., Wiley-VCH/John Wiley and Sons, New York (2003). ISBN 0-471-23585-7
R.Q. Topper, K. Chung*, C. Boelke*, D. Louie*, J.S. Kang*, R. Hannan*, T. Kiang*, L.H. Chan*, Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene, Theoretical Chemistry Accounts 109/4, 233 (2003). DOI: 10.1007/s00214-002-0409-z
J. Kritzer*, A. Deaconescu*, J. de la Parra Jr.*, D. Coluccio*, S. Mikhail*, R.Q. Topper, Benchmarking potential energy models against bulk properties for simulations of bismuth clusters, Internet Journal of Chemistry3, 12(2000).
R.Q. Topper, Adaptive path-integral Monte Carlo methods for accurate computation of molecular thermodynamic properties, in Monte Carlo Methods in Chemical Physics:Advances in Chemical Physics105, Chapter 5, pp. 117-170, D. Ferguson, I. Siepmann, and D.G. Truhlar, Eds., John Wiley & Sons, Inc., New York (1999). ISBN-13: 978-0471196303
F.M. Torres*, E. Agichtein*, L. Grinberg*, G. Yu*, R.Q. Topper, A note on the application of the “Boltzmann simplex”-simulated annealing algorithm to global optimizations of argon and water clusters, Journal ofMolecular Structure (THEOCHEM)419, 85 (1997). DOI: hS0166-1280(97)00195-4
R.Q. Topper, Visualizing molecular phase space: Non–statistical effects in reaction dynamics, in Reviews in Computational Chemistry, Vol. 10, Chapter 3, pp. 101-176, K.B. Lipkowitz and D.B. Boyd, Eds., VCH Publishers, New York (1997). ISBN:9780471186489
A. Matro, D.L. Freeman, R.Q. Topper, Computational study of the structures and thermodynamic properties of ammonium chloride clusters using a parallel jump-walking approach,Journal of Chemical Physics104, 8690 (1996). DOI: 10.1063/1.471558
R.Q. Topper, D.L. Freeman, Monte Carlo studies of the orientational order-disorder phase transition in solid ammonium chloride, Los Alamos Chemical Physics Preprint Database, #9403002 (1994). This article was not published elsewhere but was widely disseminated and has been cited in the primary literature. https://arxiv.org/abs/chem-ph/9403002
R.Q. Topper, Q. Zhang, Y.-P. Liu, D.G. Truhlar, Quantum steam tables. Free energy calculations for H2O, D2O, H2S, and H2Se by adaptively optimized Fourier path integrals, Journal of Chemical Physics98, 4991 (1993). DOI: 10.1063/1.464953
R.Q. Topper, G.J. Tawa, D.G. Truhlar, Quantum free-energy calculations: A three-dimensional test case, Journal of Chemical Physics97, 3648 (1992). DOI: 10.1063/1.462949
R.Q. Topper, D.G. Truhlar, Quantum free-energy calculations: Optimized Fourier path-integral Monte Carlo computation of coupled vibrational partition functions,Journal of Chemical Physics97, 3648 (1992). DOI: 10.1063/1.462948
N. De Leon, M.A. Mehta, R.Q. Topper, Cylindrical manifolds in phase space as mediators of chemical reaction dynamics and kinetics II. Numerical considerations and applications to molecular models with two degrees of freedom, Journal of Chemical Physics94, 8329 (1991). DOI: 10.1063/1.460065
N. De Leon, M.A. Mehta, R.Q. Topper, Cylindrical manifolds in phase space as mediators of chemical reaction dynamics and kinetics I. Theory,Journal of Chemical Physics 94, 8310 (1991). DOI: 10.1063/1.460116

PUBLISHED SOFTWARE, EDUCATIONAL MATERIALS AND BOOK REVIEWS (*=undergraduate coauthor)

S.L. Topper*, R.Q. Topper, TransRot, https://github.com/steventopper/Transrot (2021-present).
R.Q. Topper, I. Markus*, Annie 4.7.1, https://robert-topper.cargo.site/publications-1#publications-and-symposia-list (2022).
R.Q. Topper, C.R. Spray, J. Duncan, L.J. Treadwell, S.G. Sobel, How Many Atoms Are In A Nanowire?, http://www.ionicviper.org (2013). Contributed learning object. Workshop product; peer reviewed.
J.Duncan, C.R. Spray, L.J. Treadwell, R.Q. Topper, S.G. Sobel, Solid State, Semiconductors, Electrochemistry, and Nanowires for Solar Cells: Discuss! http://www.ionicviper.org (2013). Contributed learning object. Workshop product; peer reviewed.
R.Q. Topper, Trends in Measured Redox Potentials and Computed Molecular Orbital Energies of Derivatized Buckminsterfullerene, https://www.ionicviper.org/(2013). Contributed learning object, peer reviewed.
“Atomistic Approaches in Modern Biology: From Quantum Chemistry to Molecular Simulations. Topics in Current Chemistry, Volume 268,”Journal of the American Chemical Society,129(31), pp 9830 – 9831 (2007). Invited book review.
“Reviews in Computational Chemistry, Vol. 13,”Journal of the American Chemical Society,122(19), 4845 (2000). Invited book review.
“Mathematica Computer Programs for Physical Chemistry,” Theoretical Chemistry Accounts, 101, 439 (1999). Invited book review.
"Quantum Mechanics Simulations: Consortium for Upper-level Physics Software by J.R Hiller, I.D. Johnston and D.F. Styer,” Computer Physics Communications,94,272 (1995). Invited book review.

ORGANIZATION OF CONFERENCES AND SYMPOSIA

Organizing team member, Virtual Winter School on Computational Chemistry (2022-2026). See https://winterschool.cc/team .
Invited member of the Scientific Organizing Committee, 14th International Electronic Conference on Synthetic Organic Chemistry (November 2010).
Principal Organizer, 7th - 11th Electronic Computational Chemistry Conference(2001–2007).
Invited member of the Scientific Organizing Committee, Fourth Annual Electronic Computational Chemistry Conference (November 1997).
Invited session chair, Computational Chemistry in Graduate and Undergraduate Education, 213th national meeting of the ACS, San Francisco, CA (March 1997).
Invited session organizer and online session chair, “Stochastic Methods for Conformational Sampling,” First Electronic Molecular Modelling and Graphics Society Conference. (October 1996).

EDITED CONFERENCE PROCEEDINGS (**=high school student coauthor)

R.Q. Topper, and O. Dmitrenko, Eds., Abstracts of the 11th Electronic Computational Chemistry Conference, http://stores.lulu.com/eccc (2008).
R.Q. Topper, G. Sun, Eds., Proceedings of the 10th Electronic Computational Chemistry Conference, Theoretical Chemistry Accounts117(2) (2007); R.Q. Topper and G. Sun, Introduction to the Proceedings of the 10th Electronic Computational Chemistry Conference, Theoretical Chemistry Accounts117(2), p. 183 (2007).

R.Q. Topper, O. Dmitrenko, Eds., Proceedings of the 9th Electronic Computational Chemistry Conference, International Journal of Molecular Sciences Vols. 5-7(2004); R.Q. Topper and O. Dmitrenko, Introduction to the Proceedings of the9th Electronic Computational Chemistry Conference, International Journal of Molecular Sciences Vol. 5 (2004).

Structural characterization of N-acetyl-2-aminofluorene (AAF) guanine and deoxyguanosine adducts via a molecular mechanics, semi-empirical, and density functional theory cascade method, T.A. Isgro, N. Mathew**, R.Q. Topper, “Frontiers in DNA Research: An Interdisciplinary Symposium” program at the 226th national meeting of the ACS, New York, NY (2003).Contributed lecture.
R.Q. Topper, W.M.F. Fabian, Eds., Proceedings of the 8th Electronic Computational Chemistry Conference, special issue, Theoretical Chemistry Accounts 109/4(2003); R.Q. Topper, W.M.F. Fabian, Introduction to the Proceedings of the 8th Electronic Computational Chemistry Conference, Theoretical Chemistry Accounts109/4, p.1(2003).

THE ALBERT NERKEN SCHOOL OF ENGINEERING