For a list of papers, also see my Google Scholar page

For papers for download, see my pre-prints on arXiv.

For presentations, see this presentations page.

Published work, University of Iowa (16)

42. #Van Benschoten, W. Z., #Petras H.R., Shepherd, J. J. (2023). Electronic Free Energy Surface of the Nitrogen Dimer Using First-Principles Finite Temperature Electronic Structure Methods. The Journal of Physical Chemistry A 127 (32), 6842-6856. https://doi.org/10.1021/acs.jpca.3c01741 # authors contributed equally.

41. Van Benschoten, W. Z., Weiler, L., Smith, G. J., Man, S., DeMello, T., Shepherd, J. J. (2023). Electronic specific heat capacities and entropies from density matrix quantum Monte Carlo using Gaussian process regression to find gradients of noisy data. The Journal of Chemical Physics, 158, 214115; https://doi.org/10.1063/5.0150702 & on arXiv: https://doi.org/10.48550/arXiv.2305.07081

40. Paudel, A., Campbell, E. J., Van Benschoten, W. Z., Otting, G. W., Shepherd, J. J., Bowden, N. B. (2023). Polymerization of Primary Amines with Sulfur Monochloride to Yield Red Polymers with a Conjugated SN Backbone. Macromolecules. https://doi.org/10.1021/acs.macromol.2c02507

39. Mihm, T. N., Weiler, L., Shepherd, J. J. (2023). How the Exchange Energy Can Affect the Power Laws Used to Extrapolate the Coupled Cluster Correlation Energy to the Thermodynamic Limit. Journal of Chemical Theory and Computation, 19, 6, 1686–1697 https://doi.org/10.1021/acs.jctc.2c00737 & on arXiv: https://arxiv.org/abs/2302.05051

38. Weiler, L., Mihm, T. N., Shepherd, J. J. (2022). Machine learning for a finite size correction in periodic coupled cluster theory calculations. The Journal of Chemical Physics, 156, 204109; https://doi.org/10.1063/5.0086580 & on arXiv: https://arxiv.org/abs/2204.00092

37. Van Benschoten, W. Z., Shepherd, J. J. (2022). Piecewise interaction picture density matrix quantum Monte Carlo. The Journal of Chemical Physics, 156, 184107; https://doi.org/10.1063/5.0094290 & on arXiv: https://arxiv.org/abs/2108.06252

36. Mihm, T. N., Schäfer, T, Ramadugu, S. K., Weiler, L, Grüneis, A.,  Shepherd, J. J. (2021). A shortcut to the thermodynamic limit for quantum many-body calculations of metals. Nature Computational Science 1, 801–808 (2021). https://doi.org/10.1038/s43588-021-00165-1(open access)

35. #Petras, H. R., #Van Benschoten, W. Z., Ramadugu, S. K., Shepherd, J. J. (2021). The sign problem in density matrix quantum Monte Carlo. Journal of Chemical Theory and Computation, 17, 10, 6036–6052. https://pubs.acs.org/doi/abs/10.1021/acs.jctc.1c00078 & on arXiv: http://arxiv.org/abs/2102.00080 # authors contributed equally.

34. Dorian, A., Landgreen, E. J., Petras, H. R., Shepherd, J. J., Williams, F. J. (2021) Iron-catalyzed halogen exchange for trifluoromethyl arenes. Chem. Eur. J. 27, 10839. https://doi.org/10.1002/chem.202101324 

33. Mihm, T. N., Yang, B., Shepherd, J. J. (2021) Power laws used to extrapolate the coupled cluster correlation energy to the thermodynamic limit. Journal of Chemical Theory and Computation, 17, 5, 2752–2758 https://doi.org/10.1021/acs.jctc.0c01171 

32. Mihm, T. N., Van Benschoten, W. Z., Shepherd, J. J. (2021) Accelerating convergence to the thermodynamic limit with twist angle selection applied to methods beyond many-body perturbation theory. Journal of Chemical Physics 154, 024113 ; https://doi.org/10.1063/5.0033408

31. * Petras, H. R., Ramadugu, S. K., Malone, F. D., Shepherd, J. J. (2020) Using density matrix quantum Monte Carlo for calculating exact-on-average energies for ab-initio Hamiltonians in a finite basis set. Journal of Chemical Theory and Computation,  16, 2, 1029-1038. https://doi.org/10.1021/acs.jctc.9b01080 

30. * #Petras, H. R., #Graham, D. S., Ramadugu, S. K., Goodpaster, J. D., Shepherd, J. J. (2019) Fully quantum embedding with density functional theory for full configuration interaction quantum Monte Carlo. Journal of Chemical Theory and Computation, 15, 10, 5332-5342. https://dx.doi.org/10.1021/acs.jctc.9b00571 # authors contributed equally.

29. *** Spielvogel, K. D.; Coughlin, E. J.; Petras, H.; Luna, J. A.; Benson, A.; Donahue, C. M.; Kibasa, A.; Lee, K.; Salacinski, R.; Bart, S. C.; Shaw, S. K.; Shepherd, J, J.; Daly, S. R. (2019) "The Influence of Redox-Innocent Donor Groups in Tetradentate Ligands Derived from o-Phenylenediamine: Electronic Structure Investigations with Nickel." Inorganic Chemistry,  58, 19, 12756 - 12774. https://dx.doi.org/10.1021/acs.inorgchem.9b01675

28. * Mihm, T. N., McIsaac, A. R., Shepherd, J. J. (2019). An optimized twist angle to find the thermodynamic limit derived from the uniform electron gas. The Journal of Chemical Physics, 150, 191101. https://dx.doi.org/10.1063/1.5091445. Published as a Communication. 

27. *** Spencer, J. S., Blunt, N. S., Choi, S., Etrych, J., Filip, M.-A., Foulkes, W. M. C., Franklin, R. S., Handley, W. J., Malone, F. D., Neufeld, V. A., Di Remigio, R., Rogers, T. W., Scott, C. J., Shepherd, J. J., Vigor, W. A., Weston, J., Xu, R., Thom, A. J. (2019) The HANDE-QMC project: open-source stochastic quantum chemistry from the ground state up. Journal of Chemical Theory and Computation, 15, 1728-1742. https://dx.doi.org/10.1021/acs.jctc.8b01217  

Published work, before University of Iowa (26)

26. Kai Guther, Robert J. Anderson, Nick S. Blunt, Nikolay A. Bogdanov, Deidre Cleland, Nike Dattani, Werner Dobrautz, Khaldoon Ghanem, Peter Jeszenszki, Niklas Liebermann, Giovanni Li Manni, Alexander Y. Lozovoi, Hongjun Luo, Dongxia Ma, Florian Merz, Catherine Overy, Markus Rampp,  Pradipta Kumar Samanta, Lauretta R. Schwarz, James J. Shepherd, Simon D. Smart, Eugenio Vitale, Oskar Weser, George H. Booth, and Ali Alavi (2020). NECI: N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods. J. Chem. Phys. 153, 034107. https://doi.org/10.1063/5.0005754

25. Nadav Geva, James J. Shepherd, Lea Nienhaus, Moungi G. Bawendi, and Troy Van Voorhis J. Phys. Chem. C, 122, 45, 26267 (2018)

24. **** Weighold, S., Neinhaus, L., Knoller, F. L., Schweinberger, F. F., Shepherd, J. J., Lyding, J. W., Heiz, U., Gruebele, M., Esch, F. (2017). Plasmonic support-mediated activation of 1 nm platinum clusters for catalysis. Physical Chemistry Chemical Physics, 19(45), 30570-30577. http://dx.doi.org/10.1039/C7CP04882C 

23. Ricke, N. D., Murray, A. T., Shepherd, J. J., Wellborn, M. G., Fukushima, T., Van Voorhis, T., Surendranath, Y. (2017). Molecular-Level Insights into Oxygen Reduction Catalysis by Graphite-Conjugated Active Sites. ACS Catalysis, 7(11), 7680. http://dx.doi.org/10.1021/acscatal.7b03086

22. Geva, N., Vaissier, V., Shepherd, J., Van Voorhis, T. (2017). Mean field treatment of heterogeneous steady state kinetics. Chemical Physics Letters, 685, 185–190. http://dx.doi.org/10.1016/j.cplett.2017.07.011

21. Dai, P., Williams, J. K., Zhang, C., Welborn, M., Shepherd, J. J., Zhu, T., Van Voorhis, T., Hong, M., Pentelute, B. L. (2017). A structural and mechanistic study of $π$-clamp-mediated cysteine perfluoroarylation. Scientific Reports, 7, 7954. http://dx.doi.org/10.1038/s41598-017-08402-2

20. Nienhaus, L., Wu, M., Geva, N., Shepherd, J. J., Wilson, M. W., Bulović, V., Van Voorhis, T., Baldo, M. A., Bawendi, M. G. (2017). Speed Limit for Triplet-Exciton Transfer in Solid-State PbS Nanocrystal-Sensitized Photon Upconversion. ACS nano, 11(8), 7848–7857. http://dx.doi.org/10.1021/acsnano.7b02024

19. Mavros, M. G., Shepherd, J. J., Tsuchimochi, T., McIsaac, A. R., Van Voorhis, T. (2017). Computational Design Principles of Two-Center First-Row Transition Metal Oxide Oxygen Evolution Catalysts. The Journal of Physical Chemistry C, 121(29), 15665–15674. http://dx.doi.org/10.1021/acs.jpcc.7b02424

18. Dai, P., Zhang, C., Welborn, M., Shepherd, J. J., Zhu, T., Van Voorhis, T., Pentelute, B. L. (2016). Salt Effect Accelerates Site-Selective Cysteine Bioconjugation. American Chemical Society.  

17. Shepherd, J. J. (2016). Communication: Convergence of many-body wave-function expansions using a plane-wave basis in the thermodynamic limit. The Journal of Chemical Physics, 145, 031104. https://doi.org/10.1063/1.4958461

16. Malone, F. D., Blunt, N., Brown, E. W., Lee, D., Spencer, J., Foulkes, W., Shepherd, J. J. (2016). Accurate exchange-correlation energies for the warm dense electron gas. Physical Review Letters, 117(11), 115701. https://doi.org/10.1103/PhysRevLett.117.115701

15. Shepherd, J. J., Henderson, T. M., Scuseria, G. E. (2016). Using full configuration interaction quantum Monte Carlo in a seniority zero space to investigate the correlation energy equivalence of pair coupled cluster doubles and doubly occupied configuration interaction. The Journal of Chemical Physics, 144(9), 094112. https://doi.org/10.1063/1.4942770

14. Malone, F. D., Blunt, N., Shepherd, J. J., Lee, D., Spencer, J., Foulkes, W. (2015). Interaction picture density matrix quantum Monte Carlo. The Journal of Chemical Physics, 143(4), 044116. https://doi.org/10.1063/1.4927434

13. J. S. Spencer, N. S. Blunt, W. A. Vigor, F. D. Malone, W. M. C. Foulkes, James J. Shepherd, and A. J. W. Thom. Journal of Open Research Software, 3, e9 (2015)

12. Overy, C., Booth, G. H., Blunt, N., Shepherd, J. J., Cleland, D., Alavi, A. (2014). Unbiased reduced density matrices and electronic properties from full configuration interaction quantum Monte Carlo. The Journal of Chemical Physics, 141(24), 244117. https://doi.org/10.1063/1.4904313

11. Shepherd, J. J., Scuseria, G. E., Spencer, J. S. (2014). Sign problem in full configuration interaction quantum Monte Carlo: Linear and sublinear representation regimes for the exact wave function. Physical Review B, 90(15), 155130. https://doi.org/10.1103/PhysRevB.90.155130

10. Shepherd, J. J., Henderson, T. M., Scuseria, G. E. (2014). Range-separated Brueckner coupled cluster doubles theory. Physical Review Letters, 112(13), 133002. https://doi.org/10.1103/PhysRevLett.112.133002

9. Shepherd, J. J., Henderson, T. M., Scuseria, G. E. (2014). Coupled cluster channels in the homogeneous electron gas. The Journal of Chemical Physics, 140(12), 124102. https://doi.org/10.1063/1.4867783

8. Grüneis, A., Shepherd, J. J., Alavi, A., Tew, D. P., Booth, G. H. (2013). Explicitly correlated plane waves: Accelerating convergence in periodic wavefunction expansions. The Journal of Chemical Physics, 139(8), 084112. https://doi.org/10.1063/1.4818753

7. Shepherd, J. J., Grüneis, A. (2013). Many-body quantum chemistry for the electron gas: Convergent perturbative theories. Physical Review Letters, 110(22), 226401. https://doi.org/10.1103/PhysRevLett.110.226401

6. Farrell, J. D., Lines, C., Shepherd, J. J., Chakrabarti, D., Miller, M. A., Wales, D. J. (2013). Energy landscapes, structural topologies and rearrangement mechanisms in clusters of dipolar particles. Soft Matter, 9(22), 5407–5416. http://dx.doi.org/10.1039/C3SM50711D

5. Shepherd, J. J., Grüneis, A., Booth, G. H., Kresse, G., Alavi, A. (2012). Convergence of many-body wave-function expansions using a plane-wave basis: From homogeneous electron gas to solid state systems. Physical Review B, 86(3), 035111. https://doi.org/10.1103/PhysRevB.86.035111

4. Shepherd, J. J., Booth, G. H., Alavi, A. (2012). Investigation of the full configuration interaction quantum Monte Carlo method using homogeneous electron gas models. The Journal of Chemical Physics, 136(24), 244101. https://doi.org/10.1063/1.4720076

3. Shepherd, J. J., Booth, G., Grüneis, A., Alavi, A. (2012). Full configuration interaction perspective on the homogeneous electron gas. Physical Review B, 85(8), 081103. https://doi.org/10.1063/1.4720076

2. Coomes, D. A., Heathcote, S., Godfrey, E. R., Shepherd, J. J., Sack, L. (2008). Scaling of xylem vessels and veins within the leaves of oak species. Biology Letters, 4(3), 302–306. http://dx.doi.org/10.1098/rsbl.2008.0094

1. Miller, M. A., Shepherd, J. J., Wales, D. J. (2008). Structural trends in clusters of quadrupolar spheres. Molecular Physics, 106(12-13), 1655–1664. http://dx.doi.org/10.1080/00268970802270067