Publications

MC25: An accurate meta pair-density functional for multiconfiguration pair-density functional theory and linearized pair-density functional theory

  • Publication Number: 22
  • Authors: Zhang, D.; Kim, Y.; Hennefarth, M. R.; Gagliardi, L.; Truhlar, D. G.
  • Year: 2025
MC25: An accurate meta pair-density functional for multiconfiguration pair-density functional theory and linearized pair-density functional theory TOC
Full Citation
Zhang, D.; Kim, Y.; Hennefarth, M. R.; Gagliardi, L.; Truhlar, D. G. MC25: An accurate meta pair-density functional for multiconfiguration pair-density functional theory and linearized pair-density functional theory. chemRxiv, 2025.

Linearized pair-density functional theory with spin-orbit coupling

  • Publication Number: 21
  • Authors: Jangid, B.; Hennefarth, M. R.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L.
  • Year: 2025
Linearized pair-density functional theory with spin-orbit coupling TOC
Full Citation
Jangid, B.; Hennefarth, M. R.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L. Linearized pair-density functional theory with spin-orbit coupling. chemRxiv, 2025.

Analytic dipole moments for complete active space linearized pair-density functional theory

  • Publication Number: 20
  • Authors: Clifford, H.; Hennefarth, M. R.; Truhlar, D. G.; Gagliardi, L.
  • Year: 2025
Analytic dipole moments for complete active space linearized pair-density functional theory TOC
Full Citation
Clifford, H.; Hennefarth, M. R.; Truhlar, D. G.; Gagliardi, L. Analytic dipole moments for complete active space linearized pair-density functional theory. J. Phys. Chem. Lett., 2025 16, 10400-10409.

The modern era of multireference methods for chemistry and materials science

  • Publication Number: 19
  • Authors: Wardzala, J.; Hennefarth, M. R.; Agarawal, V.; Jangid, B.; Seal, A.; Hermes, M. R.; King, D. S.; Gagliardi, L.
  • Year: 2025
The modern era of multireference methods for chemistry and materials science TOC
Full Citation
Wardzala, J.; Hennefarth, M. R.; Agarawal, V.; Jangid, B.; Seal, A.; Hermes, M. R.; King, D. S.; Gagliardi, L. The modern era of multireference methods for chemistry and materials science. chemRxiv, 2025.

Weighted active space selection for multireference machine-learned potentials

  • Publication Number: 18
  • Authors: Seal, A.; Perego, S.; Hennefarth, M. R.; Raucci, U.; Bonati, L.; Ferguson, A. L.; Parrinello, M.; Gagliardi, L.
  • Year: 2025
Weighted active space selection for multireference machine-learned potentials TOC
Full Citation
Seal, A.; Perego, S.; Hennefarth, M. R.; Raucci, U.; Bonati, L.; Ferguson, A. L.; Parrinello, M.; Gagliardi, L. Weighted active space selection for multireference machine-learned potentials. Proc. Natl. Acad. Sci. U.S.A., 2025 122, 38, e2513693122, 2505.10505.

MC-PDFT nuclear gradients and L-PDFT energies with meta and hybrid meta on-top functionals for ground- and excited-state geometry optimization and vertical excitation energies

  • Publication Number: 17
  • Authors: Hennefarth, M. R.; Kim, Y.; Jangid, B.; Wardzala, J.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L.
  • Year: 2025
MC-PDFT nuclear gradients and L-PDFT energies with meta and hybrid meta on-top functionals for ground- and excited-state geometry optimization and vertical excitation energies TOC
Full Citation
Hennefarth, M. R.; Kim, Y.; Jangid, B.; Wardzala, J.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L. MC-PDFT nuclear gradients and L-PDFT energies with meta and hybrid meta on-top functionals for ground- and excited-state geometry optimization and vertical excitation energies. J. Chem. Theory Comput., 2025 21, 16, 7890--7902, 2506.03304.

Multireference embedding and fragmentation methods for classical and quantum computers: From model systems to realistic applications

  • Publication Number: 16
  • Authors: Verma, S.; Mitra, A.; Wang, Q.; D’Cunha, R.; Jangid, B.; Hennefarth, M. R.; Agarawal, V.; Otis, L.; Haldar, S.; Hermes, M. R. et al.
  • Year: 2025
Multireference embedding and fragmentation methods for classical and quantum computers: From model systems to realistic applications TOC
Full Citation
Verma, S.; Mitra, A.; Wang, Q.; D’Cunha, R.; Jangid, B.; Hennefarth, M. R.; Agarawal, V.; Otis, L.; Haldar, S.; Hermes, M. R.; Gagliardi, L. Multireference embedding and fragmentation methods for classical and quantum computers: From model systems to realistic applications. arXiv, 2025, 2505.13394.

PyCPET - Computing heterogeneous 3D protein electric fields and their dynamics

  • Publication Number: 15
  • Authors: Ajmera, P.; Vargas, S.; Chaturvedi, S.; Hennefarth, M. R.; Alexandrova, A. N.
  • Year: 2025
PyCPET - Computing heterogeneous 3D protein electric fields and their dynamics TOC
Full Citation
Ajmera, P.; Vargas, S.; Chaturvedi, S.; Hennefarth, M. R.; Alexandrova, A. N. PyCPET - Computing heterogeneous 3D protein electric fields and their dynamics. J. Chem. Theory Comput., 2025 21, 8, 4299--4308.

Semiclassical nonadiabatic molecular dynamics using linearized pair-density functional theory

  • Publication Number: 14
  • Authors: Hennefarth, M. R.; Truhlar, D. G.; Gagliardi, L.
  • Year: 2024
Semiclassical nonadiabatic molecular dynamics using linearized pair-density functional theory TOC
Full Citation
Hennefarth, M. R.; Truhlar, D. G.; Gagliardi, L. Semiclassical nonadiabatic molecular dynamics using linearized pair-density functional theory. J. Chem. Theory Comput., 2024 20, 20, 8741--8748, 2408.05434.

Analytic nuclear gradients for complete active space linearized pair-density functional theory

  • Publication Number: 13
  • Authors: Hennefarth, M. R.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L.
  • Year: 2024
Analytic nuclear gradients for complete active space linearized pair-density functional theory TOC
Full Citation
Hennefarth, M. R.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L. Analytic nuclear gradients for complete active space linearized pair-density functional theory. J. Chem. Theory Comput., 2024 20, 9, 3637--3658, 2401.12933.

Linearized pair-density functional theory for vertical excitation energies

  • Publication Number: 12
  • Authors: Hennefarth, M. R.; King, D. S.; Gagliardi, L.
  • Year: 2023
Linearized pair-density functional theory for vertical excitation energies TOC
Full Citation
Hennefarth, M. R.; King, D. S.; Gagliardi, L. Linearized pair-density functional theory for vertical excitation energies. J. Chem. Theory Comput., 2023 19, 22, 7983--7988.

Linearized pair-density functional theory

  • Publication Number: 11
  • Authors: Hennefarth, M. R.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L.
  • Year: 2023
Linearized pair-density functional theory TOC
Full Citation
Hennefarth, M. R.; Hermes, M. R.; Truhlar, D. G.; Gagliardi, L. Linearized pair-density functional theory. J. Chem. Theory Comput., 2023 19, 11, 3172--3183.

The OpenMolcas web: A community-driven approach to advancing computational chemistry

  • Publication Number: 10
  • Authors: Li M. Giovanni; Fdez. G. Ignacio; Alavi, A.; Aleotti, F.; Aquilante, F.; Autschbach, J.; Avagliano, D.; Baiardi, A.; Bao, J. J.; Battaglia, S. et al.
  • Year: 2023
The OpenMolcas web: A community-driven approach to advancing computational chemistry TOC
Full Citation
Li M. Giovanni; Fdez. G. Ignacio; Alavi, A.; Aleotti, F.; Aquilante, F.; Autschbach, J.; Avagliano, D.; Baiardi, A.; Bao, J. J.; Battaglia, S.; Birnoschi, L.; Blanco-González, A.; Bokarev, S. I.; Broer, R.; Cacciari, R.; Calio, P. B.; Carlson, R. K.; Carvalho C. Rafael; Cerdán, L.; Chibotaru, L. F.; Chilton, N. F.; Church, J. R.; Conti, I.; Coriani, S.; Cuéllar-Zuquin, J.; Daoud, R. E.; Dattani, N.; Decleva, P.; de G. Coen; Delcey, M. G.; De V. Luca; Dobrautz, W.; Dong, S. S.; Feng, R.; Ferré, N.; Filatov(Gulak), M.; Gagliardi, L.; Garavelli, M.; González, L.; Guan, Y.; Guo, M.; Hennefarth, M. R.; Hermes, M. R.; Hoyer, C. E.; Huix-Rotllant, M.; Jaiswal, V. K.; Kaiser, A.; Kaliakin, D. S.; Khamesian, M.; King, D. S.; Kochetov, V.; Krośnicki, M.; Kumaar, A. A.; Larsson, E. D.; Lehtola, S.; Lepetit, M.; Lischka, H.; López R. Pablo; Lundberg, M.; Ma, D.; Mai, S.; Marquetand, P.; Merritt, I. C. D.; Montorsi, F.; Mörchen, M.; Nenov, A.; Nguyen, V. H. A.; Nishimoto, Y.; Oakley, M. S.; Olivucci, M.; Oppel, M.; Padula, D.; Pandharkar, R.; Phung, Q. M.; Plasser, F.; Raggi, G.; Rebolini, E.; Reiher, M.; Rivalta, I.; Roca-Sanjuán, D.; Romig, T.; Safari, A. A.; Sánchez-Mansilla, A.; Sand, A. M.; Schapiro, I.; Scott, T. R.; Segarra-Martí, J.; Segatta, F.; Sergentu, D.; Sharma, P.; Shepard, R.; Shu, Y.; Staab, J. K.; Straatsma, T. P.; Sørensen, L. K.; Tenorio, B. N. C.; Truhlar, D. G.; Ungur, L.; Vacher, M.; Veryazov, V.; Voß, T. A.; Weser, O.; Wu, D.; Yang, X.; Yarkony, D.; Zhou, C.; Zobel, J. P.; Lindh, R. The OpenMolcas web: A community-driven approach to advancing computational chemistry. J. Chem. Theory Comput., 2023 19, 20, 6933--6991.

Histidine‐mediated ion specific effects enable salt tolerance of a pore‐forming marine antimicrobial peptide

  • Publication Number: 9
  • Authors: Xian, W.; Hennefarth, M. R.; Lee, M. W.; Do, T.; Lee, E. Y.; Alexandrova, A. N.; Wong, G. C. L.
  • Year: 2022
Histidine‐mediated ion specific effects enable salt tolerance of a pore‐forming marine antimicrobial peptide TOC
Full Citation
Xian, W.; Hennefarth, M. R.; Lee, M. W.; Do, T.; Lee, E. Y.; Alexandrova, A. N.; Wong, G. C. L. Histidine‐mediated ion specific effects enable salt tolerance of a pore‐forming marine antimicrobial peptide. Angew. Chem-ger. Edit., 2022 134, 25.

Mineralized Peyronie’s plaque has a phenotypic resemblance to bone

  • Publication Number: 8
  • Authors: Ustriyana, P.; Hennefarth, M. R.; Srirangapatanam, S.; Jung, H.; Wang, Y.; Chen, L.; Lue, T. F.; Lin, G.; Kang, M.; Stoller, M. L. et al.
  • Year: 2022
Mineralized Peyronie’s plaque has a phenotypic resemblance to bone TOC
Full Citation
Ustriyana, P.; Hennefarth, M. R.; Srirangapatanam, S.; Jung, H.; Wang, Y.; Chen, L.; Lue, T. F.; Lin, G.; Kang, M.; Stoller, M. L.; Ho, S. P. Mineralized Peyronie’s plaque has a phenotypic resemblance to bone. Acta Biomater., 2022 140, 457--466.

Advances in optimizing enzyme electrostatic preorganization

  • Publication Number: 7
  • Authors: Hennefarth, M. R.; Alexandrova, A. N.
  • Year: 2022
Advances in optimizing enzyme electrostatic preorganization TOC
Full Citation
Hennefarth, M. R.; Alexandrova, A. N. Advances in optimizing enzyme electrostatic preorganization. Curr. Opin. Struc. Biol., 2022 72, 1--8.

Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density

  • Publication Number: 6
  • Authors: Vargas, S.; Hennefarth, M. R.; Liu, Z.; Alexandrova, A. N.
  • Year: 2021
Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density TOC
Full Citation
Vargas, S.; Hennefarth, M. R.; Liu, Z.; Alexandrova, A. N. Machine Learning to Predict Diels–Alder Reaction Barriers from the Reactant State Electron Density. J. Chem. Theory Comput., 2021 17, 10, 6203--6213.

Heterogeneous intramolecular electric field as a descriptor of Diels–Alder reactivity

  • Publication Number: 5
  • Authors: Hennefarth, M. R.; Alexandrova, A. N.
  • Year: 2021
Heterogeneous intramolecular electric field as a descriptor of Diels–Alder reactivity TOC
Full Citation
Hennefarth, M. R.; Alexandrova, A. N. Heterogeneous intramolecular electric field as a descriptor of Diels–Alder reactivity. J. Phys. Chem. A, 2021 125, 5, 1289--1298.

Direct look at the electric field in ketosteroid isomerase and its variants

  • Publication Number: 4
  • Authors: Hennefarth, M. R.; Alexandrova, A. N.
  • Year: 2020
Direct look at the electric field in ketosteroid isomerase and its variants TOC
Full Citation
Hennefarth, M. R.; Alexandrova, A. N. Direct look at the electric field in ketosteroid isomerase and its variants. ACS Catal., 2020 10, 17, 9915--9924.

Physicochemical and biochemical spatiotemporal maps of a mouse penis

  • Publication Number: 3
  • Authors: Hennefarth, M. R.; Chen, L.; Wang, B.; Lue, T. F.; Stoller, M. L.; Lin, G.; Kang, M.; Ho, S. P.
  • Year: 2020
Physicochemical and biochemical spatiotemporal maps of a mouse penis TOC
Full Citation
Hennefarth, M. R.; Chen, L.; Wang, B.; Lue, T. F.; Stoller, M. L.; Lin, G.; Kang, M.; Ho, S. P. Physicochemical and biochemical spatiotemporal maps of a mouse penis. J. Biomech., 2020 101, 109637.

The case for enzymatic competitive metal affinity methods

  • Publication Number: 2
  • Authors: Reilley, D. J.; Hennefarth, M. R.; Alexandrova, A. N.
  • Year: 2020
The case for enzymatic competitive metal affinity methods TOC
Full Citation
Reilley, D. J.; Hennefarth, M. R.; Alexandrova, A. N. The case for enzymatic competitive metal affinity methods. ACS Catal., 2020 10, 3, 2298--2307.

A chemical biology approach to model pontocerebellar hypoplasia type 1B (PCH1B)

  • Publication Number: 1
  • Authors: François-Moutal, L.; Jahanbakhsh, S.; Nelson, A. D. L.; Ray, D.; Scott, D. D.; Hennefarth, M. R.; Moutal, A.; Perez-Miller, S.; Ambrose, A. J.; Al-Shamari, A. et al.
  • Year: 2018
A chemical biology approach to model pontocerebellar hypoplasia type 1B (PCH1B) TOC
Full Citation
François-Moutal, L.; Jahanbakhsh, S.; Nelson, A. D. L.; Ray, D.; Scott, D. D.; Hennefarth, M. R.; Moutal, A.; Perez-Miller, S.; Ambrose, A. J.; Al-Shamari, A.; Coursodon, P.; Meechoovet, B.; Reiman, R.; Lyons, E.; Beilstein, M.; Chapman, E.; Morris, Q. D.; Van K. Kendall; Hughes, T. R.; Khanna, R.; Koehler, C.; Jen, J.; Gokhale, V.; Khanna, M. A chemical biology approach to model pontocerebellar hypoplasia type 1B (PCH1B). ACS Chem. Biol., 2018 13, 10, 3000--3010.