Pan, X.; Snyder, R.; Wang, J.-N.; Lander, C.; Wickizer, C.; Van, R.; Chesney, A.; Xue, Y.; Mao, Y.; Mei, Y.; Pu, J.; Shao, Y. Training machine learning potentials for reactive systems: A Colab tutorial on basic models. J. Comput. Chem. 2024, 45, 638-647. (Link)
Pan, X.; Van, R.; Mao, Y.; Pu, J.; Nam, K.; Shao, Y. Free energy profile decomposition analysis for QM/MM simulations of enzymatic reactions. J. Chem. Theory Comput. 2023, 19, 8234–8244. (Link)
Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; Pu, J. Bridging semiempirical and ab initio QM/MM potentials by Gaussian process regression and its sparse variants for free energy simulation. J. Chem. Phys. 2023, 159, 054107. (Link)
Wang, J.-N.; Xue, Y.; Li, P.; Pan, X.; Wang, M.; Shao, Y.; Mo, Y.; Mei, Y. Perspective: Reference-potential methods for the study of thermodynamic properties in chemical processes: Theory, applications, and pitfalls. J. Phys. Chem. Lett. 2023, 14, 4866–4875. (Link)
Yao, S.; Van, R.; Pan, X.; Park, J. H.; Mao, Y.; Pu, J.; Mei, Y.; Shao, Y. Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations. RSC Adv. 2023, 13, 4565–4577. (Link)
Satalkar, V.; Benassi, E.; Mao, Y.; Pan, X.; Ran, C.; Chen, X.; Shao, Y. Computational investigation of substituent effects on the fluorescence wavelengths of oxyluciferin analogs. J. Photochem. Photobiol. A: Chem. 2022, 431, 114018. (Link)
Lander, C.; Satalkar, V.; Yang, J.; Pan, X.; Pei, Z.; Chatterji, A.; Liu, C.; Nicholas, K. M.; Cichewicz, R. H.; Yang, Z.; Shao, Y. Visualization of electron density changes along chemical reaction pathways. Mol. Phys. 2022, e2113566. (Link)
Pan, X.; Van, R.; Epifanovsky, E.; Liu, J.; Pu, J.; Nam, K.; Shao, Y. Accelerating ab initio quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations with multiple time step integration and a recalibrated semiempirical QM/MM Hamiltonian. J. Phys. Chem. B 2022, 126, 4226–4235. (Link)
Snyder, R.; Kim, B.; Pan, X.; Shao, Y.; Pu, J. Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations. Phys. Chem. Chem. Phys. 2022, 24, 25134–25143. (Link)
Xue, Y.; Wang, J.-N.; Hu, W.; Zheng, J.; Li, Y.; Pan, X.; Mo, Y.; Shao, Y.; Wang, L.; Mei, Y. Affordable ab initio path integral for thermodynamic properties via molecular dynamics simulations using semiempirical reference potential. J. Phys. Chem. A 2021, 125, 10677–10685. (Link)
Pan, X.; Yang, J.; Van, R.; Epifanovsky, E.; Ho, J.; Huang, J.; Pu, J.; Mei, Y.; Nam, K.; Shao, Y. Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions. J. Chem. Theory Comput. 2021, 17, 5745–5758. (Link)
Wang, J.-N.; Liu, W.; Li, P.; Mo, Y.; Hu, W.; Zheng, J.; Pan, X.; Shao, Y.; Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 4. Adaptive QM/MM. J. Chem. Theory Comput. 2021, 17, 1318–1325. (Link)
Pan, X.; Nam, K.; Epifanovsky, E.; Simmonett, A. C.; Rosta, E.; Shao, Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J. Chem. Phys. 2021, 154, 024115. (Link)
Hu, W.; Li, P; Wang, J.-N.; Xue, Y.; Mo, Y.; Zheng, J.; Pan, X.; Shao, Y.; Mei, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semiempirical reference potential. 3. Gaussian smoothing on density-of-states. J. Chem. Theory Comput. 2020, 16, 6814–6822. (Link)
Khatri, H. R.; Han, C.; Luong, E.; Pan, X.; Shao, Y.; Colby, D. A. Controlling the cleavage of carbon–carbon bonds to generate α,α-difluorobenzyl carbanions for the construction of difluoromethylbenzenes. J. Org. Chem. 2019, 84, 11665–11675. (Link)
Pan, X.; Li, P.; Ho, J.; Pu, J.; Mei, Y.; Shao, Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching. Phys. Chem. Chem. Phys. 2019, 21, 20595–20605. (Link)
Liu, R.; Zhang, G.; Sun, M.; Pan, X.; Yang, Z. Integrating a generalized data analysis workflow with the Single-probe mass spectrometry experiment for single cell metabolomics. Anal. Chim. Acta 2019, 1064, 71–79. (Link)
Satalkar, V.; Rusmore, T. A.; Phillips, E.; Benassi, E.; Wu, Q.; Ran, C.; Pan, X.; Shao, Y. Computational modeling of curcumin-based fluorescent probe molecules. Theor. Chem. Acc. 2019, 138, 29. (Link)
Li, P.; Jia, X.; Pan, X.; Shao, Y.; Mei. Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanics accuracy via a semi-empirical reference potential. I. Weighted thermodynamics perturbation. J. Chem. Theory Comput. 2018, 14, 5583—5596. (Link)
Pan, X.; Rosta, E.; Shao, Y. Representation of the QM subsystem for long-range electrostatic interaction in non-periodic ab initio QM/MM calculations. Molecules 2018, 23, 2500. (Link)
Pan, X.; Schwartz, S. D. Conformational heterogeneity in the Michaelis complex of lactate dehydrogenase: An analysis of vibrational spectroscopy using Markov and hidden Markov models. J. Phys. Chem. B 2016, 120, 6612–6620. (Link)
Pan, X.; Schwartz, S. D. Free energy surface of the Michaelis complex of lactate dehydrogenase: A network analysis of microsecond simulations. J. Phys. Chem. B 2015, 119, 5430–5436. (Link)
Pan, X.; Liu, W.; Liu, J. Mechanism of the glycosylation step catalyzed by human α-galactosidase: A QM/MM metadynamics study. J. Phys. Chem. B 2013, 117, 484–489. (Link)
Pan, X.; Zhou, Y.; Liu, W.; Liu, J.; Dong, H. Stereoelectronic control in the cleavage of dioxolane five-membered ring on carbohydrates. Chem. Res. Chin. Univ. 2013, 29, 551–555. (Link)
Pan, X.; Cui, F.; Liu, W.; Liu, J. QM/MM study on the catalytic mechanism of heme-containing aliphatic aldoxime dehydratase. J. Phys. Chem. B 2012, 116, 5689–5693. (Link)
Dong, H.; Zhou, Y.; Pan, X.; Cui, F.; Liu, W.; Liu, J.; Ramström, O. Stereoelectronic control in regioselective carbohydrate protection. J. Org. Chem. 2012, 77, 1457–1467. (Link)
Cui, F.; Pan, X.; Liu, W.; Liu, J. Elucidation of the methyl transfer mechanism catalyzed by chalcone O-methyltransferase: A density functional study. J. Comput. Chem. 2011, 32, 3068–3074. (Link)
Li, L.; Li, G.-D.; Yan, C.; Mu, X.; Pan, X.; Zou, X.; Wang, K.; Chen, J. Efficient sunlight-driven dehydrogenative coupling of methane to ethane over a Zn+-modified zeolite. Angew. Chem. Int. Ed. 2011, 50, 8299–8303. (Link)
Pan, X.; Cui, F.; Liu, J. Quantum mechanical/molecular mechanical molecular dynamics and free energy simulations of the thiopurine S-methyltransferase reaction with 6-mercaptopurine. J. Phys. Chem. B 2011, 115, 8033–8037. (Link)
Cui, F.; Pan, X.; Liu, J. Reaction mechanism of isoflavone O-methyltransferase: A theoretical investigation. Chem. Phys. Lett. 2011, 501, 502–507. (Link)
Cui, F.; Pan, X.; Liu, J. Catalytic mechanism of hydroxynitrile lyase from Hevea brasiliensis: A theoretical investigation. J. Phys. Chem. B 2010, 114, 9622–9628. (Link)
Li, L.; Zhou, X.; Li, G.; Pan, X.; Chen, J. Unambiguous observation of electron transfer from a zeolite framework to organic molecules. Angew. Chem. Int. Ed. 2009, 48, 6678–6682. (Link)