Published/in press 2018-2022

Our Citation Profile at Google Scholar


288. Electronic Polarization is Essential for the Stabilization and Dynamics of Buried Ion Pairs in Staphylococcal Nuclease Mutants, J. Deng, Q. Cui*, J. Am. Chem. Soc., 144, 4594-4610 (2022)

287. Factors that Determine the Variation of Equilibrium and Kinetic Properties of QM/MM enzyme simulations: QM region, Conformation and Boundary Condition, D. Demapan, J. Kussman, C. Ochsenfeld, Q. Cui*, J. Chem. Theory Comput. In Press (2022)

286. The complexin C-terminal amphipathic helix stabilizes the fusion pore open state by sculpting membranes, K. C. Courtney, L. Wu, T. Mandal, M. Swift, Z. Zhang, M. Alaghemandi, Z. Wu, M. M. Bradberry, C. Deo, L. D. Lavis, N. Volkmann, D. Hanein, Q. Cui, H. Bao and E. R. Chapman*, Nat. Struct. Mol. Biol. 29, 97-107 (2022)

285. The coiled-coil domain of Escherichia coli FtsLB is a structurally detuned element critical for modulating its activation in bacterial cell division, S. J. Craven, S. G. F. Condon, G. Diaz-Vazquez, Q. Cui, and A. Senes*, J. Biol. Chem., 298, 101460 (2022)

284. Clustering of the HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR and Molecular Dynamics Simulations, N. Tran, Y. Oh, M. Sutherland, Q. Cui*, M. Hong*, J. Mol. Biol. 434, 16735 (2022)

283. O to bR Transition in Bacteriorhodopsin Occurs Through a Proton Hole Mechanism, D. Maag, T. Mast, M. Elstner, Q. Cui and Tomas Kubar*, Proc. Natl. Acad. Sci. USA, 118, e2024803118 (2021)

282. Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis, J. Zeng, J. Weng, Y. Zhang, F. Xia*, Q. Cui, and X. Xu*, J. Phys. Chem. B 125, 8805-8813 (2021)

281. Reverse Protonation of Buried Ion-pairs in Staphylococcal Nuclease Mutants, J. Deng, Q. Cui*, J. Chem. Theory. Comput., 17, 4550-4563 (2021)

280. Protein Induced Membrane Curvature in Coarse-Grained Simulations: Binding Interface, Insertion Depth and Lipid Spontaneous Curvature, T. Mandal, S. E. Spagnolie, A. Audhya and Q. Cui*, Biophys. J., 120, 3211-3221 (2021)

279. Influence of Hydrophobic Length and Flexibility of Surface Ligands on Phospholipid Membrane Disruption by Cationic Nanoparticles, Y. Q. Zhang, U. Dahal, Z. V. Feng, Z. Rosenzweig, Q. Cui* and R. J. Hamers*, Langmuir, 37, 7600-7610 (2021)

278. Multiple deprotonation paths of the nucleophile 3′-OH in the DNA synthesis reaction, M. T. Gregory, Y. Gao, Q. Cui and W. Yang*, Proc. Natl. Acad. Sci. USA, 118, e2103990118 (2021)

277. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation, W. Ren, H. Fan, S. A. Grimm, J. J. Kim, L. Li, Y. Guo, C. J. Petell, X. -F. Tan, Z. -M. Zhang, J. P. Coan, J. Yin, D. I. Kim, L. Gao, L. Cai, N. Khudaverdyan, B. Cetin, D. J. Patel, Y. Wang, Q. Cui, B. D. Strahl, O. Gozani, K. M. Miller, S. E. O’Leary, P. A. Wade, G. G. Wang*, J. Song*, Nat. Comm., 12, 2490 (2021)

276. Substrate deformation regulates DRM2-mediated DNA methylation in plants, J. Fang, S. M. Leichter, J. Jiang, M. Biswal, J. Lu, Z-M Zhang, W. Ren, J. Zhai, Q. Cui, X. Zhong,* J. Song*, Sci. Adv. 7, eabd9224 (2021)

275. Modulation of Nanoparticle Diffusion by Surface Ligand Length and Charge: Analysis with Molecular Dynamics Simulations, A. Y. Cui and Q. Cui* J. Phys. Chem. B 125, 4555-4565 (2021)

274. Mapping temperature-dependent conformational change in the voltage-sensing domain of an engineered heat-activated K+ channel, H. B. Chen, J. H. Deng, Q. Cui, B. Chanda*, K. Henzler-Wildman*, Proc. Natl. Acad. Sci. USA 118, e2017280118 (2021)

273. Interfacial Polarization and Ionic Structure at the Ionic Liquid-Metal Interface Studied by Vibrational Spectroscopy and Molecular Dynamics Simulations, M. J. Voegtle, T. Pal, A. Pennathur, S. Menachekanian, J. G. Patrow, S. Sarkar, Q. Cui, and J. M. Dawlaty*, J. Phys. Chem. B, 125, 10, 2741-2753 (2021)

272. Hercynine imidazole side-chain sp2 C-H bond deuterium exchange: implication for an imidazol- 2-yl carbene intermediate in a rhodanase-catalyzed C-S bond formation from the anaerobic ergoth- ioneine biosynthesis, R. Cheng, R. Lai, C. Peng, J. Lopez, Z. Li, N. Naowarojna, K. Li, C. Wong, N. Lee, S. A. Whelan, L. Qiao, M. W. Grinstaff, J. Y. Wang, Q. Cui*, and P. H. Liu*, ACS Catalysis, 11, 6, 3319-3334 (2021)

271. Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorophore, B. Zhi, X. X. Yao, M. Wu, A. Mensch, Y. Cui, J. H. Deng, J. Duchimaza-Heredia, K. Trerayapiwat, T. Niehaus, Y. Nishimoto, B. Frank, Y. Q. Zhang, R. E. Lewis, R. J. Hamers, H. Fairbrother, G. Orr, C. J. Murphy, Q. Cui, and C. L. Haynes*, Chem. Sci. 12, 2441-2455 (2021)

270. Perspective: Biomolecular QM/MM Simulations: What are the “Burning Issues”? Q. Cui*, T. Pal, L. Xie, J. Phys. Chem. B, 125, 689-702 (2021)

269. Improvement of d − d interactions in Density Functional Tight Binding for Transition Metal Ions with a Ligand Field Model: Assessment of a DFTB3+U model on Nickel coordination compounds, S. Stepanovic, R. Lai, M. Elstner*, M. Gruden*, P. Garcia-Fernandez*, Q. Cui*, PCCP Special Issue on “Quantum Theory: The Challenge of Transition Metal Complexes”, 22, 27084-27095 (2020)

268. What Does the Bronsted Slope Measure in the Phosphoryl Transfer Transition State? L. Rui and Q. Cui*, ACS Catalysis, 10, 13932-13945 (2020)

267. Ligand Length and Surface Curvature Modulate Nanoparticle Surface Heterogeneity and Electrostatics, D. Y. Liang, U. Dahal, M. Wu, C. J. Murphy, and Q. Cui*, J. Phys. Chem. C, 124, 24513-24525 (2020)

266. Differences in the Nature of Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models, L. Rui and Q. Cui*, J. Phys. Chem. B, Ruth Nussinov Festschrift, 124, 9371-9384 (2020)

265. Anionic nanoparticle-induced fluidization of lipid membranes affects ion channel function, I. U. Foreman-Ortiz, D. Y. Liang, E. D. Laudadio, J. Calderin, M. Wu, P. Keshri, X. Z. Zhang, M. P. Schwartz, R. J. Hamers, V. M. Rotello, C. J. Murphy, Q. Cui and J. A. Pedersen*, Proc. Natl. Acad. Sci. USA, 117, 27854-27861 (2020)

264. Functional Plasticity and Evolutionary Adaptation of Allosteric Regulation, M. Leander, Y. C. Yuan, A. Meger, Q. Cui and S. Raman*, Proc. Natl. Acad. Sci. USA, 117, 25445-25454 (2020)

263. Interfacial water and ion distribution determine $\zeta$-potential and binding affinity of nanoparticles to biomolecules, D. Y. Liang, U. Dahal, Y. Q. Zhang, C. Lochbaum, R. J. Hamers, J. A. Pedersen and Q. Cui*, Nanoscale, 12, 18106-18123 (2020)

262. Single-step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source: An Unprecedented Transformation in Anaerobic Ergothioneine Biosynthesis, R. H. Cheng, L. Wu, R. Lai, C. Peng, N. Naowarojna, W. Y. Hu, X. H. Li, S. A. Whelan, N. Lee, J. Lopez, C. M. Zhao, Y. H. Yong, J. H. Xue, X. F. Jiang, Mark Grinstaff, Z. X. Deng, J. S. Chen*, Q. Cui*, J. H. Zhou*, P. H. Liu*, ACS Catalysis, 10, 8981-8994 (2020)

261. Multi-level Free Energy Simulation with a Staged Transformation Approach, S. Ito and Q. Cui*, J. Chem. Phys., 153, 044115 (2020)

260. Protonation-Driven Aqueous Lyotropic Self-Assembly of Synthetic Six-Tail Lipidoids, J. Jennings, M. C. D. Carter, C. Y. Son, Q. Cui, D. M. Lynn, M. K. Mahanthappa*, Langmuir, 36, 8240-8252 (2020)

259. Cholesterol Interaction with the Trimeric HIV Fusion Protein gp41 in Lipid Bilayers Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations, B. Kwon, T. Mandal, M. R. Elkins, Y. Oh, Q. Cui and M. Hong*, J. Mol. Biol., 432, 4705 (2020)

258. Direct readout of heterochromatic H3K9me3 regulates DNMT1- mediated maintenance DNA methylation, W. D. Ren, H. T. Fan, S. A. Grimm, Y. R. Guo, J. J. Kim, J. K. Yin, L. H. Li, C. J. Petell, X-F, Tan, Z-M. Zhang, J. P. Coan, L. F. Gao, L. Cai, B. Detrick, B. Cetin, Q. Cui, B. Strahl, O. Gozani, Y. S. Wang, K. M. Miller, S. O’Leary, P. A. Wade, D. J. Patel, G. G. Wang, J. K. Song*, Proc. Natl. Acad. Sci. USA 117, 18439-18447 (2020)

257. Identifying the proton loading site cluster in the Ba3 cytochrome c oxidase that loads and traps protons, X. H. Cai, C. Y. Son, J. J. Mao, D. Kaur, Y. Y. Zhang, U. Khaniya, Q. Cui, M. R. Gunner*, BBA Bioenergetics 1861, 148239 (2020)

256. Artificial Intracellular Peptide Filaments, Z. Q. Feng, H. M. Wang, F. B. Wang, C. Berciu, Y. H. Oh, Q. Cui*, E. H. Egelman*, B. Xu*, Cell Rep. Phys. Sci., 1, 100085 (2020)

255. Molecular Simulation of Mechanical Properties and Membrane Activities of the ESCRT-III complexes, T. Mandal, W. Lough, S. E. Spagnolie, A. Audhya and Q. Cui*, Biophys. J., 118, 1333-1343 (2020)

254. Photo-Disassembly of Membrane Microdomains Revives Conventional Antibiotics against MRSA, J. Hui, P-T, Dong, L. Liang, T. Mandal, J. Li, C. Ulloa, Y. W. Zhan, S. Jusuf, C. Zong, M. Seleem, G. Liu, Q. Cui, J-X, Cheng*, Adv. Sci. 7, 1903117 (2020) Cover

253. Electrostatics, Hydrogen Bonding, and Molecular Structure at Polycation and Peptide:Lipid Membrane Interfaces, N. Dalchand, Q. Cui* and F. M. Geiger*, ACS Applied Mater. & Interfaces, 12, 21149-21158 (2020)

252. Proper Thermal Equilibration of Simulations with Drude Polarizable Models : Temperature Grouped Dual-Nos ́e-Hoover Thermostat, C. Y. Son, J. G. McDaniel, Q. Cui, A. Yethiraj∗, J. Phys. Chem. Lett., 10, 7523-7530 (2019)

251. Molecular Dynamics Simulation of Interaction between Functionalized Nanoparticles with Lipid Membranes: Analysis of Coarse-grained Models, M. Das, U. Dahal, O. Mesele, D. Y. Liang and Q. Cui*, J. Phys. Chem. B 123, 10547-10561 (2019)

250. Extensive Free Energy Simulations Identify Water as the Base in Nucleotide Addition by DNA Polymerase, D. Roston, D. Demapan, Q. Cui*, Proc. Natl. Acad. Sci. USA, 116, 25048-25056 (2019)

249. Analysis of Density Functional Tight Binding (DFTB) with Natural Bonding Orbitals (NBOs), X. Lu, J. Duchimaza-Heredia, and Q. Cui*, J. Phys. Chem. A 123, 7439-7453 (2019)

248. NMR structural analysis of isolated Shake voltage-sensing domain in LPPD micelles, H. B. Chen, J. K. Pan, Q. Cui, B. Chanda, K. Henzler-Wildman*, Biophys. J., 117, 388-398 (2019)

247. Quantitative analysis and correction of QM/MM boundary artifacts in adaptive QM/MM methods, H. C. Watanabe* and Q. Cui, J. Chem. Theory Comput., 15, 3917-3928 (2019) Cover

246. A Systematic Determination of Hubbard U using the GBRV Ultrasoft Pseudopotential Set, J. W. Bennett, B. G. Hudson, I. K. Metz, D. Y. Liang, S. Spurgeon, Q. Cui, S. E. Mason*, Comput. Mater. Sci., 170, 109137 (2019)

245. Gating and Inactivation of Mechanosensitive Channels of Small Conductance: A Continuum Mechanics Study, L. L. Zhu, Q. Cui, H. Xiao, X. B. Liao and X. Chen*, J. Mech. Behavior Biomed. Mater. 90, 502-514 (2019)

244. Exploring the Applicability of Density Functional Tight Binding to Transition Metal Ions: Parametrization for Nickel with the Spin-polarized DFTB3 model, M. Vujovic, M. Huynh, S. Steiner, P. Garcia-Fernandez, M. Elstner*, Q. Cui*, M. Gruden*, J. Comp. Chem., Special memorial issue for Keiji Morokuma , 40, 400-413 (2019)

243. N6-methyldeoxyadenosine directs nucleosome positioning in eukaryotic DNA, G. Z. Luo, Z. Y. Hao, M. R. Shen, D. Sparvoli, Y. Q. Zheng, Z. J. Zhang, X. C. Weng, K. Chen, Q. Cui, A. Turkewitz and C. He*, Genome Biol. 19, 200 (2018)

242. Specificity Landscapes unmask differential sequence preferences of homologous transcription factors, D. Bhimsaria, J. A. Rodriguez-Martinez, J. K. Pan, D. Roston, E. N. Korkmaz, Q. Cui, P. Ramanathan, and A. Z. Ansari*, Proc. Natl. Acad. Sci. USA , 115, E10586-10595 (2018)

241. Structural and Mechanistic Basis for Preferential Deadenylation of U6 snRNA by Usb1, Y. Nomura, D. Roston, E. J. Montemayor, Q. Cui*, and S. E. Butcher*, Nuc. Acids Res. 46, 11488-11501 (2018)

240. Lipid Corona Formation from Nanoparticle Interactions with Bilayers and Membrane-Specific Biological Outcomes, L. L. Olenick, J. M. Troiano, A. Vartanian, E. S. Melby, A. Mensch, L. L. Zhang, J. Hong, O. Mesele, T. Qiu, J. Bozich, S. Lohse, X. Zhang, T. R. Kuech, A. Millevolte, I. Gunsolus, A. C. McGeachy, M. Dogang\”un, T. Z. Li, D. H. Hu, S. R. Walter, A. Mohaimani, A. Schmoldt, M. D. Torelli, K. R. Hurley, J. Dalluge, G. Chong, Z. V. Feng, C. L. Haynes, R. J. Hamers, J. A. Pedersen, Q. Cui, R. Hernandez, R. Klaper, G. Orr, C. J. Murphy, and F. M. Geiger*, Chem , 4, 2709-2723 (2018)

239. Conformational and Dynamic Properties of Poly(ethylene oxide) in BMIM+$BF4 : A Microsecond Computer Simulation Study Using First Principles-Based Force Fields, C. Y. Son, J. G. McDaniel, Q. Cui, and A. Yethiraj*, Macromolecules, 51, 5336-5345 (2018)

238. Network Analysis of a Proposed Exit Pathway for Protons to the P-side of Cytochrome c Oxidase, X. H. Cai, K. Haider, J. X. Lu, S. Radik, C. Y. Son, Q. Cui and M. Gunner*, BBA Bioener. 1859, 997-1005 (2018)

237. Analysis of Phosphoryl Transfer Enzymes with QM/MM Free Energy Simulations, D. Roston, X. Lu, D. Fang, D. Demapan and Q. Cui*, Methods in Enzymology: Phosphatases , 607, 53-90 (2018) Invited contribution

236. Molecular Dynamics-Decorated Finite Element Method (MDeFEM): Application to the Gating Mechanism of Mechanosensitive Channels, L. L. Zhu, Q. Cui, Y. L. Liu, Y. Yan, H. Xiao, and X. Chen*, Handbook of Nonlocal Continuum Mechanics for Materials and Structure, 1-52 (2018)

235. Comment: Membrane Mediated Interaction Drives Mitochondria ATPase Assembly and Cristae Formation, Q. Cui*, J. Gen. Physiol. , 150, 777-780 (2018)

234. Hydrogen Bond Networks Near Supported Lipid Bilayers from Vibrational Sum Frequency Generation Experiments and Atomistic Simulations, M. Dogangun, P. E. Ohno, D. Y. Liang, A. C. McGeachy, N. Dalchand, T. Li, Q. Cui* and F. M. Geiger*, J. Phys. Chem. B 122, 4870-4879 (2018)

233. Counting Charges on Membrane-bound Peptides, A. C. McGeachy, E. Caudill, D. Y. Liang, Q. Cui, J. A. Pedersen and F. M. Geiger*, Chem. Sci. 9, 4285-4298 (2018)

232. Specific Substates of Ras to Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments, Y. Li, Y. W. Zhang, F. Groberuschkamp, S. Stephan, Q. Cui, C. Kottig, F. Xia* and K. Gerwert*, J. Phys. Chem. Lett. 9, 1312-1317 (2018)

231. Essence of Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations of amino acid side chain analogs, Z. J. Xu*, Q. C. Wei, W. L. Zhao, Q. Cui and N. Sahai*, J. Phys. Chem. C , 122, 4372-4380 (2018)

230. Inspiring Molecular Quantum Chemist, Obituary for Professor Keiji Morokuma, Q. Cui*, S. Irle and J. Musaev, Angew Chim. Intl. Ed. 57, 2288-2289 (2018)

229. Multiple Pathways and Timescales for Conformational Transitions in apo-Adenylate Kinase, Y. Q. Zheng and Q. Cui*, J. Chem. Theory Comput. 14, 1716-1726 (2018)

228. Dynamics and number of trans-SNARE complexes determine nascent fusion pore properties, H. Bao, D. Das, N. A. Courtney, Y. H. Jiang, J. Briguglio, X. C. Lou, D. Roston, Q. Cui, B. Chanda and E. R. Chapman*, Nature , 554, 260-263 (2018)

227. Iron starvation inhibits late stages of bacterial cytokinesis, T. M. A. Santos, M. G. Lammers, M. Q. Zhou, I. L. Sparks, M. Rajendran, D. Fang, C. L. Y. De Jesus, G. F. R. Carneiro, Q. Cui and D. B. Weibel*, ACS Chem. Bio , 13, 235-246 (2018)

226. Structural and functional analysis of the FtsLB tetrameric complex of the bacterial divisome, D. A. Mahbuba, S. G. F. Condon, C. R. Armstrong, G. Diaz-Vazquez, S. J. Craven, L. M. LaPointe, A. S. Khadria, R. Chadda, J. A. Crooks, N. Rangarajan, D. B. Weibel, A. A. Hoskins, J. L. Robertson, Q. Cui, A. Senes*, J. Biol. Chem. , 293, 1623-1641 (2018)

225. Analysis of Conformational Properties of Amine Ligands at the Gold/Water Interface with QM, MM and QM/MM simulations, D. Y. Liang, J. W. Hong, F. Dong, J. W. Bennett, S. E. Mason, R. J. Hamers and Q. Cui*, Phys. Chem. Chem. Phys. , 20, 3349-3362 (2018)