Publications

Zheng YQ, Cui Q. Microscopic mechanisms that govern the titration response and pK(a) values of buried residues in staphylococcal nuclease mutants. Proteins-Structure Function and Bioinformatics. 2017;85:268-281.
Hong JW, Hamers RJ, Pedersen JA, Cui Q. A Hybrid Molecular Dynamics/Multiconformer Continuum Electrostatics (MD/MCCE) Approach for the Determination of Surface Charge of Nanomaterials. Journal of Physical Chemistry C. 2017;121:3584-3596.
Lu XY, Ovchinnikov V, Demapan D, Roston D, Cui Q. Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin. Biochemistry. 2017;56:1482-1497.
Troiano JM, McGeachy AC, Olenick LL, Fang D, Liang DY, Hong JW, et al.. Quantifying the Electrostatics of Polycation-Lipid Bilayer Interactions. Journal of the American Chemical Society. 2017;139:5808-5816.
Son CY, Yethiraj A, Cui Q. Cavity hydration dynamics in cytochrome c oxidase and functional implications. Proceedings of the National Academy of Sciences of the United States of America. 2017;114:E8830-E8836.
Christensen AS, Kromann JC, Jensen JH, Cui Q. Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods. Journal of Chemical Physics. 2017;147.
Roston D, Cui Q. QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes. In: Voth GA. San Diego: Elsevier Academic Press Inc; 2016. pp. 213-250.
Pham GH, Rana A, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Protein Science. 2016;25:456-471.
Jin HY, Goyal P, Das AK, Gaus M, Meuwly M, Cui Q. Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations. Journal of Physical Chemistry B. 2016;120:1894-1910.
Bai H, Xue RH, Bao H, Zhang LL, Yethiraj A, Cui Q, et al.. Different states of synaptotagmin regulate evoked versus spontaneous release. Nature Communications. 2016;7.
Son CY, McDaniel JG, Schmidt JR, Cui Q, Yethiraj A. First-Principles United Atom Force Field for the Ionic Liquid BMIM+BF4-: An Alternative to Charge Scaling. Journal of Physical Chemistry B. 2016;120:3560-3568.
Christensen AS, Kubar T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chemical Reviews. 2016;116:5301-5337.
Kromann JC, Christensen AS, Cui Q, Jensen JH. Towards a barrier height benchmark set for biologically relevant systems. Peerj. 2016;4.
Lu XY, Fang D, Ito S, Okamoto Y, Ovchinnikov V, Cui Q. QM/MM free energy simulations: recent progress and challenges. Molecular Simulation. 2016;42:1056-1078.
Zhao WL, Xu ZJ, Cui Q, Sahai N. Predicting the Structure-Activity Relationship of Hydroxyapatite-Binding Peptides by Enhanced-Sampling Molecular Simulation. Langmuir. 2016;32:7009-7022.
Cui Q, Hernandez R, Mason SE, Frauenheim T, Pedersen JA, Geiger F. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies. Journal of Physical Chemistry B. 2016;120:7297-7306.
Zhang LL, Rajendram M, Weibel DB, Yethiraj A, Cui Q. Ionic Hydrogen Bonds and Lipid Packing Defects Determine the Binding Orientation and Insertion Depth of RecA on Multicomponent Lipid Bilayers. Journal of Physical Chemistry B. 2016;120:8424-8437.
Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. Journal of the American Chemical Society. 2016;138:11946-11957.
Cui Q. Perspective: Quantum mechanical methods in biochemistry and biophysics. Journal of Chemical Physics. 2016;145.
Zhu LL, Wu JZ, Liu L, Liu YL, Yan Y, Cui Q, et al.. Gating mechanism of mechanosensitive channel of large conductance: a coupled continuum mechanical-continuum solvation approach. Biomechanics and Modeling in Mechanobiology. 2016;15:1557-1576.
Goldschen-Ohm MP, Klenchin VA, White DS, Cowgill JB, Cui Q, Goldsmith RH, et al.. Structure and dynamics underlying elementary ligand binding events in human pacemaking channels. eLife. 2016;5:e20797.
Xu ZJ, Yang Y, Zhao WL, Wang ZQ, Landis WJ, Cui Q, et al.. Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues. Biomaterials. 2015;39:59-66.
Zheng YQ, Cui Q. The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics. Physical Chemistry Chemical Physics. 2015;17:13689-13698.
Taylor KC, Buvoli M, Korkmaz EN, Buvoli A, Zheng YQ, Heinze NT, et al.. Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Proceedings of the National Academy of Sciences of the United States of America. 2015;112:E3806-E3815.
Korkmaz EN, Volkman BF, Cui Q. Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin. Journal of Physical Chemistry B. 2015;119:9547-9558.
Christensen AS, Elstner M, Cui Q. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization. Journal of Chemical Physics. 2015;143.
Gaus M, Jin HY, Demapan D, Christensen AS, Goyal P, Elstner M, et al.. DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. Journal of Chemical Theory and Computation. 2015;11:4205-4219.
Ngo V, da Silva MC, Kubillus M, Li H, Roux B, Elstner M, et al.. Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins. Journal of Chemical Theory and Computation. 2015;11:4992-5001.
Hu LL, Lu JY, Cheng JD, Rao QH, Li Z, Hou HF, et al.. Structural insight into substrate preference for TET- mediated oxidation. Nature. 2015;527:118-122.
Rajendram M, Zhang LL, Reynolds BJ, Auer GK, Tuson HH, Ngo KV, et al.. Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli. Molecular Cell. 2015;60:374-384.
Goyal P, Yang S, Cui Q. Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis. Chemical Science. 2015;6:826-841.
Xu ZJ, Yang Y, Wang ZQ, Mkhonto D, Shang C, Liu ZP, et al.. Small Molecule-Mediated Control of Hydroxyapatite Growth: Free Energy Calculations Benchmarked to Density Functional Theory. Journal of Computational Chemistry. 2014;35:70-81.
Xu DG, Cui Q, Guo H. Quantum mechanical/molecular mechanical studies of zinc hydrolases. International Reviews in Physical Chemistry. 2014;33:1-41.
Zhang LL, Yethiraj A, Cui Q. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models. Journal of Chemical Theory and Computation. 2014;10:2845-2859.
Cui Q, Elstner M. Density functional tight binding: values of semi-empirical methods in an ab initio era. Physical Chemistry Chemical Physics. 2014;16:14368-14377.
Mori T, Hamers RJ, Pedersen JA, Cui Q. Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling. Journal of Physical Chemistry B. 2014;118:8210-8220.
Cui Q, Nussinov R. Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era. Plos Computational Biology. 2014;10.
Shen QT, Schuh AL, Zheng YQ, Quinney K, Wang L, Hanna M, et al.. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly. Journal of Cell Biology. 2014;206:763-777.
Qian HJ, Irle S, Lu XY, Roston D, Mori T, Elstner M, et al.. Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models AU Goyal, P Qian, HJ Irle, S Lu, XY Roston, D Mori, T Elstner, M Cui, Q. Journal of Physical Chemistry B. 2014;118:11007-11027.
Wolf S, Freier E, Cui Q, Gerwert K. Infrared spectral marker bands characterizing a transient water wire inside a hydrophobic membrane protein. Journal of Chemical Physics. 2014;141.
Odoh SO, Bondarevsky GD, Karpus J, Cui Q, He C, Spezia R, et al.. UO22+ Uptake by Proteins: Understanding the Binding Features of the Super Uranyl Binding Protein and Design of a Protein with Higher Affinity. Journal of the American Chemical Society. 2014;136:17484-17494.
Jia CX, Wu Z, Lietz CB, Liang ZD, Cui Q, Li LJ. Gas-Phase Ion Isomer Analysis Reveals the Mechanism of Peptide Sequence Scrambling. Analytical Chemistry. 2014;86:2917-2924.
Gaus M, Lu XY, Elstner M, Cui Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. Journal of Chemical Theory and Computation. 2014;10:1518-1537.
Gaus M, Cui Q, Elstner M. Density functional tight binding: application to organic and biological molecules. Wiley Interdisciplinary Reviews-Computational Molecular Science. 2014;4:49-61.
Daily MD, Yu HB, Phillips GN, Cui Q. Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. In: Klinman J, Hammes-Schiffer S. Berlin: Springer-Verlag Berlin; 2013. pp. 139-164.
Yoo J, Jackson MB, Cui Q. A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores. Biophysical Journal. 2013;104:841-852.
Yoo J, Cui Q. Membrane-Mediated Protein-Protein Interactions and Connection to Elastic Models: A Coarse-Grained Simulation Analysis of Gramicidin A Association. Biophysical Journal. 2013;104:128-138.
Yoo J, Cui Q. Three-Dimensional Stress Field around a Membrane Protein: Atomistic and Coarse-Grained Simulation Analysis of Gramicidin A. Biophysical Journal. 2013;104:117-127.
Wu Z, Cui Q, Yethiraj A. Why Do Arginine and Lysine Organize Lipids Differently? Insights from Coarse-Grained and Atomistic Simulations. Journal of Physical Chemistry B. 2013;117:12145-12156.
Ruther RE, Cui Q, Hamers RJ. Conformational Disorder Enhances Electron Transfer Through Alkyl Monolayers: Ferrocene on Conductive Diamond. Journal of the American Chemical Society. 2013;135:5751-5761.
Pang XQ, Han KL, Cui Q. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family. Journal of Computational Chemistry. 2013;34:1620-1635.
Mori T, Hamers RJ, Pedersen JA, Cui Q. An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces. Journal of Chemical Theory and Computation. 2013;9:5059-5069.
Lu XY, Cui Q. Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins. Journal of Physical Chemistry B. 2013;117:2005-2018.
Sundlass NK, Eller CH, Cui Q, Raines RT. Contribution of Electrostatics to the Binding of Pancreatic-Type Ribonucleases to Membranes. Biochemistry. 2013;52:6304-6312.
Jarecki BW, Zheng SQ, Zhang LL, Li XX, Zhou X, Cui Q, et al.. Tethered Spectroscopic Probes Estimate Dynamic Distances with Subnanometer Resolution in Voltage-Dependent Potassium Channels. Biophysical Journal. 2013;105:2724-2732.
Hou GH, Cui Q. Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily. Journal of the American Chemical Society. 2013;135:10457-10469.
Goyal P, Lu JX, Yang S, Gunner MR, Cui Q. Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. 2013;110:18886-18891.
Fu Y, Jia GF, Pang XQ, Wang RN, Wang X, Li CJ, et al.. FTO-mediated formation of N-6-hydroxymethyladenosine and N-6-formyladenosine in mammalian RNA. Nature Communications. 2013;4.
Cui Q, Zhang LL, Wu Z, Yethiraj A. Generation and sensing of membrane curvature: Where materials science and biophysics meet. Current Opinion in Solid State & Materials Science. 2013;17:164-174.
Zienau J, Cui Q. Implementation of the Solvent Macromolecule Boundary Potential and Application to Model and Realistic Enzyme Systems. Journal of Physical Chemistry B. 2012;116:12522-12534.
Xing YN, Nukaya M, Satyshur KA, Jiang L, Stanevich V, Korkmaz EN, et al.. Identification of the Ah-Receptor Structural Determinants for Ligand Preferences. Toxicological Sciences. 2012;129:86-97.
Xia F, Rudack T, Cui Q, Kotting C, Gerwert K. Detailed Structure of the H2PO4--Guanosine Diphosphate Intermediate in Ras-GAP Decoded from FTIR Experiments by Biomolecular Simulations. Journal of the American Chemical Society. 2012;134:20041-20044.
Meuwly M, Cui Q. Protein functional dynamics: From femtoseconds to milliseconds Preface. Chemical Physics. 2012;396:1-2.
Hou GH, Zhu X, Elstner M, Cui Q. A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions. Journal of Chemical Theory and Computation. 2012;8:4293-4304.
Daily MD, Makowski L, Phillips GN, Cui Q. Large-scale motions in the adenylate kinase solution ensemble: Coarse-grained simulations and comparison with solution X-ray scattering. Chemical Physics. 2012;396:84-91.
Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-Dependent pK(a) Shift Induced by Molecular Self-Assembly: Insights from Computer Simulation. Journal of Physical Chemistry B. 2012;116:491-495.
Riccardi D, Zhu X, Goyal P, Yang S, Hou GH, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications. Science China-Chemistry. 2012;55:3-18.
Yang Y, Mkhonto D, Cui Q, Sahai N. Theoretical Study of Bone Sialoprotein in Bone Biomineralization. Cells Tissues Organs. 2011;194:182-187.
Yang S, Cui Q. Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase. Biophysical Journal. 2011;101:61-69.
Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Force Field for Membrane-Peptide Simulations. Journal of Chemical Theory and Computation. 2011;7:3793-3802.
Wu Z, Cui Q, Yethiraj A. Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models. Journal of Physical Chemistry Letters. 2011;2:1794-1798.
Wu Y, Ma L, Cheley S, Bayley H, Cui Q, Chapman ER. Permeation of Styryl Dyes through Nanometer-Scale Pores in Membranes. Biochemistry. 2011;50:7493-7502.
Ma L, Sundlass NK, Raines RT, Cui Q. Disruption and Formation of Surface Salt Bridges Are Coupled to DNA Binding by the Integration Host Factor: A Computational Analysis. Biochemistry. 2011;50:266-275.
Goyal P, Ghosh N, Phatak P, Clemens M, Gaus M, Elstner M, et al.. Proton Storage Site in Bacteriorhodopsin: New Insights from Quantum Mechanics/Molecular Mechanics Simulations of Microscopic pK(a) and Infrared Spectra. Journal of the American Chemical Society. 2011;133:14981-14997.
Goyal P, Elstner M, Cui Q. Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water. Journal of Physical Chemistry B. 2011;115:6790-6805.
Daily MD, Phillips, Jr. GN, Cui Q. Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases. Plos Computational Biology. 2011;7.
Clemens M, Phatak P, Cui Q, Bondar A-N, Elstner M. Role of Arg82 in the Early Steps of the Bacteriorhodopsin Proton-Pumping Cycle. Journal of Physical Chemistry B. 2011;115:7129-7135.
Gaus M, Cui Q, Elstner M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB). Journal of Chemical Theory and Computation. 2011;7:931-948.
Zhu X, Koenig P, Hoffmann M, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for beta- and alpha/beta-Peptides. III. Molecular Mechanical Model for Acyclic beta-Amino Acids. Journal of Computational Chemistry. 2010;31:2063-2077.
Wu Z, Cui Q, Yethiraj A. A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions. Journal of Physical Chemistry B. 2010;114:10524-10529.
Van Wynsberghe AW, Cui Q. Conservation and Variation of Structural Flexibility in Protein Families. Structure. 2010;18:281-283.
Riccardi D, Yang S, Cui Q. Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2010;1804:342-351.
Mondal J, Zhu X, Cui Q, Yethiraj A. Sequence-Dependent Interaction of beta-Peptides with Membranes. Journal of Physical Chemistry B. 2010;114:13585-13592.
Mondal J, Zhu X, Cui Q, Yethiraj A. Self-Assembly of beta-Peptides: Insight from the Pair and Many-Body Free Energy of Association. Journal of Physical Chemistry C. 2010;114:13551-13556.
Ma L, Pegram L, Record MT, Cui Q. Preferential Interactions between Small Solutes and the Protein Backbone: A Computational Analysis. Biochemistry. 2010;49:1954-1962.
Rao L, Cui Q, Xu X. Electronic Properties and Desolvation Penalties of Metal Ions Plus Protein Electrostatics Dictate the Metal Binding Affinity and Selectivity in the Copper Efflux Regulator. Journal of the American Chemical Society. 2010;132:18092-18102.
Riccardi D, Cui Q, Phillips, Jr. GN. Evaluating Elastic Network Models of Crystalline Biological Molecules with Temperature Factors, Correlated Motions, and Diffuse X-Ray Scattering. Biophysical Journal. 2010;99:2616-2625.
Yoo J, Cui Q. Chemical versus Mechanical Perturbations on the Protonation State of Arginine in Complex Lipid Membranes: Insights from Microscopic pK(a) Calculations. Biophysical Journal. 2010;99:1529-1538.
Hou GH, Zhu XA, Cui Q. An Implicit Solvent Model for SCC-DFTB with Charge-Dependent Radii. Journal of Chemical Theory and Computation. 2010;6:2303-2314.
Daily MD, Phillips GN, Cui Q. Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition. Journal of Molecular Biology. 2010;400:618-631.
Yang Y, Cui Q, Sahai N. How Does Bone Sialoprotein Promote the Nucleation of Hydroxyapatite? A Molecular Dynamics Study Using Model Peptides of Different Conformations. Langmuir. 2010;26:9848-9859.
Yi CQ, Jia GF, Hou GH, Dai Q, Zhang W, Zheng GQ, et al.. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature. 2010;468:330-U223.
Yoo J, Cui Q. Curvature Generation and Pressure Profile Modulation in Membrane by Lysolipids: Insights from Coarse-Grained Simulations. Biophysical Journal. 2009;97:2267-2276.
Yang Y, Cui Q. The Hydrolysis Activity of Adenosine Triphosphate in Myosin: A Theoretical Analysis of Anomeric Effects and the Nature of the Transition State. Journal of Physical Chemistry A. 2009;113:12439-12446.
Yang Y, Cui Q. Does Water Relay Play an Important Role in Phosphoryl Transfer Reactions? Insights from Theoretical Study of a Model Reaction in Water and tert-Butanol. Journal of Physical Chemistry B. 2009;113:4930-4939.
Tang Y, Chen X, Yoo J, Yethiraj A, Cui Q. Numerical Simulation of Nanoindentation and Patch Clamp Experiments on Mechanosensitive Channels of Large Conductance in Escherichia coli. Experimental Mechanics. 2009;49:35-46.
Riccardi D, Cui Q, Phillips GN. Application of Elastic Network Models to Proteins in the Crystalline State. Biophysical Journal. 2009;96:464-475.
Ma L, Yethiraj A, Chen X, Cui Q. A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability. Biophysical Journal. 2009;96:3543-3554.
Ghosh N, Prat-Resina X, Gunner MR, Cui Q. Microscopic pK(a) Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model. Biochemistry. 2009;48:2468-2485.
Yoo J, Cui Q. Does arginine remain protonated in the lipid membrane? Insights from microscopic pK(a) calculations. Biophysical Journal. 2008;94:L61-L63.
Yang Y, Yu HB, York D, Elstner M, Cui Q. Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization. Journal of Chemical Theory and Computation. 2008;4:2067-2084.
Yang Y, Yu H, Cui Q. Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. Journal of Molecular Biology. 2008;381:1407-1420.
Tang YY, Yoo J, Yethiraj A, Cui Q, Chen X. Mechanosensitive channels: Insights from continuum-based simulations. Cell Biochemistry and Biophysics. 2008;52:1-18.
Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating mechanisms of mechanosensitive channels of large conductance, II: Systematic study of conformational transitions. Biophysical Journal. 2008;95:581-596.
Riccardi D, Koenig P, Guo H, Cui Q. Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry. 2008;47:2369-2378.
Phatak P, Ghosh N, Yu HB, Cui Q, Elstner M. Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 2008;105:19672-19677.
Hoerter JM, Otte KM, Gellman SH, Cui Q, Stahl SS. Discovery and mechanistic study of Al-III-catalyzed transamidation of tertiary amides. Journal of the American Chemical Society. 2008;130:647-654.
Ghosh N, Cui Q. pK(a) of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. Journal of Physical Chemistry B. 2008;112:8387-8397.
Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Science. 2008;17:1295-1307.
Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating mechanisms of mechanosensitive channels of large conductance, I: A continuum mechanics-based hierarchical framework. Biophysical Journal. 2008;95:563-580.
Zhu X, Koenig P, Gellman SH, Yethiraj A, Cui Q. Establishing Effective Simulation Protocols for β- and α/β-Peptides. II. Molecular Mechanical (MM) Model for a Cyclic β-Residue. Journal of Physical Chemistry B. 2008;112:5439-5448.
Zhu X, Yethiraj A, Cui Q. Establishing effective simulation protocols for beta- and alpha/beta-mixed peptides. I. QM and QM/MM models. Journal of Chemical Theory and Computation. 2007;3:1538-1549.
Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Plos Computational Biology. 2007;3:214-230.
Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. Plos Computational Biology. 2007;3:199-213.
Yu H, Cui Q. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding. Journal of Chemical Physics. 2007;127.
Yang Y, Yu H, York D, Cui Q, Elstner M. Extension of the self-consistent-charge density-functional tight-binding method: Third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. Journal of Physical Chemistry A. 2007;111:10861-10873.
Yang Y, Cui Q. Interactions between phosphate and water in solution: A natural bond orbital based analysis in a QM/MM framework. Journal of Physical Chemistry B. 2007;111:3999-4002.
Xu D, Guo H, Cui Q. Antibiotic binding to dizinc beta-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT Studies. Journal of Physical Chemistry A. 2007;111:5630-5636.
Riccardi D, Cui Q. pK(a) analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "Multiscale" QM/MM simulations and mechanistic implications. Journal of Physical Chemistry A. 2007;111:5703-5711.
Nam K, Cui Q, Gao J, York DM. Specific reaction parametrization of the AM1/d Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms. Journal of Chemical Theory and Computation. 2007;3:486-504.
Ma L, Cui Q. Activation mechanism of a signaling protein at atomic resolution from advanced computations. Journal of the American Chemical Society. 2007;129:10261-10268.
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, Jr. GN. Protein structural variation in computational models and crystallographic data (vol 15, pg 169, 2007). Structure. 2007;15:637-637.
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips, Jr. GN. Protein structural variation in computational models and crystallographic data. Structure. 2007;15:169-177.
Kissounko DA, Hoerter JM, Guzei IA, Cui Q, Gellman SH, Stahl SS. Ti-IV-mediated reactions between primary amines and secondary carboxamides: Amidine formation versus transamidation. Journal of the American Chemical Society. 2007;129:1776-1783.
Cai Z-L, Lopez P, Reimers JR, Cui Q, Elstner M. Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules. Journal of Physical Chemistry A. 2007;111:5743-5750.
Van Wynsberghe AW, Cui Q. Interpreting correlated motions using normal mode analysis. Structure. 2006;14:1647.
Riccardi D, Koenig P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, et al.. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. Journal of the American Chemical Society. 2006;128:16302-16311.
Ma L, Cui Q. The temperature dependence of salt-protein association is sequence specific. Biochemistry. 2006;45:14466.
Li G, Van Wynsberghe A, Demerdash ONA, Cui Q. Normal mode analysis of macromolecules: from enzyme active sites to molecular machines. Normal Mode Analysis. 2006;:65-89, 4 plates.
Formaneck MS, Ma L, Cui Q. Effects of temperature and salt concentration on the structural stability of human lymphotactin: Insights from molecular simulations. Journal of the American Chemical Society. 2006;128:9506.
Formaneck MS, Cui Q. The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY). Journal of Computational Chemistry. 2006;27:1923.
Cui Q. Theoretical analysis of mechanochemical coupling in the biomolecular motor myosin. Modelling Molecular Structure and Reactivity in Biological Systems. 2006;:66-75.
Cui Q. Theoretical and computational studies of vectorial processes in biomolecular systems. Theoretical Chemistry Accounts. 2006;116:51.
Kondrashov DA, Cui Q, Phillips GN. Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data. Biophysical Journal. 2006;91:2760-2767.
Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, et al.. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes. Journal of Physical Chemistry B. 2006;110:6458-6469.
Konig PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, et al.. Toward theoretical analyis of long-range proton transfer kinetics in biomolecular pumps [Review]. Journal of Physical Chemistry A. 2006;110:548-563.
Cui Q, Thorgersen MP, Westler WM, Markley JL, Downs DM. Solution structure of YggX: A prokaryotic protein involved in Fe(II) trafficking. Proteins Structure Function & Bioinformatics. 2006;62:578-586.
Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophysical Journal. 2005;89:2939-2949.
Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules - art. no. 014905. Journal of Chemical Physics. 2005;123:14905.
Casey CP, Johnson JB, Singer SW, Cui Q. Hydrogen elimination from a hydroxycyclopentadienyl ruthenium(II) hydride: Study of hydrogen activation in a ligand-metal bifunctional hydrogenation catalyst. Journal of the American Chemical Society. 2005;127:3100-3109.
Casey CP, Bikzhanova GA, Cui Q, Guzei IA. Reduction of Imines by hydroxycyclopentadienyl ruthenium hydride: Intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal. Journal of the American Chemical Society. 2005;127:14062-14071.
Li GH, Cui Q. Direct determination of reaction paths and stationary points on potential of mean force surfaces. Journal of Molecular Graphics and Modelling. 2005;24:82-93.
Range K, Riccardi D, Cui Q, Elstner M, York DM. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Physical Chemistry Chemical Physics. 2005;7:3070-3079.
Guo H, Lipscomb WN, Cui Q, Karplus M. Molecular dynamics simulations of yeast chorismate mutase: substrate conformational transitions and enzymatic catalysis. NATO Sci. Ser., Ser. I. 2005;364:63-74.
Riccardi D, Schaefer P, Cui Q. pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols [Review]. Journal of Physical Chemistry B. 2005;109:17715-17733.
Konig PH, Hoffmann M, Frauenheim T, Cui Q. A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method [Review]. Journal of Physical Chemistry B. 2005;109:9082-9095.
Li GH, Cui Q. Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: Myosin-II and Ca2+-ATPase [Review]. Biophysical Journal. 2004;86:743-763.
Cui Q, Li GH, Ma JP, Karplus M. A normal mode analysis of structural plasticity in the biomolecular motor F-1-ATPase. Journal of Molecular Biology. 2004;340:345-372.
Xu DG, Wei YS, Wu JB, Dunaway-Mariano D, Guo H, Cui Q, et al.. QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. Journal of the American Chemical Society. 2004;126:13649-13658.
Xu DG, Guo H, Gao JL, Cui Q. A QM/MM study of a nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase. Chemical Communications. 2004;:892-893.
Van Wynsberghe A, Li GH, Cui Q. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry. 2004;43:13083-13096.
Riccardi D, Li GH, Cui Q. Importance of van der Waals interactions in QM/MM Simulations. Journal of Physical Chemistry B. 2004;108:6467-6478.
Li GH, Cui Q. Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations. Journal of Physical Chemistry B. 2004;108:3342-3357.
Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F-1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 2003;100:874-879.
Smedarchina Z, Siebrand W, Fernandez-Ramos A, Cui Q. Kinetic isotope effects for concerted multiple proton transfer: A direct dynamics study of an active-site model of carbonic anhydrase. Journal of the American Chemical Society. 2003;125:243-251.
Li GH, Cui Q. What is so special about Arg 55 in the catalysis of cyclophilin A? Insights from hybrid QM/MM simulations. Journal of the American Chemical Society. 2003;125:15028-15038.
Formaneck MS, Li GH, Zhang XD, Cui Q. Calculating accurate redox potentials in enzymes with a combined QM/MM free energy perturbation approach. Journal of Theoretical and Computational Chemistry. 2003;1:53-67.
Elstner M, Cui Q, Munih P, Kaxiras E, Frauenheim T, Karplus M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis [Review]. Journal of Computational Chemistry. 2003;24:565-581.
Li GH, Zhang XD, Cui Q. Free energy perturbation calculations with combined QM/MM Potentials complications, simplifications, and applications to redox potential calculations. Journal of Physical Chemistry B. 2003;107:8643-8653.
Li GH, Cui Q. pK(a) calculations with QM/MM free energy perturbations. Journal of Physical Chemistry B. 2003;107:14521-14528.
Guo H, Cui Q, Lipscomb WN, Karplus M. Understanding the role of active-site residues in chorismate mutase catalysis from molecular-dynamics simulations. Angewandte Chemie-International Edition. 2003;42:1508-1511.
Cui Q, Karplus M. Catalysis and specificity in enzymes: A study of triosephosphate isomerase and comparison with methyl glyoxal synthase [Review]. Protein Simulations. 2003;66:315-+.
Cui Q, Karplus M. Is a "proton wire" concerted or stepwise? A model study of proton transfer in carbonic anhydrase. Journal of Physical Chemistry B. 2003;107:1071-1078.
Zhang XD, Harrison DHT, Cui Q. Functional Specificities of methylglyoxal synthase and triosephosphate isomerase: A combined QM/MM analysis. Journal of the American Chemical Society. 2002;124:14871-14878.
Li GH, Cui Q. A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+-ATPase. Biophysical Journal. 2002;83:2457-2474.
Cui Q, Karplus M. Promoting modes and demoting modes in enzyme-catalyzed proton transfer reactions: A study of models and realistic systems [Review]. Journal of Physical Chemistry B. 2002;106:7927-7947.
Cui Q, Karplus M. Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: Effect of geometry and tunneling on proton-transfer rate constants. Journal of the American Chemical Society. 2002;124:3093-3124.
Cui Q, Guo H, Karplus M. Combining ab initio and density functional theories with semiempirical methods. Journal of Chemical Physics. 2002;117:5617-5631.
Cui Q. Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine. Journal of Chemical Physics. 2002;117:4720-4728.
Ma JP, Flynn TC, Cui Q, Leslie AGW, Walker JE, Karplus M. A dynamic analysis of the rotation mechanism for conformational change in F-1-ATPase. Structure. 2002;10:921-931.
Cui Q, Karplus M. Quantum mechanical/molecular mechanical studies of the triosephosphate isomerase-catalyzed reaction: Verification of methodology and analysis of reaction mechanisms. Journal of Physical Chemistry B. 2002;106:1768-1798.
Cui Q, Elstner M, Karplus M. A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH). Journal of Physical Chemistry B. 2002;106:2721-2740.
Guo H, Cui Q, Lipscomb WN, Karplus M. Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism. Proceedings of the National Academy of Sciences of the United States of America. 2001;98:9032-9037.
Cui Q, Karplus M. Triosephosphate isomerase: A theoretical comparison of alternative pathways. Journal of the American Chemical Society. 2001;123:2284-2290.
Cui Q, Elstner M, Kaxiras E, Frauenheim T, Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. Journal of Physical Chemistry B. 2001;105:569-585.
Cui Q, Karplus M. Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules. Journal of Physical Chemistry B. 2000;104:3721-3743.
Cui Q, Karplus M. Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations. Journal of Chemical Physics. 2000;112:1133-1149.
Kaledin AL, Cui Q, Heaven MC, Morokuma K. Ab initio theoretical studies on photodissociation of HNCO upon S-1((1)A '')<- S-0((1)A(')) excitation: The role of internal conversion and intersystem crossing. Journal of Chemical Physics. 1999;111:5004-5016.
Cui Q, Morokuma K, Bowman JM, Klippenstein SJ. The spin-forbidden reaction CH((2)Pi)+N-2 -> HCN+N(S-4) revisited. II. Nonadiabatic transition state theory and application. Journal of Chemical Physics. 1999;110:9469-9482.
Cui Q, Morokuma K. The spin-forbidden reaction CH((2)Pi)+N-2 -> HCN+N(S-4) revisited I. Ab initio study of the potential energy surfaces. Theoretical Chemistry Accounts. 1999;102:127-133.
Stevens JE, Cui Q, Morokuma K. An ab initio investigation of spin-allowed and spin-forbidden pathways of the gas phase reactions of O(P-3)+C2H5I. Journal of Chemical Physics. 1998;108:1544-1551.
Stevens JE, Cui Q, Morokuma K. An ab initio study of the dissociation of HNCO in the S-1 electronic state. Journal of Chemical Physics. 1998;108:1452-1458.
Morokuma K, Cui Q, Liu ZW. Potential-energy surfaces and their dynamic implications. Faraday Discussions. 1998;110:71-89.
Kaledin AL, Heaven MC, Lawrence WG, Cui Q, Stevens JE, Morokuma K. Ab initio molecular-orbital study of the trichlorine radical, Cl-3. Journal of Chemical Physics. 1998;108:2771-2783.
Cui Q, Musaev DG, Morokuma K. Molecular orbital study of H-2 and CH4 activation on small metal clusters. 2. Pd-3 and Pt-3. Journal of Physical Chemistry A. 1998;102:6373-6384.
Cui Q, Musaev DG, Morokuma K. Molecular orbital study of H-2 and CH4 activation on small metal clusters. I. Pt, Pd, Pt-2, and Pd-2. Journal of Chemical Physics. 1998;108:8418-8428.
Cui Q, Musaev DG, Morokuma K. Density functional study on the mechanism of palladium(0)-catalyzed thioboration reaction of alkynes. Differences between Pd(0) and Pt(0) catalysts and between thioboration and diboration. Organometallics. 1998;17:1383-1392.
Cui Q, Musaev DG, Morokuma K. Why do Pt(PR3)(2) complexes catalyze the alkyne diboration reaction, but their palladium analogues do not? A density functional study. Organometallics. 1998;17:742-751.
Cui Q, Morokuma K. Ab initio studies on the electronic excited states and photodissociation of O-3 anion. Journal of Chemical Physics. 1998;108:7684-7694.
Cui Q, Morokuma K. Ab initio study on the mechanism of C2H2+NH3 reaction: Efficient charge transfer and proton transfer processes competing with stable complex formation. Journal of Chemical Physics. 1998;108:4021-4030.
Cui Q, Morokuma K. Ab initio molecular orbital studies on the structure, energies, and photodissociation of the electronic excited states of C2H. Journal of Chemical Physics. 1998;108:626-636.
Cui Q, Liu ZW, Morokuma K. Theoretical study on the mechanism CH4+C2H2+ reaction: Mode-enhancement effect. Journal of Chemical Physics. 1998;109:56-62.
Cui Q, Musaev DG, Morokuma K. Molecular orbital study of the mechanism of platinum(0)-catalyzed alkene and alkyne diboration reactions. Organometallics. 1997;16:1355-1364.
Cui Q, Morokuma K. Ab initio study of nonadiabatic interactions in the photodissociation of ketene. Journal of Chemical Physics. 1997;107:4951-4959.
Cui Q, Morokuma K. Ab initio MO studies on the photodissociation of C2H2 from the S-1((1)A(u)) state .2. Mechanism involving triplet states. Chemical Physics Letters. 1997;272:319-327.
Liu RF, Cui Q, Dunn KM, Morokuma K. Ab initio molecular orbital study of the mechanism of photodissociation of trans-azomethane. Journal of Chemical Physics. 1996;105:2333-2345.
Huang H, Alvarez K, Cui Q, Barnhart TM, Snyder P, PennerHahn JE. Infrared spectroscopic characterization of cyanocuprates (vol 118, pg 8808, 1996). Journal of the American Chemical Society. 1996;118:12252-12252.
Cui Q, Musaev DG, Svensson M, Morokuma K. Analytical second derivatives for effective core potential. Application to transition structures of Cp(2)Ru(2)(mu-H)(4) and to the mechanism of reaction Cu+Ch(2)N(2). Journal of Physical Chemistry. 1996;100:10936-10944.
Cui Q, Morokuma K, Stanton JF. Ab initio MO studies on the photodissociation of C2H2 from the S-1((1)A(u)) state. Non-adiabatic effects and S-T interaction. Chemical Physics Letters. 1996;263:46-53.
Cui Q, Morokuma K. Ab initio MO studies on the photodissociation of the methoxy family CX(3)Y (X=H,F; Y=O,S) from the (A)over-tilda(2)A(1) state. Chemical Physics Letters. 1996;263:54-62.
Cui Q, Musaev DG, Svensson M, Sieber S, Morokuma K. N-2 CLEAVAGE BY 3-COORDINATE GROUP-6 COMPLEXES - W(III) COMPLEXES WOULD-BE BETTER THAN MO(III) COMPLEXES. Journal of the American Chemical Society. 1995;117:12366-12367.