Demian Riccardi
Demian Riccardi
Thermodynamic Research Center, NIST
Verified email at nist.gov
TitleCited byYear
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes
D Riccardi, P Schaefer, Y Yang, H Yu, N Ghosh, X Prat-Resina, P König, ...
The Journal of Physical Chemistry B 110 (13), 6458-6469, 2006
2982006
pKa Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations:  A Quantitative Test of QM/MM Protocols
D Riccardi, P Schaefer, Q Cui
The Journal of Physical Chemistry B 109 (37), 17715-17733, 2005
1592005
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
P Schaefer, D Riccardi, Q Cui
The Journal of chemical physics 123 (1), 014905, 2005
1372005
“Proton holes” in long-range proton transfer reactions in solution and enzymes: A theoretical analysis
D Riccardi, P König, X Prat-Resina, H Yu, M Elstner, T Frauenheim, Q Cui
Journal of the American Chemical Society 128 (50), 16302-16311, 2006
1252006
Importance of van der Waals interactions in QM/MM simulations
D Riccardi, G Li, Q Cui
The Journal of Physical Chemistry B 108 (20), 6467-6478, 2004
1242004
Interactions of the Osmolyte Glycine Betaine with Molecular Surfaces in Water: Thermodynamics, Structural Interpretation, and Prediction of m-Values
MW Capp, LM Pegram, RM Saecker, M Kratz, D Riccardi, T Wendorff, ...
Biochemistry 48 (43), 10372-10379, 2009
862009
Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor
D Riccardi, P König, H Guo, Q Cui
Biochemistry 47 (8), 2369-2378, 2008
822008
Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer
K Range, D Riccardi, Q Cui, M Elstner, DM York
Physical Chemistry Chemical Physics 7 (16), 3070-3079, 2005
802005
Application of elastic network models to proteins in the crystalline state
D Riccardi, Q Cui, GN Phillips Jr
Biophysical journal 96 (2), 464-475, 2009
752009
p K a Analysis for the Zinc-Bound Water in Human Carbonic Anhydrase II: Benchmark for “Multiscale” QM/MM Simulations and Mechanistic Implications
D Riccardi, Q Cui
The Journal of Physical Chemistry A 111 (26), 5703-5711, 2007
592007
Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations
D Riccardi, S Yang, Q Cui
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1804 (2), 342-351, 2010
532010
Quasi-chemical theory and the standard free energy of H+ (aq)
P Grabowski, D Riccardi, MA Gomez, D Asthagiri, LR Pratt
The Journal of Physical Chemistry A 106 (40), 9145-9148, 2002
482002
Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse X-ray scattering
D Riccardi, Q Cui, GN Phillips Jr
Biophysical journal 99 (8), 2616-2625, 2010
382010
Why mercury prefers soft ligands
D Riccardi, HB Guo, JM Parks, B Gu, AO Summers, SM Miller, L Liang, ...
The Journal of Physical Chemistry Letters 4 (14), 2317-2322, 2013
362013
Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations
D Riccardi, H Guo, JM Parks, B Gu, L Liang, JC Smith
Journal of Chemical Theory and Computation 9 (1), 555-569, 2013
342013
X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C …
P Lian, HB Guo, D Riccardi, A Dong, JM Parks, Q Xu, EF Pai, SM Miller, ...
Biochemistry 53 (46), 7211-7222, 2014
322014
Mercury methylation by HgcA: theory supports carbanion transfer to Hg (II)
J Zhou, D Riccardi, A Beste, JC Smith, JM Parks
Inorganic chemistry 53 (2), 772-777, 2013
222013
A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia
Z Xiao, D Riccardi, HA Velazquez, AL Chin, CR Yates, JD Carrick, ...
Sci. Signal. 9 (455), ra113-ra113, 2016
122016
Highly mechanosensitive ion channels from graphene-embedded crown ethers
A Fang, K Kroenlein, D Riccardi, A Smolyanitsky
Nature materials 18 (1), 76, 2019
92019
Toward molecular models of proton pumping: Challenges, methods and relevant applications
D Riccardi, X Zhu, P Goyal, S Yang, GH Hou, Q Cui
Science China Chemistry 55 (1), 3-18, 2012
82012
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Articles 1–20