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Timothy J. Giese

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Position: Associate Research Professor
Education:
University of Minnesota - Ph.D. Chemical Physics (2005)
Email: N/A
Office: CIPR-308F


About Me:

Linear-scaling electronic structure methods Linear-scaling electrostatic algorithms Multipolar interactions and polarizability




Pinned Articles:

Quantum mechanical force fields for condensed phase molecular simulations


(2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c
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Publications:

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020)
DOI: 10.1021/acs.jcim.0c00613
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme

(2020) 12, 193-201
DOI: 10.1038/s41557-019-0391-x
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Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods

(2019) 15, 5543-5562
DOI: 10.1021/acs.jctc.9b00401
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Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology

(2019) 9, 5803-5815
DOI: 10.1021/acscatal.9b01155
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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462
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A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

(2018) 14, 1564–1582
DOI: 10.1021/acs.jctc.7b01175
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A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

(2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161
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Quantum mechanical force fields for condensed phase molecular simulations

(2017) 29, 383002-383016
DOI: 10.1088/1361-648X/aa7c5c
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Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations

(2017) 56, 2985-2994
DOI: 10.1021/acs.biochem.6b01192
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Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

(2016) 12, 2611-2632
DOI: 10.1021/acs.jctc.6b00198
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VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions

(2016) 144, 164115
DOI: 10.1063/1.4946779
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A Modified Divide-and-Conquer Linear-Scaling Quantum Force Field with Multipolar Charge Densities

(2016) Chapter 2, 1-32
ISBN: 12345
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Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

(2015) 143, 234111
DOI: 10.1063/1.4937166
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Multipolar Ewald Methods. II. Applications Using a Quantum Mechanical Force Field

(2015) 11, 451-461
DOI: 10.1021/ct500799g
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Multipolar Ewald Methods. I. Theory, Accuracy, and Performance

(2015) 11, 436-450
DOI: 10.1021/ct5007983
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Nucleic acid reactivity: challenges for next-generation semiempirical quantum models

(2015) 36, 1370-1389
DOI: 10.1002/jcc.23933
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Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions

(2014) 20, 1-9
DOI: 10.1002/chem.201403862
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Recent advances toward a general purpose linear-scaling quantum force field

(2014) 47, 2812–2820
DOI: 10.1021/ar500103g
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Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

(2014) 136, 7789-7792
DOI: 10.1021/ja500180q
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Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

(2014) 10, 1538–1545
DOI: 10.1021/ct401013s
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Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

(2014) 10, 1086–1098
DOI: 10.1021/ct401035t
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A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) 9, 1417-1427
DOI: 10.1021/ct3010134
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Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization

(2012) 116, 9131-9141
DOI: 10.1021/jp306239c
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Density-functional expansion methods: Grand challenges

(2012) 131, 1145-1161
DOI: 10.1007/s00214-012-1145-7
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Density-functional expansion methods: Generalization of the auxiliary basis

(2011) 134, 194103
DOI: 10.1063/1.3587052
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Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations

(2009) 7, 377-408
ISBN: 12345
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Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities

(2008) 29, 1895-1904
DOI: 10.1002/jcc.20946
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Spherical tensor gradient operator method for integral rotation: A simple, efficient, and extendable alternative to Slater-Koster tables

(2008) 129, 016102
DOI: 10.1063/1.2945897
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Contracted auxiliary Gaussian basis integral and derivative evaluation

(2008) 128, 064104
DOI: 10.1063/1.2821745
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Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations

(2007) 127, 194101
DOI: 10.1063/1.2778428
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Simulations of phosphoryl transfer reactions using multi-scale quantum models

(2006) 181-192
ISBN: 12345
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QCRNA 1.0: A database of quantum calculations for RNA catalysis

(2006) 25, 423-433
DOI: 10.1016/j.jmgm.2006.02.011
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A semiempirical quantum model for hydrogen bonded nucleic acid base pairs

(2005) 1, 1275-1285
DOI: 10.1021/ct050102l
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Improvement of semiempirical response properties with charge-dependent response density

(2005) 123, 164108
DOI: 10.1063/1.2080007
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Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits

(2004) 120, 9903-9906
DOI: 10.1063/1.1756583
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Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields

(2004) 120, 7939
DOI: 10.1063/1.1690232
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Design and application of a multicoefficient correlatiomethod for dispersion interactions

(2004) 120, 590
DOI: 10.1063/1.1630955
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High-level ab initio methods for calculation of accurate potential energy surfaces of van der Waals complexes

(2004) 98, 388-408
DOI: 10.1002/qua.20074
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Examination of the correlation energy and second virial coefficients from accurate ab initio calculations of rare-gas dimers

(2003) 119, 2618-2622
DOI: 10.1063/1.1587684
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