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OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Perspectives on Semiempirical Molecular Orbital Theory
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Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin‐Dependent Kinase 2: Correlated Ab Initio Quantum‐Chemical, DFT and Empirical Calculations
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Accurate description of van der Waals complexes by density functional theory including empirical corrections
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Systematic QM/MM investigation of factors that affect the cytochrome P450‐catalyzed hydrogen abstraction of camphor
inferredcites →https://doi.org/10.1002/jcc.20495openalex-snapshot
Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction
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Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540100208openalex-snapshot
Optimization of parameters for semiempirical methods I. Method
inferredcites →https://doi.org/10.1002/jcc.540140704openalex-snapshot
Beyond the MNDO model: Methodical considerations and numerical results
inferredcites →https://doi.org/10.1002/prot.20660openalex-snapshot
Very fast empirical prediction and rationalization of protein pK a values
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Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1007/128_2006_084openalex-snapshot
QM/MM Methods for Biological Systems
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QM/MM: what have we learned, where are we, and where do we go from here?
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Orthogonalization corrections for semiempirical methods
inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Intermolecular forces in simple systems
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Dynamical theory of proton tunneling transfer rates in solution: general formulation
inferredcites →https://doi.org/10.1016/j.jinorgbio.2004.02.030openalex-snapshot
Validation of semiempirical methods for modeling of corrinoid systems
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Quantum mechanical tunneling in methylamine dehydrogenase
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QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis
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An approximate DFT method for QM/MM simulations of biological structures and processes
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A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs
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Estimates of the Ab Initio Limit for π−π Interactions: The Benzene Dimer
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inferredcites →https://doi.org/10.1021/jp001974gopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jp0029109openalex-snapshot
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Rotational Coherence Spectroscopy and Structure of Naphthalene Trimer
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Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations
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Strength of the Benzene−Water Hydrogen Bond
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Large rate accelerations in antibody catalysis by strategic use of haptenic charge
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Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
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Density functional theory including dispersion corrections for intermolecular interactions in a large benchmark set of biologically relevant molecules
inferredcites →https://doi.org/10.1039/b701890hopenalex-snapshot
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inferredcites →https://doi.org/10.1063/1.1329889openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.1344891openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.1412004openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.1424928openalex-snapshot
Empirical correction to density functional theory for van der Waals interactions
inferredcites →https://doi.org/10.1063/1.1630953openalex-snapshot
High-level ab initio computations of structures and interaction energies of naphthalene dimers: Origin of attraction and its directionality
inferredcites →https://doi.org/10.1063/1.1637034openalex-snapshot
Dispersion corrections to density functionals for water aromatic interactions
inferredcites →https://doi.org/10.1063/1.445724openalex-snapshot
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Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1063/1.480575openalex-snapshot
Ab initio study of (NH3)2: Accurate structure and energetics
inferredcites →https://doi.org/10.1073/pnas.0409207102openalex-snapshot
Structural origins of efficient proton abstraction from carbon by a catalytic antibody
inferredcites →https://doi.org/10.1080/0026897031000121271openalex-snapshot
Extreme tunnelling in methylamine dehydrogenase revealed by hybrid QM/MM calculations: potential energy surface profile for methylamine and ethanolamine substrates and kinetic isotope effect values
inferredcites →https://doi.org/10.1080/00268970310001593286openalex-snapshot
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inferredcites →https://doi.org/10.1080/00268978400101201openalex-snapshot
A molecular dynamics method for simulations in the canonical ensemble
inferredcites →https://doi.org/10.1103/physreva.31.1695openalex-snapshot
Canonical dynamics: Equilibrium phase-space distributions
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.