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QM/MM Methods for Biological Systems

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Atomistic Approaches in Modern Biology

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 268))

Abstract

Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus on biomolecular systems. We provide a detailed overview of the methodology of QM/MM calculations and their use within optimization and simulation schemes. A tabular survey of recent applications, mostly to enzymatic reactions, is given.

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Abbreviations

ADMP:

Atom-centred density-matrix propagation

BFGS:

Broyden–Fletcher–Goldfarb–Shanno (Hessean update algorithm in minimizations)

CASSCF:

Complete active space self-consistent field

CCSD:

Coupled-cluster theory including single and double excitations

COSMO:

Conductor-like screening model

CP-MD:

Car–Parrinello molecular dynamics

DFT:

Density-functional theory

DO:

Drude oscillator

DTSS:

Differential transition-state stabilization

EC:

Enzyme class

ECP:

Effective core potential

EFP:

Effective fragment potential

EGP:

Effective group potential

ELMO:

Extremely localized molecular orbital

ESP:

Electrostatic potential

EVB:

Empirical valence bond

FEP:

Free-energy perturbation

FQ:

Fluctuating charge

GHO:

Generalized hybrid orbital

GSBP:

Generalized solvent boundary potential

HDLC:

Hybrid delocalized coordinates

HF:

Hartree–Fock

IMOMM:

Integrated molecular orbital/molecular mechanics

KIE:

Kinetic isotope effect

L-BFGS:

Limited-memory Broyden–Fletcher–Goldfarb–Shanno algorithm

LBHB:

Low-barrier hydrogen bond

LSCF:

Local self-consistent field

MC:

Monte Carlo

MC-VEEP:

Multicentred valence-electron effective potential

MD:

Molecular dynamics

MM:

Molecular mechanics

MECP:

Minimum-energy crossing point

MEP:

Minimum-energy path

MP2:

Second-order Møller–Plesset perturbation theory

NAC:

Near-attack configuration

NEB:

Nudged elastic band

OECP:

Optimized effective core potentials

ONIOM:

Our N-layered integrated molecular orbital/molecular mechanics

PBC:

Periodic boundary conditions

PES:

Potential-energy surface

PPD:

Polarized point dipole

P-RFO:

Partial rational-function optimizer

QCP:

Quantum capping potentials

QTCP:

Quantum-mechanical thermodynamic-cycle perturbation

QM:

Quantum mechanics

QM/MM:

Combined quantum mechanics/molecular mechanics

SCC-DFTB:

Self-consistent-charge density-functional tight-binding

RFO:

Rational-function optimizer

SCF:

Self-consistent field

SLBO:

Strictly localized bond orbital

SMD:

Steered molecular dynamics

VEP:

Variational electrostatic projection

TDDFT:

Time-dependent density-functional theory

TDHF:

Time-dependent Hartree–Fock

TI:

Thermodynamic integration

TPS:

Transition-path sampling

TS:

Transition state

US:

Umbrella sampling

VTST:

Variational transition-state theory

ZPE:

Zero-point energy

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Acknowledgments

H.M.S. thanks Drs. Johannes Kästner and Tell Tuttle for insightful discussions. This work was supported by the Volkswagenstiftung.

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  1. Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany

    Hans Martin Senn & Walter Thiel

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  1. Hans Martin Senn
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  2. Walter Thiel
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Correspondence to Hans Martin Senn or Walter Thiel .

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Markus Reiher

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Senn, H.M., Thiel, W. (2006). QM/MM Methods for Biological Systems. In: Reiher, M. (eds) Atomistic Approaches in Modern Biology. Topics in Current Chemistry, vol 268. Springer, Berlin, Heidelberg . https://doi.org/10.1007/128_2006_084

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