Acronyms

AH

Augmented Hessian in RFO scheme (section 3.1)

AM1

Austin Model 1. Semiemirical Hamiltonian by Dewar and co-workers [31]

CPU

Central Processing Unit

DIIS

Direct Inversion of Iterative Space optimzation method [133]

DFT

Density Functional Theory (section 1.2.1.6)

GHO

Generalized Hybrid Orbital method for the QM/MM frontier [91]

IRC

Intrinsic Reaction Coordinate (section 1.3.5.2)

HF

Hartree-Fock method (section 1.2.1.4)

L-BFGS

Limited memory Broyden Fletcher Goldfarg Shanno method [153]

LNR

Lagrange-Newton-Raphson iterative diagonalization technique (page )

MC

Monte Carlo (section 1.4)

MD

Molecular Dynamics (section 1.4)

MEP

Minimum Energy Path (section 1.3.5)

MM

Molecular Mechanics (section 1.2.2.1)

MR

Mandelate Racemase Enzyme (section 2.1)

PBC

Periodic Boundary Conditions (section 1.2.2.2)

PES

Potential Energy Surface (section 1.2.1.2)

PGA

phenylglycidate, inhibitor of Mandelate Racemase (section 2.1)

PM3

Parametrized Model 3. Semiempirical Hamiltonian [32]

qNR

Quasi Newton-Raphson. Newton Raphson optimization using an approximated second derivative matrix. Quasi Newton methods (section 1.3.4.1)

qNR-BFGS

Quasi Newton-Raphson with BFGS update (see page )

qNR-LBFGS

Quasi Newton-Raphson with limited memory BFGS update (see page )

QM/MM

quantum mechanics /molecular mechanics strategy [66]

RFO

Rational Function Optimization [130]

RFO-mBFGS

Rational Function Optimization with modified BFGS update (see page )

RMS

Root Mean Square. In this thesis the term is used in particular for the gradient norm.

SBMD

Stochastic Boundary Molecular Dynamics method [185]

SD

Steepest Descent (section 1.3.3)

SRP

Specific Reaction Parameters. In semiempirical context some empirical parameters are modified for an specific reaction

TS

Transition state. Depending on the context this can be the term for a first-order saddle point on a PES.

ZPE

Zero Point Energy