110 research outputs found
Theoretical study of spin-orbit coupling in molecules
Theoretical models to study spin-obit coupling with multi-configurational wavefunctions have been developed both methodologically and implemented into the widely distributed quantum chemistry package GAMESS. Various aspects of making the spin-orbit coupling studies more efficient and thus more available, such as extensive usage of symmetry and parallelisation have been studied. A theoretical development of one, two and partial two electron approaches to spin-orbit coupling is given and tested on a representative set of molecules. A new accurate method to study the vibrational structure of molecules, limited in the current formulation to diatomics, has been proposed. Two chemically interesting systems have been studied, the reaction path of titanium cation and ethane, and the vibrational structure of CO+ and O 2+
Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry
We extend the Effective Fragment Molecular Orbital (EFMO) method to the
frozen domain approach where only the geometry of an active part is optimized,
while the many-body polarization effects are considered for the whole system.
The new approach efficiently mapped out the entire reaction path of chorismate
mutase in less than four days using 80 cores on 20 nodes, where the whole
system containing 2398 atoms is treated in the ab initio fashion without using
any force fields. The reaction path is constructed automatically with the only
assumption of defining the reaction coordinate a priori. We determine the
reaction barrier of chorismate mutase to be kcal mol for
MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using
EFMO-RHF/6-31G(d) for the high and low layers, respectively.Comment: SI not attache
Empirical corrections and pair interaction energies in the fragment molecular orbital method
The energy and analytic gradient are developed for FMO combined with the
Hartree-Fock method augmented with three empirical corrections (HF-3c). The
auxiliary basis set approach to FMO is extended to perform pair interaction
energy decomposition analysis. The FMO accuracy is evaluated for several
typical systems including 3 proteins. Pair interaction energies computed with
different approaches in FMO are compared for a water cluster and protein-ligand
complexes.Comment: Revised version accepted in Chemical Physics Letter
Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular Orbital Method
The frozen domain effective fragment molecular orbital method is extended to
allow for the treatment of a single fragment at the MP2 level of theory. The
approach is applied to the conversion of chorismate to prephenate by chorismate
mutase, where the substrate is treated at the MP2 level of theory while the
rest of the system is treated at the RHF level. MP2 geometry optimization is
found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations
and ONIOM energy refinement and leads to a smoother convergence with respect to
the basis set for the reaction profile. For double zeta basis sets the increase
in CPU time relative to RHF is roughly a factor of two.Comment: 11 pages, 3 figure
Multicomponent Strongly Interacting Few-Fermion Systems in One Dimension
The paper examines a trapped one-dimensional system of multicomponent
spinless fermions that interact with a zero-range two-body potential. We show
that when the repulsion between particles is very large the system can be
approached analytically. To illustrate this analytical approach we consider a
simple system of three distinguishable particles, which can be addressed
experimentally. For this system we show that for infinite repulsion the energy
spectrum is sixfold degenerate. We also show that this degeneracy is partially
lifted for finitely large repulsion for which we find and describe
corresponding wave functions.Comment: Paper in connection with the 22nd European Conference on Few-Body
Problems in Physics, Krakow, Poland, 9-13 September 201
Geometry Optimizations of Open-Shell Systems with the Fragment Molecular Orbital Method
The ability to perform geometry optimizations on large molecular systems is desirable for both closed- and open-shell species. In this work, the restricted open-shell Hartree–Fock (ROHF) gradients for the fragment molecular orbital (FMO) method are presented. The accuracy of the gradients is tested, and the ability of the method to reproduce adiabatic excitation energies is also investigated. Timing comparisons between the FMO method and full ab initio calculations are also performed, demonstrating the efficiency of the FMO method in modeling large open-shell systems
- …