11,124 research outputs found
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
How does an interacting many-body system tunnel through a potential barrier to open space?
The tunneling process in a many-body system is a phenomenon which lies at the
very heart of quantum mechanics. It appears in nature in the form of
alpha-decay, fusion and fission in nuclear physics, photoassociation and
photodissociation in biology and chemistry. A detailed theoretical description
of the decay process in these systems is a very cumbersome problem, either
because of very complicated or even unknown interparticle interactions or due
to a large number of constitutent particles. In this work, we theoretically
study the phenomenon of quantum many-body tunneling in a more transparent and
controllable physical system, in an ultracold atomic gas. We analyze a full,
numerically exact many-body solution of the Schr\"odinger equation of a
one-dimensional system with repulsive interactions tunneling to open space. We
show how the emitted particles dissociate or fragment from the trapped and
coherent source of bosons: the overall many-particle decay process is a quantum
interference of single-particle tunneling processes emerging from sources with
different particle numbers taking place simultaneously. The close relation to
atom lasers and ionization processes allows us to unveil the great relevance of
many-body correlations between the emitted and trapped fractions of the
wavefunction in the respective processes.Comment: 18 pages, 4 figures (7 pages, 2 figures supplementary information
The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
We extend the effective fragment molecular orbital method (EFMO) into
treating fragments connected by covalent bonds. The accuracy of EFMO is
compared to FMO and conventional ab initio electronic structure methods for
polypeptides including proteins. Errors in energy for RHF and MP2 are within 2
kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides
similar to FMO but obtained two to five times faster. For proteins, the errors
are also within a few kcal/mol of the FMO results. We developed both the RHF
and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures
had an RMSD of 0.40 and 0.44 {\AA} for RHF and MP2, respectively.Comment: Revised manuscrip
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