249 research outputs found
Application of the PM6 method to modeling the solid state
The applicability of the recently developed PM6 method for modeling various properties of a wide range of organic and inorganic crystalline solids has been investigated. Although the geometries of most systems examined were reproduced with good accuracy, severe errors were found in the predicted structures of a small number of solids. The origin of these errors was investigated, and a strategy for improving the method proposed
Effect of Peierls transition in armchair carbon nanotube on dynamical behaviour of encapsulated fullerene
The changes of dynamical behaviour of a single fullerene molecule inside an
armchair carbon nanotube caused by the structural Peierls transition in the
nanotube are considered. The structures of the smallest C20 and Fe@C20
fullerenes are computed using the spin-polarized density functional theory.
Significant changes of the barriers for motion along the nanotube axis and
rotation of these fullerenes inside the (8,8) nanotube are found at the Peierls
transition. It is shown that the coefficients of translational and rotational
diffusions of these fullerenes inside the nanotube change by several orders of
magnitude. The possibility of inverse orientational melting, i.e. with a
decrease of temperature, for the systems under consideration is predicted.Comment: 9 pages, 6 figures, 1 tabl
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
Topological mechanochemistry of graphene
In view of a formal topology, two common terms, namely, connectivity and
adjacency, determine the quality of C-C bonds of sp2 nanocarbons. The feature
is the most sensitive point of the inherent topology of the species so that
such external action as mechanical deformation should obviously change it and
result in particular topological effects. The current paper describes the
effects caused by uniaxial tension of a graphene molecule in due course of a
mechanochemical reaction. Basing on the molecular theory of graphene, the
effects are attributed to both mechanical loading and chemical modification of
edge atoms of the molecule. The mechanical behavior is shown to be not only
highly anisotropic with respect to the direction of the load application, but
greatly dependent on the chemical modification of the molecule edge atoms thus
revealing topological character of the graphene deformation.Comment: 9 pages, 10 figures, 1 table. arXiv admin note: text overlap with
arXiv:1301.094
The Energy Computation Paradox and ab initio Protein Folding
The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination
A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion
The present study analyzed binding of Cu2+ to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches including electron correlation effects. In order to shed light on the character of interactions between Cu2+ and peptides, which are expected to be mainly electrostatic in nature, decomposition of interaction energy into physically meaningful components was applied
A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry
We present here a review of the fundamental topics of Hartree-Fock theory in
Quantum Chemistry. From the molecular Hamiltonian, using and discussing the
Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock
equations for the electronic problem. Special emphasis is placed in the most
relevant mathematical aspects of the theoretical derivation of the final
equations, as well as in the results regarding the existence and uniqueness of
their solutions. All Hartree-Fock versions with different spin restrictions are
systematically extracted from the general case, thus providing a unifying
framework. Then, the discretization of the one-electron orbitals space is
reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition
of the basic underlying concepts related to the construction and selection of
Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we
close the review with a section in which the most relevant modern developments
(specially those related to the design of linear-scaling methods) are commented
and linked to the issues discussed. The whole work is intentionally
introductory and rather self-contained, so that it may be useful for non
experts that aim to use quantum chemical methods in interdisciplinary
applications. Moreover, much material that is found scattered in the literature
has been put together here to facilitate comprehension and to serve as a handy
reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and
subeqn package
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