10,884 research outputs found
Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals
From configuration interaction (CI) ab initio calculations, we derive an
effective two-orbital extended Hubbard model based on the gerade (g) and
ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular
conductor (TTM-TTP)I_3 and the single-component molecular conductor
[Au(tmdt)_2]. First, by focusing on the isolated molecule, we determine the
parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian
matrix. Next, we extend the analysis to two neighboring molecule pairs in the
crystal and we perform similar calculations to evaluate the inter-molecular
interactions. From the resulting tight-binding parameters, we analyze the band
structure to confirm that two bands overlap and mix in together, supporting the
multi-band feature. Furthermore, using a fragment decomposition, we derive the
effective model based on the fragment MOs and show that the staking TTM-TTP
molecules can be described by the zig-zag two-leg ladder with the
inter-molecular transfer integral being larger than the intra-fragment transfer
integral within the molecule. The inter-site interactions between the fragments
follow a Coulomb law, supporting the fragment decomposition strategy.Comment: 16 pages, 8 figures, published versio
Multi-Orbital Molecular Compound (TTM-TTP)I_3: Effective Model and Fragment Decomposition
The electronic structure of the molecular compound (TTM-TTP)I_3, which
exhibits a peculiar intra-molecular charge ordering, has been studied using
multi-configuration ab initio calculations. First we derive an effective
Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up
a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine
its full parameters: the transfer integrals, the Coulomb and exchange
interactions. The tight-binding band structure obtained from these transfer
integrals is consistent with the result of the direct band calculation based on
density functional theory. Then, by decomposing the frontier MOs into two
parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be
described by a two-leg ladder model, while the inter-fragment Coulomb energies
are scaled to the inverse of their distances. This result indicates that the
fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys.
132 (2010) 214705] successfully describes the low-energy properties of this
compound.Comment: 5 pages, 4 figures, published versio
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
Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values
We present a critical analysis of the popular fragment-orbital
density-functional theory (FO-DFT) scheme for the calculation of electronic
coupling values. We discuss the characteristics of different possible
formulations or 'flavors' of the scheme which differ by the number of electrons
in the calculation of the fragments and the construction of the Hamiltonian. In
addition to two previously described variants based on neutral fragments, we
present a third version taking a different route to the approximate diabatic
state by explicitly considering charged fragments. In applying these FO-DFT
flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole
transfer) we find that our new scheme gives improved electronic couplings for
HAB7 (-6.2% decrease in mean relative signed error) and greatly improved
electronic couplings for HAB11 (-15.3% decrease in mean relative signed error).
A systematic investigation of the influence of exact exchange on the electronic
coupling values shows that the use of hybrid functionals in FO-DFT calculations
improves the electronic couplings, giving values close to or even better than
more sophisticated constrained DFT calculations. Comparing the accuracy and
computational cost of each variant we devise simple rules to choose the best
possible flavor depending on the task. For accuracy, our new scheme with
charged-fragment calculations performs best, while numerically more efficient
at reasonable accuracy is the variant with neutral fragments
Charge migration in organic materials: Can propagating charges affect the key physical quantities controlling their motion?
Charge migration is a ubiquitous phenomenon with profound implications
throughout many areas of chemistry, physics, biology and materials science. The
long-term vision of designing functional materials with tailored molecular
scale properties has triggered an increasing quest to identify prototypical
systems where truly molecular conduction pathways play a fundamental role. Such
pathways can be formed due to the molecular organization of various organic
materials and are widely used to discuss electronic properties at the nanometer
scale. Here, we present a computational methodology to study charge propagation
in organic molecular stacks at nano and sub-nanoscales and exploit this
methodology to demonstrate that moving charge carriers strongly affect the
values of the physical quantities controlling their motion. The approach is
also expected to find broad application in the field of charge migration in
soft matter systems.Comment: 18 pages, 6 figures, accepted for publication in the Israel Journal
of Chemistr
Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis
Given the piecewise approach to modeling intermolecular interactions for
force fields, they can be difficult to parameterize since they are fit to data
like total energies that only indirectly connect to their separable functional
forms. Furthermore, by neglecting certain types of molecular interactions such
as charge penetration and charge transfer, most classical force fields must
rely on, but do not always demonstrate, how cancellation of errors occurs among
the remaining molecular interactions accounted for such as exchange repulsion,
electrostatics, and polarization. In this work we present the first generation
of the (many-body) MB-UCB force field that explicitly accounts for the
decomposed molecular interactions commensurate with a variational energy
decomposition analysis, including charge transfer, with force field design
choices that reduce the computational expense of the MB-UCB potential while
remaining accurate. We optimize parameters using only single water molecule and
water cluster data up through pentamers, with no fitting to condensed phase
data, and we demonstrate that high accuracy is maintained when the force field
is subsequently validated against conformational energies of larger water
cluster data sets, radial distribution functions of the liquid phase, and the
temperature dependence of thermodynamic and transport water properties. We
conclude that MB-UCB is comparable in performance to MB-Pol, but is less
expensive and more transferable by eliminating the need to represent
short-ranged interactions through large parameter fits to high order
polynomials
Nucleation of a sodium droplet on C60
We investigate theoretically the progressive coating of C60 by several sodium
atoms. Density functional calculations using a nonlocal functional are
performed for NaC60 and Na2C60 in various configurations. These data are used
to construct an empirical atomistic model in order to treat larger sizes in a
statistical and dynamical context. Fluctuating charges are incorporated to
account for charge transfer between sodium and carbon atoms. By performing
systematic global optimization in the size range 1<=n<=30, we find that Na_nC60
is homogeneously coated at small sizes, and that a growing droplet is formed
above n=>8. The separate effects of single ionization and thermalization are
also considered, as well as the changes due to a strong external electric
field. The present results are discussed in the light of various experimental
data.Comment: 17 pages, 10 figure
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