24,351 research outputs found
Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?
Recent years have seen vast improvements in the ability of rigorous
quantum-mechanical methods to treat systems of interest to molecular biology.
In this review article, we survey common computational methods used to study
such large, weakly bound systems, starting from classical simulations and
reaching to quantum chemistry and density functional theory. We sketch their
underlying frameworks and investigate their strengths and weaknesses when
applied to potentially large biomolecules. In particular, density functional
theory---a framework that can treat thousands of atoms on firm theoretical
ground---can now accurately describe systems dominated by weak van der Waals
interactions. This newfound ability has rekindled interest in using this
tried-and-true approach to investigate biological systems of real importance.
In this review, we focus on some new methods within density functional theory
that allow for accurate inclusion of the weak interactions that dominate
binding in biological macromolecules. Recent work utilizing these methods to
study biologically-relevant systems will be highlighted, and a vision for the
future of density functional theory within molecular biology will be discussed
Graphite and Hexagonal Boron-Nitride Possess the Same Interlayer Distance. Why?
Graphite and hexagonal boron nitride (h-BN) are two prominent members of the
family of layered materials possessing a hexagonal lattice. While graphite has
non-polar homo-nuclear C-C intra-layer bonds, h-BN presents highly polar B-N
bonds resulting in different optimal stacking modes of the two materials in
bulk form. Furthermore, the static polarizabilities of the constituent atoms
considerably differ from each other suggesting large differences in the
dispersive component of the interlayer bonding. Despite these major differences
both materials present practically identical interlayer distances. To
understand this finding, a comparative study of the nature of the interlayer
bonding in both materials is presented. A full lattice sum of the interactions
between the partially charged atomic centers in h-BN results in vanishingly
small monopolar electrostatic contributions to the interlayer binding energy.
Higher order electrostatic multipoles, exchange, and short-range correlation
contributions are found to be very similar in both materials and to almost
completely cancel out by the Pauli repulsions at physically relevant interlayer
distances resulting in a marginal effective contribution to the interlayer
binding. Further analysis of the dispersive energy term reveals that despite
the large differences in the individual atomic polarizabilities the
hetero-atomic B-N C6 coefficient is very similar to the homo-atomic C-C
coefficient in the hexagonal bulk form resulting in very similar dispersive
contribution to the interlayer binding. The overall binding energy curves of
both materials are thus very similar predicting practically the same interlayer
distance and very similar binding energies.Comment: 18 pages, 5 figures, 2 table
Exact Wave Packet Dynamics of Singlet Fission in Unsubstituted and Substituted Polyene Chains within Long-Range Interacting Models
Singlet fission (SF) is a potential pathway for significant enhancement of
efficiency in organic solar cells (OSC). In this paper, we study singlet
fission in a pair of polyene molecules in two different stacking arrangements
employing exact many-body wave packet dynamics. In the non-interacting model,
the SF yield is absent. The individual molecules are treated within Hubbard and
Pariser-Parr-Pople (PPP) models and the interaction between them involves
transfer terms, intersite electron repulsions and site-charge--bond-charge
repulsion terms. Initial wave packet is constructed from excited singlet state
of one molecule and ground state of the other. Time development of this wave
packet under the influence of intermolecular interactions is followed within
the Schr\"odinger picture by an efficient predictor-corrector scheme. In
unsubstituted Hubbard and PPP chains, excited singlet state leads to
significant SF yield while the state gives negligible fission yield.
On substitution by donor-acceptor groups of moderate strength, the lowest
excited state will have sufficient character and hence results in
significant SF yield. Because of rapid internal conversion, the nature of the
lowest excited singlet will determine the SF contribution to OSC efficiency.
Furthermore, we find the fission yield depends considerably on the stacking
arrangement of the polyene molecules.Comment: 13 pages, 8 figures, 4 table
Effect of van der Waals forces on the stacking of coronenes encapsulated in a single-wall carbon nanotube and many-body excitation spectrum
We investigate the geometry, stability, electronic structure and optical
properties of C24H12 coronenes encapsulated in a single-wall (19,0) carbon
nanotube. By an adequate combination of advanced electronic-structure
techniques, involving weak and van derWaals interaction, as well as many-body
effects for establishing electronic properties and excitations, we have
accurately characterized this hybrid carbon nanostructure, which arises as a
promising candidate for opto-electronic nanodevices. In particular, we show
that the structure of the stacked coronenes inside the nanotube is
characterized by a rotation of every coronene with respect to its neighbors
through van derWaals interaction, which is of paramount importance in these
systems. We also suggest a tentative modification of the system in order this
particular rotation to be observed experimentally. A comparison between the
calculated many-body excitation spectrum of the systems involved reveals a
pronounced optical red-shift with respect to the coronene-stacking gas-phase.
The origin of this red-shift is explained in terms of the confinement of the
coronene molecules inside the nanotube, showing an excellent agreement with the
available experimental evidence
Strength of π-Stacking, from Neutral to Cation: Precision Measurement of Binding Energies in an Isolated π-Stacked Dimer
π-Stacking interactions are ubiquitious across chemistry and biochemistry, impacting areas from organic materials and photovoltaics to biochemistry and DNA. However, experimental data is lacking regarding the strength of π-stacking forces—an issue not settled even for the simplest model system, the isolated benzene dimer. Here, we use two-color appearance potential measurements to determine the binding energies of the isolated, π-stacked dimer of fluorene (C13H10) in ground, excited, and ionic states. Our measurements provide the first precise values for π-stacking interaction energies in these states, which are key benchmarks for theory. Indeed, theoretical predictions using ab initio and carefully benchmarked DFT methods are in excellent agreement with experiment
Manganites at Quarter Filling: Role of Jahn-Teller Interactions
We have analyzed different correlation functions in a realistic spin-orbital
model for half-doped manganites. Using a finite-temperature diagonalization
technique the CE phase was found in the charge-ordered phase in the case of
small antiferromagnetic interactions between electrons. It is shown
that a key ingredient responsible for stabilization of the CE-type spin and
orbital-ordered state is the cooperative Jahn-Teller (JT) interaction between
next-nearest Mn neighbors mediated by the breathing mode distortion of
Mn octahedra and displacements of Mn ions. The topological phase
factor in the Mn-Mn hopping leading to gap formation in one-dimensional models
for the CE phase as well as the nearest neighbor JT coupling are not able to
produce the zigzag chains typical for the CE phase in our model.Comment: 16 pages with 16 figures, contains a more detailed parameter estimate
based on the structural data by Radaelli et al. (accepted for publication in
Phys. Rev. B
Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport
Several assemblies of guanine molecules are investigated by means of
first-principle calculations. Such structures include stacked and
hydrogen-bonded dimers, as well as vertical columns and planar ribbons,
respectively, obtained by periodically replicating the dimers. Our results are
in good agreement with experimental data for isolated molecules, isolated
dimers, and periodic ribbons. For stacked dimers and columns, the stability is
affected by the relative charge distribution of the pi orbitals in adjacent
guanine molecules. pi-pi coupling in some stacked columns induces dispersive
energy bands, while no dispersion is identified in the planar ribbons along the
connections of hydrogen bonds. The implications for different materials
comprised of guanine aggregates are discussed. The bandstructure of dispersive
configurations may justify a contribution of band transport (Bloch type) in the
conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations
band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.
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