2,516 research outputs found
Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion
We estimate polarizabilities of atoms in molecules without electron density,
using a Voronoi tesselation approach instead of conventional density
partitioning schemes. The resulting atomic dispersion coefficients are
calculated, as well as many-body dispersion effects on intermolecular potential
energies. We also estimate contributions from multipole electrostatics and
compare them to dispersion. We assess the performance of the resulting
intermolecular interaction model from dispersion and electrostatics for more
than 1,300 neutral and charged, small organic molecular dimers. Applications to
water clusters, the benzene crystal, the anti-cancer drug
ellipticine---intercalated between two Watson-Crick DNA base pairs, as well as
six macro-molecular host-guest complexes highlight the potential of this method
and help to identify points of future improvement. The mean absolute error made
by the combination of static electrostatics with many-body dispersion reduces
at larger distances, while it plateaus for two-body dispersion, in conflict
with the common assumption that the simple correction will yield proper
dissociative tails. Overall, the method achieves an accuracy well within
conventional molecular force fields while exhibiting a simple parametrization
protocol.Comment: 13 pages, 8 figure
Extension of the B3LYP - Dispersion-Correcting Potential Approach to the Accurate Treatment of both Inter- and Intramolecular Interactions
We recently showed that dispersion-correcting potentials (DCPs),
atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys.
Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying
functional to predict non-covalent interactions. However, the application of
B3LYP-DCP for the {\beta}-scission of the cumyloxyl radical led a calculated
barrier height that was over-estimated by ca. 8 kcal/mol. We show in the
present work that the source of this error arises from the previously developed
carbon atom DCPs, which erroneously alters the electron density in the C-C
covalent-bonding region. In this work, we present a new C-DCP with a form that
was expected to influence the electron density farther from the nucleus. Tests
of the new C-DCP, with previously published H-, N- and O-DCPs, with
B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of
non-covalently interacting dimers showed that it is one of the most accurate
methods available for treating intermolecular interactions, giving mean
absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively.
Additional testing on the S12L database of complexation systems gave an MAE of
2.6 kcal/mol, showing that the B3LYP-DCP/6-31+G(2d,2p) approach is one of the
best-performing and feasible methods for treating large systems dominated by
non-covalent interactions. Finally, we showed that C-C making/breaking
chemistry is well-predicted using the newly developed DCPs. In addition to
predicting a barrier height for the {\beta}-scission of the cumyloxyl radical
that is within 1.7 kcal/mol of the high-level value, application of
B3LYP-DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights
and energies, isomerization energies and relative conformation energies gives
performance that is amongst the best of all available dispersion-corrected
density-functional theory approaches
Stability of Chiral States, Role of Intermolecular Interactions and Molecular Parity Violation
We study the problem of stability of chiral states, also known as problem of
chirality, within the framework of a two-dimensional approximation of a
symmetric double-well potential. We show how the symmetry breaking of the
potential due to the molecular parity violation can stop the tunneling in a
coherent way, accordingly stabilize the chiral states. Then, we use the quantum
Brownian motion within a linear Lindblad-type equation to model how the
intermolecular interactions make the tunneling incoherent, thus inducing a
racemization by dephasing. Finally, we investigate the normal physical
conditions where the dephasing racemization does not suppress the effects of
the molecular parity violation, accordingly the molecular parity violation may
be observed experimentally.Comment: 5 pages, 2 Figure
Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates
Supramolecular aggregates of synthetic dye molecules offer great perspectives to prepare biomimetic functional materials for light-harvesting and energy transport. The design is complicated by the fact that structure-property relationships are hard to establish, because the molecular packing results from a delicate balance of interactions and the excitonic properties that dictate the optics and excited state dynamics, in turn sensitively depend on this packing. Here we show how an iterative multiscale approach combining molecular dynamics and quantum mechanical exciton modeling can be used to obtain accurate insight into the packing of thousands of cyanine dye molecules in a complex double-walled tubular aggregate in close interaction with its solvent environment. Our approach allows us to answer open questions not only on the structure of these prototypical aggregates, but also about their molecular-scale structural and energetic heterogeneity, as well as on the microscopic origin of their photophysical properties. This opens the route to accurate predictions of energy transport and other functional properties
An indole trimer: synthesis, self-assembly and applications
The organic semiconductor, the indole -5- carboxylic acid asymmetric trimer (ICAT), was
chemically synthesised using a new procedure. Self- assembly of ICAT in solution,
produced narrowly dispersed discotic nanoparticles that are stable in solution and
transferable between surfaces. Highly ordered ICAT bulk molecular and nanoparticle thin
films were produced through controlled assembly of ICAT at the solution /solid interface,
using glass substrates functionalised with a variety of self assembled monolayers (SAMs).
Two films, in particular, on the hydroxyl and the amine -functionalised substrates had
extremely well ordered microstructures, suitable for device application.An immersion based deposition technique was developed, where gold and SAM - functionalised glass substrates were immersed in ICAT solutions made with solvents with a
range of polarities. At short immersion times, bulk or particulate films were deposited, as a
function of immersion solvent. Longer immersion times produced size tailored vertically
aligned nanorod and nanowire arrays, as a function of immersion solvent. The immersion
time also controlled both the rod density and rod orientation on the substrates. The results
were interpreted in terms of heterogeneous nucleation and subsequent growth. Solvophobic
forces induced homogeneous nucleation rather than heterogeneous nucleation, in the
immersion systems with water and hydrocarbon based immersion solvents. Aligned
nanorods and nanowires were assembled on gold and hydroxyl -functionalised glass
substrates when polar aprotic immersion solvents were used. There was no obvious
correlation between nanostructure dimensions and solvent polarity in these experiments.
This is the first time vertically aligned nanorod arrays have been fabricated with small
organic functional molecules, through a solution based technique (non -template).Solution based deposition techniques developed here were used to deposit ICAT onto field
effect transistors (FETs), resulting in devices with a range of ICAT film morphologies.
Single crystal devices were also produced where the ICAT crystal bridged the active
channel, defined as the gap between the source and drain electrodes. Several chips, with
over 20 FETs on each chip, with each ICAT film morphology type, were fabricated.
Selected chips had consistent, reproducible current/voltage (IV) outputs that varied within
« one order of magnitude, when probed on all areas. The devices produced n and p -type
unipolar activity and the onset of ambipolar activity in ambient conditions, at low voltage
probing ranges. Carrier type was dependent on the film morphology. Device lifetime was
dependent on film thickness
Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment
Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent complexes, which stabilize and modulate (in particular blue, violet, and red) colors in flowers, berries, and food products derived from them (including wines, jams, purees, and syrups). This noncovalent association and their electronic and optical implications constitute the copigmentation phenomenon. Over the past decade, experimental and theoretical studies have enabled a molecular understanding of copigmentation. This review revisits this phenomenon to provide a comprehensive description of the nature of binding (the dispersion and electrostatic components of ÏâÏ stacking, the hydrophobic effect, and possible hydrogen-bonding between pigment and copigment) and of spectral modifications occurring in copigmentation complexes, in which charge transfer plays an important role. Particular attention is paid to applications of copigmentation in food chemistry.P.T. thanks the âConseil ReÌgional du Limousinâ for financial support and CALI (CAlcul en LImousin). Financial support from the Czech Science Foundation (P208/12/G016), the Ministry of Education, Youth and Sports of the Czech Republic (project LO1305), and the Operational Program Education for Competitiveness-European Social Fund (project CZ.1.07/2.3.00/20.0058 of the Ministry of Education, Youth and Sports of the Czech Republic) is also gratefully acknowledged. The work at IMDEA was supported by the Spanish Ministerio de EconomĂa y Competitividad (MINECO; project CTQ2014-58801)
Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchangeâcorrelation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclearâelectronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an âopen teamwareâ model and an increasingly modular design
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