16 research outputs found
Reliably Modeling the Mechanical Stability of Rigid and Flexible MetalâOrganic Frameworks
ConspectusOver the
past two decades, metalâorganic frameworks (MOFs)
have matured from interesting academic peculiarities toward a continuously
expanding class of hybrid, nanoporous materials tuned for targeted
technological applications such as gas storage and heterogeneous catalysis.
These oft-times crystalline materials, composed of inorganic moieties
interconnected by organic ligands, can be endowed with desired structural
and chemical features by judiciously functionalizing or substituting
these building blocks. As a result of this reticular synthesis, MOF
research is situated at the intriguing intersection between chemistry
and physics, and the building block approach could pave the way toward
the construction of an almost infinite number of possible crystalline
structures, provided that they exhibit stability under the desired
operational conditions. However, this enormous potential is largely
untapped to date, as MOFs have not yet found a major breakthrough
in technological applications. One of the remaining challenges for
this scale-up is the densification of MOF powders, which is generally
achieved by subjecting the material to a pressurization step. However,
application of an external pressure may substantially alter the chemical
and physical properties of the material. A reliable theoretical guidance
that can presynthetically identify the most stable materials could
help overcome this technological challenge.In this Account,
we describe the recent research the progress on
computational characterization of the mechanical stability of MOFs.
So far, three complementary approaches have been proposed, focusing
on different aspects of mechanical stability: (i) the Born stability
criteria, (ii) the anisotropy in mechanical moduli such as the Young
and shear moduli, and (iii) the pressure-versus-volume equations of
state. As these three methods are grounded in distinct computational
approaches, it is expected that their accuracy and efficiency will
vary. To date, however, it is unclear which set of properties are
suited and reliable for a given application, as a comprehensive comparison
for a broad variety of MOFs is absent, impeding the widespread use
of these theoretical frameworks.Herein, we fill this gap by
critically assessing the performance
of the three computational models on a broad set of MOFs that are
representative for current applications. These materials encompass
the mechanically rigid UiO-66Â(Zr) and MOF-5Â(Zn) as well as the flexible
MIL-47Â(V) and MIL-53Â(Al), which undergo pressure-induced phase transitions.
It is observed that the Born stability criteria and pressure-versus-volume
equations of state give complementary insight into the macroscopic
and microscopic origins of instability, respectively. However, interpretation
of the Born stability criteria becomes increasingly difficult when
less symmetric materials are considered. Moreover, pressure fluctuations
during the simulations hamper their accuracy for flexible materials.
In contrast, the pressure-versus-volume equations of state are determined
in a thermodynamic ensemble specifically targeted to mitigate the
effects of these instantaneous fluctuations, yielding more accurate
results. The critical Account presented here paves the way toward
a solid computational framework for an extensive presynthetic screening
of MOFs to select those that are mechanically stable and can be postsynthetically
densified before their use in targeted applications
Radiation Products at 77 K in Trehalose Single Crystals: EMR and DFT Analysis
The radicals obtained in trehalose dihydrate single crystals
after
77 K X-irradiation have been investigated at the same temperature
using X-band electron paramagnetic resonance (EPR), electron nuclear
double resonance (ENDOR), and ENDOR-induced EPR (EIE) techniques.
Five proton hyperfine coupling tensors were unambiguously determined
from the ENDOR measurements and assigned to three carbon-centered
radical species (T1, T1*, and T2) based on the EIE spectra. EPR angular
variations revealed the presence of four additional alkoxy radical
species (T3 to T6) and allowed determination of their g tensors. Using
periodic density functional theory (DFT) calculations, T1/T1*, T2,
and T3 were identified as H-loss species centered at C4, C1â˛,
and O2â˛, respectively. The T4 radical is proposed to have the
unpaired electron at O4, but considerable discrepancies between experimental
and calculated HFC values indicate it is not simply the (net) H-loss
species. No suitable models were found for T5 and T6. These exhibit
a markedly larger g anisotropy than T3 and T4, which were not reproduced
by any of our DFT calculations
Radiation Products at 77 K in Trehalose Single Crystals: EMR and DFT Analysis
The radicals obtained in trehalose dihydrate single crystals
after
77 K X-irradiation have been investigated at the same temperature
using X-band electron paramagnetic resonance (EPR), electron nuclear
double resonance (ENDOR), and ENDOR-induced EPR (EIE) techniques.
Five proton hyperfine coupling tensors were unambiguously determined
from the ENDOR measurements and assigned to three carbon-centered
radical species (T1, T1*, and T2) based on the EIE spectra. EPR angular
variations revealed the presence of four additional alkoxy radical
species (T3 to T6) and allowed determination of their g tensors. Using
periodic density functional theory (DFT) calculations, T1/T1*, T2,
and T3 were identified as H-loss species centered at C4, C1â˛,
and O2â˛, respectively. The T4 radical is proposed to have the
unpaired electron at O4, but considerable discrepancies between experimental
and calculated HFC values indicate it is not simply the (net) H-loss
species. No suitable models were found for T5 and T6. These exhibit
a markedly larger g anisotropy than T3 and T4, which were not reproduced
by any of our DFT calculations
Mechanical Properties from Periodic Plane Wave Quantum Mechanical Codes: The Challenge of the Flexible Nanoporous MIL-47(V) Framework
Modeling the flexibility of metalâorganic
frameworks (MOFs)
requires the computation of mechanical properties from first principles,
e.g., for screening of materials in a database, for gaining insight
into structural transformations, and for force field development.
However, this paper shows that computations with periodic density
functional theory are challenged by the flexibility of these materials:
guidelines from experience with standard solid-state calculations
cannot be simply transferred to flexible porous frameworks. Our test
case, the MIL-47Â(V) material, has a large-pore and a narrow-pore shape.
The effect of Pulay stress (cf. Pulay forces) leads to drastic errors
for a simple structure optimization of the flexible MIL-47Â(V) material.
Pulay stress is an artificial stress that tends to lower the volume
and is caused by the finite size of the plane wave basis set. We have
investigated the importance of this Pulay stress, of symmetry breaking,
and of <i>k</i>-point sampling on (a) the structure optimization
and (b) mechanical properties such as elastic constants and bulk modulus,
of both the large-pore and narrow-pore structure of MIL-47Â(V). We
found that, in the structure optimization, Pulay effects should be
avoided by using a fitting procedure, in which an equation of state <i>E</i>(<i>V</i>) (EOS) is fit to a series of energy
versus volume points. Manual symmetry breaking could successfully
lower the energy of MIL-47Â(V) by distorting the vanadiumâoxide
distances in the vanadyl chains and by rotating the benzene linkers.
For the mechanical properties, the curvature of the EOS curve was
compared with the Reuss bulk modulus, derived from the elastic tensor
in the harmonic approximation. Errors induced by anharmonicity, the
eggbox effect, and Pulay effects propagate into the Reuss modulus.
The strong coupling of the unit cell axes when the unit cell deforms
expresses itself in numerical instability of the Reuss modulus. For
a flexible material, it is therefore advisible to resort to the EOS
fit procedure
On the Thermodynamics of Framework Breathing: A Free Energy Model for Gas Adsorption in MIL-53
When
adsorbing guest molecules, the porous metalâorganic
framework MIL-53Â(Cr) may vary its cell parameters drastically while
retaining its crystallinity. A first approach to the thermodynamic
analysis of this âframework breathingâ consists of comparing
the osmotic potential in two distinct shapes only (large-pore and
narrow-pore). In this paper, we propose a generic parametrized free
energy model including three contributions: host free energy, guestâguest
interactions, and hostâguest interaction. Free energy landscapes
may now be constructed scanning all shapes and any adsorbed amount
of guest molecules. This allows us to determine which shapes are the
most stable states for arbitrary combinations of experimental control
parameters, such as the adsorbing gas chemical potential, the external
pressure, and the temperature. The new model correctly reproduces
the structural transitions along the CO<sub>2</sub> and CH<sub>4</sub> isotherms. Moreover, our model successfully explains the adsorption
versus desorption hysteresis as a consequence of the creation, stabilization,
destabilization, and disappearance of a second free energy minimum
under the assumptions of a first-order phase transition and collective
behavior. Our general thermodynamic description allows us to decouple
the gas chemical potential Îź and mechanical pressure <i>P</i> as two independent thermodynamic variables and predict
the complete (Îź, <i>P</i>) phase diagram for CO<sub>2</sub> adsorption in MIL-53Â(Cr). The free energy model proposed
here is an important step toward a general thermodynamics description
of flexible metalâorganic frameworks
Critical Analysis of the Accuracy of Models Predicting or Extracting Liquid Structure Information
This work aims at a critical assessment
of properties predicting
or extracting information on the density and structure of liquids.
State-of-the-art NVT and NpT molecular dynamics (MD) simulations have
been performed on five liquids: methanol, chloroform, acetonitrile,
tetrahydrofuran, and ethanol. These simulations allow the computation
of properties based on first principles, including the equilibrium
density and radial distribution functions (RDFs), characterizing the
liquid structure. Refinements have been incorporated in the MD simulations
by taking into account basis set superposition errors (BSSE). An extended
BSSE model for an instantaneous evaluation of the BSSE corrections
has been proposed, and their impact on the liquid properties has been
assessed. If available, the theoretical RDFs have been compared with
the experimentally derived RDFs. For some liquids, significant discrepancies
have been observed, and a profound but critical investigation is presented
to unravel the origin of these deficiencies. This discussion is focused
on tetrahydrofuran where the experiment reveals some prominent peaks
completely missing in any MD simulation. Experiments providing information
on liquid structure consist mainly of neutron diffraction measurements
offering total structure factors as the primary observables. The splitting
of these factors in reciprocal space into intra- and intermolecular
contributions is extensively discussed, together with their sensitivity
in reproducing correct RDFs in coordinate space
Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides
The concept of the atomic charge is extensively used
to model the
electrostatic properties of proteins. Atomic charges are not only
the basis for the electrostatic energy term in biomolecular force
fields but are also derived from quantum mechanical computations on
protein fragments to get more insight into their electronic structure.
Unfortunately there are many atomic charge schemes which lead to significantly
different results, and it is not trivial to determine which scheme
is most suitable for biomolecular studies. Therefore, we present an
extensive methodological benchmark using a selection of atomic charge
schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I,
electronegativity equalization method (EEM), and split-charge equilibration
(SQE)] applied to two sets of penta-alanine conformers. Our analysis
clearly shows that Hirshfeld-I charges offer the best compromise between
transferability (robustness with respect to conformational changes)
and the ability to reproduce electrostatic properties of the penta-alanine.
The benchmark also considers two charge equilibration models (EEM
and SQE), which both clearly fail to describe the locally charged
moieties in the zwitterionic form of penta-alanine. This issue is
analyzed in detail because charge equilibration models are computationally
much more attractive than the Hirshfeld-I scheme. Based on the latter
analysis, a straightforward extension of the SQE model is proposed,
SQE+Q<sup>0</sup>, that is suitable to describe biological systems
bearing many locally charged functional groups
Molecular Dynamics Kinetic Study on the Zeolite-Catalyzed Benzene Methylation in ZSMâ5
The methylation of arenes is a key
step in the production of hydrocarbons
from methanol over acidic zeolites. We performed ab initio static
and molecular dynamics free energy simulations of benzene methylation
in H-ZSM-5 to determine the factors that influence the reaction kinetics.
Special emphasis is given to the effect of the surrounding methanol
molecules on the methylation kinetics. It is found that for higher
methanol loadings, methylation may also occur from a protonated methanol
cluster, indicating that the exact location of the Brønsted acid
site is not essential for the zeolite-catalyzed methylation reaction.
However, methylations from a protonated methanol cluster exhibit higher
free energy barriers than a methylation from a single methanol molecule.
Finally, comparison with a pure methanol solvent reaction environment
indicates that the main role of the zeolite during the methylation
of benzene is to provide the acidic proton and to create a polar environment
for the reaction. The metadynamics approach, which is specifically
designed to sample rare events, allows exploring new reaction pathways,
which take into account the flexibility of the framework and additional
guest molecules in the pores and channels of the zeolite framework.
This approach goes beyond the often applied static calculations to
determine reaction kinetics
Solvent-Controlled Selective Transformation of 2-Bromomethyl-2-methylaziridines to Functionalized Aziridines and Azetidines
The reactivity of 2-bromomethyl-2-methylaziridines toward
oxygen,
sulfur, and carbon nucleophiles in different solvent systems was investigated.
Remarkably, the choice of the solvent has a profound influence on
the reaction outcome, enabling the selective formation of either functionalized
aziridines in dimethylformamide (through direct bromide displacement)
or azetidines in acetonitrile (through rearrangement via a bicyclic
aziridinium intermediate). In addition, the experimentally observed
solvent-dependent behavior of 2-bromomethyl-2-methylaziridines was
further supported by means of DFT calculations
Dominant Stable Radicals in Irradiated Sucrose: <b>g</b> Tensors and Contribution to the Powder Electron Paramagnetic Resonance Spectrum
Ionizing radiation
induces a composite, multiline electron paramagnetic
resonance (EPR) spectrum in sucrose, that is stable at room temperature
and whose intensity is indicative of the radiation dose. Recently,
the three radicals which dominate this spectrum were identified and
their proton hyperfine tensors were accurately determined. Understanding
the powder EPR spectrum of irradiated sucrose, however, also requires
an accurate knowledge of the <b>g</b> tensors of these radicals.
We extracted these tensors from angular dependent electron nuclear
double resonance-induced EPR measurements at 110 K and 34 GHz. Powder
spectrum simulations using this completed set of spin Hamiltonian
parameters are in good agreement with experimentally recorded spectra
in a wide temperature and frequency range. However, as-yet nonidentified
radicals also contribute to the EPR spectra of irradiated sucrose
in a non-negligible way