29 research outputs found
Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations
The scattering-adapted flexible inner region ensemble separator (SAFIRES) is
a partitioning scheme designed to divide a simulation cell into two regions to
be treated with different computational methodologies. SAFIRES prevents
particles from crossing between regions and resolves boundary events through
elastic collisions of the particles mediated by the boundary, conserving energy
and momenta. A multiple-time-step propagation algorithm is introduced where the
time step is scaled automatically to identify the moment a collision occurs. If
the length of the time step is kept constant, the new propagator reduces to a
regular algorithm for Langevin dynamics, and to the velocity Verlet algorithm
for classical dynamics if the friction coefficient is set to zero. SAFIRES
constitutes the exact limit of the premise behind boundary-based methods such
as FIRES, BEST, and BCC which take advantage of the indistinguishability of
molecules on opposite sides of the separator. It gives correct average ensemble
statistics despite the introduction of an ensemble separator. SAFIRES is tested
in simulations where the molecules on the two sides are treated in the same
way, for a Lennard-Jones (LJ) liquid and a LJ liquid in contact with a surface,
as well as for liquid modelling simulations using the TIP4P force field.
Simulations using SAFIRES are shown to reproduce the unconstrained reference
simulations without significant deviations.Comment: To be submitted to Journal of Chemical Theory and Computatio
Solvent-Controlled Chemoselectivity in the Photolytic Release of Hydroxamic Acids and Carboxamides from Solid Support
The
synthetic utility and theoretical basis of a photolabile hydroxylamine-linker
are presented. The developed protocols enable the efficient synthesis
and chemoselective photolytic release of either hydroxamates or carboxamides
from solid support. The bidetachable mode of the linker unit is uniquely
dependent on the solvent. Hydroxamic acids are obtained by performing
photolysis in protic solvents, whereas photolysis in aprotic solvents
enables the selective release of carboxamides
Ultrafast X-ray absorption study of longitudinal-transverse phonon coupling in electrolyte aqueous solution
Ultrafast X-ray absorption spectroscopy is applied to study the conversion of longitudinal to transverse phonons in aqueous solution.</p
Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard–Jones Parameters for Water and to Study Solvation of TiO2 Nanoparticles
Publisher's version (Ăştgefin grein)Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological
applications, where their functional environment is often an aqueous solution. The correct description
of metal oxide electronic structure is still a challenge for local and semilocal density functionals,
whereas hybrid functional methods provide an improved description, and local atomic function-based
codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional
calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes,
in a real environment. Therefore, we here present and critically assess the accuracy of our electrostatic
embedding quantum mechanical/molecular mechanical (QM/MM) coupling between CRYSTAL17
and AMBER16, and demonstrate some of its capabilities via the case study of TiO2 NPs in water.
First, we produced new Lennard–Jones (LJ) parameters that improve the accuracy of water–water
interactions in the B3LYP/TIP3P coupling. We found that optimizing LJ parameters based on water
tri- to deca-mer clusters provides a less overstructured QM/MM liquid water description than when
fitting LJ parameters only based on the water dimer. Then, we applied our QM/MM coupling
methodology to describe the interaction of a 1 nm wide multilayer of water surrounding a spherical
TiO2 nanoparticle (NP). Optimizing the QM/MM water–water parameters was found to have little to
no effect on the local NP properties, which provide insights into the range of influence that can be
attributed to the LJ term in the QM/MM coupling. The effect of adding additional water in an MM
fashion on the geometry optimized nanoparticle structure is small, but more evident effects are seen
in its electronic properties. We also show that there is good transferability of existing QM/MM LJ
parameters for organic molecules–water interactions to our QM/MM implementation, even though
these parameters were obtained with a different QM code and QM/MM implementation, but with the
same functional.National Council for Eurasian and East European Research.
Funding: This research was funded by the Icelandic Research Fund (grant 174244-051) and VILLUM FONDEN,
the European Research Council (ERC) under the European Union’s HORIZON2020 research and innovation
programme (ERC Grant Agreement No [647020]).
Acknowledgments: A.O.D. Would like to thank JĂłnsson, H. for discussions about fitting strategies. C.D.V. is
grateful to Lara Ferrighi, Massimo Olivucci, and Stefano Motta for fruitful discussions. A.O.D. Acknowledges
funding from the Icelandic Research Fund (grant 174244-051) and VILLUM FONDEN. The project has received
funding from the European Research Council (ERC) under the European Union’s HORIZON2020 research and
innovation programme (ERC Grant Agreement No [647020]).Peer Reviewe
Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses
Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined