You are here: Home / Archives for computational chemistry

Gieseking Receives NSF CAREER Award

July 8, 2021 By

Figure from Rebecca GiesekingRebecca Gieseking, Assistant Professor of Chemistry, has received an NSF CAREER award from the Chemical Theory, Models and Computational Methods program. This award will enable her research group to develop computational models that provide chemical understanding of how light interacts with metal nanoclusters.

Harnessing solar energy is crucial to reduce humanity’s dependence on fossil fuels and alleviate the environmental impact of our ever-increasing demand for energy. Noble metal nanoclusters containing tens to hundreds of metal atoms have the potential to revolutionize solar energy technologies by harnessing light to produce chemical fuels. These nanoclusters strongly absorb light because they support plasmons, which are collective oscillations of the electrons. Understanding, controlling, and manipulating the plasmon properties is key to improving the efficiency of solar energy storage.

Rebecca has shown that efficient computational models can accurately model the light absorption of metal nanocluster, and her group is now extending these models to understand the decay processes after metal nanoclusters absorb light. They are using these models to understand how these decay processes change as a function of nanocluster size, shape, and composition to design metal nanoclusters with controllable decay time scales for efficient solar energy storage.

Filed Under: awards, chemistry, division of science, division of science, labs Tagged With: , , , ,

Acid, Base and Electrical Charge at the Water Surface

April 3, 2016 By
Liquid water seems simple, but there’s a lot of chemistry going on in it.
It is common knowledge that, in pure water, under ordinary conditions, 1 in every 10 million H2O molecules is dissociated into the acid ion H+ and the base ion OH–. However, what preference, if any, these self-ions of water have to sit at the air water interface has been the subject of lengthy and heated debate. The question is consequential in a wide range of contexts, including on the surface of droplets in the atmosphere and at the surfaces of biomolecules.  The Herzfeld group has now bridged the gap between experiment and theory by using a model that efficiently balances three subtle features of water molecules (polarizability, H+ sharing, and H+ transfer) that control the ambient behavior of the liquid. The model predicts that OH– prefers the air-water interface while H+ avoids it, consistent with observations of the response of air bubbles in water to an applied electric field.
water
Bai C, Herzfeld J. Surface Propensities of the Self-Ions of Water. ACS Central Science. 2016.
Filed Under: chemistry Tagged With: , , ,

Easy Come, Easy Go

October 5, 2012 By

Whereas the diffusion of water molecules in the bulk liquid depends entirely on breaking hydrogen bonds, the diffusion of proton defects (i.e., an excess proton in acid or a proton deficit in base) is expedited by proton hopping across hydrogen bonds.  The details of this process are well understood in acid, and the process in base was believed to occur in analogous fashion. However, theoretical studies of hydroxide have given highly divergent predictions of solvation structures and diffusion rates, depending on the chosen recipe for such simulations: some predicted the traditionally expected solvation structures and some predicted the experimentally observed diffusion trends, but none do both. Now Seyit Kale, a graduate student in Prof. Judith Herzfeld’s group, has studied proton defects using the group’s recently developed LEWIS force field.[1] The LEWIS simulations obtain the correct relative diffusion rates with hydroxide solvation structures that are analogous to those of hydronium,[2] thereby supporting the traditional picture of the “proton hole”. The authors also catch and characterize proton transfer events, identifying similar “special pairs”[3] as the intermediates in both cases (see figure).

[1]       S. Kale, J. Herzfeld, J. Chem. Phys. 2012, 136, 084109.
[2]       S. Kale, J. Herzfeld, Angew. Chem. Int. Edit. 2012 in press. DOI: 10.1002/anie.201203568.
[3]       O. Markovitch, H. Chen, S. Izvekov, F. Paesani, G. A. Voth, N. Agmon, J. Phys. Chem. B. 2008, 112, 9456-9466.

 

Filed Under: chemistry, labs Tagged With: , , , , , ,

Escaping the Lattice

December 5, 2011 By

The next best thing to seeing real atoms is to mimic them in silico: we assign interactions between the atoms and then — pouf –They’re alive!

The number of particles in a visible sample is on the order of Avogadro’s constant, say ~1023, whereas a fairly muscular computer can only follow ~105-107 atoms at a time. To compensate, computational scientists typically replicate their simulation boxes infinitely in space. This creates a quandary for calculating forces across replication boxes. The simplest option, which is to neglect forces beyond a chosen cut-off, suffices for many interactions, is too crude for the particularly long-range interactions that occur between charges. To accurately account for these interactions, it is customary to use a clever 90-year-old (!) technique, called the Ewald sum.(1)

The problem with the Ewald sum is that it requires imposing a long-range periodicity that is inappropriately short for macromolecules.(2) To avoid artifacts, a number of alternatives have been suggested. One intuitive approach, called “force shifting”, smooths the interaction energy and its first derivative (the force) at the chosen cutoff. However, this creates new artifacts (see figure) when particles have very large or varying charges, as in some ionic liquids. Brandeis scientists Seyit Kale and Judith Herzfeld, have found that this problem can be solved by also smoothing the second derivative of the interaction energy (the acceleration).(3)  This approach performs virtually as well as the Ewald sum in a new reactive force field that they have been developing (see figure).

The neighbor frequencies for bulk water calculated with force shifting at a cutoff of 9 Å (red) and 12 Å (magenta) versus with the authors’ new approach at a 9 Å cutoff (blue) and the Ewald sum (black). The blue and black curves are virtually the same while the red and magenta curves contain artifacts. The inset shows a representation of a water molecule from the force field that the authors are developing.

  1. Ewald P (1921) The Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 369: 253-287.
  2. Hunenberger PH, McCammon JA (1999) Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study. Biophys. Chem. 78: 69-88.
  3. Kale S, Herzfeld J (2011) Pairwise Long-range Compensation for Strongly Ionic Systems. J. Chem. Theory Comput. 7: 3620-3624.
Filed Under: chemistry, labs Tagged With: , , , , , ,

Protected by Akismet
Blog with WordPress

Welcome Guest | Login (Brandeis Members Only)