Treating random sequential addition via the replica method.

While many physical processes are non-equilibrium in nature, the theory and modeling of such phenomena lag behind theoretical treatments of equilibrium systems. The diversity of powerful theoretical tools available to describe equilibrium systems has inspired strategies that map non-equilibrium systems onto equivalent equilibrium analogs so that interrogation with standard statistical mechanical approaches is possible. In this work, we revisit the mapping from the non-equilibrium random sequential addition process onto an equilibrium multi-component mixture via the replica method, allowing for theoretical predictions of non-equilibrium structural quantities.

Inverse design of equilibrium cluster fluids applied to a physically informed model.

Inverse design strategies have proven highly useful for the discovery of interaction potentials that prompt self-assembly of a variety of interesting structures. However, often the optimized particle interactions do not have a direct relationship to experimental systems. In this work, we show that Relative Entropy minimization is able to discover physically meaningful parameter sets for a model interaction built from depletion attraction and electrostatic repulsion that yield self-assembly of size-specific clusters.

Inverse methods for design of soft materials.

Functional soft materials, comprising colloidal and molecular building blocks that self-organize into complex structures as a result of their tunable interactions, enable a wide array of technological applications. Inverse methods provide a systematic means for navigating their inherently high-dimensional design spaces to create materials with targeted properties. While multiple physically motivated inverse strategies have been successfully implemented in silico, their translation to guiding experimental materials discovery has thus far been limited to a handful of proof-of-concept studies.

Structure and phase behavior of polymer-linked colloidal gels.

Low-density "equilibrium" gels that consist of a percolated, kinetically arrested network of colloidal particles and are resilient to aging can be fabricated by restricting the number of effective bonds that form between the colloids. Valence-restricted patchy particles have long served as one archetypal example of such materials, but equilibrium gels can also be realized through a synthetically simpler and scalable strategy that introduces a secondary linker, such as a small ditopic molecule, to mediate the bonds between the colloids. Here, we consider the case where the ditopic linker molecules are low-molecular-weight polymers and demonstrate using a model colloid-polymer mixture how macroscopic properties such as the phase behavior as well as the microstructure of the gel can be designed through the polymer molecular weight and concentration.

The role of pressure in inverse design for assembly.

Isotropic pairwise interactions that promote the self-assembly of complex particle morphologies have been discovered by inverse design strategies derived from the molecular coarse-graining literature. While such approaches provide an avenue to reproduce structural correlations, thermodynamic quantities such as the pressure have typically not been considered in self-assembly applications. In this work, we demonstrate that relative entropy optimization can be used to discover potentials that self-assemble into targeted cluster morphologies with a prescribed pressure when the iterative simulations are performed in the isothermal-isobaric ensemble.

Communication: From close-packed to topologically close-packed: Formation of Laves phases in moderately polydisperse hard-sphere mixtures.

Particle size polydispersity can help to inhibit crystallization of the hard-sphere fluid into close-packed structures at high packing fractions and thus is often employed to create model glass-forming systems. Nonetheless, it is known that hard-sphere mixtures with modest polydispersity still have ordered ground states. Here, we demonstrate by computer simulation that hard-sphere mixtures with increased polydispersity fractionate on the basis of particle size and a bimodal subpopulation favors the formation of topologically close-packed C14 and C15 Laves phases in coexistence with a disordered phase.

Gelation of plasmonic metal oxide nanocrystals by polymer-induced depletion attractions.

Gelation of colloidal nanocrystals emerged as a strategy to preserve inherent nanoscale properties in multiscale architectures. However, available gelation methods to directly form self-supported nanocrystal networks struggle to reliably control nanoscale optical phenomena such as photoluminescence and localized surface plasmon resonance (LSPR) across nanocrystal systems due to processing variabilities. Here, we report on an alternative gelation method based on physical internanocrystal interactions: short-range depletion attractions balanced by long-range electrostatic repulsions.

Inverse design of multicomponent assemblies.

Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology-relative entropy optimization-to determine isotropic interactions that promote assembly of targeted multicomponent phases, and we apply this extension to design interactions for a variety of binary crystals ranging from compact triangular and square architectures to highly open structures with dodecagonal and octadecagonal motifs. We compare the resulting optimized (self- and cross) interactions for the binary assemblies to those obtained from optimization of analogous single-component systems.

Inverse Design of Self-Assembling Frank-Kasper Phases and Insights Into Emergent Quasicrystals.

We discuss how a machine learning approach based on relative entropy optimization can be used as an inverse design strategy to discover isotropic pair interactions that self-assemble single- or multicomponent particle systems into Frank-Kasper phases. In doing so, we also gain insights into the self-assembly of quasicrystals.

Interactions and design rules for assembly of porous colloidal mesophases.

Porous mesophases, where well-defined particle-depleted 'void' spaces are present within a particle-rich background fluid, can be self-assembled from colloidal particles interacting via isotropic pair interactions with competing attractions and repulsions. While such structures could be of wide interest for technological applications (e.g.

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species.

Insights into the Electronic Structure of Molecules from Generalized Valence Bond Theory.

In this article we describe the unique insights into the electronic structure of molecules provided by generalized valence bond (GVB) theory. We consider selected prototypical hydrocarbons as well as a number of hypervalent molecules and a set of first- and second-row valence isoelectronic species. The GVB wave function is obtained by variationally optimizing the orbitals and spin coupling in the valence bond wave function.

Assembly of nothing: equilibrium fluids with designed structured porosity.

Controlled micro- to meso-scale porosity is a common materials design goal with possible applications ranging from molecular gas adsorption to particle size selective permeability or solubility. Here, we use inverse methods of statistical mechanics to design an isotropic pair interaction that, in the absence of an external field, assembles particles into an inhomogeneous fluid matrix surrounding pores of prescribed size ordered in a lattice morphology. The pore size can be tuned via modification of temperature or particle concentration.

Linking Semiconductor Nanocrystals into Gel Networks through All-Inorganic Bridges.

For colloidal semiconductor nanocrystals (NCs), replacement of insulating organic capping ligands with chemically diverse inorganic clusters enables the development of functional solids in which adjacent NCs are strongly coupled. Yet controlled assembly methods are lacking to direct the arrangement of charged, inorganic cluster-capped NCs into open networks. Herein, we introduce coordination bonds between the clusters capping the NCs thus linking the NCs into highly open gel networks.

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Bonding in O3 and SO2.

There are many well-known differences in the physical and chemical properties of ozone (O3) and sulfur dioxide (SO2). O3 has longer and weaker bonds than O2, whereas SO2 has shorter and stronger bonds than SO. The O-O2 bond is dramatically weaker than the O-SO bond, and the singlet-triplet gap in SO2 is more than double that in O3.

Insights into the electronic structure of disulfur tetrafluoride isomers from generalized valence bond theory.

Sulfur and fluorine can participate in a variety of bonding motifs, lending significant diversity to their chemistry. Prior work has identified three distinct minima for disulfur tetrafluoride (S2F4) compounds: two FSSF3 isomers and one SSF4 species. We used a combination of sophisticated explicitly correlated coupled cluster calculations and generalized valence bond (GVB) theory to characterize the electronic structure of these species as well as additional stationary points on the potential energy surface with F2SSF2 connectivity.

Effects of ligand electronegativity on recoupled pair bonds with application to sulfurane precursors.

Recoupled pair bonds (RPBs) are conditional bonds-they only form for selected central atoms and ligands. A complete theoretical description of RPBs requires an understanding of the properties of the central atom and ligands that enable such bonds to be formed. In this work, we show that ligand electronegativity is positively correlated with recoupled pair bond strength for a variety of ligands interacting with the 3p(2) pair of sulfur.

Electronic structure of H2S, SF2, and HSF and implications for hydrogen-substituted hypervalent sulfur fluorides.

It is well known that hypervalent molecules are more stable with very electronegative ligands such as fluorine. For example, while SF6 is uniquely stable and experimentally well characterized and many of the features of SF4 have been characterized, neither H4S nor H6S has been observed. Furthermore, no hypervalent sulfur species with mixed hydrogen and fluorine ligands have been experimentally characterized to date.

Bonding in Sulfur-Oxygen Compounds-HSO/SOH and SOO/OSO: An Example of Recoupled Pair π Bonding.

The ground states (X(2)A″) of HSO and SOH are extremely close in energy, yet their molecular structures differ dramatically, e.g., re(SO) is 1.

Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview.

This paper presents an overview of recent experiments and theoretical developments aimed at using vibrational spectroscopy to understand the structure and dynamics of nitrile-labeled biomolecules. Nitrile groups are excellent vibrational probes of proteins and DNA because they absorb in a region of the spectrum that is relatively free of absorption due to the biomolecule, and they have high extinction coefficients. The vibrational frequency of nitrile groups is also extraordinarily sensitive to its local environment, and thus C[triple bond, length as m-dash]N bonds have been employed in both linear and 2-D infrared (IR) spectroscopy experiments and also as vibrational Stark probes of electric fields in proteins.

Photodynamics in complex environments: ab initio multiple spawning quantum mechanical/molecular mechanical dynamics.

Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochemistry. Because most practical photochemistry occurs in solution and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies.

Optimized quantum mechanics/molecular mechanics strategies for nitrile vibrational probes: acetonitrile and para-tolunitrile in water and tetrahydrofuran.

The nitrile (Ctriple bondN) group is a powerful probe of structure and dynamics because its vibrational frequency is extraordinarily sensitive to the electrostatic and chemical characteristics of its local environment. For example, site-specific nitrile labels are useful indicators of protein structure because their infrared (IR) absorption spectra can clearly distinguish between solvent-exposed residues and residues buried in the hydrophobic core of a protein. In this work, three variants of the optimized quantum mechanics/molecular mechanics (OQM/MM) technique for computing Ctriple bondN vibrational frequencies were developed and assessed for acetonitrile in water.

Nitrile groups as vibrational probes: calculations of the CN infrared absorption line shape of acetonitrile in water and tetrahydrofuran.

The C[TRIPLE BOND]N bond is a powerful probe of protein structure and dynamics because it absorbs in a region of the infrared spectrum apart from the other vibrations that occur naturally in proteins, and because its infrared absorption line shape is sensitive to specific characteristics of the local environment. Since the polarity experienced by the probe can differ dramatically within the protein, infrared spectroscopy of a C[TRIPLE BOND]N site-specifically labeled residue can be used to infer its local environment within the protein. It has been shown experimentally that the spectrum of acetonitrile in water is different in terms of peak position and width compared to acetonitrile in tetrahydrofuran (THF).

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study.

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.