Strain and rupture of HIV-1 capsids during uncoating.

SignificanceThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.

Stability and molecular pathways to the formation of spin defects in silicon carbide.

Spin defects in wide-bandgap semiconductors provide a promising platform to create qubits for quantum technologies. Their synthesis, however, presents considerable challenges, and the mechanisms responsible for their generation or annihilation are poorly understood. Here, we elucidate spin defect formation processes in a binary crystal for a key qubit candidate-the divacancy complex (VV) in silicon carbide (SiC). Using atomistic models, enhanced sampling simulations, and density functional theory calculations, we find that VV formation is a thermally activated process that competes with the conversion of silicon (VSi) to carbon monovacancies (VC), and that VV reorientation can occur without dissociation. We also find that increasing the concentration of VSi relative to VC favors the formation of divacancies. Moreover, we identify pathways to create spin defects consisting of antisite-double vacancy complexes and determine their electronic properties. The detailed view of the mechanisms that underpin the formation and dynamics of spin defects presented here may facilitate the realization of qubits in an industrially relevant material.

Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium.

In heterogeneous catalysis, free energy profiles of reactions govern the mechanisms, rates, and equilibria. Energetics are conventionally computed using the harmonic approximation (HA), which requires determination of critical states a priori. Here, we use neural networks to efficiently sample and directly calculate the free energy surface (FES) of a prototypical heterogeneous catalysis reaction-the dissociation of molecular nitrogen on ruthenium-at density-functional-theory-level accuracy. We find that the vibrational entropy of surface atoms, often neglected in HA for transition metal catalysts, contributes significantly to the reaction barrier. The minimum free energy path for dissociation reveals an "on-top" adsorbed molecular state prior to the transition state. While a previously reported flat-lying molecular metastable state can be identified in the potential energy surface, it is absent in the FES at relevant reaction temperatures. These findings demonstrate the importance of identifying critical points self-consistently on the FES for reactions that involve considerable entropic effects.

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6).

Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6 We find that capsid hexamers and pentamers have differential binding modes for IP6 Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.

Solving the Trivial Crossing Problem While Preserving the Nodal Symmetry of the Wave Function.

In an adiabatic mixed quantum-classical simulation, the avoided crossing of weakly coupled eigenstates can lead to unphysical discontinuities in wave function dynamics, otherwise known as the trivial crossing problem. A standard solution to the trivial crossing problem eliminates spatial discontinuities in wave function dynamics by imposing changes to the eigenstate of the wave function. In this paper, we show that this solution has the side effect of introducing transient discontinuities in the nodal symmetry of the wave function. We present an alternative solution to the trivial crossing problem that preserves both the spatial and nodal structure of the adiabatic wave function. By considering a model of exciton dynamics on conjugated polymer systems, we show that failure to preserve wave function symmetry yields exciton dynamics that depends unphysically on polymer system size. We demonstrate that our symmetry-preserving solution to the trivial crossing problem yields more realistic dynamics and can thus improve the accuracy of simulations of larger systems that are prone to the trivial crossing problem.

Inverse Temperature Dependence of Charge Carrier Hopping in Quantum Dot Solids.

In semiconductors, increasing mobility with decreasing temperature is a signature of charge carrier transport through delocalized bands. Here, we show that this behavior can also occur in nanocrystal solids due to temperature-dependent structural transformations. Using a combination of broadband infrared transient absorption spectroscopy and numerical modeling, we investigate the temperature-dependent charge transport properties of well-ordered PbS quantum dot (QD) solids. Contrary to expectations, we observe that the QD-to-QD charge tunneling rate increases with decreasing temperature, while simultaneously exhibiting thermally activated nearest-neighbor hopping behavior. Using synchrotron grazing-incidence small-angle X-ray scattering, we show that this trend is driven by a temperature-dependent reduction in nearest-neighbor separation that is quantitatively consistent with the measured tunneling rate.

Molecular engineered conjugated polymer with high thermal conductivity.

Traditional polymers are both electrically and thermally insulating. The development of electrically conductive polymers has led to novel applications such as flexible displays, solar cells, and wearable biosensors. As in the case of electrically conductive polymers, the development of polymers with high thermal conductivity would open up a range of applications in next-generation electronic, optoelectronic, and energy devices. Current research has so far been limited to engineering polymers either by strong intramolecular interactions, which enable efficient phonon transport along the polymer chains, or by strong intermolecular interactions, which enable efficient phonon transport between the polymer chains. However, it has not been possible until now to engineer both interactions simultaneously. We report the first realization of high thermal conductivity in the thin film of a conjugated polymer, poly(3-hexylthiophene), via bottom-up oxidative chemical vapor deposition (oCVD), taking advantage of both strong C=C covalent bonding along the extended polymer chain and strong π-π stacking noncovalent interactions between chains. We confirm the presence of both types of interactions by systematic structural characterization, achieving a near-room temperature thermal conductivity of 2.2 W/m·K, which is 10 times higher than that of conventional polymers. With the solvent-free oCVD technique, it is now possible to grow polymer films conformally on a variety of substrates as lightweight, flexible heat conductors that are also electrically insulating and resistant to corrosion.

Including surface ligand effects in continuum elastic models of nanocrystal vibrations.

The measured low frequency vibrational energies of some quantum dots (QDs) deviate from the predictions of traditional elastic continuum models. Recent experiments have revealed that these deviations can be tuned by changing the ligands that passivate the QD surface. This observation has led to speculation that these deviations are due to a mass-loading effect of the surface ligands. In this article, we address this speculation by formulating a continuum elastic theory that includes the dynamical loading by elastic surface ligands. We demonstrate that this model is capable of accurately reproducing the l = 0 phonon energy across a variety of different QD samples, including cores with different ligand identities and epitaxially grown CdSe/CdS core/shell heterostructures. We highlight that our model performs well even in the small QD regime, where traditional elastic continuum models are especially prone to failure. Furthermore, we show that our model combined with Raman measurements can be used to infer the elastic properties of surface bound ligands, such as sound velocities and elastic moduli, that are otherwise challenging to measure.

Charge Carrier Hopping Dynamics in Homogeneously Broadened PbS Quantum Dot Solids.

Energetic disorder in quantum dot solids adversely impacts charge carrier transport in quantum dot solar cells and electronic devices. Here, we use ultrafast transient absorption spectroscopy to show that homogeneously broadened PbS quantum dot arrays (σhom2:σinh2 > 19:1, σinh/kBT < 0.4) can be realized if quantum dot batches are sufficiently monodisperse (δ ≲ 3.3%). The homogeneous line width is found to be an inverse function of quantum dot size, monotonically increasing from ∼25 meV for the largest quantum dots (5.8 nm diameter/0.92 eV energy) to ∼55 meV for the smallest (4.1 nm/1.3 eV energy). Furthermore, we show that intrinsic charge carrier hopping rates are faster for smaller quantum dots. This finding is the opposite of the mobility trend commonly observed in device measurements but is consistent with theoretical predictions. Fitting our data to a kinetic Monte Carlo model, we extract charge carrier hopping times ranging from 80 ps for the smallest quantum dots to over 1 ns for the largest, with the same ethanethiol ligand treatment. Additionally, we make the surprising observation that, in slightly polydisperse (δ ≲ 4%) quantum dot solids, structural disorder has a greater impact than energetic disorder in inhibiting charge carrier transport. These findings emphasize how small improvements in batch size dispersity can have a dramatic impact on intrinsic charge carrier hopping behavior and will stimulate further improvements in quantum dot device performance.

Modulation of Low-Frequency Acoustic Vibrations in Semiconductor Nanocrystals through Choice of Surface Ligand.

Recent experimental and theoretical results have highlighted the surprisingly dominant role of acoustic phonons in regulating dynamic processes in nanocrystals. While it has been known for many years that acoustic phonon frequencies in nanocrystals depend on their size, strategies for tuning acoustic phonon energy at a given fixed size were not available. Here, we show that acoustic phonon frequencies in colloidal quantum dots (QDs) can be tuned through the choice of the surface ligand. Using low-frequency Raman spectroscopy, we explore the dependence of the l = 0 acoustic phonon resonance in CdSe QDs on ligand size, molecular weight, and chemical functionality. On the basis of these aggregated observations, we conclude that the primary mechanism for this effect is mass loading of the QD surface and that interactions between ligands and with the surrounding environment play a comparatively minor yet non-negligible role.

Temperature dependence of acoustic vibrations of CdSe and CdSe-CdS core-shell nanocrystals measured by low-frequency Raman spectroscopy.

We measure the temperature dependence of breathing-mode acoustic vibrations of semiconductor nanocrystals using low-frequency Raman spectroscopy. In CdSe core-only nanocrystals, the lowest-energy l = 0 mode red-shifts with increasing temperature by ∼5% between 77-300 K. Changes to the interatomic bond distances in the inorganic crystal lattice, with corresponding changes to the bulk modulus and density of the material, contribute to the observed energy shift but do not fully explain its magnitude across all nanocrystal sizes. Invariance of the Raman linewidth over the same temperature range suggests that the acoustic breathing mode is inhomogeneously broadened. The acoustic phonons of CdSe/CdS core-shell composite nanocrystals display similar qualitative behavior. However, for large core-shell nanocrystals, we observe a higher-order Raman peak at approximately twice the energy of the l = 0 mode, which we identify as a higher spherical harmonic-the n = 2, l = 0 eigenmode-rather than a two-phonon scattering event.

Can Disorder Enhance Incoherent Exciton Diffusion?

Recent experiments aimed at probing the dynamics of excitons have revealed that semiconducting films composed of disordered molecular subunits, unlike expectations for their perfectly ordered counterparts, can exhibit a time-dependent diffusivity in which the effective early time diffusion constant is larger than that of the steady state. This observation has led to speculation about what role, if any, microscopic disorder may play in enhancing exciton transport properties. In this article, we present the results of a model study aimed at addressing this point. Specifically, we introduce a general model, based upon Förster theory, for incoherent exciton diffusion in a material composed of independent molecular subunits with static energetic disorder. Energetic disorder leads to heterogeneity in molecule-to-molecule transition rates, which we demonstrate has two important consequences related to exciton transport. First, the distribution of local site-specific hopping rates is broadened in a manner that results in a decrease in average exciton diffusivity relative to that in a perfectly ordered film. Second, since excitons prefer to make transitions that are downhill in energy, the steady state distribution of exciton energies is biased toward low-energy molecular subunits, those that exhibit reduced diffusivity relative to a perfectly ordered film. These effects combine to reduce the net diffusivity in a manner that is time dependent and grows more pronounced as disorder is increased. Notably, however, we demonstrate that the presence of energetic disorder can give rise to a population of molecular subunits with exciton transfer rates exceeding those of subunits in an energetically uniform material. Such enhancements may play an important role in processes that are sensitive to molecular-scale fluctuations in exciton density field.

Subdiffusive exciton transport in quantum dot solids.

Colloidal quantum dots (QDs) are promising materials for use in solar cells, light-emitting diodes, lasers, and photodetectors, but the mechanism and length of exciton transport in QD materials is not well understood. We use time-resolved optical microscopy to spatially visualize exciton transport in CdSe/ZnCdS core/shell QD assemblies. We find that the exciton diffusion length, which exceeds 30 nm in some cases, can be tuned by adjusting the inorganic shell thickness and organic ligand length, offering a powerful strategy for controlling exciton movement. Moreover, we show experimentally and through kinetic Monte Carlo simulations that exciton diffusion in QD solids does not occur by a random-walk process; instead, energetic disorder within the inhomogeneously broadened ensemble causes the exciton diffusivity to decrease over time. These findings reveal new insights into exciton dynamics in disordered systems and demonstrate the flexibility of QD materials for photonic and optoelectronic applications.

On the electronic structure of the low lying electronic states of vanadium trioxide.

The electronic structure of transition metal oxides is frequently studied using density functional theory. Nonetheless, the electronic structure of VO3 has been found to be sensitive to the choice of functional. As a consequence, the basic question of whether or not the ground electronic state exhibits a Jahn-Teller distortion has yet to be resolved. Using basis sets of triple zeta quality and multireference configuration interaction wave functions as large as 700 million configuration state functions, we determine that the ground electronic state of VO3 is a (2)A2 state in C3v symmetry. The first two excited electronic states are also characterized and found to be the components of a degenerate (2)E state, in C3v symmetry, which exhibits a small Jahn-Teller distortion. The Jahn-Teller stabilization energy is only 40 cm(-1) and the barrier to pseudo-rotation is 9 cm(-1). This (2)E state exhibits some unexpected properties. In the vicinity of the minimum energy conical intersection, the local topography appears almost quadratic, rather than linear, in the Jahn-Teller active coordinates. This gives rise to three symmetry-related seams of conical intersections in addition to the symmetry-required seam and results in the suppression of the geometric phase effect. These features, attributable to small linear Jahn-Teller parameters, are usually found in states characterized by e(2) (or e(3)e(')) electron configurations rather than the e(3) configuration found here. In addition to its Jahn-Teller minimum, the first excited state exhibits a second minimum with a structure significantly distorted from C3v. A conical intersection with Cs symmetry connects the two minima and puts an upper limit of 190 cm(-1) on the barrier connecting these minima.

Electronic structure calculations in arbitrary electrostatic environments.

Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.