Raman Spectra of Electrified Si-Water Interfaces: First-Principles Simulations.

We investigate the Raman spectra of liquid water in contact with a semiconductor surface using first-principles molecular dynamics simulations. We focus on a hydrogenated silicon-water interface and compute the Raman spectra from time correlation functions of the polarizability. We establish a relationship between Raman spectral signatures and structural properties of the liquid at the interface, and we identify the vibrational impacts of an applied electric field. We show that negative bias leads to a reduction of the number of hydrogen bonds (HBs) formed between the surface and the topmost water layer and an enhancement of the HB interactions between water molecules. Instead, positive bias leads to an enhancement of both the HB interactions between water and the surface and between water molecules, creating a semi-ordered interfacial layer. Our work provides molecular-level insights into electrified semiconductor/water interfaces and the identification of specific structural features through Raman spectroscopy.

Engineering the formation of spin-defects from first principles.

The full realization of spin qubits for quantum technologies relies on the ability to control and design the formation processes of spin defects in semiconductors and insulators. We present a computational protocol to investigate the synthesis of point-defects at the atomistic level, and we apply it to the study of a promising spin-qubit in silicon carbide, the divacancy (VV). Our strategy combines electronic structure calculations based on density functional theory and enhanced sampling techniques coupled with first principles molecular dynamics. We predict the optimal annealing temperatures for the formation of VVs at high temperature and show how to engineer the Fermi level of the material to optimize the defect's yield for several polytypes of silicon carbide. Our results are in excellent agreement with available experimental data and provide novel atomistic insights into point defect formation and annihilation processes as a function of temperature.

All-Electron Plane-Wave Electronic Structure Calculations.

We demonstrate the use of the plane wave basis for all-electron electronic structure calculations. The approach relies on the definition of an analytic, norm-conserving, regularized Coulomb potential, and a scalable implementation of the plane wave method capable of handling large energy cutoffs (up to 80 kRy in the examples shown). The method is applied to the computation of electronic properties of isolated atoms as well as the diamond and silicon crystals, MgO, solid argon, and a configuration of 64 water molecules extracted from a first-principles molecular dynamics simulation. The computed energies, band gaps, ionic forces, and stress tensors provide reference results for the validation of pseudopotentials and/or localized basis sets. A calculation of the all-electron band structure of diamond and silicon using the SCAN meta-GGA density functional allows for a validation of calculations based on pseudopotentials derived using the PBE exchange-correlation functional. In the case of (H2O)64, the computed ionic forces provide a reference from which the errors incurred in pseudopotential calculations and in localized Gaussian basis sets calculations can be estimated.

Free-Energy Landscape and Isomerization Rates of Au4 Clusters at Finite Temperatures.

In metallic nanoparticles, the geometry of atomic positions controls the particle's electronic band structure, polarizability, and catalytic properties. Analyzing the structural properties is a complex problem; the structure of an assembled cluster changes from moment to moment due to thermal fluctuations. Conventional structural analyses based on spectroscopy or diffraction cannot determine the instantaneous structure exactly and can merely provide an averaged structure. Molecular simulations offer an opportunity to examine the assembly and evolution of metallic clusters, as the preferred assemblies and conformations can easily be visualized and explored. Here, we utilize the adaptive biasing force algorithm applied to first-principles molecular dynamics to demonstrate the exploration of a relatively simple system, which permits a comprehensive study of the small metal cluster Au4 in both neutral and charged configurations. Our simulation work offers a quantitative understanding of these clusters' dynamic structure, which is significant for single-site catalytic reactions on metal clusters and provides a starting point for a detailed quantitative understanding of more complex pure metal and alloy clusters' dynamic properties.

Quantum simulations of thermally activated delayed fluorescence in an all-organic emitter.

We investigate the prototypical NAI-DMAC thermally activated delayed fluorescence (TADF) emitter in the gas phase- and high-packing fraction limits at finite temperature, by combining first principles molecular dynamics with a quantum thermostat to account for nuclear quantum effects (NQE). We find a weak dependence of the singlet-triplet energy gap (ΔEST) on temperature in both the solid and the molecule, and a substantial effect of packing. While the ΔEST vanishes in the perfect crystal, it is of the order of ∼0.3 eV in the molecule, with fluctuations ranging from 0.1 to 0.4 eV at 300 K. The transition probability between the HOMOs and LUMOs has a stronger dependence on temperature than the singlet-triplet gap, with a desirable effect for thermally activated fluorescence; such temperature effect is weaker in the condensed phase than in the molecule. Our results on ΔEST and oscillator strengths, together with our estimates of direct and reverse intersystem crossing rates, show that optimization of packing and geometrical conformation is critical to increase the efficiency of TADF compounds. Our findings highlight the importance of considering thermal fluctuations and NQE to obtain robust predictions of the electronic properties of NAI-DMAC.

Capturing the Complete Reaction Profile of a C-H Bond Activation.

The activation of C-H bonds requires the generation of extremely reactive species, which hinders the study of this reaction and its key intermediates. To overcome this challenge, we synthesized an iron(III) chloride-pyridinediimine complex that generates a chlorine radical proximate to reactive C-H bonds upon irradiation with light. Transient spectroscopy confirms the formation of a Cl·|arene complex, which then activates C-H bonds on the PDI ligand to yield HCl and a carbon-centered radical as determined by photocrystallography. First-principles molecular dynamics-density functional theory calculations reveal the trajectory for the formation of a Cl·|arene intermediate. Together, these experimental and computational results show the complete reaction profile for the preferential activation of a C-H bond in the solid state.

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.

Dissociation of salts in water under pressure.

The investigation of salts in water at extreme conditions is crucial to understanding the properties of aqueous fluids in the Earth. We report first principles (FP) and classical molecular dynamics simulations of NaCl in the dilute limit, at temperatures and pressures relevant to the Earth's upper mantle. Similar to ambient conditions, we observe two metastable states of the salt: the contact (CIP) and the solvent-shared ion-pair (SIP), which are entropically and enthalpically favored, respectively. We find that the free energy barrier between the CIP and SIP minima increases at extreme conditions, and that the stability of the CIP is enhanced in FP simulations, consistent with the decrease of the dielectric constant of water. The minimum free energy path between the CIP and SIP becomes smoother at high pressure, and the relative stability of the two configurations is affected by water self-dissociation, which can only be described properly by FP simulations.

Ensemble first-principles molecular dynamics simulations of water using the SCAN meta-GGA density functional.

We present an ensemble of 16 independent first-principles molecular dynamics simulations of water performed using the Strongly Constrained and Appropriately Normed (SCAN) meta-generalized gradient approximation exchange-correlation functional. These simulations were used to compute the structural and electronic properties of liquid water, as well as polarizabilities, Raman and infrared spectra. Overall, we find that the SCAN functional used at a simulation temperature of 330 K provides an accurate description of the structural and electronic properties of water while incurring a moderate computational cost. The availability of an ensemble of independent simulations provides a quantitative estimate of the uncertainty in computed structural and electronic properties. Results are also compared with a similar dataset generated using the Perdew, Burke, and Ernzerhof exchange-correlation functional at a temperature of 400 K. All simulation data and trajectories are available at http://quantum-simulation.org.

Finite-Field Approach to Solving the Bethe-Salpeter Equation.

We present a method to compute optical spectra and exciton binding energies of molecules and solids based on the solution of the Bethe-Salpeter equation and the calculation of the screened Coulomb interaction in a finite field. The method does not require either the explicit evaluation of dielectric matrices or of virtual electronic states, and can be easily applied without resorting to the random phase approximation. In addition, it utilizes localized orbitals obtained from Bloch states using bisection techniques, thus greatly reducing the complexity of the calculation and enabling the efficient use of hybrid functionals to obtain single particle wave functions. We report exciton binding energies of several molecules and absorption spectra of condensed systems of unprecedented size, including water and ice samples with hundreds of atoms.

A Finite-Field Approach for GW Calculations beyond the Random Phase Approximation.

We describe a finite-field approach to compute density response functions, which allows for efficient G0 W0 and G0 W0Γ0 calculations beyond the random phase approximation. The method is easily applicable to density functional calculations performed with hybrid functionals. We present results for the electronic properties of molecules and solids, and we discuss a general scheme to overcome slow convergence of quasiparticle energies obtained from G0 W0Γ0 calculations, as a function of the basis set used to represent the dielectric matrix.

The role of defects and excess surface charges at finite temperature for optimizing oxide photoabsorbers.

Computational screening of materials for solar to fuel conversion technologies has mostly focused on bulk properties, thus neglecting the structure and chemistry of surfaces and interfaces with water. We report a finite temperature study of WO3, a promising anode for photoelectrochemical cells, carried out using first-principles molecular dynamics simulations coupled with many-body perturbation theory. We identified three major factors determining the chemical reactivity of the material interfaced with water: the presence of surface defects, the dynamics of excess charge at the surface, and finite temperature fluctuations of the surface electronic orbitals. These general descriptors are essential for the understanding and prediction of optimal oxide photoabsorbers for water oxidation.

First-Principles Simulations of Liquid Water Using a Dielectric-Dependent Hybrid Functional.

We carried out first-principles simulations of liquid water under ambient conditions using a dielectric-dependent hybrid functional, where the fraction of exact exchange is set equal to the inverse of the high-frequency dielectric constant of the liquid. We found excellent agreement with experiment for the oxygen-oxygen partial correlation function at the experimental equilibrium density and 311 ± 3 K. Other structural and dynamical properties, such as the diffusion coefficient, molecular dipole moments, and vibrational spectra, are also in good agreement with experiment. Our results, together with previous findings on electronic properties of the liquid with the same functional, show that the dielectric-dependent hybrid functional accurately describes both the structural and electronic properties of liquid water.

Hierarchical Coupling of First-Principles Molecular Dynamics with Advanced Sampling Methods.

We present a seamless coupling of a suite of codes designed to perform advanced sampling simulations, with a first-principles molecular dynamics (MD) engine. As an illustrative example, we discuss results for the free energy and potential surfaces of the alanine dipeptide obtained using both local and hybrid density functionals (DFT), and we compare them with those of a widely used classical force field, Amber99sb. In our calculations, the efficiency of first-principles MD using hybrid functionals is augmented by hierarchical sampling, where hybrid free energy calculations are initiated using estimates obtained with local functionals. We find that the free energy surfaces obtained from classical and first-principles calculations differ. Compared to DFT results, the classical force field overestimates the internal energy contribution of high free energy states, and it underestimates the entropic contribution along the entire free energy profile. Using the string method, we illustrate how these differences lead to different transition pathways connecting the metastable minima of the alanine dipeptide. In larger peptides, those differences would lead to qualitatively different results for the equilibrium structure and conformation of these molecules.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Roadmap on semiconductor-cell biointerfaces.

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world.

Blind test of density-functional-based methods on intermolecular interaction energies.

In the past decade, a number of approaches have been developed to fix the failure of (semi)local density-functional theory (DFT) in describing intermolecular interactions. The performance of several such approaches with respect to highly accurate benchmarks is compared here on a set of separation-dependent interaction energies for ten dimers. Since the benchmarks were unknown before the DFT-based results were collected, this comparison constitutes a blind test of these methods.

Reproducibility in density functional theory calculations of solids.

The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.