OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy.

We present OrbNet Denali, a machine learning model for an electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing graph neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.

Analytical gradients for molecular-orbital-based machine learning.

Molecular-orbital-based machine learning (MOB-ML) enables the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. Here, we present the derivation, implementation, and numerical demonstration of MOB-ML analytical nuclear gradients, which are formulated in a general Lagrangian framework to enforce orthogonality, localization, and Brillouin constraints on the molecular orbitals. The MOB-ML gradient framework is general with respect to the regression technique (e.

Small Nuclear Quantum Effects in Scattering of H and D from Graphene.

We study nuclear quantum effects in H/D sticking to graphene, comparing scattering experiments at near-zero coverage with classical, quantized, and transition-state calculations. The experiment shows H/D sticking probabilities that are indistinguishable from one another and markedly smaller than those expected from a consideration of zero-point energy shifts of the chemisorption transition state. Inclusion of dynamical effects and vibrational anharmonicity via ring-polymer molecular dynamics (RPMD) yields results that are in good agreement with the experimental results.

Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis.

Decreasing the wall-clock time of quantum mechanics/molecular mechanics (QM/MM) calculations without sacrificing accuracy is a crucial prerequisite for widespread simulation of solution-phase dynamical processes. In this work, we demonstrate the use of embedded mean-field theory (EMFT) as the QM engine in QM/MM molecular dynamics (MD) simulations to examine polyolefin catalysts in solution. We show that employing EMFT in this mode preserves the accuracy of hybrid-functional DFT in the QM region, while providing up to 20-fold reductions in the cost per SCF cycle, thereby increasing the accessible simulation time-scales.

Imaging covalent bond formation by H atom scattering from graphene.

Viewing the atomic-scale motion and energy dissipation pathways involved in forming a covalent bond is a longstanding challenge for chemistry. We performed scattering experiments of H atoms from graphene and observed a bimodal translational energy loss distribution. Using accurate first-principles dynamics simulations, we show that the quasi-elastic channel involves scattering through the physisorption well where collision sites are near the centers of the six-membered C-rings.

Linear-Response Time-Dependent Embedded Mean-Field Theory.

We present a time-dependent (TD) linear-response description of excited electronic states within the framework of embedded mean-field theory (EMFT). TD-EMFT allows for subsystems to be described at different mean-field levels of theory, enabling straightforward treatment of excited states and transition properties. We provide benchmark demonstrations of TD-EMFT for both local and nonlocal excitations in organic molecules, as well as applications to chlorophyll a, solvatochromic shifts of a dye in solution, and sulfur K-edge X-ray absorption spectroscopy (XAS).

Embedded Mean-Field Theory with Block-Orthogonalized Partitioning.

Embedded mean-field theory (EMFT) provides a simple, flexible framework for describing subsystems at different levels of mean-field theory. Subsystems are defined by partitioning a one-particle basis set, with a natural choice being the atomic orbital (AO) basis. Although generally well behaved, EMFT with AO partitioning can exhibit unphysical collapse of the self-consistent solution.

Doping Versatile n-Type Organic Semiconductors via Room Temperature Solution-Processable Anionic Dopants.

In this study, we describe a facile solution-processing method to effectively dope versatile n-type organic semiconductors, including fullerene, n-type small molecules, and graphene by commercially available ammonium and phosphonium salts via in situ anion-induced electron transfer. In addition to the Lewis basicity of anions, we unveiled that the ionic binding strength between the cation and anion of the salts is also crucial in modulating the electron transfer strength of the dopants to affect the resulting doping efficiency. Furthermore, combined with the rational design of n-type molecules, an n-doped organic semiconductor is demonstrated to be thermally and environmentally stable.

Aromatic thiol-mediated cleavage of N-O bonds enables chemical ubiquitylation of folded proteins.

Access to protein substrates homogenously modified by ubiquitin (Ub) is critical for biophysical and biochemical investigations aimed at deconvoluting the myriad biological roles for Ub. Current chemical strategies for protein ubiquitylation, however, employ temporary ligation auxiliaries that are removed under harsh denaturing conditions and have limited applicability. We report an unprecedented aromatic thiol-mediated N-O bond cleavage and its application towards native chemical ubiquitylation with the ligation auxiliary 2-aminooxyethanethiol.

Highly Sensitive Built-In Strain Sensors for Polymer Composites: Fluorescence Turn-On Response through Mechanochemical Activation.

A new class of rationally designed mechanophores is developed for highly sensitive built-in strain sensors in polymer composites. These mechanophores are designed to regenerate the π-conjugation pathway between the electron donor and electron acceptor by force-induced cleavage of the covalent bond to form a fluorescent dipolar dye.

Approximate singly excited states from a two-component Hartree-Fock reference.

For many molecules, relaxing the spin symmetry constraint on the wave function results in the lowest energy mean-field solution. The two-component Hartree-Fock (2cHF) method relaxes all spin symmetry constraints, and the wave function is no longer an eigenfunction of the total spin, spin projection, or time-reversal symmetry operators. For ground state energies, 2cHF is a superior mean-field method for describing spin-frustrated molecules.

Ab initio two-component Ehrenfest dynamics.

We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation.

Stability of the complex generalized Hartree-Fock equations.

For molecules with complex and competing magnetic interactions, it is often the case that the lowest energy Hartree-Fock solution may only be obtained by removing the spin and time-reversal symmetry constraints of the exact non-relativistic Hamiltonian. To do so results in the complex generalized Hartree-Fock (GHF) method. However, with the loss of variational constraints comes the greater possibility of converging to higher energy minima.

Time-dependent non-equilibrium dielectric response in QM/continuum approaches.

The Polarizable Continuum Models (PCMs) are some of the most inexpensive yet successful methods for including the effects of solvation in quantum-mechanical calculations of molecular systems. However, when applied to the electronic excitation process, these methods are restricted to dichotomously assuming either that the solvent has completely equilibrated with the excited solute charge density (infinite-time limit), or that it retains the configuration that was in equilibrium with the solute prior to excitation (zero-time limit). This renders the traditional PCMs inappropriate for resolving time-dependent solvent effects on non-equilibrium solute electron dynamics like those implicated in the instants following photoexcitation of a solvated molecular species.

Ab initio non-relativistic spin dynamics.

Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely.

Quantum coherent plasmon in silver nanowires: a real-time TDDFT study.

A plasmon-like phenomenon, arising from coinciding resonant excitations of different electronic characteristics in 1D silver nanowires, has been proposed based on theoretical linear absorption spectra. Such a molecular plasmon holds the potential for anisotropic nanoplasmonic applications. However, its dynamical nature remains unexplored.

Density of States Guided Møller-Plesset Perturbation Theory.

An integral formalism using a density-of-state framework has been developed for Møller-Plesset perturbation theory. This method is designed to compute the correlation energy correction for large systems with high density of states, such as polymers and nanostructures. The framework has the potential to lower the computational cost of perturbation theory, and such perspectives are discussed in this paper.

A Guided Self-Consistent-Field Method for Excited-State Wave Function Optimization: Applications to Ligand-Field Transitions in Transition-Metal Complexes.

A guided self-consistent field (SCF) method is presented in this paper. This method uses the eigenspace update-and-following idea to improve the SCF method for optimizing wave functions that are higher-energy solutions to the Roothaan-Hall equation. In this method, the eigenvectors of the previous SCF step are used to prediagonalize the current Fock/Kohn-Sham matrix, preserving the ordering of orbital occupations.

Doping of fullerenes via anion-induced electron transfer and its implication for surfactant facilitated high performance polymer solar cells.

Simple and solution-processible tetrabutyl-ammonium salts (TBAX) can dope fullerene and its derivatives to achieve conductive thin films (σ as high as 0.56 S/m). The electron transfer between the anions of TBAXs and n-type semiconductors induces doping without encountering any harsh activation.

Solution-processible highly conducting fullerenes.

n-Doping of solution-processible organic semiconductors: highly conductive fullerenes are demonstrated through solution-processed fulleropyrrolidinium iodide (FPI) and FPI-doped PCBM to reach a high conductivity (3.2 S/m). The n-doping proceeds via anion-induced electron transfer between the iodide on FPI and the fullerene in the solid state.

An efficient method for calculating dynamical hyperpolarizabilities using real-time time-dependent density functional theory.

In this paper we present a time-domain time-dependent density functional theory (TDDFT) approach to calculate frequency-dependent polarizability and hyperpolarizabilities. In this approach, the electronic degrees of freedom are propagated within the density matrix based TDDFT framework using the efficient modified midpoint and unitary transformation algorithm. We use monochromatic waves as external perturbations and apply the finite field method to extract various orders of the time-dependent dipole moment.

Mechanisms of bridge-mediated electron transfer: a TDDFT electronic dynamics study.

We present a time-dependent density functional theory approach for probing the dynamics of electron transfer on a donor-bridge-acceptor polyene dye scaffold. Two kinds of mechanisms, namely, the superexchange mechanism and the sequential mechanism, may be involved in the electron transfer process. In this work, we have focused on the crossover between these two charge transfer mechanisms on a series of donor-bridge-acceptor polyene dye systems with varying lengths of conjugated bridges.

Polymer triplet energy levels need not limit photocurrent collection in organic solar cells.

We study charge recombination via triplet excited states in donor/acceptor organic solar cells and find that, contrary to intuition, high internal quantum efficiency (IQE) can be obtained in polymer/fullerene blend devices even when the polymer triplet state is significantly lower in energy than the intermolecular charge transfer (CT) state. Our model donor system comprises the copolymer PIDT-PhanQ: poly(indacenodithiophene-co-phenanthro[9,10-b]quinoxaline), which when blended with phenyl-C(71)-butyric acid methyl ester (PC(71)BM) is capable of achieving power conversion efficiencies of 6.0% and IQE ≈ 90%, despite the fact that the polymer triplet state lies 300 meV below the interfacial CT state.

Improved charge transport and absorption coefficient in indacenodithieno[3,2-b]thiophene-based ladder-type polymer leading to highly efficient polymer solar cells.

A novel ladder-type donor (IDTT) is developed by substituting the two outward thiophenes of the IDT donor with two thieno[3,2-b]thiophenes. The polymer derived from this donor possesses longer effective conjugation and better planarity, which improves electron delocalization along the polymer backbone and charge mobility. The polymer solar cell device using PIDTT-DFBT shows a high power conversion efficiency of 7.

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution.