Accelerating the density-functional tight-binding method using graphical processing units.

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1-6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1-2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.

Nonadiabatic Effects on Defect Diffusion in Silicon-Doped Nanographenes.

Single atom impurities in graphene, substitutional silicon defects in particular, have been observed to diffuse under electron beam irradiation. However, the relative importance of elastic and inelastic scattering in facilitating their mobility remains unclear. Here, we employ excited-state electronic structure calculations to explore potential inelastic effects, and find an electronically nonadiabatic excited-state silicon diffusion pathway involving "softened" Si-C bonding that presents an ∼2 eV lower diffusion barrier than the ground-state pathway. Beam-induced transition rates to this state indicate that the excited-state pathway is accessible through irradiation of the defect site. However, even in the limit of fully elastic scattering, upward nonadiabatic transitions are also possible along the diffusion coordinate, increasing the diffusion barrier and further demonstrating the potential for electronic nonadiabaticity to influence beam-induced atomic transformations in materials. We also propose some experimentally testable signatures of such excited-state pathways.

Electron-Beam-Induced Molecular Plasmon Excitation and Energy Transfer in Silver Molecular Nanowires.

We investigate (1) electron-beam-induced plasmon absorption spectra of Ag molecular nanowire dimers and (2) electron-beam-induced energy transfer between two nanowires. We employ linear-response time-dependent density functional theory (TDDFT) and real-time TDDFT methods to simulate the electron-beam-induced plasmonic excitations, dynamics, and corresponding electron energy loss spectrum for small models of a single molecular nanowire with four Ag atoms and for two Ag nanowires. An array of different relative orientations of nanowires and of different initial excitation conditions resulting from applying an electron beam at different positions with respect to the Ag nanowires is investigated. The results demonstrate (1) an electron beam can induce plasmonic excitations from the molecular Ag nanowire ground state to the excited states that are both optically allowed and forbidden, (2) a tunability for selective excitations that can be controlled by the position of a focused electron beam, and (3) kinetic and dynamic behaviors of time-dependent electron-beam-induced energy transfer between two Ag molecular nanowires depend on the position of the beam source and nanowire separation distance, providing insights into the spatial dependences of plasmonic couplings in nanowire arrays.

A fast scheme to calculate electronic couplings between P3HT polymer units using diabatic orbitals for charge transfer dynamics simulations.

We propose a fast and accurate calculation method to compute the electronic couplings between molecular units in a thiophene-ring-based polymer chain mimicking a real organic semiconducting polymer, poly(3-hexylthiophene). Through a unit block diabatization scheme, the method employed minimal number of diabatic orbitals to compute the site energies and electronic couplings, which were validated by comparing with benchmark density functional theory calculations. In addition, by using the obtained electronic couplings, a quantum dynamics simulation was carried out to propagate a hole initially localized in a thiophene-ring unit of the polymer chain. This work establishes a simple, efficient, and robust means for the simulation of electron or hole transfer processes in organic semiconducting materials, an important capability for study and understanding of the class of organic optoelectronic and photovoltaic materials. © 2018 Wiley Periodicals, Inc.

A computational workflow for designing silicon donor qubits.

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to perform detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. The resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.

Computational approaches to delivery of anticancer drugs with multidimensional nanomaterials.

Functionalized nanotubes (NTs), nanosheets, nanorods, and porous organometallic scaffolds are potential in vivo carriers for cancer therapeutics. Precise delivery through these agents depends on factors like hydrophobicity, payload capacity, bulk/surface adsorption, orientation of molecules inside the host matrix, bonding, and nonbonding interactions. Herein, we summarize advances in simulation techniques, which are extremely valuable in initial geometry optimization and evaluation of the loading and unloading behavior of encapsulated drug molecules. Computational methods broadly involve the use of quantum and classical mechanics for studying the behavior of molecular properties. Combining theoretical processes with experimental techniques, such as X-ray crystallography, NMR spectroscopy, and bioassays, can provide a more comprehensive understanding of the structure and function of biological molecules. This integrated approach has led to numerous breakthroughs in drug discovery, enzyme design, and the study of complex biological processes. This short review provides an overview of results and challenges described from erstwhile investigations on the molecular interaction of anticancer drugs with nanocarriers of different aspect ratios.

Quantum Chemical Simulations of CO2 and N2 Capture in Reline, a Prototypical Deep Eutectic Solvent.

Deep eutectic solvents such as reline are an emerging class of low-cost, environmentally friendly solvents with tunable properties that are potentially applicable for the capture and separation of CO2. Experimental measurements showed that a reline-based membrane contactor can capture and separate CO2 via physisorption through a dissolution process with 96.7% purity from a mixed gas containing CO2 and N2 (50:50% molar ratio). We examine the nature of the interaction of CO2 and N2 with reline employing quantum chemical methods. We focus on explaining the mechanism by which CO2 and N2 bind to reline and the reason for the high selectivity for absorption of CO2 compared to N2. We analyze the dynamics, energetics, and binding motifs for CO2 and N2 in reline employing density functional theory, density functional tight binding, and ab initio molecular dynamics. We also investigate the effect of reline on the vibrational spectra of CO2 and reline. Our simulations indicate that the selective capture of CO2 from the mixture of CO2 and N2 is due to the interplay between attractive electrostatic and charge polarization forces with opposing entropic effects, which shift the energetic balance and make the N2 absorption unfavorable in reline.

Quantum theory of electronic excitation and sputtering by transmission electron microscopy.

Many computational models have been developed to predict the rates of atomic displacements in two-dimensional (2D) materials under electron beam irradiation. However, these models often drastically underestimate the displacement rates in 2D insulators, in which beam-induced electronic excitations can reduce the binding energies of the irradiated atoms. This bond softening leads to a qualitative disagreement between theory and experiment, in that substantial sputtering is experimentally observed at beam energies deemed far too small to drive atomic dislocation by many current models. To address these theoretical shortcomings, this paper develops a first-principles method to calculate the probability of beam-induced electronic excitations by coupling quantum electrodynamics (QED) scattering amplitudes to density functional theory (DFT) single-particle orbitals. The presented theory then explicitly considers the effect of these electronic excitations on the sputtering cross section. Applying this method to 2D hexagonal BN and MoS2 significantly increases their calculated sputtering cross sections and correctly yields appreciable sputtering rates at beam energies previously predicted to leave the crystals intact. The proposed QED-DFT approach can be easily extended to describe a rich variety of beam-driven phenomena in any crystalline material.

Theoretical Examination of the Hydroxide Transport in Cobaltocenium-Containing Polyelectrolytes.

Polymers incorporating cobaltocenium groups have received attention as promising components of anion-exchange membranes (AEMs), exhibiting a good balance of chemical stability and high ionic conductivity. In this work, we analyze the hydroxide diffusion in the presence of cobaltocenium cations in an aqueous environment based on the molecular dynamics of model systems confined in one dimension to mimic the AEM channels. In order to describe the proton hopping mechanism, the forces are obtained from the electronic structure computed at the density-functional tight-binding level. We find that the hydroxide diffusion depends on the channel size, modulation of the electrostatic interactions by the solvation shell, and its rearrangement ability. Hydroxide diffusion proceeds via both the vehicular and structural diffusion mechanisms with the latter playing a larger role at low diffusion coefficients. The highest diffusion coefficient is observed under moderate water densities (around half the density of liquid water) when there are enough water molecules to form the solvation shell, reducing the electrostatic interaction between ions, yet there is enough space for the water rearrangements during the proton hopping. The effects of cobaltocenium separation, orientation, chemical modifications, and the role of nuclear quantum effects are also discussed.

Time-dependent quantum dynamical simulations of C2 condensation under extreme conditions.

We report theoretical studies of the initial phase of bulk C(2) condensation into carbon nano-structures by means of Born-Oppenheimer and time-dependent quantum mechanical Liouville-von Neumann molecular dynamics based on the density-functional tight-binding (DFTB) framework for electrons. We observe that the time-dependent quantum mechanical approach leads to faster formation of carbon nanostructures than analogous Born-Oppenheimer simulations. Our results suggest that the condensation of bulk carbon is nonadiabatic in nature, with the critical role of electronic stopping as in ion-irradiation of materials. Contrary to time-dependent quantum mechanical simulations, Born-Oppenheimer dynamics incorrectly predict that the short carbon chains obtained from initial reactive collisions between C(2) quickly evaporate, leading to much lower probability of secondary collisions and condensation. We also discuss some deficiencies in Born-Oppenheimer dynamics that lead to unphysical charge polarization and electron transfer.

MP2 energy and density for large molecular systems with internal error control using the Divide-Expand-Consolidate scheme.

Divide-Expand-Consolidate (DEC) is a local correlation method where the inherent locality of the electron correlation problem is used to express the correlated calculation on a large molecular system in terms of small independent fragment calculations employing small subsets of local HF orbitals. A crucial feature of the DEC scheme is that the sizes of the local orbital spaces are determined in a black box manner during the calculation. In this way it is ensured that the correlation energy has been determined to a predefined precision compared to a conventional calculation. In the present work we apply the DEC scheme to calculate the correlation energy as well as the electron density matrix for the insulin molecule using second order Møller-Plesset (MP2) theory. This is the first DEC calculation on a molecular system which is too large to be treated using a conventional MP2 implementation. The fragmentation errors for the insulin DEC calculation are carefully analyzed using internal consistency checks. It is demonstrated that size-intensive properties are determined to the same precision for small and large molecules. For example, the percentage of correlation energy recovered and the error per electron in the correlated density matrix depend only on the predefined precision and not on the molecular size.

Extracting Inelastic Scattering Cross Sections for Finite and Aperiodic Materials from Electronic Dynamics Simulations.

Explicit time-dependent electronic structure theory methods are increasingly prevalent in the areas of condensed matter physics and quantum chemistry, with the broad-band optical absorptivity of molecular and small condensed-phase systems nowadays routinely studied with such approaches. In this paper, it is demonstrated that electronic dynamics simulations can similarly be employed to study cross sections for the scattering-induced electronic excitations probed in nonresonant inelastic X-ray scattering and momentum-resolved electron energy loss spectroscopies. A method is put forth for evaluating the electronic dynamic structure factor, which involves the application of a momentum boost-type perturbation and transformation of the resulting reciprocal space density fluctuations into the frequency domain. Good agreement is first demonstrated between the dynamic structure factor extracted from these electronic dynamics simulations and the corresponding transition matrix elements from linear response theory. The method is then applied to some extended (quasi)one-dimensional systems, for which the wave vector becomes a good quantum number in the thermodynamic limit. Finally, the dispersion of many-body excitations in a series of hydrogen-terminated graphene flakes (and twisted bilayers thereof) is investigated to highlight the utility of the presented approach for capturing morphology-dependent effects in the inelastic scattering cross sections of nanostructured and/or noncrystalline materials.

Understanding Beam-Induced Electronic Excitations in Materials.

Optical electronic absorption spectroscopy and corresponding selection rules have played a prominent role in the development of the theory of electronic structure of materials. In this work, we expand the modern toolbox of chemistry and materials science to include electron and ion microscopies and spectroscopies, allowing spatially resolved interrogation of materials' atomic and electronic structures by beams of charged particles. Specifically, we formulate and discuss the selection rules for electronic excitation due to the interaction between materials and beams of charged particles. We show that transition probabilities for point charge-induced electronic excitations depend strongly on the position of the externally charged particles and can significantly deviate from those derived from the electric dipole (long-wavelength) approximation. We present and implement expressions within the linear response time-dependent density functional theory (TD-DFT) framework for rates of transition between the ground and excited states induced by an external point charge. The point charge-induced transition rates for particular electronic excitations from linear response TD-DFT were validated through comparison to excited state populations from real time TD-DFT simulations following an impulsive point charge perturbation, then evaluated on a three-dimensional grid to map their spatial dependence for a small polybenzoid. This method, when combined with information about excited state energy gradients, represents a first step toward an ab initio framework for probing the structural response of materials under irradiation by charged particles resulting from inelastic scattering. Engineering electron beam interaction with matter to manipulate single atoms and localized electronic states offers a revolutionary new regime beyond laser excitation.

Liouville-von Neumann molecular dynamics.

We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C(2) and retinal system.

Identification of site-specific isotopic labels by vibrational spectroscopy in the electron microscope.

The identification of isotopic labels by conventional macroscopic techniques lacks spatial resolution and requires relatively large quantities of material for measurements. We recorded the vibrational spectra of an α amino acid, l-alanine, with damage-free "aloof" electron energy-loss spectroscopy in a scanning transmission electron microscope to directly resolve carbon-site-specific isotopic labels in real space with nanoscale spatial resolution. An isotopic red shift of 4.8 ± 0.4 milli-electron volts in C-O asymmetric stretching modes was observed for 13C-labeled l-alanine at the carboxylate carbon site, which was confirmed by macroscopic infrared spectroscopy and theoretical calculations. The accurate measurement of this shift opens the door to nondestructive, site-specific, spatially resolved identification of isotopically labeled molecules with the electron microscope.

Hydrogen tunneling in an enzyme active site: a quantum wavepacket dynamical perspective.

We study the hydrogen tunneling problem in a model system that represents the active site of the biological enzyme, soybean lipoxygenase-1. Toward this, we utilize quantum wavepacket dynamics performed on potential surfaces obtained by using hybrid density functional theory under the influence of a dynamical active site. The kinetic isotope effect is computed by using the transmission amplitude of the wavepacket, and the experimental value is reproduced. By computing the hydrogen nuclear orbitals (eigenstates) along the reaction coordinate, we note that tunneling for both hydrogen and deuterium occurs through the existence of distorted, spherical s-type proton wave functions and p-type polarized proton wave functions for transfer along the donor-acceptor axis. In addition, there is also a significant population transfer through distorted p-type proton wave functions directed perpendicular to the donor-acceptor axis (via intervening pi-type proton eigenstate interactions) which underlines the three-dimensional nature of the tunneling process. The quantum dynamical evolution indicates a significant contribution from tunneling processes both along the donor-acceptor axis and along directions perpendicular to the donor-acceptor axis. Furthermore, the tunneling process is facilitated by the occurrence of curve crossings and avoided crossings along the proton eigenstate adiabats.

Non-Transition-Metal Catalytic System for N2 Reduction to NH3: A Density Functional Theory Study of Al-Doped Graphene.

The prevalent catalysts for natural and artificial N2 fixation are known to hinge upon transition-metal (TM) elements. Herein, we demonstrate by density functional theory that Al-doped graphene is a potential non-TM catalyst to convert N2 to NH3 in the presence of relatively mild proton/electron sources. In the integrated structure of the catalyst, the Al atom serves as a binding site and catalytic center while the graphene framework serves as an electron buffer during the successive proton/electron additions to N2 and its various downstream NxHy intermediates. The initial hydrogenation of N2 can readily take place via an internal H-transfer process with the assistance of a Li+ ion as an additive. In view of the recurrence of H transfer in the first step of N2 reduction observed in biological nitrogenases and other synthetic catalysts, this finding highlights the significance of heteroatom-assisted H transfer in the design of synthetic catalysts for N2 fixation.

Deuteration as a Means to Tune Crystallinity of Conducting Polymers.

The effects of deuterium isotope substitution on conjugated polymer chain stacking of poly(3-hexylthiophene) is studied experimentally by X-ray diffraction (XRD) in combination with gel permeation chromatography and theoretically using density functional theory and quantum molecular dynamics. For four P3HT materials with different levels of deuteration (pristine, main-chain deuterated, side-chain deuterated, and fully deuterated), the XRD measurements show that main-chain thiophene deuteration significantly reduces crystallinity, regardless of the side-chain deuteration. The reduction of crystallinity due to the main-chain deuteration is a quantum nuclear effect resulting from a static zero-point vibrational energy combined with a dynamic correlation of the dipole fluctuations. The quantum molecular dynamics simulations confirm the interchain correlation of the proton-proton and deuteron-deuteron motions but not of the proton-deuteron motion. Thus, isotopic purity is an important factor affecting stability and properties of conjugated polymer crystals, which should be considered in the design of electronic and spintronic devices.

Building with ions: towards direct write of platinum nanostructures using in situ liquid cell helium ion microscopy.

Direct write with a liquid precursor using an ion beam in situ, allows fabrication of nanostructures with higher purity than using gas phase deposition. Specifically, positively charged helium ions, when compared to electrons, localize the reaction zone to a single-digit nanometer scale. However, to control the interaction of the ion beam with the liquid precursor, as well as enable single digit fabrication, a comprehensive understanding of the radiolytic process, and the role of secondary electrons has to be developed. Here, we demonstrate an approach for directly writing platinum nanostructures from aqueous solution using a helium ion microscope, and discuss possible mechanisms for the beam-induced particle growth in the framework of Born-Oppenheimer and real-time electron dynamics models. We illustrate the nanoparticle nucleation and growth parameters through data analysis of in situ acquired movie data, and correlate these results to a fully encompassing, time-dependent, quantum dynamical simulation that takes into account both quantum and classical interactions. Finally, sub-15 nm resolution platinum structures generated in liquid are demonstrated.

Understanding How Isotopes Affect Charge Transfer in P3HT/PCBM: A Quantum Trajectory-Electronic Structure Study with Nonlinear Quantum Corrections.

The experimentally observed effect of selective deuterium substitution on the open circuit voltage for a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM; Nat. Commun. 2014, 5, 3180) is explored using a 221-atom model of a polymer-wrapped PCBM molecule. The protonic and deuteronic wave functions for the H/D isotopologues of the hexyl side chains are described within a quantum trajectory/electronic structure approach where the dynamics is performed with newly developed nonlinear corrections to the quantum forces, necessary to describe the nuclear wave functions; the classical forces are generated with a density functional tight binding method. The resulting protonic and deuteronic time-dependent wave functions are used to assess the effects of isotopic substitution (deuteration) on the energy gaps relevant to the charge transfer for the donor and acceptor electronic states. While the isotope effect on the electronic energy levels is found negligible, the quantum-induced fluctuations of the energy gap between the charge transfer and charge separated states due to nuclear wave functions may account for experimental trends by promoting charge transfer in P3HT:PCBM and increasing charge recombination on the donor in the deuterium substituted P3HT:PCBM.