We utilize real-time time-dependent density functional theory and Ehrenfest dynamics scheme to investigate excited-state nonadiabatic dynamics of ligand dissociation of cobalt tricarbonyl nitrosyl, ...Co(CO)
NO, which is a precursor used for cobalt growth in advanced technologies, where the precursor's reaction is enhanced by electronic excitation. Based on the first-principles calculations, we demonstrate two dissociation pathways of the NO ligand on the precursor. Detailed electronic structures are further analyzed to provide an insight into dynamics following the electronic excitations. This study sheds light on computational demonstration and underlying mechanism of the electronic-excitation-induced dissociation, especially in molecules with complex chemical bonds such as the Co(CO)
NO.
We present a computational tool, eReaxFF, for simulating explicit electrons within the framework of the standard ReaxFF reactive force field method. We treat electrons explicitly in a pseudoclassical ...manner that enables simulation several orders of magnitude faster than quantum chemistry (QC) methods, while retaining the ReaxFF transferability. We delineate here the fundamental concepts of the eReaxFF method and the integration of the Atom-condensed Kohn–Sham DFT approximated to second order (ACKS2) charge calculation scheme into the eReaxFF. We trained our force field to capture electron affinities (EA) of various species. As a proof-of-principle, we performed a set of molecular dynamics (MD) simulations with an explicit electron model for representative hydrocarbon radicals. We establish a good qualitative agreement of EAs of various species with experimental data, and MD simulations with eReaxFF agree well with the corresponding Ehrenfest dynamics simulations. The standard ReaxFF parameters available in the literature are transferrable to the eReaxFF method. The computationally economic eReaxFF method will be a useful tool for studying large-scale chemical and physical systems with explicit electrons as an alternative to computationally demanding QC methods.
What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to ...promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.
Carbon interdigitated array (IDA) electrodes with features sizes down to 1.2 μm were fabricated by controlled pyrolysis of patterned photoresist. Cyclic voltammetry of reversible redox species ...produced the expected steady-state currents. The collection efficiency depends on the IDA electrode spacing, which ranged from around 2.7 to 16.5 μm, with the smaller dimensions achieving higher collection efficiencies of up to 98%. The signal amplification because of redox cycling makes it possible to detect species at relatively low concentrations (10–5 molar) and the small spacing allows detection of transient electrogenerated species with much shorter lifetimes (submillisecond). Digital simulation software that accounts for both the width and height of electrode elements as well as the electrode spacing was developed to model the IDA electrode response. The simulations are in quantitative agreement with experimental data for both a simple fast one electron redox reaction and an electron transfer with a following chemical reaction at the IDAs with larger gaps whereas currents measured for the smallest IDA electrodes, that were larger than the simulated currents, are attributed to convection from induced charge electrokinetic flow.
Reliable and robust convergence to the electronic ground state within density functional theory (DFT) Kohn–Sham (KS) calculations remains a thorny issue in many systems of interest. In such cases, ...charge sloshing can delay or completely hinder the convergence. Here, we use an approach based on transforming the time-dependent DFT equations to imaginary time, followed by imaginary-time evolution, as a reliable alternative to the self-consistent field (SCF) procedure for determining the KS ground state. We discuss the theoretical and technical aspects of this approach and show that the KS ground state should be expected to be the long-imaginary-time output of the evolution, independent of the exchange-correlation functional or the level of theory used to simulate the system. By maintaining self-consistency between the single-particle wave functions (orbitals) and the electronic density throughout the determination of the stationary state, our method avoids the typical difficulties encountered in SCF. To demonstrate dependability of our approach, we apply it to selected systems which struggle to converge with SCF schemes. In addition, through the van Leeuwen theorem, we affirm the physical meaningfulness of imaginary-time TDDFT, justifying its use in certain topics of statistical mechanics such as in computing imaginary-time path integrals.
We present a method for real-time propagation of electronic wave functions, within time-dependent density functional theory (RT-TDDFT), coupled to ionic motion through mean-field classical dynamics. ...The goal of our method is to treat large systems and complex processes, in particular photocatalytic reactions and electron transfer events on surfaces and thin films. Due to the complexity of these processes, computational approaches are needed to provide insight into the underlying physical mechanisms and are therefore crucial for the rational design of new materials. Because of the short time step required for electron propagation (of order ∼10 attoseconds), these simulations are computationally very demanding. Our methodology is based on numerical atomic-orbital-basis sets for computational efficiency. In the computational package, to which we refer as TDAP-2.0 (Time-evolving Deterministic Atom Propagator), we have implemented a number of important features and analysis tools for more accurate and efficient treatment of large, complex systems and time scales that reach into a fraction of a picosecond. We showcase the capabilities of our method using four different examples: (i) photodissociation into radicals of opposite spin, (ii) hydrogen adsorption on aluminum surfaces, (iii) optical absorption of spin-polarized organic molecule containing a metal ion, and (iv) electron transfer in a prototypical dye-sensitized solar cell.
Band alignment between two materials is of fundamental importance for a multitude of applications. However, density functional theory (DFT) either underestimates the bandgap - as is the case with the ...local density approximation (LDA) or generalized gradient approximation (GGA) - or is highly computationally demanding, as is the case with hybrid-functional methods. The latter can become prohibitive in electronic-structure calculations of supercells which describe quantum wells. We propose to apply the DFT+U method, with U for each atomic shell being treated as set of tuning parameters, to automatically fit the bulk bandgap and the lattice constant, and then use the thus obtained U parameters in large supercell calculations to determine the band alignment. We apply this procedure to InP/In0.5Ga0.5As, In0.5Ga0.5As/In0.5Al0.5As and InP/In0.5Al0.5As quantum wells, and obtain good agreement with experimental results. Although this procedure requires some experimental input, it provides both meaningful valence and conduction band offsets while, crucially, lattice relaxation is taken into account. The computational cost of this procedure is comparable to that of LDA. We believe that this is a practical procedure that can be useful for providing accurate estimates of band alignments between more complicated alloys.
We present a new paradigm for understanding optical absorption and hot electron dynamics experiments in graphene. Our analysis pivots on assigning proper importance to phonon-assisted indirect ...processes and bleaching of direct processes. We show indirect processes figure in the excess absorption in the UV region. Experiments which were thought to indicate ultrafast relaxation of electrons and holes, reaching a thermal distribution from an extremely nonthermal one in under 5–10 fs, instead are explained by the nascent electron and hole distributions produced by indirect transitions. These need no relaxation or ad-hoc energy removal to agree with the observed emission spectra and fast pulsed absorption spectra. The fast emission following pulsed absorption is dominated by phonon-assisted processes, which vastly outnumber direct ones and are always available, connecting any electron with any hole any time. Calculations are given, including explicitly calculating the magnitude of indirect processes, supporting these views.
Despite intensive study of reactions on metals, it is unclear whether electronic excitations play an important role. Here, we show that nonadiabatic effects do indeed play a significant role in N2 ...and H2 dissociation on Ru nanoparticles. We employ nonadiabatic dynamical calculations based on real-time, time-dependent density functional theory to study energy dissipation during these exothermic reaction steps. We find that dissipation of the excess energy into excitation of electrons exceeds thermal dissipation into phonons. For isolated dissociation events, electronic friction can increase reaction barriers; furthermore, the excitations induced by a dissociation event can affect other reacting molecules. Our studies suggest that, for exothermic reactions, metal catalysts in reaction conditions may be constantly experiencing electronic excitations, and these excitations can significantly affect surface chemistry.
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