Article

SCC-DFTB Parameters for Simulating Hybrid Gold-Thiolates Compounds

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Abstract

We present a parametrization of a self-consistent charge density functional-based tight-binding scheme (SCC-DFTB) to describe gold-organic hybrid systems by adding new Au-X (X = Au, H, C, S, N, O) parameters to a previous set designed for organic molecules. With the aim of describing gold-thiolates systems within the DFTB framework, the resulting parameters are successively compared with density functional theory (DFT) data for the description of Au bulk, Aun gold clusters (n = 2, 4, 8, 20), and Aun SCH3 (n = 3 and 25) molecular-sized models. The geometrical, energetic, and electronic parameters obtained at the SCC-DFTB level for the small Au3 SCH3 gold-thiolate compound compare very well with DFT results, and prove that the different binding situations of the sulfur atom on gold are correctly described with the current parameters. For a larger gold-thiolate model, Au25 SCH3 , the electronic density of states and the potential energy surfaces resulting from the chemisorption of the molecule on the gold aggregate obtained with the new SCC-DFTB parameters are also in good agreement with DFT results. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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... 53 The auorg-1-1 parameter set, designed to describe optical excitations of organic molecules on gold nanoclusters, are employed for all computations in this work. 54 To obtain a correct desorption reaction coordinate, the DFTB parameters associated with the repulsive potential between ...
... To obtain the average absorption spectrum, vertical excitation energies and oscillator strengths of all snapshots are computed using the LR-TDDFTB. 54 For NAMD simulations, all excited state trajectories are prepared by plasmon excitation (i.e., 2.7 eV) according to the absorption spectrum and are propagated for 1 ps. The timesteps for nuclear (classical) and electronic (quantum) equations of motions are set to 0.4 fs and 0.1 fs, respectively. ...
... 2,60,61 The inset of Figure 1 shows the ground state equilibrium geometry of Au 20 −CO optimized by DFTB method. 54 This structure with CO molecule adsorbed at the apex site of the Au 20 cluster is consistent with previous findings. 62 To further confirm this adsorption configuration is favorable during the dynamic process, ground state potential energy surface (PES) along the adsorption reaction coordinate (Figure 1) is calculated. ...
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Heterogeneous catalysis of adsorbates on metallic surfaces mediated by plasmon has potential high photoelectric conversion efficiency and controllable reaction selectivity. Theoretical modeling of dynamical reaction processes provides in-depth analyses complementing experimental investigations. Especially for plasmon-mediated chemical transformations, light absorption, photoelectric conversion, electron-electron scattering, and electron-phonon coupling occur simultaneously at different timescales, rendering it very challenging to delineate the complex interplay of different factors. In this work, a trajectory surface hopping non-adiabatic molecular dynamics method is used to investigate the dynamics of plasmon excitation in an Au$_{20}$-CO system, including hot carrier generation, plasmon energy relaxation, and CO activation induced by electron-vibration coupling. The electronic properties indicate that when Au$_{20}$-CO is excited, a partial charge transfer takes place from Au$_{20}$ to CO. On the other hand, the dynamical simulations show that hot carriers generated after plasmon excitation transfer back and forth between Au$_{20}$ and CO. Meanwhile, the C-O stretching mode is activated due to the non-adiabatic couplings. The efficiency of plasmon-mediated transformation ($\sim$40\%) is obtained based on the ensemble average of these quantities. Our simulations provide important dynamical and atomistic insights into plasmon-mediated chemical transformation from the perspective of non-adiabatic simulations.
... [48][49][50] Based on a controlled approximation of density functional theory (DFT), this method has been successfully used to describe the electronic structures of large biological and organic systems, as well as their quantum properties. 50,51 Specifically, all of the DFTB calculations were performed using the DFTB+ code, 52 with the auorg set of parameters 53 in the second-order SCC-DFTB. The ground state structures of all systems were obtained with a geometry optimization with a force criterion of 10 −4 a.u, followed by a vibrational frequencies calculation to ensure that the structures correspond to a global energy minimum. ...
... The auorg set of parameters have been developed more specifically to describe gold bulk materials and surfaces or slabs decorated with organic molecules, 53 and has yet to be tested on GNCs. As a matter of fact, these GNCs possess a specific core-shell atomic arrangement, e.g., for Au 25 (SR) 18 − , the icosahedral cluster core encompasses 13 gold atoms and its outer part is built with 6 S-Au-S-Au-S staples. ...
... Indeed, as shown in a previous DFT study of this system, 11 the optical properties of such π-conjugated chromophores are more accurately reproduced when using a more sophisticated functional including a range-separation term, while a pure GGA functional returns bands which are too low in energy. It is then somewhat expected for the auorg set of parameters, created with a GGA type of functional, 53 to inherit such errors. Switching to a recent DFTB model to construct the parameters (not yet available for Au and S atoms) based on a range-separated type of functional, 61 may correct this behavior. ...
Article
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The electron flow between a metallic aggregate and an organic molecule after excitation with light is a crucial step on which are based the hybrid photovoltaic nanomaterials. So far, designing such device with the help of theoretical approaches have been heavily limited by the computational cost of quantum dynamics models able to track the evolution of the excited states over time. In this contribution we present the first application of Time-Dependent Density Functional Tight-Binding (TD-DFTB) method for an experimental nanometer-sized gold-organic system consisting in a hexyl-protected Au25 cluster labelled with a pyrene fluorophore, in which the fluorescence quenching of the pyrene is attributed to an electron transfer from the metallic cluster to the dye. The full quantum rationalization of the electron transfer is attained through quantum dynamics simulations, highlighting the crucial role of the protecting ligands shell in the electron transfer, as well as the coupling with nuclear movement. This work paves the way towards a fast and accurate theoretical design of optoelectronic nanodevices.
... Therefore, many have turned their attention to the approximate quantum methods, such as Density Functional Based Tight-Binding (DFTB), to reduce the computational time and to extend the range of system sizes that are accessible. Fihey et al. 34 have recently developed parameters for gold-thiolates systems in the DFTB framework to accurately reproduce geometries, energies and electronic properties obtained at the DFT level. Oliveira et al. 35 have conducted a benchmark of the Au-Au parameters for a series of gold clusters against DFT. ...
... 62,63 The parameters used for the systems under study were obtained from previously reported publication. 34,36 The geometry optimization of the systems was done with the conjugate gradient algorithm without any constraint. Dispersion corrections were systematically introduced using the DFTB3 framework 64 along with hydrogen bond corrections, as proposed in previous publications. ...
... In the literature, there is currently one parameter set available for Au-Au, Au-O, and Au-H interactions, named as "auorg", which was benchmarked for the Au-Au interactions and Au interactions with organic molecules (O, S, H, C) in an aqueous environment. 34 Furthermore, water-water interaction can be described by different available sets. We tested water-water parameters from mio-1-1 set which was extensively used for water and solvated Titanium systems. ...
Article
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While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water–gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNPs along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water–water interactions as well as the water–GNP interactions.
... DFTB has been used to investigate various clusters including sodium [262], ceria [295], cadmium sulfides [233,264], bore [166], silver and gold [155,157,165,172,173,[267][268][269][270][271][272], ZnO [273], molybdenum disulfide [274], iron [154,275] or nanodiamond [276,277]. In addition to the necessary work dedicated to specific DFTB parametrization for these systems [155,156,172,173,[268][269][270]278], a number of studies have been devoted to their structural characterisation [63,153,154,157,161,165,268,278]. Figure 3 illustrates examples of investigated structures for silver cluster Ag 561 [172]. ...
... DFTB has been used to investigate various clusters including sodium [262], ceria [295], cadmium sulfides [233,264], bore [166], silver and gold [155,157,165,172,173,[267][268][269][270][271][272], ZnO [273], molybdenum disulfide [274], iron [154,275] or nanodiamond [276,277]. In addition to the necessary work dedicated to specific DFTB parametrization for these systems [155,156,172,173,[268][269][270]278], a number of studies have been devoted to their structural characterisation [63,153,154,157,161,165,268,278]. Figure 3 illustrates examples of investigated structures for silver cluster Ag 561 [172]. An interesting question is the evolution with size of the competition between ordered and disordered structures [157,165,173,272]. ...
... Then, they demonstrated its ability to accurately describe the low-energy structures of Au m (SMe) n species as well as qualitatively describe their electronic structure. A similar study was latter conducted by Fihey et al. who developed a new set of DFTB parameters for Au-X (X = Au, H, C, S, N, O) elements in order to better describe the interaction of thiolates and other molecules with gold particles [269]. Those parameters were validated by considering two species: Au 3 SCH 3 and Au 25 SCH 3 for which structural, energetic and electronic properties were calculated and compared to DFT results. ...
Article
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The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare or functionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
... We first optimize the tetrahedral Au 20 structure in its ground state at the DFTB level with the auorg-1-1 parameter set. 62 This is The Journal of Chemical Physics ARTICLE scitation.org/journal/jcp followed by a 50 ps Born-Oppenheimer molecular dynamics with a classical time step Δt = 1 fs. ...
... To construct the average absorption spectrum, vertical excitation energies and oscillator strengths of all samples are computed using LR-TDDFTB. 62 For NAMD simulations, all excited state trajectories were prepared by plasmon excitation according to the absorption spectrum (see details in Appendix A) and propagated for 5 ps. The time step for nuclear and electronic motion is set to 1 and 0.25 fs, respectively. ...
Article
Hot carriers generated from the decay of plasmon excitation can be harvested to drive a wide range of physical or chemical processes. However, their generation efficiency is limited by the concomitant phonon-induced relaxation processes by which the energy in excited carriers is transformed into heat. However, simulations of dynamics of nanoscale clusters are challenging due to the computational complexity involved. Here, we adopt our newly developed Trajectory Surface Hopping (TSH) nonadiabatic molecular dynamics algorithm to simulate plasmon relaxation in Au 20 clusters, taking the atomistic details into account. The electronic properties are treated within the Linear Response Time-Dependent Tight-binding Density Functional Theory (LR-TDDFTB) framework. The relaxation of plasmon due to coupling to phonon modes in Au 20 beyond the Born–Oppenheimer approximation is described by the TSH algorithm. The numerically efficient LR-TDDFTB method allows us to address a dense manifold of excited states to ensure the inclusion of plasmon excitation. Starting from the photoexcited plasmon states in Au 20 cluster, we find that the time constant for relaxation from plasmon excited states to the lowest excited states is about 2.7 ps, mainly resulting from a stepwise decay process caused by low-frequency phonons of the Au 20 cluster. Furthermore, our simulations show that the lifetime of the phonon-induced plasmon dephasing process is ∼10.4 fs and that such a swift process can be attributed to the strong nonadiabatic effect in small clusters. Our simulations demonstrate a detailed description of the dynamic processes in nanoclusters, including plasmon excitation, hot carrier generation from plasmon excitation dephasing, and the subsequent phonon-induced relaxation process.
... Slater-Koster set [39,122,123] with orbital dependent Hubbard parameters. A periodic setup was used as well and the optimization was done at the Γ point. ...
... NEGF-DFTB was employed to compute the thermoelectric properties of OPE3 derivatives. We used the auorg-1-1 Slater-Koster set [39,122,123] with orbital dependent Hubbard parameters. A periodic setup was used, where the device is repeated perpendicular to the transport direction along the surface. ...
Thesis
Thermoelectricity is the conversion of heat to electricity and vice versa. As Seebeck discovered, a voltage applied to an electronic device generates a heat current, while a temperature difference can generate electricity. During the past decades, the size of consumer electronics has been continuously decreasing. The down-sizing of the electronic devices requires a more efficient heat management. An interesting route towards this goal is the idea of using single molecules as electronic components which gave rise to "molecular electronics".In fact, the usage of organic molecules in thermoelectric applications has at tracted a great deal of attention due to their flexibility, relatively low price and their eco-friendly nature. In this work, the thermoelectric properties of molecular junctions based on oligo(phenyleneethynylene) (OPE3) derivatives were studied. With the help of Density Functional Theory (DFT) calculations, models for the molecular junctions were constructed. The electronic transport properties were obtained using Non Equilibrium Green’s Function-Density Functional based Tight-Binding (NEGF-DFTB). Firstly, the effect of side groups on the electronic conductance and thermopower of OPE3 derivatives was quantified. It is shown that these derivatives provide structural properties that are needed for highly efficient thermoelectric materials. Next,the effect of cross-linking molecules on the thermoelectric efficiency was investigated. Classical Molecular Dynamics (MD) was used to compute the phonon transport across the junctions. Combining the results from ab-initio and MD for electron and phonon transport, respectively, the thermoelectric efficiency in terms of the figure of merit ZT was computed for OPE3 derivatives. We have found that cross-linked molecules show a high ZT value, which makes them good candidates to be used as cooling systems. Finally, we introduce a circuit model that combines electron and phonon transport channels. This model allows to determine optimal parameter ranges in order to maximize cooling. Overall, our results demonstrate that the OPE3 derivatives display the necessary structural rigidity and compatible electronic structure to enable high performance devices for cooling applications.
... Among the vast literature focused on gold clusters , numerous works are devoted to Au 20 [63,64,66,73,74,80,88,99,107] because this cluster presents a double magic number: its atomic structure is a highly symmetrical pyramid and, in the simple spherical Jellium model, its 20-electron outer electronic shell is closed (1s 2 1p 6 1d 10 2s 2 superorbital configuration). In recent studies, employing a new adaptation of DFTB parameters [109,111,112], we have investigated the potential energy surface (PES) of Au (0,+,−) 20 by combining a Parallel Tempering Molecular Content courtesy of Springer Nature, terms of use apply. Rights reserved. ...
... The DFTB parameters used were adapted [112,116,123] from those developed by Fihey et al. [111] (the "auorg" set from the www.dftb.org website). ...
Article
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We report the combination of the threshold algorithm with the Density Functional-based Tight Binding method allowing for the exploration of complex potential energy surfaces and the evaluation of probability flows between their regions, at the quantum level. This original scheme is used to explore the energy landscape of an anionic 20-atom gold cluster, Au20-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$_{20}^{-}$$\end{document}. On the basis of the relevant structures, 19 structural groups are highlighted, all of them being variations about the pyramidal shape: (1) distorted pyramids, (2) pyramids in which the atom of one of the facets has been removed, leaving a hole, and placed at different positions on the cluster and (3) pyramids on which an atom located at a vertex has been removed and placed on an edge or on a facet. Upper limits of the energies required to connect the basins of the 19 groups on the potential energy surface are evaluated. Moreover, the attractive basins are identified on the basis of the analysis of the probability flows on the landscape. The comparison of the disconnectivity tree with the results of the flux analysis provides a consistent representation of the Au20-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$_{20}^{-}$$\end{document} basins’ proximity. Finally, we show how the new scheme allowed for the identification of counter-intuitive transition pathways. Graphical abstract
... 51 While the AO energies and the Hubbard parameters U are normally taken from DFT calculations of the free atom, the other electronic parameters and pairwise repulsive potentials are subject to optimization with the goal to reproduce certain desired properties; for instance, electronic band structure, atomization energies, reaction energies, and geometries (energy gradients or atomic forces). In order to parameterize the Au and P interactions for DFTB2, we adopted the Au electronic parameters from the "auorg" set published by Fihey et al. (referred to as auorg a ), 58 and a modied version of "auorg" by Oliveira et al. (referred to as auorg c ). 59 The difference between these two parameter sets lies in the Au 6p-orbital energy; in the auorg a set it was taken as the true PBE orbital energy, while in the auorg c set it was empirically shied upward by z+0.0279 hartree. The main purpose for this orbital energy shi was to obtain improved values for cohesive energies of pure gold nanoclusters with respect to PBE. 59 Following the work of "auorg", only 5d and 6 s valence electrons are considered, in total 11 valence electrons per Au atom. ...
... Structures Weights À65.01 1.0 [Au 6 (planar)] 2+ + PH 3 0 [Au 6 (planar)-PH 3 ] 2+ À64. 58 1.0 12 TELMUV 26 in the calculations generating the training set in order to avoid complications originating from a possible convolution of DFTB repulsive energy terms and the long-distance dispersion term. In order to benchmark the accuracy of the new parameters, ligand binding energies and optimized geometries were compared to their TPSS counterparts for various complexes of PH 3 , PMe 3 , PPh 3 and small-to moderate-sized gold clusters. ...
Article
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We report a parameterization of the second-order density-functional tight-binding (DFTB2) method for the quantum chemical simulation of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces. Our parameterization extends the previously released DFTB2 "auorg" parameter set by connecting it to the electronic parameter of phosphorus in the "mio" parameter set. Although this connection could technically simply be accomplished by creating only the required additional Au-P repulsive potential, we found that the Au 6p and P 3d virtual atomic orbital energy levels exert a strong influence on the overall performance of the combined parameter set. Our optimized parameters are validated against density functional theory (DFT) geometries, ligand binding and cluster isomerization energies, ligand dissociation potential energy curves, and molecular orbital energies for relevant phosphine-ligated Au n clusters (n = 2-70), as well as selected experimental X-ray structures from the Cambridge Structural Database. In addition, we validate DFTB simulated far-IR spectra for several phosphine- and thiolate-ligated gold clusters against experimental and DFT spectra. The transferability of the parameter set is evaluated using DFT and DFTB potential energy surfaces resulting from the chemisorption of a PH3 molecule on the gold (111) surface. To demonstrate the potential of the DFTB method for quantum chemical simulations of metalloid gold clusters that are challenging for traditional DFT calculations, we report the predicted molecular geometry, electronic structure, ligand binding energy, and IR spectrum of Au108S24(PPh3)16.
... 386 atoms are included in the central region, and the remaining gold atoms are distributed to the electrodes in six layers each. The auorg-1-1 parameter set was used 109 . After the calculation of the transmission function in a non-SCC approximation and using the wide band approximation, the zero-bias conductance was evaluated at a Fermi energy of −5 eV by G = G 0 T (E F ). ...
Preprint
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Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way towards their routine evaluation.
... Recently, DFTB has been coupled with the vdW and MBD methods 29,30 to incorporate long-range dispersion, but unfortunately few reliable DFTB parametrizations for metal-organic interfaces exist to date. 31 Machine learning-based interatomic potentials (MLIPs) offer high computational efficiency whilst retaining the accuracy of the underlying training data based on electronic structure theory. Atomistic MLIP methods include Gaussian Approximation Potentials [32][33][34] or neural network (NN) potentials (e.g. ...
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The computational prediction of the structure and stability of hybrid organic-inorganic interfaces provides important insights into the measurable properties of electronic thin film devices, coatings, and catalyst surfaces and plays an important role in their rational design. However, the rich diversity of molecular configurations and the important role of long-range interactions in such systems make it difficult to use machine learning (ML) potentials to facilitate structure exploration that otherwise require computationally expensive electronic structure calculations. We present an ML approach that enables fast, yet accurate, structure optimizations by combining two different types of deep neural networks trained on high-level electronic structure data. The first model is a short-ranged interatomic ML potential trained on local energies and forces, while the second is an ML model of effective atomic volumes derived from atoms-in-molecules partitioning. The latter can be used to connect short-range potentials to well-established density-dependent long-range dispersion correction methods. For two systems, specifically gold nanoclusters on diamond (110) surfaces and organic $\pi$-conjugated molecules on silver (111) surfaces, we train models on sparse structure relaxation data from density functional theory and show the ability of the models to deliver highly efficient structure optimizations and semi-quantitative energy predictions of adsorption structures.
... partially based on the DFTB+ [41][42] software package. We also used the density functional based tight-binding method with auorg-1-1 parametrization [43][44] as implemented in the DFTB+ package. We considered a realistic atomistic system including the STM tip and the substrate, both connected to semi-infinite electrodes. ...
Article
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The rapid development of on‐surface synthesis provides a unique approach toward the formation of carbon‐based nanostructures with designed properties. Herein, we present the on‐surface formation of CN‐substituted phenylene vinylene chains on the Au(111) surface, thermally induced by annealing the substrate stepwise at temperatures between 220°C and 240°C. The reaction is investigated by scanning tunneling microscopy and density functional theory. Supported by the calculated reaction pathway, we assign the observed chain formation to a Knoevenagel condensation between an aldehyde and a methylene nitrile substituent.
... We performed self-consistent density-functional-based tight-binding simulations for geometric and electronic structural properties as implemented in the program package DFTB+ 7 . The parameter set "auorg-1-1" has been utilized in all our calculations 34 , which is an extension of the "mio-1-1" 35 parameter set to include gold. The "mio-1-1" set has been developed for organic molecules including O, N, C, H, and S atoms and works well for conformational energies and geometries of H-bonded systems 36 Determining minimum configurations. ...
Article
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Due to the low corrugation of the Au(111) surface, 1,4-bis(phenylethynyl)-2,5-bis(ethoxy)benzene (PEEB) molecules can form quasi interlocked lateral patterns, which are observed in scanning tunneling microscopy experiments at low temperatures. We demonstrate a multi-dimensional clustering approach to quantify the anisotropic pair-wise interaction of molecules and explain these patterns. We perform high-throughput calculations to evaluate an energy function, which incorporates the adsorption energy of single PEEB molecules on the metal surface and the intermolecular interaction energy of a pair of PEEB molecules. The analysis of the energy function reveals, that, depending on coverage density, specific types of pattern are preferred which can potentially be exploited to form one-dimensional molecular wires on Au(111).
... Implementations use Slater-Koster parametrisations, which provide the orbital coefficients and potentials. In this study, Slater-Koster files generated by Arnaud and Fihey et al for SCC-DFTB simulations of gold were used [18]. The classical energy generated by the LAMMPS simulation (E classical ) and the total Mermin energy from the DFTB+ energy calculation (E electronic ) were extracted during labelling. ...
Article
Classical simulations of materials and nanoparticles have the advantage of speed and scalability but at the cost of precision and electronic properties, while electronic structure simulations have the advantage of accuracy and transferability but are typically limited to small and simple systems due to the increased computational complexity. Machine learning can be used to bridge this gap by providing correction terms that deliver electronic structure results based on classical simulations, to retain the best of both worlds. In this study we train an artificial neural network (ANN) as a general ansatz to predict a correction of the total energy of arbitrary gold nanoparticles based on general (material agnostic) features, and a limited set of structures simulated with an embedded atom potential and the self-consistent charge density functional tight binding (SCC-DFTB) method. We find that an accurate model with an overall precision of 14 eV or 8.6 % can be found using a diverse range of particles and a large number of manually generated features which were then reduced using automatic data-driven approach to reduce evaluation bias. We found the ANN reduces to a linear relationship if a suitable subset of important features are identified prior to training, and that the prediction can be improved by classifying the nanoparticles into kinetically limited and thermodynamically limited subsets based prior to training the ANN corrections. The results demonstrate the potential for machine learning to enhance classical molecular dynamics simulations without adding significant computational complexity, and provides methodology that could be used to predict other electronic properties which cannot be calculated solely using classical simulations.
... They are more thermally, and chemically resistant compared to the polyacetylene molecules studied as the linkers in our previous work 27 , which motivates us to study them here. Geometry optimization and calculations of band structures of two periodical chains, consisting of Au 309 nanoparticle and fragment of polypyrrole or polythiophene ( Fig. 4 and Fig. 6), respectively, were carried out by the self-consistent-charge density-functional tight-binding method (SCC DFTB) 40 with use of DFTB+ code (Version 19.1) 41 and parameters set that is appropriate for the description of the interaction between the atoms in the series of carbon, nitrogen, oxygen, hydrogen, sulfur and gold 40,42,43 . Although the simulations were performed for periodical systems in the three-dimensional space, the periodicity of these chains was considered along x-direction. ...
Article
Thermoelectric and plasmonic properties of systems comprised of small golden nanoparticles (NP) linked by narrow conductive polymer bridges are studied using the original hybrid quantum‐classical model. The bridges considered here to be either conjugated polyacetylene, or polypyrrole, or polythiophene chain molecules terminated by thiol groups. The parameters required for the model were obtained using DFT and DFTB simulations. We found that charge‐transfer plasmons in the considered dumbbell structures possess the frequency in the infrared region for all considered molecular linkers. The appearance of plasmon vibrations and the existence of charge flow through the conductive molecule, with manifestation of quantum properties, were confirmed using frequency‐dependent polarizability calculations implemented in the Coupled Perturbed Kohn‐Sham method. To study the thermoelectric properties of the 1D periodical systems, we have derived a universal equation for the Seebeck coefficient. Phonon part of the thermal conductivity for the periodical −NP−S−C8H8‐ system was calculated by the classical molecular dynamics. The thermoelectric figure of merit ZT was calculated by considering the electrical quantum conductivity of the systems in the ballistic regime. It is shown that for Au309 nanoparticles connected by polyacetylene, polypyrrole, or polythiophene chains at T=300 K, ZT∼{0.08;0.45;0.40}, respectively.
... 41 DFTB is an approximate DFT method with an appealing cost/accuracy ratio and has been successfully used in a variety of applications in the field of molecular electronics. [42][43][44] Here we employed the auorg-0-1 Slater-Koster set 45,46 with orbital dependent Hubbard parameters and used a periodic setup, where the device is replicated perpendicular to the transport direction along the surface. This entails a solution of the Poisson equation under periodic boundary conditions to obtain the charge density in the device region. ...
Article
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We report the synthesis and the single-molecule transport properties of three new oligo(phenyleneethynylene) (OPE3) derivatives possessing terminal dihydrobenzo[b]thiophene (DHBT) anchoring groups and various core substituents (phenylene, 2,5-dimethoxyphenylene and 9,10-anthracenyl). Their electronic conductance and their Seebeck coefficient have been determined using scanning tunneling microscopy-based break junction (STM-BJ) experiments between gold electrodes. The transport properties of the molecular junctions have been modelled using DFT-based computational methods which reveal a specific binding of the sulfur atom of the DHBT anchor to the electrodes. The experimentally determined Seebeck coefficient varies between -7.9 and -11.4 μV K-1 in the series and the negative sign is consistent with charge transport through the LUMO levels of the molecules.
... Similarly, description of different crystal phases with the same chemical composition but with very different coordination numbers can be challenging. Recent examples show, 21,22 however, that it is possible to reach a reasonable accuracy if special care is taken during the parameterization process. ...
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DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green’s functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.
... Geometry optimization end calculations of electronic properties of a family consisting of six icosahedron shaped similar gold nanoparticles consisting of 55, 147, 309, 561, 923, and 1415 atoms (see Fig. 5) were carried out by the DFTB method 50 with use of a parameter set that is appropriate for the description of bulk gold clusters and bulk material, as well as AunSCH 3 clusters. 51 A calculation of the band structure for the periodical structure -[Au 147 SC 8 H 8 S]-was also made. Furthermore, for using in (6) the total energies Etot of the isolated gold nanoparticles having different total charges, Q(e) ∈ {−2, −1, 0, 1, 2} were calculated (Table I). ...
Article
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We analyze a new type of plasmon system arising from small metal nanoparticles linked by narrow conductive molecular bridges. In contrast to the well-known charge-transfer plasmons, the bridge in these systems consists only of a narrow conductive molecule or polymer in which the electrons move in a ballistic mode, showing quantum effects. The plasmonic system is studied by an original hybrid quantum-classical model accounting for the quantum effects, with the main parameters obtained from first-principles density functional theory simulations. We have derived a general analytical expression for the modified frequency of the plasmons and have shown that its frequency lies in the near-infrared (IR) region and strongly depends on the conductivity of the molecule, on the nanoparticle-molecule interface, and on the size of the system. As illustrated, we explored the plasmons in a system consisting of two small gold nanoparticles linked by a conjugated polyacetylene molecule terminated by sulfur atoms. It is argued that applications of this novel type of plasmon may have wide ramifications in the areas of chemical sensing and IR deep tissue imaging.
... The Au substrate was described as a slab with two dimensional PBC and theoretically optimized lattice parameter of 4.159 Å [31] was used. The Au substrate was optimized using DFTB platform employing DFTB.org parameter directory [32]. For the pEDA calculations without the thiol linker, the terminal hydrogen was attached to the gold with a bond length of 1.980 Å as shown in Scheme 1(A). ...
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Atomic scale manufacturing is a necessity of the future to develop atomic scale devices with high precision. A different perspective of the quantum realm, that includes the tunnelling effect, leakage current at the atomic-scale, Coulomb blockade and Kondo effect, is inevitable for the fabrication and hence, the mass production of these devices. For these atomic-scale device development, molecular level devices must be fabricated. Proper theoretical studies could be an aid towards the experimental realities. Electronic transport studies are the basis to realise and interpret the problems happening at this minute scale. Keeping these in mind, we present a periodic energy decomposition analysis (pEDA) of two potential candidates for moletronics: phthalocyanines and porphyrins, by placing them over gold substrate cleaved at the (111) plane to study the adsorption and interaction at the interface and then, to study their application as a channel between two electrodes, thereby, providing a link between pEDA and electronic transport studies. pEDA provides information regarding the bond strength and the contribution of electrostatic energy, Pauli’s energy, orbital energy and the orbital interactions. Combining this analysis with electronic transport studies, can provide novel directions for atomic/close-to-atomic-scale manufacturing (ACSM). Literature survey shows that this is the first work which establishes a link between pEDA and electronic transport studies and a detailed pEDA study on the above stated molecules. The results show that among the molecules studied, porphyrins are more adsorbable over gold substrate and conducting across a molecular junction than phthalocyanines, even though, both molecules show a similarity in adsorption and conduction when a terminal thiol linker is attached. A further observation establishes the importance of attractive terms, which includes interaction, orbital and electrostatic energies, in correlating the pEDA study with the transport properties. By progressing this research, further developments could be possible in atomic-scale manufacturing in the future.
Article
Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way toward their routine evaluation.
Thesis
To increase the number of electronic components in a single integrated circuit chip, the functional feature size should be reduced to the atomic and close-to-atomic scale (ACS). For this, the application of molecules could be utilised as a channel for current conduction. This thesis focuses on the fundamental aspects of this theme to help us achieve atomic scale device fabrication in the future. A literature review on advances in moletronics and atomic and close-to-atomic scale manufacturing (ACSM) research with the application of atomic force microscopy (AFM) is given in chapter 1. ACS device manufacturing using molecules as the building block requires to overcome mainly three fundamental problems. Firstly the orientation of the molecule when placed between the electrodes plays a critical role in electronic transport. This is explained in chapter 2, which gives a detailed ab-initio simulation studies of current flow in inorganic molecule, such as polyoxometalates (POMs) and organic molecules such as phthalocyanines (Pc) and porphyrins (Pr), by incorporating them between gold electrodes. For the POM molecule, longitudinal orientation showed better conduction than lateral orientation, whereas for Pc and Pr molecules, the geometrically optimised orientation displayed better electronic transport properties than the tautomerized structure. Secondly, the bonding interaction between the electrode and the molecular terminal atoms helps us to determine the rate of electronic transport at the junction. Chapter 3 inspects this interaction through a periodic energy decomposition analysis on Pc and Pr derivatives. The attractive and repulsive energy terms of the bonding interactions proved that Pr molecules are better interactive over the gold substrate in comparison to Pc molecules. Electronic transport studies performed on their derivatives with and without thiol linkers further supported this result. Thus, a link between these two studies were established. This paves path for future work to select appropriate molecules and electrodes to demonstrate transistor actions for atomic scale device fabrication. Finally, the possibility of the fabrication of ACS electrodes with a single atomic protrusion for the attachment of molecules needs to be experimentally validated. As a first step towards this, fundamental studies using AFM to achieve atomic layer removal were carried out taking into account different machining parameters. This is given in chapter 4 and chapter 5. In chapter 4, mechanical AFM-based scratching techniques over gold and silicon using diamond tips were performed. In silicon substrate, material removal having a minimum depth of 3.2Å which is close to about 3 silicon atom thickness, has been achieved. On gold, a minimum depth of 9.7Å, close to 7 atom thickness has been achieved. In chapter 5, electrochemical AFM-based lithography over HOPG and silicon using platinum coated tips were carried out. Results showed that in bare silicon local anodic oxidation took place instead of material removal. Even in hydrofluoric (HF) treated silicon, oxidation occurred but in a controlled and well defined manner. From this, it can be deduced that HF treated silicon is better suited for structure fabrication than bare silicon. In the case of HOPG, different patterns such as nano-holes, nanolines and intrinsic patterns were machined and material removal close-to-a single atomic layer, ~3.35Å was achieved. Results from chapter 4 and 5 reveal that controlled AFM-based scratching techniques can ensure the fabrication of well-defined atomic structures for the application of molecular devices. Since ACSM represents the next phase of manufacturing, this thesis proposes some of the primary works required to realise ACSM using the currently available techniques and simulation methodologies to bring us one step closer in achieving considerable advancements in this field in the near future.
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Gold Nanoparticles (GNPs), owing to their unique properties and versatile preparation strategy, have been demonstrated to exhibit promising applications in diverse fields, which include bio-sensors, catalysts, nanomedicines and radiotherapy. Yet, the nature of the interfacial interaction of GNPs with their chemical environment remains elusive. Experimental vibrational spectroscopy can reveal different interactions of aromatic biological molecules absorbed on GNPs, that may result from changes in the orientation of the molecule. However, the presence of multiple functional groups and the aqueous solvent introduces competition, and complexifies the spectral interpretations. Therefore, our objective is to theoretically investigate the adsorption of aromatic molecules containing various functional groups on the surface of GNPs to comparatively study their preferred adsorption modes. The interaction between Au32, as a model of GNPs, and a series of substituted aromatic compounds that includes benzene, aniline, phenol, toluene, benzoic acid, acetophenone, methyl benzoate, and thiophenol, is investigated. Our computed interaction energies highlight the preference of the aromatic ring to lie flat on the surface. The orientations of the molecules can be distinguished using infrared spectroscopy along with strong changes in intensity and significant shifts of some vibrational modes when the molecule interacts with the GNP. The interaction energy and the electron transfer between the nanoparticle and the aromatic molecule are not found to correlate, possibly because of significant back donation of electrons from GNPs to organic molecules as revealed by charge decomposition analysis. A thorough quantum topological analysis identifies multiple non-covalent interactions and assigns the nature of the interaction mostly to dative interactions between the aromatic ring and the GNP as well as dispersive interaction. Finally, energy decomposition analyses point out the role of the charge transfer energy contribution in the subtle balance of the different physical components.
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Dihydroazulene/vinylheptafulvene pairs are known as molecular dipole switches that undergo a ring-opening/-closure reaction by UV irradiation or thermal excitation. Herein, we show that the ring-closure reaction of a single vinylheptafulvene adsorbed on the Au(111) surface can be induced by voltage pulses from the tip of a scanning tunneling microscope. This cyclization is accompanied by the elimination of HCN, as confirmed by simulations. When inducing lateral movements by applying voltage pulses with the STM tip, we observe that the response of the single molecules changes with the ring closing reaction. This behaviour is discussed by comparing the dipole moment and the charge distribution of the open and closed forms on the surface.
Preprint
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Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way towards their routine evaluation.
Article
Understanding photon-electron conversion on the nanoscale is essential for future innovations in nano-optoelectronics. In this article, based on nonequilibrium Green's function (NEGF) formalism, we develop a quantum-mechanical method for modeling energy conversion in nanoscale optoelectronic devices. The method allows us to study photoinduced charge transport and electroluminescence processes in realistic devices. First, we investigate the electroluminescence properties of a two-level model with two different treatments of inelastic scatterings. We show the regime where self-consistency between electron and photon is important for correct description of the inelastic scatterings. The method is then applied to model single-molecule junctions based on the density-functional tight-binding approach. The predicted emission spectra are found to be in very good agreement with experimental measurements. For nanostructured materials, the method is further applied to study the photoresponse of a two-dimensional graphene/graphite-C3N4 heterojunction photovoltaic device. The simulations demonstrate clearly the impact of atomistic details on the optoelectronic properties of nanodevices. This work provides a practical theoretical framework that can be applied to model and design realistic nanodevices.
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In this work, a general tight-binding based energy decomposition analysis (EDA) scheme for intermolecular interactions is proposed. Different from the earlier version [Xu et al., J. Chem. Phys. 154, 194106 (2021)], the current tight-binding based density functional theory (DFTB)-EDA is capable of performing interaction analysis with all the self-consistent charge (SCC) type DFTB methods, including SCCDFTB2/3 and GFN1/2-xTB, despite their different formulas and parameterization schemes. In DFTB-EDA, the total interaction energy is divided into frozen, polarization, and dispersion terms. The performance of DFTB-EDA with SCC-DFTB2/3 and GFN1/2-xTB for various interaction systems is discussed and assessed
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Due to their structured density of states, molecular junctions provide rich resources to filter and control the flow of electrons and phonons. Here we compute the out of equilibrium current-voltage characteristics and dissipated heat of some recently synthesized oligophenylenes (OPE3) using the Density Functional based Tight-Binding (DFTB) method within Non-Equilibrium Green's Function Theory (NEGF). We analyze the Peltier cooling power for these molecular junctions as function of a bias voltage and investigate the parameters that lead to optimal cooling performance. In order to quantify the attainable temperature reduction, an electro-thermal circuit model is presented, in which the key electronic and thermal transport parameters enter. Overall, our results demonstrate that the studied OPE3 devices are compatible with temperature reductions of several K. Based on the results, some strategies to enable high performance devices for cooling applications are briefly discussed.
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The computational prediction of the structure and stability of hybrid organic-inorganic interfaces provides important insights into the measurable properties of electronic thin film devices, coatings, and catalyst surfaces and plays an important role in their rational design. However, the rich diversity of molecular configurations and the important role of long-range interactions in such systems make it difficult to use machine learning (ML) potentials to facilitate structure exploration that otherwise requires computationally expensive electronic structure calculations. We present an ML approach that enables fast, yet accurate, structure optimizations by combining two different types of deep neural networks trained on high-level electronic structure data. The first model is a short-ranged interatomic ML potential trained on local energies and forces, while the second is an ML model of effective atomic volumes derived from atoms-in-molecules partitioning. The latter can be used to connect short-range potentials to well-established density-dependent long-range dispersion correction methods. For two systems, specifically gold nanoclusters on diamond (110) surfaces and organic π-conjugated molecules on silver (111) surfaces, we train models on sparse structure relaxation data from density functional theory and show the ability of the models to deliver highly efficient structure optimizations and semi-quantitative energy predictions of adsorption structures.
Thesis
The computational studies developed in this thesis are divided in two research projects. The first part concerns a theoretical study of luminescent polynuclear copper (I) complexes. The second chapter report computational results that are compared to experimental data obtained by C. Lescop and collaborators (ISCR - INSA Rennes) for copper dimers bridged by three diphosphines. Different levels of calculations are tested in order to quantify the accuracy of the results. The following chapter brings together the study of related metallacyclic compounds comprising respectively 6 and 8 copper atoms. These studies show the importance of the geo-metric reorganization of excited states and intermolecular interactions at the solid state. The second part of this thesis aims at providing a theoretical support to the development of molecular devices presenting high thermoelectric performance. The first chapter reports on the state of the art and the factors influencing the variation of thermoelectric properties. Chapters II and III present the theoretical tools available for the study of the transmission properties of molecular junctions and their thermoelectric characteristics. The advantages of organometallic compounds in inducing thermoelectric properties are treated in chapters IV and V. A significant increase in conductance and See-beck coefficients is calculated. A computational molecular design implies the use of cheap computational methods. The density functional tight-binding methods are evaluated for this purpose in the last chapter.
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Charge transport properties in single-walled carbon nanotubes (SWCNTs) can be significantly modified through doping, tuning their electrical and thermoelectric properties. In our study, we used more than 40 nitrogen-bearing compounds as dopants and determined their impact on the material’s electrical conductivity. The application of nitrogen compounds of diverse structures and electronic configurations enabled us to determine how the dopant nature affects the SWCNTs. The results reveal that the impact of these dopants can often be anticipated by considering their Hammett’s constants and pKa values. Furthermore, the empirical observations supported by first-principles calculations indicate that the doping level can be tuned not only by changing the type and the concentration of dopants but also by varying the orientation of nitrogen compounds around SWCNTs.
Article
In an effort to gain insight into enantiomeric transitions, their transition mechanism, time span of transitions and distribution of time spans etc., we performed molecular dynamics (MD) simulations on chiral clusters Au10, Au15 and Au18, and found that viable reaction coordinates can be deduced from simulation data for enlightening the enantiomeric dynamics for Au10 and Au15, but not so for Au18. The failure in translating the Au18-L ⇌ Au18-R transitions by MD simulations has been chalked up to the thermal energy kBT at 300 K being much lower than energy barriers separating the enantiomers of Au18. Two simulation strategies were taken to resolve this simulation impediment. The first one uses the well-tempered metadynamics MD (MMD) simulation, and the second one adeptly applies first a somewhat crude MMD simulation to locate a highly symmetrical isomer Au18S and subsequently employed it as initial configuration in the MD simulation. In both strategies, we work in collective variable space of lower dimensionality. The well-tempered MMD simulation tactic was carried out aiming to offer a direct verification of Au18 enantiomers, while the tactic to conduct MMD/MD simulations in two consecutive simulation steps was intended to provide an indirect evidence of the existence of enantiomers of Au18 given that energy barriers separating them are much higher than ca. kBT at 300 K. This second tactic, in addition to confirming indirectly Au18-L and Au18-R starting from the symmetrical cluster Au18S, the simulation results shed light also on the mechanism akin to associative/nonassociative reaction transitions.
Article
Deoxyribonucleic acid (DNA) sequencing has found wide applications in medicine including treatment of diseases, diagnosis and genetics studies. Rapid and cost-effective DNA sequencing has been achieved by measuring the transverse electronic conductance as a single-stranded DNA is driven through a nanojunction. With the aim of improving the accuracy and sensitivity of DNA sequencing, we investigate the electron transport properties of DNA nucleobases within gold nanogaps based on first-principles quantum transport simulations. Considering the fact that the DNA bases can rotate within the nanogap during measurements, different nucleobase orientations and their corresponding residence time within the nanogap are explicitly taken into account based on their energetics. This allows us to obtain an average current that can be compared directly to experimental measurements. Our results indicate that bare gold electrodes show low distinguishability among the four DNA nucleobases while the distinguishability can be substantially enhanced with sulfur atom decorated electrodes. We further optimized the size of the nanogap by maximizing the residence time of the desired orientation.
Preprint
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The harnessing of plasmon-induced hot carriers promises to open new avenues for the development of clean energies and chemical catalysis. The extraction of carriers before thermalization and recombination is of primordial importance to obtain appealing conversion yields. Here, hot carrier injection in the paradigmatic Au-TiO$_{2}$ system is studied by means of electronic and electron-ion dynamics. Our results show that pure electronic features (without considering many-body interactions or dissipation to the environment) contribute to the electron-hole separation stability. These results reveal the existence of a dynamic contribution to the interfacial potential barrier (Schottky barrier) that arises at the charge injection pace, impeding electronic back transfer. Furthermore, we show that this charge separation stabilization provides the time needed for the charge to leak to capping molecules placed over the TiO$_{2}$ surface triggering a coherent bond oscillation that will lead to a photocatalytic dissociation. We expect that our results will add new perspectives to the interpretation of the already detected long-lived hot carrier lifetimes, their catalytical effect, and concomitantly to their technological applications.
Preprint
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Due to their structured density of states, molecular junctions provide rich resources to filter and control the flow of electrons and phonons. Here we compute the out of equilibrium current-voltage characteristics and dissipated heat of some recently synthesized oligophenylenes (OPE3) using the Density Functional based Tight-Binding (DFTB) method within Non-Equilibrium Green's Function Theory (NEGF). We analyze the Peltier cooling power for these molecular junctions as function of a bias voltage and investigate the parameters that lead to optimal cooling performance. In order to quantify the attainable temperature reduction, an electro-thermal circuit model is presented, in which the key electronic and thermal transport parameters enter. Overall, our results demonstrate that the studied OPE3 devices are compatible with temperature reductions of several K. Based on the results, some strategies to enable high performance devices for cooling applications are briefly discussed.
Article
The harnessing of plasmon-induced hot carriers promises to open new avenues for the development of clean energies and chemical catalysis. The extraction of carriers before thermalization and recombination is of fundamental importance to obtain appealing conversion yields. Here, hot carrier injection in the paradigmatic Au-TiO2 system is studied by means of electronic and electron-ion dynamics. Our results show that pure electronic features (without considering many-body interactions or dissipation to the environment) contribute to the electron-hole separation stability. These results reveal the existence of a dynamic contribution to the interfacial potential barrier (Schottky barrier) that arises at the charge injection pace, impeding electronic back transfer. Furthermore, we show that this charge separation stabilization provides the time needed for the charge to leak to capping molecules placed over the TiO2 surface triggering a coherent bond oscillation that will lead to a photocatalytic dissociation. We expect that our results will add new perspectives to the interpretation of the already detected long-lived hot carrier lifetimes and their catalytical effect, and concomitantly to their technological applications.
Article
The electronic and geometrical structure of 1,4-bis(phenylethynyl)-2,5-bis(ethoxy)benzene (PEEB) molecules adsorbed on a Au(111) surface is investigated by low temperature scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) in conjunction with density-functional-based tight-binding (DFTB) simulations of the density of states and the interaction with the substrate. Our density functional theory calculations indicate that the PEEB molecule is physisorbed on the Au(111) substrate, with negligible distortion of the molecular geometry and charge transfer between molecule and substrate.
Article
The DFTB theory was combined with the isothermal Brownian‐type molecular dynamics (MD) and metadynamics molecular dynamics (MMD) algorithms to perform simulation studies for Au clusters. Two representative DFTB parametrizations were investigated. In one parametrization, the DFTB‐A, the Slater–Koster parameters in the DFTB energy function were determined focusing on the ionic repulsive energy part, Erep and the other, the DFTB‐B, due attention was paid to the electronic band‐structure energy part, Eband. Minimized structures of these two parametrizations were separately applied in MD and MMD simulations to generate unbiased and biased trajectories in collective variable (CV) space, respectively. Here, we found the MD simulations monitored at 300 K manifest fluxional characteristics in planar cluster Au9/DFTB‐A, but give no discernible tracts of fluxionality for planar Au8/DFTB‐A and Au8/DFTB‐B, for nonplanar Au10/DFTB‐A and, to some extent, for nonplanar Au9/DFTB‐B; they are plausibly being hindered by higher‐than kBT energy barriers. Very recent FIR‐MPD spectroscopy measurements, however, were reported to have detected at 300 K both the planar and nonplanar neutral Aun clusters in the size range 5 ≤ n ≤ 13. The failure of MD simulations has prompted us to apply the MMD simulation and construct the free energy landscape (FEL) in CV space. Through scrutinizing the FELs of these clusters and their associated structures, we examine the relative importance of Erep/DFTB‐A and Eband/DFTB‐B in unraveling the covalent‐like behavior of valence electrons in Aun. Most important of all, we shall evaluate the DFTB parametrization in MMD strategy through comparing extensively the simulation data recorded with the gas‐phase experimental data.
Article
Among the different mechanisms that can be used to drive a molecule on a surface by the tip of a scanning tunneling microscope at low temperature, we used voltage pulses to move azulene-based single molecules and nanostructures on Au(111). Upon evaporation, the molecules partially cleave and form metallo-organic dimers while single molecules are very scarce, as confirmed by simulations. By applying voltage pulses to the different structures under similar conditions, we observe that only one type of dimer can be controllably driven on the surface, which has the lowest dipole moment of all investigated structures. Experiments under different bias and tip height conditions reveal that the electric field is the main driving force of the directed motion. We discuss the different observed structures and their movement properties with respect to their dipole moment and charge distribution on the surface.
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Molecular rotors with controllable functions are promising for molecular machines and electronic devices. Especially, fast rotation in molecular rotor enables switchable molecular conformations and charge transport states for electronic applications. However, the key to molecular rotor-based electronic devices comes down to a trade-off between fast rotational speed and thermal stability. Fast rotation in molecular rotor requires a small energy barrier height, which disables its controllability under thermal excitation at room temperature. To overcome this trade-off dilemma, we design molecular rotors with co-axial polar rotating groups to achieve wide-range mechanically controllable rotational speed. The interplay between polar rotating groups and directional mechanical load enables a “stop-go” system with a wide-range rotational energy barrier. We show through density functional calculations that directional mechanical load can modulate the rotational speed of designed molecular rotors. At a temperature of 300 K, these molecular rotors operate at low rotational speed in native state and accelerates tremendously (up to 10 ¹⁹ ) under mechanical load.
Thesis
L’interface M-thiol(ate) composant la surface de nanoparticules cristallines d’Or ou d’Argent a été étudiée à l’aide d’outils de la chimie quantique (DFT,QTAIM,ELF,NBO) à deux échelles différentes : d’un agrégat pyramidal M20 (modèle des bords et de défauts des nanoparticules), et de surfaces périodiques (111) et (100), en interaction avec un ligand méthyle thiol ou un radical méthyle thiolate. Après la mise en place d’une procédure permettant pour la première fois une analyse topologique quantitative fiable sur des systèmes périodiques traités en ondes planes, il a été montré que : MeSH se physisorbe systématiquement en position « Top », une liaison dative se formant entre le soufre et un atome métallique, accompagnée d’un mécanisme de transfert de charge complexe ; MeS se chimisorbe principalement en position pontée, une compétition se produisant entre la récupération d’un électron conduisant à MeS- et la formation de 2 liaisons datives accompagnées d’un transfert de charge S->M ; les liaisons Au-S sont toujours plus fortes que les liaisons Ag-S, induit par les effets relativistes de l’Or. Un champ de force réactif Ag-thiolate a été optimisé par une méthode d’apprentissage supervisé, et reproduit correctement les sites et énergies d’adsorption. Il a permis la comparaison avec des modèles existants Au-thiolate et d’envisager des simulations de nanoparticules complètes.
Article
A recently developed modified basin hopping (MBH) optimization algorithm, combined with an energy function calculated by the semiempirical density functional tight-binding (DFTB) theory, was applied to determine the lowest-energy structures of Au n clusters with size n = 3-20. It was predicted from the DFTB/MBH optimization algorithm calculations that clusters Au10, Au15, and Au18 exhibit chiral properties; i.e., each of these three clusters possesses the same energy value and associated with it are two nonsuperposable mirror-image clusters. In the potential energy landscape, there thus exist multidimensional barriers separating the two enantiomers, and this lowest-energy double-well morphology is surrounded by potential-energy minima of higher energies. In this paper, we have chosen to study the chiral cluster Au15 by employing an isothermal Brownian-type molecular dynamics simulation to discern in greater detail its conformational transition from one enantiomer, say left, to its right counterpart. To facilitate our analysis of the simulation data, we transpose the multidimensional configurational space description to a lower dimensional collective variable (CV) space spanned by two geometry-relevant CVs. The thermally driven progression and mechanism of enantiomeric transitions between the left and right enantiomers will be our main focus, and the strategy is to dissect the time development of the CVs collected from different sets of independent simulation runs. From simulation data, we found that an understanding of the dynamics of enantiomeric transitions needs first to seek out the left and right enantiomers through a molecular modeling and visualizing program, then to ferret out and identify between the left and right enantiomers a symmetrical structure, and finally to define from the latter a reaction coordinate. We showed in this work that this single reaction coordinate is predictive in unraveling the left ⇌ right enantiomeric transition events, providing a specific inkling of the transition time span and its associated distribution which can be checked further for its reasonableness by the autocorrelation function and a vibrational analysis, all of which shed light on the mechanisms of transition.
Article
A new reactive force field based on the ReaxFF formalism is effectively parametrized against an extended training set of quantum chemistry data (containing more than 120 different structures) to describe accurately silver- and silver-thiolate systems. The results obtained with this novel representation demonstrate that the novel ReaxFF paradigm is a powerful methodology to reproduce more appropriately average geometric and energetic properties of metal clusters and slabs when compared to the earlier ReaxFF parametrizations dealing with silver and gold. ReaxFF cannot describe adequately specific geometrical features such as the observed shorter distances between the under-coordinated atoms at the cluster edges. Geometric and energetic properties of thiolates adsorbed on a silver Ag20 pyramid are correctly represented by the new ReaxFF and compared with results for gold. The simulation of self-assembled monolayers of thiolates on a silver (111) surface does not indicate the formation of staples in contrast to the results for gold-thiolate systems.
Article
We report the first-hyperpolarizability, β(-2ω; ω,ω), of gold nanoclusters Au6(GSH)2(MPA)2 having six gold atoms capped by 3-mercaptopropionic acid (MPA) and glutathione (GSH) that is unprecedented. Here, we used the concentration of 2.1×10¹⁶ nanoclusters/mL to determine β(-2ω; ω,ω) applying the hyper-Rayleigh scattering technique by using a 1064 nm laser and analyzing the scattered light at 532 nm. The measured hyperpolarizability is found to be β(-2ω; ω,ω) =760×10⁻³⁰ esu which corresponds to ≈127× 10⁻³⁰ esu per gold atom. The static hyperpolarizability, β(0) = 52×10⁻³⁰ esu per gold atom, was determined by using a two-level model approximation. The large β(-2ω; ω,ω) is attributed to quantum confinement effect and the geometry of the nanoclusters that have no inversion symmetry. Preliminary computer calculations based on the DFT method were performed and the numerical results present the same order of magnitude than the experimental values.
Article
Semiempirical quantum mechanical (SEQM) methods offer an attractive middle ground between fully ab initio quantum chemistry and force-field simulations, allowing for a quantum mechanical treatment of the system at a relatively low computational cost. However, SEQM methods have not been frequently utilized in the study of transition metal systems, mostly due to the difficulty in obtaining reliable parameters. This paper examines the accuracy of the PM6 and PM7 semiempirical methods to predict geometries, ionization potentials, and HOMO-LUMO energy gaps of several bare gold clusters (Au n ) and thiolate-protected gold nanoclusters (AuSNCs). Contrary to PM6, the PM7 method can predict qualitatively correct geometries and ionization potentials when compared to DFT. PM6 fails to predict the characteristic gold core and gold-sulfur ligand shell (staple motifs) of the AuSNC structures. Both the PM6 and PM7 methods overestimate the HOMO-LUMO gaps. Overall, PM7 provides a more accurate description of bare gold and gold-thiolate nanoclusters than PM6. Nevertheless, refining the gold parameters could help achieve better quantitative accuracy.
Article
Graphene nanoribbons (GNRs) with atomically precise heterojunction interfaces are exploited as nanoscale light emitting devices with modulable emission frequencies. By connecting GNRs with different widths and lengths, topological boundary states can be formed and manipulated. Using first-principles-based atomistic simulations, we studied the luminescence properties of a STM GNR junction and explore the applications of these topological states as nanoscale light sources. Taking advantage of the ultrahigh resolution of STM tip, direct injection of high energy carriers at selected boundary states can be achieved. In this way, emission color can be controlled by precisely changing the tip position. The GNR heterojunction can therefore represent a robust and controllable light-emitting device that takes a step forward towards the fabrication of nanoscale graphene-based optoelectronic devices.
Article
We report the results of a study of the isomeric thiolate monolayer capping of two gold nanocluster molecules, namely Au92 and Au102 , both protected by 44 4-tert-butylbenzene thiolate (TBBT) ligands. The finding of an isomeric monolayer of the same ligand in a series of metal nanocluster molecules in this large size range, is unprecedented. Au92 and Au102 possess entirely different structures and properties. The Au92 has an 84 atom face centered cubic (FCC) core whereas Au102 has a 79 atom Marks-decahedral core. Nevertheless, despite the metal core structural diversity and the complexities of the interfacial staples, both of these have the same number of ligands. The Au92 core is protected by 28 bridging ligands and 8 monomeric staple motifs whereas Au102 is protected by 19 monomeric and 2 dimeric staple motifs. The Au92 and Au102 cores have cuboidal and globular structures, respectively. As a result, Au92 has longer {100} facets and exhibits c(2x2) monolayer arrangement for bridging ligands similar to what has been observed on {100} facets of bulk gold, whereas Au102 has only staple motifs. We prepared the Au102 in TBBT series using a ligand-exchange-based approach and characterized them by mass spectrometry and UV-Vis spectroscopy. Mass spectrometry revealed that the compound has a mixture of isoelectronic species with the formula of Au102(TBBT)44, Au103(TBBT)45, and Au104(TBBT)46. Concurrent first-principles electronic structure computational studies provide insights into the stability and nature of these two isomeric-monolayer capped gold nanomolecules.
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In the last decades, theoretical and experimental studies of nanostructured materials have gathered the efforts of a big slice of the scientific community. Light-nanostructure interaction has been a preponderant research topic fueled by the interest in the plasmonic properties of metallic nanostructures. More recently, the study of plasmon-induced hot carrier generation has drawn the attention of scientists because of their potential application in optoelectronics, photovoltaics and photocatalysis. In this contribution, we study the real-time electronic dynamics associated with the generation of hot carriers in silver and gold nanoparticles focusing on its energy distribution and atomic shell population/depopulation dynamics. Revisiting our previous results from the perspective of a generalized 2d correlation analysis paves the way to disentangle complex dynamic outcomes, like the dissipation of the sp-band energy absorbed during plasmonic excitation. We show that this mechanism is founded in the dynamic cross-correlation between sp-band and d-band electronic populations.
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Analytical expressions are derived for the evaluation of energy gradients in the zeroth order regular approximation (ZORA) to the Dirac equation. The electrostatic shift approximation is used to avoid gauge dependence problems. Comparison is made to the quasirelativistic Pauli method, the limitations of which are highlighted. The structures and first metal-carbonyl bond dissociation energies for the transition metal complexes W(CO)6, Os(CO)5, and Pt(CO)4 are calculated, and basis set effects are investigated. © 1999 American Institute of Physics.
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We extend an approximate density functional theory DFT method for the description of long-range dispersive interactions which are normally neglected by construction, irrespective of the correlation function applied. An empirical formula, consisting of an R 6 term is introduced, which is appropriately damped for short distances; the corresponding C 6 coefficient, which is calculated from experimental atomic polarizabilities, can be consistently added to the total energy expression of the method. We apply this approximate DFT plus dispersion energy method to describe the hydrogen bonding and stacking interactions of nucleic acid base pairs. Comparison to MP2/6-31G*0.25 results shows that the method is capable of reproducing hydrogen bonding as well as the vertical and twist dependence of the interaction energy very accurately. © 2001 American Institute of Physics.
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We present an efficient scheme for calculating the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrices will be discussed. Our approach is stable, reliable, and minimizes the number of order N-atoms(3) operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special ''metric'' and a special ''preconditioning'' optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent calculations. It will be shown that the number of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order N-atoms(2) scaling is found for systems up to 100 electrons. If we take into account that the number of k points can be implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable.
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Over the last three decades, self-assembled molecular films on solid surfaces have attracted widespread interest as an intellectual and technological challenge to chemists, physicists, materials scientists, and biologists. A variety of technological applications of nanotechnology rely on the possibility of controlling topological, chemical, and functional features at the molecular level. Self-assembled monolayers (SAMs) composed of chemisorbed species represent fundamental building blocks for creating complex structures by a bottom-up approach. These materials take advantage of the flexibility of organic and supramolecular chemistry to generate synthetic surfaces with well-defined chemical and physical properties. These films already serve as structural or functional parts of sensors, biosensors, drug-delivery systems, molecular electronic devices, protecting capping for nanostructures, and coatings for corrosion protection and tribological applications.
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The formal relationship between ultrasoft (US) Vanderbilt-type pseudopotentials and Blöchl's projector augmented wave (PAW) method is derived. It is shown that the total energy functional for US pseudopotentials can be obtained by linearization of two terms in a slightly modified PAW total energy functional. The Hamilton operator, the forces, and the stress tensor are derived for this modified PAW functional. A simple way to implement the PAW method in existing plane-wave codes supporting US pseudopotentials is pointed out. In addition, critical tests are presented to compare the accuracy and efficiency of the PAW and the US pseudopotential method with relaxed core all electron methods. These tests include small molecules (H2, H2O, Li2, N2, F2, BF3, SiF4) and several bulk systems (diamond, Si, V, Li, Ca, CaF2, Fe, Co, Ni). Particular attention is paid to the bulk properties and magnetic energies of Fe, Co, and Ni.
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In this paper we propose an extension of the self-consistent charge-density-functional tight-binding (SCC-DFTB) method [M. Elstner et al., Phys. Rev. B 58, 7260 (1998)], which allows the calculation of the optical properties of finite systems within time-dependent density-functional response theory (TD-DFRT). For a test set of small organic molecules low-lying singlet excitation energies are computed in good agreement with first-principles and experimental results. The overall computational cost of this parameter-free method is very low and thus it allows us to examine large systems: we report successful applications to C60 and the polyacene series.
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We present a systematically improvable density fitting scheme designed for accurate Coulomb potential evaluation of periodic and molecular systems. The method does not depend on the way the density is calculated, allowing for a basis set expansion as well as a numerical representations of the orbitals. The scheme is characterized by a partitioning of the density into local contributions that are expanded by means of cubic splines. For three-dimensional periodic systems, the long-range contribution to the Coulomb potential is treated with the usual reciprocal space representation of the multipole moments, while in one- and two-dimensional systems, it is calculated via a new algorithm based on topological extrapolation. The efficiency and numerical robustness of the scheme is assessed for a number of periodic and nonperiodic systems within the framework of density-functional theory.
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The Density Functional Tight Binding (DFTB) and Time Dependent DFTB (TD-DFTB) methods have been coupled with the Polarizable Continuum Model (PCM) of solvation, aiming to study spectroscopic properties for large systems in condensed phases. The calculation of the ground and the excited state energies, together with the analytical gradient and Hessian of the ground state energy, have been implemented in a fully analytical and computationally effective approach. After sketching the theoretical background of both DFTB and PCM, we describe the details of both the formalism and the implementation. We report a number of examples ranging from vibrational to electronic spectroscopy, and we identify the strengths and the limitations of the DFTB/PCM method. We also evaluate DFTB as a component in a hybrid approach, together with a more refined quantum mechanical (QM) method and PCM, for the specific case of anharmonic vibrational spectra.
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In this work, we present binding energies of acetic acid on the (110), (100), and (011) surfaces of rutile TiO2 calculated with the two density functional theory (DFT) exchange-correlation functionals PBE and PBEsol. It is shown that the binding energies can be influenced, in this case slightly reduced for all three surfaces, via preadsorption of hydrogen. Additionally, we tested the performance of the density-functional based tight-binding (DFTB) method applied to these adsorbate systems. Analysis of the electronic density of states shows that DFTB provides qualitatively comparable results to DFT calculations as long as the Fermi energy level remains within the band gap.
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We investigate magnetic and structural properties of iron clusters up to Fe 32, well extending into the size range accessible by experiment. A density-functional based tight-binding scheme fully incorporating the effects of spin polarisation and charge transfer in a self-consistent manner has been used. The potential hypersurfaces have been scanned by an unconstrained search using a genetic algorithm. Results for smaller clusters up to Fe 17 are validated against more sophisticated density functional theory calculations. Our magnetic moment data show a strong change around Fe 13 being unique in this size range. For the larger cluster sizes a smooth decrease of the clusters average spin magnetic moments is found in good agreement with experimental data.
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In this work, we review recent extensions of the density functional tight binding (DFTB) methodology and its application to organic and biological molecules. DFTB denotes a class of computational models derived from density functional theory (DFT) using a Taylor expansion around a reference density. The first- and second-order models, DFTB1 and DFTB2, have been reviewed recently (WIREs Comput Mol Sci 2012, 2:456–465). Here, we discuss the extension to third order, DFTB3, which in combination with a modification of the Coulomb interactions in the second-order formalism and a new parametrization scheme leads to a significant improvement of the overall performance. The performance of DFTB2 and DFTB3 for organic and biological molecules are discussed in detail, as well as problems and limitations of the underlying approximations. WIREs Comput Mol Sci 2014, 4:49–61. doi: 10.1002/wcms.1156 The authors have declared no conflicts of interest in relation to this article. For further resources related to this article, please visit the WIREs website.
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The adsorption of multivalent thiols on gold (111) surface was investigated using density functional theory applying the Perdew-Burke-Ernzerhof functional. Through the comparison of differences in energetics, structure and charge density distribution of a set of monodentate and polydentate thiols, we have described in detail the factors affecting the adsorption energy and the role played by the multivalence, which causes a decreasing of adsorption energy because of both electronic and steric hindrance effects. Finally, the comparison between the adsorption of 1,2- and 1,3-disulfides revealed how the chain length may affect the cleavage of the SS bond when they adsorb on Au(111) surface. © 2013 Wiley Periodicals, Inc.
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We have performed ion mobility measurements on gold cluster cations Aun+ generated by pulsed laser vaporization. For clusters with n<14, experimental cross sections are compared with theoretical results from density functional calculations. This comparison allows structural assignment. We find that room temperature gold cluster cations have planar structures for n=3–7. Starting at n=8 they form three dimensional structures with (slightly distorted) fragments of the bulk phase structure being observed for n=8–10.
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Small gold clusters Aum (m ≤ 16) were analyzed step by step using the density functional theory at B3LYP level with a Lanl2DZ pseudopotential to understand the rules governing the structures obtained for the most stable clusters. After a characterization by means of the NBO population analysis and spin densities, the particular electronic structure of such species was confronted to their structural parameters and stability. It appears that the most stable structures can be described in an original way through resonance structures resulting from an analysis of Aum clusters into dimeric Au2 subunits. These are arranged so as to promote: 1. A good overlap between bonding σ and anti-bonding σ* areas belonging to different Au2 units. 2. A cyclic flow of electrons over the whole cluster. This model uses relatively simple chemical concepts in order to justify most of the structures already found in the literature as well as to establish a new approach explaining the structural transition from two- to three-dimensional configurations.
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The prolate-to-spherical shape transition in GroupIV clusters has been a puzzle since its discovery over a decade ago. Here we explain this phenomenon by elucidating the structures of Sin and Si+n with n=20 27. The geometries were obtained in unbiased searches using a new big bang'' optimization method. They are substantially more stable than any found to date, and their ion mobilities and dissociation energies are in excellent agreement with experiment. The present results prove that the packing of midsize clusters is thermodynamically controlled and open the door to understanding the evolution of semiconductor nanosystems towards the bulk.
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The formation of gold-thiolate nanoparticles via oxidation of gold clusters by thiols is examined in this work. Using the BP86 density functional with a triple ζ basis set, the adsorption of methylthiol onto various gold clusters Aun(Z) (n = 1-8, 12, 13, 20; Z = 0, -1, +1) and Au38(4+) is investigated. The rate-limiting step for the reaction of one thiol with the gold cluster is the dissociation of the thiol proton; the resulting hydrogen atom can move around the gold cluster relatively freely. Addition of a second thiol can lead to H2 formation and the generation of a gold-thiolate staple motif.
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In this article, we document a new implementation of the fuzzy cells scheme for numerical integration in polyatomic systems [Becke, J. Chem. Phys. 1998, 88, 2547] and compare its efficiency and accuracy with respect to an integration scheme based on the Voronoi space partitioning. We show that the accuracy of both methods is comparable, but that the fuzzy cells scheme is better suited for geometry optimization. For this method, we also introduce the locally dense grid concept and present a proof-of-concept application. © 2013 Wiley Periodicals, Inc.
Article
The time-dependent density functional based tight-binding (TD-DFTB) approach is generalized to account for fractional occupations. In addition, an on-site correction leads to marked qualitative and quantitative improvements over the original method. Especially, the known failure of TD-DFTB for the description of \sigma -> \pi* and n -> \pi* excitations is overcome. Benchmark calculations on a large set of organic molecules also indicate a better description of triplet states. The accuracy of the revised TD-DFTB method is found to be similar to first principles TD-DFT calculations at a highly reduced computational cost. As a side issue, we also discuss the generalization of the TD-DFTB method to spin-polarized systems. In contrast to an earlier study [Trani et al., JCTC 7 3304 (2011)], we obtain a formalism that is fully consistent with the use of local exchange-correlation functionals in the ground state DFTB method.
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We present GW calculations for small and large gap systems comprising typical semiconductors (Si, SiC, GaAs, GaN, ZnO, ZnS, CdS, and AlP), small gap semiconductors (PbS, PbSe, and PbTe), insulators (C, BN, MgO, and LiF), and noble gas solids (Ar and Ne). It is shown that the G0W0 approximation always yields too small band gaps. To improve agreement with experiment, the eigenvalues in the Green’s function G (GW0) and in the Green’s function and the dielectric matrix (GW) are updated until self-consistency is reached. The first approximation leads to excellent agreement with experiment, whereas an update of the eigenvalues in G and W gives too large band gaps for virtually all materials. From a pragmatic point of view, the GW0 approximation thus seems to be an accurate and still reasonably fast method for predicting quasiparticle energies in simple sp-bonded systems. We furthermore observe that the band gaps in materials with shallow d states (GaAs, GaN, and ZnO) are systematically underestimated. We propose that an inaccurate description of the static dielectric properties of these materials is responsible for the underestimation of the band gaps in GW0, which is itself a result of the incomplete cancellation of the Hartree self-energy within the d shell by local or gradient corrected density functionals.
Article
A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold–gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold–gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold–gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge, and face-centered sites; sites in the first subsurface layer show still small positive shifts. © 1997 American Institute of Physics.
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We outline details about an extension of the tight-binding (TB) approach to improve total energies, forces, and transferability. The method is based on a second-order expansion of the Kohn-Sham total energy in density-functional theory (DFT) with respect to charge density fluctuations. The zeroth order approach is equivalent to a common standard non-self-consistent (TB) scheme, while at second order a transparent, parameter-free, and readily calculable expression for generalized Hamiltonian matrix elements may be derived. These are modified by a self-consistent redistribution of Mulliken charges (SCC). Besides the usual band structure'' and short-range repulsive terms the final approximate Kohn-Sham energy additionally includes a Coulomb interaction between charge fluctuations. At large distances this accounts for long-range electrostatic forces between two point charges and approximately includes self-interaction contributions of a given atom if the charges are located at one and the same atom. We apply the new SCC scheme to problems where deficiencies within the non-SCC standard TB approach become obvious. We thus considerably improve transferability.
Article
The LCAO, or Bloch, or tight binding, approximation for solids is discussed as an interpolation method, to be used in connection with more accurate calculations made by the cellular or orthogonalized plane-wave methods. It is proposed that the various integrals be obtained as disposable constants, so that the tight binding method will agree with accurate calculations at symmetry points in the Brillouin zone for which these calculations have been made, and that the LCAO method then be used for making calculations throughout the Brillouin zone. A general discussion of the method is given, including tables of matrix components of energy for simple cubic, face-centered and body-centered cubic, and diamond structures. Applications are given to the results of Fletcher and Wohlfarth on Ni, and Howarth on Cu, as illustrations of the fcc case. In discussing the bcc case, the splitting of the energy bands in chromium by an antiferromagnetic alternating potential is worked out, as well as a distribution of energy states for the case of no antiferromagnetism. For diamond, comparisons are made with the calculations of Herman, using the orthogonalized plane-wave method. The case of such crystals as InSb is discussed, and it is shown that their properties fit in with the energy band picture.
Article
The adsorption energetics of methanethiolate and benzenethiolate on Au(111) have been calculated using periodic density functional theory (DFT), based on the SIESTA methodology, with an internal coordinates implementation for geometry input and structure optimisation. Both molecules are covalently bound with interaction energies of 1.85 and 1.43 eV for methanethiolate and benzenethiolate, respectively. The preferred binding site is slightly offset from the bridge site in both cases towards the fcc-hollow. The potential energy surfaces (PES) have depths of 0.36 and 0.22 eV, the hollow sites are local maxima in both cases, and there is no barrier to diffusion of the molecule at the bridge site. The corresponding dimers are weakly bound for methanethiolate and benzenethiolate, with binding energies of 0.38 and 0.16 eV, respectively, and the preferred binding geometry is with the two sulphur atoms close to adjacent atop sites. The barrier to dissociation of the dimer dimethyl disulphide is estimated to lie between 0.3 and 0.35 eV.
Article
a b s t r a c t A theoretical study based on periodic DFT calculations of the structure, the surface bonding, and the ener-getics of butanethiols adsorbed on the Au(1 1 1) surface is reported. Several sites and coverage have been considered, and neutral and charged metal surfaces have been simulated. Whatever the coverage is, the preferred site is a hollow-bridge type-site in which sulfur atom simultaneously binds to two gold atoms. Thiol adsorption parameters are sensitive to the coverage, especially the adsorption energy that shows a clear response to the number of thiols adsorbed, and the thiol-surface interaction decreases when the coverage grows as the lateral repulsion between the alkyl tails weaken the strength of the Au-S bond. The thiol-surface interaction parameters are also sensitive to the charge of the metal. Also, we found that the adsorption becomes more favorable when the metal surface is negatively charged, and less favorable on positive surfaces. Finally, in order to analyze dynamical effects, we performed a molecular dynamics (MD) simulation considering a system with ethanethiol on an Au slab pre-covered by water. The MD sim-ulation shows that the proton transfer occurs within a few femtoseconds and that prior to the transfer itself, the sulfur atom binds to a gold surface atom. This Au atom is clearly pulled out of the surface, what could be interpreted as the onset of the islands and cluster formation already observed in the low cover-age regime.
Article
We investigated the formation and stability of layers of methylthiolate prepared on the Au(111) surface by the method of immersion in an ethanolic solution of dimethyl disulfide (DMDS). The surface species were characterized by electrochemical reductive desorption and high-resolution photoelectron spectroscopy. Both techniques confirmed the formation of a methylthiolate monolayer at short immersion times (around 1 min). As the immersion time increased, the electrochemical experiments showed the disappearance of the methylthiolate reductive desorption current peak and the appearance of a current peak at ca. −0.9 V which was attributed to sulfur species. At long immersion times, the XPS measurements showed two main components for the S 2p signal: a component at ca. 161 eV which corresponds to atomic sulfur and a component at ca. 162 eV which we attributed to polysulfide species. We propose that the breakage of the S−C bond of methylthiolate is responsible for the appearance of sulfur species on the surface. Density functional theory (DFT) calculations were performed to identify the elementary steps that may lead to the decomposition of methylthiolate. We found that the cleavage of the S−C bond is only activated by the oxidative dehydrogenation of the methyl group of methylthiolate. Thio-oxymethylene, SCH2O, is the key intermediate leading to the breakage of the S−C bond because it decomposes into atomic sulfur and formaldehyde with an activation energy barrier of only 1.1 kcal/mol.
Article
A quantum mechanical/molecular mechanical (QM/MM) approach based on an approximate density functional theory, the so-called self-consistent charge density functional tight binding (SCC-DFTB) method, has been implemented in the CHARMM program and tested on a number of systems of biological interest. In the gas phase, SCC-DFTB gives reliable energetics for models of the triosephosphate isomerase (TIM) catalyzed reactions. The rms errors in the energetics compared to B3LYP/6-31+G(d,p) are about 2−4 kcal/mol; this is to be contrasted with AM1, where the corresponding errors are 9−11 kcal/mol. The method also gives accurate vibrational frequencies. For the TIM reactions in the presence of the enzyme, the overall SCC-DFTB/CHARMM results are in somewhat worse agreement with the B3LYP/6-31+G(d,p)/CHARMM values; the rms error in the energies is 5.4 kcal/mol. Single-point B3LYP/CHARMM energies at the SCC-DFTB/CHARMM optimized structures were found to be very similar to the full B3LYP/CHARMM values. The relative stabilities of the αR and 310 conformations of penta- and octaalanine peptides were studied with minimization and molecular dynamics simulations in vacuum and in solution. Although CHARMM and SCC-DFTB give qualitative different results in the gas phase (the latter is in approximate agreement with previous B3LYP calculations), similar behavior was found in aqueous solution simulations with CHARMM and SCC-DFTB/CHARMM. The 310 conformation was not found to be stable, and converted to the αR form in about 15 ps. The αR conformation was stable in the simulation with both SCC-DFTB/CHARMM and CHARMM. The i,i+3 CO···HN distances in the αR conformation were shorter with the SCC-DFTB method (2.58 Å) than with CHARMM (3.13 Å). With SCC-DFTB/CHARMM, significant populations with i,i+3 CO···HN distances near 2.25 Å, particularly for the residues at the termini, were found. This can be related to the conclusion from NMR spectroscopy that the 310 configuration contributes for alanine-rich peptides, especially at the termini.
Article
How thiols and disulfides bind to gold surfaces to form self-assembled monolayers is a long-standing open question. In particular, determining the nature itself of the anchor groups and of their interaction with the metal is a priority issue, which has so far been approached only with oversimplified models. We present ab initio calculations of the adsorption configurations (dissociative and not) of methanethiol and dimethyl disulfide on Au(111) at low coverage, which are based on density functional theory using gradient-corrected exchange-correlation functionals. A complete characterization of their structure, binding energies, and type of bonding is obtained. It is established that dissociation is clearly favored for the disulfide with subsequent formation of strongly bound thiolates, in agreement with experimental evidence, whereas thiolates resulting from S−H bond cleavage in thiols can coexist with the adsorbed “intact” species and become favored if accompanied by the formation of molecular hydrogen.
Article
A new self-consistent-charge density-functional tight-binding (SCC-DFTB) set of parameters for Ti−X pairs of elements (X = Ti, H, C, N, O, S) has been developed. The performance of this set has been tested with respect to TiO2 bulk phases and small molecular systems. It has been found that the band structures, geometric parameters, and cohesive energies of rutile and anatase polymorphs are in good agreement with the reference DFT data and with experiment. Low-index rutile and anatase surfaces were also tested. For molecular systems, binding and atomization energies close to their DFT analogues have been achieved. Large errors, however, have been found for systems in high-spin states and/or having multireference character of their wave functions. The correct performance of SCC-DFTB for surface reactions has been demonstrated via the water splitting on anatase (001) surface. The current SCC-DFTB set is a suitable tool for future in-depth investigation of chemical processes occurring on the surfaces of TiO2 polymorphs as well as for other processes of physicochemical interest.
Article
A new method is described to evaluate integrals of quadratically interpolated functions over the three-dimensional Brillouin zone. The method is based on the method of the authors for analytic quadratic integration over the two-dimensional Brillouin zone. It uses quadratic interpolation not only for the dispersion relation epsilon (k), but for property functions f(k) as well. The method allows a 'machine accuracy' evaluation of the integrals and may therefore be regarded as equivalent to a truly analytic evaluation of the integrals. It is compared to other methods of integral approximation by calculating tight-binding Brillouin zone integrals using the same number of k-points for all methods. Also shown are cohesive energy calculations for a number of elements. When the quadratic method is compared to the commonly used linear method, it is found that far fewer k-points are needed to obtain a desired accuracy.
Article
An approach for electronic structure calculations is described that generalizes both the pseudopotential method and the linear augmented-plane-wave (LAPW) method in a natural way. The method allows high-quality first-principles molecular-dynamics calculations to be performed using the original fictitious Lagrangian approach of Car and Parrinello. Like the LAPW method it can be used to treat first-row and transition-metal elements with affordable effort and provides access to the full wave function. The augmentation procedure is generalized in that partial-wave expansions are not determined by the value and the derivative of the envelope function at some muffin-tin radius, but rather by the overlap with localized projector functions. The pseudopotential approach based on generalized separable pseudopotentials can be regained by a simple approximation.
Article
The 20-nanogold cluster Au20 exhibits a large variety of two- and three-dimensional isomeric forms. Among them is the ground-state isomer Au20(Td) representing the stable cluster with a unique tetrahedral shape, with all atoms on the surface, and large HOMO-LUMO gap which even slightly exceeds that of the buckyball fullerene C60. The anionic cluster Au(Td) that holds its parent tetrahedral symmetry features a high catalytic activity. The list of the properties of the 20-nanogold clusters surveyed in the present work ranges from the energetic order of stability of its isomers to the optical absorption and excitation spectra of the Au20(Td) cluster. We also report the structures and properties of its doubly charged clusters Au and Au and computationally confirm that Au is indeed stable. The zero-point-energy-corrected adiabatic second electron affinity of Au20(Td) amounts to 0.43–0.53 eV that is consistent with the experimental data. In addition, we provide computational evidence of the existence of the novel, hollow cage isomer of Au20 and analyze its key properties. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Article
A hybrid quantum mechanical (QM) and molecular mechanical (MM) approach has been developed and used to study the aqueous solvation effect on biological systems. The self-consistent charge density functional tight-binding (SCC-DFTB) method is employed to perform the quantum mechanical calculations in the QM part, while the AMBER 4.1 force field is used to perform the molecular mechanical calculations in the MM part. The coupling terms between these two parts include electrostatic and van der Waal's interactions. As a test of feasibility, this approach has been first applied to some small systems H-bonded with water molecule(s), and very good agreement with the ab initio results has been achieved. The hybrid potential was then used to investigate the solvation effect on the capped (L-Ala)n helices with n=4, 5, 8 and 11. (L-Ala)n was treated with the SCC-DFTB method and the water molecules with the TIP3P water model. It has been shown that, in gas phase, the α helices of (L-Ala)n are less stable than the corresponding 310 helices. In water solution, however, the α helices are stabilized and, compared with 310 helices, the α helices have stronger charge–charge interactions with the surrounding water molecules. This may be explained by the larger dipole moment of α helices in aqueous solution, which will influence and organize the orientations of the surrounding water molecules. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 459–479, 2000
Article
Gold nanoparticles typically have a metallic core, and the electronic conduction band consists of quasicontinuous energy levels (i.e. spacing δ ≪ kBT, where kBT is the thermal energy at temperature T (typically room temperature) and kB is the Boltzmann constant). Electrons in the conduction band roam throughout the metal core, and light can collectively excite these electrons to give rise to plasmonic responses. This plasmon resonance accounts for the beautiful ruby-red color of colloidal gold first observed by Faraday back in 1857.