Computing the Properties of Materials from First Principles with SIESTA

Polar Polymorphism: A New Intermediate Structure toward the Thin-Film Phase in Asymmetric Benzothieno[3,2-b][1]-benzothiophene Derivatives

Understanding structure and polymorphism is relevant for any organic device optimization, and it is of particular relevance in 7-decyl-2-phenyl[1]benzothieno[3,2-b][1]benzothiophene (Ph-BTBT-10) since high carrier mobility in Ph-BTBT-10 thin films has been linked to the structural transformation from the metastable thin-film phase to the thermodynamically stable bilayer structure via thermal annealing. We combine here a systematic nanoscale morphological analysis with local Kelvin probe force microcopy (KPFM) that demonstrates the formation of a polar polymorph in thin films as an intermediate structure for thicknesses lower than 20 nm. The polar structure develops with thickness a variable amount of structural defects in the form of individual flipped molecules (point defects) or sizable polar domains, and evolves toward the reported nonpolar thin-film phase. The direct experimental evidence is supported by electronic structure density functional theory calculations. The structure of the film has dramatic effects on the electronic properties, leading to a decrease in the film work function (by up to 1 eV) and a considerable broadening of the occupied molecular orbitals, attributed to electrostatic disorder. From an advanced characterization point of view, KPFM stands out as a valuable tool for evaluating electrostatic disorder and the conceivable emergence of polar polymorphs in organic thin films. The emergence of polar assemblies introduces a critical consideration for other asymmetric BTBT derivatives, which may be pivotal to understanding the structure-property relationships in organic field-effect transistors (OFETs). A precise determination of any polar assemblies close to the dielectric interface is critical for the judicious design and upgrading of high-performance OFETs.

Accelerated Deep Learning Dynamics for Atomic Layer Deposition of Al(Me)3 and Water on OH/Si(111)

Knowledge of the detailed mechanism behind the atomic layer deposition (ALD) can greatly facilitate the optimization of the manufacturing process. Computational modeling can potentially foster the understanding; however, the presently available capabilities of the accurate ab initio computational techniques preclude their application to modeling surface processes occurring on a long time scale, such as ALD. Although the situation can be greatly improved using machine learning (ML), this technique requires an enormous amount of data for training datasets. Here, we propose an iterative protocol for optimizing ML training datasets and apply ML-assisted ab initio calculations to model surface reactions occurring during the Al(Me)₃/H₂O ALD process on the OH-terminated Si (111) surface. The protocol uses a recently developed low-dimensional projection technique (TDUS), greatly reducing the amount of information required to achieve high accuracy (ca. 1 kcal/mol or less) of the developed ML models. The resulting free energy landscapes reveal fine details of various aspects of the target ALD process, such as the surface proton transfer, zwitterionic surface configurations, elimination-addition/addition-elimination, and S_N2 reactions as well as the role of the surface entropic and temperature effects. Simulations of adsorption dynamics predict that the maximum physisorption rate of ca. 70% is achieved at the incidence velocity u_rms of the reactants in the range of 15-20 Å/ps. Hence, the proposed protocol furnishes a very effective tool to study complex chemical reaction dynamics at a much reduced computational cost.

Prediction of the near-IR spectra of ices by ab initio molecular dynamics

Use of ab initio molecular dynamics to predict the near-IR spectra of ices and application to astronomical models.

Simulations and spectra of water in CO matrices

Models for the inclusion of water molecules in carbon monoxide matrices are developed using density functional theory applied to amorphous solid systems. The models cover a large range of systems for smaller or larger CO matrices with different water content, consisting of either individual H₂O molecules or small clusters linked by H-bonds. The vibrational spectra of the samples are predicted at the minimum of their potential energy surface. The spectra allow instances where the water molecules remain isolated or form aggregates to be discerned, and they also provide an indication of the strength of the H-bonding, when present. The calculations support recent experimental observations that linked IR bands at 3707 cm^-1 and 3617 cm^-1 to the presence of unbound water molecules in water-poor CO/H₂O mixed ices. Assignment of some observed bands to water dimers or trimers is suggested as well. The residual static pressure in fixed-volume simulation cells is also calculated.

Localization versus Delocalization in Chiral Single Component Conductors of Gold Bis(dithiolene) Complexes

The first examples of chiral single component conductors are reported. Both (S,S) and (R,R) enantiomers of 5,6-dimethyl-5,6-dihydro-1,4-dithiin-2,3-dithiolate (dm-dddt) ligand have been used to prepare anionic metal bis(dithiolene) complexes formulated as ([(n-Bu)4N][M(dm-dddt)2] (M = Au, Ni), which are isostructural according to single crystal X-ray analysis. Single crystal transport measurements indicate semiconducting behavior for the anionic radical Ni complexes, with low room temperature conductivity values and high activation energies. Electrocrystallization experiments provided neutral [M(dm-dddt)2] (M = Au, Ni) complexes. The neutral radical gold compounds show intermolecular S···S interactions in the solid state giving rise to layers interconnected through weak C-H···S hydrogen bonds. The most peculiar structural feature concerns a dissymmetry between the two dithiolene moieties, while the nickel counterpart is symmetric. Single crystal resistivity measurements show thermally activated behavior for the open-shell gold complexes, with room temperature conductivity values of 0.02-0.04 S·cm(-1) and activation energies strongly influenced by hydrostatic pressure. A thorough theoretical study on nickel anion radical and gold neutral radical bis(dithiolene) complexes applied to the chiral complexes [M(dm-dddt)2] (M = Au, Ni(-)) and to a series of previously reported compounds addressed the issue of symmetry versus asymmetry from an electronic coupling perspective between the two dithiolene ligands. It results that neutral gold complexes with dithiolene ligands without extended delocalization are Class II mixed-valent compounds in the Robin and Day classification, presenting an inherent tendency toward asymmetric structures, which can be however modulated by the intermolecular organization in the solid state.

Magnetic and transport properties of Fe4single-molecule magnets: a theoretical insight

DFT methods have been employed to analyse the magnetic and transport properties of a family of Fe₄complexes showing single-molecule magnet behaviour deposited on gold surfaces.

Structural and electronic control of the metal to insulator transition and local orderings in the θ-(BEDT-TTF)2X organic conductors

A first-principles density functional theory (DFT) study of [Formula: see text]-(BEDT-TTF)2X molecular conductors with X  =  I3, CsCo(SCN)4 (ambient pressure, 7.5 kbar and 10 kbar), CsZn(SCN)4, TlCo(SCN)4, RbCo(SCN)4 and RbZn(SCN)4 (220 K and 90 K) is reported. It is shown that these salts exhibit three different types of band structure each of them associated with a different physical behavior. In contrast with previous proposals it is found that the key electronic parameter behind the differences in the band structures is the intrastack transfer integral, t c . A new mechanism for the metal to insulator transition in the [Formula: see text]-(BEDT-TTF)2MM'(SCN)4 ([Formula: see text], Tl; [Formula: see text], Co) salts is proposed, where an order-disorder structural transition of the ethylenedithio groups doubling the periodicity along the stack direction drives the system into an electronically pseudo-1D system along the interstack direction that is subject to a 4k F charge localization of holes. The structural rearrangement is such that the holes are not distributed equally between the two donors; the larger hole density is associated with the B donors which establish the strongest hydrogen bonds with the anion layers. A detailed microscopic description of how disorder of the ethylenedithio groups, the θ dihedral angle and the electronic structure intermingle and lead to the unusual phase diagram of these salts is presented. In this framework the role of pressure and uniaxial strain in controlling the physical behavior of these salts is discussed.

Links between the Crystal and Electronic Structure in the New Family of Unconventional Superconductors A2Cr3As3 (A = K, Rb, Cs)

The electronic structure of a new family of superconductors is examined through density functional theory calculations. In contrast with other quasi-1D superconductors, these phases exhibit a relatively complex electronic structure and the Fermi surface contains both 1D and 3D components. It is shown that cations have an almost nil influence on the electronic structure. The absence of a structural Peierls modulation is discussed, and the differences with the structurally related M2Mo6Se6 (M = Tl, In, ...) superconductors are stressed. The large electron mass renormalization and the lack of clear correlation between N(EF) and Tc suggest the existence of strong electron correlations and an unconventional origin of the superconductivity.

Electronic Structure and Magnetic Properties of CuFeS2

Chalcopyrite (CuFeS2) is an antiferromagnetic semiconductor with unusual magnetic and electrical properties, which are still not clearly understood. Neutron diffraction experiments reveal a phase transition at ∼50 K that has been attributed to an unexpected appearance of magnetic moments on Cu ions, having a paramagnetic arrangement down to 50 K and then ordering to an antiferromagnetic state at lower temperatures. In this study we use DFT-based computational methods to investigate the electronic structure and magnetic properties of CuFeS2 in order to obtain a reliable source of information for the interpretation of the observed magnetic behavior, and in particular to shed some light on the magnetic behavior of copper atoms in this compound. We have calculated the electronic structure of the ground and low-energy magnetically excited states and deduced a set of exchange coupling constants that are used afterward in classical Monte Carlo simulations to obtain magnetic susceptibility data, which compare successfully with our experimental results above ∼170 K. From our results it can be inferred that copper atoms remain in a diamagnetic state in this temperature range, although spin delocalization from neighboring iron atoms results in a non-negligible spin density on the copper atoms at high temperatures.

Donor–anion interactions at the charge localization and charge ordering transitions of (TMTTF)2AsF6 probed by NEXAFS

Detection of the charge localization and charge ordering transitions of (TMTTF)₂AsF₆ at T_ρ ≈ 230 K and T_CO ≈ 102 K, respectively.

Second harmonic generation in carbon nanotubes induced by transversal electrostatic field

Carbon nanotubes (CNTs) of armchair and zigzag type contain an inversion centre, and are thus intrinsically unable to generate dipole even-order nonlinearities, such as second harmonic generation (SHG). Breaking the inversion symmetry by application of an external voltage transversal to the CNT axis will, however, induce a second harmonic response. Similarly, additional non-vanishing second harmonic tensor elements will be induced in chiral tubes already displaying an intrinsic response. Many geometries realizing such a setup can be envisaged, e.g., an experimental gate setup or deposition of CNTs on, or integration in, strongly polarized host media, perhaps facilitating a tunable second harmonic response. In this work, we calculate the SHG signal from CNTs under transversally applied electric fields based on a tight-binding model.

Structure and magnetism of disordered carbon

Motivated by the observation of ferromagnetism in carbon foams, we perform a massive search for (meta)stable disordered structures of elemental carbon by a generate and test approach. We use the density functional based program SIESTA to optimize the structures and calculate the electronic spectra and spin densities. About 1% of the 24,000 optimized structures present magnetic moments, a necessary but not sufficient condition for intrinsic magnetic order. We analyse the results using elements of graph theory. Although the relation between the structure and the occurrence of magnetic moments is not yet fully clarified, we give some minimal requirements for this possibility, such as the existence of three-fold coordinated atoms surrounded by four-fold coordinated atoms. We discuss in detail the most promising structures.

Adsorption configuration effects on the surface diffusion of large organic molecules: the case of Violet Lander

Violet Lander (C(108)H(104)) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology.

Density functional theory for transition metals and transition metal chemistry

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Electronic structure of the A(8)Tr(11) (A = K, Rb, Cs; Tr = Ga, In, Tl) Zintl phases: possible chemical reasons behind their activated versus non activated conductivity

The electronic structure of the A(8)Tr(11) (A = K, Cs; Tr = Ga, In, Tl) Zintl phases has been studied by means of first-principles density functional theory (DFT) calculations. It is shown that the hypoelectronic Tr(11) cluster in these phases must be considered as Tr(11)(8-) even if it would require just a 7- charge to maximize its bonding, filling all its bonding and nonbonding levels. Our calculations show that the lowest empty orbital of the isolated Tr(11)(7-) clusters is an a(1)-type orbital. However, a degenerate e-type set of orbitals is higher but quite close in the case of the Ga(11)(7-) clusters. Thus, for the isolated Tr(11)(8-) clusters, the extra electron occupies always an a(1)-type antibonding orbital that contains, however, some Tr-Tr bonding component thus leading to a weak global antibonding character. In the solid, cluster-alkali-metal bonding interactions occur and spread the cluster levels into bands, but the extra electron still fills the a(1)-type cluster level for most of the A(8)Tr(11) phases. The cluster-alkali-metal interactions have a minor role in stabilizing this orbital but they provide the necessary delocalization to lead to the metallic character of these phases. In contrast, the e-type antibonding levels of the Ga(11)(7-) isolated cluster are those which become filled by the extra electron in the Cs(8)Ga(11) solid. This phase should be metallic, but occupation of this degenerate pair of cluster levels would lead to a structural instability that may be avoided by reducing the interactions of the alkali-metal atoms with the cluster levels. In that way the occupation appropriate for the isolated cluster is restored (i.e., one electron fills the a(1) cluster orbital), but the extra electron now remains localized on the cluster, thus leading to the unexpected activated conductivity observed for the Cs(8)Ga(11) phase.

Chemical functionalization of graphene

Experimental and theoretical results on chemical functionalization of graphene are reviewed. Using hydrogenated graphene as a model system, general principles of the chemical functionalization are formulated and discussed. It is shown that, as a rule, 100% coverage of graphene by complex functional groups (in contrast with hydrogen and fluorine) is unreachable. A possible destruction of graphene nanoribbons by fluorine is considered. The functionalization of infinite graphene and graphene nanoribbons by oxygen and by hydrofluoric acid is simulated step by step.

Host-guest interactions, uniform vs fragmented linear atom chains and likeliness of Peierls distortions in the (Ca7N4)[M(x)] (M = Ag, Ga, In) phases

The electronic structure of the recently reported (Ca(7)N(4))[M((x))] (M = Ag, Ga, and In) phases has been studied by means of first principles density functional theory (DFT) calculations. It is shown that under the assumption of very weak host-guest interactions: (a) four calcium atoms per formula unit may be considered as Ca(1.5+), whereas the remaining three may be considered as Ca(2+) so that the guest atoms would be neutral, and (b) the Peierls distortions which could set in the guest linear chains are unlikely. These results are compatible with the experimental information. However, the first principles DFT calculations clearly show that very sizable host-guest interactions occur and drastically modify this situation. As a result, there is a substantial electron transfer from the framework to the guest atoms, and all calcium atoms of the framework are better described as Ca(2+). The stoichiometry and structure of these systems result from a competition between the natural tendency of the bare guest atoms to form uniform linear chains within the reduced space of the channels and the attempt to optimize their positions within the channels through interactions with the calcium atoms. Model calculations suggest that indium has a weaker tendency to form uniform linear chains and interacts in a stronger way with the host. It is shown that, for the (Ca(7)N(4))[M(1.33)] (M = Ag and Ga) phases, a structure built from three repeat units of the Ca(7)N(4) host framework containing uniform linear chains with a repeat unit of four guest metal atoms is compatible with the strong interaction scenario and the lack of correlation between the different linear guest chains. These phases should be metallic conductors, and the carriers have both host and guest character. In contrast, the guest atoms in (Ca(7)N(4))[In(1.0)] prefer to occur as a series of trimeric units. Although this phase is found to have a metallic band structure, the conductivity should be smaller than those of the (Ca(7)N(4))[M(1.33)] (M = Ag and Ga) phases.

The SIESTA method; developments and applicability

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

l-Alanine in a Droplet of Water: A Density-Functional Molecular Dynamics Study

We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and alpha-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C(alpha)-site bond.

A density-functional study of the structures, binding energies and total spins of Ni–Fe clusters using nonlocal norm-conserving pseudopotentials and the generalized gradient approximation

We report ab initio calculations of the structures, binding energies, and total spins of the clusters Ni(13), Ni(19), Ni(23), Ni(26), Ni(12)Fe, Ni(11)Fe(2), Ni(18)Fe, Ni(17)Fe(2), Ni(22)Fe, Ni(20)Fe(3), and Ni(25)Fe using a density-functional method that employs linear combination of atomic orbitals as basis sets, nonlocal norm-conserving pseudopotentials, and the generalized gradient approximation for exchange and correlation. Our results show that the Fe-doped Ni clusters, which have icosahedral or polyicosahedral ground-state structures similar to those of the corresponding pure Ni clusters, are most stable with the Fe atoms occupying internal positions, as has also been inferred from experimental results on the adsorption of molecular nitrogen on the cluster surfaces. We also rule out the possibility that the experimentally observed difference between the (nonpolyicosahedral) configurations of N(2)-saturated Ni(26) and N(2)-saturated Ni(25)Fe be due to the influence of the Fe atom on the energy of the underlying metal cluster.