Developed Density Functional Theory Research Articles

Performance of density-functional-theory and random-phase-approximation methods on the study of transition-metal clusters: the Tan clusters as an example

Recently developed density-functional-theory (DFT) and random-phase-approximation (RPA) methods are used to study competing isomers of some negatively charged Ta clusters, namely Ta12 - and Ta10 -, in an attempt to find a suitable strategy towards accurate studies of transition-metal clusters based on DFT. Also the neutral and cationic forms Ta12 (0,+) of the twelve-atom cluster are studied. The results are compared with experimental information obtained by several methods that differ in the property under study and the total electric charge of the clusters. We find that a careful choice of the density functional, the use of relativistic two-component methods, eventually in combination with all-electron basis sets, and the application of RPA-type methods, may all be necessary steps for a good assessment. Such an assessment should be made in relation to several experimental properties as much as possible.

Substrate-Induced Changes on the Optical Properties of Single-Layer WS2.

Among the most studied semiconducting transition metal dichalcogenides (TMDCs), WS2 showed several advantages in comparison to their counterparts, such as a higher quantum yield, which is an important feature for quantum emission and lasing purposes. We studied transferred monolayers of WS2 on a drilled Si3N4 substrate in order to have insights about on how such heterostructure behaves from the Raman and photoluminescence (PL) measurements point of view. Our experimental findings showed that the Si3N4 substrate influences the optical properties of single-layer WS2. Beyond that, seeking to shed light on the causes of the PL quenching observed experimentally, we developed density functional theory (DFT) based calculations to study the thermodynamic stability of the heterojunction through quantum molecular dynamics (QMD) simulations as well as the electronic alignment of the energy levels in both materials. Our analysis showed that along with strain, a charge transfer mechanism plays an important role for the PL decrease.

Electronic Spectra of C60 Films Using Screened Range Separated Hybrid Functionals.

We study computationally the electronic spectra of C60 thin films using the recently developed density functional theory (DFT) framework combining a screened range separated hybrid (SRSH) functional with a polarizable continuum model (PCM). The SRSH-PCM approach achieves excellent correspondence between the frontier orbital's energy levels and the ionization potential and electron affinity of the molecular system at the condensed phase and consequently leads to high quality electronic excitation energies when used in time-dependent DFT calculations. Our calculated excited states reproduce the experimentally main reported spectral peaks at the 3.6-4.6 eV energy range and when addressing excitonic effects also reproduce the red-shifted spectral feature. Notably, we analyze the low-lying peak at 2.7 eV and associate it to an excitonic state.

Toward Engineering of Solution Microenvironments for the CO2 Reduction Reaction: Unraveling pH and Voltage Effects from a Combined Density-Functional-Continuum Theory.

Engineering the electrolyte microenvironment represents an attractive route to tuning the selectivity of electrocatalytic reactions beyond catalyst composition and morphology. However, harnessing the full potential of this approach requires understanding the interplay between voltage, electrolyte composition, and adsorbate binding within the electrical double layer, which is absent from the usual theoretical approaches. In this work, we apply a recently developed density functional theory (DFT)-continuum approach based on the effective screening medium method and reference interaction site model (ESM-RISM) to explore electrolyte effects with an enhanced description of the electrochemical interface. Applying this method to the binding of CO adsorbates in potassium-containing electrolytes on copper, a problem of direct relevance to CO2 electroreduction to value-added products, we show that the interdependence of voltage and pH leads to an unexpected change in adsorption site preference on Cu(001) terraces. Our findings highlight the often-overlooked importance of the electrical double-layer structure for predicting catalyst operation.

The Mechanism of the Propagation in the Anionic Polymerization of Polystyryllithium in Non-Polar Solvents Elucidated by Density Functional Theory Calculations. A Study of the Negligible Part Played by Dimeric Ion-Pairs under Usual Polymerization Conditions.

The elementary processes occurring in the anionic polymerization of styrene with dimerically associated polystyryllithium (propagation during the anionic polymerization of dimeric polystyryllithium) in the gas phase and cyclohexane were studied using MX062X/6-31+G(d), a recently developed density functional theory (DFT) method and compared with the polymerization of styrene with non-associated polystyryllithium, which was described in a previous study. The most stable transition state in the reaction of styrene with dimeric polystyryllithium has a structure in which the side chains of styrene and the two chain end units of polystyryllithium are located in the same direction around the Li atom near the reactive site. The relative enthalpy for this transition state in cyclohexane is 28 kJ·mol−1, which is much lower than that for the reaction of non-associated polystyryllithium (51 kJ·mol−1). However, the relative free energy (which determines the rate constant) for the former is 93 kJ·mol−1, which is greater than that for the latter by 7 kJ·mol−1, indicating that the latter reaction (reaction with non-associated polystyryllithium) is advantageous over the former (reaction with dimeric polystyrylllithium). Their rates of reaction are also affected by initiator concentrations; in the case of reactions with low initiator concentrations, from which high molecular weight polymers are usually obtained, the rate of reaction corresponding to non-associated polystyryllithium is much larger than that corresponding to dimeric polystyryllithium.

Evaluation of DFT-D3 dispersion corrections for various structural benchmark sets

We present an evaluation of our newly developed density functional theory (DFT)-D3 dispersion correction D3(CSO) in comparison to its predecessor D3(BJ) for geometry optimizations. Therefore, various benchmark sets covering bond lengths, rotational constants, and center of mass distances of supramolecular complexes have been chosen. Overall both corrections give accurate structures and show no systematic differences. Additionally, we present an optimized algorithm for the computation of the DFT-D3 gradient, which reduces the formal scaling of the gradient calculation from O(N3) to O(N2).

New Vistas on the Anionic Polymerization of Styrene in Non-Polar Solvents by Means of Density Functional Theory.

The elementary processes of anionic styrene polymerization in the gas phase and in cyclohexane were studied using M062X (a recently developed density functional theory (DFT) method) combined with the 6-31+G(d) basis sets, in order to clarify the complicated phenomena caused by the association of the active chain-ends and elucidate the details of the polymerization mechanism. Three types of HSt2Li (a model structure of polystyryllithium chain-ends) were obtained; the well-known first structure in which Li is coordinated to the side chain, the second structure in which Li is coordinated to the phenyl ring, (both without the penultimate unit coordination), and the third structure in which Li is coordinated to both the chain-end unit and the penultimate styrene unit. Although the third HSt2Li is the most stable as expected, the free energy for the transition state of its reaction with styrene is higher than those for the other two transition states due to its steric hindrance. The free energy for the transition state of the reaction of the second HSt2Li with styrene is the lowest, suggesting that the route through it is the predominant reaction path. The penultimate unit effect, slower addition of styrene to HSt2Li than to HStLi, is attributed to coordination of the penultimate styrene units of the polystyryllithium dimer (one of the starting materials) to its Li atoms. The calculated enthalpy for the reaction barrier of the second HSt2Li with styrene in cyclohexane was found to agree with the observed apparent activation energy in benzene.

Design of Nanostructured Heterogeneous Solid Ionic Coatings through a Multiscale Defect Model.

Understanding of the electrical conduction, that is, ionic and electronic conduction, through the solid electrolyte interphase (SEI) is critical to the design of durable lithium-ion batteries (LIBs) with high rate capability and long life. It is believed that an ideal SEI should not only be an ionic conductor, but also an electronic insulator. In this study, we present a theoretical design of an artificial SEI consisting of lithium fluoride (LiF) and lithium carbonate (Li2CO3) on a LIB anode based on a newly developed density functional theory (DFT) informed space charge model. We demonstrate that the migration of lattice Li ions from LiF phase to form Li interstitials in Li2CO3 is energetically favorable near the LiF/Li2CO3 interface. At equilibrium, this interfacial defect reaction establishes a space charge potential across the interface, which causes the accumulation of ionic carriers but the depletion of electronic carriers near the LiF/Li2CO3 interface. To utilize this space charge effect, we propose a computationally designed, nanostructured artificial SEI structure with high density of interfaces of LiF and Li2CO3 perpendicular to the electrode. On the basis of this structure, the influences of grain size and volume ratio of the two phases were studied. Our results reveal that reducing the grain size of Li2CO3 in the nanostructured composite can promote ionic carriers and increase the ionic conductivity through the composite SEI by orders of magnitude. At the same time, the electronic conductivity is reduced due to electron depletion near the LiF/Li2CO3 interface. Furthermore, an optimal volume fraction that ensures high ionic and low electronic conduction was predicted.

Improved DFT-Based Interpretation of ESI-MS of Aqueous Metal Cations

We present results showing that our recently developed density functional theory (DFT)-based speciation model of the aqueous Al(3+) system has the potential to improve the interpretations of ESI-MS studies of aqueous metal cation hydrolytic speciation. The main advantages of our method are that (1) it allows for the calculation of the relative abundance of a given species which may be directly assigned to the signal intensity in a mass spectrum; (2) in cases where species with identical m⁄z ratios may coexist, the assignment can be unambiguously assigned based on their theoretical relative abundances. As a demonstration of its application, we study four pairs of monomer and dimer aqueous Al(3+) species, each with identical m/z ratio. For some of these pairs our method predicts that the dominant species changes from the monomer to the dimer species under varying pH conditions.

Theoretical investigation of the dispersion interaction in argon dimer and trimer

The ultimate aim of the present work is to establish an acceptable level of computation for the van der waals (vdw) complexes that is able to pick up appreciable amount of dispersion interaction energy, reproduce the equilibrium separation within the acceptable limits and at the same time cost and time effective. In order to reach this aim vdw clusters where pure isotropic dispersion interaction occur, namely, Ar dimer and trime were investigated. Computations using different basis sets and at different levels of theory have been carried out. Three basis sets, namely, the 6-31++G**, the 6-311++G** and the aug-cc-pvdz basis set, were found superior to all other basis sets used. The high performance and relative small CPU time of the 6-31++G** basis set make it a good candidate for use with large vdw clusters, especially those of interest in biology. Three compound methods were applied in the present work, namely G1, G2 and G2 Moller-Plesset (MP2) and the complete basis set method, CBS-Q. These methods failed to detect the attraction dispersion interaction in the dimer. The predicted repulsive interaction seems dominant in all these methods. Some of the recently developed Density Functional Theory (DFT) methods that were parameterized to account for the dispersion interaction were also evaluated in the present work. Results come to the conclusion that, in contrast to the claims made, state-of-the-art Density Functional Theory methods are incapable of accounting for dispersion effects in a quantitative way, although these methods predict correctly the inter-atomic separations and are thus considered a real improvement over the conventional methods. BS-SE has been computed, analyzed and discussed.

First Principle Simulation of the Temperature Dependent Magnetic Circular Dichroism of a Trinuclear Copper Complex in the Presence of Zero Field Splitting

We present a test of a recently developed density functional theory (DFT) based methodology for the calculation of magnetic circular dichroism (MCD) spectra in the presence of zero-field splitting (ZFS). The absorption and MCD spectra of the trinuclear copper complex μ(3)O ([Cu(3)(L)(μ(3)-O)](4+)), which models the native intermediate produced in the catalytic cycle of the multicopper oxidases, have been simulated from first principle within the framework of adiabatic time dependent density functional theory. The effects of the ZFS of the quartet (4)A(2) ground state on the theoretical MCD spectrum of μ(3)O have been analyzed. The simulated spectra are consistent with the experimental ones. The theoretical assignments of the MCD spectra are based on direct simulation as well as a detailed analysis of the molecular orbitals in μ(3)O. Some of the assignments differ from those given in previous studies. The ZFS effects in the presence of a strong external magnetic field (7 T) prove negligible. The change of the sign of the ZFS changes systematically the intensity of the MCD bands of the z-polarized excitations. The effect of the ZFS on the x,y-polarized excitations is not uniform.

The oxidation of tyrosine and tryptophan studied by a molecular dynamics normal hydrogen electrode

The thermochemical constants for the oxidation of tyrosine and tryptophan through proton coupled electron transfer in aqueous solution have been computed applying a recently developed density functional theory (DFT) based molecular dynamics method for reversible elimination of protons and electrons. This method enables us to estimate the solvation free energy of a proton (H(+)) in a periodic model system from the free energy for the deprotonation of an aqueous hydronium ion (H(3)O(+)). Using the computed solvation free energy of H(+) as reference, the deprotonation and oxidation free energies of an aqueous species can be converted to pK(a) and normal hydrogen electrode (NHE) potentials. This conversion requires certain thermochemical corrections which were first presented in a similar study of the oxidation of hydrobenzoquinone [J. Cheng, M. Sulpizi, and M. Sprik, J. Chem. Phys. 131, 154504 (2009)]. Taking a different view of the thermodynamic status of the hydronium ion, these thermochemical corrections are revised in the present work. The key difference with the previous scheme is that the hydronium is now treated as an intermediate in the transfer of the proton from solution to the gas-phase. The accuracy of the method is assessed by a detailed comparison of the computed pK(a), NHE potentials and dehydrogenation free energies to experiment. As a further application of the technique, we have analyzed the role of the solvent in the oxidation of tyrosine by the tryptophan radical. The free energy change computed for this hydrogen atom transfer reaction is very similar to the gas-phase value, in agreement with experiment. The molecular dynamics results however, show that the minimal solvent effect on the reaction free energy is accompanied by a significant reorganization of the solvent.

Density Functional Study on Core Ionization Spectra of Cytidine and Its Fragments

Abstract The sugar–base correlation of cytosine (base) and deoxyribose (sugar) moieties of cytidine is investigated based on their inner-shell electronic structural information. A recently developed density functional theory (DFT) model, CV-B3LYP, with a Gaussian-type basis set of 6-311G**, and the DFT-LB94 model with a Slater-type basis set of TZ2P are employed to calculate inner shell ionization energies. The results reveal that the corresponding geometry of cytidine is not significantly different from its fragments, i.e., cytosine and deoxyribose. Changes in charge distribution of cytidine with respect to cytosine and deoxyribose concentrate on the local C sites in the base pyrimidine ring and sugar ring, as indicated by the atomic Hirshfeld charges. The O-K, N-K, and C-K spectra of cytidine inherit the aromatic signature in cytosine, suggesting that the role of the aromatic ring is a buffer to diffuse the changes brought in by the addition of the deoxyribose moiety. Formation of cytidine, however, substantially changes the C-K spectra of the deoxyribose moiety. In general, the correlated O-K, N-K, and C-K sites of cytidine exhibit small red shifts with respect to the cytosine base, whereas the O-K and C-K sites of cytidine show blue shifts in comparison with those of deoxyribose.

Metahybrid Density Functional Theory and Correlated ab Initio Studies on Microhydrated Adenine−Thymine Base Pairs

Monohydrated and dihydrated adenine-thymine base pairs are characterized using metahybrid density functional theory and correlated ab initio approaches. The motivation of this work is twofold. First, the high-level geometries and interaction energies computed for different complexes serve as a reference for the testing of recently developed density functional theory (DFT) with respect to its ability to correctly describe the balance between the electrostatic and the dispersion contributions that bind these complexes. Second, these studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for a better understanding of the influence of the solvent on the stability of the structure of DNA duplexes.

DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations versus Experiment in Vacuo

A complete scan of the potential-energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller-Plesset second-order perturbation theory (RI-MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol(-1). The different behaviors of nonmethylated and methylated trimers is also discussed. The high-level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple-zeta basis set predicts 11 uracil trimer interaction energies with a root-mean-square error of 2.3 kcal mol(-1) relative to highly correlated ab initio theoretical calculations.

Density Functionals for Noncovalent Interaction Energies of Biological Importance.

Forty density functionals and one wavefunction method are assessed against a recently published database of accurate noncovalent interaction energies of biological importance. The comparison shows that two newly developed density functional theory (DFT) methods, PWB6K and M05-2X, give the best performance for this benchmark database of 22 noncovalent complexes, including both hydrogen-bonding and dispersion-dominated complexes. In contrast, the more popular B3LYP and PBEh functionals fail to describe the interactions in the dispersion-dominated complexes. The local spin density approximation and BHandH functionals give good performance for dispersion-dominated interactions at the expense of a large error for hydrogen bonding. PWB6K and M05-2X constitute a new generation of DFT methods based on simultaneously optimized exchange and correlation functionals that include kinetic energy density in both the exchange and correlation functional, and the present study confirms that they have greatly improved performance for noncovalent interactions as compared to previous DFT methods. We interpret this as being due to an improved treatment of medium-range correlation effects by the exchange-correlation functional. We recommend the PWB6K and M05-2X methods for investigating large biological systems and soft materials.

How Well Can Density Functional Methods Describe Hydrogen Bonds to π Acceptors?

We employed four newly developed density functional theory (DFT) methods for the calculation of five pi hydrogen bonding systems, namely, H2O-C6H6, NH3-C6H6, HCl-C6H6, H2O-indole, and H2O-methylindole. We report new coupled cluster calculations for HCl-C6H6 that support the experimental results of Gotch and Zwier. Using the best available theoretical and experimental results for all five systems, our calculations show that the recently proposed MPW1B95, MPWB1K, PW6B95, and PWB6K methods give accurate energetic and geometrical predictions for pi hydrogen bonding interactions, for which B3LYP fails and PW91 is less accurate. We recommend the most recent DFT method, PWB6K, for investigating larger pi hydrogen bonded systems, such as those that occur in molecular recognition, protein folding, and crystal packing.

The colloidal force of bead-spring chains in a good solvent

A recently developed density functional theory (DFT) for tethered bead-spring chains is used to investigate colloidal forces for the good solvent case. A planar surface of tethered chains is opposed to a bare, hard wall and the force exerted on the bare wall is calculated by way of the contact density. Previously, the case of large wall separation was investigated. The density profiles of the unperturbed chains, in that case, were found to be neither stepfunctions nor parabolas and were shown to accurately predict computer simulation results. In the present paper, the surface forces that result from the distortion of these density profiles at finite wall separation is studied. The resulting force function is analyzed for varying surface coverages, wall separations, and chain lengths. The results are found to be in near quantitative agreement with the scaling predictions of Alexander [S. Alexander, J. Phys. (Paris) 38, 983 (1977)] when the layer thickness is "correctly" defined. Finally, a hybrid Alexander-DFT theory is suggested for the analysis of experimental results.

Assessment of recently developed density functionals for the calculation of enthalpies of formation in challenging cases

The errors in computed enthalpies of formation for a test set of molecules are compared for some recently developed density functional theory (DFT) functionals (PBE, VSXC, and PBE1PBE) with B3LYP and experiment. The test molecules studied here are an atypical set that includes molecules found to have larger enthalpy of formation errors for DFT methods. Overall, the B3LYP and VSXC functionals yield the best results, with VSXC yielding slightly better results even though, unlike B3LYP, VSXC does not contain any Hartree–Fock exchange.

Spin–orbit corrections to NMR shielding constants from density functional theory. How important are the two-electron terms?

A recently developed density functional theory (DFT) ansatz for the calculation of one-electron spin–orbit (SO) corrections to NMR chemical shifts has been extended to include two-electron SO operators. The performance of different approximations is evaluated in calculations of 1 H and 13 C nuclear shieldings in the hydrogen halides, the halomethanes, and in iodobenzene. Two-electron contributions are significant relative to the one-electron contributions for fluorine substituents (ca. 30–35%) but decrease for the heavier halogens (ca. 6–7% for iodine). A mean-field approximation to the two-electron SO integrals performs excellently, with negligible deviations from the `exact' results, thus opening the way to calculations on large systems.