Influence of atomistic physics on electro-osmotic flow: An analysis based on density functional theory

Efficient charge-transfer (CT) phosphorescence in the near-IR (NIR) spectral region is reported for four substituted Ru-(R-dipyrrinato) complexes, [Ru(bpy)2(R-dipy)](PF6), where bpy is 2,2'-bipyridine and the substituent R is phenyl (ph), 2,4,6-trimethylphenyl, 4-carboxyphenyl (HOOC-ph), or 4-pyridinyl. The experimentally determined phosphorescence efficiency, ιem(p) = kRAD(p)/(νem(p))3 (where kRAD(p) and νem(p) are the phosphorescence rate constant and the phosphorescence frequency, respectively), of the [Ru(bpy)2(R-dipy)]+ complexes was approximately double that of [Ru(bpy)(Am)4]2+ complexes (Am = ammine ligand) in the NIR region. Density functional theory (DFT) modeling indicated two strikingly different electronic configurations of the triplet emitting state (Te) in the two types of complexes. The Te of [Ru(bpy)2(R-dipy)]+ complexes shows a CT-type corresponding to the metal-to-ligand charge transfer (MLCT)-(Ru-(R-dipy)) and the ππ*-(R-dipy) moiety configurations, and the Te state in the [Ru(bpy)(Am)4]2+ complexes corresponds to an approximately MLCT excited state consisting of mostly MLCT-(Ru-bpy) with a minimal ππ*(bpy) contribution. DFT modeling also indicated that the low-energy singlet excited states in the Te geometry (Sn(T)) of the [Ru(bpy)2(ph-dipy)]+ complex consist of numerous CT-Sn(T)-type states of the Ru-dipy and Ru-bpy moieties, whereas the [Ru(bpy)(Am)4]2+ ions show quite simple MLCT-Sn(T)-type states of the Ru-bpy moiety. Based on experimental observations, DFT modeling, and the plain spin-orbit coupling (SOC) principle, we conclude that the remarkably high ιem(p) amplitudes of the [Ru(bpy)2(R-dipy)]+ complexes relative to those of [Ru(bpy)(Am)4]2+ complexes can be attributed to the relatively substantial contribution of intrinsic SOC-mediated intensity stealing from the numerous low-energy CT-type Sn(T) states.

AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.

In the Comment by S\oderlind et al. [Phys. Rev. B 90, 157101 (2014)], the authors argue that (1) density functional theory (DFT), especially with all-electron methods, already models U metal and U-Zr alloy accurately; and (2) $\mathrm{DFT}+U$ results calculated at ${U}_{\mathrm{eff}}=1.24$ for volume, enthalpy, and magnetic moments that they select from our study [Phys. Rev. B 88, 235128 (2013)] suggest adding the Hubbard $U$ potential in $\mathrm{DFT}+U$ reduces accuracy compared to DFT. With respect to argument (1) by S\oderlind et al., we argue that previously neglected and very recent experimental data suggest that DFT in S\oderlind's full-potential linear muffin-tin orbital calculations [Phys. Rev. B 66, 085113 (2002)] still models the bulk modulus and elastic constants of \ensuremath{\alpha}U with errors considerably larger than other related elements, e.g., most transition metals. In addition, we demonstrate that the assertion by S\oderlind et al. that our DFT results are not satisfactory because deficiency exists in our projector augmented wave calculation is unfounded. With respect to argument (2) by S\oderlind et al., we argue that they have inappropriately focused on just one phase [the bcc phase \ensuremath{\gamma}(U,Zr)], neglecting the other phases which represent the majority of our evidence; made overgeneralizations based on results at only one ${U}_{\mathrm{eff}}$ value of 1.24 eV; and supported their argument with inaccurate assertions that $\mathrm{DFT}+U$ predicts for \ensuremath{\gamma}(U,Zr) an unprecedentedly large positive volume of mixing and an enthalpy of mixing that is inconsistent with the experimental miscibility gap. We therefore hold to our original conclusion that the accuracy of DFT for modeling U and U-Zr has room for improvement and $\mathrm{DFT}+U$ is a good candidate.

The present study is concerned with unsteady electroosmotic flow (EOF) in a microchannel with the electric charge distribution described by the Poisson-Boltzmann (PB) equation. The nonlinear PB equation is solved by a systematic perturbation with respect to the parameter λ which measures the strength of the wall zeta potential relative to the thermal potential. In the small λ limits (λ<<1), we recover the linearized PB equation - the Debye-Hückel approximation. The solutions obtained by using only three terms in the perturbation series are shown to be accurate with errors <1% for λ up to 2. The accurate solution to the PB equation is then used to solve the electrokinetic fluid transport equation for two types of unsteady flow: transient flow driven by a suddenly applied voltage and oscillatory flow driven by a time-harmonic voltage. The solution for the transient flow has important implications on EOF as an effective means for transporting electrolytes in microchannels with various electrokinetic widths. On the other hand, the solution for the oscillatory flow is shown to have important physical implications on EOF in mixing electrolytes in terms of the amplitude and phase of the resulting time-harmonic EOF rate, which depends on the applied frequency and the electrokinetic width of the microchannel as well as on the parameter λ.

Li's paper [Phys. Rev. B 85, 235407 (2012)] presents density functional theory (DFT) results of stress as a function of different strain states. The work of Cooper et al. [Phys. Rev. B 87, 035423 (2013)] performs the same DFT calculations as part of an investigation into the nonlinear elastic properties of ${\mathrm{MoS}}_{2}$. Some of the DFT results of Li are substantially different from our recently published paper, Cooper et al. [Phys. Rev. B 87, 035423 (2013)]. Although both papers agree on states of equibiaxial stress, there is substantial disagreement on states of uniaxial tensile stress. In this Comment we show that our DFT computations are properly executed and consistent across three different DFT codes, including the one used by Li.

Density functional theory (DFT) molecular dynamics (MD) and classical MD simulations of the principal shock Hugoniot are presented for two hydrocarbon polymers, polyethylene (PE) and poly(4-methyl-1-pentene) (PMP). DFT results are in excellent agreement with experimental data, which is currently available up to 80 GPa. Further, we predict the PE and PMP Hugoniots up to 350 and 200 GPa, respectively. For comparison, we studied two reactive and two nonreactive interaction potentials. For the latter, the exp-6 interaction of Borodin et al. showed much better agreement with experiment than OPLS. For the reactive force fields, ReaxFF displayed decidedly better agreement than AIREBO. For shocks above 50 GPa, only the DFT results are of high fidelity, establishing DFT as a reliable method for shocked macromolecular systems.

The terahertz absorption spectra of aspirin and benzoic acid have been measured in the range 200-500 cm-1 (6-15 THz). Density-functional theory (DFT) modeling has assigned fundamental vibrational modes to the observed absorption bands. Hydrogen bonds between the crystalline planes of aspirin resulted in better agreement between the experimental and modeled spectra than for benzoic acid. The similar structure of these two molecules suggests a similar absorption spectrum, which indeed was obtained experimentally. However, the detailed crystal structure and molecular differences result in some of the apparently common absorption bands being assigned to different vibrational modes through the DFT modeling. Thus, our study importantly reveals that even though crystalline forms of two similar molecules may have similar experimental terahertz spectra, the resemblance may be superficial rather than fundamental.

Density functional theory (DFT) has been applied to modeling molecular interactions in water for over three decades. The ubiquity of water in chemical and biological processes demands a unified understanding of its physics, from the single molecule to the thermodynamic limit and everything in between. Recent advances in the development of data-driven and machine-learning potentials have accelerated simulation of water and aqueous systems with DFT accuracy. However, anomalous properties of water in the condensed phase, where a rigorous treatment of both local and non-local many-body (MB) interactions is in order, are often unsatisfactory or partially missing in DFT models of water. In this review, we discuss the modeling of water and aqueous systems based on DFT and provide a comprehensive description of a general theoretical/computational framework for the development of data-driven many-body potentials from DFT reference data. This framework, coined MB-DFT, readily enables efficient many-body molecular dynamics (MD) simulations of small molecules, in both gas and condensed phases, while preserving the accuracy of the underlying DFT model. Theoretical considerations are emphasized, including the role that the delocalization error plays in MB-DFT potentials of water and the possibility to elevate DFT and MB-DFT to near-chemical-accuracy through a density-corrected formalism. The development of the MB-DFT framework is described in detail, along with its application in MB-MD simulations and recent extension to the modeling of reactive processes in solution within a quantum mechanics/MB molecular mechanics (QM/MB-MM) scheme, using water as a prototypical solvent. Finally, we identify open challenges and discuss future directions for MB-DFT and QM/MB-MM simulations in condensed phases.

The core structure of -type screw dislocations in hexagonal close packed titanium is investigated computationally using periodic supercells with quadrupolar configurations in combination with density functional theory (DFT) and a modified embedded atom method (MEAM) classical potential. Two arrangements of the quadrupolar supercell configurations are examined, and within each arrangement two initial dislocation positions are compared. (Meta)stable pyramidal and prismatic dislocation core structures exist within both DFT and MEAM methods, and the relaxed structure from a given configuration resulting from our anisotropic elasticity theory solution depends only on the assumed initial dislocation positions. Within DFT we find the ground state core structure to be spread on the pyramidal plane. We find that it is necessary to include the semi-core 3p electrons as valence states in the DFT calculations in order to converge the ground state dislocation core configuration and difference in energy between structures. In terms of k-point sampling, it is found that at least a k-point mesh is necessary to converge the dislocation core structure for a supercell one Burgers vector deep. Use of higher k-point densities or inclusion of additional semi-core electronic states as valence electrons results in the same core structure. With the MEAM potential considered in this work, we find the ground state core configuration to be spread predominantly on the prismatic plane, in contrast with the DFT results.

We have investigated the importance of polarization by the enzyme dihydrofolate reductase (DHFR) on its substrates, folate and dihydrofolate, using a series of quantum mechanical (QM) techniques (Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2), local density approximation (LDA) and generalized gradient approximation (GGA) density functional theory (DFT) calculations) in which the bulk enzyme is included in the calculations as point charges. Polarization, in terms of both charges on components (residues) of the folate and dihydrofolate molecules and changes in the electron density, particularly of the pterin ring of the substrates, and the implications for the catalytic reduction are discussed. Significant differences in polarization behavior are observed for the different theoretical methods employed. The consequences of this, particularly for choosing an appropriate model for quantum mechanical/molecular mechanical (QM/MM) calculations, are pointed out. The HF and MP2 QM methods show small polarizations (approximately 0.04 electrons) of the pterin ring but quite large polarizations with both LDA and GGA DFT methods (0.3-0.5 electrons). This large difference in polarization for both folate and dihydrofolate arises as a result of substantial differences between the charge distributions for the gasphase DFT and HF calculations, specifically the charges on the dianionic glutamate side chain. Some recent literature reports of incorrect representation of anionic systems by DFT methods are noted. The DFT results are similar to the previously reported LDA DFT results of Bajorath et al. predicting a large polarization of the pterin ring of folate (Proteins 9:217-224, 1991) and dihydrofolate (PNAS 88:6423-6426, 1991) of approximately 0.5-0.6 electrons.

Modeling palladium surfaces with density functional theory, neural networks and molecular dynamics

Establishing the fundamental possibility of the existence of the heteroligand macrotetracyclic complexes of vanadium, chromium, manganese, and iron-containing in the inner coordination sphere phthalocyanine, oxygen (O2-) and fluorine (F-) ions and having general [MPc(O)F] formula (M= V, Cr, Mn, Fe), by using of quantum-chemical calculation of parameters of their molecular/electronic structures and thermodynamical characteristics. The molecular and electronic structures of the above-mentioned heteroligand macrotetracyclic chelates of 3d-elements (M) of the type [MPc(O)F] (M= V, Cr, Mn, Fe) which are unknown at present, were theoretically investigated. Standard thermodynamic parameters of formation (standard enthalpy ΔH0 f, 298, entropy S0 f, 298, and Gibbs’s energy ΔG0 f, 298) for these macrocyclic compounds were calculated, too. Identifying details of molecular and electronic structures of compounds indicated above. Density functional theory (DFT) model chemistries (B3PW91/TZVP and OPBE/TZVP) with a combination of the D3 version of Grimme’s dispersion. The data on the geometric parameters of the molecular structure of these complexes are presented; it was shown that MN4 chelate nodes, all metal-chelate and 6-membered non-chelate rings in each of these macrocyclic coordination compounds, are practically planar with a small deviation from coplanarity (not more 3o); nonetheless, N4 grouping from donor nitrogen atoms and 5-membered non-chelate rings are strictly planar. Wherein, the bond angles between two donor nitrogen atoms and M atom are not equal to 90o; a similar situation occurs for the bond angles between donor atoms N, M, and O or F (notwithstanding the bond angles formed by M, O, and F atoms are exactly 180°). Also, NBO analysis data and the values of the standard enthalpy, entropy, and Gibbs energy of the formation of these compounds were presented. Specific features of DFT calculated molecular and electronic structures of the heteroligand metal macrocyclic compounds have been discussed. It has been shown that good agreement between the parameters of molecular structures obtained by two various DFT model chemistries takes place. Also, it has been noted that predicting the possibility of the existence of exotic coordination compounds and modeling their molecular/electronic structures using modern quantum chemical calculations (and, in particular, using DFT of various levels) is a very useful tool for solving problems associated with such synthesis.

Density functional theory (DFT) calculations allow us to reproduce the SERS (surface-enhanced Raman scattering) spectra of molecules adsorbed on nanostructured metal surfaces and extract the most information this spectroscopy is potentially able to provide. The latter point mainly concerns the anchoring mechanism and the bond strength between molecule and metal as well as the structural and electronic modifications of the adsorbed molecule. These findings are of fundamental importance for the application of this spectroscopic technique. This review presents and discusses some SERS–DFT studies carried out in Italy as a collaboration between the universities of Modena and Reggio-Emilia and of Florence, giving an overview of the information that we can extract with a combination of experimental SERS spectra and DFT modeling. In addition, a selection of the most recent studies and advancements on the DFT approach to SERS spectroscopy is reported with commentary.

We report a detailed study, using state-of-the-art simulation and theoretical methods, of the effective (depletion) potential between a pair of big hard spheres immersed in a reservoir of much smaller hard spheres, the size disparity being measured by the ratio of diameters q ≡ σ(s)/σ(b). Small particles are treated grand canonically, their influence being parameterized in terms of their packing fraction in the reservoir η(s)(r). Two Monte Carlo simulation schemes--the geometrical cluster algorithm, and staged particle insertion--are deployed to obtain accurate depletion potentials for a number of combinations of q ≤ 0.1 and η(s)(r). After applying corrections for simulation finite-size effects, the depletion potentials are compared with the prediction of new density functional theory (DFT) calculations based on the insertion trick using the Rosenfeld functional and several subsequent modifications. While agreement between the DFT and simulation is generally good, significant discrepancies are evident at the largest reservoir packing fraction accessible to our simulation methods, namely, η(s)(r) = 0.35. These discrepancies are, however, small compared to those between simulation and the much poorer predictions of the Derjaguin approximation at this η(s)(r). The recently proposed morphometric approximation performs better than Derjaguin but is somewhat poorer than DFT for the size ratios and small-sphere packing fractions that we consider. The effective potentials from simulation, DFT, and the morphometric approximation were used to compute the second virial coefficient B(2) as a function of η(s)(r). Comparison of the results enables an assessment of the extent to which DFT can be expected to correctly predict the propensity toward fluid-fluid phase separation in additive binary hard-sphere mixtures with q ≤ 0.1. In all, the new simulation results provide a fully quantitative benchmark for assessing the relative accuracy of theoretical approaches for calculating depletion potentials in highly size-asymmetric mixtures.

Comparative density functional theory and density functional tight binding study of 2-anthroic acid on TiO2