HAB79: A new molecular dataset for benchmarking DFT and DFTB electronic couplings against high-level ab initio calculations

A new molecular dataset called HAB79 is introduced to provide ab initio reference values for electronic couplings (transfer integrals) and to benchmark density functional theory (DFT) and density functional tight-binding (DFTB) calculations. The HAB79 dataset is composed of 79 planar heterocyclic polyaromatic hydrocarbon molecules frequently encountered in organic (opto)electronics, arranged to 921 structurally diverse dimer configurations. We show that CASSCF/NEVPT2 with a minimal active space provides a robust reference method that can be applied to the relatively large molecules of the dataset. Electronic couplings are largest for cofacial dimers, in particular, sulfur-containing polyaromatic hydrocarbons, with values in excess of 0.5 eV, followed by parallel displaced cofacial dimers. V-shaped dimer motifs, often encountered in the herringbone layers of organic crystals, exhibit medium-sized couplings, whereas T-shaped dimers have the lowest couplings. DFT values obtained from the projector operator-based diabatization (POD) method are initially benchmarked against the smaller databases HAB11 (HAB7-) and found to systematically improve when climbing Jacob’s ladder, giving mean relative unsigned errors (MRUEs) of 27.7% (26.3%) for the generalized gradient approximation (GGA) functional BLYP, 20.7% (15.8%) for hybrid functional B3LYP, and 5.2% (7.5%) for the long-range corrected hybrid functional omega-B97X. Cost-effective POD in combination with a GGA functional and very efficient DFTB calculations on the dimers of the HAB79 database give a good linear correlation with the CASSCF/NEVPT2 reference data, which, after scaling with a multiplicative constant, gives reasonably small MRUEs of 17.9% and 40.1%, respectively, bearing in mind that couplings in HAB79 vary over 4 orders of magnitude. The ab initio reference data reported here are expected to be useful for benchmarking other DFT or semi-empirical approaches for electronic coupling calculations

Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins

Multi-heme cytochromes (MHCs) are fascinating proteins used by bacterial organisms to shuttle electrons within, between, and out of their cells. When placed in solid-state electronic junctions, MHCs support temperature-independent currents over several nanometers that are 3 orders of magnitude higher compared to other redox proteins of similar size. To gain molecular-level insight into their astonishingly high conductivities, we combine experimental photoemission spectroscopy with DFT+Σ current–voltage calculations on a representative Gold-MHC-Gold junction. We find that conduction across the dry, 3 nm long protein occurs via off-resonant coherent tunneling, mediated by a large number of protein valence-band orbitals that are strongly delocalized over heme and protein residues. This picture is profoundly different from the electron hopping mechanism induced electrochemically or photochemically under aqueous conditions. Our results imply that the current output in solid-state junctions can be even further increased in resonance, for example, by applying a gate voltage, thus allowing a quantum jump for next-generation bionanoelectronic devices

Correction to “Electronic Couplings for Charge Transfer across Molecule/Metal and Molecule/Semiconductor Interfaces: Performance of the Projector Operator-Based Diabatization Approach”

The POD electronic coupling values computed at the hybrid-functional DFT level for He2 + (Table 1 in ref 1), Zn2 + (Table 2 in ref 1), and the HAB11 database (Table 3 in ref 1) are incorrect. The apparent “cluster boundary” calculations for B3LYP, PBE0, and PBE50, as described in the original article, were erroneously carried out in periodic boundary conditions (PBC) where the long-range Hartree-Fock exchange (HFX) was screened using a large range-separation parameter ? = 14 bohr-1. As a result, the global-hybrid functionals were in fact described as strongly screened range-separated hybrid functionals with only the GGA fraction in the longe-range part remaining (beyond 1/? ~ 0.07 bohr) where the HFX, mixed with the GGA exchange in the short-range, was attenuated. This incorrect setup yielded the values listed in the published article. Recently, we have reinvestigated the POD couplings on HAB7-, HAB11, and the new HAB79 data sets using the neutral-dimer approach in cluster boundary conditions.2 Range-separated hybrid (RSH) functionals such as LRC-wPBEh and wB97X with mixed GGA and HF exchange in the short-range and pure HF in the long-range were shown to be the most accurate giving a mean relative unsigned error of ~5%. The corrected POD electronic coupling values for He2 +, Zn2 +, and HAB11 in cluster boundary conditions are summarized in Tables 1-3. Here, results are reported for a more diverse set of functionals than those in the original publication, including GGA, hybrid, and range-separated hybrid functionals HSE06, LRC-wPBEh, and (Table Presented). wB97X. The couplings reported here for GGA functionals differ somewhat from those reported in the original publication. This is because all calculations presented herein were carried out for charge-neutral dimers, consistent with the approach taken in ref 2, whereas previous calculations were carried out for dimers with a net charge of +1

Electronic Couplings for Charge Transfer across Molecule/Metal and Molecule/Semiconductor Interfaces: Performance of the Projector Operator-Based Diabatization Approach

One principal parameter determining charge transfer rates between molecules and metals is the electronic coupling strength between the discrete electronic states of the molecule and the band states of the metal. Their calculation with computational chemistry methods remains challenging, both conceptually and in practice. Here, we report the implementation of the projection-operator diabatization (POD) approach of Kondov et al. (<i>J. Phys. Chem. C</i> <b>2007</b>, 111, 11970–11981) in the CP2K program package, which extends the range of applications to charge transfer at infinite periodic surfaces. In the POD approach the self-consistent Kohn–Sham Hamiltonian of the full system is partitioned in donor (e.g., molecule) and acceptor (e.g., metal) blocks which are block-diagonalized. The coupling matrix elements between donor and acceptor states are simply identified with the matrix elements of the off-diagonal block. We find that the POD method performs similarly well as constrained DFT (CDFT) on the HAB11 database for excess hole transfer between simple organic dimers, with a mean relative unsigned error of 9.3 %, compared to 5.3 % in CDFT. By studying two case examples, electron injection from a dye molecule to TiO₂ and electron transfer from a molecule, that forms self-assembled monolayers, to metallic Au(111), we demonstrate that the POD method is a useful and cost-effective tool for estimation of electronic coupling across heterogeneous interfaces

Tunneling-to-Hopping Transition in Multiheme Cytochrome Bioelectronic Junctions

Multiheme cytochromes (MHCs) have attracted much interest for use in nanobioelectronic junctions due to their high electronic conductances. Recent measurements on dry MHC junctions suggested that a coherent tunneling mechanism is operative over surprisingly long long distances (>3 nm), which challenges our understanding of coherent transport phenomena. Here we show that this is due to (i) a low exponential distance decay constant for coherent conduction in MHCs (β = 0.2 Å-1) and (ii) a large density of protein electronic states which prolongs the coherent tunneling regime to distances that exceed those in molecular wires made of small molecules. Incoherent hopping conduction is uncompetitive due to the large energy level offset at the protein-electrode interface. Removing this offset, e.g., by gating, we predict that the transport mechanism crosses over from coherent tunneling to incoherent hopping at a protein size of ∼7 nm, thus enabling transport on the micrometer scale with a shallow polynomial (∼1/r) distance decay

Exploring Rutile (110) and Anatase (101) TiO₂ Water Interfaces by Reactive Force-Field Simulations

We have investigated static/structural as well as dynamical properties of anatase (101) and rutile (110) TiO₂ interfaces with liquid bulk water by reactive force fields (ReaxFF). Layered, well-organized structure of water in the interface region was clearly observed within 6.5 Å of the surfaces. The first-hydration layer molecules adsorbed to unsaturated surface Ti atoms undergo spontaneous dissociation leading, rather controversially, to full coverage of O_2c/O_b by H⁺ and partial coverage of Ti_5c by OH^–. Expected large variations of intrinsic electric field on the interfaces, and drop of electrostatic potential, were detected. Interfacial water was found to be heavily confined with a self-diffusion constant of 2 orders of magnitude lower than 2.28 × 10^–9 m²/s measured in the bulk water region. Moreover, the rotational movement of adsorbed water molecules was found to be considerably hindered as well. On the other hand, the calculated hydrogen-bond lifetime on the interface was shorter than in bulk water for both surface types. Finally, the IR spectra obtained from collective-water-dipole variations in the interfacial region revealed stronger effects on stretching vibrations on anatase (101) than on rutile (110); however, description of liquid-water bond-stretching vibrations generally suffers from lack of accuracy in the applied reactive potential

Binding of piano-stool Ru(II) complexes to DNA; QM/MM study

Ru(II) “piano-stool” complexes belong to group of biologically active metallocomplexes with promising anticancer activity. In this study, we investigate the reaction mechanism of [(η6-benzene)Ru(II)(en)(H2O)]2+ (en = ethylenediamine) complex binding to DNA by hybrid QM/MM computational techniques. The reaction when the Ru(II) complex is coordinated on N7-guanine from major groove is explored. Two reaction pathways, direct binding to N7 position and two-step mechanism passing through O6 position, are considered. It was found that the reaction is exothermic and the direct binding process is preferred kinetically. In analogy to cisplatin, we also explored the possibility of intrastrand cross-link formation where the Ru(II) complex makes a bridge between two adjacent guanines. Two different pathways were found, leading to a final structure with released benzene ligand. This process is exothermic; however, one pathway is blocked by relatively high initial activation barrier. Geometries, energies, and electronic properties analyzed by atoms in molecules and natural population analysis methods are discussed

Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study

Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer

Hydrogen Intramolecular Stretch Redshift in the Electrostatic Environment of Type II Clathrate Hydrates from Schrödinger Equation Treatment

The one-dimensional Schr&ouml;dinger equation, applied to the H2 intramolecular stretch coordinate in singly to quadruply occupied large cages in extended Type II (sII) hydrogen clathrate hydrate, was solved numerically herein via potential-energy scans from classical molecular dynamics (MD), employing bespoke force-matched H2&ndash;water potential. For both occupation cases, the resultant H&ndash;H stretch spectra were redshifted by ~350 cm&minus;1 vis-&agrave;-vis their classically sampled counterparts, yielding semi-quantitative agreement with experimental Raman spectra. In addition, ab initio MD was carried out systematically for different cage occupations in the extended sII hydrate to assess the effect of differing intra-cage intrinsic electric field milieux on H&ndash;H stretch frequencies; we suggest that spatial heterogeneity of the electrostatic environment is responsible for some degree of peak splitting