Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds

Rationalization of the light-induced electron injection mechanism in a model 1D ZnO nanowire-dye complex: insights from real-time TD-DFTB simulations

Zinc oxide nanowires (ZnO NWs) possess a unique one-dimensional (1D) morphology that offers a direct pathway for charge transport. In this article, we present the first application of the real-time time-dependent density functional tight-binding (real-time TD-DFTB) method for a model hybrid system consisting of a catechol molecule adsorbed on a ZnO nanowire. The rationalization of the photoinduced electron injection to the 1D nanostructure is attained through quantum dynamics simulations, stressing the role of charge transfer in the new optical transitions upon dye adsorption. We provide a momentum-resolved picture of the photoexcitation dynamics, highlighting the charge accumulation in certain k-points, which could improve our understanding of these ultrafast processes. Finally, in the context of dye-sensitized solar cells (DSSCs) based on ZnO NW arrays, we provide a method to calculate the photoresponse obtaining similar results to experiments. This work paves the way towards the fast and accurate theoretical design of 1D optoelectronic nanodevices.

Polarization Controlled Assembly of Ultrathin Thiorphan Nanostructures on ZnO Surface Facets

Despite the importance of thiorphan as a small molecule with vital biological roles, its interactions with zinc oxide (ZnO) nanomaterials that are prospective in drug delivery and theranostic applications have not yet been sufficiently explored. Here the impact of surface polarity of different ZnO facets on thiorphan adsorption is studied both experimentally by atomic force microscopy (AFM) and angle resolved X-ray photoelectron spectroscopy (XPS) and theoretically by force field molecular dynamics (FFMD) and density functional tight binding simulations (DFTB). Polar ZnO surfaces cause the formation of thiorphan nanodots, where the size of the nanodots depends on the direction of dipoles: small (4 nm) nanodots are formed on Zn-face ZnO, while large (25 nm) nanodots are formed on O-face ZnO. Nonpolar ZnO surfaces cause self-assembly into layered nanoislands with characteristic 4 nm layer thickness, which subsequently merge into rigid nanolayers. The self-assembly is shown to be controlled solely by the effect of surface dipole electric field orientation and magnitude, whereas effects of surface chemistry or solution are negligible. The results thus also show a way for controlling the assembly of thiorphan and other molecular nanomaterials for diverse applications.

Unusual CO2 Adsorption in ZIF-7: Insight from Raman Spectroscopy and Computational Studies

Here, we use Raman spectroscopy to investigate temperature-dependent changes in the atomic-scale structure of the zeolitic imidazolate framework ZIF-7 in a CO₂ atmosphere and uncover the mechanism of maximal CO₂ adsorption at 206 K. At 301 K, the Raman spectra of ZIF-7 at various CO₂ gas pressures reveal a narrow-pore (np) to large-pore (lp) phase transition commencing at 0.1 bar as a result of adsorption of CO₂, as evident in the appearance of Fermi resonance bands of CO₂ at 1272 and 1376 cm^-1. Moreover, the Raman inactive bending mode of CO₂ becomes active due to geometrical distortion of adsorbed CO₂. It further splits into two peaks due to hydrogen bonding interactions between CO₂ and the benzene ring of the benzimidazole linker ZIF-7, as supported by our computational studies. In addition, the interaction between CO₂ molecules plays a key role. Upon reducing the temperature at 1 bar CO₂ gas pressure, ZIF-7 exhibits softening of the imidazole puckering mode and the Fermi resonance CO₂ band due to interactions between CO₂ and the framework through hydrogen bonding. At 206 K, substantial modification in the lattice mode and disappearance of the Raman inactive CO₂ bending mode confirm the changes in the size of the pore cavity through structural rearrangements of CO₂.

Nonlinear Reaction Coordinate of an Enzyme Catalyzed Proton Transfer Reaction

We present an in-depth study on the theoretical calculation of an optimum reaction coordinate as a linear or nonlinear combination of important collective variables (CVs) sampled from an ensemble of reactive transition paths for an intramolecular proton transfer reaction catalyzed by the enzyme human carbonic anhydrase (HCA) II. The linear models are optimized by likelihood maximization for a given number of CVs. The nonlinear models are based on an artificial neural network with the same number of CVs and optimized by minimizing the root-mean-square error in comparison to a training set of committor estimators generated for the given transition. The nonlinear reaction coordinate thus obtained yields the free energy of activation and rate constant as 9.46 kcal mol^-1 and 1.25 × 10⁶ s^-1, respectively. These estimates are found to be in quantitative agreement with the known experimental results. We have also used an extended autoencoder model to show that a similar analysis can be carried out using a single CV only. The resultant free energies and kinetics of the reaction slightly overestimate the experimental data. The implications of these results are discussed using a detailed microkinetic scheme of the proton transfer reaction catalyzed by HCA II.

Strong Structural and Electronic Binding of Bovine Serum Albumin to ZnO via Specific Amino Acid Residues and Zinc Atoms

ZnO biointerfaces with serum albumin have attracted noticeable attention due to the increasing interest in developing ZnO-based materials for biomedical applications. ZnO surface morphology and chemistry are expected to play a critical role on the structural, optical, and electronic properties of albumin-ZnO complexes. Yet there are still large gaps in the understanding of these biological interfaces. Herein we comprehensively elucidate the interactions at such interfaces by using atomic force microscopy and nanoshaving experiments to determine roughness, thickness, and adhesion properties of BSA layers adsorbed on the most typical polar and non-polar ZnO single-crystal facets. These experiments are corroborated by force field (FF) and density-functional tight-binding (DFTB) calculations on ZnO-BSA interfaces. We show that BSA adsorbs on all the studied ZnO surfaces while interactions of BSA with ZnO are found to be considerably affected by the atomic surface structure of ZnO. BSA layers on the ( 000 1 ‾ ) surface have the highest roughness and thickness, hinting at a specific upright BSA arrangement. BSA layers on ( 10 1 ‾ 0 ) surface have the strongest binding, which is well correlated with DFTB simulations showing atomic rearrangement and bonding between specific amino acids (AAs) and ZnO. Besides the structural properties, the ZnO interaction with these AAs also controls the charge transfer and HOMO-LUMO energy positions in the BSA-ZnO complexes. This ZnO facet-specific protein binding and related structural and electronic effects can be useful for improving the design and functionality of ZnO-based materials and devices.

Visualizing the {110} surface structure of equilibrium-form ZIF-8 crystals by low-dose Cs-corrected TEM

The properties of zeolitic imidazolate framework (ZIF) crystals highly depend on the structures of the low-energy surfaces, such as {110} of ZIF-8. However, the atomic/molecular configurations of the ZIF-8 {110} surfaces remain debated. In this study, the near-atomic-scale characterization of {110} surfaces of ZIF-8 is conducted by low-dose aberration-corrected transmission electron microscopy (TEM). The real-space images with mitigated surface delocalization by minimized spherical aberration of TEM, together with the solvent corrected surface energy calculations, demonstrate that the {110} surfaces of ZIF-8 crystals with an equilibrium-form rhombic morphology have a zigzag-type termination. This study provides experimental evidence to clarify the debated structure of {110} ZIF-8 surfaces and has important implications in understanding the crystal growth and surface related properties of ZIF-8.

Development of Density-Functional Tight-Binding Parameters for the Molecular Dynamics Simulation of Zirconia, Yttria, and Yttria-Stabilized Zirconia

In this work, a set of density-functional tight-binding (DFTB) parameters for the Zr-Zr, Zr-O, Y-Y, Y-O, and Zr-Y interactions was developed for bulk and surface simulations of ZrO₂ (zirconia), Y₂O₃ (yttria), and yttria-stabilized zirconia (YSZ) materials. The parameterization lays the ground work for realistic simulations of zirconia-, yttria-, and YSZ-based electrolytes in solid oxide fuel cells and YSZ-based catalysts on long timescales and relevant size scales. The parameterization was validated for the zirconia and yttria polymorphs observed under standard conditions based on density functional theory calculations and experimental data. Additionally, we performed DFTB-based molecular dynamics (MD) simulations to compute structural and vibrational properties of these materials. The results show that the parameters can give a qualitatively correct phase ordering of zirconia, where the tetragonal phase is more stable than the cubic phase at a lower temperature. The lattice parameters are only slightly overestimated by 0.05-0.1 Å (2% error), still within the typical accuracy of first-principles methods. Additionally, the MD results confirm that zirconia and yttria phases are stable against transformations under standard conditions. The parameterization also predicts that vibrational spectra are within the range of 100-1000 cm^-1 for zirconia and 100-800 cm^-1 for yttria, which is in good agreement with predictions both from full quantum mechanics and a recently developed classical force field. To further demonstrate the advantage of the developed DFTB parameters in terms of computational resources, we conducted DFTB/MD simulations of the YSZ4 and YS12 models containing approximately 750 atoms.

Role of Host-Guest Interaction in Understanding Polymerisation in Metal-Organic Frameworks

Metal-organic frameworks, MOFs, offer an effective template for polymerisation of polymers with precisely controlled structures within the sub-nanometre scales. However, synthetic difficulties such as monomer infiltration, detailed understanding of polymerisation mechanisms within the MOF nanochannels and the mechanism for removing the MOF template post polymerisation have prevented wide scale implementation of polymerisation in MOFs. This is partly due to the significant lack in understanding of the energetic and atomic-scale intermolecular interactions between the monomers and the MOFs. Consequently in this study, we explore the interaction of varied concentration of styrene, and 3,4-ethylenedioxythiophene (EDOT), at the surface and in the nanochannel of Zn₂(1,4-ndc)₂ (dabco), where 1,4-ndc = 1,4-naphthalenedicarboxylate and dabco = 1,4-diazabicyclo[2.2.2]octane. Our results showed that the interactions between monomers are stronger in the nanochannels than at the surfaces of the MOF. Moreover, the MOF-monomer interactions are strongest in the nanochannels and increase with the number of monomers. However, as the number of monomers increases, the monomers turn to bind more strongly at the surface leading to a potential agglomeration of the monomers at the surface.

ParAMS: Parameter Optimization for Atomistic and Molecular Simulations

This work introduces ParAMS-a versatile Python package that aims to make parametrization workflows in computational chemistry and physics more accessible, transparent, and reproducible. We demonstrate how ParAMS facilitates the parameter optimization for potential energy surface (PES) models, which can otherwise be a tedious specialist task. Because of the package's modular structure, various functionality can be easily combined to implement a diversity of parameter optimization protocols. For example, the choice of PES model and the parameter optimization algorithm can be selected independently. An illustration of ParAMS' strengths is provided in two case studies: (i) a density functional-based tight binding (DFTB) repulsive potential for the inorganic ionic crystal ZnO and (ii) a ReaxFF force field for the simulation of organic disulfides.

Curvature Constrained Splines for DFTB Repulsive Potential Parametrization

The Curvature Constrained Splines (CCS) methodology has been used for fitting repulsive potentials to be used in SCC-DFTB calculations. The benefit of using CCS is that the actual fitting of the repulsive potential is performed through quadratic programming on a convex objective function. This guarantees a unique (for strictly convex) and optimum two-body repulsive potential in a single shot, thereby making the parametrization process robust, and with minimal human effort. Furthermore, the constraints in CCS give the user control to tune the shape of the repulsive potential based on prior knowledge about the system in question. Herein, we developed the method further with new constraints and the capability to handle sparse data. We used the method to generate accurate repulsive potentials for bulk Si polymorphs and demonstrate that for a given Slater-Koster table, which reproduces the experimental band structure for bulk Si in its ground state, we are unable to find one single two-body repulsive potential that can accurately describe the various bulk polymorphs of silicon in our training set. We further demonstrate that to increase transferability, the repulsive potential needs to be adjusted to account for changes in the chemical environment, here expressed in the form of a coordination number. By training a near-sighted Atomistic Neural Network potential, which includes many-body effects but still essentially within the first-neighbor shell, we can obtain full transferability for SCC-DFTB in terms of describing the energetics of different Si polymorphs.

Analytical approach to phonon calculations in the SCC-DFTB framework

Detailed derivation of the analytical, reciprocal-space approach of Hessian calculation within the self-consistent-charge density-functional based tight-binding framework (SCC-DFTB) is presented. This approach provides an accurate and efficient way for obtaining the SCC-DFTB Hessian of periodic systems. Its superiority with respect to the traditional numerical force differentiation method is demonstrated for doped graphene, graphene nanoribbons, boron-nitride nanotubes, bulk zinc-oxide, and other systems.

SARS-CoV-2 Virion Stabilization by Zn Binding

Zinc plays a crucial role in the process of virion maturation inside the host cell. The accessory Cys-rich proteins expressed in SARS-CoV-2 by genes ORF7a and ORF8 are likely involved in zinc binding and in interactions with cellular antigens activated by extensive disulfide bonds. In this report we provide a proof of concept for the feasibility of a structural study of orf7a and orf8 proteins. A conceivable hypothesis is that lack of cellular zinc, or substitution thereof, might lead to a significant slowing down of viral maturation.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

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 orfunctionalized 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.

Orthogonal order parameters to model the reaction coordinate of an enzyme catalyzed reaction

The choice of suitable collective variables in formulating an optimal reaction coordinate is a challenging task for activated transitions between a pair of stable states especially when dealing with biochemical changes such as enzyme catalyzed reactions. A detailed benchmarking study is carried out on the choice of collective variables that can distinguish between the stable states unambiguously. We specifically address the issue if these variables may be directly used to model the optimal reaction coordinate, or if it would be better to use their orthogonalized counterparts. The proposed computational scheme is applied to the rate determining intramolecular proton transfer step in the enzyme human carbonic anhydrase II. The optimum reaction coordinate is determined with and without orthogonalization of the collective variables pertinent to a key conformational fluctuation and the actual proton transfer step at the active site of the enzyme. Suitability of the predicted reaction coordinates in different processes is examined in terms of the free energy profile projected along the reaction coordinate, the rate constant of transition and the underlying molecular mechanism of barrier crossing. Our results indicate that a better agreement with earlier simulation and experimental data is obtained when the orthogonalized collective variables are used to model the reaction coordinate.

Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold

Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical properties of gold and silver materials. After a brief overview of the theoretical basis of DFTB, its parametrization and its transferability, we report its past and recent applications to gold and silver systems, including small clusters, nanoparticles, bulk and surfaces, bare and interacting with various organic and inorganic compounds. The range of applications covered by those studies goes from plasmonics and molecular electronics, to energy conversion and surface chemistry. Finally, perspectives of DFTB in the field of gold and silver surfaces and NPs are outlined.

Characterization of ZnO as substrate for DSSC

We present a complete analysis of the photoinjection process in 3 nm spherical ZnO nanoparticles with different dyes attached to their surface.

Molecular dynamics simulations of zinc oxide solubility: From bulk down to nanoparticles

The solubility of metal oxides is one of the key descriptors for the evaluation of their potential toxic effects, both in the bulk form and in nanoparticulated aggregates. Current work presents a new methodology for the in silico assessment of the solubility of metal oxides, which is demonstrated using a well-studied system, ZnO. The calculation of the solubility is based on statistical thermodynamics tools combined with Density Functional Tight Binding theory for the evaluation of the free energy exchange during the dissolution process. Models of small ZnO clusters are used for describing the final dissolved material, since the complete ionic dissolution of ZnO is hindered by the formation of O^2- anions in solution, which are highly unstable. Results show very good agreement between the computed solubility values and experimental data for ZnO bulk, up to 0.5 mg L^-1 and equivalents of 50 μg L^-1 for the free Zn²⁺ cation in solution. However, the reference model for solid nanoparticles formed by free space nanoparticles can only give a limited quantitative solubility evaluation for ZnO nanoparticles.

On-the-Fly QM/MM Docking with Attracting Cavities

We developed a hybrid quantum mechanical/molecular mechanical (QM/MM) on-the-fly docking algorithm to address the challenges of treating polarization and selected metal interactions in docking. The algorithm is based on our classical docking algorithm Attracting Cavities and relies on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. We benchmarked the performance of this approach on three very diverse data sets: (1) the Astex Diverse set of 85 common noncovalent drug/target complexes formed both by hydrophobic and electrostatic interactions; (2) a zinc metalloprotein data set of 281 complexes, where polarization is strong and ligand/protein interactions are dominated by electrostatic interactions; and (3) a heme protein data set of 72 complexes, where ligand/protein interactions are dominated by covalent ligand/iron binding. Redocking performance of the on-the-fly QM/MM docking algorithm was compared to the performance of classical Attracting Cavities, AutoDock, AutoDock Vina, and GOLD. The results demonstrate that the QM/MM code preserves the high accuracy of most classical scores on the Astex Diverse set, while it yields significant improvements on both sets of metalloproteins at moderate computational cost.

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.

Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome

Sotos syndrome is an overgrowth syndrome caused by mutations within the functional domains ofNSD1 gene coding for NSD1, a multidomain protein regulating chromatin structure and gene expression. In particular, PHDVC5HCHNSD1 tandem domain, composed by a classical (PHDV) and an atypical (C5HCH) plant homeo-domain (PHD) finger, is target of several pathological missense-mutations. PHDVC5HCHNSD1 is also crucial for NSD1-dependent transcriptional regulation and interacts with the C2HR domain of transcriptional repressor Nizp1 (C2HRNizp1)in vitro To get molecular insights into the mechanisms dictating the patho-physiological relevance of the PHD finger tandem domain, we solved its solution structure and provided a structural rationale for the effects of seven Sotos syndrome point-mutations. To investigate PHDVC5HCHNSD1 role as structural platform for multiple interactions, we characterized its binding to histone H3 peptides and to C2HRNizp1 by ITC and NMR. We observed only very weak electrostatic interactions with histone H3 N-terminal tails, conversely we proved specific binding to C2HRNizp1 We solved C2HRNizp1 solution structure and generated a 3D model of the complex, corroborated by site-directed mutagenesis. We suggest a mechanistic scenario where NSD1 interactions with cofactors such as Nizp1 are impaired by PHDVC5HCHNSD1 pathological mutations, thus impacting on the repression of growth-promoting genes, leading to overgrowth conditions.

Computational prediction of optimal metal ions to induce coordinated polymerization of muscle-like [c2]daisy chains

Schematic representations of the polymerized [c2]daisy chain linked with Fe²⁺ in contracted vs. elongated forms by computational simulation.

Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations

Snake venom metalloproteinases are important toxins that play fundamental roles during envenomation. They share a structurally similar catalytic domain, but with diverse hemorrhagic capabilities. To understand the structural basis for this difference, we build and compare two dynamical models, one for the hemorrhagic atroxlysin-I from Bothrops atrox and the other for the non-hemorraghic leucurolysin-a from Bothrops leucurus. The analysis of the extended molecular dynamics simulations shows some changes in the local structure, flexibility and surface determinants that can contribute to explain the different hemorrhagic activity of the two enzymes. In agreement with previous results, the long Ω-loop (from residue 149 to 177) has a larger mobility in the hemorrhagic protein. In addition, we find some potentially-relevant differences at the base of the S1' pocket, what may be interesting for the structure-based design of new anti-venom agents. However, the sharpest differences in the computational models of atroxlysin-I and leucurolysin-a are observed in the surface electrostatic potential around the active site region, suggesting thus that the hemorrhagic versus non-hemorrhagic activity is probably determined by protein surface determinants.

DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters

We report the parametrization of a density functional tight binding method (DFTB3) for copper in a spin-polarized formulation. The parametrization is consistent with the framework of 3OB for main group elements (ONCHPS) and can be readily used for biological applications that involve copper proteins/peptides. The key to our parametrization is to introduce orbital angular momentum dependence of the Hubbard parameter and its charge derivative, thus allowing the 3d and 4s orbitals to adopt different sizes and responses to the change of charge state. The parametrization has been tested by applying to a fairly broad set of molecules of biological relevance, and the properties of interest include optimized geometries, ligand binding energies, and ligand proton affinities. Compared to the reference QM level (B3LYP/aug-cc-pVTZ, which is shown here to be similar to the B97-1 and CCSD(T) results, in terms of many properties of interest for a set of small copper containing molecules), our parametrization generally gives reliable structural properties for both Cu(I) and Cu(II) compounds, although several exceptions are also noted. For energetics, the results are more accurate for neutral ligands than for charged ligands, likely reflecting the minimal basis limitation of DFTB3; the results generally outperform NDDO based methods such as PM6 and even PBE with the 6-31+G(d,p) basis. For all ligand types, single-point B3LYP calculations at DFTB3 geometries give results very close (∼1-2 kcal/mol) to the reference B3LYP values, highlighting the consistency between DFTB3 and B3LYP structures. Possible further developments of the DFTB3 model for a better treatment of transition-metal ions are also discussed. In the current form, our first generation of DFTB3 copper model is expected to be particularly valuable as a method that drives sampling in systems that feature a dynamical copper binding site.

Gold as an intruder in ZnO nanowires

Several techniques for obtaining ZnO nanowires (ZnO NWs) have been reported in the literature. In particular, vapour-liquid-solid (VLS) with Au as a catalyst is widely used. During this process, Au impurities in the ZnO NWs can be incorporated accidentally, and for this reason we named these impurities as intruders. It is thought that these intruders may produce interesting alterations in the electronic characteristics of nanowires. In the experiment, it is not easy to detect either Au atoms in these nanowires, or the modification that intruders produce in different electrical, optical and other properties. For this reason, in this density functional theory investigation, the effect of Au intruders on ZnO NWs is analysed. Au extended (thread) and point defects (atoms replacing Zn or O, or Au interstitials) are used to simulate the presence of gold atoms. Optimised geometries, band-gaps and density of states indicate that the presence of small amounts of Au drastically modifies the electronic states of ZnO NWs. The results reported here clearly indicate that small amounts of Au have a strong impact on the electronic properties of ZnO NWs, introducing states in the band edges that may promote transitions in the visible spectral region. The presence of Au as an intruder in ZnO NWs enhances the potential use of this system for photonic and photovoltaic applications.

Temperature-dependent and bistable current-voltage measurements in zinc porphyrin molecular junctions

We report bistability in current-voltage curves from di(PEP)PorZn in an electromigrated molecular junction. Bistability was observed at ±0.3 V at 300 K but did not occur at 4 K. No bistability was identified at 300 K for another porphyrin molecule (di(Xyl)PorZn), where the phenyl-ethnyl-phenyl (PEP) side groups were replaced with a flexible p-xylene. Molecular dynamics simulations show that bistability may be due to conformation changes related to the fluctuation of the dihedral angle surrounding the zinc and/or the rotation of the porphyrin central plane of the molecule. Results suggest that other mechanisms may play a role in the current-voltage characteristics observed.

Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications

We report the parametrization of the approximate density functional theory, DFTB3, for magnesium and zinc for chemical and biological applications. The parametrization strategy follows that established in previous work that parametrized several key main group elements (O, N, C, H, P, and S). This 3OB set of parameters can thus be used to study many chemical and biochemical systems. The parameters are benchmarked using both gas-phase and condensed-phase systems. The gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization (MIO). The results indicate that DFTB3/3OB is particularly successful at predicting structures, including rather complex dinuclear metalloenzyme active sites, while being semiquantitative (with a typical mean absolute deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point calculations with high-level quantum mechanics (QM) methods generally lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic properties. DFTB3/MM simulations for solution and two enzyme systems also lead to encouraging structural and energetic properties in comparison to available experimental data. The remaining limitations of DFTB3, such as the treatment of interaction between metal ions and highly charged/polarizable ligands, are also discussed.

Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications

We report the parametrization of the approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The parametrization is done in a framework consistent with our previous 3OB set established for O, N, C, and H, thus the resulting parameters can be used to describe a broad set of organic and biologically relevant molecules. The 3d orbitals are included in the parametrization, and the electronic parameters are chosen to minimize errors in the atomization energies. The parameters are tested using a fairly diverse set of molecules of biological relevance, focusing on the geometries, reaction energies, proton affinities, and hydrogen bonding interactions of these molecules; vibrational frequencies are also examined, although less systematically. The results of DFTB3/3OB are compared to those from DFT (B3LYP and PBE), ab initio (MP2, G3B3), and several popular semiempirical methods (PM6 and PDDG), as well as predictions of DFTB3 with the older parametrization (the MIO set). In general, DFTB3/3OB is a major improvement over the previous parametrization (DFTB3/MIO), and for the majority cases tested here, it also outperforms PM6 and PDDG, especially for structural properties, vibrational frequencies, hydrogen bonding interactions, and proton affinities. For reaction energies, DFTB3/3OB exhibits major improvement over DFTB3/MIO, due mainly to significant reduction of errors in atomization energies; compared to PM6 and PDDG, DFTB3/3OB also generally performs better, although the magnitude of improvement is more modest. Compared to high-level calculations, DFTB3/3OB is most successful at predicting geometries; larger errors are found in the energies, although the results can be greatly improved by computing single point energies at a high level with DFTB3 geometries. There are several remaining issues with the DFTB3/3OB approach, most notably its difficulty in describing phosphate hydrolysis reactions involving a change in the coordination number of the phosphorus, for which a specific parametrization (3OB/OPhyd) is developed as a temporary solution; this suggests that the current DFTB3 methodology has limited transferability for complex phosphorus chemistry at the level of accuracy required for detailed mechanistic investigations. Therefore, fundamental improvements in the DFTB3 methodology are needed for a reliable method that describes phosphorus chemistry without ad hoc parameters. Nevertheless, DFTB3/3OB is expected to be a competitive QM method in QM/MM calculations for studying phosphorus/sulfur chemistry in condensed phase systems, especially as a low-level method that drives the sampling in a dual-level QM/MM framework.

Stacking Faults and Mechanical Behavior beyond the Elastic Limit of an Imidazole-Based Metal Organic Framework: ZIF-8

We determine the nonlinear mechanical behavior of a prototypical zeolitic imidazolate framework (ZIF-8) along two modes of mechanical failure in response to tensile and shear forces using first-principles simulations. Our generalized stacking fault energy surface reveals an intrinsic stacking fault of surprisingly low energy comparable to that in copper, though the energy barrier associated with its formation is much higher. The lack of vibrational spectroscopic evidence for such faults in experiments can be explained with the structural instability of the barrier state to form a denser and disordered state of ZIF-8 seen in our analysis, that is, large shear leads to its amorphization rather than formation of faults.

An SCC-DFTB Repulsive Potential for Various ZnO Polymorphs and the ZnO-Water System

We have developed an efficient scheme for the generation of accurate repulsive potentials for self-consistent charge density-functional-based tight-binding calculations, which involves energy-volume scans of bulk polymorphs with different coordination numbers. The scheme was used to generate an optimized parameter set for various ZnO polymorphs. The new potential was subsequently tested for ZnO bulk, surface, and nanowire systems as well as for water adsorption on the low-index wurtzite (101̅0) and (112̅0) surfaces. By comparison to results obtained at the density functional level of theory, we show that the newly generated repulsive potential is highly transferable and capable of capturing most of the relevant chemistry of ZnO and the ZnO/water interface.