Pseudodiagonalization-based wavefunction optimization with contracted planewave basis functions.

Electronic structure calculations representing the molecular orbitals (MOs) with contracted planewave basis functions (CPWBFs) have been reported recently. CPWBFs are Fourier-series representations of atom-centered basis functions. The mathematical features of CPWBFs permit the construction of matrix-vector products, FC o , involving the application of the Fock matrix, F, to the set of occupied MOs, C o , without the explicit evaluation of F. This approach offers a theoretical speed-up of M/n over F-based methods, where M and n are the number of basis functions and occupied MOs, respectively. The present study reports methodological advances that permit FC o -based optimization of wavefunction formed from CPWBFs. In particular, a technique is reported for optimizing wavefunctions by combining pseudodiagonalization techniques based on an exact representation of FC o , approximate information regarding the virtual orbital energies, and direct inversion of the iterative subspace optimization schemes to guide the wavefunction to a converged solution. This method is found to speed-up wavefunction optimizations by factors of up to ~6 - 8 over F-based optimization methods while providing identical results. Further, the computational cost of this technique is relatively insensitive to basis set size, thus providing further benefits in calculations using large CPWBF basis sets. The results of density functional theory calculations show that this method permits the use of hybrid exchange-correlation (XC) functionals with a small increase in effort over analogous calculations using generalized gradient approximation XC functionals. © 2019 Wiley Periodicals, Inc.

Direct inversion of the iterative subspace with contracted planewave basis functions.

Ways to reduce the computational cost of periodic electronic structure calculations by using basis functions corresponding to linear combinations of planewaves have been examined recently. These contracted planewave (CPW) basis functions correspond to Fourier series representations of atom-centered basis functions, and thus provide access to some beneficial properties of planewave (PW) and localized basis functions. This study reports the development and assessment of a direct inversion of the iterative subspace (DIIS) method that employs unique properties of CPW basis functions to efficiently converge electronic wavefunctions. This method relies on access to a PW-based representation of the electronic structure to provide a means of efficiently evaluating matrix-vector products involving the application of the Fock matrix to the occupied molecular orbitals. These matrix-vector products are transformed into a form permitting the use of direct diagonalization techniques and DIIS methods typically employed with atom-centered basis sets. The abilities of this method are assessed through periodic Hartree-Fock calculations of a range of molecules and solid-state systems. The results show that the method reported in this study is approximately five times faster than CPW-based calculations in which the entire Fock matrix is calculated. This method is also found to be weakly dependent upon the size of the basis set, thus permitting the use of larger CPW basis sets to increase variational flexibility with a minor impact on computational performance. © 2018 Wiley Periodicals, Inc.

Density-functional tight-binding investigation of the structure, stability and material properties of nickel hydroxide nanotubes.

Nickel hydroxide is a material composed of two-dimensional layers that can be rolled up to form cylindrical nanotubes belonging to a class of inorganic metal hydroxide nanotubes that are candidates for applications in catalysis, energy storage, and microelectronics. The stabilities and other properties of this class of inorganic nanotubes have not yet been investigated in detail. The present study uses self-consistent-charge density-functional tight-binding calculations to examine the stabilities, mechanical properties, and electronic properties of nickel hydroxide nanotubes along with the energetics associated with the adsorption of water by these systems. The tight-binding model was parametrized for this system based on the results of first-principles calculations. The stabilities of the nanotubes were examined by calculating strain energies and performing molecular dynamics simulations. The results indicate that single-walled nickel hydroxide nanotubes are stable at room temperature, which is consistent with experimental investigations. The nanotubes possess size-dependent mechanical properties that are similar in magnitude to those of other inorganic nanotubes. The electronic properties of the nanotubes were also found to be size-dependent and small nickel oxyhydroxide nanotubes are predicted to be semiconductors. Despite this size-dependence, both the mechanical and electronic properties were found to be almost independent of the helical structure of the nanotubes. The calculations also show that water molecules have higher adsorption energies when binding to the interior of the nickel hydroxide nanotubes when compared to adsorption in nanotubes formed from other two-dimensional materials such as graphene. The increased adsorption energy is due to the hydrophilic nature of nickel hydroxide. Due to the broad applications of nickel hydroxide, the nanotubes investigated here are also expected to be used in catalysis, electronics, and clean energy production.

Molecular structure and interactions of water intercalated in nickel hydroxide.

The structure and properties of α-Ni(OH)2 containing water and nitrate have been investigated computationally. The adsorption of water molecules on the Ni(OH)2 surface is also investigated to provide insight into the nature of the water-Ni(OH)2 interactions. The spectroscopic and dynamical behaviour of the intercalated species has been characterized and used to explain experimental findings reported for this material. The results presented here indicate that the water molecules interact non-covalently with Ni(OH)2, with a binding energy that is comparable in magnitude with that of the water dimer hydrogen bond. The presence of the intercalated species increases the distance between the Ni(OH)2 layers such that the interlayer interactions are negligible. The weakening of the interlayer interactions facilitates the horizontal displacement of the layers relative to one another, providing a possible origin for stacking faults observed in α-Ni(OH)2. Comparison of the vibrational frequencies calculated here with the experimental spectra confirms that α-Ni(OH)2 containing only water molecules can be synthesized. The structures of the water molecules intercalated in α-Ni(OH)2 were found to be analogous to those absorbed in γ-NiOOH, while the water-layer interactions are stronger in γ-NiOOH. The results presented here characterize the structure and interactions of water intercalated in nickel hydroxides and also provide insights into the effects of intercalated water on the properties of layered metal hydroxides.

N-Heterocyclic Carbene Self-assembled Monolayers on Copper and Gold: Dramatic Effect of Wingtip Groups on Binding, Orientation and Assembly.

Self-assembled monolayers of N-heterocyclic carbenes (NHCs) on copper are reported. The monolayer structure is highly dependent on the N,N-substituents on the NHC. On both Cu(111) and Au(111), bulky isopropyl substituents force the NHC to bind perpendicular to the metal surface while methyl- or ethyl-substituted NHCs lie flat. Temperature-programmed desorption studies show that the NHC binds to Cu(111) with a desorption energy of Edes =152±10 kJ mol-1 . NHCs that bind upright desorb cleanly, while flat-lying NHCs decompose leaving adsorbed organic residues. Scanning tunneling microscopy of methylated NHCs reveals arrays of covalently linked dimers which transform into adsorbed (NHC)2 Cu species by extraction of a copper atom from the surface after annealing.

Effects of reduced dimensionality on the properties of magnesium hydroxide and calcium hydroxide nanostructures.

Metal hydroxides are a class of layered materials that contain two-dimensional metal hydroxide layers that can be isolated to form layered nanostructures. In this work, density functional theory (DFT) and self-consistent-charge density-functional tight-binding (SCC-DFTB) methods have been used to investigate the properties of magnesium hydroxide and calcium hydroxide nanostructures. The properties of single layer and multi layer structures with up to 10 metal hydroxide sheets and nanoparticles containing more than 2000 atoms have been calculated and compared with the bulk properties of these systems. The accuracy of the DFT methods employed and SCC-DFTB parameters developed in this study were validated against available experimental data. The results of the calculations indicate that significant differences exist between the properties of the nanostructures and the corresponding bulk values. In particular, the interlayer binding energies, electronic band gaps, and spectroscopic features are size-dependent and tend to converge to the bulk values as the size of the nanosystem is increased. The calculated binding energies and shear moduli show that all nanostructures are mechanically stable, in agreement with the experimental reports; although, their stabilities may be affected by the presence of intercalated species. Energy decomposition analyses reveal that the intralayer interactions in the investigated systems are predominantly electrostatic in nature, while the interlayer interactions are dominated by dispersion and polarization components. The results presented here quantify various properties of magnesium hydroxide and calcium hydroxide nanostructures, and could be used to understand the properties of other nanosystems containing layers of metal hydroxides in their structure.

Exact exchange with non-orthogonal generalized Wannier functions.

The evaluation of exact exchange (EXX) is an important component of quantum chemical calculations performed with ab initio and hybrid density functional methods. While evaluating exact exchange is routine in molecular quantum chemical calculations performed with localized basis sets, the non-local nature of the exchange operator presents a major impediment to the efficient use of exact exchange in calculations that employ planewave basis sets. Non-orthogonal generalized Wannier functions (NGWFs) corresponding to planewave expansions of localized basis functions are an alternative form of basis set that can be used in quantum chemical calculations. The periodic nature of these functions renders them suitable for calculations of periodic systems, while the contraction of sets of planewaves into individual basis functions reduces the number of variational parameters, permitting the construction and direct diagonalization of the Fock matrix. The present study examines how NGWFs corresponding to Fourier series representations of conventional atom-centered basis sets can be used to evaluate exact exchange in periodic systems. Specifically, an approach for constructing the exchange operator with NGWFs is presented and used to perform Hartree-Fock calculations with a series of molecules in periodically repeated simulation cells. The results demonstrate that the NGWF approach is significantly faster than the EXX method, which is a standard approach for evaluating exact exchange in periodic systems.

High pressure chemistry of thioaldehydes: A first-principles molecular dynamics study.

First-principles molecular dynamics simulations are used to investigate the chemical behavior of bulk thioacetaldehyde (MeC(H)S) in response to changes in pressure, P. The simulations show that these molecules oligomerize in response to applied P. Oligomerization is initiated through C-S bond formation, with constrained dynamics simulations showing that the barrier to this reaction step is lowered significantly by applied P. Subsequent reactions involving the formation of additional C-S bonds or radical processes that lead to S-S and C-C bonds lengthen the oligomers. Oligomerization is terminated through proton transfer or the formation of rings. The mechanistic details of all reactions are examined. The results indicate that the P-induced reactivity of the MeC(H)S-based system differs significantly from that of analogous MeC(H)O-based systems, which have been reported previously. Comparison with the MeC(H)O study shows that replacing oxygen with sulfur significantly lowers the P required to initiate oligomerization (from 26 GPa to 5 GPa), increases the types of reactions in which systems of this type can take part, and increases the variety of products formed through these reactions. These differences can be explained in terms of the electronic structures of these systems, which may be useful for certain high P applications.

Theoretical Approaches for Understanding the Interplay Between Stress and Chemical Reactivity.

The use of mechanical stresses to induce chemical reactions has attracted significant interest in recent years. Computational modeling can play a significant role in developing a comprehensive understanding of the interplay between stresses and chemical reactivity. In this review, we discuss techniques for simulating chemical reactions occurring under mechanochemical conditions. The methods described are broadly divided into techniques that are appropriate for studying molecular mechanochemistry and those suited to modeling bulk mechanochemistry. In both cases, several different approaches are described and compared. Methods for examining molecular mechanochemistry are based on exploring the force-modified potential energy surface on which a molecule subjected to an external force moves. Meanwhile, it is suggested that condensed phase simulation methods typically used to study tribochemical reactions, i.e., those occurring in sliding contacts, can be adapted to study bulk mechanochemistry.

Tuning the mesomorphic properties of phenoxy-terminated smectic liquid crystals: the effect of fluoro substitution.

The mesomorphic properties of phenoxy-terminated 5-alkoxy-2-(4-alkoxyphenyl)pyrimidine liquid crystals can be tuned in a predictable fashion with fluoro substituents on the phenoxy end-group. We show that an ortho-fluoro substituent promotes the formation of a tilted smectic C (SmC) phase whereas a para-fluoro substituent promotes the formation of an orthogonal smectic A (SmA) phase. The balance between SmA and SmC phases may be understood in terms of the energetic preference of the phenoxy end-groups to self-assemble via arene-arene interactions in a parallel or antiparallel geometry, and how these non-covalent interactions may cause either a suppression or enhancement of out-of-layer fluctuations at the interface of smectic layers. Calculations of changes in the potential energy of association ΔE for non-covalent dimers of fluoro-substituted n-butyloxybenzene molecules in parallel and antiparallel geometries support this hypothesis. We also show how mesomorphic properties can be further tuned by difluoro and perfluoro substitution, including difluoro substitution at the ortho positions, which uniquely promotes the formation of a SmC-nematic phase sequence.

DFT computational study of the methanolytic cleavage of DNA and RNA phosphodiester models promoted by the dinuclear Zn(II) complex of 1,3-bis(1,5,9-triazacyclododec-1-yl)propane.

A density functional theory study of the cleavage of a DNA model [p-nitrophenyl methyl phosphate (2)] and two RNA models [p-nitrophenyl 2-hydroxypropyl phosphate (3) and phenyl 2-hydroxypropyl phosphate (4)] promoted by the dinuclear Zn((II)) complex of 1,3-bis(1,5,9-triazacyclododec-1-yl)propane formulated with a bridging methoxide (1a) was undertaken to determine possible mechanisms for the transesterification processes that are consistent with experimental data. The initial substrate-bound state of 2:1a or 3:1a has the two phosphoryl oxygens bridging Zn((II))1 and Zn((II))2. For each of 2 and 3, four possible mechanisms were investigated, three of which were consistent with the overall free energy for the catalytic cleavage step for each substrate. The computations revealed various roles for the metal ions in the three mechanisms. These encompass concerted or stepwise processes, where the two metal ions with associated alkoxy groups [Zn((II))1:((-)OCH3) and Zn((II))1:((-)O-propyl)] play the role of a direct nucleophile (on 2 and 3, respectively) or where Zn((II))1:((-)OCH3) can act as a general base to deprotonate an attacking solvent molecule in the case of 2 or the attacking 2-hydroxypropyl group in the case of 3. The Zn((II))2 ion can serve as a spectator (after exerting a Lewis acid role in binding one of the phosphates' oxygens) or play active additional roles in providing direct coordination of the departing aryloxy group or positioning a hydrogen-bonding solvent to assist the departure of the leaving group. An important finding revealed by the calculations is the flexibility of the ligand system that allows the Zn-Zn distance to expand from ~3.6 Å in 1a to over 5 Å in the transforming 2:1a and 3:1a complexes during the catalytic event.

Photo- and thermal-induced multistructural transformation of 2-phenylazolyl chelate boron compounds.

The new N,C-chelate boron compounds B(2-phenylazolyl)Mes2 [Mes = mesityl; azolyl = benzothiazolyl (1a), 4-methylthiazolyl (2a), benzoxazolyl (3a), benzimidazolyl (4a)] undergo an unprecedented multistructural transformation upon light irradiation or heating, sequentially producing isomers b, c, d, and e. The dark isomers b generated by photoisomerization of a undergo a rare thermal intramolecular H-atom transfer (HAT), reducing the azole ring and generating new isomers c, which are further transformed into isomers d. Remarkably, isomers d can be converted to their diastereomers e quantitatively by heating, and e can be converted back to d by irradiation at 300 nm. The structures of isomers 1d and 1e were established by X-ray diffraction. The unusual HAT reactivity can be attributed to the geometry of the highly energetic isomers b and the relatively low aromaticity of the azole rings. The boryl unit plays a key role in the reversible interconversion of d and e, as shown by mechanistic pathways established through DFT and TD-DFT calculations.

Stepwise intramolecular photoisomerization of NHC-chelate dimesitylboron compounds with C-C bond formation and C-H bond insertion.

C,C-chelate dimesitylboron (BMes(2)) compounds containing an N-heterocyclic carbene (NHC) donor have been obtained. Single-crystal X-ray diffraction analyses established that the boron atom in these compounds is bound by four carbon atoms in a distorted tetrahedral geometry. Compared to previously reported N,C-chelate dimesitylboron compounds, the new C,C-chelate boron compounds have a much larger HOMO-LUMO energy gap (>3.60 eV). They do, however, respond to UV irradiation (300 nm) in the same manner as N,C-chelate BMes(2) compounds do, undergoing photoisomerization and converting to an intensely colored (yellow or orange) isomer A quantitatively, with a high quantum efficiency (0.60-0.75). NMR and single-crystal X-ray diffraction analyses established that the structure of A is similar to the dark isomers obtained from N,C-chelate BMes(2) compounds. However, unlike the N,C-chelate dark isomers that have the tendency to thermally reverse back to the light colored isomers, the isomers A of the C,C-chelate BMes(2) are thermally stable and no reverse isomerization was observed even when heated to 80 °C (or 110 °C) for hours. The most unusual finding is that isomers A undergo further photoisomerization when irradiated at 350 nm, forming a new colorless species B nearly quantitatively. NMR and single-crystal X-ray diffraction analyses established the structure of isomer B, which may be considered as an intramolecular C-H insertion product via a borylene intermediate. Mechanistic aspects of this unusual two-step photoisomerization process have been examined by DFT computational studies.

Prediction of reaction barriers and force-induced instabilities under mechanochemical conditions with an approximate model: a case study of the ring opening of 1,3-cyclohexadiene.

Mechanochemistry, the use of mechanical stresses to activate chemical reactions, has emerged as a topic of significant interest. The present study examines the use of an approximate model for the prediction of reaction barriers under mechanochemical conditions using the ring opening of 1,3-cyclohexadiene along conrotatory and disrotatory directions as a specific test case. To do this, reaction barriers are evaluated using quantum chemical methods with an external force applied between various pairs of atoms. The results show that the consequent effects on the barrier exhibit a significant dependence on the locations of the atoms used to apply the external force, and in some cases, force-induced instabilities occur that alter the fundamental nature of the reaction pathway. The ability of an approximate model based on a second-order expansion of the force-modified potential energy with respect to nuclear coordinates to reproduce this behavior is then assessed. Good agreement between the results obtained through the quantum chemical calculations and approximate model is attained when force-induced instabilities do not occur. In addition, a strategy for predicting when such instabilities occur is presented and found to yield results that are in qualitative agreement with the quantum chemical calculations. Finally, the response of the system to the external force is interpreted in terms of the parameters entering the model, which correspond to interatomic distances and stiffnesses, and possibly sheds lights on ways to design molecules that exhibit a desired chemical response to mechanochemical conditions.

Methanolysis of thioamide promoted by a simple palladacycle is accelerated by 10(8) over the methoxide-catalyzed reaction.

Palladacycle 1 catalyzes the methanolytic cleavage of N-methyl-N-(4-nitrophenyl)thiobenzamide (4) via a mechanism involving formation of a Pd-bound tetrahedral intermediate (TI). The rate constant for decomposition of the complex formed between 1, methoxide, and 4 is 9.3 s(-1) at 25 °C; this reaction produces methyl thiobenzoate and N-methyl-4-nitroaniline. The ratio of the second-order rate constant for the catalyzed reaction, given as k(cat)/K(d), relative to that of the methoxide-promoted reaction is 3 × 10(8), representing a very large catalysis of thioamide bond cleavage by a synthetic metal complex.

Amine exchange in formamidines: an experimental and theoretical study.

N-H-containing formamidines combine a reasonably strong association to carboxylic acids to form complexes of well-defined geometries with a simultaneous proton-induced electrophilicity enhancement that allows for the exchange of their amine portion. The N=C(H)-NH fragment, therefore, undergoes "imine-like" exchange with N-containing nucleophiles. Because of the prototropic equilibrium, the N=C(H)-NH fragment may behave as a "bisimine" centred on the same carbon, in which both N-containing fragments can be exchanged. Considering the proton-induced sensitisation of both C-N units and the well-defined formamidine-carboxylic acid complex geometry, it should be possible to use carboxylic acids as templates for the synthesis of defined architectures by dynamic amine exchange within formamidines. This study highlights three exchange regimes based on the nature of the incoming amine (aliphatic amines, aromatic amines and alkoxyamines), as well as exchange rules based on the amine leaving groups. Following this analysis, a proof of concept for carboxylic acid templated macrocycle formation through dynamic exchange is provided.

The tensile strengths of heterogeneous interfaces: a comparison of static and dynamic first-principles calculations.

First-principles molecular dynamics (FPMD) simulations and static quantum chemical (QC) calculations are used to evaluate the tensile strengths, σ(c), of interfaces consisting of (0001) surfaces of α-Al(2)O(3) separated by small organic species. The evaluation of σ(c) with FPMD was achieved by performing simulations in which the simulation cell was extending in a direction normal to the fracture plane until rupture of the interface occurred. The static QC calculations employed an approach which treated fracture of the interface as a competition between uniform extension of the simulation cell and crack formation at the rupture site, which is analogous to that used in the construction of universal binding energy relationships. The results showed that the static QC calculations accurately reproduced the FPMD simulations with respect to tensile strength and the cell extension at which rupture occurred, provided that the rupture site employed in the static calculations matched the site at which rupture occurred during the FPMD simulations. A simple strategy for identifying the rupture site, even in complex systems containing many potential rupture sites, is proposed. Overall, the work extends the calculation of tensile strengths with static QC methods to highly heterogeneous interfaces, thus providing a computationally efficient alternative to demanding FPMD simulations for this purpose.

Chemical response of aldehydes to compression between (0001) surfaces of α-alumina.

First-principles molecular dynamics simulations are used to investigate the chemical response of acetaldehyde molecules (MeCHO) to compression and decompression between (0001) surfaces of α-alumina (Al(2)O(3)), with pressures reaching approximately 40 GPa. The results demonstrate that the MeCHO molecules are transformed into other chemical species through a range of chemical processes involving the formation of C-O and C-C bonds between MeCHO monomers as well as proton transfer. The mechanistic details of a representative set of the observed reactions are elucidated through analysis of maximally localized Wannier functions. Analysis of the changes in structure demonstrates that the main role of compression is to reduce the distances between MeCHO molecules to facilitate the formation of C-O bonds. Additional examination of the electronic structure demonstrates that the surface plays a role in facilitating proton transfer by both rendering hydrogen atoms in adsorbed MeCHO molecules more acidic and by acting as a proton acceptor. In addition, adsorption of the MeCHO molecules on the surface renders the sp(2) carbon atoms in these molecules more electrophilic, which promotes the formation of C-C and C-O bonds. It is suggested that the reaction products may be beneficial in the context of wear inhibition. Comparison of the surface structure before compression and after decompression demonstrates that the aldehydes and reaction products are capable of inhibiting irreversible changes in the structure as long as there is at least a monolayer coverage of these species. As a whole, the study sheds light on the chemical behavior of the aldehydes in response to uniaxial compression in nanoscopic contacts that likely applies to other molecules containing carbonyl groups and other metal oxide surfaces.

Exciting clusters, what does off-resonance actually mean?

Noble metal clusters have unique photophysical properties, especially as a new class of materials for multiphoton biomedical imaging. The previously studied Au25SR18 exhibits "giant" two-photon absorbance cross sections. Herein, we investigate the origins of the large two photon absorption for Au25SR18, as well as 10 other Au and Ag clusters using femtosecond pump/probe transient absorption spectroscopy (fsTAS). Excited state absorbance (ESA) ubiquitous to thiolated Au and Ag clusters is used herein as an optical signature of two-photon absorbances of the 11 different Au and Ag clusters, which does not require high quantum yields of emission. The large selection of clusters, studied with a single laser system, allows us to draw conclusions on the role of the particular metal, cluster size/structure, and the effects of the ligands on the ability to absorb multiple NIR photons. The use of a laser with a 1028 nm excitation also allows us to investigate the dramatic effect of excitation wavelength and explain why laser wavelength has led to large variances in the non-linear responses reported for clusters to date. We discuss the double resonance mechanism, responsible for giant two photon absorbance cross-sections, helping match properties of metal clusters with experimental conditions for maximizing signal/response in multiphoton applications.

In Situ Formation of Nano Ni-Co Oxyhydroxide Enables Water Oxidation Electrocatalysts Durable at High Current Densities.

The oxygen evolution reaction (OER) limits the energy efficiency of electrocatalytic systems due to the high overpotential symptomatic of poor reaction kinetics; this problem worsens over time if the performance of the OER electrocatalyst diminishes during operation. Here, a novel synthesis of nanocrystalline Ni-Co-Se using ball milling at cryogenic temperature is reported. It is discovered that, by anodizing the Ni-Co-Se structure during OER, Se ions leach out of the original structure, allowing water molecules to hydrate Ni and Co defective sites, and the nanoparticles to evolve into an active Ni-Co oxyhydroxide. This transformation is observed using operando X-ray absorption spectroscopy, with the findings confirmed using density functional theory calculations. The resulting electrocatalyst exhibits an overpotential of 279 mV at 0.5 A cm-2 and 329 mV at 1 A cm-2 and sustained performance for 500 h. This is achieved using low mass loadings (0.36 mg cm-2 ) of cobalt. Incorporating the electrocatalyst in an anion exchange membrane water electrolyzer yields a current density of 1 A cm-2 at 1.75 V for 95 h without decay in performance. When the electrocatalyst is integrated into a CO2 -to-ethylene electrolyzer, a record-setting full cell voltage of 3 V at current density 1 A cm-2 is achieved.