Bond formation insights into the Diels-Alder reaction: A bond perception and self-interaction perspective.

The behavior of electrons during bond formation and breaking cannot commonly be accessed from experiments. Thus, bond perception is often based on chemical intuition or rule-based algorithms. Utilizing computational chemistry methods, we present intrinsic bond descriptors for the Diels-Alder reaction, allowing for an automatic bond perception. We show that these bond descriptors are available from localized orbitals and self-interaction correction calculations, e.g., from Fermi-orbital descriptors. The proposed descriptors allow a sparse, simple, and educational inspection of the Diels-Alder reaction from an electronic perspective. We demonstrate that bond descriptors deliver a simple visual representation of the concerted bond formation and bond breaking, which agrees with Lewis' theory of bonding.

A theoretical investigation into gallic acid pyrolysis.

Thermodynamic and kinetic information on the first two steps of gallic acid pyrolysis, a decarboxylation followed by a dehydrogenation, is obtained based on density functional theory and quantum chemistry. For the kinetics, transition states are identified with the help of the climbing image nudged elastic band method. Both reactions exhibit two transition states. One of them is related to the rotation of OH groups, and the other one is related to the breaking and forming of bonds. The gallic acid pyrolysis as a whole is judged to be endothermal, and it changes from endergonic to exergonic between 500 and 750 K. The second reaction, the dehydrogenation of pyrogallol, is identified as the rate-determining step of gallic acid pyrolysis, with reaction rate constants below 1 s-1 for temperatures below 1250 K.

Chemical bonding theories as guides for self-interaction corrected solutions: Multiple local minima and symmetry breaking.

Fermi-Löwdin orbitals (FLOs) are a special set of localized orbitals, which have become commonly used in combination with the Perdew-Zunger self-interaction correction (SIC) in the FLO-SIC method. The FLOs are obtained for a set of occupied orbitals by specifying a classical position for each electron. These positions are known as Fermi-orbital descriptors (FODs), and they have a clear relation to chemical bonding. In this study, we show how FLOs and FODs can be used to initialize, interpret, and justify SIC solutions in a common chemical picture, both within FLO-SIC and in traditional variational SIC, and to locate distinct local minima in either of these approaches. We demonstrate that FLOs based on Lewis theory lead to symmetry breaking for benzene-the electron density is found to break symmetry already at the symmetric molecular structure-while ones from Linnett's double-quartet theory reproduce symmetric electron densities and molecular geometries. Introducing a benchmark set of 16 planar cyclic molecules, we show that using Lewis theory as the starting point can lead to artifactual dipole moments of up to 1 D, while Linnett SIC dipole moments are in better agreement with experimental values. We suggest using the dipole moment as a diagnostic of symmetry breaking in SIC and monitoring it in all SIC calculations. We show that Linnett structures can often be seen as superpositions of Lewis structures and propose Linnett structures as a simple way to describe aromatic systems in SIC with reduced symmetry breaking. The role of hovering FODs is also briefly discussed.

PyFLOSIC: Python-based Fermi-Löwdin orbital self-interaction correction.

We present pyflosic, an open-source, general-purpose python implementation of the Fermi-Löwdin orbital self-interaction correction (FLO-SIC), which is based on the python simulation of chemistry framework (pyscf) electronic structure and quantum chemistry code. Thanks to pyscf, pyflosic can be used with any kind of Gaussian-type basis set, various kinds of radial and angular quadrature grids, and all exchange-correlation functionals within the local density approximation, generalized-gradient approximation (GGA), and meta-GGA provided in the libxc and xcfun libraries. A central aspect of FLO-SIC is the Fermi-orbital descriptors, which are used to estimate the self-interaction correction. Importantly, they can be initialized automatically within pyflosic; they can also be optimized within pyflosic with an interface to the atomic simulation environment, a python library that provides a variety of powerful gradient-based algorithms for geometry optimization. Although pyflosic has already facilitated applications of FLO-SIC to chemical studies, it offers an excellent starting point for further developments in FLO-SIC approaches, thanks to its use of a high-level programming language and pronounced modularity.

Interpretation and Automatic Generation of Fermi-Orbital Descriptors.

We present an interpretation of Fermi-orbital descriptors (FODs) and argue that these descriptors carry chemical bonding information. We show that a bond order derived from these FODs agrees well with reference values, and highlight that optimized FOD positions used within the Fermi-Löwdin orbital self-interaction correction (FLO-SIC) method correspond to expectations from Linnett's double-quartet theory, which is an extension of Lewis theory. This observation is independent of the underlying exchange-correlation functional, which is shown using the local spin density approximation, the Perdew-Burke-Ernzerhof generalized gradient approximation (GGA), and the strongly constrained and appropriately normed meta-GGA. To make FOD positions generally accessible, we propose and discuss four independent methods for the generation of Fermi-orbital descriptors, their implementation as well as their advantages and drawbacks. In particular, we introduce a re-implementation of the electron force field, an approach based on the centers of mass of orbital densities, a Monte Carlo-based algorithm, and a method based on Lewis-like bonding information. All results are summarized with respect to future developments of FLO-SIC and related methods. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Analytic atomic gradients in the fermi-löwdin orbital self-interaction correction.

We derived, implemented, and thoroughly tested the complete analytic expression for atomic forces, consisting of the Hellmann-Feynman term and the Pulay correction, for the Fermi-Löwdin orbital self-interaction correction (FLO-SIC) method. Analytic forces are shown to be numerically accurate through an extensive comparison to forces obtained from finite differences. Using the analytic forces, equilibrium structures for a small set of molecules were obtained. This work opens the possibility of routine self-interaction free geometrical relaxations of molecules using the FLO-SIC method. © 2018 Wiley Periodicals, Inc.

Stretched or noded orbital densities and self-interaction correction in density functional theory.

Semilocal approximations to the density functional for the exchange-correlation energy of a many-electron system necessarily fail for lobed one-electron densities, including not only the familiar stretched densities but also the less familiar but closely related noded ones. The Perdew-Zunger (PZ) self-interaction correction (SIC) to a semilocal approximation makes that approximation exact for all one-electron ground- or excited-state densities and accurate for stretched bonds. When the minimization of the PZ total energy is made over real localized orbitals, the orbital densities can be noded, leading to energy errors in many-electron systems. Minimization over complex localized orbitals yields nodeless orbital densities, which reduce but typically do not eliminate the SIC errors of atomization energies. Other errors of PZ SIC remain, attributable to the loss of the exact constraints and appropriate norms that the semilocal approximations satisfy, suggesting the need for a generalized SIC. These conclusions are supported by calculations for one-electron densities and for many-electron molecules. While PZ SIC raises and improves the energy barriers of standard generalized gradient approximations (GGAs) and meta-GGAs, it reduces and often worsens the atomization energies of molecules. Thus, PZ SIC raises the energy more as the nodality of the valence localized orbitals increases from atoms to molecules to transition states. PZ SIC is applied here, in particular, to the strongly constrained and appropriately normed (SCAN) meta-GGA, for which the correlation part is already self-interaction-free. This property makes SCAN a natural first candidate for a generalized SIC.

Fermi-Löwdin orbital self-interaction corrected density functional theory: Ionization potentials and enthalpies of formation.

The Fermi-Löwdin orbital self-interaction correction (FLO-SIC) methodology is applied to atoms and molecules from the standard G2-1 test set. For the first time FLO-SIC results for the GGA-type PBE functional are presented. In addition, examples where FLO-SIC like any proper SIC provides qualitative improvements compared to standard DFT functionals are discussed in detail: the dissociation limit for H 2 + , the step-wise linearity behavior for fractional occupation, as well as the significant reduction of the error of static polarizabilities. Further, ionization potentials and enthalpies of formation obtained by means of the FLO-SIC DFT method are compared to other SIC variants and experimental values. The self-interaction correction gives significant improvements if used with the LDA functional but shows worse performance in case of enthalpies of formation if the PBE-GGA functional is used. The errors are analyzed and the importance of the overbinding of hydrogen is discussed. © 2018 Wiley Periodicals, Inc.

Theoretical and experimental investigations of 129Xe NMR chemical shift isotherms in metal-organic frameworks.

The pressure dependence of the 129Xe chemical shift in the metal-organic frameworks (MOFs) UiO-66 and UiO-67 (UiO - University of Oslo) has been investigated using both theory and experiment. The resulting chemical shift isotherms were analyzed with a theoretical approach based on model systems (as proposed by K. Trepte, J. Schaber, S. Schwalbe, F. Drache, I. Senkovska, S. Kaskel, J. Kortus, E. Brunner and G. Seifert, Phys. Chem. Chem. Phys., 2017, 19, 10020-10027) and experimental 129Xe NMR measurements at different pressures. All investigations were carried out at T = 237 K while the pressure range was chosen according to the maximum pressure at which Xe liquifies (p0 = 1.73 MPa or 17.3 bar), thus 0 < p ≤ p0. The theoretically predicted chemical shift isotherms agree well with the experimental ones. Additionally, a comparison of the chemical shift isotherms with volumetric adsorption isotherms was carried out to determine the similarities and differences of both isotherms.

The origin of the measured chemical shift of 129Xe in UiO-66 and UiO-67 revealed by DFT investigations.

The NMR chemical shift of the xenon isotope 129Xe inside the metal-organic frameworks (MOFs) UiO-66 and UiO-67 (UiO - University of Oslo) has been investigated both with density functional theory (DFT) and in situ high-pressure 129Xe NMR measurements. The experiments reveal a decrease of the total chemical shift comparing the larger isoreticular MOF (UiO-67) with the smaller one (UiO-66), even though one may expect an increase due to the higher amount of adsorbed Xe atoms. We are able to calculate contributions to the chemical shift individually. This allows us to evaluate the shift inside the different pores independently. To compare the theoretical results with the experimental ones, we performed molecular dynamics simulations of Xe in the MOFs. For this purpose, the pores were completely filled with Xe to gain insight into the distribution of Xe at high pressures. The resulting trend of the total shift agrees well between the theoretical predictions and the experiments. Moreover, we are able to describe specific contributions to the total shift per pore, explaining the experimental behavior at an atomistic level.

Self-consistent self-interaction corrected density functional theory calculations for atoms using Fermi-Löwdin orbitals: Optimized Fermi-orbital descriptors for Li-Kr.

In the Fermi-Löwdin orbital method for implementing self-interaction corrections (FLO-SIC) in density functional theory (DFT), the local orbitals used to make the corrections are generated in a unitary-invariant scheme via the choice of the Fermi orbital descriptors (FODs). These are M positions in 3-d space (for an M-electron system) that can be loosely thought of as classical electron positions. The orbitals that minimize the DFT energy including the SIC are obtained by finding optimal positions for the FODs. In this paper, we present optimized FODs for the atoms from Li-Kr obtained using an unbiased search method and self-consistent FLO-SIC calculations. The FOD arrangements display a clear shell structure that reflects the principal quantum numbers of the orbitals. We describe trends in the FOD arrangements as a function of atomic number. FLO-SIC total energies for the atoms are presented and are shown to be in close agreement with the results of previous SIC calculations that imposed explicit constraints to determine the optimal local orbitals, suggesting that FLO-SIC yields the same solutions for atoms as these computationally demanding earlier methods, without invoking the constraints.

Screening for high-spin metal organic frameworks (MOFs): density functional theory study on DUT-8(M1,M2) (with Mi = V, ,Cu).

We present a first principles study of low-spin (LS)/high-spin (HS) screening for 3d metal centers in the metal organic framework (MOF) DUT-8(Ni). Various density functional theory (DFT) codes have been used to evaluate numerical and DFT related errors. We compare highly accurate all-electron implementations with the widely used plane wave approach. We present electronically and magnetically stable DUT-8(Ni) HS secondary building units (SBUs). In this work we show how to tune the magnetic and electronic properties of the original SBU only by changing the metal centers.

Phthalocyanine dimers in a blend: spectroscopic and theoretical studies of MnPc(δ +)/F(16)CoPc(δ -).

We have prepared mixed phthalocyanine films out of MnPc and F(16)CoPc, which were characterized by means of photoemission spectroscopy and electron energy-loss spectroscopy. Our data reveal the formation of MnPc/F(16)CoPc charge transfer dimers in analogy to the related heterojunction. The electronic excitation spectrum of these blends is characterized by a new low energy excitation at 0.6 eV. Density functional theory calculations show that the new signal is caused by a strong absorption between the states of the interface induced two level system.

Investigating the Thermodynamics and Kinetics of Catechin Pyrolysis for Environmentally Friendly Binders.

The thermodynamics and kinetics of the pyrolysis of (+)-catechin, a building block of the condensed tannins found in recipes for sustainable binders, are evaluated at the DLPNO-CCSD(T) level and compared to other methods from quantum chemistry. Using the climbing image nudged elastic band method coupled with transition state optimization, minimum energy paths and highest-energy transition states are identified for the first two pyrolysis steps, a catechol split-off with subsequent dehydrogenation. While the catechol split-off path was very smooth, the dehydrogenation featured an additional transition state in the form of an OH group rotation. The combined reaction was judged endothermic in the range of 0 to 1250 K and exergonic at 1000 K and above. It is shown that the catechol split-off is the rate-determining step of the pyrolysis of catechin, which is equivalent to kinetic inhibition at all investigated temperatures.

Hybrid states and charge transfer at a phthalocyanine heterojunction: MnPc(δ+)/F16CoPc(δ-).

Using photoelectron spectroscopy we demonstrate charge transfer at an interface between two well-known transition metal phthalocyanines, MnPc and F16CoPc, resulting in charged MnPc(δ+) and F16CoPc(δ-) species. Moreover, the transferred charge is substantially confined to the two transition metal centers. Density functional theory calculations reveal that a hybrid state is formed between the two types of phthalocyanines, which causes this charge transfer. For the hybrid state the Mn 3d(xz) interacts with the Co 3d(z2) orbital leading to a two-level system. As only the lower of the two hybrid states is occupied, the charge is directly transferred to the Co 3d(z2) orbital.

Stabilization of hypophosphite in the binding pocket of a dinuclear macrocyclic complex: synthesis, structure, and properties of [Ni(2)L(µ-O(2)PH(2))]BPh(4) (L = N(6)S(2) donor ligand).

The dinickel(II) complex [Ni2L(ClO4)]ClO4 (1), where L(2-) represents a 24-membered macrocyclic hexaamine-dithiophenolate ligand, reacts with [nBu4N]H2PO2 to form the hypophosphito-bridged complex [Ni2L(µ-O2PH2)](+), which can be isolated as an air-stable perchlorate [Ni2L(µ-O2PH2)]ClO4 (2) or tetraphenylborate [Ni2L(µ-O2PH2)]BPh4 (3) salt. 3·MeCN crystallizes in the triclinic space group P1̅. The bisoctahedral [Ni2L(µ-O2PH2)](+) cation has a N3Ni(µ1,3-O2PH2)(µ-S)2NiN3 core structure with the hypophosphito ligand attached to the two Ni(II) ions in a µ1,3-bridging mode. The hypophosphito ligand is readily replaced by carboxylates, in agreement with a higher affinity of the [Ni2L](2+) dication for more basic oxoanions. Treatment of [Ni2L(µ-O2PH2)]ClO4 with H2O2 or MCPBA results in the oxidation of the bridging thiolato to sulfonato groups. The hypophosphito group is not oxidized under these conditions due to the steric protection offered by the supporting ligand. An analysis of the temperature-dependent magnetic susceptibility data for 3 reveals the presence of ferromagnetic exchange interactions between the Ni(ii) (S = 1) ions with a value for the magnetic exchange coupling constant J of +22 cm(-1) (H = -2JS1S2). These results are additionally supported by DFT (density functional theory) calculations.

Unexpected Phonon Behaviour in BiFexCr1-xO3, a Material System Different from Its BiFeO3 and BiCrO3 Parents.

The dielectric function and the bandgap of BiFe0.5Cr0.5O3 thin films were determined from spectroscopic ellipsometry and compared with that of the parent compounds BiFeO3 and BiCrO3. The bandgap value of BiFe0.5Cr0.5O3 is lower than that of BiFeO3 and BiCrO3, due to an optical transition at ~2.27 eV attributed to a charge transfer excitation between the Cr and Fe ions. This optical transition enables new phonon modes which have been investigated using Raman spectroscopy by employing multi-wavelengths excitation. The appearance of a new Raman mode at ~670 cm-1 with a strong intensity dependence on the excitation line and its higher order scattering activation was found for both BiFe0.5Cr0.5O3 thin films and BiFexCr1-xO3 polycrystalline bulk samples. Furthermore, Raman spectroscopy was also used to investigate temperature induced structural phase transitions in BiFe0.3Cr0.7O3.

Electronic structure and transport properties of coupled CdS/ZnSe quantum dots.

Electronic structure and transport characteristics of coupled CdS and ZnSe quantum dots are studied using density functional theory and non equilibrium Greens function method respectively. Our investigations show that in these novel coupled dots, the Frontier occupied and unoccupied molecular orbitals are spatially located in two different parts, thereby indicating the possibility of asymmetry in electronic transport. We have calculated electronic transport through the coupled quantum dot by varying the coupling strength between the individual quantum dots in the limits of weak and strong coupling. Calculations reveal asymmetric current vs voltage curves in both the limits indicating the rectifying properties of the coupled quantum dots. Additionally we discuss the possibility to tune the switching behavior of the coupled dots by different gate geometries.

How to build molecules with large magnetic anisotropy.

Predicting single-molecule magnets? Magnetic anisotropy, a property that plays a key role in single-molecule magnets (SMMs), has been analyzed by using theoretical methods. Mononuclear complexes and the dependence of the magnetic anisotropy on their geometrical and electronic structure, as well as how such mononuclear complexes must be combined as building blocks to obtain polynuclear complexes with large anisotropy (see figure) are considered.The magnetic anisotropy of mononuclear transition-metal complexes has been studied by means of electronic structure calculations based on density functional theory. The variation of the zero-field splitting (ZFS) parameters has been analyzed for the following characteristic distortions: a tetragonal Jahn-Teller distortion, the Bailar twist, the Berry pseudorotation, and the planarization of tetrahedral complexes. Finally, the coupling of mononuclear building blocks in polynuclear complexes to obtain a large negative magnetic anisotropy necessary to improve their single-molecule-magnet (SMM) behavior has been studied.

Ferroelastic domain identification in BiFeO3 crystals using Raman spectroscopy.

Multiferroic BiFeO3 crystals were investigated by means of micro-Raman spectroscopy using the laser wavelengths of 442 nm (resonant conditions) and 633 nm (non-resonant conditions). The azimuthal angle dependence of the intensity of the Raman modes allowed their symmetry assignment. The experimental data are consistent with a simulation based on Raman tensor formalism. Mixed symmetries were taken into account, considering the orientation of the crystal optic axis along a pseudo-cubic <111> direction. The strong anisotropic intensity variation of some of the polar Raman modes was used for line scans and mappings in order to identify ferroelastic domain patterns. The line scans performed with different excitation wavelengths and hence different information depths indicate a tilt of the domain walls with respect to the sample surface. The domain distribution found by Raman spectroscopy is in very good agreement with the finding of electron back scattering diffraction.