Electronic Descriptors for Supervised Spectroscopic Predictions.

Spectroscopic properties of molecules hold great importance for the description of the molecular response under the effect of UV/vis electromagnetic radiation. Computationally expensive ab initio (e.g., MultiConfigurational SCF, Coupled Cluster) or TDDFT methods are commonly used by the quantum chemistry community to compute these properties. In this work, we propose a (supervised) Machine Learning approach to model the absorption spectra of organic molecules. Several supervised ML methods have been tested such as Kernel Ridge Regression (KRR), Multiperceptron Neural Networs (MLP), and Convolutional Neural Networks. [Ramakrishnan et al. J. Chem. Phys. 2015, 143, 084111. Ghosh et al. Adv. Sci. 2019, 6, 1801367.] The use of only geometrical-atomic number descriptors (e.g., Coulomb Matrix) proved to be insufficient for an accurate training. [Ramakrishnan et al. J. Chem. Phys. 2015, 143, 084111.] Inspired by the TDDFT theory, we propose to use a set of electronic descriptors obtained from low-cost DFT methods: orbital energy differences (Δϵia = ϵa - ϵi), transition dipole moment between occupied and unoccupied Kohn-Sham orbitals (⟨ϕi|r|ϕa⟩), and when relevant, charge-transfer character of monoexcitations (Ria). We demonstrate that with these electronic descriptors and the use of Neural Networks we can predict not only a density of excited states but also get a very good estimation of the absorption spectrum and charge-transfer character of the electronic excited states, reaching results close to chemical accuracy (∼2 kcal/mol or ∼0.1 eV).

Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems.

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

Covalent C-N Bond Formation through a Surface Catalyzed Thermal Cyclodehydrogenation.

The integration of substitutional dopants at predetermined positions along the hexagonal lattice of graphene-derived polycyclic aromatic hydrocarbons is a critical tool in the design of functional electronic materials. Here, we report the unusually mild thermally induced oxidative cyclodehydrogenation of dianthryl pyrazino[2,3-g]quinoxalines to form the four covalent C-N bonds in tetraazateranthene on Au(111) and Ag(111) surfaces. Bond-resolved scanning probe microscopy, differential conductance spectroscopy, along with first-principles calculations unambiguously confirm the structural assignment. Detailed mechanistic analysis based on ab initio density functional theory calculations reveals a stepwise mechanism featuring a rate determining barrier of only ΔE⧧ = 0.6 eV, consistent with the experimentally observed reaction conditions.

Revising the common understanding of metamagnetism in the molecule-based bisdithiazolyl BDTMe compound.

The BDTMe molecule-based material is the first example of a thiazyl radical to exhibit metamagnetic behavior. Contrary to the common idea that metamagnetism occurs in low-dimensional systems, it is found that BDTMe magnetic topology consists of a complex 3D network of almost isotropic ferromagnetic spin-ladders that are coupled ferromagnetically and further connected by some weaker antiferromagnetic interactions. Calculated magnetic susceptibility χT(T) data is in agreement with experiment. Calculated M(H) data clearly show the typical sigmoidal shape of a metamagnet at temperatures below 2 K. The calculated critical field becomes more apparent in the dM/dH(H) plot, being in very good agreement with experiment. Our computational study concludes that the magnetic topology of BDTMe is preserved throughout the entire experimental range of temperatures (0-100 K). Accordingly, the ground state is the same irrespective of the temperature at which we study the BDTMe crystal. Revising the commonly accepted understanding of a metamagnet explained as ground state changing from antiferromagnetic to ferromagnetic, the Boltzmann population of the different states is here suggested to be the key concept: at 2 K the ground singlet state has more weight (24%) than at 10 K (1.5%), where excited states have an important role. Changes in the antiferromagnetic interactions that couple the ferromagnetic skeleton of BDTMe will directly affect the population of the distinct states that belong to a given magnetic topology and thus its magnetic response. Accordingly, this strategy could be valid for a wide range of bisdithiazolyl BDT-compounds whose magnetism can be tuned by means of weak antiferromagnetic interactions.

Real-Time Propagation TDDFT and Density Analysis for Exciton Coupling Calculations in Large Systems.

Photoactive systems are characterized by their capacity to absorb the energy of light and transform it. Usually, more than one chromophore is involved in the light absorption and excitation transport processes in complex systems. Linear-Response Time-Dependent Density Functional (LR-TDDFT) is commonly used to identify excitation energies and transition properties by solving the well-known Casida's equation for single molecules. However, in practice, LR-TDDFT presents some disadvantages when dealing with multichromophore systems due to the increasing size of the electron-hole pairwise basis required for accurate evaluation of the absorption spectrum. In this work, we extend our local density decomposition method that enables us to disentangle individual contributions into the absorption spectrum to computation of exciton dynamic properties, such as exciton coupling parameters. We derive an analytical expression for the transition density from Real-Time Propagation TDDFT (P-TDDFT) based on Linear Response theorems. We demonstrate the validity of our method to determine transition dipole moments, transition densities, and exciton coupling for systems of increasing complexity. We start from the isolated benzaldehyde molecule, perform a distance analysis for π-stacked dimers, and finally map the exciton coupling for a 14 benzaldehyde cluster.

A Definition of the Magnetic Transition Temperature Using Valence Bond Theory.

Macroscopic magnetic properties are analyzed using Valence Bond theory. Commonly the critical temperature TC for magnetic systems is associated with a maximum in the energy-based heat capacity Cp(T). Here a more broadly applicable definition of the magnetic transition temperature TC is described using the spin moment expectation value (i.e., applying the spin exchange density operator) instead of energy. Namely, the magnetic capacity Cs(T) reflects variation in the spin multiplicity as a function of temperature, which is shown to be related to ∂[χT(T)]/∂T. Magnetic capacity Cs(T) depends on long-range spin interactions that are not relevant in the energy-based heat capacity Cp(T). Differences between Cs(T) and Cp(T) are shown to be due to spin order/disorder within the crystal that can be monitored via a Valence Bond analysis of the corresponding magnetic wave function. Indeed the concept of the Boltzmann spin-alignment order is used to provide information about the spin correlation between magnetic units. As a final illustration, the critical temperature is derived from the magnetic capacity for several molecular magnets presenting different magnetic topologies that have been experimentally studied. A systematic shift between the transition temperatures associated with Cs(T) and Cp(T) is observed. It is demonstrated that this shift can be attributed to the loss of long-range spin correlation. This suggests that the magnetic capacity Cs(T) can be used as a predictive tool for the magnetic topology and thus for the synthetic chemists.

Insights into colour-tuning of chlorophyll optical response in green plants.

First-principles calculations within the framework of real-space time-dependent density functional theory have been performed for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible the studies of the optical response of individual Chl molecules subjected to the influence of the remainder of the chromophore network. The spectra calculated using our real-space TDDFT method agree with previous suggestions that weak interaction with the protein microenvironment should produce only minor changes in the absorption spectrum of Chl chromophores in LHC-II. In addition, relative shifting of Chl absorption energies leads the stromal and lumenal sides of LHC-II to absorb in slightly different parts of the visible spectrum providing greater coverage of the available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC-II complex.

Vertical transition energies vs. absorption maxima: illustration with the UV absorption spectrum of ethylene.

We revisit the validity of making a direct comparison between measured absorption maxima and computed vertical transition energies within 0.1 eV to calibrate an excited-state level of theory. This is illustrated on the UV absorption spectrum of ethylene for which the usual experimental values of 7.66 eV (V←N) and 7.11 eV (R(3s)←N) cannot be compared directly to the results of electronic structure calculations for two very different reasons. After validation of our level of theory against experimental data, a new experimental reference of 7.28 eV is suggested for benchmarking the Rydberg state, and the often-cited average transition energy (7.80 eV) is confirmed as a safer estimate for the valence state.

Dividing the spoils: role of pyrazine ligands and perchlorate counterions in the magnetic properties of bis(pyrazine)diperchloratecopper(II), [Cu(pz)2](ClO4)2.

A complete first-principles bottom-up computational study of the magnetic properties of [Cu(pz)2](ClO4)2 is presented. A remarkable agreement is observed in the whole range of temperatures between simulated and experimental magnetic susceptibility data. Interestingly, the simulated heat capacity values show an anomaly close to the Néel temperature of 4.21 K associated with a transition from a two-dimensional (2D) antiferromagnet to a three-dimensional (3D) ordered state. The antiferromagnetic behavior of [Cu(pz)2](ClO4)2 is due to a 2D magnetic topology owing to two antiferromagnetic J(AB) interactions through pyrazine ligands. Although presenting a very similar molecular arrangement, the numerical values of the two magnetically significant J(AB) couplings differ by 25% (-10.2 vs -7.3 cm(-1)). This difference can be ascribed to three main contributions: (i) the central pyrazine ring shearing-like distortion, (ii) the effect of the orientation of the perchlorate counterions, and (iii) a hitherto unrecognized skeleton-counterion cooperation arising from different hydrogen bonding contributions in the two most significant J(AB) couplings. The impact of the orientation of the perchlorate counterions is disclosed by comparison to J(AB) studies using structurally similar ligands but with different electronegativity (namely, BF4(-), BCl4(-), and BBr4(-)). Pyrazine ligands and perchlorate counterions prove to be noninnocent.

A generalised 17-state vibronic-coupling Hamiltonian model for ethylene.

In a previous work [B. Lasorne, M. A. Robb, H.-D. Meyer, and F. Gatti, "The electronic excited states of ethylene with large-amplitude deformations: A dynamical symmetry group investigation," Chem. Phys. 377, 30-45 (2010); and ibid. 382, 132 (2011) (Erratum)], we investigated the electronic structure of ethylene (ethene, C(2)H(4)) in terms of 17 dominant configurations selected at the multiconfiguration self-consistent field level of theory. These were shown to be sufficient to recover most of the static electron correlation among the first valence and Rydberg states at all geometries. We also devised a strategy to build a 17-quasidiabatic-state matrix representation of the electronic Hamiltonian for curvilinear coordinates using dynamical symmetry. Here, we present fitted surfaces in the form of a generalised vibronic-coupling Hamiltonian model for two nuclear coordinates, CC bond stretching and torsion. Dynamic electron correlation is included into the electronic structure to improve the energetics of the Rydberg states at the multireference configuration interaction level of theory. The chemical interpretation of the adiabatic states of interest does not change qualitatively, which validates our choice of underlying quasidiabatic states in the model. The absorption spectrum is calculated with quantum dynamics and partially assigned. This first two-dimensional model shows a surprisingly good agreement with the experimental spectrum.

Synthesis, structure, magnetic behavior, and theoretical analysis of diazine-bridged magnetic ladders: Cu(quinoxoline)X2 and Cu(2,3-dimethylpyrazine)X2 (X = Cl, Br).

The synthesis, structure, and magnetic behavior of the complexes Cu(qnx)Br(2) (1), Cu(2,3-dmpz)Br(2) (2), Cu(qnx)Cl(2) (3), and Cu(2,3-dmpz)Cl(2) (4) (qnx = quinoxaline, dmpz = dimethylpyrazine) are described. Both X-ray structural data and fitting of the magnetic data suggest that the compounds are well-described as strong-rung, two-leg magnetic ladders with J(rung) ranging from -30 K to -37 K, and J(rail) ranging from -14 K to -24 K. An unexpected decrease in the exchange constant for J(rail) (through the diazine ligand) is observed when the halide ion is changed from bromide to chloride, along with a small decrease in the magnetic exchange through the halide ion. Theoretical calculations on 2 and 4 via a first-principles bottom-up approach confirmed the description of the complexes as two-leg magnetic ladders. Furthermore, the calculations provide an explanation for the experimentally observed change in the value of the magnetic exchange through the dmpz ligand when the halide ion is changed from bromide to chloride, and for the very small change observed in the exchange through the different halide ions themselves via a combination of changes in geometry, bond lengths, and anion volume.

Origin of the magnetic bistability in molecule-based magnets: a first-principles bottom-up study of the TTTA crystal.

The magnetic bistability present in some molecule-based magnets is investigated theoretically at the microscopic level using the purely organic system TTTA (1,3,5-trithia-2,4,6-triazapentalenyl). The TTTA crystal is selected for being one of the best-studied molecule-based systems presenting magnetic bistability. The magnetic properties of the high- and low-temperature structures (HT and LT phases, respectively) are accurately characterized by performing a First-Principles Bottom-Up study of each phase. The changes that the magnetic exchange coupling constants (J(AB)) undergo when the temperature is raised (LT → HT) or lowered (HT → LT) are also fully explored in order to unravel the reasons behind the presence of these two different pathways. The triclinic LT phase is diamagnetic due to the fact that the nearly eclipsed π dimer is effectively magnetically silent and not to formation of a covalent bond between two TTTA molecules. It is also shown that bistability in TTTA results from the coexistence of the monoclinic HT and triclinic LT phases in the temperature range studied.

The magnetism of (5MAP)2CuBr4 [5MAP = 5-methyl-2-aminopyridinium]: a quasi-2D or a 3D magnetic system?

In order to determine if its magnetic topology is actually two- or three-dimensional (2D or 3D), the mechanism of the magnetic interaction in (5MAP)(2)CuBr(4), a previously thought quasi-2D antiferromagnet, is re-examined using the first-principles bottom-up methodology. Once the magnitude and sign of all unique magnetic interactions present in the room-temperature (5MAP)(2)CuBr(4) crystal are evaluated, it is found that, even at room temperature, the magnetic topology of the crystal corresponds to a 3D antiferromagnet. Such 3D nature cannot be determined by examination of the magnetic susceptibility curve, chi(T), because it is found that the chi(T) curve computed using this 3D magnetic topology is very similar to that obtained using a 2D model where all interplane interactions have been deleted. However, its 3D magnetic dimensionality can be confirmed by examination of the shape of the magnetization curve, M(H); the computed curve is similar to the experimental one for the 3D case.