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).

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 state-of-the-art theoretical evaluation and rationalization of the magnetic interactions (J(AB)) in molecule-based magnets is discussed in this critical review, focusing first on isolated radical···radical pair interactions and afterwards on how these interactions cooperate in the solid phase. Concerning isolated radical pairwise magnetic interactions, an initial analysis is done on qualitative grounds, concentrating also on the validity of the most commonly used models to predict their size and angularity (namely, McConnell-I and McConnell-II models, overlap of magnetic orbitals,…). The failure of these models, caused by their oversimplified description of the magnetic interactions, prompted the introduction of quantitative approaches, whose basic principles and relative quality are also evaluated. Concerning the computation of magnetic interactions in solids, we resort to a sum of pairwise magnetic interactions within the Heisenberg Hamiltonian framework, and follow the First-principles Bottom-Up procedure, which allows the accurate study of the magnetic properties of any molecule-based magnet in an unbiased way. The basic principles of this approach are outlined, applied in detail to a model system, and finally demonstrated to properly describe the magnetic properties of molecule-based systems that show a variety of magnetic topologies, which range from 1D to 3D (152 references).

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 studies of the optical response of individual Chl molecules subject to the influence of the remainder of the chromophore network. The spectra calculated with 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 available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC–II complex.

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.

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.

On the basis of magnetic susceptibility and heat capacity data, copper pyrazine dinitrate crystal [abbreviated CuPz(NO(3))(2)] has long been considered a good prototype for S = (1)/(2) antiferromagnetic (AFM) Heisenberg chain behavior down to 0.05 K. However, a recent muon-spin rotation experiment indicated the presence of a previously unnoticed 1D to 3D magnetic transition below 0.107 K. Our aim in this work is to perform a rigorous quantitative study of the mechanism of this 1D-3D magnetic transformation, by doing a first-principles bottom-up study of the CuPz(NO(3))(2) crystal at 158 K, where the magnetic properties are clearly 1D, and at 2 K, at which the neutron structure (reported in this work) is considered nearly identical with that below 0.1 K (due to small thermal effects). A change in the magnetic topology is found between these two structures: at 158 K, there are isolated AFM spin chains (J(intra) = -5.23 cm(-1)), while at 2 K, the magnetic chains (J(intra) = -5.96 cm(-1)) weakly interact (the largest of the J(inter) parameters is -0.09 cm(-1)). This change is caused by thermal contraction upon cooling (no crystallographic phase transition is detected down to 2 K, and one will not likely occur below that temperature). The computed and experimental magnetic susceptibility chi(T) curves are nearly identical. The calculated heat capacity C(p)(T) curve has a maximum at 6.92 K, close to the 5.20 K maximum found in the experimental curve at zero external field. In spite of the 3D magnetic topology of the crystal at low temperature, the magnetic susceptibility and heat capacity curves behave as a pure 1D AFM chain in all regions because of the large J(intra)/J(inter) ratio (66.2 in absolute value) and the effect of including the J(inter) interactions will not be easily appreciated in any of these experiments. The impact of the presence of odd- and even-membered regular AFM finite chains in the CuPz(NO(3))(2) crystal has also been evaluated. Odd-membered interacting chains produce an increase in both chi(T) and C(p)(T) curves when the temperature is very close to zero, in agreement with the experimental observations, while even-membered chains produce a small shoulder in the C(p)(T) curve between 0.8 and 5 K. No changes are seen in the remaining regions. Concerning the spin gap, odd-membered chains present a quasi-zero gap but the finite even-membered chains still have a sizable one. Finally, the effect of increasing the magnitude of J(inter) was investigated by fixing the value of J(intra) to that found for the 2 K CuPz(NO(3))(2) crystal. The magnetic susceptibility and heat capacity curves remain practically unchanged.

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.