Fernando Nogueira

University of Coimbra | UC · Department of Physics

In this study we analyze the dielectric properties of a recently published dataset to identify high-refractive-index and high-band-gap materials that are crucial for modern optoelectronic applications. We employ advanced crystal graph convolutional neural networks and density functional perturbation theory calculations to accelerate the discovery o...

An algorithm for wildfire suppression based on graph theory and that builds on realistic simulations of the propagation, is efficient, produces results in a short period of time and has the potential to help achieving a faster suppression of a real fire is reported.The suppression algorithm looks for the selection of the best locations to attack th...

The family of recently described salts based on the electron donor CNB-EDT-TTF and different anions A, with general formula (CNB-EDT-TTF) 4 A, constitutes an unprecedented type of molecular conductor based on a bilayer structure of the donors.

The physics of surface plasmons has a long tradition in condensed matter theory but as the dimension of the systems reaches the nano scale, new effects appear. In this work, by calculating the absorption spectra of a single wall carbon nanotube, using time dependent density functional theory, the effect of adding/removing electrons on the surface p...

In certain materials, and for certain voltage ranges, electrical current flowing through the material decreases when the voltage across the sample is increased. This negative differential conductance (NDC) is important for oscillators, amplifiers, and fast switching devices. In this work, using real-time quantum simulations, we show that this pheno...

First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate th...

First-principles calculations have been used to investigate the potential use of circular dichroism (CD) spectroscopy in single molecule sensing. Using a real-space implementation of time-dependent density functional theory (TDDFT), several systems involving single-walled carbon nanotubes (SWCNT) and small molecules have been studied to evaluate th...

Delafossite crystals are fascinating ternary oxides that have demonstrated transparent conductivity and ambipolar doping. Here we use a high-throughput approach based on density functional theory to find delafossite and related layered phases of composition ABX2, where A and B are elements of the periodic table, and X is a chalcogen (O, S, Se, and...

The determination of the optical spectrum of single-wall carbon nanotubes (SWCNTs) is essential for the development of optoelectronic components and sensors with application in many fields. Real SWCNTs are finite, but almost all the studies performed so far use infinite SWCNTs. However, the spectra of finite and infinite systems are different. In t...

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...

The dream of any solid-state theorist is to be able to predict new materials with tailored properties from scratch, i.e., without any input from experiment. Over the past decades, we have steadily approached this goal. Recent developments in the field of high-throughput calculations focused on finding the best material for specific applications. Ho...

A novel erbium(III) complex with acetylacetone (Hacac) and bathophenanthroline (4,7-diphenyl-1,10-phenanthroline, bath) ligands, formulated as [Er(acac)3(bath)], has been characterized by elemental analysis, X-ray diffraction, thermogravimetric analysis, Fourier transform infrared spectroscopy, Raman spectroscopy, absorption and emission spectrosco...

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These prop...

In this work we present the improvements made to the Octopus code in order to reduce the memory requirements and to optimise parallel data distribution. Both topics are central for efficiency and feasibility of calculations when the system must be run in a large HPC environment. These modifications were mainly made in the real-space mesh partitioni...

The firefly luciferin/luciferase system, a famous example of fluorescent proteins, has been successfully used in various bio-imaging techniques, as a reporter for ATP generation, gene expression, and as a biosensor for environmental pollutants. In all these diverse applications, some special marking demands require an extensive color modulation of...

Systematic study of the optical and magnetic excitations of twelve MSi$_{12}$ and four MSi$_{10}$ transition metal encapsulating Si cages has been carried out by employing real time time-dependent density functional theory. Criteria for the choice of transition metals (M) are clusters' stability, synthesizability, and diversity. It was found that b...

Theoretical analysis using quadratic response theory within the time-dependent density functional theory (TDDFT) formalism shows that the dermacozines, a group of phenazine-based compounds isolated from cultures of Dermacoccus abyssi found in the Mariana Trench, possess large first hyperpolarisability (β) values at common incident laser wavelengths...

A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive since it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here we use action spectroscopy to c...

Nitrogen is a common structural element in the acceptor moieties of organic donor-acceptor nonlinear optical (NLO) chromophores. In order to assess the effect of substitution with heavier group 15 elements, computational studies of the nonlinear optical properties of betaine derivatives, (CH(3))(3)X(+)CH(2)CO(2)(-) (X = N, P, As, Sb, Bi), have been...

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time....

Part I Theory and Experiment - Why We Need TDDFT.- Part II Basic Theory.- PartIII Advanced Concepts.- Part IV Real-Time Dynamics.- Part V Numerical Aspects.- Part VI TDDFT vs Other Theoretical Techniques.

Marine natural products: a new source of novel chromophores for nonlinear optics

The special interest in molecular design for the development of novel second-order nonlinear optical (SONLO) materials is driven by their potential applications in new optoelectronic technologies. Various strategies are currently employed to enhance the molecular SONLO activity, and studies revealed that species having open-shell electronic states...

Although many microenvironmental factors contribute to the color shift of light emission from the firefly chromophore, the dominant one is the local electrostatic field. This opens up the possibility of accurate color tuning the bioluminescent absorption and emission by adjusting the local charged residues. With this aim, the optical response of ox...

Gas phase spectroscopy of the firefly luciferin anion: comparison of experiment with TDDFT predictions

In the current manuscript we present the results of a computational study on a series of chromophores with enhanced intrinsic hyperpolarizability. The high hyperpolarizability values of these molecules were previously reported and were achieved by making use of aromatic moieties in order to modulate the aromatic stabilization energy along the conju...

Firefly bioluminescence displays a sensitivity to pH changes through an alteration of the energy of the emitted photon leading to yellow-green light above ∼pH 6.5 and red light below this value. Calculations using the fragment molecular orbital method have been performed on the active site of the luciferase enzyme from the Japanese firefly Luciola...

We propose the heterojunction effect in the analysis of the fluorescence mechanism of the firefly chromophore. Following this analysis, and with respect to the HOMO-LUMO gap alignment between the chromophore's functional fragments, three main heterojunction types (I, II, and I*) are identified. Time-dependent density-functional theory optical absor...

Upon ionization, rare-gas (like Ar and Xe) clusters shift their absorption spectrum from the ultraviolet to the visible. This happens as bonding becomes much stronger due to the removal of an electron from a strongly antibonding orbital. In this article, we study the absorption spectrum of small cationic xenon clusters (Xe(n) (+), with n=3,...,35)...

Bio-heteroJunction effect on fluorescence origin and efficiency improvement of firefly chromophores

Fragment molecular orbital studies of luciferase from the Japanese firefly Luciola cruciata

Fragment molecular orbital studies of luciferase from the Japanese firefly Luciola cruciata

Fragment molecular orbital studies of luciferase from the Japanese firefly Luciola cruciata

Recent Hyper Rayleigh Scattering measurements report a significant increase of second-order hyperpolarizability upon introduction of positive charges at the pyridyl end groups in trispyridyl octopolar chromophores. We calculated the geometries, linear response, and first-order hyperpolarizabilities of a series of six trispyridyl molecules both in t...

The crystal structure of a new phase of triphenylguanidine has been solved by X-ray diffraction. The crystals are monoclinic, space group P21/c, with a=12.4060(4)Å, b=15.1653(6)Å, c=8.7028(3)Å, β=103.2482(15)°, Z=4 and R=0.0572. The crystal structure of the common orthorhombic phase of triphenylguanidine has been redetermined. The hydrogen bond pat...

Various combinations of density functionals and pseudopotentials with associated valence basis-sets are compared for reproducing the known solid-state structure of [V 2O 2(OO) 2 l-lact 2] (2-) cis . Gas-phase optimizations at the B3LYP/SBKJC level have been found to provide a structure that is close to that seen in the solid state by X-ray diffract...

We present a computer package designed to generate and test norm-conserving pseudo-potentials within Density Functional Theory. The generated pseudo-potentials can be either non-relativistic, scalar relativistic or fully relativistic and can explicitly include semi-core states. A wide range of exchange–correlation functionals is included.

Triphenylguanidinium chloride was synthesized and the corresponding infrared (IR) spectra was measured. Four different conformers of triphenylguanidine, two neutral and two protonated forms, have been studied by means of ab-initio calculations. The four geometries were optimized using Hartree–Fock and DFT/B3LYP 6-31G(d,p)+ level of theory. The calc...

It was recently reported that second-order hyperpolarizability increases significantly upon introduction of positive charges at the pyridyl end groups in trispyridyl octopolar chromophores, when compared with the neutral species. We performed ab-initio and semi-empirical calculations for the geometries, electronic localization function and first hy...

Charged rare-gas clusters are markedly different from their neutral, van der Waals bonded counterparts. The removal of an electron from a strongly antibonding orbital causes the bonding to become much stronger and shifts the optical absorption to the visible region. We report a fully ab-initio determination of the geometry, electronic structure, an...

The success of density functional theory (DFT) is clearly demonstrated by the overwhelming amount of research articles describing results obtained within DFT that were published in the last decades. There is also a fair number of books reviewing the basics of the theory and its extensions (e.g., the present volume, [1] and [2]). These works fall ma...

Guanidine compounds have attracted much interest due to the donor and acceptor abilities of the nitrogen and their potencial nonlinear optical properties. Octupolar molecules are particularly interesting from the point of view of nonlinear optics. Their null dipole moment does not stand as a drawback for its crystallization and still allows the cry...

Magnetic properties of transition-metal clusters have been the subject of intensive study in the last decades both theoretical and experimentaly. In particular, the importance of noncollinear effects and spin-orbit coupling in those systems has recently gained great interest. In this work we use time dependent density functional theory (TDDFT) to s...

In strict accordance with special relativity, locality is defined in terms of observed results. In a non-deterministic "hidden-parameter" theory, admitting "statistical independence" of the outcomes for a single pair, locality and a restriction ("primary locality") at the level of "primary probabilities", Bell's inequalities are recollected. Their...

The task of finding a flow at the top of the core that fits geomagnetic observations at the Earth's surface is an underdetermined problem. Weighted regularized least squares together with the tangential geostrophy hypothesis strongly constrain the flow, inhibiting both medium- to small-scale flow features from emerging and low-latitude currents fro...

This paper deals with the application of pattern search methods to the numerical solution of a class of molecular geometry problems with important applications in molecular physics and chemistry. The goal is to nd a conguration of a cluster or a molecule with minimum total energy. The minimization problems in this class of geometry molecular proble...

Density Functionals for Non-relativistic Coulomb Systems in the New Century.- Orbital-Dependent Functionals for the Exchange-Correlation Energy: A Third Generation of Density Functionals.- Relativistic Density Functional Theory.- Time-Dependent Density Functional Theory.- Density Functional Theories and Self-energy Approaches.- A Tutorial on Densit...

We solve a weighted regularized least-squares problem to invert a geomagnetic field model for the flow at the top of the Earth's liquid core. In this process we assess both small scale features by using a weak regularization and the 'non-geostrophic belt' by alleviating the tangential geostrophic constraint. Two very distinct classes of solutions c...

We show how pattern search methods can be adapted to the optimization problem contexts where there are ways to provide points that can lead to an objective function decrease. The paradigm here is that it is the user and the optimization algorithm together, and not the optimization algorithm alone, that lead the calculation of new points. We are es...

This paper deals with the application of pattern search methods to the numerical solution of a class of molecular geometry problems with important applications in molecular physics and chemistry. The goal is to nd a conguration of a cluster or a molecule with minimum total energy. The minimization problems in this class of geometry molecular proble...

Within a perturbative treatment of realistic local electron-ion pseudopotentials for the simple metals, we study structural phase transitions under pressure in Na and other monovalent metals, Mg and other divalent metals, and Al and other trivalent metals. For the "good local pseudopotential" metals Na, Mg, and Al, our results are in reasonable agr...

One of the most efficient approaches in computational cluster physics uses a plane-wave basis set and pseudopotentials to describe electron–ion interactions. This method – where the clusters are placed inside supercells – is restricted in its usual form to neutral systems because of the long-range interaction between a charged cluster and its perio...

The properties of simple metals are fixed primarily by the equilibrium average valence-electron density parameter rs, and secondarily by the valence z. The simplest level of theory that can account quantitatively for these trends invokes a “universal” local electron-ion pseudopotential, defined for each pair (rs,z) and treated as a second-order per...

We comment on a recently published criticism of our analysis of the paradox of Einstein, Podolsky and Rosen.

A comprehensive study of the lattice dynamics, elastic moduli, and liquid metal resistivities for 16 simple metals in the bcc and fcc crystal structures is made using a density-based local pseudopotential. The phonon frequencies exhibit excellent agreement with both experiment and nonlocal pseudopotential theory. The bulk modulus is evaluated by th...

A new local pseudopotential, called the `'evanescent core" pseudopotential, has recently been proposed for sp-bonded metals. It is fitted to dominant density parameters of the solid state (valence, average equilibrium valence electron density, and interstitial valence electron density), and it yields an overall good description of physical properti...

The Einstein, Podolsky and Rosen paradox, in Bohm's version, is re-examined with emphasis on the spin correlation operators, which represent the correlations in the mathematical theory as created in our mind. It is justified, in this approach, that these spin correlation operators acquire the status of physical concepts only in the context of a spe...

A new local pseudopotential based on solid state properties has been applied to the simple metals(C. Fiolhais et al.), Phys. Rev. B 51, 14001 (1995). (Erratum submitted).. Its transferability to clusters and atoms has been studied(F. Nogueira et al.), J. Phys.: Cond. Matt. (1996), in print.. The parameters of this so-called ``evanescent core'' pote...

Local electron - ion pseudopotentials fitted to dominant density parameters of the solid state (valence, equilibrium average electron density and interstitial electron density) have been constructed and tested for sixteen simple metals. Calculated solid-state properties present little evidence of the need for pseudopotential non-locality, but this...

Discusses, for a product of several operators and in relation to commutativity, the requirements for the establishment of meaningful expectation values. A published example relating to the product of spin operators, where not all pairs commute, is critically examined on the basis of the strict properties of the Pauli operators.