From Fundamentals to Spectroscopic Applications of Density Functional Theory

Density functional theory (DFT) and its time-dependent counterpart (TDDFT) are crucial tools in material discovery, drug design, biochemistry, catalysis, and nanoscience. However, despite its exact theoretical basis, approximations are necessary throughout, from the description of electron exchange and correlation (xc) interactions to the representation of wavefunctions for ever larger systems and the use of calculated quantities to explain and predict real-world phenomena. To address long-standing problems related to the speed and accuracy of approximations to the xc functional, we develop neural networks to emulate two such approximations, the local density (LDA) and generalized gradient (PBE) approximations, within the DFT code gpaw. We present a strategy for retraining the network and assess which training data is necessary to optimize performance for total energies over a wide class of molecules and crystals. While certain classes of materials proved difficult to describe, neural network implementations were able to reproduce the LDA and PBE xc functionals with high accuracy and a reasonable computation time. In an effort to develop a more efficient, robust, and accurate method for predicting the optical properties of low-dimensional systems, we introduce the LCAO-TDDFT-k-ω code within gpaw, where a linear combination of atomic orbitals (LCAO) representation of the Kohn-Sham wavefunctions and TDDFT implementation in wavenumber k and frequency ω space provides substantial memory and time savings, and a first order derivative discontinuity correction to the electronic gap brings the optical spectra in line with experimental measurements. Convergence of the basis set, the use of low-dimensional response functions, and different ways to incorporate the energy correction are explored for a series of materials across all dimensions: 0D fullerene and chlorophyll monomers, 1D single-walled carbon nanotubes, 2D graphene and phosphorene monolayers, and 3D anatase and rutile titanium dioxide. We develop a set of visualization tools for resolving the energetic, spatial, and reciprocal space distributions of excitations, and find LCAO-TDDFT-k-ω yields qualitative and semi-quantitative agreement with other TDDFT methods and implementations at a fraction of the time and memory cost. Finally, we introduce a phenomenological hydrodynamic model for the optical conductivity of graphene, with contributions due to universal conductivity, Pauli blocking, and intraband transitions included in a systematic way, is fit empirically with results from TDDFT, and manages to reproduce experimental spectra across a wide range of energies within energy loss equations derived for 2D materials. We find experimental parameters such as the amount of doping in graphene, the size of the collection aperture, and the energy of incoming electrons influence the shape of the spectra in important ways, especially in the energy region accessible to higher resolution probing techniques

Analysis of Plasmons Sustained on the Surface of Graphene

This thesis is broken into two parts, both dealing with the role of two-dimensional graphene in electronic and optical applications. The first section develops a phenomenological relationship for the polarizability of the graphene sheet using a hybrid semi-classical and QFT-derived (Quantum Field Theory) model for different energy regimes. Fits are made and our results are compared to data from two distinct experimental setups. The effects of contamination and rippling of the sheet are considered. The second section shows a phenomenological model for the rough surfaces of graphene and its underlying substrate for a sheet grown on a conducting material. Three different perturbative mathematical models are then explored to justify the shift in the plasmon frequency and the energy loss dispersion due to roughness, using input from experimental roughness data. The models are compared and corrected to include physical effects like crumpling

Optical Excitations of Chlorophyll a and b Monomers and Dimers

11 pages, 9 figuresPreprin

Simulations of magnetic Bragg scattering in transmission electron microscopy

We have simulated the magnetic Bragg scattering in transmission electron microscopy in two antiferromagnetic compounds, NiO and LaMnAsO. This weak magnetic phenomenon was observed in NiO experimentally by Loudon. We have computationally reproduced Loudon's experimental data, and for comparison we have performed calculations for the LaMnAsO compound as a more challenging case, containing lower concentration of magnetic elements and strongly scattering heavier non-magnetic elements. We have also described thickness and voltage dependence of the intensity of the antiferromagnetic Bragg spot for both compounds. We have employed two computational approaches, one assuming a static lattice with Debye-Waller smeared potentials, and another explicitly considering the atomic vibrations within the quantum excitations of phonons model (thermal diffuse scattering). The structural analysis shows that the antiferromagnetic Bragg spot appears in between (111) and (000) reflections for NiO, while for LaMnAsO the antiferromagnetic Bragg spot appears at the position of the (110) reflection in the diffraction pattern, which corresponds to a forbidden reflection of the crystal structure. Calculations predict that the intensity of the magnetic Bragg spot in NiO is significantly stronger than thermal diffuse scattering at room temperature. For LaMnAsO, the magnetic Bragg spot is weaker than the room-temperature thermal diffuse scattering, but its detection can be facilitated at reduced temperatures

Short-course combination treatment for experimental chronic Chagas disease.

Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, affects millions of people in the Americas and across the world, leading to considerable morbidity and mortality. Current treatment options, benznidazole (BNZ) and nifurtimox, offer limited efficacy and often lead to adverse side effects because of long treatment durations. Better treatment options are therefore urgently required. Here, we describe a pyrrolopyrimidine series, identified through phenotypic screening, that offers an opportunity to improve on current treatments. In vitro cell-based washout assays demonstrate that compounds in the series are incapable of killing all parasites; however, combining these pyrrolopyrimidines with a subefficacious dose of BNZ can clear all parasites in vitro after 5 days. These findings were replicated in a clinically predictive in vivo model of chronic Chagas disease, where 5 days of treatment with the combination was sufficient to prevent parasite relapse. Comprehensive mechanism of action studies, supported by ligand-structure modeling, show that compounds from this pyrrolopyrimidine series inhibit the Qi active site of T. cruzi cytochrome b, part of the cytochrome bc1 complex of the electron transport chain. Knowledge of the molecular target enabled a cascade of assays to be assembled to evaluate selectivity over the human cytochrome b homolog. As a result, a highly selective and efficacious lead compound was identified. The combination of our lead compound with BNZ rapidly clears T. cruzi parasites, both in vitro and in vivo, and shows great potential to overcome key issues associated with currently available treatments

DNDI-6174 is a preclinical candidate for visceral leishmaniasis that targets the cytochrome bc1.

New drugs for visceral leishmaniasis that are safe, low cost, and adapted to the field are urgently required. Despite concerted efforts over the last several years, the number of new chemical entities that are suitable for clinical development for the treatment of Leishmania remains low. Here, we describe the discovery and preclinical development of DNDI-6174, an inhibitor of Leishmania cytochrome bc1 complex activity that originated from a phenotypically identified pyrrolopyrimidine series. This compound fulfills all target candidate profile criteria required for progression into preclinical development. In addition to good metabolic stability and pharmacokinetic properties, DNDI-6174 demonstrates potent in vitro activity against a variety of Leishmania species and can reduce parasite burden in animal models of infection, with the potential to approach sterile cure. No major flags were identified in preliminary safety studies, including an exploratory 14-day toxicology study in the rat. DNDI-6174 is a cytochrome bc1 complex inhibitor with acceptable development properties to enter preclinical development for visceral leishmaniasis

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Safety, immunogenicity, and reactogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines given as fourth-dose boosters following two doses of ChAdOx1 nCoV-19 or BNT162b2 and a third dose of BNT162b2 (COV-BOOST): a multicentre, blinded, phase 2, randomised trial

Background Some high-income countries have deployed fourth doses of COVID-19 vaccines, but the clinical need, effectiveness, timing, and dose of a fourth dose remain uncertain. We aimed to investigate the safety, reactogenicity, and immunogenicity of fourth-dose boosters against COVID-19.Methods The COV-BOOST trial is a multicentre, blinded, phase 2, randomised controlled trial of seven COVID-19 vaccines given as third-dose boosters at 18 sites in the UK. This sub-study enrolled participants who had received BNT162b2 (Pfizer-BioNTech) as their third dose in COV-BOOST and randomly assigned them (1:1) to receive a fourth dose of either BNT162b2 (30 µg in 0·30 mL; full dose) or mRNA-1273 (Moderna; 50 µg in 0·25 mL; half dose) via intramuscular injection into the upper arm. The computer-generated randomisation list was created by the study statisticians with random block sizes of two or four. Participants and all study staff not delivering the vaccines were masked to treatment allocation. The coprimary outcomes were safety and reactogenicity, and immunogenicity (antispike protein IgG titres by ELISA and cellular immune response by ELISpot). We compared immunogenicity at 28 days after the third dose versus 14 days after the fourth dose and at day 0 versus day 14 relative to the fourth dose. Safety and reactogenicity were assessed in the per-protocol population, which comprised all participants who received a fourth-dose booster regardless of their SARS-CoV-2 serostatus. Immunogenicity was primarily analysed in a modified intention-to-treat population comprising seronegative participants who had received a fourth-dose booster and had available endpoint data. This trial is registered with ISRCTN, 73765130, and is ongoing.Findings Between Jan 11 and Jan 25, 2022, 166 participants were screened, randomly assigned, and received either full-dose BNT162b2 (n=83) or half-dose mRNA-1273 (n=83) as a fourth dose. The median age of these participants was 70·1 years (IQR 51·6–77·5) and 86 (52%) of 166 participants were female and 80 (48%) were male. The median interval between the third and fourth doses was 208·5 days (IQR 203·3–214·8). Pain was the most common local solicited adverse event and fatigue was the most common systemic solicited adverse event after BNT162b2 or mRNA-1273 booster doses. None of three serious adverse events reported after a fourth dose with BNT162b2 were related to the study vaccine. In the BNT162b2 group, geometric mean anti-spike protein IgG concentration at day 28 after the third dose was 23 325 ELISA laboratory units (ELU)/mL (95% CI 20 030–27 162), which increased to 37 460 ELU/mL (31 996–43 857) at day 14 after the fourth dose, representing a significant fold change (geometric mean 1·59, 95% CI 1·41–1·78). There was a significant increase in geometric mean anti-spike protein IgG concentration from 28 days after the third dose (25 317 ELU/mL, 95% CI 20 996–30 528) to 14 days after a fourth dose of mRNA-1273 (54 936 ELU/mL, 46 826–64 452), with a geometric mean fold change of 2·19 (1·90–2·52). The fold changes in anti-spike protein IgG titres from before (day 0) to after (day 14) the fourth dose were 12·19 (95% CI 10·37–14·32) and 15·90 (12·92–19·58) in the BNT162b2 and mRNA-1273 groups, respectively. T-cell responses were also boosted after the fourth dose (eg, the fold changes for the wild-type variant from before to after the fourth dose were 7·32 [95% CI 3·24–16·54] in the BNT162b2 group and 6·22 [3·90–9·92] in the mRNA-1273 group).Interpretation Fourth-dose COVID-19 mRNA booster vaccines are well tolerated and boost cellular and humoral immunity. Peak responses after the fourth dose were similar to, and possibly better than, peak responses after the third dose