APPLICATION AND DEVELOPMENT OF THE LINEAR COMBINATION OF ATOMIC ORBITALS B-SPLINE DENSITY FUNCTIONAL THEORY METHOD FOR THE MOLECULAR ELECTRONIC CONTINUUM

2004/2005Lo scopo della presente tesi è l'applicazione e lo sviluppo del metodo LCAO B-spline DFT, basato sulla Combinazione Lineare degli Orbitali Atomici (LCAO), sulla Teoria del Funzionale Densità (DFT) e sull'impiego delle funzioni di base Bspline, per lo studio della fotoionizzazione molecolare. Nel Capitolo 1 viene considerata una breve introduzione al processo di fotoionizzazione e alla teoria della fotoionizzazione molecolare. Nel Capitolo 2 vengono presentati i metodi computazionali utilizzati durante il presente lavoro di tesi. I risultati ottenuti sono presentati nei successivi Capitoli della tesi. Il lavoro è suddiviso in tre parti. Nella prima parte (Capitoli 3-6) il metodo LCAO B-spline DFT è applicato allo studio del Dicroismo Circolare nella Distribuzione Angolare (CDAD) dei fotoelettroni emessi da molecole chirali, ionizzate da luce circolarmente polarizzata di definita elicità. Un primo studio computazionale sull'effetto CDAD è focalizzato su una serie di derivati chirali dell'ossirano, con lo scopo di identificare tendenze lungo la serie molecolare. I risultati evidenziano una inaspettata sensibilità da parte del dicroismo circolare verso cambiamenti nella struttura elettronica molecolare. Inoltre i valori calcolati sottolineano come lintensità dell'effetto CD AD è da attribuire non tanto alla chiralità dello stato iniziale, ma bensì alla capacità della funzione d'onda del fotoelettrone (completamente delocalizzata su tutta la molecola) di sondare l'asimmetria nel potenziale molecolare effettivo. Il metodo LCAO B-spline DFT è quindi applicato allo studio del dicroismo circolare nella distribuzione angolare dei fotoelettroni emessi dai livelli di core e di valenza degli enantiomeri della canfora. I risultati sono confrontati con i valori calcolati attraverso l'approccio Continuum Multiple Scattering: i due metodi teorici mostrano un sostanziale accordo nei risultati. Inoltre, un confronto dei risultati calcolati con i dati sperimentali disponibili mostra un accordo sostanziale se non addirittura quantitativo. E' inoltre presentato uno studio teorico e sperimentale sul dicroismo circolare nella distribuzione angolare dei fotoelettroni emessi dai livelli di valenza del 3- idrossitetraidrofurano, il quale è una molecola relativamente flessibile. Questo lavoro mette luce su nuove caratteristiche del dicroismo in fotoemissione, il quale appare molto sensibile a fattori di tipo conformazionale. L'influenza degli effetti conformazionali sui parametri dinamici di fotoionizzazione, con particolare attenzione all'effetto CDAD, è quindi investigata in dettaglio. Il metodo LCAO E-spline DFf è applicato ai conformeri della molecola (1R,2R)-1,2-dibromo-1,2-dicloro-1,2-difluoroetano. Il parametro dicroico mostra una significativa sensibilità verso il conformero della molecola. Ciò suggerisce che il profilo energetico del parametro dicroico potrebbe essere utilizzato come un fingerprint dei conformeri di una molecola chirale. Il metodo computazionale è anche applicato alla rotazione del metile nella molecola (S)-ossirano, in modo da verificare l'assunzione che la rotazione del metile non influisca in maniera significativa sui valori calcolati dell'effetto CDAD. Si verifica invece come la rotazione del gruppo metile provochi variazioni inaspettate e drammatiche sul profilo del parametro dicroico. La seconda parte del lavoro (Capitolo 7) riguarda l'investigazione teorica sulla correttezza dell'assunzione che il Eranching Ratio nella ionizzazione dei livelli di core di siti atomici chimicamente diversi dello stesso elemento, segua il rapporto statistico. Il metodo LCAO E-spline DFT è stato impiegato per calcolare in maniera accurata le sezioni d'urto associate alla ionizzazione degli orbitali ls dei carboni per un set di molecole organiche scelte. I risultati mostrano che deviazioni nella sezione d'urto inducono forti andamenti non statistici da parte dei Eranching Ratios relativi alla ionizzazione dei livelli core, fino a diversi e V sopra la soglia di ionizzazione. La parte finale della tesi (Capitolo 8) riguarda il problema delle shape resonances. La razionalizzazione delle strutture risonanti, spesso presenti nello spettro molecolare del continuo, è un problema ampiamente discusso. Nel presente lavoro una nuova metodologia per localizzare e caratterizzare in termini molecolari le shape resonances viene proposta. Partendo da un sistema modello, è stato sviluppato un metodo per caratterizzare le risonanze in termini di contributo da parte degli orbitali virtuali di valenza. Il metodo sviluppato è quindi esteso al caso molecolare ed applicato alla localizzazione e caratterizzazione delle shape resonances che appaiono nella fotoionizzazione dei livelli crg di core e di valenza di N1.XVIII Ciclo1977Versione digitalizzata della tesi di dottorato cartacea

Molecular graph transformer: stepping beyond ALIGNN into long-range interactions

Graph Neural Networks (GNNs) have revolutionized material property prediction by learning directly from the structural information of molecules and materials. However, conventional GNN models rely solely on local atomic interactions, such as bond lengths and angles, neglecting crucial long-range electrostatic forces that affect certain properties. To address this, we introduce the Molecular Graph Transformer (MGT), a novel GNN architecture that combines local attention mechanisms with message passing on both bond graphs and their line graphs, explicitly capturing long-range interactions. Benchmarking on MatBench and Quantum MOF (QMOF) datasets demonstrates that MGT's improved understanding of electrostatic interactions significantly enhances the prediction accuracy of properties like exfoliation energy and refractive index, while maintaining state-of-the-art performance on all other properties. This breakthrough paves the way for the development of highly accurate and efficient materials design tools across diverse applications

Computational screening of metalloporphyrin catalysts for the activation of carbon dioxide

Electrocatalytic CO2 reduction (eCO2R) to value-added chemicals offers a promising route for carbon capture and utilization. Metalloporphyrin (M-POR) is a class of catalysts for eCO2R that has drawn attention due to its tuneable electronic and structural properties. This work presents a computational screening, based on density functional theory calculations, of one of the key steps in the eCO2R: the adsorption of CO2 on 110 M-PORs with varying peripheral ligands, metal centres, and oxidation states, to understand how these factors can influence CO2 activation. A set of criteria was used to shortlist M-PORs based on their ability to lengthen the C–O bond, bend the O–C–O angle, bind CO2, and donate charge from the metal of the M-POR to the carbon of CO2. 16 systems were selected for their potential to activate CO2. These systems predominantly have the electron configuration of the metal centre in the d[6] and d[7] configurations. Natural bond orbital analysis revealed the impact of electron-withdrawing groups in the system, which increases orbital splitting and, consequently, lowers the ability of the M-POR to activate CO2. Second-order perturbation theory analysis confirms that the presence of electron-donating groups in the ligand structure enhances CO2 activation. This work demonstrates the interconnected effect of peripheral ligands, metal centres, and oxidation states in M-PORs on their ability to adsorb and activate CO2, thereby establishing structure-activity relationships within M-PORs

Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions

We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell

Sulfate and molybdate incorporation at the calcite–water interface: insights from ab initio molecular dynamics

Sulfur and molybdenum trace impurities in speleothems (stalagmites and stalactites) can provide long and continuous records of volcanic activity, which are important for past climatic and environmental reconstructions. However, the chemistry governing the incorporation of the trace element-bearing species into the calcium carbonate phases forming speleothems is not well understood. Our previous work has shown that substitution of tetrahedral oxyanions [XO4]2– (X = S and Mo) replacing [CO3]2– in CaCO3 bulk phases (except perhaps for vaterite) is thermodynamically unfavorable with respect to the formation of competing phases, due to the larger size and different shape of the [XO4]2– tetrahedral anions in comparison with the flat [CO3]2– anions, which implied that most of the incorporation would happen at the surface rather than at the bulk of the mineral. Here, we present an ab initio molecular dynamics study, exploring the incorporation of these impurities at the mineral–water interface. We show that the oxyanion substitution at the aqueous calcite (10.4) surface is clearly favored over bulk incorporation, due to the lower structural strain on the calcium carbonate solid. Incorporation at surface step sites is even more favorable for both oxyanions, thanks to the additional interface space afforded by the surface line defect to accommodate the tetrahedral anion. Differences between sulfate and molybdate substitutions can be mostly explained by the size of the anions. The molybdate oxyanion is more difficult to incorporate in the calcite bulk than the smaller sulfate oxyanion. However, when molybdate is substituted at the surface, the elastic cost is avoided because the oxyanion protrudes out of the surface and gains stability via the interaction with water at the interface, which in balance results in more favorable surface substitution for molybdate than for sulfate. The detailed molecular-level insights provided by our calculations will be useful to understand the chemical basis of S- and Mo-based speleothem records

Hydrogen-bond structure and low-frequency dynamics of electrolyte solutions: Hydration numbers from ab Initio water reorientation dynamics and dielectric relaxation spectroscopy

We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl2 ) solutions at different concentrations (0.6-2.8 mol kg-1 ) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl2 has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction

Theoretical insights into the role of defects in the optimization of the electrochemical capacitance of graphene

Graphene-based frameworks suffer from a low quantum capacitance due to graphene’s Dirac point at the Fermi level. This theoretical study investigated the effect structural defects, nitrogen and boron doping, and surface epoxy/hydroxy groups have on the electronic structure and capacitance of graphene. Density functional theory calculations reveal that the lowest energy configurations for nitrogen or boron substitutional doping occur when the dopant atoms are segregated. This elucidates why the magnetic transition for nitrogen doping is experimentally only observed at higher doping levels. We also highlight that the lowest energy configuration for a single vacancy defect is magnetic. Joint density functional theory calculations show that the fixed band approximation becomes increasingly inaccurate for electrolytes with lower dielectric constants. The introduction of structural defects rather than nitrogen or boron substitutional doping, or the introduction of adatoms leads to the largest increase in density of states and capacitance around graphene’s Dirac point. However, the presence of adatoms or substitutional doping leads to a larger shift of the potential of zero charge away from graphene’s Dirac point

Silicon Radical-Induced CH4 Dissociation for Uniform Graphene Coating on Silica Surface

Due to the manufacturability of highly well-defined structures and wide-range versatility in its microstructure, SiO2 is an attractive template for synthesizing graphene frameworks with the desired pore structure. However, its intrinsic inertness constrains the graphene formation via methane chemical vapor deposition. This work overcomes this challenge by successfully achieving uniform graphene coating on a trimethylsilyl-modified SiO2 (denote TMS-MPS). Remarkably, the onset temperature for graphene growth dropped to 720 °C for the TMS-MPS, as compared to the 885 °C of the pristine SiO2 . This is found to be mainly from the Si radicals formed from the decomposition of the surface TMS groups. Both experimental and computational results suggest a strong catalytic effect of the Si radicals on the CH4 dissociation. The surface engineering of SiO2 templates facilitates the synthesis of high-quality graphene sheets. As a result, the graphene-coated SiO2 composite exhibits a high electrical conductivity of 0.25 S cm-1 . Moreover, the removal of the TMP-MPS template has released a graphene framework that replicates the parental TMS-MPS template on both micro- and nano- scales. This study provides tremendous insights into graphene growth chemistries as well as establishes a promising methodology for synthesizing graphene-based materials with pre-designed microstructures and porosity

Correction: Resolving nanoscopic structuring and interfacial THz dynamics in setting cements

Correction for ‘Resolving nanoscopic structuring and interfacial THz dynamics in setting cements’ by Fu V. Song et al., Mater. Adv., 2022, 3, 4982–4990, https://doi.org/10.1039/D1MA01002F.Funder: Horizon 2020 Framework Programme; FundRef: https://doi.org/10.13039/10.13039/100010661; Grant(s): ACT, No. 299668 Funder: Engineering and Physical Sciences Research Council; FundRef: https://doi.org/10.13039/10.13039/501100000266; Grant(s): EP/K000128/1, EP/L000202 Funder: Science and Technology Facilities Council; FundRef: https://doi.org/10.13039/10.13039/501100000271; Grant(s): RB1100006, RB1110428 and RB1310334 Funder: Sapienza Università di Roma; FundRef: https://doi.org/10.13039/10.13039/501100004271 Funder: McMaster University; FundRef: https://doi.org/10.13039/10.13039/100009776 Funder: University of British Columbia; FundRef: https://doi.org/10.13039/10.13039/501100005247 Funder: Natural Sciences and Engineering Research Council of Canada; FundRef: https://doi.org/10.13039/10.13039/501100000038; Grant(s): RGPIN 04598, RY

A thermodynamically favorable route to the synthesis of nanoporous graphene templated on CaO via chemical vapor deposition

Template-assisted chemical vapor deposition (CVD) is a promising approach for fabricating nanoporous materials based on graphene walls. Among conventional metal oxide templates, CaO, produced through the thermal decomposition of CaCO3, offers improved environmental sustainability and lower production costs, thereby potentially making it a viable candidate for green template materials. Nevertheless, the underlying reaction mechanisms of the interaction on the CaO surface during the CVD process remain indeterminate, giving rise to challenges in regulating graphene formation and obtaining high-quality materials. In this work, a comprehensive experimental-theoretical investigation has unveiled the CVD mechanism on CaO. CaO exhibits efficient catalytic activity in the dissociation of CH4, thereby facilitating a thermodynamically favorable conversion of CH4 to graphene. These findings highlight the potential of using CaO as a substrate for graphene growth, combining both sustainability and cost-effectiveness. When the shell-like graphene layer deposited on CaO particles is released through the dissolution of CaO with HCl, the resulting nanoporous graphene-based materials can be readily compacted by the capillary force of the liquid upon drying. The folded surfaces, however, can become available for electric double-layer capacitance via electrochemical exfoliation under a low applied potential (<1.2 V vs. Ag/AgClO4)