Elucidating the Electronic Origins of Intermolecular Forces in Crystalline Solids

It is not possible to study almost any physical system without considering intermolecular forces (IMFs), no matter how insignificant they may appear relative to other energetic factors. Countless studies have shown that IMFs are responsible for governing a wide variety of physical properties, but often the atomic-origins of such interactions elude experimental detection. A considerable amount of work throughout the course of this research was therefore placed on using quantum mechanical simulations, specifically density functional theory (DFT), to calculate the electronic properties of solid-materials. The goal of these calculations was a better understanding of the precise origins of interatomic energies, down to the single-electron level. Furthermore, experimental X-ray diffraction and terahertz spectroscopy were both utilized because they are able to broadly probe the potential energy surfaces of molecular crystals, enhancing the theoretical data. Combining DFT calculations with experimental measurements enabled in-depth studies into the nature of specific non-covalent interactions, with results that were often unexpected based on conventional descriptions of IMFs. Overall, this work represents a significant advancement in understanding how subtle changes in characteristics like orbital occupation or electron density can have profound effects on bulk properties, highlighting the fragile relationship that exists between the numerous energetic parameters occurring within condensed phase systems

Applications of density functional theory (DFT) to investigate the structural, spectroscopic and magnetic properties of lanthanide(III) complexes

[Abstract] Density functional theory (DFT) has become a general tool to investigate the structure and properties of complicated inorganic molecules, such as lanthanide(III) coordination compounds, due to the high accuracy that can be achieved at relatively low computational cost. Herein, we present an overview of different successful applications of DFT to investigate the structure, dynamics, vibrational spectra, NMR chemical shifts, hyperfine interactions, excited states, and magnetic properties of lanthanide(III) complexes. We devote particular attention to our own work on the conformational analysis of LnIII-polyaminocarboxylate complexes. Besides, a short discussion on the different approaches used to investigate lanthanide(III) complexes, i. e. all-electron relativistic calculations and the use of relativistic effective core potentials (RECPs), is also presented. The issue of whether the 4f electrons of the lanthanides are involved in chemical bonding or not is also shortly discussed.Ministerio de Educación y Ciencia; CTQ2009-10721Xunta de Galicia; IN845B-2010/06

Теорија Функционала Густине у проучавању електронских стања аква- и оксо- комплекса прве серије прелазних метала

In the scope of present doctoral thesis, the complicated electronic structure of aqua- and oxo- complexes of the first row transition metals is studied. Energies of the ground and excited electronic states of transition metal complexes are calculated using DFT-based theoretical methods. The performance of different DFAs was investigated in order to find an unambiguous way to determine the ground spin state of oxo- and hydroxo-iron complexes, which is one of the most demanding tasks, both from theoretical and experimental point of view. The results direct us to use S12g for optimization as well as for the determination of the ground spin state.For calculation of excited states, two different methods (TD-DFT and LF-DFT) are utilized, whereas the results are rationalized and compared with those obtained experimentally. The results indicate a significantly better performance of LF-DFT method for calculation of excited states and reproduction of experimental spectra. In addition, EDA study of a series of oxo- and hydroxo- iron model complexes was performed. The binding energy is decomposed into chemically meaningful contributions. Obtained results show that the most important factor, responsible for the energy differentiation, is the destabilizing preparation energy based on excitation energy requirements and oxidation state of the metal. And the other is the stabilizing orbital interaction energy established when chemical bonds are created. The primary challenge was to establish an appropriate level of theory able to explain the relationships between structural features and electronic structure, and in turn rationalize the experimentally obtained results. The scientific content of this dissertation proposes computational steps which make DFT reliable for explaining, interpreting and predicting the characteristics and properties of first row transition metal complexes. By rationally applying the proposed methodologies, we have an exclusive opportunity to clarify the experimental blindspots and apply the basic principles in order to understand the chemical complexities.У оквиру ове докторске тезе проучавана је компликована електронска структура аква- и оксо- комплекса прве серије прелазних метала. Теоријским методама, заснованим на DFT, израчунате су енергије основних и побуђених електронских стања комплекса прелазних метала. Испитано је понашање различитих DFA у циљу проналажења недвосмисленог начина за одређивање основног спинског стања оксо- и хидроксо- комплекса гвожђа, што је захтевaн задатак, и са теоријског и са експерименталног становишта. Резултати нас усмеравају на коришћење S12g за оптимизацију, као и за одређивање основног спинског стања. За рачунање побуђених стања употребљене су две различите методе (TD-DFT и LF-DFT) а резултати рационализовани и упоређени са експериментално добијеним. Резултати указују на знатно боље понашање LF-DFT методе за рачунање побуђених стања и репродукцију експерименталних спектара. У склопу ове дисертације изведено је и EDA изучавање серије оксо- и хидроксо- модел комплекса гвожђа. Енергија везивања разложена је на хемијски смислене доприносе. Резултати показују да је најбитнији фактор, одговоран за енергетску диференцијацију енергија побуђивања, неопходна да се метални јон из изолованог електронског стања доведе у електронско стање које поседује у комплексном једињењу. Следећи допринос по важности је орбитална стабилизација услед успостављања метал-лиганд хемијске везе. Примарни изазов је представљало успостављање одговарајућег нивоа теорије, објашњење међусобних односа између структурних особина и металног окружења са електронском структуром, као и рационализација добијених резултата и експерименталних података. Научни садржај ове дисертације предлаже рачунарске кораке којима чине DFT поузданом у објашњавању, тумачењу и предвђању карактеристика и својства комплекса прве серије прелазних метала. Рационалном применом предложених методологија, имамо прилику да разјаснимо експерименталне недоумице и искористимо основна начела како бисмо разумели хемијске сложености

Computational Approach to Aluminum Biochemistry and Development of New Chelation Strategies

299 p.DIPC:Donostia International Physics Center SmartLigs Bioinformatica Universidade do Port

Computational investigations of the spectroscopy, vibronic coupling, and photo(stereo)chemistry in inorganic systems

This thesis focuses on the spectroscopy and photo-stereochemistry of relatively large closed-shell and open-shell transition metal complexes, investigated with an array of modern computational methodologies. The presence of the metal electrons/orbitals results in a greater number of low-lying excited states, and these states are vibronically coupled resulting in Jahn-Teller or pseudo-Jahn-Teller (pJT) effects, or general surface crossings. These features are very challenging to calculate but are vitally important to explain the observed behavior in such systems. Computational investigations using the multiconfigurational CASSCF method on the pJT effect occurring in ammonia, and Mo2(DXylF)2(O2CCH3)2(μ2-O)2 complex are presented. These definitively show that in the latter case the experimentally observed structure is due to a vibronic coupling of the ground electronic state with that of a nondegenerate 1πδ* state, resulting in a rhomboidal rather than square motif at the bimetallic centre. The (BQA)PtMe2I (BQA= bis(8-quinolinyl)amide) complex has been found to undergo unexpected meridial to facial isomerisation induced by light. The TD-DFT method was used to examine the spectroscopy of this system, and the CASSCF method was used to examine excited state relaxation pathways. The system relaxes on an excited state potential energy surface, of an essentially localised ππ* excited state of the BQA ligand, and reaches a facial excited minimum that is located adjacent to a sloped conical intersection connecting the excited and ground electronic states. Chromium (III) complexes have been investigated for many years and many aspects of their photochemistry are still not very well understood. The photochemistry of paradigm Cr (III) complexes, such as chromium oxalate [Cr(C2O4)3]3-, chromium tris- (1,3diaminopropane) [Cr(tn)3]3+ and Cr(tn)2(CN)2, have been investigated using TDDFT and CASSCF methods. Non-radiative relaxation pathways have been documented showing mechanism of both internal conversion in the quartet manifold, as well as inter-system crossing into the doublet manifold. The results explain photostereochemical features of the photo-induced racemization of [Cr(C2O4)3]3- and the photoaquation of [Cr(tn)3]3+ and Cr(tn)2(CN)2.Engineering and Physical Sciences Research Council (EPSRC) grant No. EP/F01709

Kvantově-chemické studium adsorpce v mikroporézních materiálech

Microporous materials play a crucial role in a wide range of applications in chemical engineering, chemistry, material science or lately even in medicine. Zeolites and metal- organic frameworks (MOFs) take a prominent place among them. The most important fields of applications include gas separation, purification or gas storage. A detailed understanding of adsorption properties of these materials represents a long-standing effort from experimental as well as computational chemistry community. However, ac- curate computational description of adsorption in microporous materials represents a significant challenge for computational chemists as: (i) unit cells of the crystalline mi- croporous materials are typically large, (ii) dispersion interactions are of importance, and (iii) there are metal cations, often with open-shell electronic structure, present in the framework interacting strongly and specifically with adsorbing molecules. Despite a significant progress made in theoretical description of adsorption mechanisms in both zeolites and MOFs in last decade, there is a number of applications and systems for which the commonly used computational approaches fail to provide a needed accuracy. A whole class of such systems is represented, for example, by MOFs containing tran- sition metal coordinatively...Mikroporézní materiály hrají významnou roli v mnoha oblastech aplikace chemického inženýrství, chemie, materiálového výzkumu a v poslední době dokonce i v oblasti medicíny. Nejvýznamnější z nich jsou zeolity a mikroporézní koordinační polymery (angl. Metal Organic Frameworks, zkráceně MOF), které se používají především k rozdělování plynů, jejich čištění a k jejich uskladňování. Dlouhodobým cílem expe- rimentálních a výpočetních chemiků je pochopit mechanismus adsorpce v těchto ma- teriálech. Nicméně přesný popis tohoto procesu představuje velkou výzvu, protože (i) jednotkové cely krystalických forem těchto materiálů jsou obvykle velké, (ii) disperzní interakce musí být zohledněny, (iii) ve struktuře jsou přítomny kationty kovů, často s otevřenou elektronovou slupkou, které interagují silně a specificky s adsorbujícími se molekulami. Přes významný pokrok v teoretickém popisu mechanismu adsorpce v ze- olitech a MOFech zaznamenaný v posledních letech, stále zůstává množství aplikací a systémů, pro které obecně používané výpočetní přístupy selhávají. Příkladem celé třídy takovýchto systému jsou MOFy obsahující v adsorpčních místech přechodné kovy, které jsou koordinačně...Department of Physical and Macromolecular ChemistryKatedra fyzikální a makromol. chemieFaculty of SciencePřírodovědecká fakult

CatSD: structural database and high-throughout predictive workflows for homogeneous catalyst design

Identification of highly active catalysts is an important process across multiple industries including drug development, process chemistry and agrochemicals. The lack of understanding of ligand properties and catalytic pathways are limiting factors for the uptake of more sustainable and highly active catalysts. Herein we report a novel method for the identification of ligands and the prediction of their activity for homogeneous catalysts from the Cambridge Structural Database. We present CatSD, a structural database complete with catalytically relevant features to enable the mining of organometallic ligands from the CSD. We also present a high-throughput computational workflow for the prediction of activation energies and mechanistic exploration. This workflow is on a timescale similar to experimental high-throughput screening and provides energies with an accuracy of 3.9 kcal mol-1 . CatSD and the prediction workflow were applied to the Ullmann-Goldberg reaction to identify novel ligands for amine and amide coupling partners. Over 10,000 ligands were identified from the CSD for both coupling partners. The workflow showed excellent reliability for the generation of starting structures (99.7%) and good reliability for the optimisation of important intermediates (>84%) and transition states (TSOA: 33-61%, TSSig: 83-85%). Several ligands were validated experimentally identifying a previously unreported active ligand class. The effect of ligand properties was explored using machine learning to identify several key characteristics for both nucleophile coupling partners. Machine learning was also used to predict activation energies without the need to calculate the transition state. Models were optimised providing accuracy on par with the accuracy of the workflow calculations. It is our hope that the methodologies presented in this work will aid the discovery and design of ligands for homogeneous catalysts for the wider chemistry community as well as stimulate further research in this field