Being a program written primarily in Python that strictly adheres to modern object-oriented software engineering and parallel programming practices, VeloxChem is shown to be suitable for the development of (semi)automatized workflows that extend its scope from first-principles quantum chemical purism to hybrid quantum-classical interoperability and some degree of semiempiricism. Methods are presented for building complex systems such as metal-organic frameworks, constructing molecular mechanics and interpolation mechanics force fields, conformer searches, system solvation, determining free energies of solvation, and determining free energy profiles of reaction pathways using the empirical valence bond method. The implementations are made intuitive with opportunities for interactive plotting and 3D molecular structure illustrations through the use of Jupyter notebooks.

The Ru(tda) catalyst has been a major milestone in the development of molecular water oxidation catalysts due to its outstanding performance at neutral pH. The role of the noncoordinating carboxylate group is to act as a nucleophile, donating an oxygen atom to the oxo group, thereby acting as an oxide relay (OR) mechanism for O-O bond formation. A substitution of the carboxylates for phosphonate groups has been proposed, resulting in the Ru(tPaO) catalyst, which has shown even more efficient performance in experimental characterization. In this study, we explore the feasibility of the OR mechanism in the newly reported Ru(tPaO) molecular catalyst. We investigated the catalytic cycle using density functional theory and identified a variation of the OR mechanism that involves radical oxygen atoms in O-O bond formation. We have also determined that the subsequent hydroxide nucleophilic attack is the sole rate-limiting step in the catalytic cycle. All activation free energies are very low, with a free-energy barrier of 2.1 kcal/mol for O-O bond formation and 4.2 kcal/mol for OH- nucleophilic attack.

To avoid the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive regions, which is also known as complete active space methods. However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree-Fock energies. We will explore classical and quantum computation methods for orbital optimization and compare the chemically inspired ansatz, UCCSD, with the classical full CI approach for describing the active space in both weakly and strongly correlated molecules. Finally, we will investigate the practical implementation of a quantum CASSCF, where hardware-efficient circuits must be used and noise can interfere with accuracy and convergence. Additionally, we will examine the impact of using canonical and noncanonical active orbitals on the convergence of the quantum CASSCF routine in the presence of noise.

To increase the stability and current density of molecular-catalyst-based electroanodes for water oxidation, immobilization of the catalysts at the electrode surface is a common strategy. A prominent example is the oligomerized Ru(tda) molecular catalyst, which showed outstanding current densities even at neutral pH values. One of the most challenging aspects of immobilized catalysts is to understand the interaction between the catalyst and the surface under operando conditions. Experiments are often performed under model conditions, and computational methods to study reaction steps are typically limited to a few hundred atoms. In this study, we combined three computational methods, density functional theory electronic structure computations, molecular dynamics for large-scale simulations of the catalyst-solid interaction, and empirical valence bond for reaction modeling the catalyst at the interface of a large carbon support and a phosphate water buffer. These techniques allowed us to explore the combined effects of solvent, hydrophobic directionality, and electric field on the attachment and reactivity of a Ru(tda) pentamer at a graphene surface. Our simulations have a perfect agreement with the experimental characterization under model conditions. However, we find that under operando conditions, where the catalyst is oxidized to the active RuV state, with a phosphate-containing electrolyte and an applied electric field, the attachment is completely reversed compared to the model conditions with RuII and organic solvents. This reversed attachment leads to a water-excluded region close to the active RuV═O center. The EVB reaction modeling showed that the reaction could still proceed to form an O-O bond via an oxide relay mechanism, where a dangling carboxylate reacts with the oxo via nucleophilic attack. We find that the activation energies are identical in water solution and at the electrode surface, showing how this mechanism is key to highly active molecular water oxidation catalysts immobilized on surfaces. Since attachment to surfaces could have a strong, and often negative, influence on the reactions, this study provides a guideline on how to model reactions without compromising the complexity of the electrode environment.

The Ru(tda) catalyst has been a major milestone in the development of molecular water oxidation catalysts due to its outstanding performance at neutral pH. The role of the non-coordinating carboxylate group is to act as a nucleophile, donating an oxygen atom to the oxo group, acting as an oxide relay mechanism the the O-O bond formation. A substitution of the carboxylates for phosphonate groups has been proposed, the Ru(tPaO), and its experimental characterization has shown an even more efficient performance. In this study, we explore the feasibility of the oxide relay mechanism in the newly reported Ru(tPaO) molecular catalyst. We have explored the catalytic cycle using density functional theory and we have identified a variation of the oxide relay mechanism that involves radical oxygen atoms in the O-O bond formation. We have explored the origin of the radical character in this complex and we have identified the hydroxyl nucleophilic attack as the sole rate limiting step in the catalytic cycle. The barriers are very low in all the steps, the O-O bond formation has a free energy barrier of 2.1 kcal/mol and the OH- nucleophilic attack 4.2 kcal/mol.

The industrial revolution thrived our society to great technological advancement and a shift from an agrarian to an industrial society. Besides this fact, the side effect has been the development of a society highly dependent on energy, and the main sources of energy are based on non-renewable fossil fuels. This issue calls for the quest for new renewable energy sources that can address the energy dependency minimizing its side effects of it. In this quest, hydrogen is a promising source due to its high energy capacity and clean sub-products.

The first chapter of this thesis will revise more in deep this environmental issues and what is needed to implement sustainable hydrogen production by water splitting. As well, as how the water source is extremely relevant, and solutions for using seawater are required to scale up hydrogen production. Also, an introduction to molecular catalysts for water oxidation based on Ru will be exposed, including a historical perspective and the state of the art at this day. The first chapter will finish with the strategies explored in this thesis to overcome the limitations of molecular catalysts in water splitting devices i.e, stability and current density.

This work uses an ample set of computational tools to explore the reactivity and supramolecular properties of molecular catalysts. The second chapter will start with the treatment of molecules as electronic systems utilizing molecular quantum mechanics. Wave function formalism and density functional formalism of molecular quantum mechanics will be exposed and explained to the extent that is needed to ground the results of this thesis. The next section will introduce the treatment of molecules as atomic systems employing molecular mechanics and how we derive relevant supramolecular effects such as hydrophobicity, means of attachment to electrode surfaces, solvent, and electric field effects. Finally, this chapter will revise the Empirical Valence Bond approach to study the reactivity dependence on the molecular environment.

The last chapter will go over the results of this thesis that correspond to the annexed papers at the end of this work. Starting from the characterization of the oxide relay mechanism in the highly efficient catalyst Ru(tda) where a novel function for the non-coordinating carboxylate ligand is proposed. To increase the stability of the Ru(tda) an attachment to carbon surfaces has been proposed and proved to increase significantly the stability. A study of the oxide relay mechanism at the surface revealed that the water-excluded environment of the active site in the reactive intermediate does not affect the key steps of this mechanism, in agreement with the experimental results reported. Next, the Ru(bda) has been shown to effectively catalyze the formation of molecular nitrogen from ammonia in an apolar solvent. The Ru(bda) has been well studied for water oxidation due to its high efficiency and the key step has been identified as the dimerization of two complexes driven by the aqueous solvent. The study of the dimerization process in acetonitrile has revealed the crucial role of solvent in supramolecular effects since acetonitrile promotes complex-counterion pairing aiding the dimerization of the Ru(bda) and. To increase the current density is needed a strategy to increase the catalyst density at the surface. Oligomerization of the Ru(tda) has shown to be an effective strategy to increase the current density of the hybrid electroanode to levels that are comparable to commercial electrolyzers. The exploration of the ways of attachment to the carbon surface revealed high dependency on the metal center oxidation state, the solvent, and the electric field. Also, the reactivity of the oligomer has been explored using the Empirical Valence Bond approach, revealing that the O-O bond formation remains unaltered in the oligomer and the reactivity remains unaltered in this complex environment, in agreement with experimental results. Finally, the substitution of the carboxylates in the Ru(tda) by phosphonates (Ru(tPaO)) has been proved to double the efficiency of the molecular catalyst at neutral pH. Due to the similarities between carboxylates and phosphonates the oxide relay mechanism has been tested in the Ru(tPaO), revealing that the origin of the extreme reactivity comes from low barriers in all the steps. The O-O bond formation involves an intramolecular radical coupling lowering the activation barrier to 2.1 kcal/mol. This radical coupling revealed a variation of the oxide relay mechanism called the radical oxide relay mechanism.

Den industriella revolutionen blomstrade vårt samhälle till stora tekniska framsteg och en övergång från ett jordbrukssamhälle till ett industrisamhälle. Förutom detta faktum har bieffekten varit utvecklingen av ett samhälle starkt beroende av energi, och de huvudsakliga energikällorna är baserade på ickeförnybara fossila bränslen. Denna fråga kräver en strävan efter nya förnybara energikällor som kan hantera energiberoendet och minimera dess bieffekter av det. I denna strävan är väte en lovande källa på grund av dess höga energikapacitet och rena delprodukter.

Det första kapitlet i denna avhandling kommer att gå igenom mer på djupet av dessa miljöfrågor och vad som behövs för att implementera hållbar väteproduktion genom vattenklyvning. Liksom hur vattenkällan är extremt relevant, och lösningar för att använda havsvatten krävs för att skala upp väteproduktionen. Dessutom kommer en introduktion till molekylära katalysatorer för vattenoxidation baserade på Ru att exponeras, inklusive ett historiskt perspektiv och den senaste tekniken i dag. Det första kapitlet kommer att avslutas med de strategier som utforskas i denna avhandling för att övervinna begränsningarna hos molekylära katalysatorer i vattenklyvningsanordningar, dvs stabilitet och strömtäthet.

Detta arbete använder en riklig uppsättning beräkningsverktyg för att utforska reaktiviteten och supramolekylära egenskaperna hos molekylära katalysatorer. Det andra kapitlet kommer att börja med behandlingen av molekyler som elektroniska system som använder molekylär kvantmekanik. Vågfunktionsformalism och densitetsfunktionell formalism inom molekylär kvantmekanik kommer att exponeras och förklaras i den utsträckning som behövs för att grunda resultaten av denna avhandling. Nästa avsnitt kommer att introducera behandlingen av molekyler som atomsystem som använder molekylär mekanik och hur vi härleder relevanta supramolekylära effekter såsom hydrofobicitet, sätt att fästa på elektrodytor, lösningsmedel och elektriska fälteffekter. Slutligen kommer detta kapitel att revidera den empiriska valensbindningsmetoden för att studera reaktivitetsberoendet av den molekylära miljön.

Det sista kapitlet kommer att gå igenom resultaten av denna avhandling som motsvarar de bifogade artiklarna i slutet av detta arbete. Utgående från karakteriseringen av oxidrelämekanismen i den högeffektiva katalysatorn Ru(tda) där en ny funktion för den icke-koordinerande karboxylatliganden föreslås. För att öka stabiliteten hos Ru(tda) har en vidhäftning till kolytor föreslagits och visat sig öka stabiliteten avsevärt. En studie av oxidrelämekanismen vid ytan avslöjade att den vattenexkluderade miljön för den aktiva platsen i den reaktiva intermediären inte påverkar nyckelstegen i denna mekanism, i överensstämmelse med de experimentella resultaten som rapporterats. Därefter har Ru(bda) visat sig effektivt katalysera bildningen av molekylärt kväve från ammoniak i ett opolärt lösningsmedel. Ru(bda) har studerats väl för vattenoxidation på grund av dess höga effektivitet och nyckelsteget har identifierats som dimerisering av två komplex som drivs av det vattenhaltiga lösningsmedlet. Studien av dimeriseringsprocessen i acetonitril har avslöjat lösningsmedlets avgörande roll i supramolekylära effekter eftersom acetonitril främjar komplex-motjonparning som hjälper till att dimerisera Ru(bda) och. För att öka strömtätheten behövs en strategi för att öka katalysatordensiteten vid ytan. Oligomerisering av Ru(tda) har visat sig vara en effektiv strategi för att öka strömtätheten hos hybridelektranoden till nivåer som är jämförbara med kommersiella elektrolysatorer. Utforskningen av sätten att fästa på kolytan avslöjade ett stort beroende av metallcentrumets oxidationstillstånd, lösningsmedlet och det elektriska fältet. Oligomerens reaktivitet har också undersökts med användning av Empirical Valence Bond-metoden, vilket avslöjar att O-O-bindningsbildningen förblir oförändrad i oligomeren och reaktiviteten förblir oförändrad i denna komplexa miljö, i överensstämmelse med experimentella resultat. Slutligen har substitutionen av karboxylaterna i Ru(tda) med fosfonater (Ru(tPaO)) visat sig fördubbla effektiviteten av den molekylära katalysatorn vid neutralt pH. På grund av likheterna mellan karboxylater och fosfonater har oxidrelämekanismen testats i Ru(tPaO), vilket avslöjar att ursprunget till den extrema reaktiviteten kommer från låga barriärer i alla steg. O-O-bindningsbildningen involverar en intramolekylär radikalkoppling som sänker aktiveringsbarriären till 2,1 kcal/mol. Denna radikalkoppling avslöjade en variation av oxidrelämekanismen som kallas radikaloxidrelämekanismen.

The decentralisation of accurate determination of the ammonium ion (NH4+) is relevant for environmental monitoring (i. e., nitrogen cycle) and certain clinical applications (e. g., kidney and liver diseases). Potentiometric ionophore-based sensors are one alternative for these purposes in terms of versatile implementation, though the potassium ion (K+) is known to be a major source of interference. We herein investigate the use of three different tripodal tris(pyrazolyl) compounds derived from 1,3,5-triethylbenzene as NH4+ ionophores. A complete set of potentiometric experiments together with theoretical simulations reveals suitable analytical performance while demonstrating a suppression of the K+ interference given the formation of an adequate cavity in the ionophore to host NH4+ over K+ in the membrane environment. The results support the use of these electrodes in the analytical detection of NH4+ in a wide range of samples with variable contents.

To increase the stability and current density of molecular-catalyst-based electroan- odes for water oxidation immobilization of the catalysts at the electrode surface is a common strategy. A prominent example it the oligomerized Ru(tda) molecular cat- alyst which showed outstanding current densities even at neutral pH values. One of the most challenging aspects of immobilized catalysts is to understand the interaction between the catalyst and the surface under operando conditions. Experiments are of- ten performed under model conditions and computational methods to study reaction steps are typically limited to a few hundred atoms. In this study, we combined three computational methods, density functional theory electronic structure computations, molecular dynamics for large scale simulations of the catalyst-solid interaction, and empirical valence bond for reaction modeling the catalyst at the interface of a large carbon support and a phosphate water buffer. These techniques allowed us to explore the combined effects of solvent, hydrophobic directionality, and electric field on the at- tachment and reactivity of a Ru(tda) pentamer at a graphene surface. Our simulations have perfect agreement with the experimental characterization under model conditions. However, we find that under operando conditions, where the catalyst is oxidized to the active RuV state, with a phosphate containing electrolyte and an applied electric field, the attachment is completely reversed compared to the model conditions with RuII and organic solvents. This reversed attachment leads to a water excluded region close to the active RuV=O center. The EVB reaction modeling showed that the reaction could still proceed to form an O-O bond via the oxide relay mechanism where a dangling carboxylate reacts with the oxo via nucleophilic attack. We find that the activation energy is identical in water solution and at the electrode surface, showing how this mechanism is key to highly active molecular water oxidation catalysts immobilized on surfaces. Since attachment to surfaces could have strong, and often negative, influence on the reactions this study provides a guideline in how to model reactions without compromising the complexity of the electrode environment.

Intermolecular radical coupling (also interaction of two metal centers I2M) is one of the main mechanisms for O-O bond formation in water oxidation catalysts. For Ru(bda)L-2 (H(2)bda = 2,2'-bipyridine-6,6'-dicarboxylate, L = pyridine or similar nitrogen containing heterocyclic ligands) catalysts a significant driving force in water solution is the hydrophobic effects driven by the solvent. The same catalyst has been successfully employed to generate -N2 from ammonia, also via I2M, but here the solvent was acetonitrile where hydrophobic effects are absent. We used a classical force field for the key intermediate [(RuN)-N-VI(bda)(py)(2)](+) to simulate the dimerization free energy by calculation of the potential mean force, in both water and acetonitrile to understand the differences and similarities. In both solvents the complex dimerizes with similar free energy profiles. In water the complexes are essentially free cations with limited ion paring, while in acetonitrile the ion-pairing is much more significant. This ion-pairing leads to significant screening of the charges, making dimerization possible despite lower solvent polarity that could lead to repulsion between the charged complexes. In water the lower ion pairing is compensated by the hydrophobic effect leading to favorable dimerization despite repulsion of the charges. A hypothetical doubly charged [(RuIN)-I-VI(bda)py(2)](2+) was also studied for deeper understanding of the charge effect. Despite the double charge the complexes only dimerized favorably in the lower dielectric solvent acetonitrile, while in water the separated state is more stable. In the doubly charged catalyst the effect of ion-pairing is even more pronounced in acetonitrile where it is fully paired similar to the 1+ complex, while in water the separation of the ions leads to greater repulsion between the two catalysts, which prevents dimerization. 

In order to combine the advantages of molecular catalysts with the stability of solid-state catalysts, hybrid systems with catalysts immobilized on carbon nanotubes are prominent candidates. Here we explore our recent mechanistic proposal for Ru(tda)(py)2, the oxide relay mechanism, in a hybrid system from an experimental study. It reacts with the same efficiency but with increased stability compared to the homogeneous molecular catalyst. We used the empirical valence bond method and molecular dynamics with enhanced sampling approaches to investigate the two key steps in the mechanism: the intramolecular O–O bond formation and the OH– nucleophilic attack. The results on these calculations show that the oxide relay mechanism remains unaltered in the new environment. We believe that the principles should apply to other oxide containing dangling groups and to other metal centers, opening new possibilities of future developments on hybrid molecular catalyst-based water splitting devices.