Yes / A new type of model, FFLUX, to describe the interaction between atoms has been developed as an alternative to traditional force fields. FFLUX models are constructed from applying the kriging machine learning method to the topological energy partitioning method, Interacting Quantum Atoms (IQA). The effect of varying parameters in the construction of the FFLUX models is analyzed, with the most dominant effects found to be the structure of the molecule and the number of conformations used to build the model. Using these models the optimization of a variety of small organic molecules is performed, with sub kJ mol-1 accuracy in the energy of the optimized molecules. The FFLUX models are also evaluated in terms of their performance in describing the potential energy surfaces (PESs) associated with specific degrees of freedoms within molecules. While the accurate description of PESs presents greater challenges than individual minima, FFLUX models are able to achieve errors of <2.5 kJ mol-1 across the full C-C-C-C dihedral PES of n-butane, indicating the future possibilities of the technique.

Understanding pattern formation in nature is an important topic in applied mathematics. For more than three decades, the Ohta–Kawasaki energy has attracted considerable attention from applied mathematicians. This energy functional, which combines surface energy and electrostatic potential energy, captures the intricate patterns observed in various physical and biological systems. Despite its apparent simplicity, the Ohta–Kawasaki energy serves as a versatile framework for describing a wide range of pattern formation phenomena induced by competing interactions. In this dissertation, we aim to gain a better understanding of the important properties of the Ohta–Kawasaki energy, specifically its stationary points, global minimizers, and energy landscape. We explore these properties in the context of broad applications such as nuclear physics, block copolymers, and biological membranes. In order to investigate the complicated geometries in these applications, we utilize asymptotic analysis and numerical simulations. Firstly, we explore the stationary points of the Ohta–Kawasaki energy. Specifically, we study how a three-dimensional ball loses stability as the nonlocal coefficient increases in the binary case. Our approach combines numerical simulations and bifurcation analysis. We calculate the minimum energy path for the transition from a single ball to two separate balls, as well as the bifurcation branch orginating from the ball. In the context of nuclear physics, this bifurcation branch is known as the Bohr–Wheeler branch. Our simulations suggest that, unlike the previous understanding, all the stationary points on this bifurcation branch are unstable. Similar results are observed in two dimensions. This finding illustrates the unexpected mechanism governing the stability loss of balls and disks. Secondly, we explore the global minimizers of the Ohta–Kawasaki energy. We numerically compute the one-dimensional energy minimizers of relatively short patterns in the non-degenerate ternary case. Inspired by our numerical results, we propose an array of periodic candidates. We then show that our candidates can have lower energy than the previously conjectured global minimizer which is of the cyclic pattern. Our results are consistent with simulations based on other theories and physical experiments of triblock copolymers, in which noncyclic lamellar patterns have been found. This finding indicates that even in one dimension, the global minimizers of the Ohta–Kawasaki energy can exhibit unexpected richness. Lastly, we explore the energy landscape of the Ohta–Kawasaki energy. We propose a phase-field reformulation which is shown to Gamma-converge to the original sharp interface model in the degenerate ternary case. Our phase-field simulations and asymptotic results suggest that the limit of the recovery sequence exhibits behaviors similar to the self-assembly of amphiphiles, including the formation of lipid bilayer membranes. This finding reveals the intricate landscape of the Ohta–Kawasaki energy. In summary, this dissertation sheds light on three important aspects of the Ohta–Kawasaki energy: its stationary points, global minimizers, and energy landscape. Our findings are timely contributions to the ongoing research on pattern formation driven by energetic competition.

No / Nonadiabatic Monte Carlo transition-state theory is used to explore competing C¿Cl and C¿Br bond fission processes in a simple model of 1[n,pi*(CO)] photoexcited bromoacetyl chloride. Morse potentials are used to represent bond stretching coordinates, and the positions and magnitudes of nonadiabatic coupling between excited state potentials are modeled using ab initio data. The main effect of nonadiabaticity is to favor C¿Cl fission over C¿Br, despite a larger barrier to C¿Cl dissociation. The absolute values of the rate constants are smaller than observed experimentally, but the calculated branching ratios are close to the experimental value. For C¿Cl fission, it is shown that the minimum energy crossing point is not sufficient to describe the rate constant, suggesting that care must be taken when using alternative models which make this assumption.

Noncovalent interactions in complex chemical systems are examined by considering model systems which capture the essential physics of the interactions and applying correlated electronic structure techniques to these systems. Noncovalent interactions are critical to understanding a host of energetic and structural properties in complex chemical systems, from base pair stacking in DNA to protein folding in organic solids. Complex chemical and biophysical systems, such as enzymes and proteins, are too large to be studied using computational techniques rigorous enough to capture the subtleties of noncovalent interactions. Thus, the larger chemical system must be truncated to a smaller model system to which rigorous methods can be applied in order to capture the essential physics of the interaction. Computational methodologies which can account for high levels of electron correlation, such as second-order perturbation theory and coupled-cluster theory, must be used. These computational techniques will be used to study several types (pi stacking, S/pi, and C-H/pi) of noncovalent interactions in two chemical contexts: biophysical systems and organic solids.

<p dir="ltr">Hypergolic propellants contain a fuel and an oxidizer that ignite on contact without the need for an external ignition source. Hydrazines are often used as the fuel, despite health and environmental safely concerns. Monomethylhydrazine (MMH) is a commonly used fuel in conjunction with dinitrogen tetroxide as the oxidizer for in-space maneuvering, although the mechanisms for the reactions of these two compounds are not fully understood. Based on the spontaneous generation of product ions in liquid phase experiments, quantum chemical calculations using the SMD model of implicit solvation were used to probe proposed reaction mechanisms. The reactions of hydrazine and MMH with the nitrosonium cation and the nitronium cation, which included the formation of the corresponding fuel radical cation, were explored. The reactions of hydrazines with the nitronium cation in model solvents were found to be highly exergonic, by as much as 70 kcal mol^-1. Further reactions of the MMH radical cation were also explored, including the formation of tetrazanes. Developing a complete mechanism to explain the formation of the most abundant product ions can further the understanding of hypergolicity and aid in the development of safer fuels.</p><p dir="ltr">The ASTM D2425 method was originally developed in 1965 and updated in 2019 for analyzing aviation fuels. However, a method using two dimensional gas chromatography coupled to a flame ionization detector (GCxGC/FID) was previously developed at Purdue University for the analysis of aviation fuels, including those derived from traditional sources and those derived from sustainable feedstocks. The established ASTM D2425 method was compared to the GCxGC/FID method for the analysis of Jet A-1, a sustainable aviation fuel, and a model compound mixture. The peak areas of eleven compound classes were compared across the three different samples by using a Pearson coefficient to determine skewness, an Anderson-Darling test for normality, Levene’s test and F-test for equal variances (depending on the normality of the data), and a 2-sample t-test. The results of these statistical analyses were somewhat vague and further studies should be done to fully compare the ASTM D2425 method with the GCxGC/FID method.</p>

Disertacijoje nagrinėjamas galimas aplinkos poveikis organinių molekulių elektroninių būsenų savybėms. Tam tikslui yra naudojami kompiuterizuotieji kvantinės mechanikos metodai, kuriais remiantis nagrinėjamos įvairių molekulių savybės. Ištirtos 2-(N-metil-α-iminoethyl)-fenol ir N-triphenylmethylsalicylidene imine molekelulių, esančių poliniame tirpiklyje, struktūros pagrindinėje ir sužadintose elektroninėse būsenose. Pirmą kartą parodyta, kad, norint gauti teisingą kokybinį ir artimą kiekybiniam vidujmolekulinės protono pernašos potencinės energijos paviršių, būtina atsižvelgti į polinių tirpiklio molekulių kuriamą vandenilinių ryšių tinklą bei į nulinių svyravimų energijas. Pastarieji ir nulemia protono pernašos vyksmo kryptį bei efektyvumą. Parodyta, kad anilų klasės molekulių konformerų susiformavimas priklauso nuo tirpiklio poliškumo, o jų susidarymas savo ruožtu konkuruoja su klasterių iš tirpiklio molekulių susiformavimo galimybėmis. Pirmą kartą parodyta, kad dipolinio momento vertė bakteriorodopsine yra nulemta membranos paviršiuose esančių radikalų. Pademonstruota, kad stilbazolio molekulė deformuojasi ir sudaro naujus konformerus (pademonstruota dviejų formų atsiradimo galimybė) tik esant molekulėms tirpalo apsuptyje. Šis rezultatas paaiškino eksperimente stebimus skirtuminių spektrinių pokyčių evoliucijos prigimtį. Apskaičiuotos ir išanalizuotos karotinoidų - luteino, violaksantino ir zeaksantino molekulių - žemiausios sužadintos elektroninės būsenos. Parodyta... [toliau žr. visą tekstą] / To explore changes caused by the environment on the internal characteristics of an organic molecule is the objective of the thesis. For this purpose we investigate a variety of organic molecules. Using various methods of quantum mechanics calculations possible influence of a polar solvent on the ground and excited states of 2-(N-metil-α-iminoethyl)-fenol and N-triphenylmethylsalicylidene imine is considered. It is shown for the first time that in order to obtain the correct qualitative and quantitative interpretation of possible pathways of the intermolecular proton transfer the hydrogen network of the polar solvent molecules together with the zero point energy have to be taken into consideration. It is also shown that conformational variability of anil-type molecules in polar solvents is competing with clusters formation of solvent molecules. It is shown for the first time that the dipole moment of bacteriorhodopsin is mainly defined by cytoplasmic and extracellular coils on the surfaces of the membrane. It is also demonstrated that the stilbazole molecule experiences the deformation resulting in formation of new conformers (at least two forms are present) in the solvent surrounding. The experimental data of the transient spectroscopy were explained in the basis of these model calculations. The lowest excited states of carotinoids, such as lutein, zeaxanthin and violoxantin are calculated and analyzed. Sensitivity of the excited electronic state on the polar environment is... [to full text]

Elektroninio sužadinimo evoliucija šviesai jautriose molekulėse yra reiškinys, kuriuo remiantis įmanoma nagrinėti daugelį natūralių ir dirbtinių procesų: augalų ir bakterijų fotosintezę, regos mechanizmą, optomechaninių bei optoelektroninių prietaisų (pavyzdžiui, organinių šviestukų) veikimą. Teoriškai šis reiškinys modeliuojamas sprendžiant laikinę Šriodingerio lygtį. Deja, toks sprendimas realiems, praktiškai panaudojamiems junginiams šiandien yra per sudėtingas uždavinys, todėl jį tenka keisti supaprastinant nagrinėjamų junginių modelius arba sprendimo metodiką. Šioje disertacijoje aprašomų tyrimų tikslas buvo elektroninės struktūros skaičiavimų metodais (t. y. sprendžiant paprastesnę nuostoviąją Šriodingerio lygtį) ištirti elektroninio sužadinimo sukeltus procesus fotoaktyviose molekulėse ir sudaryti sužadinimo relaksaciją apibūdinančius potencinės energijos paviršių modelius. Parodoma, jog ta pačia metodika atliekamų tyrimų rezultatai paaiškina įvairiuose junginiuose vykstančius reiškinius: bakteriorodopsino baltymo funkcinės grupės vykdomą protono pernašą poliniame tirpiklyje, indolo-benzoksazino junginio optomechaninį ciklą, našią fosforescenciją organiniame silicio polimere bei šviestukams naudojamo metaloorganinio komplekso su prijungtomis krūvininkų pernašos grupėmis ypatybes. / Evolution of the electronic excitation is a general process that can be used to explain many natural and artificial phenomena, such as photosynthesis in plants and bacteria, biological mechanism of vision, and operating principles of optomechanical and optoelectronic devices. This process is theoretically modeled by solving the time-dependent Schroedinger equation. However, such treatment is too computationally expensive to be used for practical molecular systems. Therefore, either models of the structure of the systems or the solving procedure itself must be simplified to get the desired results. The main goal of the research presented in this dissertation was to study processes caused by the electronic excitation in photoactive molecules using computational methods of electronic structure (i. e. solving the simpler time-independent Schroedinger equation) and to construct the potential energy surface models describing the energy relaxation in the investigated molecules. It is shown that the results of different investigations performed using the same procedure provide explanations of different phenomena in various compounds, such as: proton transfer in polar solvent, performed by a functional group of the bacteriorhodopsin protein; optomechanical cycle of the indolo-benzoxazine compound; efficient phosphorescence of the silicon-based organic polymer; and optical properties of organometallic emitter compound with additional charge-carrier groups.

Evolution of the electronic excitation is a general process that can be used to explain many natural and artificial phenomena, such as photosynthesis in plants and bacteria, biological mechanism of vision, and operating principles of optomechanical and optoelectronic devices. This process is theoretically modeled by solving the time-dependent Schroedinger equation. However, such treatment is too computationally expensive to be used for practical molecular systems. Therefore, either models of the structure of the systems or the solving procedure itself must be simplified to get the desired results. The main goal of the research presented in this dissertation was to study processes caused by the electronic excitation in photoactive molecules using computational methods of electronic structure (i. e. solving the simpler time-independent Schroedinger equation) and to construct the potential energy surface models describing the energy relaxation in the investigated molecules. It is shown that the results of different investigations performed using the same procedure provide explanations of different phenomena in various compounds, such as: proton transfer in polar solvent, performed by a functional group of the bacteriorhodopsin protein; optomechanical cycle of the indolo-benzoxazine compound; efficient phosphorescence of the silicon-based organic polymer; and optical properties of organometallic emitter compound with additional charge-carrier groups. / Elektroninio sužadinimo evoliucija šviesai jautriose molekulėse yra reiškinys, kuriuo remiantis įmanoma nagrinėti daugelį natūralių ir dirbtinių procesų: augalų ir bakterijų fotosintezę, regos mechanizmą, optomechaninių bei optoelektroninių prietaisų (pavyzdžiui, organinių šviestukų) veikimą. Teoriškai šis reiškinys modeliuojamas sprendžiant laikinę Šriodingerio lygtį. Deja, toks sprendimas realiems, praktiškai panaudojamiems junginiams šiandien yra per sudėtingas uždavinys, todėl jį tenka keisti supaprastinant nagrinėjamų junginių modelius arba sprendimo metodiką. Šioje disertacijoje aprašomų tyrimų tikslas buvo elektroninės struktūros skaičiavimų metodais (t. y. sprendžiant paprastesnę nuostoviąją Šriodingerio lygtį) ištirti elektroninio sužadinimo sukeltus procesus fotoaktyviose molekulėse ir sudaryti sužadinimo relaksaciją apibūdinančius potencinės energijos paviršių modelius. Parodoma, jog ta pačia metodika atliekamų tyrimų rezultatai paaiškina įvairiuose junginiuose vykstančius reiškinius: bakteriorodopsino baltymo funkcinės grupės vykdomą protono pernašą poliniame tirpiklyje, indolo-benzoksazino junginio optomechaninį ciklą, našią fosforescenciją organiniame silicio polimere bei šviestukams naudojamo metaloorganinio komplekso su prijungtomis krūvininkų pernašos grupėmis ypatybes.

Este projeto tem dois objetivos. Primeiramente estudou-se a aplicabilidade dos splines tricúbicos para a construção de superfícies de energia potencial globais. Um dos obstáculos que este método tem de superar e a escolha de um sistema de coordenadas apropriado, que minimize a influência de pontos não físicos. Para isto, propôs-se o uso do sistema de coordenadas de Pekeris, nunca usado para este fim. Este procedimento foi realizado para três sistemas químicos bem descritos na literatura, [Cl,H2], [F,H,D] e [H,O,Cl], cujas superfícies de energia potencial e propriedades das reações foram usadas como referência. Com base nestes modelos, aplicamos o método proposto variando-se a quantidade e a disposição dos nós das interpolações, a fim de verificar sua influência na qualidade das superfícies interpoladas. Os resultados mostram que as superfícies construídas por este método reproduzem muito bem os cálculos de dinâmica química, tanto por métodos quânticos quanto por métodos clássicos. Para isto, os nós da interpolação devem cobrir as regiões mais importantes da superfície de energia potencial e os valores mais baixos das coordenadas de Pekeris devem ser priorizados. O segundo objetivo consiste na aplicação deste procedimento na construção da superfície de energia potencial [H,S,F]. Com esta superfície, diversas características deste sistema foram analisadas, tais como geometrias dos pontos estacionários, energias relativas e frequências vibracionais. Os valores obtidos estão de acordo com os dados descritos na literatura. A superfície construída também foi usada para a realização de cálculos de dinâmica para a reação F+HS &#8594; S+FH. Observamos a existência de dois tipos de mecanismos, um com a formação de um intermediário de longa duração e outro com a abstração direta do átomo de hidrogênio. / This project has two goals. First, we studied the applicability of the tricubic splines to construct global potential energy surfaces. One of the diculties this approach has to overcome is the choice of an appropriate coordinate system that minimises the in uence of non-physical points. For such, we proposed the use of the Pekeris coordinate system, never employed for this purpose. This procedure was carried out for three well described systems, [Cl,H2], [F,H,D] and [H,O,Cl], whose potential energy surfaces and reaction properties were taken as references. Based on these models, we applied the proposed method varying the amount and arrangement of the interpolation knots, to verify their influence on the quality of the interpolated surfaces. The results showed that surfaces constructed by this approach reproduce very well the chemical dynamics calculations, both for the quantum as well as for the classical methods, provided that the interpolation knots cover the most important regions of the potential energy surfaces, and the lower values of the Pekeris coordinates are prioritised. The second goal was the application of this procedure to the construction of the [H,S,F] potential energy surface. With this surface, several characteristics of this system were analysed, such as the geometry of the stationary points, relative energies and vibrational frequencies. The values obtained are in agreement with the data described in the literature. The constructed surface was also used for quantum dynamics calculations on the reaction F + HS &#8594; S + FH. We observed two kinds of mechanisms, one of them with the formation of a long-living intermediate and the other with the direct abstraction of the hydrogen atom.

Proteins are involved in numerous functions in the human body, including chemical transport, molecular recognition, and catalysis. To perform their function most proteins must adopt a specific structure (often referred to as the folded structure). A microscopic description of folding is an important prerequisite for elucidating the underlying basis of protein misfolding and rational drug design. However, protein folding occurs on heterogeneous length and time scales, presenting a grand challenge to both experiments and simulations. In computer simulations, challenges are generally mitigated by adopting coarse-grained descriptions of the physical environment, employing enhanced sampling strategies, and improving computing code and hardware. While significant advances have been made in these areas, for numerous systems a large spatiotemporal gap between experiment and simulations still exists, due to the limited time and length scales achieved by simulation, and the inability of many experimental techniques to probe fast motions and short distances. In this thesis, kinetic transition networks (KTNs) are constructed for various protein folding systems, via approaches based on the potential energy landscape (PEL) framework. By applying geometry optimisation techniques, the PEL is discretised into stationary points (i.e.~low-energy minima and the transition states that connect them). Essentially, minima characterise the low-lying regions of the PEL (thermodynamics) and transition states encode the motion between these regions (dynamics). Principles from statistical mechanics and unimolecular rate theory may then be employed to derive free energy surfaces and folding rates, respectively, from the KTN. Furthermore, the PEL framework can take advantage of parallel and distributed computing, since stationary points from separate simulations can be easily integrated into one KTN. Moreover, the use of geometry optimisation facilitates greater conformational sampling than conventional techniques based on molecular dynamics. Accordingly, this framework presents an appealing means of probing complex processes, such as protein folding. In this dissertation, we demonstrate the application of state-of-the-art theory, combining PEL analysis and KTNs to three diverse protein systems. First, to improve the efficiency of protein folding simulations, the intrinsic rigidity of proteins is exploited by implementing a local rigid body (LRB) approach. The LRB approach effectively integrates out irrelevant degrees of freedom from the geometry optimisation procedure and further accelerates conformational sampling. The effects of this approach on the underlying PEL are analysed in a systematic fashion for a model protein (tryptophan zipper\,1). We demonstrate that conservative local rigidification can reproduce the thermodynamic and dynamic properties for the model protein. Next, the PEL framework is employed to model large-scale conformational changes in proteins, which have conventionally been difficult to probe in silico. Methods based on geometry optimisation have proved useful in overcoming the broken ergodicity issue, which is associated with proteins that switch morphology. The latest PEL-based approaches are utilised to investigate the most extreme case of fold-switching found in the literature:~the α-helical hairpin to β-barrel transition of the C-terminal domain of RfaH, a bacterial transcription factor. PEL techniques are employed to construct the free energy landscape (FEL) for the refolding process and to discover mechanistic details of the transition at an atomistic level. The final part of the thesis focuses on modelling intrinsically disordered proteins (IDPs). Due to their inherent structural plasticity, IDPs are generally difficult to characterise, both experimentally and via simulations. An approach for studying IDPs within the PEL framework is implemented and tested with various contemporary potential energy functions. The cytoplasmic tail of the human cluster of differentiation 4 (CD4), implicated in HIV-1 infection, is characterised. Metastable states identified on the FEL help to unify, and are consistent with, several earlier predictions.