Academic literature on the topic 'Open Shell Molecular Systems'

This PhD thesis reports original research results concerning the development of theoretical models and computational protocols for the quantification and analysis of two of the most important quantum observables of open-shell systems: the electron spin density and the phosphorescence energy gap. In the first part, a comprehensive theory of the electron spin density topology is proposed for the first time [1]. Several new notions (spin density critical points, molecular spin graphs, spin density basins, spin maxima and spin minima joining paths etc.) and descriptors (local and integral spin polarization indeces, basin average spin density etc.) are introduced. This analysis reveals that the spin density topology, based on precise mathematical notions, can unveil precious information on the physical structure of spin-polarized systems. In particular, it enables to describe and quantify spin polarization and delocalization mechanisms and, at the same time, to evaluate the dependence of spin density distributions on the adopted level of theory. In the second part instead, the performance of the domain-based local pair natural orbital (DLPNO) variant of the “gold standard” CCSD(T) method for the prediction of phosphorescence energies of aromatic chromophores is investigated for the first time [2]. An extensive analysis of both accuracy and computational cost of the main parameters of the method (basis set, triples correction approximation, dimension of PNOs space) is conducted. Two procedures, the Gold DLPNO-CCSD(T) aimed at maximizing the accuracy and the Silver DLPNO-CCSD(T) aimed at minimizing the computational cost, which result in an excellent agreement with experimental data, are proposed. 1. G. Bruno, G. Macetti, L. Lo Presti and C. Gatti, “Spin Density Topology,” Molecules, 25, 3537, 2020. 2. G. Bruno, B. de Souza, F. Neese, and G. Bistoni, “Can domain-based local pair natural orbitals approaches accurately predict phosphorescence energies?,” Phys. Chem. Chem. Phys., 24, 14228–14241, 2022.

This thesis focuses on two different, but equally challenging, areas of computational chemistry: transition metal organic molecule interactions and parameterisation of organic conjugated polymers for molecular dynamics simulations. The metal-binding properties are important for understanding of biomolecular action of type 2 diabetes drug and development of novel protocols for redox calculations of copper systems. In this area the challenge is mainly related to the complex electronic structure of the open-shell transition metals. The main challenges for the parameterisation of conjugated polymers are due to the size of the studied systems, their conjugated nature and inclusion of environment. Metal-binding properties as well as electronic structures of copper complexes of type 2 diabetes drug metformin (Metf) and other similar, but often inactive, compounds were examined using DFT method. It was found that for neutral compounds it is not possible to explain the differences in their biological effects solely by examining the copper-binding properties. Further, the proposed mechanism potentially explaining the difference in the biomolecular mode of action involves a possible deprotonation of biguanide and Metf compounds under higher mitochondrial pH which would lead to formation of more stable copper complexes and potentially affecting the mitochondrial copper homeostasis. In addition, redox properties of copper-biguanide complexes could interfere with the sensitive redox chemistry or interact with important metalloproteins in the mitochondria. Understanding the copper-binding properties is also important for a systematic development and testing of computational protocols for calculations of reduction potentials of copper complexes. Copper macrocyclic complexes previously used as model systems for redox-active metalloenzymes and for which experimentally determined redox potentials are available were used as model systems. First adequacy of using single reference methods such as DFT was examined for these systems and then various DFT functionals and basis sets were tested in order to develop accurate redox potential protocol. It was shown that good relative cor-relations were obtained for several functionals while the best absolute agreement was obtained with either the M06/cc-pVTZ functional with the SMD or either M06L or TPSSTPSS functional with cc-pVTZ basis set and the PCM solvation model. Organic conjugated polymers have a great potential due to their application in organic optoelectronics. Various wavefunction and DFT methods are utilized in order to systematically develop parameterisation scheme that can be used to derive selected force-field parameters such as torsional potentials between monomer units that are critical for these systems and partial charges. Moreover, critical points of such a parameterisation are addressed in order to obtain accurate MD simulations that could provide valuable insight into material morphology and conformation that affect their optical properties and conductivity. It was shown that a two step approach of geometry optimisation with CAM-B3LYP/631G* and single point (SP) energy scan with CAM-B3LYP/cc-pVTZ is able to yield accurate dihedral potentials in agreement with the potentials calculated using higher level methods such as MP2 and CBS limit CCSD(T). Further, investigating partial charge distribution for increasing backbone length of fluorene and thiophene it has been found that it is possible to obtain a three residue model of converged charge distributions using the RESP scheme. The three partial charge residues can be then used to build and simulate much longer polymers without the need to re-parametrize charge distributions. In the case of side-chains, it was found that it is not possible to obtain converged charge sets for sidechain lengths of up to 10 carbons due to the strong asymmetry between the side-chain ends. Initial validation of derived force-field parameters performed by simulations of 32mers of fluorene with octyl side-chains (PF8) and thiophene with hexyl side-chains (P3HT) in chloroform and calculation of persistence lengths and end-to-end lengths showed close correspondence to experimentally obtained values.

In this thesis, the implementation of the incremental scheme for open-shell systems with unrestricted Hartree-Fock reference wave functions is described. The implemented scheme is tested within robustness and performance with respect to the accuracy in the energy and the computation times. New approaches are discussed to implement a fully automated incremental scheme in combination with the domain-specific basis set approximation. The alpha Domain Partitioning and Template Equalization are presented to handle unrestricted wave functions for the local correlation treatment. Both orbital schemes are analyzed with a test set of structures and reactions. As a further goal, the DSBSenv orbital basis sets and auxiliary basis sets are optimized to be used as environmental basis in the domain-specific basis set approach. The performance with respect to the accuracy and computation times is analyzed with a test set of structures and reactions. In another project, a scheme for the optimization of auxiliary basis sets for uranium is presented. This scheme was used to optimize the MP2Fit auxiliary basis sets for uranium. These auxiliary basis enable density fitting in quantum chemical methods and the application of the incremental scheme for systems containing uranium. Another project was the systematical analysis of the binding energies of four water dodecamers. The incremental scheme in combination with the CCSD(T) and CCSD(T)(F12*) method were used to calculate benchmark energies for these large clusters.

The question posed in this work is how one would model and predict the rotational spectrum of open-shell open-shell van der Waals complexes. There are two secondary questions that arise: the nature of radical-radical interactions in such systems and the modelling of the large amplitude motion of the constituent molecules. Four different systems were studied in this work, each providing part of the answer to the main question. Starting with the large amplitude motion, there are two theoretical approaches that may be adopted: to either model the whole complex as a semi-rigid molecule, or to perform quantum dynamical calculations. We recorded and analysed the rotational spectrum (using Fourier transform microwave spectroscopy) of the molecule of tertiary butyl acetate (TBAc) which exhibits a high degree of internal rotation; and of the weakly-bound complex between a neon atom and a nitrogen dioxide molecule (Ne-NO2). We used the semi-rigid approach for TBAc and the quantum dynamical approach for Ne-NO2. We also explored the compatibility of these two approaches. Moreover, we were able to predict and analyse the fine and hyperfine structure of the Ne-NO2 spectrum using spherical tensor operator algebra and the results of our dynamics calculations. To explore the nature of the interactions in an radical-radical van der Waals complex we calculated the PESs of the possible states that the complex may be formed in, when an oxygen and a nitrogen monoxide molecule meet on a plane using a number of high level ab initio methods. Finally, our conclusions were tested and applied when we performed the angular quantum dynamics to predict the rotational spectrum of the complex between an oxygen and a nitrogen dioxide molecule, and account for the effect of nuclear spin statistics in that system.

The microwave spectrum of the open-shell van der Waals complex NO-HF has been recorded in the region 6-20GHz using a pulsed nozzle Fourier transform microwave spectrometer. This is the first observation of the microwave spectrum of a open-shell van der Waals complex between two molecules. The spectrum exhibits a rich hyperfine structure with the observation of intermolecular hyperfine interactions in an isolated system providing a sensitive probe of electron transfer in the complex. The spectrum consists of four fine structure transitions 5/2(e)-3/2(e), 3/2(e)-1/2(e), 5/2(f)-3/2(f), 3/2(f)-1/2(f) which have been fitted to a semi-rigid Hamiltonian developed to include the effects of the orbital and spin angular momenta of the unpaired electron on NO. A new treatment to account for the intermolecular hyperfine interaction was developed. The structure of the complex has been determined and is significantly bent with an angle of between 37 degrees and 49 degrees between the NO internuclear axis and the a-axis of the complex. The Renner-Teller parameter, epsilon 2, is very large and negative having the value of -10 449.32(4)GHz indicating that configuration with the unpaired electron in the plane of the complex is more stable. The analysis of the hyperfine interactions of the hydrogen and fluorine nuclei uses two constants for each nucleus, one for the spatial relationship between the magnetic moments of the unpaired electron and the nuclear magnetic moment and a Fermi-contact term. The Fermi-contact term for hydrogen is the first strong evidence of intermolecular charge transfer in an isolated van der Waals molecule.

This thesis investigates the applicability of a range of computational techniques across a range of open shell chemical systems from the geometrically simple but electronically complex to the geometrically complex but electronically simple. Initially an investigation into a range of geometrically simple but electronically complicated systems is presented. The Monte Carlo Configuration Interaction method (MCCI) is applied to challenging transition metals dimers such as ScNi in order to establish the ground state potential energy surface, from equilibrium bond lengths through to dissociation using highly compact wavefunctions compared to Full Configuration Interaction (FCI). It shall be demonstrated that the ScNi dimer represents the current limit of this technique. Software development of MCCI is then undertaken in order to perform calculations of spin-orbit coupling interactions. Results on B, C, O, F, Si, S, F, Cl, OH, NO, CN and C2 species are shown to be comparable with other techniques using the one-electron Breit-Pauli Hamiltonian. The application of quantum chemistry to geometrically complex but electronically simple systems is then considered. Density Functional Theory (DFT) is used to investigate the mechanism and energetic barriers leading to ring inversion of the biscalix[4]arene supra-molecule. A minimum barrier height of 19.31 kcalmol−1 to inversion is elucidated along with details of the complete mechanistic pathway to inversion. The focus then moves to polymetallic clusters of calix[4]arene. A DFT study is made of the preferential binding of calix[4]arene towards first row transition metals of various oxidation and spin states. Results indicate that Cu3+ (singlet) species will preferentially bind to the lower rim over other metals in the study. The final DFT-related work presented is a study of the preferential binding at the upper rim of polymetallic calix[4]arene clusters towards a range of important small gas molecules. It was found that gases such as NH3 and SO2 bind most strongly to the upper rim with the inclusion of a transition metal at the lower rim providing strengthening of the host-guest binding.