Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method

In large biomolecular systems such as protein complexes, there are huge numbers of combinations of inter-residue interactions whose comprehensive analyses are often beyond the intuitive processing by researchers. Here we propose a computational method to allow for a systematic analysis of these interactions based on the fragment molecular orbital calculations, in which the inter-fragment interaction energies are comprehensively processed by the singular value decomposition. For a trimer complex of SARS-CoV-2 spike protein, three-body interactions among residues belonging to three chains are analyzed to elicit a small number of essential interaction modes or networks crucial for the structural stability of complex.

Studies towards the Synthesis of a Heterobimetallic Zirconium Germanium Complex from Imidozirconocenes, Germanimines and Germylenes

<p>Early-late transition metal heterobimetallic complexes with direct metal to metal interactions are desirable synthetic targets due to the complementary reactivity of the two different metals present in these compounds. The electron-rich late transition metal (often Rh, Ir, Fe, or Mo), and electron-poor early transition metal create an ideal environment for heterolytic bond cleavage in what is often termed ‘cooperative reactivity’. This project aimed to synthesise a zirconium-germanium heterobimetallic complex based on a known heterobimetallic ligand scaffold; 1. The synthesis of the desired heterobimetallic 1 was attempted using two different synthetic approaches. The first involved the investigating the reactivity between an unsaturated zirconium nitrogen bond (an imidozirconocene) and a germanium(II) source with a lone pair of electrons (known as a germylene). The second approach investigated the reactivity between an unsaturated germanium nitrogen bond (a germanimine) and a zirconium(II) source. In order to have the highest chance of success, a wide range of germanium and zirconium complexes were synthesised. The novel germylenes include [Ge(NAPHTMS)] (NAPHTMS = [1,8-((CH3)3Si)N)2C10H6]) and [Ge(BIANMes)] (BIANMes = [((2,4,6-Me(C6H2)N)2)C12H6)]). These proved to be unreactive towards the imidozirconium species [Cp2Zr(NAr*)(THF)] and [Cp2Zr(NDipp)(THF)] (Ar* = (2,6-(C6H5)2CH)-4-(tBu)C6H2), Dipp = (2,6-((CH3)2CH)C6H3)) as well as other amidozirconocenes. However, within these studies, the mixed coordination germanium species [[Ge(NAPHTMS)Ge(Bu)(NAPHTMS)]-[Li(THF4)]+] and [[Ge(NAPHTMS)Ge(Me)(NAPHTMS)]-[Li(THF4)]+]were synthesised. Density functional theory (DFT) molecular orbital calculations were used to help explain the observed reactivity. With regards to the second approach, routes to new germanimine complexes such as [(HMDS)2Ge(NMes)] ((HMDS) = ((CH3)3Si)2N), Mes = (2,4,6-CH3(C6H3))), were explored, and several methods for generating “Cp2Zr” were examined. Although these conditions proved unsuccessful for generating 1, the reaction between dialkyl zirconocene with azides to form novel zirconocene triazenido complexes was discovered and the sterics affecting the synthesis of new germanimine complexes was investigated.</p>

Studies towards the Synthesis of a Heterobimetallic Zirconium Germanium Complex from Imidozirconocenes, Germanimines and Germylenes

<p>Early-late transition metal heterobimetallic complexes with direct metal to metal interactions are desirable synthetic targets due to the complementary reactivity of the two different metals present in these compounds. The electron-rich late transition metal (often Rh, Ir, Fe, or Mo), and electron-poor early transition metal create an ideal environment for heterolytic bond cleavage in what is often termed ‘cooperative reactivity’. This project aimed to synthesise a zirconium-germanium heterobimetallic complex based on a known heterobimetallic ligand scaffold; 1. The synthesis of the desired heterobimetallic 1 was attempted using two different synthetic approaches. The first involved the investigating the reactivity between an unsaturated zirconium nitrogen bond (an imidozirconocene) and a germanium(II) source with a lone pair of electrons (known as a germylene). The second approach investigated the reactivity between an unsaturated germanium nitrogen bond (a germanimine) and a zirconium(II) source. In order to have the highest chance of success, a wide range of germanium and zirconium complexes were synthesised. The novel germylenes include [Ge(NAPHTMS)] (NAPHTMS = [1,8-((CH3)3Si)N)2C10H6]) and [Ge(BIANMes)] (BIANMes = [((2,4,6-Me(C6H2)N)2)C12H6)]). These proved to be unreactive towards the imidozirconium species [Cp2Zr(NAr*)(THF)] and [Cp2Zr(NDipp)(THF)] (Ar* = (2,6-(C6H5)2CH)-4-(tBu)C6H2), Dipp = (2,6-((CH3)2CH)C6H3)) as well as other amidozirconocenes. However, within these studies, the mixed coordination germanium species [[Ge(NAPHTMS)Ge(Bu)(NAPHTMS)]-[Li(THF4)]+] and [[Ge(NAPHTMS)Ge(Me)(NAPHTMS)]-[Li(THF4)]+]were synthesised. Density functional theory (DFT) molecular orbital calculations were used to help explain the observed reactivity. With regards to the second approach, routes to new germanimine complexes such as [(HMDS)2Ge(NMes)] ((HMDS) = ((CH3)3Si)2N), Mes = (2,4,6-CH3(C6H3))), were explored, and several methods for generating “Cp2Zr” were examined. Although these conditions proved unsuccessful for generating 1, the reaction between dialkyl zirconocene with azides to form novel zirconocene triazenido complexes was discovered and the sterics affecting the synthesis of new germanimine complexes was investigated.</p>

Molecular Interactions between Methylene Blue and Sodium Alginate Studied by Molecular Orbital Calculations

A methylene blue (MB) indicator embedded in sodium alginate (SA) film was previously examined for detecting active oxygen species. In a previous study, spectrometry was used to identify and characterize the MB/SA complex. However, the decolorization mechanism was not fully assessed. In this study, our aim is to conduct computational calculations at the B3LYP/6-31G(d) level to clarify the exact types and positions of the interaction that cause the decolorization in MB. The results demonstrate that MB/SA interacts with carboxylates (-COO(superscript)-(superscript)) of SA and the N, C, and S atoms of MB, confirming previous experimental observations.

Hyperfine Interactions in Organic Fragments

<p>This thesis, the first thesis in theoretical chemistry submitted for the degree of Master of Science at Victoria University of Wellington, has been designed to illustrate two alternative approaches to theoretical studies. The first five chapters illustrate the modern use of operator methods; the last two are concerned mainly with molecular orbital calculations for large organic molecules, using a giant high speed electronic computer. I am deeply indebted to Mr Keith Morris, of the Applied Mathematics Division, Department of Scientific and Industrial Research, for his generous and highly competent help in writing computing programs, and operating computers, at all odd hours of the day and night, for the calculations in this thesis. I would also like to thank Dr R.M. Golding, for useful discussions, and the Director, Applied Mathematics Division, Department of Scientific and Industrial Research, for making computing facilities available.</p>

Hyperfine Interactions in Organic Fragments

<p>This thesis, the first thesis in theoretical chemistry submitted for the degree of Master of Science at Victoria University of Wellington, has been designed to illustrate two alternative approaches to theoretical studies. The first five chapters illustrate the modern use of operator methods; the last two are concerned mainly with molecular orbital calculations for large organic molecules, using a giant high speed electronic computer. I am deeply indebted to Mr Keith Morris, of the Applied Mathematics Division, Department of Scientific and Industrial Research, for his generous and highly competent help in writing computing programs, and operating computers, at all odd hours of the day and night, for the calculations in this thesis. I would also like to thank Dr R.M. Golding, for useful discussions, and the Director, Applied Mathematics Division, Department of Scientific and Industrial Research, for making computing facilities available.</p>

Synthesis, Structural and Physicochemical Characterization of a Titanium(IV) Compound with the Hydroxamate Ligand N,2-Dihydroxybenzamide

The siderophore organic ligand N,2-dihydroxybenzamide (H2dihybe) incorporates the hydroxamate group, in addition to the phenoxy group in the ortho-position and reveals a very rich coordination chemistry with potential applications in medicine, materials, and physical sciences. The reaction of H2dihybe with TiCl4 in methyl alcohol and KOH yielded the tetranuclear titanium oxo-cluster (TOC) [TiIV4(μ-O)2(HOCH3)4(μ-Hdihybe)4(Hdihybe)4]Cl4∙10H2O∙12CH3OH (1). The titanium compound was characterized by single-crystal X-ray structure analysis, ESI-MS, 13C, and 1H NMR spectroscopy, solid-state and solution UV–Vis, IR vibrational, and luminescence spectroscopies and molecular orbital calculations. The inorganic core Ti4(μ-O)2 of 1 constitutes a rare structural motif for discrete TiIV4 oxo-clusters. High-resolution ESI-MS studies of 1 in methyl alcohol revealed the presence of isotopic distribution patterns which can be attributed to the tetranuclear clusters containing the inorganic core {Ti4(μ-O)2}. Solid-state IR spectroscopy of 1 showed the presence of an intense band at ~800 cm−1 which is absent in the spectrum of the H2dihybe and was attributed to the high-energy ν(Ti2–μ-O) stretching mode. The ν(C=O) in 1 is red-shifted by ~10 cm−1, while the ν(N-O) is blue-shifted by ~20 cm−1 in comparison to H2dihybe. Density Functional Theory (DFT) calculations reveal that in the experimental and theoretically predicted IR absorbance spectra of the ligand and Ti-complex, the main bands observed in the experimental spectra are also present in the calculated spectra supporting the proposed structural model. 1H and 13C NMR solution (CD3OD) studies of 1 reveal that it retains its integrity in CD3OD. The observed NMR changes upon addition of base to a CD3OD solution of 1, are due to an acid–base equilibrium and not a change in the TiIV coordination environment while the decrease in the complex’s lability is due to the improved electron-donating properties which arise from the ligand deprotonation. Luminescence spectroscopic studies of 1 in solution reveal a dual narrow luminescence at different excitation wavelengths. The TOC 1 exhibits a band-gap of 1.98 eV which renders it a promising candidate for photocatalytic investigations.