From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases

The amyloid β-protein is an intrinsically disordered protein that has the potential to assemble into myriad structures, including oligomers and fibrils. These structures are neurotoxic and are thought to initiate a cascade of events leading to Alzheimer's disease. Understanding this pathogenetic process and elucidating targets for drug therapy depends on elucidation of the structural dynamics of Aβ assembly. In this chapter, we describe work packages required to determine the three-dimensional structures of Aβ and of smaller bioactive fragments thereof, which may be important in AD pathogenesis. These packages include density functional theory, Car-Parrinello molecular dynamics simulations, temperature-dependent replica exchange molecular dynamics simulations, disorder predictors based on bioinformatics, and neural network deep learning.

Challenges and limitations in the studies of glycoproteins: A computational chemist's perspective

Experimenters face challenges and limitations while analyzing glycoproteins due to their high flexibility, stereochemistry, anisotropic effects, and hydration phenomena. Computational studies complement experiments and have been used in characterization of the structural properties of glycoproteins. However, recent investigations revealed that computational studies face significant challenges as well. Here, we introduce and discuss some of these challenges and weaknesses in the investigations of glycoproteins. We also present requirements of future developments in computational biochemistry and computational biology areas that could be necessary for providing more accurate structural property analyses of glycoproteins using computational tools. Further theoretical strategies that need to be and can be developed are discussed herein.

Observation of Induced Luminescence and Thermochromism in Achiral Hydrogen Bonded Liquid Crystal Complexes

A novel hydrogen bonded liquid crystal (HBLC) complexes are obtained from the non-mesogenic (benzylmalonic acid) and mesogenic (p-n-alkyloxybenzoic acid, where n = 6, 7 and 8) compound via intermolecular hydrogen bonds (H-bond). H-bonds are experimentally confirmed by the Fourier transform infrared spectroscopic (FT-IR) studies and the same is validated using density functional theory (DFT). Induced thermochromism is observed by the polarizing optical microscope (POM) and its possible applications are reported. Phase transition temperature and their analogous enthalpy values, stability factor and span width are determined by the differential scanning calorimetry (DSC) studies. Band gap energy is calculated using UV-visible and photoluminescence spectrum. Hyper conjugative stabilization energy and atomic charge distribution is studied by the natural bond orbital (NBO) studies. Mulliken analysis clearly reveals the intermolecular interaction and steric effect of the HBLC complexes. An interesting phenomenon is that the observation of luminescence and thermochromism in the highly fluidity nematic phase. This peculiar behavior is attributed due to the intermolecular H-bonding interaction between the BMA and nOBA compounds and the effect of rotatory motion of the molecules in nematic phase. Luminescence increases when the spacer moiety decreases in the present complexes is also reported. In nematic phase, the molecules are in different degrees of the excited state which is correlated with the hyper conjugative energy through NBO studies.