: Computational modeling has become an important tool for scientists to both predict the properties of materials and systems and to gain a better understanding of the underlying mechanisms. This chapter is a brief yet holistic introduction to computational modeling, focusing on density functional theoretical (DFT) methods. The different types of computational modeling methods, including molecular mechanics, semiempirical, and ab initio methods, as well as the different software available for computational calculations are discussed. A step-by-step guide is presented using Gaussian16 software to introduce the basics of computational modeling based on our work with biomimetic polymer beads. However, the guide presented here is not limited to this particular system; it can be applied to any computational modeling case. The computational modeling methods for the building of the structures are described, and the calculation parameters, such as basis sets and exchange-correlation functionals, are explained. The output data and results are presented and discussed. Two simulation features were the focus of this work: (1) the simulation of the Raman spectra and (2) the different solvation environments. While some researchers in the field believe that computational simulation should be performed before the lab experiments, in fact they should be done simultaneously. This is so that the output of the experimental data can be used as the input of the computational parameters, as a form of semiempirical modeling, in order to achieve more accurate results for predicting the behavior of future experiments and understanding the atomic forces and mechanisms.

Last. Nageh K. Allam(The: American University in Cairo)H-Index: 36

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CO adsorption on Cu(100), (110), and (111) surfaces has been extensively studied using Kohn–Sham density functional theory calculations. A holistic analysis of adsorption energies, charge transfer, and structural changes has been employed to highlight the variations in adsorption mechanisms upon changing the surface type and the adsorption site. Each surface, with its unique arrangement of atoms, resulted in a varying adsorbate behavior, although the same adsorption site is considered. This dire...

#2Nageh K. Allam(The: American University in Cairo)H-Index: 36

The gas sensing process involves complicated and precise adsorption mechanisms, and the selection of the right material is mainly based on “guess-and-check” procedures, which necessitates the search for a more systematic approach to discover optimum materials with required specifications. Herein, we report the use of ab initio first-principles methods to expedite the process of finding the material with the highest potential compared to in-lab trial and error. We focused on the NO2 adsorption me...

A detailed computational investigation of the 5,6-dihydroxyindole (DHI)-based porphyrin-type tetramer first described by Kaxiras as a theoretical structural model for eumelanin biopolymers is reported herein, with a view to predicting the technological potential of this unique bioinspired tetracatechol system. All possible tautomers/conformers, as well as alternative protonation states, were explored for the species at various degrees of oxidation and all structures were geometry optimized at th...

This article presents a perspective on Kohn-Sham density functional theory (KS-DFT) for electronic structure calculations in chemical physics. This theory is in widespread use for applications to both molecules and solids. We pay special attention to several aspects where there are both concerns and progress toward solutions. These include: 1. The treatment of open-shell and inherently multiconfigurational systems (the latter are often called multireference systems and are variously classified a...

The accurate description of open-shell molecules, in particular of transition metal complexes and clusters, is still an important challenge for quantum chemistry. Although density-functional theory (DFT) is widely applied in this area, the sometimes severe limitations of its currently available approximate realizations often preclude its application as a predictive theory. Here, we review the foundations of DFT applied to open-shell systems, both within the nonrelativistic and the relativistic f...

During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science—promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of ...

Three pathways for the reaction of bispidine-iron(II) complexes (where bispidine is a rigid tetradentate amine/pyridine ligand) with H2O2 have been studied by DFT calculations. For all oxidation states the high-spin and low-spin (intermediate-spin) forms have been optimized, and the computed data have been compared with the readily available experimental results. It is concluded that there is a direct conversion of the bispidine-iron(II)-hydrogen peroxide complex to the corresponding iron(IV)-di...

CASTEP Computer program / Density functional theory / Pseudopotentials / ab initio study / Plane-wave method / Computational crystallography Abstract. The CASTEP code for first principles electro- nic structure calculations will be described. A brief, non- technical overview will be given and some of the features and capabilities highlighted. Some features which are un- ique to CASTEP will be described and near-future devel- opment plans outlined.

1: An outline of what computational chemistry is all about. 1.1. What you can do with computational chemistry. 1.2. The tools of computational chemistry. 1.3. Putting it all together. 1.4. The philosophy of computational chemistry. 1.5. Summary of Chapter 1. References. 2: The concept of the potential energy surface. 2.1. Perspective. 2.2. Stationary points. 2.3. The Born-Oppenheimer approximation. 2.4. Geometry optimization. 2.5. Stationary points and normal-mode vibrations. Zero point energy. ...

Array-based biosensors have shown as effective and powerful tools to distinguish intricate mixtures with infinitesimal differences among analytes such as nucleic acids, proteins, microorganisms, and other biomolecules. In array-based bacterial sensing, the recognition of bacteria is the initial step that can crucially influence the analytical performance of a biosensor array. Bacteria recognition as well as the signal readout and mathematical analysis are indispensable to ensure the discriminati...