Research Topics in Bioactivity, Environment and Energy: Experimental and Theoretical Tools

Preface
Contents
Energy, Materials and Environment
Theory and Computation in Photo-Electro-Chemical Catalysis: Highlights, Challenges, and Prospects
1 Introduction
2 Photo-Electro-Chemical Catalysis and the Role of Computation
2.1 Fundamental Science Concepts for Photo-Electro-Chemical Conversions
2.2 Fundamental Challenges in Photo-Electro-Chemical Conversions
2.3 Computation and Simulation for Photo-Electro-Chemical Catalysis
3 Computation and Modeling of Carrier Structure, Dynamics, and Utilization
3.1 Overview of Our Multiscale Modeling Framework
3.2 Mesoscale Modeling in Photo-Electro-Catalysis
3.3 Highlights
4 Challenges in Computation and Modeling in Photo-Electro-Catalysis
4.1 Challenge to DFT: Accurate and Reliable Functionals for Polarons and Excitons
4.2 Exciton Structure and Dynamics: Cross-Validation of Theory and Experiment.
5 Conclusion and Outlook
References
Emerging Metal-Halide Perovskite Materials for Enhanced Solar Cells and Light-Emitting Applications
1 Introduction
2 Emerging Metal-Halide Perovskite Structures
2.1 Homovalent Elements
2.2 Heterovalent Elements
3 Synthesis Protocol for Emerging Metal-Halide Perovskites
3.1 One-Step Deposition
3.2 Two-Step Deposition
3.3 Solvent-Engineering
4 Opportunities in Optoelectronic Technologies
4.1 Applications as Light Emitters
4.2 Applications as Solar Cells
5 Conclusions and Outlook
References
SrTi1-xSnxO3 Thin Films as Photocatalysts for Organic Dye Degradation: Influence of the Composition, Deposition Method, and Growth Orientation
1 Introduction
2 Experimental Details
3 Results
3.1 Influence of the Thin Film Composition and Deposition Method on the Photocatalytic Activity
3.2 Influence of the Thin Film Growth
4 Conclusions
References
SrSnO3 Applied in the Reduction of NO by CO: Influence of Transition Metal Doping on the Catalytic Activity
1 Introduction
1.1 Catalytic Abatement of NO
1.2 ASnO3 Perovskites
1.3 Perovskites Applied in the Reduction of NO by CO
2 Materials and Methods
2.1 Reagents
2.2 Modified Pechini Method
2.3 Characterization of the Catalysts
2.4 Catalytic Activity
3 Results and Discussion
3.1 Influence of Doping on the Catalytic Activity of SrSnO3: Me (Me: Fe, Ni, Cu)
3.2 Influence of the Synthesis Procedure on the Catalytic Results of SrSnO3: Fe
3.3 Influence of the Dopant Amount on the Catalytic Properties of SrSnO3: Cu
4 Conclusions
References
Advances in the Synthesis and Applications of Self-Activated Fluorescent Nano- and Micro-Hydroxyapatite
1 Introduction and General Concepts
2 Crystallographic Structure of HA
3 Synthesis of Luminescent HA
3.1 Chemical Precipitation
3.2 Synthesis from Natural Bio-Resources
3.3 Hydrothermal-Assisted Precipitation
3.4 Sol–Gel Method
4 Self-Activated Luminescence
5 Applications
5.1 Plain Fluorescence Imaging
5.2 Fluorescence-Guided Therapy
5.3 Biosensing
5.4 Bone Treatment and Regeneration
5.5 Other Applications
6 Conclusions and Perspectives
References
Spintronic Properties in Complex Perovskites: A Concordance Between Experiments and Ab-Initio Calculations
1 Introduction
2 Experimental Techniques
3 Calculation Methods
4 Semiconductor Ferromagnetic Features and Thermophysical Properties of Superstructurated (La,Tb)2CoFeO6 Double Perovskites
4.1 Structural Characteristics
4.2 Ferromagnetic Behavior
4.3 Electric Response
4.4 Electronic Structures
4.5 Thermophysical Properties
5 Conclusions
References
Graphenylene-Like Structures as a New Class of Multifunctional Materials Alternatives to Graphene
1 Introduction
2 Graphenylene
2.1 Structural and Physical Properties
2.2 Gas Separation
2.3 Catalysis and Gas Sensing
2.4 Energy Storage and Similar Systems
2.5 Electronic Transport
3 Experimental Synthesis
4 Graphenylene-Like (Inorganic Analogs)
4.1 Boron Nitride (BN)
4.2 Silicon (Si)
4.3 Zinc Oxide (ZnO)
4.4 Silicon Carbide (SiC)
4.5 Gallium Nitride (GaN)
5 Concluding Remarks
References
Computer Simulations of MOF Systems: Key Applications
1 Introduction
2 Most Used Theoretical Methods
3 Fuel Gas Storage
4 Polluting Gas Capture
5 Gas Separation
6 Drug Delivery
7 Final Remarks
References
Advanced DFT Atomistic Approaches for Electronic, Optical, and Structural Properties of Semiconductor Oxides
1 Early Overview
2 Structural Disorder and Photoluminescence
3 Conclusions
References
Computational Simulations to Predict the Morphology of Nanostructures and Their Properties
1 Introduction
2 Methodology
2.1 Computational Model
2.2 Surfaces
2.3 Eletronic and Structural Descriptors
2.4 Representation of Morphological Transformations
3 H2 Production by Water-Splitting Using ABO4 Compounds
4 Concluding Remarks
References
Unraveling the Surface Chemistry of the Heterogeneous Catalytic Decomposition of O3 for Selectivity Concerning O2 or HO• Formation
1 Introduction
2 Reaction Mechanism of O3 Decomposition
3 O3 Decomposition on Metal Oxides/Hydroxides
4 O3 Decomposition on Carbon-Based Materials
5 O3 Decomposition on Zeolites
6 Modelling Studies of O3 Decomposition
7 Conclusions
References
NH3 Synthesis by Electrochemical Process Under Ambient Condition
1 Introduction
2 N2 Reduction Mechanism and the Most Favorable Metals and Oxides Electrodes for the Reaction
3 Most Relevant Catalysts for the Electrochemical Reduction of N2
3.1 Noble Metals
3.2 Transition Metal Oxides
3.3 Sulfide-Based Catalysts for NRR
3.4 Transition Metal Phosphide-Based Catalysts
3.5 Rational Catalyst/Support Design
4 Electrochemical Reactors Types for the N2 Reduction Reaction
5 Conclusions and Future Perspectives
References
Overview: Catalysts, Feedstocks in Biodiesel Production
1 Introduction
2 Fame Production
3 Edible, Non-edible, Waste, Cooking Oils, Waste Fats, Algal Oil
4 Experimental Characterization
5 Homogeneous Catalysts
6 Acid Catalyst
7 Heterogeneous Catalysts
8 Basic Heterogeneou Catalysts
9 Alkaline Earth Metal Oxides
10 Transition Metal Oxides
11 Zeolites
12 Supported Catalyst
13 Hydrocalcite
14 Mixed Metal Oxides
15 Biomass Based Catalyst
16 Ion Exchange Resin
17 Sulfated Catalyst and Sulfonated Carbon-Based Catalyst
18 Enzyme Catalyst
19 Bifunctional Solid Catalyst
20 Nanomaterial Stimulants
21 Electrocatalytic Process for Transesterification
22 Artificial Inteligence and Machine Learning Methods
23 Comparison of Catalysts in the Production Process
24 Comparison of Industrial Production Methods
25 Conclussions and Outlook
References
Bioactivity
In Silico Drug Design and in Vivo Acute Toxicity Assay of Chalcone Analogs with Biological Antiparkinsonian Activity
1 Introduction
2 Results and Discussion
2.1 A Bibliographic Search of Natural Substances
2.2 Derivation of the Pharmacophoric Pattern
2.3 Molecular Docking Study
2.4 Prediction of Pharmacokinetics (ADME) and Toxicological Properties
2.5 Structural Modifications, Activity Prediction and Synthetic Viability
2.6 Synthesis of Planned Molecules by Claisen-Schmidt Reaction
2.7 Pharmacological Activity in a Zebrafish Model
3 Conclusion
4 Experimental Session
4.1 Search for the Structures of Natural Substances
4.2 Derivation of the Pharmacophoric Pattern
4.3 Molecular Docking Study
4.4 Prediction of Pharmacokinetics (ADME) and Toxicological Properties
4.5 Structural Modifications, Activity Prediction and Synthetic Viability
4.6 Synthesis of Planned Molecules by Claisen-Schmidt Reaction
4.7 Acute Toxicity in a Zebrafish Model
5 Ethical considerations
References
Electronic and Structural Insights of BCR-ABL Inhibitors Under LMC Treatment Perspective
1 Introduction
1.1 Chronic Myeloid Leukemia and Tyrosine Kinase Inhibitors
1.2 BCR-ABL Protein
2 Methodology
2.1 PDB Structures and Molecular Docking
2.2 Electronic Structure
3 Results and Discussion
3.1 Frontier Molecular Orbitals
3.2 Docking and the Electronic Structure Correlation
3.3 Comparison of the Docking at P1 and S1 Sites of the Wild and Mutated Proteins
References
Pathophysiology, Molecular Interaction Mechanism, Metabolism, Pharmacotherapy and New Perspectives in the Pharmacological Treatment of Chemical Dependence on the Main Illicit Drugs Consumed in the World
1 Introduction
2 Method
3 Cannabis sativa
3.1 Cannabis
3.2 Lysergic Acid Diethylamide (LSD)
3.3 Amphetamine
3.4 Cocaine
4 Physiopathology of Chemical Dependence
4.1 Cannabis
4.2 LSD
4.3 Cocaine
4.4 Amphetamines
5 Symptomatology of Withdrawal Syndrome
5.1 Cannabis
5.2 Cocaine
5.3 Amphetamines
5.4 LSD
6 Pharmacological Treatment for Withdrawal Syndrome
7 Conclusion
References
MAO Inhibitors from Natural Sources for Major Depression Treatment
1 Introduction
2 Antidepressant Drugs
3 Medicinal Herbs Against Depression
4 Pharmacophoric Features of MAO Inhibitors and Phytochemicals
5 Conclusion
References
Advances in Computational Techniques for Discovery and Development of Drugs Against Leishmaniasis, a Brief Review
1 Introduction
1.1 Genomic, Transcriptomic and Proteomic Approaches in Leishmaniasis
2 Comparative Genomics Between L. Major, L. Infantum and L. Braziliensis
2.1 Transcriptomic
2.2 Transcriptomics of the Parasite-Vector Interaction
2.3 Proteomics
2.4 Genetic Target Validation in Leishmanial
3 Aspects of Drug Discovery in Antileishmania Therapy
3.1 Insights Based in Bioinformatics Techniques
4 Considerations and Perspectives
References
Lead Optimization in Drug Discovery
1 Introduction
2 Computational Methods Used in Lead Optimization
2.1 Fragment-Based,  Pharmacophore and Bioisosterism
2.2 Conformational Studies
2.3 Structure–Activity Studies, Machine Learning/Deep Learning, and ADMETox Studies
3 Conclusion
References
Pulsed Electric Field and Ultrasound Applied to Proteins, Enzymes and Peptides
1 Protein Sources for Obtaining Amino Acids: Current and New Trends
2 Enzymatic Stimulation
3 Effect of Ultrasound on Enzymes and Peptides
4 Electrostimulation on Proteins and Enzymes for the Production of Value-Added Peptides
References
Vaccine History: From Smallpox to Covid-19
1 Introduction
2 Vaccination History
3 Vaccines Imunology
4 Current Vaccines
4.1 BCG
4.2 Influenza
4.3 Rubella
4.4 Dengue
4.5 HIV
4.6 HPV
5 Messenger RNA Vaccines and COVID-19
6 COVID-19 Vaccines
6.1 Pfizer/BioNTech
6.2 Oxford/AstraZeneca
6.3 Coronavac
6.4 Janssen
7 COVID-19 Childhood Vaccines
References
Structural Aspects of Organic Compounds as Proteasome Inhibitors Addressed to Several Diseases
1 General Aspects About Proteasome: Structure and Function
2 Proteasome Inhibitors in Inflammatory Diseases
3 Proteasome Inhibitors in Protozoal Diseases
4 Proteasome Inhibitors in Cancer Treatment
5 Conclusions
References
Phytotechnological and Pharmaceutical Potential of Eugenia Genus
1 Introduction
2 The Pharmaceutical Potential of the Eugenia Genus
3 Phytotechnological Potential of the Eugenia Genus
4 Food Application of Eugenia spp.
5 Conclusion
References
How Basic Programming Knowledge can Help the Drug Discovery Process
1 Introduction
2 Hosting Scripts and Software
3 Process Automation in the Discovery and Planning of New Drugs Through Python Programming Language
4 Python Language Application in Automation Processes
5 The Python Programming Language Applied to Drug Research and Drug Discovery
6 The Use of Basic Concepts in Python for the Development of Scripts in Drug Discovery: A Practical Approach
6.1 Practical Examples
6.2 Automating Some Tasks of Gromacs
6.3 Automation and Integration of OpenEye Company Software
6.4 ROC/AUC Validations for ROCS and GOLD Software
7 Conclusion
References
Ligand-Based Drug Design for Selection of Molecules with Pharmacological Activity in Essential Tremor
1 Introduction
2 Material and Methods
2.1 Molecules Selection
2.2 Identification of Pharmacophore Groups
2.3 Pharmacophore-Based Virtual Screening
2.4 Determination of Physical and Chemical Properties
2.5 Prediction of Pharmacokinetic Properties
2.6 Prediction of Toxicological Properties
2.7 Activity Prediction: SEA and PASS
2.8 Modifications of the Selected Prototype
2.9 Molecular Docking Using the Gold Software
3 Results and Discussion
3.1 Molecules Selection
3.2 Pharmacophoric  Model
3.3 Pharmacophore-Based Virtual Screening
3.4 Determination of Physical and Chemical Properties
3.5 Prediction of Pharmacokinetic Properties
3.6 Prediction of Toxicological Properties
3.7 Activity Prediction: SEA and PASS
3.8 Selection and Modification of the Prototype
3.9 Molecular Docking of Modifications
4 Conclusion
References
Intramolecular Hydrogen Bonding Patterns and Conformational Preferences of Ouabain—A Molecule with Cardiotonic and Antiviral Activities
1 Introduction
2 Computational Details
3 Results
3.1 Conformational Preferences and Energetics
3.2 Characteristics of the Intramolecular Hydrogen Bonds
3.3 Other Molecular Properties
4 Discussion and Conclusions
References
Molecular Modeling of Acetylcholinesterase Inhibitors for the Treatment of Alzheimer's Disease
1 Introduction
2 Materials and Method
2.1 Inhibitors and Crystallographic Structure of PDB Studied
2.2 Calculation of Molecular Properties
2.3 Electrostatic Potential Maps—MEP
2.4 Molecular Docking
2.5 Hypothesis of the Pharmacophoric Group
2.6 ADME/Tox Screenning
3 Results and Discussions
3.1 Structures Studied
3.2 Analysis of Physicochemical Properties
3.3 Calculation of Molecular Properties
3.4 Molecular Electrostatic Potential Maps—MEP
3.5 Molecular Docking
3.6 Hypothesis of the Pharmacophoric Group
3.7 ADME/Tox Screenning
4 Conclusion
Supplementary Material
References