Quantum Chemistry Simulation of Biological Molecules

Cover
Half-title
Title page
Copyright information
Contents
Preface
Figure Credits
1 Basic Properties of Quantum Chemistry
	1.1 Introduction
	1.2 The Schrödinger Equation
	1.3 Chemical Bonds
	1.4 Classical Calculations
	1.5 Quantum Calculations
	1.6 Density Functional Theory
	1.7 Exchange-Correlation Energy
	1.8 Molecular Fractionation with Conjugate Caps Method
	1.9 Conclusions
2 Charge Transport in the DNA Molecule
	2.1 Introduction
	2.2 Quasiperiodic Structures
	2.3 Tight-Binding Hamiltonian
	2.4 Charge Transport in DNA
	2.5 Conclusions
3 Electronic Transmission Spectra of the DNA Molecule
	3.1 Introduction
	3.2 Electrical Conductivity
	3.3 Twisted Geometry
	3.4 Methylated States
	3.5 Diluted Base-Pairing
	3.6 Conclusions
4 Thermodynamic Properties of the DNA Molecule
	4.1 Introduction
	4.2 Classical Statistics: The Single-Strand DNA Structure
	4.3 Classical Statistics: The Double-Strand DNA Structure
	4.4 Quantum Statistics: The Single-Strand DNA Structure
	4.5 Quantum Statistics: The Double-Strand DNA Structure
	4.6 Nonextensive Thermodynamics
	4.7 DNA Denaturation
	4.8 Conclusions
5 Properties of the DNA/RNA Nucleobases
	5.1 Introduction
	5.2 Experimental Procedure and Computational Details
	5.3 Crystal Structures
	5.4 Electronic Band Structure
	5.5 Effective Masses
	5.6 Absorption Spectra
	5.7 Conclusions
6 Molecular Electronics
	6.1 Introduction
	6.2 Molecular Diode
	6.3 Alpha3-Helical Polypeptide and Its Biochemical Variants
	6.4 Single Micro-RNAs Chains and the Autism Spectrum Disorder
	6.5 Conclusions
7 Amino Acid Anhydrous Crystals
	7.1 Introduction
	7.2 Structural, Electronic, and Optical Properties
	7.3 Infrared and Raman Spectra of the L-Aspartic Acid
	7.4 Role of Water on the Vibrational Spectra of L-Aspartic Acid
	7.5 Conclusions
8 Protein–Protein Systems
	8.1 Introduction
	8.2 The Protein Data Bank
	8.3 Improving PDB through Molecular Dynamics
	8.4 The Dielectric Function of Proteins
	8.5 The Importance of Protein–Protein Interactions
	8.6 Conclusions
9 Ascorbic Acid and Ibuprofen Drugs
	9.1 Introduction
	9.2 Ascorbic Acid
	9.3 Ibuprofen
	9.4 Human Serum Albumin
	9.5 Conclusions
10 Cholesterol-Lowering Drugs
	10.1 Introduction
	10.2 Crystallographic Data
	10.3 Chemical Structure
	10.4 Binding Interaction Energy Profiles
	10.5 Conclusions
11 Collagen-Based Biomaterials
	11.1 Introduction
	11.2 Chemical Structure of the Collagen-Like Peptide T3-785
	11.3 Energetic Description
	11.4 Interaction Binding Energies
	11.5 Graphical Panel of the Most Relevant Interactions
	11.6 Integrin–Collagen Triple-Helix Complex Interaction
	11.7 Structural Representation
	11.8 Interaction Energy Profiles
	11.9 Conclusions
12 Antimigraine Drugs
	12.1 Introduction
	12.2 Serotonin Receptors and the Antimigraine Drugs
	12.3 Drug–Receptor Complex Data
	12.4 Interaction Energy of the Amino Acid Fragments
	12.5 Total Binding Energy
	12.6 Conclusions
13 Antiparkinson Drugs
	13.1 Introduction
	13.2 Levodopa Molecule
	13.3 Carbidopa Molecule
	13.4 Conclusions
14 Central Nervous System Disorders
	14.1 Introduction
	14.2 The iGluR2-AMPA Receptors
	14.3 Crystallographic Data of the Different Types of Willardiines
	14.4 Willardiines Partial Agonism in iGluR2-AMPA Receptors
	14.5 Interaction Energies
	14.6 Conclusions
15 The Biology of Cancer
	15.1 Introduction
	15.2 Estrogen Receptor and Its Agonists/Antagonists
	15.3 Energetic Description of Cilengitide Bound to Integrin
	15.4 Cancer Immunotherapy
	15.5 Conclusions
16 Concluding Remarks
	16.1 Introduction
	16.2 Past Achievements
	16.3 The Road Ahead
	16.4 Conclusions
References
Index