Leszczynski / Shukla Practical Aspects of Computational Chemistry

Methods, Concepts and Applications
1. Auflage 2009
ISBN: 978-90-481-2687-3
Verlag: Springer Netherlands
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 465 Seiten

'Practical Aspects of Computational Chemistry' presents contributions on a range of aspects of Computational Chemistry applied to a variety of research fields. The chapters focus on recent theoretical developments which have been used to investigate structures and properties of large systems with minimal computational resources. Studies include those in the gas phase, various solvents, various aspects of computational multiscale modeling, Monte Carlo simulations, chirality, the multiple minima problem for protein folding, the nature of binding in different species and dihydrogen bonds, carbon nanotubes and hydrogen storage, adsorption and decomposition of organophosphorus compounds, X-ray crystallography, proton transfer, structure-activity relationships, a description of the REACH programs of the European Union for chemical regulatory purposes, reactions of nucleic acid bases with endogenous and exogenous reactive oxygen species and different aspects of nucleic acid bases, base pairs and base tetrads.

Autoren/Hrsg.

Leszczynski, Jerzy

Shukla, Manoj

Inhaltsverzeichnis

1;186715_1_En_FM1_OnlinePDF.pdf;1
2;186715_1_En_1_Chapter_OnlinePDF.pdf;15
2.1;1 Efficient and Accurate Electron Propagator Methods and Algorithms;15
2.1.1;1.1 Introduction;15
2.1.2;1.2 Superoperator Formulation;16
2.1.3;1.3 Quasiparticle Methods;20
2.1.3.1;1.3.1 Transition Operator Method;20
2.1.3.2;1.3.2 Reduction of Virtual Space;21
2.1.3.3;1.3.3 Resolution of Identity;22
2.1.4;1.4 Performance;23
2.1.4.1;1.4.1 Transition Operator Method;23
2.1.4.2;1.4.2 Reduction of Virtual Space;25
2.1.4.3;1.4.3 Resolution of the Identity;27
2.1.5;1.5 Conclusions;28
2.1.6;References;29
3;186715_1_En_2_Chapter_OnlinePDF.pdf;32
3.1;2 Properties of Excited States of Molecules in Solution Described with Continuum Solvation Models;32
3.1.1;2.1 Introduction;32
3.1.2;2.2 The Basic PCM;35
3.1.3;2.3 The PCM for Excited States;36
3.1.3.1;2.3.1 Equilibrium vs. Nonequilibrium Solvation;36
3.1.3.2;2.3.2 The QM Description of the Excited States:State Specific vs. LR;37
3.1.3.3;2.3.3 Excited State Properties Calculated as Energy Analytical Gradients;38
3.1.3.4;2.3.4 Electronic Coupling Between Chromophores in Solution;38
3.1.4;2.4 Numerical Examples;39
3.1.4.1;2.4.1 Absorption/Emission in Homogeneous and Heterogeneous Environments;39
3.1.4.2;2.4.2 How Solvent Controls EET and Light Harvesting;43
3.1.5;2.5 Conclusions;46
3.1.6;References;47
4;186715_1_En_3_Chapter_OnlinePDF.pdf;50
4.1;Chapter Chapter 3: Chirality and Chiral Recognition;50
4.1.1;Introduction;50
4.1.1.1;Chiral Objects;50
4.1.1.2;Chirality in Chemistry;53
4.1.1.3;The Chirality of Biomolecules;55
4.1.2;General Considerations;56
4.1.2.1;Magnitude (Large vs. Small Effects);56
4.1.2.2;Phase Effects;57
4.1.2.3;Sign (Positive vs. Negative);57
4.1.3;Discussion;60
4.1.3.1;Experimental and Theoretical Results;61
4.1.3.2;Pure Theoretical Studies;67
4.1.3.3;Solvent Effects on Chiral Recognition;86
4.1.3.4;The Use of Metals to Bring Together the Chiral Entities;86
4.1.3.5;Optical Rotatory Power Studies;90
4.1.4;Conclusions;92
4.1.5;References;93
5;186715_1_En_4_Chapter_OnlinePDF.pdf;100
5.1;Chapter Chapter 4: Multiscale Modeling: A Review;100
5.1.1;Introduction;100
5.1.2;Multiscale modeling publications;102
5.1.3;Bridging Between Scales: A Difference of Disciplines;104
5.1.3.1;Solid Mechanics Bridging (Hierarchical Methods);104
5.1.3.2;Numerical Methods (Concurrent Methods);108
5.1.3.3;Materials Science Bridging;110
5.1.3.4;Physics Perspective;114
5.1.3.5;Mathematics Perspective;115
5.1.4;Multiscale Modeling of Different Materials;118
5.1.4.1;Metals;118
5.1.4.2;Ceramics;118
5.1.4.3;Polymers;118
5.1.4.3.1;Monolithic Synthetic Polymer Multiscale Modeling;119
5.1.4.3.2;Composite Synthetic Polymer Multiscale Modeling;119
5.1.4.3.3;Human and Animal Multiscale Modeling;121
5.1.4.3.4;Multiscale Modeling of Vegetation-Based Structural Materials;122
5.1.5;Multiscale Modeling for Design;122
5.1.6;Multiscale Modeling in Manufacturing;123
5.1.7;Engineering Designs in Practice Using Multiscale Modeling;124
5.1.7.1;Plasticity-Damage Multiscale Modeling Example of Automotive Cadillac Control Arm Design;124
5.1.7.2;Multiscale Fatigue Modeling Example of Automotive Corvette Cradle;130
5.1.8;Summary;134
5.1.9;References;136
6;186715_1_En_5_Chapter_OnlinePDF.pdf;149
6.1;Chapter Chapter 5: Challenging the Multiple Minima Problem: Example of Protein Folding;149
6.1.1;Introduction;149
6.1.2;Energy Landscape of Protein Molecule;151
6.1.3;Coarse-Graining of the Landscape;151
6.1.4;Coarse-Grained Conformational Energy;154
6.1.5;Monte Carlo Procedure;154
6.1.5.1;Example: Ab novo Prediction;155
6.1.5.2;Example: Conformational Autocatalysis (A Model of Prion Propagation);156
6.1.6;Concluding Remarks;157
6.1.7;References;159
7;186715_1_En_6_Chapter_OnlinePDF.pdf;161
7.1;Chapter Chapter 6: An Overview of sigma-Hole Bonding, an Important and Widely-Occurring Noncovalent Interaction;161
7.1.1;The sigma-Hole Concept: Origin;161
7.1.2;The sigma-Hole Concept: Expansion;163
7.1.3;Computational Results;167
7.1.4;On the Nature of sigma-Hole Bonding;170
7.1.5;Significance of sigma-Hole Interactions;172
7.1.6;References;172
8;186715_1_En_7_Chapter_OnlinePDF.pdf;176
8.1;Chapter Chapter 7: sigma-Bond Prevents Short pi-Bonds: A Detailed Theoretical Study on the Compounds of Main Group and Transiti;176
8.1.1;Introduction;176
8.1.2; Computational Details;179
8.1.3;Results and Discussion;180
8.1.3.1; Short Bonds in Main Group Compounds;180
8.1.3.2; Five Valence Electron Diatomic Species;181
8.1.3.3;Six Valence Electron Diatomic Species;182
8.1.3.4;Seven Valence Electron Diatomic Species;183
8.1.3.5; Eight Valence Electron Diatomic Species;183
8.1.3.6;Short Bonds in Transition Metal Complexes;185
8.1.4;Conclusions;189
8.1.5;References;190
9;186715_1_En_8_Chapter_OnlinePDF.pdf;193
9.1;Chapter Chapter 8: QSAR Models for Regulatory Purposes: Experiences and Perspectives;193
9.1.1;The Modeling Context for QSAR;193
9.1.2;The QSAR Model Theory;194
9.1.3;The QSAR Model Practice;196
9.1.4;The Regulatory Perspective;198
9.1.4.1;Identifying the Legislative Target;198
9.1.4.2;Satisfying the Legislative Context;199
9.1.4.3;Specific Requirements;200
9.1.5;The Practical Issues and Feasibility;202
9.1.6;European Projects on QSAR and Regulations;204
9.1.6.1;The DEMETRA Project;204
9.1.6.2;The CAESAR Project;205
9.1.6.3;The CHEMOMENTUM Project;205
9.1.6.4;The OSIRIS Project;206
9.1.7;Open Issues;207
9.1.8;References;209
10;186715_1_En_9_Chapter_OnlinePDF.pdf;211
10.1;Chapter Chapter 9: Quantitative Structure-Activity Relationships (QSARs) in the European REACH System: Could These Approaches b;211
10.1.1;Role of Computational Chemistry in REACH;211
10.1.2;(Q)SAR Methodology;212
10.1.3;Problematic Nanomaterials;216
10.1.4;Nano-QSAR Challenges;218
10.1.5;Conclusions;222
10.1.6;References;223
11;186715_1_En_10_Chapter_OnlinePDF.pdf;227
11.1;Chapter Chapter 10: Structure-Activity Relationships in Nitro-Aromatic Compounds;227
11.1.1;Introduction;228
11.1.2;The Ames Salmonella Typhimurium Assay;229
11.1.3;Metabolic Activation;231
11.1.4;Structural and Electronic Factors Modulating Biological Activity;232
11.1.4.1;Orientation and Position of the Nitro Group;232
11.1.4.2;Effect of the Reduction Potential of the Nitro-Aromatic Compound;235
11.1.4.3;Molecular Size, Number of Nitro Groups, and Structural Arrangement;236
11.1.4.4;Substituents Other than Nitro Group;237
11.1.4.5;Summary of the Structural and Electronic Factors Influencing the Mutagenic Activity;239
11.1.5;Quantitative Structure-Activity Relationships (QSARs);239
11.1.5.1;Summary on the QSAR Models;243
11.1.6;Outlook;244
11.1.7;References;246
12;186715_1_En_11_Chapter_OnlinePDF.pdf;251
12.1;Chapter 11: Molecular Modeling as an Auxiliary Method in Solving Crystal Structures Based on Diffraction Techniques;251
12.1.1;Introduction;251
12.1.2;Analysis of Partially Disordered Structures;252
12.1.2.1;Solving the Structural Problem;252
12.1.2.2;Correcting Erroneously Determined Geometry of Molecules;254
12.1.2.3;Correcting Disordered Structures;256
12.1.3;Long Range Ordering Problems;257
12.1.3.1;Polytypism in Layered Structures;257
12.1.3.2;Long Range Structural Correlations;260
12.1.3.3;Multicomponent Inclusion - Structural Models;261
12.1.4;Concluding Remarks;263
12.1.5;References;264
13;186715_1_En_12_Chapter_OnlinePDF.pdf;265
13.1;Chapter Chapter 12: Dihydrogen Bonds: Novel Feature of Hydrogen Bond Interactions;265
13.1.1;Hydrogen Bond and Dihydrogen Bond Interactions;265
13.1.2;The Theoretical Methods Applied to Analyze and Characterize the Hydrogen and Dihydrogen Bonds;269
13.1.2.1;The Hydrogen Bond Energy;269
13.1.2.2;The Quantum Theory of ``Atoms in Molecules´´ (QTAIM);272
13.1.3;Variety of Dihydrogen Bonds Interactions;274
13.1.4;Dihydrogen Bonds and the Other Nonbonding Interactions;278
13.1.5;Summary;282
13.1.6;References;283
14;186715_1_En_13_Chapter_OnlinePDF.pdf;286
14.1;Chapter Chapter 13: Catalytic Decomposition of Organophosphorus Compounds;286
14.1.1;Introduction;287
14.1.1.1;Organophosphorus Compounds, Clay Minerals, and Metal Oxides;287
14.1.1.1.1;Organophosphorus Compounds;287
14.1.1.1.2;Clay Minerals and Metal Oxides;289
14.1.2;Computational Methods and Models;291
14.1.2.1;Quantum-Chemical Approximations for the Modeling of Surface Reactivity;292
14.1.3;Adsorption and Decomposition of Organophosphorus Compounds on Clay Minerals and Metal Oxides;293
14.1.3.1;Interactions of Nerve Agents with Clay Minerals;293
14.1.3.2;Interactions of Nerve Agents and Their Simulants with Metal Oxides;296
14.1.4;Summary;301
14.1.5;References;302
15;186715_1_En_14_Chapter_OnlinePDF.pdf;306
15.1;Chapter Chapter 14: Toward Understanding of Hydrogen Storage in Single-Walled Carbon Nanotubes by Investigations of Chemisorpti;306
15.1.1;Introduction;306
15.1.2;Experimental Studies on the Hydrogenation of SWNTs;309
15.1.3;Theoretical Studies on the Chemisorption of Hydrogen Atoms on SWNTs;312
15.1.3.1;Computed Vibrational Frequencies of Hydrogen Chemisorbed SWNTs;318
15.1.3.2;Hydrogenation of SWNT Beyond Hydrogen Storage;319
15.1.4;Summary and Outlook;320
15.1.5;References;321
16;186715_1_En_15_Chapter_OnlinePDF.pdf;323
16.1;Chapter Chapter 15: Quantum Monte Carlo for Electronic Structure;323
16.1.1;Introduction;323
16.1.2;The QMC Method;325
16.1.2.1;Variational Monte Carlo;326
16.1.2.2;Diffusion Monte Carlo;326
16.1.2.2.1;Importance Sampling;327
16.1.2.2.2;Trial Functions;327
16.1.2.2.3;The Fixed-Node Approximation;328
16.1.2.2.4;Excited States;328
16.1.2.2.5;Pseudopotentials in QMC;329
16.1.3;Applications of DMC;329
16.1.3.1;O4;329
16.1.3.2;Free Base Porphyrin;330
16.1.3.3;EPLF for Spheroidene;330
16.1.4;Closing Statement;330
16.1.5;References;331
17;186715_1_En_16_Chapter_OnlinePDF.pdf;334
17.1;Chapter Chapter 16: Sequential Monte Carlo and Quantum Mechanics Calculation of the Static Dielectric Constant of Liquid Argon;334
17.1.1;Introduction;334
17.1.2;Methods;335
17.1.2.1;Monte Carlo Simulation;335
17.1.2.2;Quantum Mechanical Calculations;336
17.1.2.2.1;The Separability of the Dipole Polarizability;337
17.1.3;Results;338
17.1.3.1;The Structure of Liquid Argon;338
17.1.3.2;Polarizability and Dielectric Constant of Liquid Argon;339
17.1.4;Concluding Remarks;342
17.1.5;References;342
18;186715_1_En_17_Chapter_OnlinePDF.pdf;344
18.1;Chapter Chapter 17: CO2(aq) Parameterization Through Free Energy Perturbation/Monte Carlo Simulations for Use in CO2 Sequestrat;344
18.1.1;Introduction;344
18.1.2;Computational Methods;346
18.1.2.1;Gas Phase Calculations;346
18.1.2.2;Classical Simulations;347
18.1.2.3;Solubility Calculations;348
18.1.3;Results and Discussion;351
18.1.3.1;Gas Phase Calculations;351
18.1.3.2;CO2 Solubility and Local Solvent Structure;355
18.1.4;Conclusions;362
18.1.5;References;363
19;186715_1_En_18_Chapter_OnlinePDF.pdf;365
19.1;Chapter Chapter 18: Free Energy Perturbation Monte Carlo Simulations of Salt Influences on Aqueous Freezing Point Depression;365
19.1.1;Introduction;365
19.1.2;Methodology;366
19.1.3;Results;368
19.1.3.1;Determination of Aqueous Freezing Points;368
19.1.4;Conclusions;374
19.1.5;References;375
20;186715_1_En_19_Chapter_OnlinePDF.pdf;377
20.1;Chapter Chapter 19: The Potential Energy Shape for the Proton Motion in Protonated Naphthalene Proton Sponges (DMAN-s) and its ;377
20.1.1;Introduction;377
20.1.2;Main Properties of Protonated DMAN-s;378
20.1.2.1;Geometry of [NHN]+ Hydrogen Bonds;378
20.1.2.2;Infrared Spectra;380
20.1.2.3;NMR Spectra;381
20.1.2.4;2J(N,N) and J(N,H) Coupling Constants;384
20.1.3;Theoretical Treatment;385
20.1.4;General Remarks on the Accuracy of Ab Initio Calculations of Barrier Height for Proton Transfer;386
20.1.5;References;390
21;186715_1_En_20_Chapter_OnlinePDF.pdf;393
21.1;20 Nucleic Acid Base Complexes: Elucidationof the Physical Origins of Their Stability;393
21.1.1;20.1 Quantum–Chemical Approach to Evaluationof Noncovalent Interactions for Nucleic Acid Base Complexes: The Basics, the Pros, and the Cons;393
21.1.1.1;20.1.1 Supermolecular Approach;394
21.1.1.2;20.1.2 Perturbation-Theory Approach;395
21.1.2;20.2 The Nature of Interactions in Nucleic AcidBase Complexes;396
21.1.2.1;20.2.1 H-Bonded DNA Base Pairs;396
21.1.2.2;20.2.2 Stacked DNA Base Pairs;397
21.1.3;20.3 Summary and Outlook;400
21.1.4;References;401
22;186715_1_En_21_Chapter_OnlinePDF.pdf;404
22.1;Chapter Chapter 21: Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases;404
22.1.1;Introduction;404
22.1.2;Ab Initio Studies of Conformational Flexibility in Nucleic Acid Bases;406
22.1.3;Conclusions;415
22.1.4;References;416
23;186715_1_En_22_Chapter_OnlinePDF.pdf;419
23.1;Chapter Chapter 22: DNA Lesions Caused by ROS and RNOS: A Review of Interactions and Reactions Involving Guanine;419
23.1.1;Introduction;419
23.1.2;Basic Information About ROS and RNOS;420
23.1.3;Reactions at the C8 Site of Guanine;423
23.1.3.1;Methods of Study;424
23.1.3.2;Reaction of Guanine with OHc Radicals: Formation of 8-oxoG;427
23.1.3.3;Reaction of Guanine with H2O2: Formation of 8-oxoG;430
23.1.3.4;Reaction of Guanine with H2O3: Formation of 8-oxoG;431
23.1.3.5;Reaction of Guanine with ONOO-: Formation of 8-oxoG and 8-nitroG;434
23.1.3.6;Reaction of Guanine with ONOOCO2-: Formation of 8-oxoG and 8-nitroG;436
23.1.3.7;Reactions of Imidazole with HOCl and NO2Cl;439
23.1.4;Conclusions;440
23.1.5;References;441
24;186715_1_En_23_Chapter_OnlinePDF.pdf;448
24.1;Chapter Chapter 23: Stability and Structures of the DNA Base Tetrads: A Role of Metal Ions;448
24.1.1;Introduction;448
24.1.2;Guanine Tetrad;449
24.1.3;Isoguanine Tetrad;449
24.1.4;Tetrads Formed by Adenine, Cytosine, Thymine, and Uracil;450
24.1.5;Tetrads with Mixed Bases;451
24.1.6;Interaction Between Metal Ions and the NAB Tetrads;452
24.1.7;Summary;454
24.1.8;References;454
25;186715_1_En_BM2_OnlinePDF.pdf;457
25.1;: Index;457