Advances in Chemical Modeling. Volume 6

Mihai V. Putz (Editor)
Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry,West University of Timişoara, Timișoara, Romania

Series: Chemistry Research and Applications
BISAC: MED078000

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In today’s modern economy, and in strategic management more precisely, which is often driven by scientific and technological research-development and innovations, the best position in a market is held by the so called advantage – competitive, sustainable, or perennial! Competitive associates are in the so called “red oceans” where firms, products, and organizations offer and compete for the same customer segment. Perennial advantage associates, in contrast, create “blue oceans” by which new products and markets couple and create “peaceful waves” and a no-competition landscape! But what about sustainability? Sustainability may be regarded as a sub-class of perenniality and might eventually end the disruptive innovation that potentially attracts and converts non-customers to actual customers in a “blue ocean” enterprise! However, sustainability is not necessarily related to durability – that is a measure of time after all; it instead address a strategic development by which a product or service, once created, can be returned to its original components without affecting the environment, whenever it is necessary, by present of future generations! It is therefore a two sided attribute of products, services and processes, with a high degree of “cybernetics” inside, in the sense of inverse-connections, feed-back, and integrated-parts-in-whole construct. In modern chemistry, the so called nano-chemistry, sustainability means: controlling design, controlling synthesis, atomic-and-molecular memory, intelligent materials that are able to reverse their entropy at certain stimulus and triggering points, etc. This is what we may call sustainable nano-chemistry! It is still a large idealization of most chemical processes, yet it is fulfilled by certain parts of chemical research, especially those involved in nano-science and technology with sustainable degrees! Aiming to document this desirable and sustainable future of nano-chemistry, the present volume, while continuing the precedent in the series, contains world class chapters in the allied fields of Structural Physical Chemistry, Structural Modeling Chemistry, Nano-chemistry by Graph Theory, Nano-chemistry by Molecular Topology, QSAR (Quantitative-Structure-Activity Relationships), and Frontier Theories in Physical-Chemistry. (Imprint: Nova)

Preface: Sustainable Nano-Chemistry
Mihai V. Putz

Structural Physical Chemistry

Chapter 1. Bondonic Effects on the Topo-Reactivity of PAHs
Mihai V. Putz and Marina A. Tudoran

Chapter 2. Anti-Bondonic Effects on the Topo-Reactivity of PAHs
Mihai V. Putz and Marina A. Tudoran

Chapter 3. Adamantyl Super-Structures: Hyper-Adamantane, Hyper-Hyper-Adamantane, toward Fractality and More
D. J. Klein, D. Bhattacharya, A. Panda, and L. L. Griffin

Chapter 4. Calcite Lattice Parameters in the PT-Plane to 7.62 Kb and 533°C
Michael J. Bucknum and Eduardo A. Castro

Chapter 5. Interaction of TNT with Melatonin Biosynthesis
Lemi Türker

Chapter 6. Interaction of TNT with Epinephrine Biopathway
Lemi Türker

Chapter 7. Effect of Dioxetane Group on the Ballistic Properties of Hexanitrostilbene (HNS)
Lemi Türker and Serhat Varis

Chapter 8. Cone Model for the Detonation Velocity
Lemi Türker

Structural Modeling Chemistry

Chapter 9. Valence Isomerizations of Bicyclo[4.2.0]octatriene or Bicyclo[6.2.0]decatetraene and of Their Hetero-analogs: A Computational Study
Alexandru T. Balaban, Debojit Bhattacharya, and Douglas J. Klein

Chapter 10. Molecular Classification of Styrylquinolines as Human Immunodeficiency Virus Integrase Inhibitors
Francisco Torrens and Gloria Castellano

Chapter 11. Models for Human Soluble Epoxy Hydrolase Inhibitory Activity of 1-aryl-3-(1-acylpiperidin-4-yl) Urea Analogues
Neelam Mahajan, Viney Lather, S.S. Sambi, and A.K. Madan

Chapter 12. Encoding and Clustering of Proteins in Mycobacterium Tuberculosis Proteome
Viktor Drgan, Jaros³aw J. Panek, Marjan Vracko, and Marjana Novic

Chapter 13. LigandMiner Algorithm for Repositioning of Known Ligands between Similar Protein Binding Sites
Janez Konc and Dusanka Janezic

Chapter 14. On the Novel ETE2 and BDE2 Molecular Descriptors of Flavonoid Free Radical Scavenging Potency
Dragan Amic, Bono Lucic, Ana Amic, and Zoran Markovic

Chapter 15. Modeling of Simultaneous Heat and Mass Transfer in Hollow Fiber Membranes
Hosein Hayer and Ahad Ghaemi

Nanochemistry by Graph Theory

Chapter 16. The Possibility of Impossible in Chemical Graph Theory
Istvan Laszlo

Chapter 17. Mean Molecular Connectivity Indices
Lionello Pogliani and Jesus Vicente De Julián-Ortiz

Chapter 18. Augmented Eccentric Connectivity Indices of a Molecular Graph
Mohammad Reza Farahani

Chapter 19. Extensions of Euler’s Polyhedron Formula
E. C. Kirby, R. B. Mallion, P. Pollak, and P. J. Skrzynski

Chapter 20. Zagreb Group Indices and Beyond
Ivan Gutman and Tamas Reti

Chapter 21. Prediction of Stability Constants for Copper(Ii) Binding to Tetrapeptides Containing Histidyl Residue with Graph-Theoretical Method
Ante Milicevic and Nenad Raos

Nanochemistry by Molecular Topology

Chapter 22. Topological Resonance Energy - 40 Years Later
Ivan Gutman

Chapter 23. Topological Symmetry of Multi-Shell Clusters with Octahedral Symmetry
Fatemeh Koorepazan-Moftakhar, Atena Parvan-Moldovan, and Mircea V. Diudea

Chapter 24. Using the Cut Method to Compute GA3 of Circumcoronene Series of Benzenoid Hk
Mohammad Reza Farahani

QSAR

Chapter 25. Pyrimidine Derivatives with Biological Activity in Anti-HIV Therapy. The Spectral-Diagonal-SAR Approach
Nicoleta A. Dudaș and Mihai V. Putz

Chapter 26. Refined Variable Zagreb Indices: Highly Discriminating Topological Descriptors for QSAR/QSPR
Monika Singh, Kinkar Ch. Das, S. Gupta, and A. K. Madan

Chapter 27. A Quantitative Structure-Activity Relationship and Molecular Docking Study on a Series of Indole-5-carboxamides Acting as Anti-hepatitis C Virus Agents
Sakshi Gupta, Neeraj Agarwal, Vijay K. Agarwal, Satya P. Gupta, and Basheerulla Shaik

Chapter 28. Path Eccentricity-Based Highly Discriminating Molecular Descriptors for QSAR/QSPR. Part I: Development and Evaluation
Rakesh Kumar Marwaha, Harish Jangra, Kinkar C. Das, P.V. Bharatam, and A.K. Madan

Chapter 29. Path Eccentricity Based Highly Discriminating Molecular Descriptors for QSAR/QSPR. Part II: Application in Development of Models for Prediction of a Biological Activity
Rakesh Kumar Marwaha and A.K. Madan

Frontier Theories in Physical-Chemistry

Chapter 30. Failure of Principle of Equalisation of Atomic Hardnesses on Molecule Formation. Implications
Nirmal K. Shee and Dipankar Datta

Chapter 31. How Quantum Mechanics Prohibits Regional Virialism in Molecules. I. Regional
Gerald F. Thomas

Chapter 32. How Quantum Mechanics Prohibits Regional Virialism in Molecules. II. Fragment
Gerald F. Thomas

Chapter 33. How Quantum Mechanics Prohibits Regional Virialism in Molecules. III. Transferability
Gerald F. Thomas

Chapter 34. How Quantum Mechanics Prohibits Regional Virialism in Molecules. IV. Closure
Gerald F. Thomas

Index

Chapter 1

[1] Putz, M.V. The Bondons: The Quantum Particles of the Chemical Bond, Int. J. Mol. Sci. 2010, 11, 4227-4256.
[2] Putz M.V. Quantum Theory: Density, Condensation, and Bonding. Apple Academic Press and CRC Press, Toronto-New Jersey, Canada-USA, 2012.
[3] Putz M.V. Chemical Orthogonal Spaces. In: Mathematical Chemistry Monographs, Vol. 14, University of Kragujevac, Serbia, 2012.
[4] Putz M.V., Ori O. Bondonic Characterization of Extended Nanosystems: Application to Graphene's Nanoribbons Chemical Physics Letters 2012, 548, 95-100.
[5] Putz M.V., Ori O. Bondonic Effects in Group-IV Honeycomb Nanoribbons with Stone-Wales Topological Defects. Molecules 2014, 19(4), 4157-4188.
[6] Putz M.V., Ori O. Predicting Bondons by Goldstone Mechanism with Chemical Topological Indices. International Journal of Quantum Chemistry 2015, 115 (3), 137–143.
[7] Putz M.V. Quantum Nanochemistry. A Fully Integrated Approach: Vol. III. Quantum Molecules and Reactivity. Apple Academic Press and CRC Press, Toronto-New Jersey, Canada-USA, 2015.
[8] Putz M.V. Quantum Nanochemistry. A Fully Integrated Approach: Vol. IV. Quantum Solids and Orderability. Apple Academic Press and CRC Press, Toronto-New Jersey, Canada-USA. 2015.
[9] Putz M.V., Ori O. Bondonic Chemistry: Physical Origins and Entanglement Prospects, In: Exotic Properties of Carbon Nanomatter: Advances in Physics and Chemistry. Mihai V. Putz, Ottorino Ori (Eds.), Springer Verlag, Dordrecht, NL, Chapter 10, 2015.
[10] Putz M.V., Pitulice L., Dascălu D., Isac D. Bondonic Chemistry: Non-Classical Implications on Classical Carbon Systems, In: Exotic Properties of Carbon Nanomatter: Advances in Physics and Chemistry. Mihai V. Putz, Ottorino Ori (Eds.), Springer Verlag, Dordrecht, NL, Chapter 11, 2015.
[11] Putz M.V., Duda-Seiman C., Duda-Seiman D.M., Bolcu C. Bondonic Chemistry: Consecrating Silanes as Metallic Precursors for Silicenes Materials, In: Exotic Properties of Carbon Nanomatter: Advances in Physics and Chemistry. Mihai V. Putz, Ottorino Ori (Eds.), Springer Verlag, Dordrecht, NL, Chapter 12, 2015.
[12] Putz M.V., Dudaș N.A., Putz A.-M. Bondonic Chemistry: Predicting Ionic Liquids’ (IL) Bondons by Raman-IR Spectra, In: Exotic Properties of Carbon Nanomatter: Advances in Physics and Chemistry. Mihai V. Putz, Ottorino Ori (Eds.), Springer Verlag, Dordrecht, NL, Chapter 13, 2015.
[13] Putz M.V. Hidden Side of Chemical Bond: The Bosonic Condensate. In: Advances in Chemistry Research. Volume 10, James C. Taylor (Ed.) Series: Advances in Chemistry Research, NOVA Science Publishers, Inc., New York, USA, Chapter 8, pp. 261-298, 2011.
[14] Putz M.V. Conceptual Density Functional Theory: from Inhomogeneous Electronic Gas to Bose-Einstein Condensates. In: Chemical Information and Computational Challenges in 21st Century. A Celebration of 2011 International Year of Chemistry, Mihai V. Putz (Ed.) Series: Chemistry Research and Applications and Series: Chemical Engineering Methods and Technology, NOVA Science Publishers, Inc., New York, USA, Chapter 1, pp. 1-60, 2011.
[15] Putz M.V. Density Functional Theory of Bose-Einstein Condensation: Road to Chemical Bonding Quantum Condensate. Structure and Bonding 2012, 149, 1-50.
[16] Tudoran M.A., Putz M.V. Molecular Graph Theory: From Adjacency Information to Colored Topology by Chemical Reactivity. Current Organic Chemistry 2015, in press.
[17] Putz M.V., Dudaş N.A. Variational principles for mechanistic quantitative structure –activity relationship (QSAR) studies: application on uracil derivatives’ anti-HIV action. Struct. Chem. 2013, 24, 1873-1893.
[18] Putz M.V. Quantum Nanochemistry. A Fully Integrated Approach: Vol. V. Quantum Structure-Activity Relationships (Qu-SAR). Apple Academic Press and CRC Press, Toronto-New Jersey, Canada-USA. 2015.
[19] Putz M.V., Dudaș N.A. Determining Chemical Reactivity Driving Biological Activity from SMILES Transformations: The Bonding Mechanism of Anti-HIV Pyrimidines. Molecules 2013, 18, 9061-9116.
[20] Putz M.V., Tudoran M.A., Putz A.M. Structure Properties and Chemical-Bio/Ecological of PAH Interactions: From Synthesis to Cosmic Spectral Lines, Nanochemistry, and Lipophilicity-Driven Reactivity. Curr. Org. Chem. 2013, 17, 2845-2871.
[21] Putz M.V., Putz A.M. DFT Chemical Reactivity Driven by Biological Activity: Applications for the Toxicological Fate of Chlorinated PAHs. Struct. Bond. 2013, 150, 181–232.
[22] Program Package, HyperChem 7.01; Hypercube, Inc.: Gainesville, FL, USA, 2002.

Chapter 2

[1] Putz, M.V.; Tudoran M.A. Bondonic effects on Topo-Reactivity of PAHs. Int. J. Chem. Model. 2014, 6(2-3), 311-346.
[2] Putz M.V., Ori O. Bondonic Chemistry: Physical Origins and Entanglement Prospects, In: Exotic Properties of Carbon Nanomatter: Advances in Physics and Chemistry. Mihai V. Putz, Ottorino Ori (Eds.), Springer Verlag, Dordrecht, NL, Chapter 10, 2015.
[3] Putz, M.V. The Bondons: The Quantum Particles of the Chemical Bond, Int. J. Mol. Sci. 2010, 11, 4227-4256.
[4] Tudoran M.A., Putz M.V. Molecular Graph Theory: From Adjacency Information to Colored Topology by Chemical Reactivity. Current Organic Chemistry 2015, in press.
[5] Putz M.V. Quantum Nanochemistry. A Fully Integrated Approach: Vol. V. Quantum Structure-Activity Relationships (Qu-SAR). Apple Academic Press and CRC Press, Toronto-New Jersey, Canada-USA. 2015.
[6] Putz M.V., Putz A.M. DFT Chemical Reactivity Driven by Biological Activity: Applications for the Toxicological Fate of Chlorinated PAHs. Struct. Bond. 2013, 150, 181–232.
[7] Putz M.V., Tudoran M.A., Putz A.M. Structure Properties and Chemical-Bio/Ecological of PAH Interactions: From Synthesis to Cosmic Spectral Lines, Nanochemistry, and Lipophilicity-Driven Reactivity. Curr. Org. Chem. 2013, 17, 2845-2871.
[8] Program Package, HyperChem 7.01; Hypercube, Inc.: Gainesville, FL, USA, 2002.

Chapter 3

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29, 107-130.
[6] Plavsić, D.; Trinajstić, N.; Klein, D. J. Clar Structures in Fractal Benzenoids. Croat. Chem. Acta 1992,

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13-131.
[14] Balaban, A. T. Partitioned-Formula Periodic Tables for Diamond Hydrocarbons (Diamondoids). J. Chem. Inf. Mod. 2012, 52, 2856-2863.
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[20] Schwertfeger, H.; Fokin, A. A.; Schreiner. Diamonds are a Chemist’s Best Friend: Diamondoid Chemistry Beyond Adamantane. Angew Chem., Intl. Edn. 2008, 47, 1022-1036.
[21] Semenov, S. G.; Sigolaev, F. Y.; Belyakov, A. V. Adamant-1,3,5-triyl Super Dodecahedranes. J. Struct. Chem. 2013, 54, 960-962.
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Functionalized Nanodiamonds Part I. An Experimental Assessment of Diamantane and Computational Predictions for Higher Diamondoids. Chem. Eur. J. 2005, 11, 7091-7101.
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Chapter 4

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Chapter 5

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Chapter 10

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Chapter 15

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Chapter 16

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Chapter 17

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Chapter 18

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Chapter 19

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Chapter 20

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Chapter 25

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