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Special Issue "The Chemical Bond and Bonding"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (1 May 2008)

Special Issue Information

The Guest Editor's Introduction to the Special Issue

Dear Colleagues,

cbb-logoYou may have noticed that 90 years have passed since the publication of the cornerstone and perplexing paper of Gilbert Newton Lewis (entitled The Atom and the Molecule, J. Am. Chem. Soc. 1916, 38, 762) from where the quantum chemistry begins it own quest for the elucidation of the nature of chemical bond and bonding. This is the historical argument, a celebration year for chemical bonding, a moment of re-thinking about it.

An epistemological argument can be also formulated. As physical sciences seek the Grand Unifications of the existing Forces in Nature, a similar endeavor seems appropriate in Chemistry as well, since all manifest modes of bonding may be seen as facets of a basic chemical bonding content of different degrees of action, in different contexts and environments.

Then, recently, many exotic chemical situations have been reported, such as sextupole bonds, nano- and bio-molecules and aggregates that need both conceptual and computational explanations. The increased need of molecular design for assessing biotargets through pharmacophores, the practical demands of predictions of acute toxicity of medicines and environmental waste compounds, all these actual realities of chemistry in both its principles and applications deserve a special forum.

Finally, among other reputed journals similar projects have also appeared, thus underlying the importance in revisiting or reviewing the actual modes of bonding. Worth note is the recent 500-page special issue of the Journal of Computational Chemistry (JCC) of January 2007 (www3.interscience.wiley.com/cgi-bin/jissue/113493174).

For all these reasons I strongly believe that a special IJMS issue dedicated to CHEMICAL BOND AND BONDING would be highly appreciated by both theorists and experimentalists exploring the chemical state (for the BOND appellative) and reactivity (for the BONDING one).

On a personal ground I am fully engaged in scientific projects concerning unification of chemical bonding modes through quantum principles and indices. In this respect I bring to your attention my recent invited book chapter “Unifying absolute and chemical electronegativity and hardness density functional formulations through the chemical action concept”, in “Progress in Quantum Chemistry Research”; Erik O. Hoffman (ed.); Nova Publishers: New York, 2007 (in press); (www.novapublishers.com/catalog/product_info.php?products_id=5571) as well my invited expert commentary: “Can quantum-mechanical description of chemical bond be considered complete?”, in “Quantum Chemistry Research Trends”, Mikas P. Kaisas (ed.); Nova Publishers: New York 2007 (in press); (www.novapublishers.com/catalog/product_info.php?products_id=5570).

Therefore, in order to create a high quality platform for communication on the topic, I invite you to actively contribute to the special issue on “The Chemical Bond and Bonding”. As Guest Editor I am ready to examine in-depth all papers submitted for this volume and to provide my remarks to improve them for best publication.

Kind regards,
Dr. Mihai V. Putz

Leading Review Papers:

  1. Lewis, G.N. The Atom and the Molecule. J. Am. Chem. Soc. 1916, 38, 762-785.
  2. Pauling, L. The Nature of the Chemical Bond. III. The Transition from One Extreme Bond Type to Another. J. Am. Chem. Soc. 1932, 54, 988-1003.
  3. Feynman, R.P. Forces in Molecules. Phys. Rev. 1939, 56, 340-343.
  4. Hohenberg, P.; Kohn, W. Inhomogeneous Electronic Gas. Phys. Rev. 1964, 136, B864-B871.
  5. Kohn, W.; Sham, L.J. Self-Consistent Equations Including Exchange and Correlation Effects. Phys. Rev. 1965, 140, A1133-A1138.
  6. Deb, B.M. The Force Concept in Chemistry. Rev. Mod. Phys. 1973, 45, 22-43.
  7. Bamzai, A.S.; Deb, B.M. The Role of Single-Particle Density in Chemistry. Rev. Mod. Phys. 1981, 53, 95-126.
  8. Kohn, W.; Becke, A.D.; Parr, R.G. Density Functional Theory of Electronic Structure. J. Phys. Chem. 1996, 100, 12974-12980.
  9. Krokidis, X.; Noury, S.; Silvi, B. Characterization of Elementary Chemical Processes by Catastrophe Theory. J. Phys. Chem. A 1997, 101, 7277-7282.
  10. Bürgi, H.B. Structure Correlation and Chemistry. Acta Cryst. 1998, A54, 873-885.
  11. Le Guennec, P. Towards a Theory of Molecular Recognition. Theor. Chem. Acc. 1999, 101, 151-158.
  12. Ayers, P.W.; Parr, R.G. Variational Principles for Describing Chemical Reactions: The Fukui Function and Chemical Hardness Revisited. J. Am. Chem. Soc. 2000, 122, 2010-2018.
  13. Ayers, P.W.; Parr, R.G. Variational Principles for Describing Chemical Reactions. Reactivity Indices Based on the External Potential. J. Am. Chem. Soc. 2001, 123, 2007-2017.
  14. Ghosh, D.C.; Biswas, R. Theoretical Calculation of Absolute Radii of Atoms and Ions. Part 1. The Atomic Radii. Int. J. Mol. Sci. 2002, 3, 87-113.
  15. Pérez, P.; Andrés, J.; Safont, V.S.; Tapia, O.; Contreras, R. Spin-Philicity and Spin-Donicity as Auxiliary Concepts to Quantify Spin-Catalysis Phenomena. J. Phys. Chem. A 2002, 106, 5353-5357.
  16. Politzer, P.; Lane, P.; Concha, M.C. Atomic and Molecular Energies in Terms of Electrostatic Potentials at Nuclei. Int. J. Quantum Chem. 2002, 90, 459-463.
  17. Nalewajski, R.F. Applications of the Information Theory to Problems of Molecular Electronic Structure and Chemical Reactivity. Int. J. Mol. Sci. 2002, 3, 237-259.
  18. March, N.H. Classic Ionic Crystals and Quantal Wigner Electron Solids: Role of Electron Correlation. Int. J. Quantum Chem. 2003, 92, 11-21
  19. Bian, Q.; Talman, J.D. Method for Evaluation of Density Functional Integrals in Molecular Calculations. Theor. Chem. Acc. 2004, 112, 141-144.
  20. Genoni, A.; Sironi, M. A Novel Approach to Relax Extremely Localized Molecular Orbitals: The Extremely Localized Molecular Orbital-Valence Bond Method. Theor. Chem. Acc. 2004, 112, 254-262.
  21. Kędzierski, P.; Wielgus, P.; Sikora, A.; Sokalski, W.A.; Leszczyński, J. Visualization of the Differential Transition State Stabilization within the Active Site Environment. Int. J. Mol. Sci. 2004, 5, 186-195.
  22. Tomasi, J. Thirty Years of Continuum Solvation Chemistry: A Review, and Prospects for the Near Future. Theor. Chem. Acc. 2004, 112, 184-203.
  23. Putz, M.V. Markovian Approach of the Electron Localization Functions. Int. J. Quantum Chem. 2005, 105, 1-11.
  24. Bredow, T.; Jug, K. Theory and Range of Modern Semiempirical Molecular Orbital Methods. Theor. Chem. Acc. 2005, 113, 1-14.
  25. Yesylevskyy, S.O.; Kharkyanen, V.N.; Demchenko, A.P. Hierarchical Clustering of the Correlation Patterns: New Method of Domain Identification in Proteins. Biophys. Chem. 2006, 119, 84-93.
  26. Putz, M.V. Systematic Formulation for Electronegativity and Hardness and Their Atomic Scales within Density Functional Softness Theory. Int. J. Quantum Chem. 2006, 106, 361-389.
  27. Putz, M.V. Semiclassical Electronegativity and Chemical Hardness. J. Theor. Comp. Chem. 2007, 6, 33-47.
  28. Bader, R.F.W.; Hernández-Trujillo, J.; Cortés-Guzmán, F. Chemical Bonding: From Lewis to Atoms in Molecules. J. Comput. Chem. 2007, 28, 4-14.
  29. Kutzelnigg, W. What I Like About Hückel Theory. J. Comput. Chem. 2007, 28, 25-34.
  30. Alabugin, I.V.; Manoharan, M. Rehybridization as a General Mechanism for Maximizing Chemical and Supramolecular Bonding and a Driving Force for Chemical Reactions. J. Comput. Chem. 2007, 28, 373-390.

Keywords

  • Ab initio methods
  • atoms-in-molecule methods
  • biological interaction
  • biomolecules
  • Born-Oppenheimer and Non-Born-Oppenheimer modes
  • catalysis
  • chemical action
  • chemical education in treating bonding
  • chemical hardness
  • clusters
  • configuration interaction
  • covalent bond
  • density functional theory
  • electron deficient molecules
  • electronegativity
  • electronic localization
  • enzymic interactions
  • frontier orbitals
  • fukui function
  • gas-phase and solvent reactions
  • Hartree-Fock theory
  • history of chemical bond
  • Hückel methods
  • hybridization schemes
  • hydrogen bond
  • hypervalences
  • interfaces
  • ionic bond
  • lone and pair electrons
  • macromolecules
  • meaning of chemical bond
  • metallic bond
  • molecular orbitals
  • molecular quantum information
  • nanosystems
  • natural orbitals
  • nature of chemical bond
  • octet rule
  • orthogonalization schemes
  • population analysis
  • principles of chemical hardness
  • principles of electronegativity
  • quantitative structure-activity relationships
  • quantitative structure-property relationships
  • quantum partition of molecules
  • quantum topology of molecules
  • reactivity principles
  • self-consistent field
  • semiempirical methods
  • softness
  • solid state reactions
  • unification of the chemical modes of bonding
  • valence

Related Special Issue

Published Papers (10 papers)

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Research

Jump to: Review

Open AccessCommunication Anomalously Strong Effect of the Ion Sign on the Thermochemistry of Hydrogen Bonded Aqueous Clusters of Identical Chemical Composition
Int. J. Mol. Sci. 2009, 10(2), 507-517; doi:10.3390/ijms10020507
Received: 23 May 2008 / Revised: 5 January 2009 / Accepted: 7 January 2009 / Published: 5 February 2009
Cited by 8 | PDF Full-text (309 KB) | HTML Full-text | XML Full-text
Abstract
The sign preference of hydrogen bonded aqueous ionic clusters Χ±(H2O)i(n =1-5, Χ = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large
[...] Read more.
The sign preference of hydrogen bonded aqueous ionic clusters Χ±(H2O)i (n =1-5, Χ = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large difference in formation free energies between cations and anions of identical chemical composition. The effect of vibrational anharmonicity on stepwise Gibbs free energy changes has been investigated, and possible uncertainties associated with the harmonic treatment of vibrational spectra have been discussed. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessCommunication Effect of Ammonia on the Gas-Phase Hydration of the Common Atmospheric Ion HSO4-
Int. J. Mol. Sci. 2008, 9(11), 2184-2193; doi:10.3390/ijms9112184
Received: 23 May 2008 / Revised: 20 October 2008 / Accepted: 23 October 2008 / Published: 7 November 2008
Cited by 17 | PDF Full-text (408 KB) | HTML Full-text | XML Full-text
Abstract
Hydration directly affects the mobility, thermodynamic properties, lifetime and nucleation rates of atmospheric ions. In the present study, the role of ammonia on the formation of hydrogen bonded complexes of the common atmospheric hydrogensulfate (HSO4-) ion with water has been
[...] Read more.
Hydration directly affects the mobility, thermodynamic properties, lifetime and nucleation rates of atmospheric ions. In the present study, the role of ammonia on the formation of hydrogen bonded complexes of the common atmospheric hydrogensulfate (HSO4-) ion with water has been investigated using the Density Functional Theory (DFT). Our findings rule out the stabilizing effect of ammonia on the formation of negatively charged cluster hydrates and show clearly that the conventional (classical) treatment of ionic clusters as presumably more stable compared to neutrals may not be applicable to pre-nucleation clusters. These considerations lead us to conclude that not only quantitative but also qualitative assessment of the relative thermodynamic stability of atmospheric clusters requires a quantum-chemical treatment. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Figures

Open AccessArticle Lix@C60: Calculations of the Encapsulation Energetics and Thermodynamics
Int. J. Mol. Sci. 2008, 9(9), 1841-1850; doi:10.3390/ijms9091841
Received: 30 July 2008 / Revised: 8 August 2008 / Accepted: 15 August 2008 / Published: 17 September 2008
Cited by 5 | PDF Full-text (695 KB) | HTML Full-text | XML Full-text
Abstract
Li@C60 and Li@C70 can be prepared and thus, their calculations at higher levels of theory are also of interest. In the report, the computations are carried out on Li@C60, Li2@C60 and Li3@C60 with the B3LYP
[...] Read more.
Li@C60 and Li@C70 can be prepared and thus, their calculations at higher levels of theory are also of interest. In the report, the computations are carried out on Li@C60, Li2@C60 and Li3@C60 with the B3LYP density-functional theory treatment in the standard 3-21G and 6-31G* basis sets. The computed energetics suggests that Lix@C60 species may be produced for a few small x values if the Li pressure is enhanced sufficiently. In order to check the suggestion, a deeper computational evaluation of the encapsulation thermodynamics is carried out. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessArticle Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition
Int. J. Mol. Sci. 2008, 9(9), 1652-1664; doi:10.3390/ijms9091652
Received: 14 February 2008 / Revised: 28 July 2008 / Accepted: 28 August 2008 / Published: 2 September 2008
Cited by 1 | PDF Full-text (319 KB) | HTML Full-text | XML Full-text
Abstract
In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I) and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT) terms, was introduced
[...] Read more.
In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I) and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT) terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5) with net attractive effects and Arg1 (with a net repulsive effect), responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessArticle Bonding in Mercury-Alkali Molecules: Orbital-driven van der Waals Complexes
Int. J. Mol. Sci. 2008, 9(6), 926-942; doi:10.3390/ijms9060926
Received: 29 April 2008 / Revised: 2 June 2008 / Accepted: 2 June 2008 / Published: 2 June 2008
Cited by 5 | PDF Full-text (481 KB) | HTML Full-text | XML Full-text
Abstract
The bonding situation in mercury-alkali diatomics HgA (2Σ+) (A = Li, Na, K, Rb) has been investigated employing the relativistic all-electron method Normalized Elimination of the Small Component (NESC), CCSD(T), and augmented VTZ basis sets. Although Hg,A interactions are
[...] Read more.
The bonding situation in mercury-alkali diatomics HgA (2Σ+) (A = Li, Na, K, Rb) has been investigated employing the relativistic all-electron method Normalized Elimination of the Small Component (NESC), CCSD(T), and augmented VTZ basis sets. Although Hg,A interactions are typical of van der Waals complexes, trends in calculated De values can be explained on the basis of a 3-electron 2-orbital model utilizing calculated ionization potentials and the De values of HgA+(1Σ+) diatomics. HgA molecules are identified as orbital-driven van der Waals complexes. The relevance of results for the understanding of the properties of liquid alkali metal amalgams is discussed. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessArticle Closing in on Chemical Bonds by Opening up Relativity Theory
Int. J. Mol. Sci. 2008, 9(3), 272-298; doi:10.3390/ijms9030272
Received: 4 December 2007 / Revised: 15 February 2008 / Accepted: 26 February 2008 / Published: 12 March 2008
Cited by 5 | PDF Full-text (904 KB) | HTML Full-text | XML Full-text
Abstract
This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization
[...] Read more.
This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization potentials in elements. Striking patterns in ionization potentials are revealed when the data are viewed in an element-independent way, where element-specific details are removed via an appropriate scaling law. The scale factor involved is not explained by quantum mechanics; it is revealed only when one goes back further, to the development of Einstein’s special relativity theory. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessArticle Chromatographic Retention Times of Polychlorinated Biphenyls: from Structural Information to Property Characterization
Int. J. Mol. Sci. 2007, 8(11), 1125-1157; doi:10.3390/i8111125
Received: 16 August 2007 / Revised: 9 November 2007 / Accepted: 13 November 2007 / Published: 22 November 2007
Cited by 19 | PDF Full-text (372 KB) | HTML Full-text | XML Full-text
Abstract
The paper presents a unitary approach of the use of a Molecular DescriptorsFamily in structure-property/activity relationships, particularly in modelling thechromatographic retention times of polychlorinated biphenyls. Starting from molecularstructure, viewed as a graph, and considering the bonds and bond types, atom types andoften the
[...] Read more.
The paper presents a unitary approach of the use of a Molecular DescriptorsFamily in structure-property/activity relationships, particularly in modelling thechromatographic retention times of polychlorinated biphenyls. Starting from molecularstructure, viewed as a graph, and considering the bonds and bond types, atom types andoften the 3D geometry of the molecule, a huge family of molecular descriptors called MDFwas calculated. A preliminary selection of MDF members was done by simple linearregression (LR) against the measured property. The best fitted MDF subset is thensubmitted to multivariate linear regression (MLR) analysis in order to find the best pairs ofMDF members that produce a reliable QSPR (Quantitative Structure-PropertyRelationship) model. The predictive capability was finally tested by randomly splitting ofdata into training and test sets. The best obtained models are presented and the results arediscussed. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessArticle Three Dimensional Pharmacophore Modelling of Monoamine oxidase-A (MAO-A) inhibitors
Int. J. Mol. Sci. 2007, 8(9), 894-919; doi:10.3390/i8090894
Received: 2 May 2007 / Revised: 25 July 2007 / Accepted: 30 July 2007 / Published: 3 September 2007
PDF Full-text (874 KB) | HTML Full-text | XML Full-text
Abstract
Flavoprotein monoamine oxidase is located on the outer membrane ofmitochondria. It catalyzes oxidative deamination of monoamine neurotransmitters such asserotonin, norepinephrine and dopamine and hence is a target enzyme for antidepressantdrugs. MAO (mono amine oxidase) has two isoforms, namely MAO-A and MAO-B.MAO-A isoform has
[...] Read more.
Flavoprotein monoamine oxidase is located on the outer membrane ofmitochondria. It catalyzes oxidative deamination of monoamine neurotransmitters such asserotonin, norepinephrine and dopamine and hence is a target enzyme for antidepressantdrugs. MAO (mono amine oxidase) has two isoforms, namely MAO-A and MAO-B.MAO-A isoform has higher affinity for serotonin and norepinephrine, while; MAO-Bpreferentially deaminates phenylethylamine and benzylamine. These important propertiesdetermine the clinical importance of MAO inhibitors. Selective MAO-A inhibitors are usedin the treatment of neurological disorders such as depression. In this article we havedeveloped a Hypogen pharmacophore for a set of 64 coumarin analogs and tried to analyzethe intermolecular H-bonds with receptor structure. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)

Review

Jump to: Research

Open AccessReview Chemical Interactions and Their Role in the Microphase Separation of Block Copolymer Thin Films
Int. J. Mol. Sci. 2009, 10(9), 3671-3712; doi:10.3390/ijms10093671
Received: 6 August 2009 / Accepted: 14 August 2009 / Published: 25 August 2009
Cited by 58 | PDF Full-text (5091 KB) | HTML Full-text | XML Full-text
Abstract
The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are
[...] Read more.
The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) systems. BCP systems self-assemble via a thermodynamic driven process where chemical dis-affinity between the blocks driving them part is balanced by a restorative force deriving from the chemical bond between the blocks. These systems are attracting much interest because of their possible role in nanoelectronic fabrication. This form of self-assembly can obtain highly regular nanopatterns in certain circumstances where the orientation and alignment of chemically distinct blocks can be guided through molecular interactions between the polymer and the surrounding interfaces. However, for this to be possible, great care must be taken to properly engineer the interactions between the surfaces and the polymer blocks. The optimum methods of structure directing are chemical pre-patterning (defining regions on the substrate of different chemistry) and graphoepitaxy (topographical alignment) but both centre on generating alignment through favourable chemical interactions. As in all self-assembling systems, the problems of defect formation must be considered and the origin of defects in these systems is explored. It is argued that in these nanostructures equilibrium defects are relatively few and largely originate from kinetic effects arising during film growth. Many defects also arise from the confinement of the systems when they are ‘directed’ by topography. The potential applications of these materials in electronics are discussed. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)
Open AccessReview Density Functionals of Chemical Bonding
Int. J. Mol. Sci. 2008, 9(6), 1050-1095; doi:10.3390/ijms9061050
Received: 30 April 2008 / Revised: 9 June 2008 / Accepted: 10 June 2008 / Published: 26 June 2008
Cited by 29 | PDF Full-text (728 KB) | HTML Full-text | XML Full-text
Abstract
The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps
[...] Read more.
The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. Full article
(This article belongs to the Special Issue The Chemical Bond and Bonding)

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