E-Mail Alert

Add your e-mail address to receive forthcoming issues of this journal:

Journal Browser

Journal Browser

Special Issue "Atoms in Molecules and in Nanostructures"

Quicklinks

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 (31 October 2012)

Special Issue Editor

Guest Editor
Dr. Dr.-Habil. Mihai V. Putz (Website)

Associate Professor of Theoretical Physical Chemistry, Biology-Chemistry Department & PhD School of Chemistry - West University of Timisoara, Str. Pestalozzi No. 16, Timisoara, RO-300115, Romania & Principal Investigator of Nanochemistry, Laboratory of Renewable Energy – Photovoltaics, National Institute of Research and Development in Electrochemistry and Condensed Matter Timișoara (INCEMC), Romania; Str. Dr. A. Păunescu Podeanu, no.144, Timişoara RO-300569, Romania
Fax: +40 256 592620
Interests: quantum physical chemistry; nanochemistry; reactivity indices and principles; electronegativity; density functional theory; path integrals; enzyme kinetics; QSAR; epistemology and philosophy of science

Special Issue Information

Dear Colleagues,

Due to the ever increasing focus on modeling the chemical structures based on electrons-in-atoms quantum character, the recent achievements give credit to the necessity of generalization of the fashioned valence paradigm of the chemical bond at various many-electronic manifestations of matter, from atoms, to molecules, to nanostructures.

Reviewing only some of the pre-eminent examples worth noting the sigmatropic shiftamers (a kind of polymers in which the σ and π bonds are migrating back and forth along the hydrocarbon framework); the charge-shift bonding concept – a new binding class between the electronic pairs somehow different from the ionic and covalent traditional ones in the sense that it is seen as a kind of their resonance as it appears in the molecular systems like F2, O2, N2 (with impact in the environmental chemistry) or in polar compounds like C-F (specific to ecotoxicology) or in the reactions that imply a competition between the exchange in the hydrogen or halogen (e.g. HF); the typical quantum results that have been recorded in the biosynthesis of antibiotics; the aromaticity feature of molecules and macro-molecules, now extended to the nanostructures. All these cutting-edge cases of molecular sciences, along many others relating the chemical structure and reactivity have to find their proper atomic based quantum pattern for being controlled and designed as the society demanding bio-, eco- or pharmaco- logical actions.

This is why the present IJMS special issue dedicated on how “atoms in molecules and atoms in nanostructures” synergistically behave toward chemical reactivity and biological activity is equally envisaged for presenting the most advanced computational and/or experimental works reporting and/or modeling new or fundamental/paradigmatic molecules and nanostructures. It aims to steep across Mathematical, Physical and Quantum Chemistry tools for providing a unified view of the atomic manifestation in molecule and nanostructure realms.

Dr. Mihai V. Putz
Guest Editor

Keywords

  • atoms-in-molecules
  • chemical bonding
  • nanostructures
  • reactivity indices
  • topological indices
  • crystallography
  • computational chemistry
  • molecular and nanostructure design
  • nanostructure synthesis
  • aromaticity

Published Papers (9 papers)

View options order results:
result details:
Displaying articles 1-9
Export citation of selected articles as:

Research

Open AccessArticle Spectral Inverse Quantum (Spectral-IQ) Method for Modeling Mesoporous Systems: Application on Silica Films by FTIR
Int. J. Mol. Sci. 2012, 13(12), 15925-15941; doi:10.3390/ijms131215925
Received: 26 September 2012 / Revised: 19 November 2012 / Accepted: 22 November 2012 / Published: 28 November 2012
Cited by 8 | PDF Full-text (560 KB) | HTML Full-text | XML Full-text
Abstract
The present work advances the inverse quantum (IQ) structural criterion for ordering and characterizing the porosity of the mesosystems based on the recently advanced ratio of the particle-to-wave nature of quantum objects within the extended Heisenberg uncertainty relationship through employing the quantum [...] Read more.
The present work advances the inverse quantum (IQ) structural criterion for ordering and characterizing the porosity of the mesosystems based on the recently advanced ratio of the particle-to-wave nature of quantum objects within the extended Heisenberg uncertainty relationship through employing the quantum fluctuation, both for free and observed quantum scattering information, as computed upon spectral identification of the wave-numbers specific to the maximum of absorption intensity record, and to left-, right- and full-width at the half maximum (FWHM) of the concerned bands of a given compound. It furnishes the hierarchy for classifying the mesoporous systems from more particle-related (porous, tight or ionic bindings) to more wave behavior (free or covalent bindings). This so-called spectral inverse quantum (Spectral-IQ) particle-to-wave assignment was illustrated on spectral measurement of FT-IR (bonding) bands’ assignment for samples synthesized within different basic environment and different thermal treatment on mesoporous materials obtained by sol-gel technique with n-dodecyl trimethyl ammonium bromide (DTAB) and cetyltrimethylammonium bromide (CTAB) and of their combination as cosolvents. The results were analyzed in the light of the so-called residual inverse quantum information, accounting for the free binding potency of analyzed samples at drying temperature, and were checked by cross-validation with thermal decomposition techniques by endo-exo thermo correlations at a higher temperature. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Figures

Open AccessArticle Errors in the Calculation of 27Al Nuclear Magnetic Resonance Chemical Shifts
Int. J. Mol. Sci. 2012, 13(11), 15420-15446; doi:10.3390/ijms131115420
Received: 10 October 2012 / Revised: 2 November 2012 / Accepted: 6 November 2012 / Published: 21 November 2012
Cited by 4 | PDF Full-text (2386 KB) | HTML Full-text | XML Full-text
Abstract
Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III) in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was [...] Read more.
Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III) in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was evaluated by comparing the calculated and experimental chemical shifts in more than one hundred aluminum(III) complexes. In order to differentiate the error due to the chemical shielding tensor calculation from that due to the inadequacy of the molecular geometry prediction, single-crystal X-ray diffraction determined structures were used to build the isolated molecule models for calculating the chemical shifts. The results were compared with those obtained using the calculated geometries at the B3LYP/6-31G(d) level. The isotropic chemical shielding constants computed at different levels have strong linear correlations even though the absolute values differ in tens of ppm. The root-mean-square difference between the experimental chemical shifts and the calculated values is approximately 5 ppm for the calculations based on the X-ray structures, but more than 10 ppm for the calculations based on the computed geometries. The result indicates that the popular theoretical models are adequate in calculating the chemical shifts while an accurate molecular geometry is more critical. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Figures

Open AccessArticle On the Electrophilic Character of Molecules Through Its Relation with Electronegativity and Chemical Hardness
Int. J. Mol. Sci. 2012, 13(2), 2160-2175; doi:10.3390/ijms13022160
Received: 31 December 2011 / Revised: 6 February 2012 / Accepted: 7 February 2012 / Published: 17 February 2012
Cited by 10 | PDF Full-text (245 KB) | HTML Full-text | XML Full-text
Abstract
Electrophilicity is an intrinsic property of atoms and molecules. It probably originates logistically with the involvement in the physical process of electrostatics of soaked charge in electronic shells and the screened nuclear charge of atoms. Motivated by the existing view of conceptual [...] Read more.
Electrophilicity is an intrinsic property of atoms and molecules. It probably originates logistically with the involvement in the physical process of electrostatics of soaked charge in electronic shells and the screened nuclear charge of atoms. Motivated by the existing view of conceptual density functional theory that similar to electronegativity and hardness equalization, there should be a physical process of equalization of electrophilicity during the chemical process of formation of hetero nuclear molecules, we have developed a new theoretical scheme and formula for evaluating the electrophilicity of hetero nuclear molecules. A comparative study with available bench marking reveals that the hypothesis of electrophilicity and equalization, and the present method of evaluating equalized electrophilicity, are scientifically promising. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Open AccessArticle On the Several Molecules and Nanostructures of Water
Int. J. Mol. Sci. 2012, 13(1), 1066-1094; doi:10.3390/ijms13011066
Received: 30 September 2011 / Revised: 4 January 2012 / Accepted: 5 January 2012 / Published: 19 January 2012
PDF Full-text (353 KB) | HTML Full-text | XML Full-text
Abstract
This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for [...] Read more.
This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Open AccessArticle QSAR Study and Molecular Design of Open-Chain Enaminones as Anticonvulsant Agents
Int. J. Mol. Sci. 2011, 12(12), 9354-9368; doi:10.3390/ijms12129354
Received: 15 September 2011 / Revised: 7 November 2011 / Accepted: 24 November 2011 / Published: 14 December 2011
Cited by 32 | PDF Full-text (262 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling [...] Read more.
Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling approaches are applied with the purpose of comparing the consistency of our results: (a) the search of molecular descriptors via multivariable linear regressions; and (b) the calculation of flexible descriptors with the CORAL (CORrelation And Logic) program. Among the results found, we propose some potent candidate open-chain enaminones having ED50 values lower than 10 mg·kg−1 for corresponding pharmacological studies. These compounds are classified as Class 1 and Class 2 according to the Anticonvulsant Selection Project. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Open AccessArticle Topological Anisotropy of Stone-Wales Waves in Graphenic Fragments
Int. J. Mol. Sci. 2011, 12(11), 7934-7949; doi:10.3390/ijms12117934
Received: 31 August 2011 / Revised: 24 October 2011 / Accepted: 7 November 2011 / Published: 15 November 2011
Cited by 12 | PDF Full-text (462 KB) | HTML Full-text | XML Full-text
Abstract
Stone-Wales operators interchange four adjacent hexagons with two pentagon-heptagon 5|7 pairs that, graphically, may be iteratively propagated in the graphene layer, originating a new interesting structural defect called here Stone-Wales wave. By minimization, the Wiener index topological invariant evidences a marked anisotropy [...] Read more.
Stone-Wales operators interchange four adjacent hexagons with two pentagon-heptagon 5|7 pairs that, graphically, may be iteratively propagated in the graphene layer, originating a new interesting structural defect called here Stone-Wales wave. By minimization, the Wiener index topological invariant evidences a marked anisotropy of the Stone-Wales defects that, topologically, are in fact preferably generated and propagated along the diagonal of the graphenic fragments, including carbon nanotubes and graphene nanoribbons. This peculiar edge-effect is shown in this paper having a predominant topological origin, leaving to future experimental investigations the task of verifying the occurrence in nature of wave-like defects similar to the ones proposed here. Graph-theoretical tools used in this paper for the generation and the propagation of the Stone-Wales defects waves are applicable to investigate isomeric modifications of chemical structures with various dimensionality like fullerenes, nanotubes, graphenic layers, schwarzites, zeolites. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Figures

Open AccessArticle First Principles Study on the Electronic Properties of Zn64Sb64−xTex Solid Solution (x = 0, 2, 3, 4)
Int. J. Mol. Sci. 2011, 12(5), 3162-3169; doi:10.3390/ijms12053162
Received: 29 March 2011 / Revised: 25 April 2011 / Accepted: 4 May 2011 / Published: 13 May 2011
Cited by 4 | PDF Full-text (396 KB) | HTML Full-text | XML Full-text
Abstract
The electronic properties of Te doped-ZnSb systems are investigated by first-principles calculations. We focus on the Zn64Sb64−xTex systems (x = 0, 2, 3, 4), which respond to the 0, 1.56at%, 2.34at% and 3.12at% of Te [...] Read more.
The electronic properties of Te doped-ZnSb systems are investigated by first-principles calculations. We focus on the Zn64Sb64−xTex systems (x = 0, 2, 3, 4), which respond to the 0, 1.56at%, 2.34at% and 3.12at% of Te doping concentration. We confirm that the amount of Te doping will change the conductivity type of ZnSb. In the cases of x = 2 and 3, we find that the Te element in ZnSb introduces some bands originating from Te s and p orbits and a donor energy level in the bottom of the conduction band, which induce the n-type conductivity of ZnSb. From these findings for the electronic structure and the conductivity mechanism, we predict that Te doping amounts such as 1.56at% and 2.34at% can be considered as suitable candidates for use as donor dopant. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Open AccessArticle The Bondons: The Quantum Particles of the Chemical Bond
Int. J. Mol. Sci. 2010, 11(11), 4227-4256; doi:10.3390/ijms11114227
Received: 23 August 2010 / Revised: 11 October 2010 / Accepted: 21 October 2010 / Published: 28 October 2010
Cited by 18 | PDF Full-text (509 KB) | HTML Full-text | XML Full-text
Abstract
By employing the combined Bohmian quantum formalism with the U(1) and SU(2) gauge transformations of the non-relativistic wave-function and the relativistic spinor, within the Schrödinger and Dirac quantum pictures of electron motions, the existence of the chemical field is revealed along the [...] Read more.
By employing the combined Bohmian quantum formalism with the U(1) and SU(2) gauge transformations of the non-relativistic wave-function and the relativistic spinor, within the Schrödinger and Dirac quantum pictures of electron motions, the existence of the chemical field is revealed along the associate bondon particle  characterized by its mass (mΒ), velocity (vΒ), charge (eΒ), and life-time (tΒ). This is quantized either in ground or excited states of the chemical bond in terms of reduced Planck constant ħ, the bond energy Ebond and length Xbond, respectively. The mass-velocity-charge-time quaternion properties of bondons’ particles were used in discussing various paradigmatic types of chemical bond towards assessing their covalent, multiple bonding, metallic and ionic features. The bondonic picture was completed by discussing the relativistic charge and life-time (the actual zitterbewegung) problem, i.e., showing that the bondon equals the benchmark electronic charge through moving with almost light velocity. It carries negligible, although non-zero, mass in special bonding conditions and towards observable femtosecond life-time as the bonding length increases in the nanosystems and bonding energy decreases according with the bonding length-energy relationship Ebond[kcal/mol]*Xbond[A]=182019, providing this way the predictive framework in which the particle may be observed. Finally, its role in establishing the virtual states in Raman scattering was also established. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Figures

Open AccessArticle Compactness Aromaticity of Atoms in Molecules
Int. J. Mol. Sci. 2010, 11(4), 1269-1310; doi:10.3390/ijms11041269
Received: 26 January 2010 / Revised: 8 March 2010 / Accepted: 8 March 2010 / Published: 26 March 2010
Cited by 12 | PDF Full-text (567 KB) | HTML Full-text | XML Full-text
Abstract
A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing [...] Read more.
A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a03 for Hydrogen is provided, where a0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules). With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Figures

Journal Contact

MDPI AG
IJMS Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
ijms@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to IJMS
Back to Top