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Int. J. Mol. Sci., Volume 7, Issue 3 (March 2006) – 3 articles , Pages 71-110

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185 KiB  
Article
Dipole Correlation of the Electronic Structures of theConformations of Water Molecule Evolving Through theNormal Modes of Vibrations Between Angular (C2v) to Linear(D∝h) Shapes
by Dulal C. Ghosh and Arindam Chakraborty
Int. J. Mol. Sci. 2006, 7(3), 71-96; https://doi.org/10.3390/i7030071 - 17 Mar 2006
Cited by 6 | Viewed by 10958
Abstract
In order to settle the issue of equivalence or non-equivalence of the two lone pairsof electrons on oxygen atom in water molecule, a quantum chemical study of the dipolecorrelation of the electronic structure of the molecule as a function of conformationsgenerated following the [...] Read more.
In order to settle the issue of equivalence or non-equivalence of the two lone pairsof electrons on oxygen atom in water molecule, a quantum chemical study of the dipolecorrelation of the electronic structure of the molecule as a function of conformationsgenerated following the normal modes of vibrations between the two extremeconformations, C2v (∠HOH at 90o) and D∝h (∠HOH at 180o), including the equilibrium one,has been performed. The study invokes quantum mechanical partitioning of moleculardipoles into bond moment and lone pair moment and localization of delocalized canonicalmolecular orbitals, CMO’s into localized molecular orbitals, LMO’s. An earlier suggestion,on the basis of photoelectron spectroscopy, that one lone pair is in p-type and the other is ins-type orbital of O atom of water molecule at its equilibrium shape, and also the qualitative“Squirrel Ears” structure are brought under serious scrutiny. A large number ofconformations are generated and the charge density matrix, dipole moment of eachconformation is computed in terms of the generated canonical molecular orbitals, CMO’sand then Sinanoğlu’s localization method is invoked to localize the CMO’s of eachconformation and the quantum mechanical hybridizations of all the bonds and lone pairs onO center are evaluated in terms of the localized molecular orbitals. Computed datademonstrate that the electronic structures i.e. two bond pairs and two lone pairs and itshybridization status of all conformations of water molecule are straightforward in terms ofthe LMO’s. It is further revealed that the pattern of orbital hybridization changescontinuously as a function of evolution of molecular shape. The close analysis of thegenerated LMO’s reveals that one lone pair is accommodated in a pure p orbital and anotherlone pair is in a hybrid orbital in almost all conformations. One more important result of the present study is that, with the physical process of structural evolution from close angular shape to the linear transition state, the length of the σ (O–H) decreases and its strength increases as a monotone function of reaction coordinates. The bond length is shortest and the strength is largest at the transition state of structural inversion. Result of structural effect of the present study during the evolution of molecular conformations is quite consistent with the result of a very refined calculation that one physically significant feature of force field that the stretching force constants at the linear geometry are considerably larger than their equilibrium counter parts. The variation of bond strength and the hybridization of s and p orbitals on O atom center to form the σ (O–H) bond as a function of evolution of conformations is in accordance with Coulson’s prediction. The total dipole moment of all conformations is partitioned into the contribution from bonds and lone pairs and correlated in terms of the computed hybridization in lone pairs. The analysis of the variation of dipole moment as a function of angular to linear structural evolution reveals that the dipole moment of H2O molecule is not due to the bond moments only but a significant contribution comes from a lone pair. It is strongly established that the dipole moment of water molecule at and around the equilibrium geometry is not due to the bond moments only and the major part of the molecular dipole comes from the contribution of lone pair electrons. This necessitates the accommodation of a lone pair of electrons in a hybrid orbital on O atom. The computed LMO’s webbed with partitioned molecular dipole reveal that one lone pair is in a pure p- type orbital and the other lone pair is in a hybrid of s and p, and not in a pure s type orbital as suggested on the basis of photoelectron spectra. The possibility of qualitative “Squirrel Ears” structure is also ruled out. The problem of equivalence or non-equivalence of the two lone pairs of the O atom in water seems to have been finally resolved by the present quantum chemical calculation. An attempt of locating the origin of barrier to the physical process of inversion of water molecule is made in terms of energy partitioning method. It is found that the dipole can be used as a descriptor for the elucidation of electronic structure of molecules. Full article
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130 KiB  
Article
The Principle of Substance Stability Is Applicable to All Levels of Organization of Living Matter
by Georgi P. Gladyshev
Int. J. Mol. Sci. 2006, 7(3), 98-110; https://doi.org/10.3390/i7030098 - 29 Mar 2006
Cited by 10 | Viewed by 6749
Abstract
The principle of substance stability – the feedback principle – is applicable to allbiological systems. It boils down for different temporal hierarchies to the following: duringthe formation (self-assembly) of the most thermodynamically stable structures at the highesthierarchical level (j), e.g., the supramolecular level, [...] Read more.
The principle of substance stability – the feedback principle – is applicable to allbiological systems. It boils down for different temporal hierarchies to the following: duringthe formation (self-assembly) of the most thermodynamically stable structures at the highesthierarchical level (j), e.g., the supramolecular level, in accordance with the second law,Nature spontaneously uses predominantly the (available for the given local part of thebiological system) least thermodynamically stable structures belonging to a lower level, forexample, the molecular level (j-1). The principle can be also applied to understructurehierarchical levels of any temporal hierarchy. It helps in understanding the causes of cancerformation and the origin of some other diseases. Full article
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Correction
Study of Polymorph Prediction for L-Ascorbic Acid [Int. J. Mol. Sci. 2005, 6, 291-302]
by Ali Arslantas, Walter C. Ermler, Rahmi Yazici and Dilhan M. Kalyon
Int. J. Mol. Sci. 2006, 7(3), 97; https://doi.org/10.3390/i7030097 - 27 Mar 2006
Cited by 1 | Viewed by 5642
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