By moving away from the traditional reductionist reading of the quantum theory of atoms in molecules (QTAIM), in this paper we analyze the role played by QTAIM in the relationship between molecular ...chemistry and quantum mechanics from an emergentist perspective. In particular, we show that such a relationship involves two steps: an
intra
-
domain emergence
and an
inter
-
domain emergence
. Intra-domain emergence, internal to quantum mechanics, results from the fact that the electron density, from which all the other QTAIM’s concepts are defined, arises from the wavefunction as a coarse-grained magnitude. Inter-domain emergence involves an analogical link, a mapping, between QTAIM’s entities, such as topological atoms and bond paths, and the entities that populate the molecular-chemistry domain, such as chemical atoms and chemical bonds.
The possibility and mechanism of water desalination using newly designed doped graphene sheets is reported. It is hereby demonstrated, through molecular dynamics (MD) simulations, that an electric ...field-assisted selective ion separation is possible using boron- and nitrogen-doped nano-porous graphene sheets. The sheets are shown to behave as nano-sponges, with potential future applications in water desalination by electrodialysis, for example. Ion separation is found to increase as the extent of ion hydration decreases under increasing field strengths. Boron- and nitrogen-doped graphene sheets are found to exhibit acceptable mechanical properties and, simultaneously, good ion selectivities and that they may be candidates for future technological applications in desalination and other refining processes.
•Water desalination through NEMD simulations for electrodialysis process is studied.•Newly designed B and N doped graphene sheet is investigated for salt rejection.•Doped graphene sheets exhibit acceptable Young's Modulus and mechanical properties.•Force, velocity and RDF of species under external electrical field are calculated.•It is shown doped graphene demonstrate well candidate for desalination technology.
Long before the phrases “climate change” and “butterfly effect” were incorporated into the mainstream literature, these phrases appeared in an appropriate context almost verbatim in the first Chapter ...of a book entitled “The Emigrant” published in the mid-nineteenth century (in
1846
) by Sir Francis Bond Head (1793–1875). Head was Upper Canada’s sixth Lieutenant Governor under King George IV and Queen Victoria. Head claimed that forest wildfires were “
changing the climate
” of North America as manifested in a warming effect “
on the thermometer
”. In that author’s account, these fires were provoked by First Nations to create fly-free zones meant to attract game that they could then hunt more readily. Head used language such as “
swarms of little flies, strange as it may sound, are, and for many years have been, most materially altering the climate…
” which is remarkably reminiscent of E. N. Lorenz’s (1917–2008) “butterfly effect” of the theory of chaotic dynamical systems. The historical context and the rationales that may have led Head to use this contemporary environmental language in a proper context are briefly discussed.
There is a need for an
a priori method with which to demonstrate the physical similarities between non-classical bioisosteres. In this study we explore the utility of the electron density and the ...electrostatic potential as the basis for a systematic investigation of the physical and chemical similarities between bioisosteres. The tetrazole and carboxylate bioisosteric pair is used as an illustrative example. It is shown that tetrazole and carboxylate anions give rise to electrostatic potentials (ESP) that exhibit a remarkable local similarity in the disposition of four coplanar local minima at positions consistent with lone pairs. The similarity of the disposition of these ESP minima generated by the two bioisosteres is in sharp contrast with their differences in the number and types of atoms, their nuclear geometrical arrangements, their total volumes, their partial charges, and their electron populations. The topology and geometrical disposition of these minima are shown to be independent of the capping group used in the model, and thus an inherent property of this bioisosteric pair. A model of the receptor region responsible for binding to either of these bioisosteres is proposed on the basis of an electrostatic “lock-and-key”.
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•Various number of sterols have chosen to form niosome bilayers computationally.•Different sterol concentrations have considered with Span60 to formed niosomes.•Molecular dynamics ...results such as RDF, H-bond and area per molecules presented.•β-sitosterol effectiveness has decreased the fluid arrangement of Span60 bilayers.•40 mol% sterol addition modifies the geometrical arrangement of the Span60 chains.
Niosome vesicles as potential nanocarriers for drug delivery systems have been in development since the mid-1980s. These vesicles form by self-assembly of cholesterol and nonionic surfactants in an aqueous phase. The aim of the present molecular dynamics (MD) simulation study is to determine how changes in the sterol side chain and ring affect the structure and stability of sorbitan monostearate (Span60) niosome bilayers. Five sterols are examined: cholesterol (CHL), β-sitosterol (BST), ergosterol (ERG), stigmasterol (STS), and lanosterol (LST). Different sets of simulations were performed by varying the number of molecules (30, 40, and 50 % sterol concentration). The interactions between Span60 and the different sterols are found to be strongly dependent on the sterol’s side chain and head group. BST is found to markedly reduce the effectiveness of the sterol on the ordering of the bilayers, a result that persists over the whole range of concentrations examined in this work.
Alanine is used as a transfer standard dosimeter for gamma ray and electron beam calibration. An important factor affecting its dosimetric response is humidity which can lead to errors in absorbed ...dose calculations. Ab initio molecular dynamics calculations were performed to determine the environmental effects on the electron paramagnetic resonance (EPR) parameters of L‐α‐alanine radicals in acidic and alkaline solutions. A new result, not dissimilar to the closed‐shell amino acid molecule alanine, is that the non‐zwitterionic form of the alanine radical is the stable form in the gas phase while the zwitterionic neutral alanine radical is not a stable structure in the gas phase. Geometric and EPR parameters of radicals in both gas and solution phases are found to be dependent on hydrogen bonding of water molecules with the polar groups and on dynamic solvation. Calculations on the optimized free radicals in the gas phase revealed that for the neutral radical, hydrogen bonding to water molecules drives a decrease in the magnitudes of g‐tensor components g
xx and g
yy without affecting neither g
zz component nor the hyperfine coupling constants (HFCCs). The transfer from the gas to solution phase of the alanine radical anion is accompanied with an increase in the spin density on the carboxylic group's oxygen atoms. However, for the neutral radical, this transfer from gas to solution phase is accompanied with the decrease in the spin density on oxygen atoms. Calculated isotropic HFCCs and g‐tensor of all radicals are in good agreement with experiment in both acidic and alkaline solutions.
Solvation and pH effects on g‐tensor and hyperfine coupling constants of L‐α‐Alanine radicals are elucidated by ab initio molecular dynamics simulations. The effects of humidity on electron paramagnetic resonance (EPR) parameters are quantified to elucidate the possible effects they have on radiation dosimetry using alanine. EPR parameters are found to be good diagnostics of hydrogen bonding with water of solvation.
The properties of carbon monoxide in its ground and two lowest lying excited states are investigated by conventional and time-dependent (TD) density functional theory (DFT). The dipole moment is ...decomposed into atomic polarisation (AP) and inter-atomic charge transfer (CT) contributions according to the quantum theory of atoms in molecules (QTAIM). Considerable AP and CT contributions cancel in the ground state (S 0) resulting in its known negligible dipole moment. This balance is disturbed in the lowest triplet (T 1) and singlet (S 1) excited states, resulting in dipole moments of 1.57 D for T 1 and 0.49 D for S 1 . The AP decreases by 2.5 D on excitation to either state but the opposing CT is reduced by 0.8 D for T 1 and by 1.8 D for S 1, insufficient for cancellation. These excitations induce charge transfer from O to C which drives dipole changes accompanied by a weakening of the C-O bond, more pronounced in the S 1 state, as trends in bond lengths, vibrational frequencies, and QTAIM properties suggest. The charge-charge flux-dipole flux (CCFDF) model in terms of QTAIM parameters reveals that the vibrational stretching band weakening on excitation is predominantly due to changes in atomic charges.
An Experimentalist's Reply to “What Is an Atom in a Molecule?” Matta, Chérif F; Bader, Richard F. W
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
05/2006, Letnik:
110, Številka:
19
Journal Article
Recenzirano
Parr, Ayers and Nalewajski have opined in this Journal that the concept of an atom in a molecule “is an object knowable by the mind or intellect, not by the senses.” This view is countered by the two ...hundred years of experimental chemistry underlying the realization that the properties of some total system are the sum of its atomic contributions. This paper concludes that an experimentalist has no doubt but that he or she is measuring the properties of atoms when performing an experiment.
The charge on an atom in a molecule is defined by the quantum theory of atoms in molecules (QTAIM) as the expectation value of the number operator, a Dirac observable. An atomic charge is measurable ...and it, together with its change, contributes to numerous measurable properties: to all molecular moments, to molecular polarizability, to intensities of electronic, infrared, and Raman absorption intensities, and to the polarization of a dielectric. The properties resulting from an applied magnetic field parallel those induced by an electric field, with the induced atomic charge being replaced by the atomic current. The phenomena of polarization and magnetization, permanent or induced, have a common physical basis when described in terms of the physics of an open system, all expressions exhibiting a single underlying structure in terms of their atomic contributions. The paper points out that this physics and the appeal the experiment it affords are lost when one employs other definitions of an atomic charge.
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