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A series of pentaatomic species has been investigated theoretically with relativistic DFT using the M06-L functional with both ZORA scalar relativistic correction, and including spin-orbit coupling effects. The distorted quasi-octahedral local minima for PtNO3+, PtN2O2 and PtN3O- corresponding to decavalent Pt were found to be unstable with respect to the elimination of O2, NO or N2. However, barriers surrounding these minima suggest that these species could be achieved under low-temperature conditions, similar to what was predicted for PtO42+ dications. Decavalent platinum sets the upper limit for high oxidation states of the chemical elements.
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Rhodium, a 4d transition metal and a lighter analogue of iridium, is known to exhibit its highest VIth oxidation state in RhF6 molecule. In this report, the stability and decomposition pathways of two species containing rhodium at a potentially formal +IX oxidation state, [RhO4]+ and RhNO3, have been investigated theoretically within the framework of the relativistic two-component Hamiltonian calculations. Possible rearrangement into isomers featuring lower formal oxidation numbers has been explored. We found that both species studied are metastable with respect to elimination of O2 or NO. However, the local minima containing Rh(IX) are protected by sufficient energy barriers on the decomposition pathway, and they could in principle be prepared. The analysis of a broader set of compounds containing group 8 and 9 metals in high formal oxidation states that correspond to the group number showed that, in contrast to a standard trend, the limits of formally attainable oxidation state correlate with high level of covalent bonding character in the complexes studied.
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The discovery of properties and applications of unknown materials is one of the hottest research areas in materials science. In this work, we navigate a route towards these goals by the development of a new type of graphyne nanostructure. It is synthesised by a Sonogashira cross-coupling reaction of 1,3,5-triethynylbenzene with cyanuric chloride resulting in an extended carbon-based material called TCC. Also, we modify the obtained TCC via fluorination using XeF2 at various concentrations to investigate the effect of fluorination on the triple bonds and the conjugated structure of graphyne. In this study, we put special emphasis on the determination of the impact of the fluorine content and the type of CF functionalities on the morphology, chemical and electronic structure, biocompatibility, electrical conductivity and possible applicability as anode materials for Li-ion batteries. The obtained results indicate that the character of C-F bonds influences the final properties of fluorinated materials. The polar C-F bonds are preferable for cell proliferation while CF2 groups are most suitable for battery devices, however, the appearance of PTFE-like units may have a negative impact on battery specific capacitance as well as on cell viability.
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Theoretical calculations utilizing relativistic ZORA Hamiltonian point to the conceivable existence of an IrNO3 molecule in C3v geometry. This minimum is shown to correspond to genuine nonavalent iridium nitride trioxide, which is a neutral analogue of cationic [IrO4 ]+ species detected recently. Despite the presence of nitride anion, the molecule is protected by substantial barriers exceeding 200â kJ mol-1 against transformations leading, for example, to global minimum (O=)2 Ir-NO, which contains metal at a lower formal oxidation state.
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The classical, in its nature, concept of atomic or ionic radii, although profitable in many fields, is represented by an ambiguous choice of formulations. In this work, we propose a definition of atomic and ionic radii rooted in chemical principles and conceptual density functional theories. The estimation based on electron density fundamental response functions has been successfully tested. The generalized approach has been shown to be applicable to atoms in any oxidation state. The radii display good correlation with classical estimates, such as Shannon. The atomic and ionic radii obtained according to this scheme are directly comparable between different elements, without any adjustment procedures requiring fitting constants. The definition also has a clear physical interpretation, which supports understanding of size-related phenomena and trends.
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Theoretical calculations for the first tri-iron-based extended metal atom chain (EMAC) molecule are reported. The studied triple-high-spin (S = 6) complex exhibits ferromagnetic ordering (according to Ising and spin-projection approximations), which renders it unique among all previously prepared and theoretically calculated EMAC compounds. This ordering originates from the prevailing ferromagnetic nearest-neighbor interactions, while the magnetic superexchange between terminal Fe(2+) sites is weaker and antiferromagnetic. Calculations indicate that this linear chain system based on a tri-iron core shows potential for the development of spin-frustrated behavior, which could be achieved through rational modification of the equatorial and axial ligands.
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Encouraged by our previous theoretical results that indicated the stabilization of the HeO unit inside the ferroelectric cavity composed of two parallel LiF dipoles, we have now undertaken the theoretical study for the related noble gas systems, (NgO)(MF)2, Ng = Ar, Kr, Xe, M = Li, Na, K. The computational results indicate that all such molecules constitute local minima, which are protected by sizable energy barriers especially for M = Li, Na, and thus these systems might constitute interesting synthetic targets at low temperatures.
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The simple relationship between size of an atom, the Pearson hardness, and electronic polarizability is described. The estimated atomic radius correlates well with experimental as well as theoretical covalent radii reported in the literature. Furthermore, the direct connection of atomic radius to HOMO electron density and important notions of conceptual DFT (such as frontier molecular orbitals and Fukui function) has been shown and interpreted. The radial maximum of HOMO density distribution at (αη)(1/2) minimizes the system energy. Eventually, the knowledge of the Fukui function of an atom is sufficient to estimate its electronic polarizability, chemical potential, and hardness.
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The concept of the polarization justified Fukui functions has been tested for the set of model molecules: imidazole, oxazole, and thiazole. Calculations of the Fukui functions have been based on the molecular polarizability analysis, which makes them a potentially more sensitive analytical tool as compared to the classical density functional theory proposals, typically built on electron density only. Three selected molecules show distinct differences in their reactivity patterns, despite very close geometry and electronic structure. The maps of the polarization justified Fukui functions on the molecular plane correctly identify important features of the molecules: the site for the preferential electrophilic attack in imidazole (-NH, see the TOC image) and oxazole (5-C), as well as uniquely aromatic character of the thiazole molecule and the acidic forms XH(+) of all three species.
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The Fukui functions based on the computable local polarizability vector have been presented for a group of simple molecules. The necessary approximation for the density functional theory softness kernel has been supported by a theoretical analysis unifying and generalizing early concepts produced by the several authors. The exact relation between local polarizability vector and the derivative of the nonlocal part of the electronic potential over the electric field has been demonstrated. The resulting Fukui functions are unique and represent a reasonable refinement when compared to the classical ones that are calculated as the finite difference of the density in molecular ions. The new Fukui functions are strongly validated by their direct link to electron dipole polarizabilities that are reported experimentally and by other computational methods.
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Existing approximation to the softness kernel, successfully explored in earlier work, has been extended; the normal Gauss distribution function has been used instead of the Dirac delta. The softness kernel becomes continuous functions in space and may be used to calculate the linear response function of the electron density. Three-dimensional visualization of the softness kernel and the linear response function are presented for a nitrogen atom as a working example. By using a single parameter of the spatial Gauss distribution, the novel softness kernel has been adjusted to be consistent with the standard form of the hardness kernel, representing the leading fraction of the electronic interactions in the system.
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New Fukui functions have been derived within the conceptual density functional theory by the analysis of the polarization effect of a system in static electric field. Resulting Fukui functions accurately reproduce the global softness and electronic dipolar polarizability; they meet the condition integral[f(r)/r]dr = -(partial differential mu/partial differential Z)(N) and lead to very reasonable values of the global hardness for atoms for the group of 29 main group elements. Computational clarity makes the new Fukui functions a promising tool in studies of molecular reactivity.
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The local reactivity of hydrogenated platinum clusters (Pt clusters) has been studied using the regional density functional theory method. We observed that antibond orbitals constitute the preferable binding site for hydrogen molecules H(2). Those sites are characterized by lowered electronic chemical potential and strong directionality and exhibit electrophilic nature. The platinum-dihydrogen (Pt-H(2)) sigma complexes were formed only by occupation of the lowest electronic chemical potential sites associated with Pt-H antibonds (sigma(PtH) ( *)) in saturated platinum clusters. The formation of sigma complexes caused mutual stabilization with the trans Pt-H bond. Such activated H(2) molecules on Pt clusters in a sense resemble heme-oxygen (heme-O(2)) complex with interaction strength greater than physisorption or hydrogen bonding but below chemisorption strength.
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The stress tensors are used widely for description of internal forces of matter. For some time it is also applied in quantum theory in studies of molecular properties in chemical systems. Electronic stress tensors measure effects caused by internal forces acting on electrons in molecules and particularly those between bonded atoms. Utilized here stress tensor originated bond orders express bond strengths in terms of these internal forces. The unique concept of energy density and electronic chemical potential based bond orders gives natural evaluation of interaction strength compared with classical definition, considering delocalized nature of electrons. In addition to other causes, the relation to electronic energy may be used to predict relative stabilities of geometrical isomers or even conformers.
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The origin of enzyme catalytic activity may be effectively explored within the nonempirical theory of intermolecular interactions. The knowledge of electrostatic, exchange, delocalization, and correlation components of the transition state and substrates stabilization energy arising from each enzyme active site residue allows to examine the most essential physical effects involved in enzymatic catalysis. Consequently, one can build approximate models of the catalytic activity in a systematic and legitimate manner. Whenever the dominant role of electrostatic interactions is recognized or assumed, the properties of an optimal catalytic environment could be simply generalized and visualized by means of catalytic fields that, in turn, aids the design of new catalysts. Differential transition state stabilization (DTSS) methodology has been applied herein to the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA). The MP2 results correlate well with the available experimental data and theoretical findings indicating that Lys72, Asp166, and the two magnesium ions contribute -22.7, -13.3, -32.4, and -15.2 kcal/mol to differential transition state stabilization, respectively. Although all interaction energy components except that of electron correlation contribution are meaningful, the first-order electrostatic term correlates perfectly with MP2 catalytic activity. Catalytic field technique was also employed to visualize crucial electrostatic features of an ideal catalyst and to compare the latter with the environment provided by PKA active site. The map of regional electronic chemical potential was used to analyze the unfavorable catalytic effect of Lys168. It was found that locally induced polarization of TS atoms thermodynamically destabilizes electrons, pulling them to regions displaying higher electronic chemical potential.
Asunto(s)
Proteínas Quinasas Dependientes de AMP Cíclico/química , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Ácido Aspártico/química , Ácido Aspártico/metabolismo , Catálisis , Dominio Catalítico , Iones , Lisina/química , Lisina/metabolismo , Magnesio/química , Magnesio/metabolismo , Modelos Moleculares , Datos de Secuencia Molecular , Fosforilación , Teoría Cuántica , Homología de Secuencia de Aminoácido , Electricidad Estática , TermodinámicaRESUMEN
How the mode of bonding affects stability and reactivity of molecule on the frame of nonrelativistic limit of the rigged quantum electrodynamics using new indices for description of bond properties related to bond orders have been characterized here. These indices are in close relation with tensorial interpretation of bond that among others allows discriminating covalent bonds using spindle structure concept. The real three-dimensional space representation of new interaction energy density utilized in this study contribute to better understanding of interaction phenomena between atoms and molecules. The differences in reactivity and stabilities of molecules have their root in the redistribution of interaction energy density.