Use of the bond-projected superposition principle in determining the conditional probabilities of orbital events in molecular fragments

The problem of defining and determining the multi-conditional probabilities of many-orbital events in the chemical bond system of a molecule is addressed anew within theoretical framework of the one-determinantal orbital representation of molecular electronic structure. Its solution is vital for determining the information-theoretic indices of bond couplings between molecular fragments or the reactant/product subsystems in chemical reactions. The superposition principle of quantum mechanics, appropriately projected into the occupied subspace of molecular orbitals, is used to condition the atomic orbitals or general basis functions of the self-consistent-field calculations. The conditional probabilities between the subspaces of basis functions (atomic orbitals) are derived from an appropriate generalization of the bond-projected superposition principle. They are then used to define the triply-conditional probabilities, relating one conditional event to another. The resulting expression is shown to satisfy the relevant non-negativity and symmetry requirements. It is applied to probe the π-bond coupling in butadiene and benzene.     

Structure of valence band in cluster model for cytochrome-<Emphasis Type="Italic">c</Emphasis>-oxidase active centers

The electron structure of cluster model for active centers of cytochrome-c-oxidase has been calculated by DFT (PBE) method in 6-31G basis. The cluster model was constructed on the basis of experimental PDB-structure and included 1105 hemoprotein atoms. The valence band ceiling of cytochromeoxidase active centers is shown to be formed by the atoms of carbon and nitrogen from porphyrin ring of cytochrome heme a₃ and atoms of carbon and nitrogen from imidazol moieties of histidine connected with Cu atom in cytochrome a₃. D-orbitals of Cu and Fe atoms from heme a₃ and d-orbital of Fe atom from heme a contribute mainly to the orbital group. A conclusion is made that the catalytic activity of the structure is determined by these two types of orbitals. Cu d-orbitals of cytochrome a are substantially low in energy. It is suggested that Cu atoms of cytochrome a shift the chemical potential of d-orbitals belonging to the active center that results in their easier electron accepting and releasing. This can be a decisive factor in the electron transport process.     

Electronic structures and spectra of cyanoethylene derivatives

Results of two different types of molecular orbital calculations of severalπ-orbital systems containing nitrile groups are reported and compared. The bidentate ligandbis-(methylmercapto) maleonitrile and related molecules are included. Electronic spectra of these molecules are reported and assigned in terms of the calculated energies.     

A feasibility study on obtaining <Emphasis Type="Italic">d</Emphasis>-orbital populations from aspherical-atom refinements on three spin crossover compounds

Although compounds undergoing thermally induced spin crossover have been widely studied, their experimental d-orbital populations from single-crystal X-ray diffraction have rarely been reported. Three pairs of structures of iron/manganese coordination compounds were re-evaluated. Least-squares refinements relied on aspherical scattering factors obtained from molecular quantum-mechanical DFT single-point computations of the respective solid-state conformation, initiated by accurate starting structures from preliminary invariom refinements of the ligand environment. Further evaluation concerned d-orbital populations of metal ions from (a) single-point computations projected onto the Hansen-Coppens multipole model and from (b) experimental refinements of the metal atoms only. The latter were successful for good-quality data, independent of temperature, and provided only one spin state was exclusively present in the crystal. Crystals that underwent light-induced excited spin state trapping were not showing the expected d-orbital populations.     

Synthesis,Spectroscopic and Computational Studies of CT Complexes of Amino Acids with Iodine as σ Acceptor

Understanding the charge transfer process between bioactive molecules and inorganic or organic molecules is significant as this interaction can be used to interpret bioactive molecule–receptor interactions. A comprehensive spectrophotometric study has been performed to explore the complexation chemistry of the amino acids, tyrosine, lysine and arginine, with iodine as σ acceptor. The molecular structure, spectroscopic characteristics and the interactive modes have been deduced from UV–Vis and IR spectra. The binding ratio of complexation has been determined to be 1:1 for iodine with the amino acids. The association constant (K), extinction coefficient (ε _max), ionization potential (IP), energy of the charge transfer complex (E _CT), resonance energy (R _N ), dissociation energy (W) and standard Gibbs energy (ΔG°) have been computed. An in silico study has been carried out using GAMESS computations to understand the structural features. Highest occupied molecular orbital and lowest unoccupied molecular orbital calculations helped us in characterizing the chemical reactivity and kinetic stability of the molecules. A good consistency between experimental and computational results has been found.     

A theoretical study of the strong interactions between carbon dioxide and OH<Superscript>+</Superscript> and NH<Subscript>2</Subscript><Superscript>+</Superscript> products resulting from protonation of 1,2-dioxirane-3-one and 1,2-oxaziridine-3-one,respectively

In this work, we investigate the nature of the O–O and O–N interactions in protonated 1,2-dioxirane-3-one derivatives and protonated 1,2-oxaziridine-3-one derivatives, respectively. The quantum theory of atoms in molecules and the natural bond orbital (NBO) method in conjunction with the localized molecular orbital energy decomposition analysis (LMOEDA) have been used. LMOEDA and NBO analyses reveal that the O–O and O–N interactions exhibit characteristics of dative covalent bonds. In addition, the L(r) = ??² ρ(r) function reveals that the O–O and O–N interactions can be categorized as strong hole–lump interactions.     

Theoretical Study of Substituent Effect in Aryl Group Migration in (<Emphasis Type="Italic">para</Emphasis>-C<Subscript>6</Subscript>H<Subscript>4</Subscript>X)Mn(CO)5 Complexes

In this study, we report substituent effect on aryl group migration in (para-C₆H₄X)Mn(CO)₅ complexes using mpw1pw91 quantum chemical calculations. These calculations reveal good linear relationships between barrier energy (ΔE), activation energy (ΔH^?), activation free energy (ΔG^?) values and rate constants with Hammett constants of X-substituents. The occupancy values of Mn–CO_cis and Mn–C(O)-(para-C₆H₄X) bonds in reactant, transition state and product were calculated by Natural bond orbital (NBO) method.     

Evaluation of the <Emphasis Type="Italic">Q</Emphasis><Subscript><Emphasis Type="Italic">y</Emphasis></Subscript> absorption band maximum in a light-harvesting complex of the bacterial photosynthetic center <Emphasis Type="Italic">Thermochromatium tepidum</Emphasis>

Excitation energies of the bacteriochlorophyll (BChl) chromophores embedded in the photosynthetic light-harvesting complex of the purple bacterium Thermochromatium tepidum are computed using the time-dependent density functional theory based upon the fragmental molecular orbital (FMO-TDDFT) method. The results are correlated with the empirically based estimates of the Q _y absorption maximum, as well as with the observed large red shift induced by the binding of calcium.     

Formation of solvate structures by the <Emphasis Type="Italic">ortho</Emphasis>-, <Emphasis Type="Italic">meta</Emphasis>-, and <Emphasis Type="Italic">para</Emphasis>-isomers of hydroxybenzoic acid in supercritical fluid

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid (o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm³ and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.     

Aromaticity of Bare Iridium Trimers and Ir3M0/+ and $$\rm{Ir}_3M_2^{+/3+}$$ (M = Li,Na, K,and Be,Ca) Bimetallic Clusters

The structural stabilities, bonding nature, electronic properties, and aromaticity of bare iridium trimers \(\rm{Ir}_3^{+/-}\) with different geometries and spin multiplicities are studied at the DFT/B3LYP level of theory. The ground state of the \(\rm{Ir}_3^{+}\) cation is found to be the ³A₂ (C_2v) triplet state and the ground state of the \(\rm{Ir}_3^{-}\) anion the ⁵A₂ (C_2v) quintet state. A detailed molecular orbital (MO) analysis indicates that the ground-state \(\rm{Ir}_3^{+}\) ion (C_2v, ³A₂) possesses double (σ and partial δ) aromaticity as well as the ground-state \(\rm{Ir}_3^{-}\) ion (C_2v, ⁵A₂). The multiple d-orbital aromaticity is responsible for the totally delocalized three-center metal-metal bond of the triangular Ir₃ framework. \(\rm{Ir}_3^{-}\) (C_2v, ¹A₁) structure motif is perfectly preserved in pyramidal Ir₃M^0/+ (C_s, ¹A′) and bipyramidal \(\rm{Ir}_3M_2^{+/3+}\) (C_2v, ¹A₁) (M = Li, Na, K and Be, Ca) bimetallic clusters which also possess the corresponding d-orbital aromatic characters.     

Electronic structure and excited states of molecular crystals of antimony and tellurium hexahalogenides

The article examines the electronic structure and orbital nature of luminescence excitation in a series of molecular crystals with the general formula E _n AX₆, where E _n are organic and inorganic cations (diphenylguanidinium, guanidinium, and cesium); n is the number of cations; AX₆ are Te(IV) and Sb(III) anions; X are the atoms of halogens Cl or Br. The electronic structure of these molecular crystals is determined from the data of X–ray photoelectron spectroscopy of the core and valence levels and еру quantum chemical modeling фе the density functional theory level together with the previously obtained single crystal X–ray diffraction data.     

On the chemical bonding features in palladium containing compounds: A combined QTAIM/DFT topological analysis

Topological analyses of the electron density on N-benzoyl-L-pheylalanine and its palladium(II) complexes are carried out using the quantum theory of atoms in molecules (QTAIM) at the M06/6-31G(d) theoretical level. The topological parameters derived from the Bader theory are also analyzed; these are characteristics of Pd bond critical points and ring critical points. The calculated structural parameters are the highest occupied molecular orbital energy (E _HOMO), the lowest unoccupied molecular orbital energy (E _LUMO), the hardness (η), the softness (S), the absolute electronegativity (χ), the electrophilicity index (ω), and the fractions of electrons transferred (ΔN) from ethylenediamine, 2,2′-bipyridine and 1,10-phenanthroline complexes to N-benzoyl-L-pheylalanine. The numerous correlations and dependences between the energy terms of the symmetry adapted perturbation theory approach, geometrical, topological, and energy parameters are detected and described.     

Transformations of 3(4)-amino-4(3)-(<Emphasis Type="Italic">tert</Emphasis>-butyl-<Emphasis Type="Italic">NNO</Emphasis>-azoxy)furoxans in the annulation reactions into 1,2,3,4-tetrazine 1,3-dioxides

Reactions of 3(4)-amino-4(3)-(tert-butyl-NNO-azoxy)furoxans with excess (NO₂)₂S₂O₇ or with a HNO₃—H₂SO₄—Ac₂O mixture unexpectedly produce [1,2,5]oxadiazolo[3,4-e]?[1,2,3,4]tetrazine 4,6-di-N-oxide (furazanotetrazine dioxide) and products of amino group oxidation (mainly to the corresponding azofuroxans) instead of the expected furoxanotetrazine dioxides. In some cases, individual (Z)-3,3´-((E)-diazene-1,2-diyl)-bis-((Z)-2-tert-butyl-1-oxidodiazenyl)-1,2,5-oxadiazole 2-oxide) was isolated. Formation of furazanotetrazine dioxides was observed in the reaction of 3-nitramino-4-(tert-butyl-NNO-azoxy)furoxan sodium salt with H₂SO₄ in Ac₂O. Quantum chemical calculation at the DFT/B3LYP/6-31G(d) level of theory was used to estimate several aspects of the reactivity of 3(4)-nitramino-4(3)-(tert-butyl-NNO-azoxy)furoxans in a comparison with 3(4)-nitramino-4(3)-phenylfuroxans and the possible causes of the observed transformations were revealed.     

Modeling of half-Heusler crystals with the chalcopyrite structure: Li<Subscript>2</Subscript>MgZn<Emphasis Type="Italic">X</Emphasis><Subscript>2</Subscript> (X = N,P, As,Sb)

A model of Li₂MgZnX ₂ half-Heusler compounds with the chalcopyrite structure is considered. The electronic structure is studied from first principles, showing that Li₂MgZnX ₂ are direct-gap crystals, except for pseudo-direct-gap Li₂MgZnP₂, with a band gap of 2.7 eV, 2.2 eV, 3.3 eV, and 2.5 eV for X = N, P, As, and Sb, respectively. The band structure and chemical bonding in the model crystals are found to be similar to those in LiMgX and LiZnX half-Heusler crystals. Total electron density and deformation electron density distributions are obtained. It is found that Mg–X and Zn–X ionic-covalent bonds are stronger than Li–X ionic bonds in Li₂MgZnX ₂ crystals, which allows Li atoms to move in the space between MgX ₄ and ZnX ₄ cation tetrahedra.     

Influence of <Emphasis Type="Italic">gauche</Emphasis> effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies

The neutral oxime reactivator RS194B with a seven-membered ring has shown better efficacy towards the tabun-inhibited AChE than that of RS69N with a six-membered ring and RS41A with a five-membered ring. The difference in the efficacy of these reactivators has remained unexplored. We report here the origin of the difference of efficacy of these reactivators based on the conformational analysis, quantum chemical calculations and steered molecular dynamics (SMD) simulations. The conformational analysis using B3LYP/6-31G(d) level of theory revealed that RS41A and RS194B are more stable in gauche conformation due to the gauche effect (–N–C–C–N– bonds) whereas RS69N prefers anti-conformation. The SMD simulations show that RS194B retains in more stable gauche conformation inside the active gorge of AChE during different time intervals that experiences more hydrogen bonding, hydrophobic interactions with the catalytic anionic site (CAS) residues and weaker interactions with the peripheral anionic site (PAS) residues compared to RS41A and RS69N. In an effort to design an even superior reactivator, RS194B-S has been chosen with a subtle change in the geometry of RS194B by replacing the carbonyl oxygen with the sulfur atom. The newly designed reactivator RS194B-S can also be a promising candidate to reactivate tabun-inhibited AChE.