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1.
The electronic structures of heme a of cytochrome c oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe ion are determined by the orbital interactions of the d orbitals of the Fe ion with the π orbitals of the porphyrin ring and the His residues. The redox reaction of the Fe ion influences the charge density on the formyl group through the π conjugation of the porphyrin ring. In addition, we found the charge transfer from the Fe ion to the propionate group of heme a in the redox change despite the lack of the π‐conjugation. We elucidated that the charge propagation originates from the heme a structure itself and that the origin of the charge delocalization to the heme propionate is the orbital interactions between the d orbital of the Fe ion and the p orbitals of the carboxylate part of the heme propionate via the π conjugation of the porphyrin ring and the σ* orbital of the C? C bond of the propionate group. The electrostatic effect by surrounding proteins enhances the charge transfer from the Fe ion to the propionate group. These results indicate that heme propionate groups serve electron mediators in electron transfer as well as electrostatic anchors, and that proteins surrounding the active site reinforce the congenital abilities of the cofactors. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010  相似文献   

2.
Although silylene-carbonyl complexes are known for decades, only recently isolable examples have been accomplished. In this work, the bonding situation is re-evaluated to explain the origins of their remarkable stability within the Kohn-Sham molecular orbital theory framework. It is shown that the chemical bond can be understood as CO interaction with the silylene via a donor-acceptor interaction: a σ-donation from the σCO into the empty p-orbital of silicon, and a π-back donation from the sp2 lone pair of silicon into the π*CO antibonding orbitals. Notably, it was established that the driving force behind the surprisingly stable Si−CO compounds, however, is another π-back donation from a perpendicular bonding R−Si σ-orbital into the π*CO antibonding orbitals. Consequently, the pyramidalization of the central silicon atom cannot be associated with the strength of the π-back donation, in sharp contrast to the established chemical bonding model. Considering this additional bonding interaction not only shed light on the bonding situation, but is also an indispensable key for broadening the scope of silylene-carbonyl chemistry.  相似文献   

3.
The theoretical study of the dehydrogenation of 2,5‐dihydro‐[furan ( 1 ), thiophene ( 2 ), and selenophene ( 3 )] was carried out using ab initio molecular orbital (MO) and density functional theory (DFT) methods at the B3LYP/6‐311G**//B3LYP/6‐311G** and MP2/6‐311G**//B3LYP/6‐311G** levels of theory. Among the used methods in this study, the obtained results show that B3LYP/6‐311G** method is in good agreement with the available experimental values. Based on the optimized ground state geometries using B3LYP/6‐311G** method, the natural bond orbital (NBO) analysis of donor‐acceptor (bond‐antibond) interactions revealed that the stabilization energies associated with the electronic delocalization from non‐bonding lone‐pair orbitals [LP(e)X3] to δ*C(1)  H(2) antibonding orbital, decrease from compounds 1 to 3 . The LP(e)X3→δ*C(1)  H(2) resonance energies for compounds 1 – 3 are 23.37, 16.05 and 12.46 kJ/mol, respectively. Also, the LP(e)X3→δ*C(1)  H(2) delocalizations could fairly explain the decrease of occupancies of LP(e)X3 non‐bonding orbitals in ring of compounds 1 – 3 ( 3 > 2 > 1 ). The electronic delocalization from LP(e)X3 non‐bonding orbitals to δ*C(1)  H(2) antibonding orbital increases the ground state structure stability, Therefore, the decrease of LP(e)X3→δ*C(1)  H(2) delocalizations could fairly explain the kinetic of the dehydrogenation reactions of compounds 1 – 3 (k 1 >k 2 >k 3 ). Also, the donor‐acceptor interactions, as obtained from NBO analysis, revealed that the (C(4)C(7)→δ*C(1)  H(2) resonance energies decrease from compounds 1 to 3 . Further, the results showed that the energy gaps between (C(4)C(7) bonding and δ*C(1)  H(2) antibonding orbitals decrease from compounds 1 to 3 . The results suggest also that in compounds 1 – 3 , the hydrogen eliminations are controlled by LP(e)→δ* resonance energies. Analysis of bond order, natural bond orbital charges, bond indexes, synchronicity parameters, and IRC calculations indicate that these reactions are occurring through a concerted and synchronous six‐membered cyclic transition state type of mechanism.  相似文献   

4.
Electron transfer in the cations of bis(hydrazines), bridged by six different π‐systems (compounds 1–6) is studied using ab initio and density functional theory (DFT) methods. Due to ionization from an antibonding combination of the lone‐pair orbitals of the nitrogens in one of the hydrazine units, conjugation is introduced in the N? N bond of that unit. This leads to a shortening of the N? N bond distance and an increase of the planarity around the nitrogens. Due to steric hindrance, this causes an increase of the angle, called φ, between the lone‐pair orbital on the nitrogen attached to the bridge and the p‐orbital on the adjacent bridge carbon for the ionized unit in the charge localized, relaxed state of the molecule. This angle controls the magnitude of the electronic coupling. In the fully delocalized symmetric transition state of the ion, however, this angle is low for both units, due to the fact that the conjugation introduced at the ionized hydrazine unit is now shared between both units. An extended π‐system is formed including the orbitals of the hydrazine units and the bridge, which leads to a large electronic coupling. The electronic coupling derived by optical methods, corresponding to the structure of the relaxed, asymmetric cation with a large φ for the ionized unit, appears to be much smaller. We believe this is due to an approximate cosine dependence on φ of the coupling. The calculations carried out support these conclusions. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 655–664, 2001  相似文献   

5.
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.  相似文献   

6.
In this work, the tuneability of the π acceptor or donor properties of a set of N‐heterocyclic carbenes (NHCs) with a wide spectrum of electronic characteristics is established by means of density functional theory and energy decomposition analysis (EDA) tools. Even though the main orbital interaction contribution to the NHC coordination is the σ donation, a significant contribution of the π interactions to the bond is observed. By means of carefully selected coordination sites, different contributions to the π interactions could be identified and isolated. It includes not only the well known back donation and donation interactions, but also the intrafragment polarization, which has not been considered in previous studies. This can be obtained through the use of the extended transition state method for EDA combined with the natural orbitals for chemical valence and the constrained space orbital variation analysis. The contributions vary with the position of the heteroatoms and the presence of exocyclic substituents; the donation/backdonation π interactions between NHC and the coordination site can range between 2 and 61% of the total π orbital interactions, while the rest is owed to intrafragment polarization. Our results do not only contribute to the understanding of the electronic structure of NHC‐based complexes, giving ways to improve their catalytic properties, but also provide comprehension on the modelization methods used to study their donor–acceptor interactions. © 2015 Wiley Periodicals, Inc.  相似文献   

7.
The electronic structure of methane adsorbed on Pt(977) is investigated using angle-resolved x-ray absorption spectroscopy (XAS) in combination with density functional theory spectrum calculations. XAS, which probes the unoccupied states atom specifically, shows the appearance of the symmetry-forbidden gas-phase lowest unoccupied molecular orbital due to s-p rehybridization. In addition new adsorption-induced states appear just above the Fermi level. A systematic investigation, where computed XA spectra are compared with the experiment, indicates elongation of the C-H bond pointing toward the surface to 1.18+/-0.05 A. The bond elongation arises due to mixing between bonding and antibonding C-H orbitals. Computed charge density difference plots show that no covalent chemical bond is formed between the adsorbate and substrate upon adsorption. The changes in electronic structure arise in order to minimize the Pauli repulsion by polarizing charge away from the surface toward the carbon atom of the methane molecule.  相似文献   

8.
The electronic structure of borabenzene (C5H5B, known also as borinane, borinine, borine) is studied using modern valence bond theory in its spin-coupled (SC) form. Three different types of SC wave functions—with six active π orbitals and with four and eight active σ orbitals—are used to describe the π system of the molecule and the σ-bond framework around the boron atom. It is demonstrated that the SC picture of the π space in borabenzene is very similar to that in benzene: The spins of six distorted nonorthogonal 2pπ orbitals are combined in a spin-coupling pattern involving two dominating Kekulétype and three less important Dewar-type Rumer spin functions. This indicates that it is appropriate to consider the π-electron sextet in borabenzene as aromatic and that the reason for the reactivity of this molecule should lie with its σ framework. The two SC models of the σ bonding around B show that the boron-carbon σ bonds in borabenzene involve orbitals are “bent” to the outer side of the six-membered ring. This creates an orbital “hole” at the boron, which should represent the preferred attachment site for Lewis acids. © 1997 John Wiley & Sons, Inc.  相似文献   

9.
The bond order of the ground electronic state of the carbon dimer has been analyzed in the light of natural orbital functional theory calculations carried out with an approximate, albeit strictly N‐representable, energy functional. Three distinct solutions have been found from the Euler equations of the minimization of the energy functional with respect to the natural orbitals and their occupation numbers, which expand upon increasing values of the internuclear coordinate. In the close vicinity of the minimum energy region, two of the solutions compete around a discontinuity point. The former, corresponding to the absolute minimum energy, features two valence natural orbitals of each of the following symmetries, σ, σ*, π and π*, and has three bonding interactions and one antibonding interaction, which is very suggestive of a bond order large than two but smaller than three. The latter, features one σ–σ* linked pair of natural orbitals and three degenerate pseudo‐bonding like orbitals, paired each with one triply degenerate pseudo‐antibonding orbital, which points to a bond order larger than three. When correlation effects, other than Hartree–Fock for example, between the paired natural orbitals are accounted for, this second solution vanishes yielding a smooth continuous dissociation curve. Comparison of the vibrational energies and electron ionization energies, calculated on this curve, with their corresponding experimental marks, lend further support to a bond order for C 2 intermediate between acetylene and ethylene.  相似文献   

10.
Sulfur ylides are useful synthetic intermediates that are formed from the interaction between singlet carbenes and sulfur-containing molecules. Partial double-bond character frequently has been proposed as a key contributor to the stability of sulfur ylides. Calculations at the B3LYP, MP2, and CCSD(T) levels of theory employing various basis sets have been performed on the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) in order to investigate the structure and bonding of these systems. The following general properties of sulfur ylides were observed from the computational studies: C-S bond distances that are close in length to that of a typical C-S double bond, high charge transfer from the sulfide to the carbene, and large torsional rotation barriers. Analysis of the sulfur ylide charge distribution indicates that the unusually short C-S bond distance can be attributed in part to the electrostatic attraction between highly oppositely charged carbon and sulfur atoms. Furthermore, n --> sigma* stabilization arising from donation of electron density from the carbon lone pair orbital into S-H or S-C antibonding orbitals leads to larger than expected torsional barriers. Finally, natural resonance theory analysis indicates that the bond order of the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) is 1.4-1.5, intermediate between a single and double bond.  相似文献   

11.
We combine photoelectron and x-ray absorption spectroscopy with density functional theory to derive a molecular orbital picture of the hydrogen bond in ice. We find that the hydrogen bond involves donation and back-donation of charge between the oxygen lone pair and the O-H antibonding orbitals on neighboring molecules. Together with internal s-p rehybridization this minimizes the repulsive charge overlap of the connecting oxygen and hydrogen atoms, which is essential for a strong attractive electrostatic interaction. Our joint experimental and theoretical results demonstrate that an electrostatic model based on only charge induction from the surrounding medium fails to properly describe the internal charge redistributions upon hydrogen bonding.  相似文献   

12.
The hydroxycyclohexadienyl peroxy radicals (HO? C6H6? O2) produced from the reaction of OH‐benzene adduct with O2 were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical IIs and 4‐hydroxycyclohexadienyl peroxy radical IIIs were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical IIs is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical IIIs, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007  相似文献   

13.
The direct dissociation of ethylene into two methylenes is studied along the least motion reaction path by means of an ab initio multiconfiguration self-consistent-field (MCSCF ) calculation. All eight configurations arising from those valence orbitals that form the CC bonds, seven of them singlet coupled and one triplet coupled, are taken into account. The HCH bond angle is optimized along the entire reaction path. Separate MCSCF optimizations are carried through for the lowest two states of 1Ag symmetry. The (1Agσ2π2) ethylene ground state dissociates into two (3B1σπ) ground-state methylenes. The (1Agσ2π*2) excited state of ethylene dissociates into two (1A1σ2) excited methylenes. It is established that both these dissociations proceed without any barrier in the energy curve. In the ground state, where orbital symmetry is conserved, the π-bond breaks before the σ-bond, and the calculated heat of reaction agrees within 6 kcal/mol with the experimental value. In the excited state, where orbital symmetry is not conserved, the nonbonded repulsion between methylene σ2 lone pairs is found to blend into the antibonding character of the excited ethylene, yielding an energy curve that is everywhere repulsive. However, the variation of the HCH angle during the dissociation process is not simple, initially it expands and subsequently it contracts. Quantitative analytical approaches are developed which furnish conceptual interpretations of the orbital changes and configurational changes along the reaction path.  相似文献   

14.
Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH4 complex formed by water and methane molecules, in which water is a proton donor and methane carbon (sp3) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial С–H bond of methane directed along the line of the O–H···C hydrogen bridge and the antibonding σ* orbital of the О–H bond of the water molecule. Topological analysis of electron density in the HOH···CH4 complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O–H···C interaction are typical for Н-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an Н bond of O–H···σ(С–H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).  相似文献   

15.
The geometries, electronic structures, and hyperfine coupling constants of azafullerene C59N (a π-electron radical) and its derivatives, C59NH and endofullerene H@C59N, were calculated at the B3LYP level of the density functional theory. Analysis of calculated potential energy profiles along trajectories of the motion of encapsulated hydrogen atom from the center of the fullerene sphere toward different atoms of C59N revealed formation of a chemical bond between the H atom and a carbon atom that is involved in the 6,6-bond with the N atom and bears the most part of the π-electron spin density. The C—H endo-bond length is 1.12 Å, the bond dissociation energy being equal to 26.4 kcal mol−1. The C—H exo-bond involving the same carbon atom is 0.02 Å shorter than the endo-bond, the bond dissociation energy being much higher (78.4 kcal mol−1).__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 51–54, January, 2005.  相似文献   

16.
A relativistic density functional theory (DFT) study is reported which aims to understand the complexation chemistry of An4+ ions (An = Th, U, Np, and Pu) with a potential decorporation agent, 5-LIO(Me-3,2-HOPO). The calculations show that the periodic change of the metal binding free energy has an excellent correlation with the ionic radii and such change of ionic radii also leads to the structural modulation of actinide–ligand complexes. The calculated structural and binding parameters agree well with the available experimental data. Atomic charges derived from quantum theory of atoms in molecules (QTAIM) and natural bond order (NBO) analysis shows the major role of ligand-to-metal charge transfer in the stability of the complexes. Energy decomposition analysis, QTAIM, and electron localization function (ELF) predict that the actinide–ligand bond is dominantly ionic, but the contribution of orbital interaction is considerable and increases from Th4+ to Pu4+. A decomposition of orbital contributions applying the extended transition state-natural orbital chemical valence method points out the significant π-donation from the oxygen donor centers to the electron-poor actinide ion. Molecular orbital analysis suggests an increasing trend of orbital mixing in the context of 5f orbital participation across the tetravalent An series (Th-Pu). However, the corresponding overlap integral is found to be smaller than in the case of 6d orbital participation. An analysis of the results from the aforementioned electronic structure methods indicates that such orbital participation possibly arises due to the energy matching of ligand and metal orbitals and carries the signature of near-degeneracy driven covalency.  相似文献   

17.
The frontier orbital theory is applied to ruthenium olefin metathesis. The formal [2+2] cycloaddition step, that is, the key step involved in the catalytic cycle of the reaction, is found to be favored by the phases of the HOMO and LUMO, in sharp contrast to [2+2] cycloaddition reactions between olefins. In the LUMO of transition metal part, a d-orbital overlaps out of phase with the vacant p-orbital of the carbene in the inner space of the metal–carbon π bond as is expected, but the remote lobe of the d orbital overlaps in phase in the outer space of the bond. This is a characteristic feature of the antibonding orbitals of transition metal bonds. The outer orbital phase plays more important role in the interaction.  相似文献   

18.
Classical organic anode materials for Na‐ion batteries are mostly based on conjugated carboxylate compounds, which can stabilize added electrons by the double‐bond reformation mechanism. Now, 1,4‐cyclohexanedicarboxylic acid (C8H12O4, CHDA) with a non‐conjugated ring (?C6H10?) connected with carboxylates is shown to undergo electrochemical reactions with two Na ions, delivering a high charge specific capacity of 284 mA h g?1 (249 mA h g?1 after 100 cycles), and good rate performance. First‐principles calculations indicate that hydrogen‐transfer‐mediated orbital conversion from antibonding π* to bonding σ stabilize two added electrons, and reactive intermediate with unpaired electron is suppressed by localization of σ‐bonds and steric hindrance. An advantage of CHDA as an anode material is good reversibility and relatively constant voltage. A large variety of organic non‐conjugated compounds are predicted to be promising anode materials for sodium‐ion batteries.  相似文献   

19.
The nature of methyl internal rotational barrier in thioacetaldehyde has been investigated by relaxation effect, natural bond orbital (NBO) analysis and Pauling exchange interactions. The true experimental barrier can be obtained by considering fully relaxed rotation. Nuclear-electron attraction term is a barrier forming term in the fully relaxed rotation, but it appears as an antibarrier for rigid rotation. It is seen that during methyl rotation, the torsional mode is coupled with the aldehydic hydrogen out-of-plane wagging motion. Natural bond orbital analysis shows that the principal barrier forming term originates from the C-C bond. The lengthening of the C-C bond is explained by considering charge transfer interaction between several bonding and antibonding orbitals in the C-C bond region, which leads to higher bonding overlap for the eclipsed conformer compared to the staggered conformer. S-C(σ)/Cme-Hp and C-Hald/Cme-Hop interactions appear to be the main barrier-forming Pauling exchange terms but have less contribution to make to the barrier compared to the C-C bond interaction.  相似文献   

20.
The aim of this study was to investigate both the electronic and steric effects of the ancillary phosphine ligand L on the reductive elimination of Me-Me from a series of L2PdMe2 and LPdMe2 complexes. Density functional theory was used to study these processes with the model ligands L = PMe3, PH3, PCl3 and with the experimentally reported ligands L = PPh3, PPh2Me, PPhMe2. For the model ligands we confirm that electron donation from L affects the barrier for reductive elimination from L2PdMe2 but not from LPdMe2. In the former case the greater the electron donation or basicity of L, the greater the barrier and the later the transition state. This is because electron donation increases the σ antibonding between Pd and L in the transition structure. On the other hand, if L is a good π acceptor this stabilizes the occupied dπ orbital of Pd in the transition structure and lowers the barrier to reductive elimination. In the case of the reactions involving LPdMe2 as the intermediate, it is the loss of the first L (L2PdMe2 → LPdMe2 + L) which determines the differences in the barrier height. Greater electron donation leads to greater L-to-Pd σ donation and a stronger Pd-L bond, and thus a greater overall barrier. A comparison of these results with the reductive elimination of 1,3-butadiene from divinyl palladium complexes L2PdR2 shows that the barriers are lower in the vinyl case because of a mix of orbital factors. Our results show that there is a significant stabilizing interaction between the Pd dπ orbital and the vinyl-vinyl hybrid σ orbitals in the reductive elimination transition structure. At the same time this Pd-R2 orbital stabilization alleviates the potential antibonding interactions between Pd and L and makes the vinyl elimination much less susceptible to ancillary ligand effects. Energy-decomposition analyses have been used to elucidate the contributing factors to the activation energies for the reductive eliminations with the model phosphine ligands. These analyses have also been used to disentangle the electronic and steric effects involved in the larger ligand systems. The electronic effects of the experimentally reported ligands are found to be very similar to each other. On the other hand, steric effects lead to a destabilization of the reactant L2PdMe2 complexes but not the transition structures, which results in a decrease in the barriers to reductive elimination compared to the smaller phosphine ligands. These steric effects do not play a role in reductive elimination from LPdMe2. These detailed analyses of the electronic and steric factors may be used to assist the design of systems which enhance or retard reductive elimination behaviour.  相似文献   

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