Mechanism of the electronic stabilization of the 3MR and divalent carbon of bis(diisopropylamino)cyclopropenylidene

Analysis of the topology of the electron density of bis(dimethylamino)cyclopropenylidene as a model of the recently synthesized, stable bis(diisopropylamino)cyclopropenylidene with the quantum theory of atoms in molecules is used to investigate the stabilizing electronic effects at the reactive carbene site by amino substitution. This work demonstrates that the plane perpendicular lone pairs of nitrogen utilize in-plane sigma-aromaticity as a conduit to delocalize charge to the carbene carbon C2, where it is transferred preferentially back into the pi-plane at the site through sigma-pi polarization. C2 is thus stabilized relative to the parent cyclopropenylidene, c-C(3)H(2), by a very different mechanism than that suggested in the orbital view of n(pi)(N) and pi(C=C) conjugation and n(pi)(N) --> p(pi)*(C2) hyperconjugation. Validation of this premise is also found in properties of asymmetric atomic quadrupole tensors, bond path ellipticities, and diamagnetic/paramagnetic components of NMR shielding tensors.     

Theoretical study of the electronic spectroscopy of CO adsorbed on Pt(111)

The excited states of CO adsorbed on the Pt(111) surface are studied using a time-dependent density functional theory formalism. To reduce the computational cost, electronic excitations are computed within a reduced single excitation space. Using cluster models of the surface, excitation energies are computed for CO in the on-top, threefold, and bridge binding sites. On adsorption, there is a lowering of the 5sigma orbital energy. This leads to a large blueshift in the 5sigma- -> pi(CO*) excitation energy for all adsorption sites. The 1pi and 4sigma orbital energies are lowered to a lesser extent, and smaller shifts in the corresponding excitation energies are predicted. For the larger clusters, pi* excitations at lower energies are observed. These transitions correspond to excitations to virtual orbitals of pi* character which lie below the pi* orbitals of gas phase CO. These orbitals are associated predominantly with the metal atoms of the cluster. The excitation energies are also found to be sensitive to changes in the adsorption geometry. The electronic spectrum of CO on Pt(111) is simulated and the assignment of the bands observed in experimental electron energy loss spectroscopy discussed.     

Core molecular orbital contribution to N2O isomerization as studied using theoretical electron momentum spectroscopy

Core molecular orbital contribution to the electronic structure of N2O isomers has been studied using quantum mechanical density functional theory combined with a plane wave impulse approximation method. Momentum distributions of wave functions for inner shell molecular orbitals of the linear NNO, cyclic and linear NON isomers of N2O are calculated through the (e, 2e) differential cross sections in momentum space. This is possible because this momentum distribution is directly proportional to the modulus squared of the momentum space wave function for the molecular orbital in question. While the momentum distributions of the NNO and cyclic N2O isomers demonstrate strong atomic orbital characteristics in their core space, the outer core molecular orbitals of the linear NON isomer exhibit configuration interactions between them and the valence molecular orbitals. It is suggested that the frozen core approximation breaks down in the prediction of the electronic structure of such an isomer. Core molecular orbital contributions to the electronic structure can alter the order of total energies of the isomers and lead to incorrect conclusions of the stability among the isomers. As a result, full electron calculations should be employed in the study of N2O isomerization.     

Lead-poisoned zinc fingers: quantum mechanical exploration of structure, coordination, and electronic excitations

Density functional theory (DFT) structure calculations and time-dependent DFT electronic excitation calculations on simple mononuclear lead structures confirm recent reports on the stabilization of tricoordinated structural domains in poisoned proteins. However, the possibility of the formation of tetracoordinated lead complexes should not be disregarded in studies on mechanisms of lead toxicity because structures with both coordination modes are plausible and might contribute to observed UV spectra. Reported calculations along with detailed molecular orbital analysis confirm that the intense UV signal at around 260 nm is an indicator of the ligand-to-metal charge transfer (LMCT) band where the electrons are transferred from the sulfur 3p orbital to the lead 6p orbital. The composition of the LMCT band reveals significant excitations not only from the Pb-S bonding orbitals but also from sulfur lone-pair orbitals to the Pb-S antibonding orbitals for which the electron density is largely localized on the Pb "6p-like" molecular orbitals. There is a solid indication that the stereochemically active pair orbital of lead is not strongly hybridized and remains largely of the 6s character in tricoordinated lead structures and is minimally hybridized in tetracoordinated lead structures. Computed UV spectra of lead model complexes are compared to experimental UV spectra of model lead peptides. The comparison shows a good agreement with the major spectral trends and changes observed in these experiments.     

Orbital views of molecular conductance perturbed by anchor units

Site-specific electron transport phenomena through benzene and benzenedithiol derivatives are discussed on the basis of a qualitative Hu?ckel molecular orbital analysis for better understanding of the effect of anchoring sulfur atoms. A recent work for the orbital control of electron transport through aromatic hydrocarbons provided an important concept for the design of high-conductance connections of a molecule with anchoring atoms. In this work the origin of the frontier orbitals of benzenedithiol derivatives, the effect of the sulfur atoms on the orbitals and on the electron transport properties, and the applicability of the theoretical concept on aromatic hydrocarbons with the anchoring units are studied. The results demonstrate that the orbital view predictions are applicable to molecules perturbed by the anchoring units. The electron transport properties of benzene are found to be qualitatively consistent with those of benzenedithiol with respect to the site dependence. To verify the result of the Hu?ckel molecular orbital calculations, fragment molecular orbital analyses with the extended Hu?ckel molecular orbital theory and electron transport calculations with density functional theory are performed. Calculated results are in good agreement with the orbital interaction analysis. The phase, amplitude, and spatial distribution of the frontier orbitals play an essential role in the design of the electron transport properties through aromatic hydrocarbons.     

Efficient Synthesis of 1,4‐Bis‐heteroatom‐substituted Tetraselanylbenzenes via 1,4‐Dilithiation of Hexaselanylbenzene and Investigation on Their Electronic Properties

We successfully synthesized mono‐ and bis‐substituted polyselanylbenzenes 3 and 5 via mono‐ and dilithiation of hexakis(phenylselanyl)benzene ( 1 ), respectively. Introduction of various heteroatom functionalities into hexaselanylbenzene changed the electronic properties dependent on the σ‐symmetric circular orbitals that were formed by the interactions between neighboring heteroatoms. In the cyclic voltammetry and theoretical studies on bis‐heteroatom‐substituted benzenes 5 , the extent of the interactions in the circular orbitals with σ‐symmetry affected the stability of the cationic species of 5 . This study would give insight into the molecular design for new σ‐delocalized systems and inspire the development of tuning electronic properties of benzene derivatives by σ‐type orbital interactions derived from heteroatom functionalities.     

Application of natural bond orbital analysis to delocalization and aromaticity in C-substituted tetrazoles.

Energies of two tautomeric forms of 10 tetrazole derivatives substituted at C5 were established by DFT/B3LYP calculations carried out at the 6-311++G level. In each case the calculated energy of the 2H-tautomer was lower than that of the 1H. Furthermore, three geometric aromaticity indices of both forms were calculated, as were the values of nuclear independent nuclear shift and aromatic stabilization energy. The electronic properties were evaluated with the help of the natural bonding orbital theory. Following this a new pi-delocalization parameter, the root-mean square of pi-electron density localized on the atoms of the five-membered tetrazole ring, SDn, was introduced. It was concluded that the electronic delocalization can be described equally well by three different parameters: SDn, the extent of the transfer of electron density from the p(z) orbital of one nitrogen to the rest of the pi electron system, and population of two antibonding pi orbitals. Arguably, the information provided by the electronic parameters is similar to that contained in the geometric (structural) aromaticity indices except for tetrazole substituted by -BH(2).     

Valence orbital response to pseudorotation of tetrahydrofuran: a snapshot using dual space analysis

The pseudorotation of tetrahydrofuran (THF) (C(4)H(8)O) has been studied using density functional theory, with respect to the valence orbital responses to the ionization potentials and to orbital electron and momentum distributions. Three conformations of THF, the global minimum structure C(s), local minimum structure C(2), and a transition state structure C(1), which are characteristic configurations on the potential energy surface, are examined using the SAOP/et-pVQZ//B3LYP/6-311++G** models with the aforementioned dual space analysis. It is noted in the ionization energy spectra that the minimum structures C(s) and C(2) are not directly connected by pseudorotation, but through the transition state structure C(1). As a result, some orbitals of the C(s) conformer are able to "correlate" to orbitals of the C(2) conformer without a strict symmetry constraint, i.e., orbital 7a' of the C(s) conformer is correlated to orbital 5b of the C(2) conformer. It is also noted that although the valence orbital ionization potentials are not significantly altered by the pseudorotation of THF, their spectra (mainly due to excitation) are quite different indeed. Detailed orbital analysis based on dual space analysis is given. The valence orbital behavior of the conformations is orbital dependent. It can be approximately divided into three groups: the "signature group" is associated with orbitals experiencing significant changes. The frontier orbitals are in this group. The "nearly identical group" includes orbitals without apparent changes across the conformations. Most of the orbitals showing a certain degree of distortion during the pseudorotation process belong to the third group. The present study demonstrates that a comprehensive understanding of the pseudorotation of THF and its dynamics requires multidimensional information and that the information gained from momentum space is complementary to that from the more familiar coordinate space.     

The ligand field as a pseudo-potential

The introduction of a pseudo-potential in crystal field theory is shown to lead to an expression for the orbital splittings which depend upon the squares of the group overlap integrals between the metal and ligand orbitals. A formula is derived whereby the group overlap integral can be directly expressed in terms of the diatomic sigma- and pi-integrals.     

Electronic charge density and mean kinetic energy of lithium orbitals in LiH,LiH+, Li2, Li2+, LiH2+, and Li2H+

The electron density near the lithium nucleus in the species LiH, LiH⁺, Li₂, Li₂⁺, LiH₂⁺, and Li₂H⁺ was analyzed by transforming the SCF molecular orbitals into a sum of atomic contribnutions, for both core and valence orbitals. These “hybrid-atomic” orbitals were used to compare: electron densities, orbital polarizations, and orbital mean kinetic energies with the corresponding lithium atom quantities. Core-orbital electron densities at the lithium nucleus were observed to increase by up to 0.5% relative to the lithium atom 1s orbital. Lithium cores also exhibited polarization but, surprisingly, in the direction away from the internuclear region. Similar dramatic changes were seen in the electron densities of the valence orbitals of lithium: The electron density at the nucleus for these orbitals increased two-fold for homonuclear species and twenty-fold for heteronuclear triatomic species relative to the electron density at the nucleus in lithium atom. The polarization of the valence orbital electronic charge, in the vicinity of the lithium nucleus, was also away from the internuclear region. The mean “hybrid-atomic” orbital kinetic energies associated with the lithium atom in the molecules also showed changes relative to the free lithium atom. Such changes, accompanying bond formation, were relatively small for the lithium core orbitals (within 0.2% of the value for lithium atom). The orbital kinetic energies for the lithium valence electrons, however, increased considerably relative to the lithium atom: By a factor of about 2 in homonuclear diatomics, by a factor of 7 in heteronuclear diatomics, and by a factor of 11 in the triatomic species. In summary, the total electronic density (core plus valence) at the lithium nucleus remained remarkably constant for all of the species studied, regardless of the effective charge on lithium. Thus, the drastic changes noted in the individual lithium orbitals occurred in a cooperative fashion so as to preserve a constant total electron density in the vicinity of the lithium nucleus. In all cases, bond formation was accompanied by an increase in the orbital kinetic energy of the lithium valence orbital. We suggest that these two observations represent important and significant features of chemical bonding which have not previously been emphasized.     

Nature of the near‐IR band in the electronic absorption spectra of neutral bis(tetrapyrrole) rare earth(III) complexes: Time‐dependent density functional theory calculations

The nature of the near‐IR band in the electronic absorption spectra of bis(tetrapyrrole) rare earth(III) complexes Y(Pc)₂ (1), La(Pc)₂ (2), Y(Pc)(Por) (3), Y(Pc)[Pc(α‐OCH₃)₄] (4), Y(Pc)[Pc(α‐OCH₃)₈] (5), and Y(Pc)[Pc(β‐OCH₃)₈] (6) was studied on the basis of time‐dependent density functional theory (TD‐DFT) calculations. The electronic dipole moment along the z‐axis in the electronic transition of the near‐IR band in all the studied neutral bis(tetrapyrrole) yttrium(III) and lanthanum(III) double‐deckers is well explained on the basis of the composition analysis of the orbitals involved. The electronic transition in the near‐IR band causes the reversion of the orbital orientation of one tetrapyrrole ring in both homoleptic and heteroleptic bis(tetrapyrrole) rare earth complexes and induces electron transfer from the tetrapyrrole ring with lower orbital energy to the other ring in the heteroleptic bis(tetrapyrrole) rare earth(III) complexes. The near‐IR band can work as an ideal characteristic absorption band to reflect the π–π interaction between the two tetrapyrrole rings in bis(tetrapyrrole) rare earth(III) double‐decker complexes because of its peculiar electronic transition nature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

Intramolecular interactions between fragments of L ‐phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L ‐phenylalanine, benzene and L ‐alanine are studied using density functional theory methods. While fully resolved experimental PES of L ‐phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e_1g and 1a_2u orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L ‐phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14‐20 eV, rather than outside of this region. This study presents a competent orbital based fragments‐in‐molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D‐PDF technique. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Electronic structures of heme a of cytochrome c oxidase in the redox states—Charge density migration to the propionate groups of heme a

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     

Ligand-derived oxidase activity. Catalytic aerial oxidation of alcohols (including methanol) by Cu(II)-diradical complexes

Seven new bis(o-iminosemiquinonato)copper(II) complexes, 1- 5, 1a, 1b, derived from differently substituted N-phenyl-2-aminophenol-based ligands, are described. Their crystal structures were determined by X-ray diffraction, and their electronic structures were established by various physical methods including electron paramagnetic resonance and variable-temperature (2-290 K) susceptibility measurements. Like complex 6, which was reported recently by us, all complexes exhibit an S t = (1)/ 2 ground state, based on the "isolated" copper(II)-spin character resulting from the dominating antiferromagnetic spin coupling between the two radicals; the ground-state electronic configuration can thus be designated as (increasing, increasing, decreasing)[R-Cu-R]. In addition, broken spin symmetry density functional solutions have been obtained. From the set of unrestricted canonical Kohn-Sham orbitals, the magnetic orbitals have been identified. The identification procedure is based on the nonvanishing overlap integrals between the space parts of orbitals occupied by electrons of opposite spin. The theoretically determined magnetic orbitals support the spin configurations suggested by the experiments. Electrochemical measurements (cyclic voltammetry and square-wave voltammetry) indicate ligand-centered redox processes. Complex 1 is found to be the best catalyst among the Cu(II) complexes for oxidation of primary alcohols with aerial oxygen as the sole oxidant to afford aldehydes under mild conditions. Thus, the function of the copper-containing enzyme Galactose Oxidase has been mimicked. Kinetic measurements in conjunction with electron paramagnetic resonance and electronic spectral studies have been used to decipher the catalytic oxidation process. A ligand-derived redox activity has been proposed as a mechanism for the aerial oxidation of primary alcohols.     

Orbital signatures of methyl in L-alanine

Molecular orbital signatures of the methyl substituent in L-alanine have been identified with respect to those of glycine from information obtained in coordinate and momentum space, using dual space analysis. Electronic structural information in coordinate space is obtained using ab initio (MP2/TZVP) and density functional theory (B3LYP/TZVP) methods, from which the Dyson orbitals are simulated based on the plane wave impulse approximation into momentum space. In comparison to glycine, relaxation in geometry and valence orbitals in L-alanine is found as a result of the attachment of the methyl group. Five orbitals rather than four orbitals are identified as methyl signatures. That is, orbital 6a in the core shell, orbitals 11a and 12a in the inner valence shell, and orbitals 19a and 20a in the outer valence shell. In the inner valence shell, the attachment of methyl to glycine causes a splitting of its orbital 10a' into orbitals 11a and 12a of L-alanine, whereas in the outer valence shell the methyl group results in an insertion of an additional orbital pair of 19a and 20a. The frontier molecular orbitals, 24a and 23a, are found without any significant role in the methylation of glycine.     

The electronic origin of unusually large nJFN coupling constants in some fluoroximes

SOPPA(CCSD) calculations show that the FC term is the most important contribution to the through‐space transmission of J_FN coupling constants for the fluoroximes studied in this work. Because of the well‐known behavior of FC term, a new rationalization for the experimental ^TSJ_FN SSCC is presented. It is mainly based on the overlap matrix (S_ij) between fluorine and nitrogen lone pairs obtained from NBO analyses. An expression is proposed to take into account the influence of the electronic density (D_ij) between coupled nuclei as well as the s% character at the site of the coupling nuclei of bonds and non‐bonding electron pairs involved in D_ij. In using this approach, a linear correlation between ^TSJ_FN versus D_ij is obtained. The most important aspect of this rationalization is related to the facility for understanding the behavior of some unusual experimental coupling constants. It is shown that, at least in this case, the electronic origin of the so‐called through‐space coupling is transmitted through to the overlap of orbitals on the coupled atoms, suggesting that, at least for these compounds, instead of through‐space coupling, it should better be dubbed as ‘through overlapping orbital coupling’. Copyright © 2013 John Wiley & Sons, Ltd.     

饱和烷烃分子C_nH_(2n+2)(n=4-6)的电子动量光谱(英文)

使用B3LYP/TZVP//B3LYP/aug-cc-pVTZ方法系统研究了饱和烷烃分子CnH2n+2(n=4-6)的轨道电子动量光谱,比较了同分异构体CnH2n+2(n=4-6)对轨道动量分布的影响.结合二维空间分析方法对电子在坐标空间中的密度分布进行了系统的研究.计算结果表明,最内价壳层电荷分布主要由s电子贡献,第二近邻芯价壳层则主要由p电子贡献,而其余的价壳层则为sp杂化.最内价轨道表现出最大的谱线强度并且远大于其它轨道的谱线强度,而且正烷烃的谱线强度要大于异烷烃等同分异构体的谱线强度,表现出了明显的与甲基移动的个数有关的性质.     

Importance of energy level matching for bonding in Th(3+)-Am(3+) actinide metallocene amidinates, (C(5)Me(5))(2)[(i)PrNC(Me)N(i)Pr]An

The synthesis of a rare trivalent Th(3+) complex, (C(5)Me(5))(2)[(i)PrNC(Me)N(i)Pr]Th, initiated a density functional theory analysis on the electronic and molecular structures of trivalent actinide complexes of this type for An = Th, Pa, U, Np, Pu, and Am. While the 6d orbital is found to accommodate the unpaired spin in the Th(3+) species, the next member of the series, Pa, is characterized by an f(2) ground state, and later actinides successively fill the 5f shell. In this report, we principally examine the evolution of the bonding as one advances along the actinide row. We find that the early actinides (Pa-Np) are characterized by localized f orbitals and essentially ionic bonding, whereas the f orbitals in the later members of the series (Pu, Am) exhibit significant interaction and spin delocalization into the carbon- and nitrogen-based ligand orbitals. This is perhaps counter-intuitive since the f orbital radius and hence metal-ligand overlap decreases with increasing Z, but this trend is counter-acted by the fact that the actinide contraction also leads to a stabilization of the f orbital manifold that leads to a near degeneracy between the An 5f and cyclopentadienyl π-orbitals for Pu and Am, causing a significant orbital interaction.