A new strategy for hyperconjugative antiaromatic compounds utilizing negative charges: a dibenzo[b,f]silepinyl dianion.

Herein we propose a new strategy for hyperconjugative antiaromatic compounds utilizing negative charges and design the 5,5-diphenyldibenzo[b,f]silepinyl dianion (pseudo 16π-electron system) in which negative hyperconjugation occurs between the anionic π-cloud and the σ*(Si-Ph) orbital. Essentially, reduction of the dibenzo[b,f]silepin with lithium readily generated a dilithium salt of the dibenzosilepinyl dianion, and its hyperconjugative antiaromaticity has been evidenced by the upfield shifts of 1H NMR signals and theoretical calculations, including large NICSzz values and ACID plots.

Theoretical analysis of the kinetic isotope effect on carboxylation in RubisCO.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) fixes atmospheric carbon dioxide into bioavailable sugar molecules. It is also well known that a kinetic isotope effect (KIE; CO2 carbon atoms) accompanies the carboxylation process. To describe the reaction and the KIE α, two different types of molecular dynamics (MD) simulations (ab initio MD and classical MD) have been performed with an Own N-layered Integrated molecular Orbitals and molecular Mechanics (ONIOM)-hybrid model. A channel structure for CO2 transport has been observed during the MD simulation in RubisCO, and assuming the reaction path from the inlet to the product through the coordinate complex with Mg2+ , simulations have been performed on several molecular configuration models fixing several distances between CO2 and ribulose-1,5-bisphosphate along the channel. Free energy analysis and diffusion coefficient analysis have been evaluated for different phases of the process. It is confirmed that the isotopic fractionation effect for CO2 containing either 13 C or 12 C would appear through the transiting path in the channel structure identified in RubisCO. The estimated isotope fractionation constant was quite close to the experimental value.

Catalysis of Cu Cluster for NO Reduction by CO: Theoretical Insight into the Reaction Mechanism.

Density functional theory calculations here elucidated that Cu38-catalyzed NO reduction by CO occurred not through NO dissociative adsorption but through NO dimerization. NO is adsorbed to two Cu atoms in a bridging manner. NO adsorption energy is much larger than that of CO. N-O bond cleavage of the adsorbed NO molecule needs a very large activation energy (ΔG°‡). On the other hand, dimerization of two NO molecules occurs on the Cu38 surface with small ΔG°‡ and very negative Gibbs reaction energy (ΔG°) to form ONNO species adsorbed to Cu38. Then, a CO molecule is adsorbed at the neighboring position to the ONNO species and reacts with the ONNO to induce N-O bond cleavage with small ΔG°‡ and very negative ΔG°, leading to the formation of N2O adsorbed on Cu38 and CO2 molecule in the gas phase. N2O dissociates from Cu38, and then it is readsorbed to Cu38 in the most stable adsorption structure. N-O bond cleavage of N2O easily occurs with small ΔG°‡ and significantly negative ΔG° to form the N2 molecule and the O atom adsorbed on Cu38. The O atom reacts with the CO molecule to afford CO2 and regenerate Cu38, which is rate-determining. N2O species was experimentally observed in Cu/γ-Al2O3-catalyzed NO reduction by CO, which is consistent with this reaction mechanism. This mechanism differs from that proposed for the Rh catalyst, which occurs via N-O bond cleavage of the NO molecule. Electronic processes in the NO dimerization and the CO oxidation with the O atom adsorbed to Cu38 are discussed in terms of the charge-transfer interaction with Cu38 and Frontier orbital energy of Cu38.

Reaction Behavior of the NO Molecule on the Surface of an Mn Particle (M = Ru, Rh, Pd, and Ag; n = 13 and 55): Theoretical Study of Its Dependence on Transition-Metal Element.

Reaction of NO molecule on M13 and M55 clusters (M = Ru, Rh, Pd, and Ag) was theoretically investigated to elucidate why its reaction behavior depends on the position of metal element in the periodic table. DFT computations show that NO dissociative adsorption occurs on M = Ru and Rh, NO molecular adsorption occurs on M = Pd, and NO dimerization occurs on M = Ag, which agree with experimental findings. The d-band center and d-band top become lower in energy following the order Ru > Rh > Pd > Ag; this is one of the characteristic features of the periodic table. In the Ag cluster, the valence band-top consists of Ag 5s orbital and its energy is higher than the d-band top of Pd. For NO dissociative adsorption, the M-N and M-O bond strengths are crucially important at the transition state and the product, to which the metal d orbital contributes very much. Ru and Rh clusters have a high energy d-band center and d-valence band top, leading to the formation of strong M-N and M-O bonds. Pd and Ag clusters have a low energy d-band center and d-band top, leading to the formation of weak M-N and M-O bonds. Because the Ag cluster has a high energy 5s valence band that can overlap well with the π* + π* MO of ONNO (NO dimer) moiety due to the same symmetry, charge transfer (CT) occurs from the Ag cluster to the π* + π* MO, which is indispensable for NO dimerization. The 4d-valence band top of Ru and Rh clusters does not fit to the π* + π* MO because of the different symmetry. Though the d-valence band top of the Pd cluster can overlap with the π* + π* MO, its energy is low, which is not good for the CT. Thus, the reactivity of metal cluster for NO is determined by the energy and type (4d or 5s) of the valence band top, which both depend on the position of element in the periodic table; accordingly, Ru and Rh clusters are reactive for NO dissociative adsorption, the Ag cluster is reactive for NO dimerization, but the Pd cluster is not reactive for both and only NO molecular adsorption is possible.

Electronic processes in NO dimerization on Ag and Cu clusters: DFT and MRMP2 studies.

Experimentally observed NO dimerization on Cu and Ag surfaces is surprising because binding energy of NO dimer is very small in gas phase. MRMP2, MP2 to MP4, CCSD(T), and DFT studies of NO dimerization on Ag2 and Cu2 clusters disclosed that the CCSD(T) method could be applied to this reaction on Ag2 and Cu2 unlike NO dimerization in gas phase which exhibits significantly large nondynamical electron correlation effect. Charge-transfer (CT) from Ag2 and Cu2 to NO moieties plays important role in NN bond formation between two NO molecules. This CT considerably decreases nondynamical correlation effect. Also, the DFT method could be applied to this NO dimerization, if appropriate DFT functional is used; all pure functionals examined here and most of the hybrid functionals underestimated the activation barrier (Ea ), while only ωB97X provided Ea similar to CCSD(T)-calculated value. NO dimerization on similar Cu2 and Cu5 needs moderately larger Ea than those on Ag2 and Ag5 , because frontier orbital participating in the CT exists at lower energy in Cu2 and Cu5 than in Ag2 and Ag5 . The Ea decreases in the order Ag2 >> Ag38 > Ag7 ∼ Ag5 and the reaction energy (ΔE) is positive (endothermic) in Ag2 but significantly negative in Ag38 , Ag7 , and Ag5 , indicating that various Ag clusters could be effective for NO dimerization except for Ag2 . The decreasing order of Ea and increasing order of exothermicity are attributed to increasing order of the frontier orbital energy of Ag2 < Ag38 < Ag7 ∼ Ag5 . © 2018 Wiley Periodicals, Inc.

First-Order Interacting Space Approach to Excited-State Molecular Interaction: Solvatochromic Shift of p-Coumaric Acid and Retinal Schiff Base.

A triple-layer QM/sQM/MM method was developed for accurately describing the excited-state molecular interactions between chromophore and the molecular environment (Hasegawa, J.; Yanai, K.; Ishimura, K. ChemPhysChem 2015, 16, 305). A first-order-interaction space (FOIS) was defined for the interactions between QM and secondary QM (sQM) regions. Moreover, configuration interaction singles (CIS) and its second-order perturbation theory (PT2) calculations were performed within this space. In this study, numerical implementation of this FOISPT2 method significantly reduced the computing time, which realized application to solvatochromic systems, p-coumaric acid in neutral ( p-CA) and anionic forms in aqueous solution, retinal Schiff base in methanol (MeOH) solution, and bacteriorhodopsin (bR). The results were consistent with the experimentally observed absorption spectra of the applied systems. The QM/sQM/MM result for the opsin shift was in better agreement to the experimental result than that of the ordinary QM/MM. A decomposition analysis was performed for the excited-state molecular interactions. Among the electronic interactions, charge-transfer (CT) effect, excitonic interaction, and dispersion interaction showed significant large contributions, while the electronic polarization effect presented only minor contribution. Furthermore, the result was analyzed to determine the contributions from each environmental molecule and was interpreted based on the distance of the molecules from the π system in the chromophores.

Electronic Polarization Effect of the Water Environment in Charge-Separated Donor-Acceptor Systems: An Effective Fragment Potential Model Study.

The electronic polarization (POL) of the surrounding environment plays a crucial role in the energetics of charge-separated systems. Here, the mechanism of POL in charge-separated systems is studied using a combined quantum mechanical and effective fragment potential (QM/EFP) method. In particular, the POL effect caused by charge separation (CS) is investigated at the atomic level by decomposition into the POL at each polarizability point. The relevance of the electric field generated by the CS is analyzed in detail. The model systems investigated are Na+-Cl- and guanine-thymine solvated in water. The dominant part of the POL arises from solvent molecules close to the donor (D) and acceptor (A) units. At short D-A distances, the electric field shows both positive and negative interferences. The former case enhances the POL energy. At longer distances, the interference is weakened, and the local electric field determines the POL energy.

How Can We Understand Au8 Cores and Entangled Ligands of Selenolate- and Thiolate-Protected Gold Nanoclusters Au24(ER)20 and Au20(ER)16 (E = Se, S; R = Ph, Me)? A Theoretical Study.

The geometries and electronic structures of selenolate-protected Au nanoclusters, Au24(SeR)20 and Au20(SeR)16, and their thiolate analogues are theoretically investigated with DFT and SCS-MP2 methods, to elucidate the electronic structure of their unusual Au8 core and the reason why they have the unusual entangled "staple-like" chain ligands. The Au8 core is understood to be an [Au4](2+) dimer in which the [Au4](2+) species has a tetrahedral geometry with a closed-shell singlet ground state. The SCS-MP2 method successfully reproduced the distance between two [Au4](2+) moieties, but the DFT with various functionals failed it, suggesting that the dispersion interaction is crucial between these two [Au4](2+) moieties. The SCS-MP2-calculated formation energies of these nanocluster compounds indicate that the thiolate staple-like chain ligands are more stable than the selenolate ones, but the Au8 core more strongly coordinates with the selenolate staple-like chain ligands than with the thiolate ones. Though Au20(SeR)16 has not been reported yet, its formation energy is calculated to be large, suggesting that this compound can be synthesized as a stable species if the concentration of Au(SeR) is well adjusted. The aurophilic interactions between the staple-like chain ligands and between the Au8 core and the staple-like chain ligand play an important role for the stability of these compounds. Because of the presence of this autophilic interaction, Au24(SeR)20 is more stable than Au20(SeR)16 and the unusual entangled ligands are involved in these compounds.

Quantum mechanical molecular interactions for calculating the excitation energy in molecular environments: a first-order interacting space approach.

Intermolecular interactions regulate the molecular properties in proteins and solutions such as solvatochromic systems. Some of the interactions have to be described at an electronic-structure level. In this study, a commutator for calculating the excitation energy is used for deriving a first-order interacting space (FOIS) to describe the environmental response to solute excitation. The FOIS wave function for a solute-in-solvent cluster is solved by second-order perturbation theory. The contributions to the excitation energy are decomposed into each interaction and for each solvent.

First-principles computational visualization of localized surface plasmon resonance in gold nanoclusters.

Cluster-size dependence of localized surface plasmon resonance (LSPR) for Aun nanoclusters (n = 54, 146, 308, 560, 922, 1414) is investigated by using our recently developed computational program of first-principles calculations for photoinduced electron dynamics in nanostructures. The size of Au1414 (3.9 nm in diameter) is unprecedentedly large in comparison with those addressed in previous first-principles calculations of optical response in nanoclusters. These computations enable us to clearly see that LSPR gradually grows and the LSPR peaks red shift with increasing cluster size. The growth of LSPR is visualized in real space, demonstrating that electron charge distributions oscillate in a collective manner around the outermost surface region of the clusters. We further illustrate that the core d electrons screen the collective oscillation of the conduction-like s electrons.

Facile synthesis of dibenzopentalene dianions and their application as new π-extended ligands.

Reduction of phenyl(silyl)ethynes with potassium followed by quenching with iodine gave dibenzopentalenes in moderate yields. The intermediates of the reactions, dipotassium dibenzopentalenides, were isolated. The first dibenzopentalene-transition-metal complex was successfully synthesized. The ruthenium atoms are located above the six-membered rings. However, X-ray diffraction analysis and theoretical calculations revealed that the aromatic nature of the five-membered rings was retained. The cyclic voltammetry of the Ru complex revealed two oxidation waves with relatively large separation.

Interaction Energy of Large Molecules from Restrained Denominator MP2-F12.

A new one-parameter correction scheme to second-order Møller-Plesset many-body perturbation theory (MP2) has been proposed to correctly evaluate intermolecular interaction energies of large π-π dispersion interaction systems as well as hydrogen-bonded and σ-σ dispersion interaction ones. The scheme restrains the denominator of the MP2 correlation energy expression based on the observation that larger corrections to MP2 are required as the orbital energy gaps become small as in large π-π stacking systems. The root-mean-square-deviation of the restrained denominator MP2 with F12 correction (RD-MP2-F12) on the S66 set of 0.346 kcal/mol is less than half of that of MP2-F12. The interaction energies of RD-MP2 are similar to those of dispersion corrected density functional theory for a series of polyaromatic hydrocarbon dimers. For the C60-fullerene dimer, however, the RD-MP2-F12 result somewhat deviates from the experimental estimate, indicating that an explicit inclusion of higher order correlation is required for the system.

Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method.

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order Møller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.

Dilithioplumbole: a lead-bearing aromatic cyclopentadienyl analog.

Although the concept of aromaticity has long played an important role in carbon chemistry, it has been unclear how applicable the stabilizing framework is to the heaviest elements. Here we report the synthesis of dilithiotetraphenylplumbole by reduction of hexaphenylplumbole. X-ray crystallography revealed a planar structure with no alternation of carbon-carbon bond lengths in the five-membered ring core. Nuclear magnetic resonance spectra and relativistic theoretical calculations show considerable aromatic character in the molecule, thus extending aromaticity to carbon's heaviest congener.

Mechanism and dynamic correlation effects in cycloaddition reactions of singlet difluorocarbene to alkenes and disilene.

Mechanisms of the cycloaddition reactions of singlet difluorocarbene (CF(2)) to alkenes and disilene were studied using CASSCF, MR-MP2, CR-CC(2,3), and UB3LYP methods in combination with basis sets up to 6-311++G(3d,p). The CASSCF(4,4) energies suggest that the cycloadditions all follow the stepwise mechanism. However, energies calculated using the MR-MP2(4,4) and CR-CC(2,3) methods in combination with the 6-311G(d) or larger basis sets consistently show that the reactions follow a concerted mechanism. The stepwise mechanisms predicted at the CASSCF level are "artificial" because of their neglect of dynamic electron correlation effects. The importance of dynamic electron correlation in determining the mechanistic nature of the reactions is explained through knowledge of the reacting system's geometries and charges along the reaction path.

Dichlorocarbene addition to C60 from the trichloromethyl anion: carbene mechanism or Bingel mechanism?

The reactions of C(60) and trichloromethyl anion (CCl(3)(-)) via both the Bingel mechanism and the carbene mechanism were comparably studied by means of density functional theory (DFT) computations. The Bingel mechanism is highly competitive as compared with the carbene mechanism that leads to the formation of C(60)(CCl(2)). Unlike the carbene mechanism with a weak regioselectivity and solvent sensitivity, the Bingel mechanism yields the [6,6]-C(60)(CCl(2)) isomer as the exclusive product and favors highly polar solvents. The results receive strong experimental support and simultaneously rationalize these experimental findings.

Synthesis, structure and reactions of a trianion equivalent, trilithiostannane.

Transmetallation reaction of trisilylstannane ArSn(SiHMe(2))(3) (Ar = 2,6-bis(2,4,6-triisopropylphenyl)phenyl), bearing a bulky substituent on the tin atom, with methyllithium in THF at room temperature gave the first trianion equivalent, trilithiostannane ArSnLi(3), the generation of which was confirmed by trapping experiments with some electrophiles as well as by (119)Sn and (7)Li NMR spectroscopy.