A Fischer-Type Ruthenium Carbene Complex as a Metathesis Catalyst for the Synthesis of Enol Ethers.

The Grubbs G-I or G-II catalyst gives the ruthenium ethoxy carbene complex, which catalyzes ring-opening cross metathesis (ROCM) of a strained cyclic alkene to give a diene where one of the two alkene moieties in the product contains an ethoxy substituent. No polymeric products are detected. Hydrocarbons such as parent norbornene or substituted cyclopropenes can proceed with the reaction smoothly. Tertiary amines, N-alkylimides, esters, and aryl or alkyl bromides remain intact under the reaction conditions. In addition to vinyl ethers, vinylic esters can also be used. The time required to reach a 50% yield of the ROCM product t50 varies from 0.01 to 140 h depending on the strain and nucleophilicity of the double bond. Anchimeric participation of an electron-rich group would result in significant enhancement of the reactivity, and the t50 could be as short as several minutes. A similar substrate without such a neighboring group shows a much slower rate. An exo-norborne derivative reacts much faster than the corresponding endo-isomer. Alkenes with poor nucleophilicity are less favored for the ROCM process, so is less strained cyclooctene.

Frozen-mode small polaron quantum master equation with variational bound for excitation energy transfer in molecular aggregates.

The small polaron quantum master equation (SPQME) is a powerful method for describing quantum dynamics in molecular systems. However, in the slow-bath regime where low-frequency vibrational modes dominate the dynamics, the fully dressed small polaron coordinates lead to errors in the SPQME theory. Furthermore, low-frequency modes also cause infrared divergence in the SPQME method, making the theory applicable only to systems described by spectral densities of the super-Ohmic form. In this study, we propose to treat these low-frequency vibrations as dynamically arrested "frozen" modes in a semiclassical representation and apply the small polaron representation only to the high-frequency vibrations. Furthermore, we show that a variational polaron approach can be utilized to determine the frequency upper bound of the frozen modes, allowing dynamical simulations free of manually tuned parameters. This frozen-mode SPQME is applied to models describing excitation energy transfer (EET) in molecular aggregates and comprehensively compared with the quasiadiabatic path integral method a well as the Redfield theory to demonstrate the applicability of this new method. We show that errors due to slow baths in the original SPQME theory are significantly reduced by the frozen-mode approximation. More significantly, we show that the new approach successfully extends the SPQME theory to be applicable to systems with the Drude-Lorentz spectral density, resulting in a great expansion of the applicability of the SPQME theory for EET problems. In summary, we demonstrate a "frozen-mode" SPQME that provides efficient and accurate simulations of EET dynamics of molecular systems in a broad parameter regime.

Band Structures of Quasi-One-Dimensional Incommensurate Helical Systems: A Case Study of Infinite Chromium Extended Metal Atom Chain.

Extended metal atom chains (EMACs) are promising candidates for molecular wires but their band structures remain to be explored. As a quasi-one-dimensional (Q1D) system, the incommensurate helical nature of EMACs hinders such calculations. In this work, we resolved this issue via explicit implementation of helical symmetry. Moreover, the pattern of metal d bands was rationalized by a systematic investigation on a series of related Q1D helical systems. Two critical factors, helical ligand field and chemically asymmetric ligand field, are proposed and identified. We found that the symmetry and ligand fields of the system dominate the pattern of the metal d bands, instead of specific chemical composition of ligands. The presented method and rationale are applicable to not only EMACs but also related Q1D helical systems.

Theory of charge transport in molecular junctions: Role of electron correlation.

We extend the quasi-particle renormalized perturbation theory developed in our previous work [Y.-W. Chang and B.-Y. Jin, J. Chem. Phys. 141, 064111 (2014)] based on nonequilibrium Green's function techniques to study the effects of electron correlation on the charge transport process in molecular junctions. In this formalism, the single-impurity Anderson's model is used as the zeroth-order Hamiltonian of each channel orbital, and the inter-channel interactions are treated by perturbation corrections. Within this scheme, the on-channel Coulomb repulsion and the single-particle spectral line-broadening can be incorporated in the zeroth-order approximation, and thus the Coulomb blockade and coherent tunneling through individual channels can be described properly. Beyond the zeroth-order description, electron correlation can be included through the self-energy corrections in the forms of the second-Born approximation and the GW approximation. The effects of electron correlation on molecular junctions are manifested as the orbital energy correction, correlated transport process, and collisional line-broadening. As an application, we have applied the present formalism to phenyl-based molecular junctions described by the Pariser-Parr-Pople Hamiltonian. The signatures of electron correlation in the simulated current-voltage curves are identified and discussed.

A simple molecular orbital treatment of current distributions in quantum transport through molecular junctions.

A simple molecular orbital treatment of local current distributions inside single molecular junctions is developed in this paper. Using the first-order perturbation theory and nonequilibrium Green's function techniques in the framework of Hückel theory, we show that the leading contributions to local current distributions are directly proportional to the off-diagonal elements of transition density matrices. Under the orbital approximation, the major contributions to local currents come from a few dominant molecular orbital pairs which are mixed by the interactions between the molecule and electrodes. A few simple molecular junctions consisting of single- and multi-ring conjugated systems are used to demonstrate that local current distributions inside molecular junctions can be decomposed by partial sums of a few leading contributing transition density matrices.

Hexahalogenated and their mixed benzene derivatives as prototypes for the understanding of halogen···halogen intramolecular interactions: New insights from combined DFT, QTAIM-, and RDG-based NCI analyses.

A large number of fully halogenated benzene derivatives containing the fluorine, chlorine, bromine, and iodine atoms have been experimentally synthesized both as single- and co-crystals (e.g., Desiraju et al., Chem. Eur. J. 2006, 12, 2222), yet the natures of the halogen ··· halogen interactions between the vicinal halogens in these compounds within the intramolecular domain are undisclosed. Given a fundamental understanding of these interactions is incredibly important in many areas of chemical, biological, supramolecular, and material sciences, we present here our newly discovered theoretical results that delineate whilst the nature of an F···F interaction in a pair of two adjacent fluorine atoms in either of the hexafluorobenzene and 1,4-dibromotetrafluorobenzene compounds examined is almost unclear, each of the latter three hexahalogenated benzene derivatives (viz., C6 Cl6 , C6 Br6 , and C6 I6 ), and each of the seven of their fully mixed hexahalogenated benzene analogues, are found to be stabilized by means of a number of halogen···halogen interactions, each a form of long-range attraction within the intramolecular domain. The Molecular Electrostatic Surface Potential model was found to be unsurprisingly unsuitable in unraveling any of the aforesaid attractions between the halogen atoms. However, such interactions successfully enunciated by a set of noncovalent interaction descriptors of geometrical, topological, and electrostatic origins. These latter properties were extracted combining the results of the Density Functional Theory electronic structure calculations with those revealed from Atoms in Molecules, and Reduced Density Gradient charge density-based topological calculations, and are expounded in detail to formalize the conclusions. © 2015 Wiley Periodicals, Inc.

Unusual bonding modes of perfluorobenzene in its polymeric (dimeric, trimeric and tetrameric) forms: entirely negative fluorine interacting cooperatively with entirely negative fluorine.

The F(δ-)···F(δ-) intermolecular synthon was recently observed to be useful for generating a two-dimensional layered supramolecular architecture on the Ag(111) surface (Kawai, et al., ACS Nano, 2015). This was formed when the entirely negative covalently bonded fluorine atoms in phenyleneethynylene(bis(2,3,5,6-tetrafluoro-4-(2,3,4,5,6-pentafluorophenylethynyl)phenyl)-ethyne (BPEPE-F18)) were in close proximity to the same atoms in another BPEPE-F18 molecule. With a view to provide rigorous insights into the physical chemistry of such an intermolecular synthon, we have selected perfluorobenzene (C6F6) as a model compound, and have performed extensive DFT-M06-2X/6-311++G(d,p) investigations on a number of its homomolecular dimers, trimers, and tetramers. Of the twelve (C6F6)2 dimers investigated, a displaced-parallel arrangement with an uncorrected binding energy (ΔE) of -7.4 kcal mol(-1) was found to be the most stable, and an incorporation of the basis set superposition error (BSSE) has significantly reduced its ΔE to -4.7 kcal mol(-1). Besides, the ΔE for a minimum-energy least stable conformation of the same dimer, which involves a single σhole(-)···σhole(-) type F(δ-)···F(δ-) intermolecular bonding interaction, amounts to -0.62 and -0.24 kcal mol(-1) without and with BSSE, respectively. The geometry of another conformation of the dimer, which accompanies a set of three F(δ-)···F(δ-) intermolecular interactions somehow similarly to those observed in the layered supramolecular structure formed by the BPEPE-F18 molecules, lies at a relative energy of 6.5 kcal mol(-1) above the most stable conformation. Passing from the latter dimer to an analogous (C6F6)3 trimer, as well as from the trimer to an analogous (C6F6)4 tetramer, the latter two clusters comprising windmill-type F(δ-)···F(δ-) intermolecular topologies, we have marked a preferential increase in the value of ΔE from -0.94 (dimer) to -2.76 (trimer) to -4.49 kcal mol(-1) (tetramer), thereby suggesting the presence of cooperative binding. An energy decomposition analysis has revealed that dispersion and polarization are the principal driving forces that bring the C6F6 molecules together in complex configurations. While a reasonable agreement was found between the charge density based topological results of the intermolecular bonding interactions that emerged from the application of Quantum Theory of Atoms in Molecules (QTAIM) and Reduced Density Gradient approaches to all the polymeric compounds, the results of the latter method were found to be too vague especially near the (3, +1) ring critical point regions. QTAIM's source function analysis has suggested that the fully negatively charged fluorine atoms in C6F6 serve as sinks for the F(δ-)···F(δ-) bond formation.

Ligand(s)-to-metal charge transfer as a factor controlling the equilibrium constants of late first-row transition metal complexes: revealing the Irving-Williams thermodynamical series.

A unified relationship between the experimental formation constants and the ligand(s)-to-metal charge transfer values of versatile ligand complexes of late transition series first-row bivalent metal ions is uncovered. The latter property not only explicates the Irving-Williams series but also rationalizes quantitatively Pearson's concept of hard and soft acids and bases by correlating the gas-phase to aqueous solution-phase chemistry in a broad sense.

Energy-Level Alignment for Single-Molecule Conductance of Extended Metal-Atom Chains.

The use of single-molecule junctions for various functions constitutes a central goal of molecular electronics. The functional features and the efficiency of electron transport are dictated by the degree of energy-level alignment (ELA), that is, the offset potential between the electrode Fermi level and the frontier molecular orbitals. Examples manifesting ELA are rare owing to experimental challenges and the large energy barriers of typical model compounds. In this work, single-molecule junctions of organometallic compounds with five metal centers joined in a collinear fashion were analyzed. The single-molecule i-V scans could be conducted in a reliable manner, and the EFMO levels were electrochemically accessible. When the electrode Fermi level (EF ) is close to the frontier orbitals (EFMO ) of the bridging molecule, larger conductance was observed. The smaller |EF -EFMO | gap was also derived quantitatively, unambiguously confirming the ELA. The mechanism is described in terms of a two-level model involving co-tunneling and sequential tunneling processes.

Significant evidence of C···O and C···C long-range contacts in several heterodimeric complexes of CO with CH3-X, should one refer to them as carbon and dicarbon bonds!

Noncovalent interactions in 18 weakly bound binary complexes formed between either of the two end-on orientations of the CO molecule and the methylated carbon positive σ-hole associated with the hydrophobic part of the CH3-X molecules are exploited using the density functional theory to examine the physical chemistry of the recently introduced 'carbon bonds' (Phys. Chem. Chem. Phys., 2013, 15, 14377), where X = -NO2, -CN, -F, -Cl, -Br, -OH, -CF3, -CCl3, and -NH2. The two important types of interactions are identified as C···O and C···C, the latter has probably never studied before, and are found to be stabilized by charge-transfer delocalizations between the electron-acceptor and -donor natural bond orbitals of the interacting partners involved, unveiled using natural bond orbital analysis. Application of atoms in molecular theory revealed preferable quantum mechanical exchange-correlation energy channels and (3, -1) bond critical points (bcps) between the atoms of noncovalently bonded pairs in these complexes, in excellent agreement with the results of the noncovalent-interaction reduced-density-gradient (NCI-RDG) theory that revealed expected isosurfaces and troughs in the low density region of the RDG vs. sign(λ2)ρ plots. The dependencies of the C···O and C···C bcp charge densities on their corresponding local energy densities, as well as on their corresponding bond electron delocalization indices are found to exhibit nontrivial roles of these topological descriptors to explain the stabilities of the investigated binary complexes. Moreover, the vibrational red- and blue-shifts in the CO bond stretching frequencies, and concomitant elongations and contractions of the corresponding bond lengths, both with respect to the monomer values, are observed upon the formation of the C···O- and C···C-bonded complexes, respectively. The increase and decrease in the complex dipole moments, relative to the sum of their respective monomer values, are found to be a characteristic that separates the aforementioned red- and blue-shifted interactions. In analogy with dihydrogen bonding, as well as that with the charge and electrostatic surface potential model descriptions, we suggest the C···C interactions to be referred to as dicarbon bonds.

Halogen bonding interaction of chloromethane with several nitrogen donating molecules: addressing the nature of the chlorine surface σ-hole.

With the goal of understanding the reason for the specific binding affinity of the chlorine in Cl-CH3 in the H2C=O···Cl-CH3 complex, we performed molecular electrostatic surface potential (MESP) analysis for isolated H3C-Cl with B3PW91, M06-2X, and MP2(full), all in conjunction with twenty-three Dunning- and Pople-type basis sets of double- and triple-ς valence qualities. The results obtained were benchmarked against the best level of theory employed, CCSD/6-311++G(3d,2p). It was found that the local maximum of the electrostatic potential, Vs,max, on the surface of the chlorine along the outermost extension of the C-Cl bond in Cl-CH3 would vary dramatically from slightly negative to slightly positive values with respect to the basis set sizes and correlation methods employed. Its value, mapped on the 0.001 electrons per bohr(3) isodensity surface, is approximately +1.0 kcal mol(-1) at the best level. This specific nature of the chlorine's Vs,max is ipso facto more plausible, and is clarified considering the 0.0015 and 0.002 electrons per bohr(3) isodensity envelopes, in which cases, Vs,max is apparently small and positive despite the varied basis sets and methods utilized. The thirteen binary complexes investigated using MP2(full)/6-311++G(3d,2p) are thus formed upon the interaction of chlorine's positive σ-hole in Cl-CH3 with the local most negative areas of electrostatic potential, Vs,min, confined on the surface of the nitrogen in the RN series of thirteen monomers, where RN = FCN, ClCN, BrCN, CH3CN, HOCN, HSCN, PCCN, PN, CCl3CN, SiH3CN, NCCN, CNCN, and NaCN. In all instances, the NCl intermolecular distances of separation evaluated are less than the sum of the chlorine and nitrogen van der Waals radii, 3.48 Å. The NCl contacts are all stable and have quasi-linear geometries (∠N···Cl-C ≅ 175-180°), unraveling the directional nature of the chlorine's positive σ-hole. The effect of substituents -R on the binding energies ΔE of the RNCl-CH3 complexes was found to be marginal, with values ranging from -0.39 to -1.29 kcal mol(-1) with MP2(full) and values from -0.02 to -0.84 kcal mol(-1) with CCSD(T). Applications of atoms in molecules and noncovalent interaction reduced-density-gradient methods revealed the N···Cl interactions to be of electrostatic origin. The red- and blue-shifts in the vibrational stretching frequencies of the C-Cl bonds estimated with MP2(full) were found to be accompanied with an increase and decrease in the corresponding bonds upon formation of the RN···Cl-CH3 complexes, respectively. Natural bond orbital analysis showed that there are several weak interorbital charge transfer interactions persisting between the electron-acceptor and -donor orbitals of the monomers interacting in the RN···Cl-CH3 complexes.

Theory of charge transport in molecular junctions: from Coulomb blockade to coherent tunneling.

We study charge transport through molecular junctions in the presence of electron-electron interaction using the nonequilibrium Green's function techniques and the renormalized perturbation theory. In the perturbation treatment, the zeroth-order Hamiltonian of the molecular junction is composed of independent single-impurity Anderson's models, which act as the channels where charges come through or occupy, and the interactions between different channels are treated as the perturbation. Using this scheme, the effects of molecule-lead, electron-electron, and hopping interactions are included nonperturbatively, and the charge transport processes can thus be studied in the intermediate parameter range from the Coulomb blockade to the coherent tunneling regimes. The concept of quasi-particles is introduced to describe the kinetic process of charge transport, and then the electric current can be studied and calculated. As a test study, the Hubbard model is used as the molecular Hamiltonian to simulate dimeric and trimeric molecular junctions. Various nonlinear current-voltage characteristics, including Coulomb blockade, negative differential resistance, rectification, and current hysteresis, are shown in the calculations, and the mechanisms are elucidated.

Correspondence between Gentile oscillators and N-annulenes.

The cyclic hydrocarbon polyenes with the general formula CNHN are called N-annulenes. In this paper, we discover that Gentile oscillators and N-annulenes in the Hückel approximation have the same energy spectra determined by the contact points of a regular polygon inscribed on a circle. This correspondence is derived from the symmetry of a C(n + 1) rotational group and dihedral group DihN. On the basis of their energy spectra, we further demonstrate that these two kinds of systems have the same partition functions and, thus, the same thermodynamics properties. N-annulenes can, therefore, be viewed as the natural realization of Gentile systems.

Correlation effects of π electrons on the band structures of conjugated polymers using the self-consistent GW approximation with vertex corrections.

Many-body perturbation theory is used to investigate the effect of π-electron correlations on the quasi-particle band structures of conjugated polymers at the level of the Pariser-Parr-Pople model. The self-consistent GW approximation with vertex corrections to both the self-energy and the polarization in Hedin's equations is employed in order to eliminate self-interaction errors and include the effects of electron-hole attraction in screening processes. The dynamic inverse dielectric function is constructed from the generalized plasmon-pole approximation with the static dressed polarization given by the coupled-perturbed Hartree-Fock equation. The bandgaps of trans-polyacetylene, trans-polyphenylenevinylene and poly(para)phenylene are calculated by both the Hartree-Fock and GW approximation, and a lowering of bandgaps due to electron correlations is found. We conclude that both dielectric screening and vertex corrections are important for calculating the quasi-particle bandgaps of conjugated polymers.

Interchain interactions in organic conjugated dimers: a composite-molecule approach.

A theoretical composite-molecule (CM) model is adopted for evaluating the electronic excited states and excitonic couplings of cofacial conjugated dimers where the contributions of charge-transfer (CT) exciton, unavailable by the commonly used supermolecular approach due to the inadequate basis set construction, can be unambiguously identified within this methodology. This method builds up with the basis set of individual molecules and then constructs combined electronic states for the dimer by considering intermolecular interactions including charge-transfer interactions. The dependences of the matrix elements on intermolecular distance and conjugation length are examined. At the short distance region between two of the polyene molecules in the dimer, the CT transitions are apparently mixing to both first and second excited states. Also, some of the matrix elements for the mixing of CT transitions with local transitions which related to the second excited state are found to be considerably larger than the exciton-type elements. An interesting finding is that with increasing the chain size the CT contribution to the second excited state reveals a minimum and indicates HOMO to LUMO charge transfer is not the major CT contribution to the second excited state in the face-to-face polyene dimer with larger chain size and interchain separation in the region of 3.6-4.0 A. A detail analysis reveals that HOMO-1 to LUMO and HOMO to LUMO+1 charge transfers are major CT contributions to the second excited state in the condition under study.

Transport through a mixed-valence molecular transistor in the sequential-tunneling regime: Theoretical insight from the two-site Peierls-Hubbard model.

Transport through a mixed-valence system in the sequential-tunneling region is investigated using the master equation method and a simple two-site Peierls-Hubbard model that includes electron-phonon (e-p) coupling, electron hopping, and electron-electron (e-e) repulsion. The characteristics of Coulomb diamonds in the conductance spectra under three regimes are discussed. In the regime of zero e-p coupling, we found that the widths of Coulomb diamonds are dominated by the competition of electron-hopping and Coulomb repulsion. In the regime of weak and intermediate e-p coupling, by virtue of the normal-mode transformation we found that coupling to the symmetric-mode decreases the widths of Coulomb diamonds. In the regime of strong e-p coupling, an analytical expression for the widths of Coulomb diamonds can be derived using the small polaron transformation. The derived formula provides a new way to estimate e-e interactions and e-p couplings experimentally.

The synthesis and magnetic properties of a linear mixed-valence [Ni3]5+ in an anthyridine tri-nickel complex.

A novel trinuclear complex [Ni3(µ3-dbay)4Cl2]I3 (1) with a mixed-valence state was prepared by reacting the tridentate ligand 1,13,14-triaza-dibenz[a,j]anthracene (dibenzanthyridine = dbay) with anhydrous NiCl2 and sodium tetraphenylborate. The title compound provides the first example of a trinuclear nickel-anthyridine-based string complex in which the metal framework of complex 1 consists of NiII-NiI-NiII. X-ray crystallography, magnetic susceptibility and detailed EPR measurements were performed to characterize the structure and magnetic properties of this unique complex.

One-handed helical double stranded polybisnorbornenes.

Helical double stranded polymers incorporated with a covalently bound chiral ferrocene linker are synthesised and characterized by CD spectra and STM images and molecular dynamics simulations.

Three-dimensional through-space/through-bond delocalization in cyclophane systems: a molecule-in-molecule approach.

In this article, we propose a simple strategy to identify the nature of excitonic couplings in a series of cyclophanedienes based on the "molecule-in-molecule" (MIM) theory. The contributions of charge-transfer (CT) exciton, unavailable by the commonly used supermolecular approach due to the inadequate basis set, can be unambiguously identified within this methodology. Combining the CT contributions calculated on the cyclophanedienes and the corresponding hypothetical molecules with tethers removed, one can infer the information on the relative importance of through-bond and through-space contributions in the low-lying excited states. Particularly, we discovered that the tether effect for the meta-linkage cyclophanedienes is crucial, whereas those for para-linkage cyclophanedienes are vanishingly small. The changes in the coupling between two moieties for both the six-membered meta-linkage and five-membered cyclophanedienes arise primarily from an increase in the through-bond charge-transfer component of the coupling (>70%). Within the MIM model, the delocalization pathway of the dimer in the excited state can be explained quantitatively by a CT exciton, which differs from the approach based on the conventional orbital interaction analysis.

Nonhelical heterometallic [Mo2M(npo)4(NCS)2] string complexes (M = Fe, Co, Ni) with high single-molecule conductance.

Using the planar 1,8-naphthyridin-2(1H)-one (Hnpo) ligand, novel nonhelical HMSCs [Mo2M(npo)4(NCS)2] (M = Fe, Co, Ni) were synthesised and they exhibited high single-molecule conductance.