Search Results (18)

Trinuclear and tetranuclear ruthenium carbonyls of the types Ru₃(CO)_n(NO)₂, Ru₃(N)(CO)_n(NO), Ru₃(N)₂(CO)_n, Ru₃(N)(CO)_n(NCO), Ru₃(CO)_n(NCO)(NO), Ru₄(N)(CO)_n(NO), Ru₄(N)(CO)_n(NCO), and Ru₄(N)₂(CO)_n related to species observed experimentally in the chemistry of Ru₃(CO)₁₀(µ-NO)₂ have been investigated using density functional theory. In all cases, the experimentally observed structures have been found to be low-energy structures. The low-energy trinuclear structures typically have a central strongly bent Ru–Ru–Ru chain with terminal CO groups and bridging nitrosyl, isocyanate, and/or nitride ligands across the end of the chain. The low-energy tetranuclear structures typically have a central Ru₄N unit with terminal CO groups and a non-bonded pair of ruthenium atoms bridged by a nitrosyl or isocyanate group. Full article

In this work, we use density functional theory to investigate the electronic structure of poly(3,4-ethylenedioxythiophene) (PEDOT) oligomers with co-located AlCl₄⁻ anions, a promising combination for energy storage. The 1980s bipolaron model remains the dominant interpretation of the electronic structure of PEDOT despite recent theoretical progress that has provided new definitions of bipolarons and polarons. By considering the influence of oligomer length, oxidation or anion concentration and spin state, we find no evidence for many of the assertions of the 1980s bipolaron model and so further contribute to a new understanding. No self-localisation of positive charges in PEDOT is found, as predicted by the bipolaron model at the hybrid functional level. Instead, our results show distortions that exhibit a single or a double peak in bond length alternations and charge density. Either can occur at different oxidation or anion concentrations. Rather than representing bipolarons or polaron pairs in the original model, these are electron distributions driven by a range of factors. Distortions can span an arbitrary number of nearby anions. We also contribute a novel conductivity hypothesis. Conductivity in conducting polymers has been observed to reduce at anion concentrations above 0.5. We show that at high anion concentrations, the energy of the localised, non-bonding anionic orbitals approaches that of the system HOMO due to Coulombic repulsion between anions. We hypothesize that with nucleic motion in the macropolymer, these orbitals will interfere with the hopping of charge carriers between sites of similar energy, lowering conductivity. Full article

Generic polymer models capturing the chain connectivity and the non-bonded excluded-volume interactions between polymer segments can be classified into hard- and soft-core models depending on their non-bonded pair potential. Here we compared the correlation effects on the structural and thermodynamic properties of the hard- and soft-core models given by the polymer reference interaction site model (PRISM) theory, and found different behaviors of the soft-core models at large invariant degree of polymerization (IDP) depending on how IDP is varied. We also proposed an efficient numerical approach, which enables us to accurately solve the PRISM theory for chain lengths as large as 10⁶. Full article

Single-molecule force spectroscopy methods, such as AFM and magnetic tweezers, have proved extremely beneficial in elucidating folding pathways for soluble and membrane proteins. To identify factors that determine the force rupture levels in force-induced membrane protein unfolding, we applied our near-atomic-level Upside molecular dynamics package to study the vertical and lateral pulling of bacteriorhodopsin (bR) and GlpG, respectively. With our algorithm, we were able to selectively alter the magnitudes of individual interaction terms and identify that, for vertical pulling, hydrogen bond strength had the strongest effect, whereas other non-bonded protein and membrane–protein interactions had only moderate influences, except for the extraction of the last helix where the membrane–protein interactions had a stronger influence. The up–down topology of the transmembrane helices caused helices to be pulled out as pairs. The rate-limiting rupture event often was the loss of H-bonds and the ejection of the first helix, which then propagated tension to the second helix, which rapidly exited the bilayer. The pulling of the charged linkers across the membrane had minimal influence, as did changing the bilayer thickness. For the lateral pulling of GlpG, the rate-limiting rupture corresponded to the separation of the helices within the membrane, with the H-bonds generally being broken only afterward. Beyond providing a detailed picture of the rupture events, our study emphasizes that the pulling mode greatly affects the factors that determine the forces needed to unfold a membrane protein. Full article

The fluorine-adsorption-induced local bond relaxation and valence-energy-state evolution of the Ti(0001) surface were examined through density functional theory calculations. The predicted bond–band–barrier (3 B) correlation notation framework for the interaction of the fluorine adsorbate with Ti atoms formed a tetrahedral structure through the creation of four valence density-of-state features, namely bonding electron pairs, nonbonding lone pairs, holes, and antibonding dipoles. The bonding states resulted in the passivation of metal Ti surfaces, the formation of Ti^p dipoles and Ti^+/p H-like bonds modulated the work function of the Ti(0001) surface, and the conversion of metallic Ti to semiconducting titanium fluoride by the holes. The findings of this study confirm the universal applicability of the 3 B correlation notation in the dynamics of fluorine chemisorption and the associated valence electrons involved in fluorination. Full article

The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers of consecutively hydrophobic residues with the same chain length were simulated under a broad temperature range. We concluded that the proteins with higher ratio or larger number of sequentially hydrophobic residues present more orientated and compact structure under a certain low temperature. It is attributed to the lower non-bonded potential energy between H-H residual pairs, especially more hydrophobic residues in a procession among the protein chain. Considering the microscopic structure of the protein, more residue contacts are achieved with the proteins with higher ratios and sequential H residues under the low temperature. Meanwhile, with the ratio and consecutive number of H residues increasing, the distribution of stem length showed a transition from exponential decline to unimodal and even multiple peaks, indicating the specific ordered structure formed. These results provide an insight into 3D structural properties of proteins from their residue sequences, which has a primary structure at molecular level and, ultimately, a practical possibility of applying in biotechnological applications. Full article

The crystal structure of magnussonite, ideally Mn²⁺₁₈[As³⁺₆(Mn¹⁺_x)O₁₈]₂[(H₂O, Cl_x, ☐) (H₂O, ☐)]₂, from Långban, Sweden, was refined to an R₁-index of 1.19% and the structure proposed by Moore and Araki (1979) is confirmed. Magnussonite has a densely packed structure of (Mnφ_n) polyhedra, φ = (O²⁻, H₂O, Cl⁻), and (As³⁺O₃) triangular pyramids that is best envisaged as layers of polyhedra in the same way as many of the other manganese-arsenite-arsenate structures from Långban. There are two distinct layers in magnussonite; the two layers may be combined into a slab that stacks along the a-direction with rotations between adjacent slabs. A surprising feature of the dense-packed magnussonite atomic arrangement is an array of structural channels along [111] that contain much of the disorder that occurs in the magnussonite structure. The channels contain the partly occupied MX site on the central axis of the channel, and the CLW2 site (with extremely low occupancy), also on the central axis of the channel. The CLW2 site, previously unrecognized in the magnussonite structure, contains H₂O, whereas the minor Cl in the structure resides in the CLW1 channel site, balancing the charge of the MX-site occupant. The MX site on the central axis of the channels displays a coordination known only in Långban minerals. In the local arrangement around the unoccupied MX site, the neighboring (As³⁺O₃) groups project their associated stereoactive lone-pairs of electrons into the channel. Where the MX site is occupied by Mn, there are six lone-pairs of electrons pointing toward Mn; the 18-electron rule predicts/rationalizes formulae for this stable transition-metal cluster. The (As³⁺O₃) groups and MX occupant form a [Mn⁺(As³⁺O₃)₆] arrangement in accord with the 18-electron rule where Mn⁺ contributes 6 3d electrons and the six lone-pairs of the [(As³⁺O₃)₆] arrangement contribute 12 electrons for a total of 18 electrons that form nine molecular orbitals that are metal-ligand bonds or non-bonding. Magnussonite and dixenite, another basic manganese-iron arsenate-arsenite-silicate mineral of the Långban-type deposits in Bergslagen, Sweden, are the only two minerals known with such local [M⁺(As³⁺O₃)_n] transition-metal clusters. The presence of these exotic clusters in structures containing densely packed Mn²⁺ octahedra is not understood at present. Full article

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1–3 and some 1–4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine–thymine and cytosine–guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds. Full article

Tin monoxide, SnO, and its analog, lead monoxide, PbO, have the same tetragonal P4/nmm structure, shaped by nonbonding dispersion forces and lone pairs. The high-pressure phases of SnO and PbO have been explored in several experimental and theoretical studies, with conflicting results. In this study, the high-pressure structures of SnO and PbO are investigated using density functional theory calculations combined with an evolutionary algorithm to identify novel high-pressure phases. We propose that the monoclinic P2₁/m SnO and orthorhombic Pmmn PbO phases, which are metastable at 0 GPa, are a slight rearrangement of the tetragonal P4/nmm-layered structure. These orthorhombic (and their closely related monoclinic) phases become more favored than the tetragonal phase upon compression. In particular, the transition pressures to the orthorhombic γ-phase Pmn2₁ of SnO/PbO and the monoclinic phase P2₁/m of SnO are found to be consistent with experimental studies. Two new high-pressure SnO/PbO polymorphs are predicted: the orthorhombic Pbcm phase of SnO and the monoclinic C₂/m of PbO. These phases are stabilized in our calculations when P > 65 GPa and P > 50 GPa, respectively. The weakening of the lone pair localization and elastic instability are the main drivers of pressure-induced phase transitions. Modulations of the SnO/PbO electronic structure due to structural transitions upon compression are also discussed. Full article

Monolayer group-IV tellurides with phosphorene-derived structures are attracting increasing research interest because of their unique properties. Here, we systematically studied the quasiparticle electronic and optical properties of two-dimensional group-IV tellurides (SiTe, GeTe, SnTe, PbTe) using the GW and Bethe–Salpeter equation method. The calculations revealed that all group-IV tellurides are indirect bandgap semiconductors except for monolayer PbTe with a direct gap of 1.742 eV, while all of them are predicted to have prominent carrier transport ability. We further found that the excitonic effect has a significant impact on the optical properties for monolayer group-IV tellurides, and the predicted exciton binding energy is up to 0.598 eV for SiTe. Interestingly, the physical properties of monolayer group-IV tellurides were subject to an increasingly isotropic trend: from SiTe to PbTe, the differences of the calculated quasiparticle band gap, optical gap, and further exciton binding energy along different directions tended to decrease. We demonstrated that these anisotropic electronic and optical properties originate from the structural anisotropy, which in turn is the result of Coulomb repulsion between non-bonding electron pairs. Our theoretical results provide a deeper understanding of the anisotropic properties of group-IV telluride monolayers. Full article

From a tight-binding approach to the instability of nonbonding electronic states, along a double-well potential, we consider here how the coupling of these states with a phonon mode can open a superconducting gap at the Fermi level. The alternation of broken- and unbroken-symmetry states, along the phonon breathing distortion, induces the mixing of band-edge states on a very short timescale, according to the noncrossing rule of chemists. We show that this mixing may generate cationic and anionic disproportionation. The negative U mechanism is thus justified here, leading to the mixing of occupied and unoccupied pair states, for the opening of a 2Δ superconducting gap. The closeness of broad σ* and narrow π* bands in the vicinity of the Fermi level should favor the superconducting phase over the insulating or metallic state, in agreement with Micnas et al.’s studies. We applied this approach to several families of superconducting materials, i.e., doped strontium titanate, high-T_C cuprates and iron selenide. Full article

Geometries, equilibrium dissociation energies (D_e), intermolecular stretching, and quadratic force constants (k_σ) determined by ab initio calculations conducted at the CCSD(T)/aug-cc-pVTZ level of theory, with D_e obtained by using the complete basis set (CBS) extrapolation [CCSD(T)/CBS energy], are presented for the B···BeR₂ and B···MgR₂ complexes, where B is one of the following Lewis bases: CO, H₂S, PH₃, HCN, H₂O or NH₃, and R is H, F or CH₃. The BeR₂ and MgR₂ precursor molecules were shown to be linear and non-dipolar. The non-covalent intermolecular bond in the B···BeR₂ complexes is shown to result from the interaction of the electrophilic band around the Be atom of BeR₂ (as indicated by the molecular electrostatic potential surface) with non-bonding electron pairs of the base, B, and may be described as a beryllium bond by analogy with complexes such as B···CO₂, which contain a tetrel bond. The conclusions for the B···MgR₂ series are similar and a magnesium bond can be correspondingly invoked. The geometries established for B···BeR₂ and B···MgR₂ can be rationalized by a simple rule previously enunciated for tetrel-bonded complexes of the type B···CO₂. It is also shown that the dissociation energy, D_e, is directly proportional to the force constant, k_σ, in each B···MR₂ series, but with a constant of proportionality different from that established for many hydrogen-bonded B···HX complexes and halogen-bonded B···XY complexes. The values of the electrophilicity, E_A, determined from the D_e for B···BeR₂ complexes for the individual Lewis acids, A, reveal the order A = BeF₂ > BeH₂ > Be(CH₃)₂—a result that is consistent with the −I and +I effects of F and CH₃ relative to H. The conclusions for the MgR₂ series are similar but, for a given R, they have smaller electrophilicities than those of the BeR₂ series. A definition of alkaline-earth non-covalent bonds is presented. Full article

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in S_N2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the S_N2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the S_N2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors. Full article

Geometries, equilibrium dissociation energies (D_e), and intermolecular stretching, quadratic force constants (k_σ) are presented for the complexes B⋯CO₂, B⋯N₂O, and B⋯CS₂, where B is one of the following Lewis bases: CO, HCCH, H₂S, HCN, H₂O, PH₃, and NH₃. The geometries and force constants were calculated at the CCSD(T)/aug-cc-pVTZ level of theory, while generation of D_e employed the CCSD(T)/CBS complete basis-set extrapolation. The non-covalent, intermolecular bond in the B⋯CO₂ complexes involves the interaction of the electrophilic region around the C atom of CO₂ (as revealed by the molecular electrostatic surface potential (MESP) of CO₂) with non-bonding or π-bonding electron pairs of B. The conclusions for the B⋯N₂O series are similar, but with small geometrical distortions that can be rationalized in terms of secondary interactions. The B⋯CS₂ series exhibits a different type of geometry that can be interpreted in terms of the interaction of the electrophilic region near one of the S atoms and centered on the C_∞ axis of CS₂ (as revealed by the MESP) with the n-pairs or π-pairs of B. The tetrel, pnictogen, and chalcogen bonds so established in B⋯CO₂, B⋯N₂O, and B⋯CS₂, respectively, are rationalized in terms of some simple, electrostatically based rules previously enunciated for hydrogen- and halogen-bonded complexes, B⋯HX and B⋯XY. It is also shown that the dissociation energy D_e is directly proportional to the force constant k_σ, with a constant of proportionality identical within experimental error to that found previously for many B⋯HX and B⋯XY complexes. Full article

The electrostatic potential near to the oxygen atom in each of the cyclic ethers 2,5-dihydrofuran, oxetane and oxirane has been calculated by using a distributed multipole analysis (DMA) of each molecule. The electrostatic potential energy V(φ) of a unit non-perturbing positive charge was calculated (via the DMA of the cyclic ether molecule) as a function of the angle φ between the C₂ axis of the cyclic ether and a vector of length r from the O atom to the unit charge. The resulting potential energy functions each has two equivalent minima. The angles φ_min at the minima are compared with the angles φ₀ and φ_e made by the O⋯H bond with the C₂ axes in the cyclic ether⋯HF complexes, as determined by rotational spectroscopy and ab initio calculations at the CCSD(T)-F12c/cc-pVTZ-F12 level of theory, respectively. An electrostatic model of cyclic ether⋯HF complexes in which the DMA of the cyclic ether interacts with a simple extended electric dipole representation of HF is also used to calculate the variation of the potential energy V_HF(φ) of the HF molecule with φ. The angles φ_min generated by this model are also compared with φ₀ and φ_e. The extent to which the electrostatic potential and the extended electric dipole HF model can be used as probes for the directions of non-bonding electron pairs carried by O in these cyclic ethers is discussed. Full article