Short Bond Length Research Articles

Lewis Acid Enhanced Axial Ligation of [Mo2]4+ Complexes

We report here the syntheses, X-ray crystal structures, electrochemistry, and density functional theory (DFT) single-point calculations of three new complexes: tetrakis(monothiosuccinimidato)dimolybdenum(II) [Mo2(SNO5)4, 1a], tetrakis(6-thioxo-2-piperidinonato)dimolybdenum(II) [Mo2(SNO6)4, 1b], and chlorotetrakis(monothiosuccinimidato)pyridinelithiumdimolybdenum(II) [pyLiMo2(SNO5)4Cl, 2-py]. X-ray crystallography shows unusually short axial Mo2-Cl bond lengths in 2-py, 2.6533(6) Å, and dimeric 2-dim, 2.644(1) Å, which we propose result from an increased Lewis acidity of the Mo2 unit in the presence of the proximal Li(+) ion. When 2-py is dissolved in MeCN, the lithium reversibly dissociates, forming an equilibrium mixture of (MeCNLiMo2(SNO5)4Cl) (2-MeCN) and [Li(MeCN)4](+)[Mo2(SNO5)4Cl](-) (3). Cyclic voltammetry was used to determine the equilibrium lithium binding constant (room temperature, K(eq) = 95 ± 1). From analysis of the temperature dependence of the equilibrium constant, thermodynamic parameters for the formation of 2-MeCN from 3 (ΔH° = -6.96 ± 0.93 kJ mol(-1) and ΔS° = 13.9 ± 3.5 J mol(-1) K(-1)) were extracted. DFT calculations indicate that Li(+) affects the Mo-Cl bond length through polarization of metal-metal bonding/antibonding molecular orbitals when lithium and chloride are added to the dimolybdenum core.

Ab initio study of symmetrical tilt grain boundaries in bcc Fe: structural units, magnetic moments, interfacial bonding, local energy and local stress

We present first-principle calculations on symmetric tilt grain boundaries (GBs) in bcc Fe. Using density functional theory (DFT), we studied the structural, electronic and magnetic properties of Σ3(111) and Σ11(332) GBs formed by rotation around the [110] axis. The optimized structures, GB energies and GB excess free volumes are consistent with previous DFT and classical simulation studies. The GB configurations can be interpreted by the structural unit model as given by Nakashima and Takeuchi (2000 ISIJ 86 357). Both the GBs are composed of similar structural units of three- and five-membered rings with different densities at the interface according to the rotation angle. The interface atoms with larger atomic volumes reveal higher magnetic moments than the bulk value, while the interface atoms with shorter bond lengths have reduced magnetic moments in each GB. The charge density and local density of states reveal that the interface bonds with short bond lengths have more covalent nature, where minority-spin electrons play a dominant role as the typical nature of ferromagnetic Fe. In order to understand the structural stability of these GBs, we calculated the local energy and local stress for each atomic region using the scheme of Shiihara et al (2010 Phys. Rev. B 81 075441). In each GB, the interface atoms with larger atomic volumes and enhanced magnetic moments reveal larger local energy increase and tensile stress. The interface atoms constituting more covalent-like bonds with reduced magnetic moments have lower local energy increase, contributing to the stabilization, while compressive stress is generated at these atoms. The relative stability between the two GBs can be understood by the local energies at the structural units. The local energy and local stress analysis is a powerful tool to investigate the structural properties of GBs based on the behavior of valence electrons.

Introducing Dinamo: A Package for Calculating Protein Circular Dichroism using Classical Electromagnetic Theory

The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.

Microstructural study of high-temperature Cr–Ni–Al–Ti alloys supported by first-principles calculations

Refractory metals present a potential for development of future high-temperature structural materials due to their high melting temperature and good high-temperature strength. However, their poor high-temperature oxidation resistance, creep resistance, and low fracture toughness at low temperatures have to be addressed. The microstructure of two Cr–Ni–Ti–Al alloys is characterized using XRD, LOM, SEM, and TEM. The microstructure of both alloys is comprised of very dilute Cr solid solution grains, intergranular L21 Ni2AlTi phase, and fine NiTi-rich B2 precipitates dispersed in the Cr-rich grains. The small spherical precipitates have a well-defined orientation relationship with the Cr-matrix, and the lattice mismatch between the precipitates and the Cr-alloy matrix is accommodated by the interface dislocations. In order to explain measured composition of L21 and B2, the site preference in these phases is further studied using the first-principles density functional theory (DFT) method at the low temperature limit. The theoretical calculations predict that Al prefers substituting for the Ti site in B2 NiTi. Structure analysis reveals that Al substituting for Ti results in the formation of strong Al–Ni bonds that have much shorter bond lengths than the Al substitution for the Ni site. The predicted Al site or Cr site preference is consistent with established Al–Ni–Ti ternary experiments. As for the L21-Ni2AlTi phase, DFT calculations predict that Cr prefers substitution with the Ni site over Al or Ti sites. This is related to the smallest relaxation effect and formation of stronger Al–Cr and Ti–Cr bonds that have much shorter nearest neighbor bond length compared to other substitution scenarios.

Ionic semiconductor: DC and AC conductivity of anilinium tetrathiafulvalene-2-carboxylate

A single crystal of anilinium tetrathiafulvalene-2-carboxylate exhibits a characteristic electrical conduction; it is a semiconductor with activation-type transport above 200 K; σ(rt) = 0.16 S cm(-1) with an activation energy of 0.11 eV. On the other hand, below 200 K, it does not obey the Arrhenius relation but is conductive even at 4 K with 2.1 × 10(-4) S cm(-1) at a frequency of 2 MHz. Its behavior exhibits strong frequency dependence and suggests a particular conduction coupled with dielectric relaxation, reflecting its ionic nature. The crystal structure of the salt shows that conducting molecules are assembled supramolecularly with multiple nonbonding interactions, such as the hydrogen bond, and the π/π and CH/π interactions. The hydrogen bond and CH/π interactions have a short bond length, which is similar to the charge-assisted-type interaction observed in organometallics.

Theoretical prediction on the structures and stability of the noble-gas containing anions FNgCC− (Ng=He, Ar, Kr, and Xe)

We have made high-level theoretical study on a new type of noble-gas (Ng) containing anions FNgCC(-). The calculated short Ng-CC bond lengths of 1.13, 1.77, 1.89, and 2.04 Å for Ng=He, Ar, Kr, and Xe, respectively, and the electron density distributions indicated strong covalent interactions between the Ng and CC induced by the polarizing fluoride ion. Except for FHeCC(-), the structures of all other FNgCC(-) were predicted to be linear. The intrinsic stability of the FNgCC(-) was studied by calculating the energies of the three-body dissociation reaction: FNgCC(-) → F(-) + Ng + CC and by calculating the energy barriers of the two-body dissociation reaction: FNgCC(-) → Ng + FCC(-). The results showed that FNgCC(-) (Ng=Ar, Kr, Xe) could be kinetically stable in the gas phase with the three-body dissociation energies of 17, 37, and 64 kcal/mol and two body-dissociation barriers of 22, 31, and 42 kcal/mol, respectively, at the coupled-cluster single double (triple)/aug-cc-pVQZ level of theory. The structures and the stability were also confirmed using the multi-reference CASPT2 calculation. Future experimental identification of the FNgCC(-) anions is expected under cryogenic conditions.

Reactions of Group 3 Metals with OF2: Infrared Spectroscopic and Theoretical Investigations of the Group 3 Oxydifluoride OMF2 and Oxyfluoride OMF Molecules

The oxidifluoride molecules, OYF(2) and OLaF(2), are produced via the reactions of laser ablated metal atoms with OF(2) in solid argon. The product structures are characterized using matrix isolation infrared spectroscopy as well as theoretical calculations. Similar to the very recently characterized OScF(2) molecule, OYF(2) is predicted to have a (2)B(2) ground state with C(2v) symmetry while the heavier OLaF(2) has a (2)A″ ground state with near C(2v) symmetry. The unpaired electron is mainly located on the terminal oxygen atom, suggesting radical character for the group 3 OMF(2) molecules. In addition, the closed shell singlet OMF molecules with bent geometries are also observed, and they are found to have triple metal-oxygen bonds with higher stretching frequencies and shorter bond lengths than their OMF(2) counterparts. α-Fluorine transfer from OF(2) to metal centers is predicted to be highly exothermic, which is very favorable for the formation of new OMF(2) and OMF species.

Spin-ordering mediated orbital hybridization in CoO at high pressures

We demonstrate a strong dependence of high-resolution 1$s$3$p$ (or ${K}_{\ensuremath{\beta}}$) resonant x-ray emission spectroscopy (RXES) on local spin correlations at high pressure. We show that the pre-edge region in ${K}_{\ensuremath{\beta}}$ RXES of CoO can be separated into a local quadrupolar contribution and nonlocal dipolar intensity, which arises from the mixing of cobalt 4$p$ states with neighboring cobalt 3$d$ orbitals. For pressures of 0--12 GPa, we observe a twofold increase in nonlocal contributions with respect to local contributions. For pressures greater than 12 GPa, the ratio remains nearly constant. The observed pressure dependence and strong intensity changes cannot be explained by a conventional picture of bond-length shortening and is ascribed to increased intersite 4$p$-3$d$ mixing due to changes in magnetic ordering. These results are supported by theoretical calculations.

Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Nonperiodic Materials.

We develop a nonempirical atoms-in-molecules (AIM) method for computing net atomic charges that simultaneously reproduce chemical states of atoms in a material and the electrostatic potential V(r) outside its electron distribution. This method gives accurate results for a variety of periodic and nonperiodic materials including molecular systems, solid surfaces, porous solids, and nonporous solids. This method, called DDEC/c3, improves upon our previously published DDEC/c2 method (Manz, T. A.; Sholl, D. S. J. Chem. Theory Comput. 2010, 6, 2455-2468) by accurately treating nonporous solids with short bond lengths. Starting with the theory all AIM charge partitioning functionals with spherically symmetric atomic weights must satisfy, the form of the DDEC/c3 functional is derived from first principles. The method is designed to converge robustly by avoiding conditions that lead to nearly flat optimization landscapes. In addition to net atomic charges, the method can also compute atomic multipoles and atomic spin moments. Calculations performed on a variety of systems demonstrate the method's accuracy, computational efficiency, and good agreement with available experimental data. Comparisons to a variety of other charge assignment methods (Bader, natural population analysis, electrostatic potential fitting, Hirshfeld, iterative Hirshfeld, and iterative stockholder atoms) show that the DDEC/c3 net atomic charges are well-suited for constructing flexible force-fields for atomistic simulations.

Nature of the Ga-Ga bonding in Na2[Arx*GaGaArx*] (Arx* = C6H3-2,6-(C6H5)2): Electron localization function analysis

The nature of the Ga-Ga bonding in Na2[Arx*GaGaArx*] (Arx* = C6H3-2,6-(C6H5)2) has been investigated and compared with that of in H2[Arx*GaGaArx*] using electron localization function (ELF) and orbital analysis. The calculation results show that in Na2[Arx*GaGaArx*], the Ga-Ga interaction is a non-classical triple bond, the heart of Na2[Arx*GaGaArx*] is the Ga2Na2 cluster rather than a simple Ga-Ga bond, and the contribution of the sodium atoms to the short Ga-Ga bond length is considerable. As the two sodium atoms are substituted by two hydrogen atoms, the Ga-Ga bond is replaced by two 3-center, 2-electron (3c-2e) Ga-H-Ga covalent bridged bonding.

Enhanced electrocatalytic performance due to anomalous compressive strain and superior electron retention properties of highly porous Pt nanoparticles

The shape and structure of electrocatalysts at the nanoscale level have a decisive effect on their activity and durability in low-temperature fuel cells. Herein, we report the discovery of unexpected structural phenomena in exotic nanostructures: the anomalous compressive strain and superior electron retention properties of highly porous Pt (HP-Pt) nanoparticles synthesized using a weakly interacting organic capping agent, tetradecyl trimethyl ammonium bromide. Even though the particle size of the HP-Pt nanoparticles was much larger than those of commercial electrocatalysts, bond length shortening occurred anomalously, and the downshifted d-band center eventually led to increased oxygen reduction reaction activity. This is because the HP-Pt nanoparticles had a highly porous urchin-like dendritic structure, interestingly in the single-crystalline phase, despite the large particle size. In addition, their electron retention properties were superior to those of commercial samples, which led to drastically enhanced stability against Pt dissolution at high potentials.

ZrFe, a Sextuply-Bonded Diatomic Transition Metal?

Diatomic ZrFe has been spectroscopically investigated for the first time, with the optical spectrum recorded in the range from 13890 cm(-1) to 18870 cm(-1). In the region from 13890 to 17500 cm(-1), a single exceptionally weak vibrational progression is found. Band origins, excited state vibrational frequencies and anharmonicities, excited state lifetimes, and the ground state vibrational interval, ΔG"(1/2), are reported for the five most abundant isotopomers. For the most abundant species, (90)Zr(56)Fe (47.2%), these values are: T(0) = 13931.9(1.2) cm(-1), ω'(e) = 325.05(54) cm(-1), ω'(e)x'(e) = 1.589(40) cm(-1), and ΔG"(1/2) = 452.2 cm(-1). Rotationally resolved studies have revealed ground and excited state rotational constants and Ω values, bond lengths and rotation-vibration constants, giving B(0)" = 0.138786(30) cm(-1) and r(0)" = 1.87685(20) Å for (90)Zr(56)Fe. The ground state and all observed excited states have Ω = 0. On the basis of the short bond length, the ground state of ZrFe is assigned as a nominally sextuply bonded (1)Σ(+) (Ω = 0(+)) state deriving from the 1σ(2)1π(4)2σ(2)1δ(4) electronic configuration. Above 18000 cm(-1), the spectrum becomes much more intense and congested, indicating the onset of electronically allowed transitions in this region.

Effect of thermally induced relaxation on passivity and corrosion of an amorphous Al–Co–Ce alloy

The corrosion behavior of Al87Co7Ce6 alloy was investigated in the amorphous as-quenched, amorphous thermally relaxed, and two partially devitrified conditions using AC and DC electrochemical methods combined with high resolution microscopy in the active dissolution and passivity-local breakdown regimes. The best corrosion resistance was observed after relaxation. Intermediate behavior was observed in a partially devitrified treatment that formed small fcc Al particles and intermetallic phases. Further devitrification decreased the corrosion resistance. The amorphous “relaxed condition”, characterized by EXAFS, is an Al–Co–Ce solid solution with short bond length, high coordination number and reduced free volume compared to the as-quenched amorphous state.

Theoretical study of CO adsorption on the surface of BN, AlN, BP and AlP nanotubes

Behavior of CO adsorption on the surface of BN, AlN, BP, and AlP nanotubes was investigated using density functional theory calculations, by means of B3LYP and B97D functionals. It was found that energetic feasibility of this process depends on several factors including LUMO energy level of tubes, electron density, and length of the surrounding bonds of adsorbing atoms plus their hybridization. These factors compete against each other to specify the adsorption behavior of the tubes. Frontier molecular orbital theory (FMO) and structural analyses show that high energy level of LUMO and short bond lengths of the tube surfaces prevent the adsorption of CO on BN nanotubes. The results suggest that the AlN nanotubes are energetically the most favorable cases toward the CO adsorption. It was found that B97D functional changes the absolute energy values of B3LYP results, but it doesn't change their relative-order of magnitudes.

EXAFS and DFT Investigations of Uranyl Arsenate Complexes in Aqueous Solution

Uranium and arsenic often co-occur in nature, for example, in acid mine drainage waters. Interaction with arsenic is thus important to understand uranium mobility in aqueous solutions. For the present study, EXAFS spectroscopy was used to investigate the formation and identify the structure of aqueous uranyl arsenate species at pH 2. The nearest U-As distance of 3.39 Å, observed in shock-frozen liquid samples, was significantly shorter than that observed in solid uranyl arsenate minerals. The shorter bond length indicated that the solution contained a bidentate-coordinated species, in contrast to the monodentate coordination in solid uranyl arsenate minerals. The U-As coordination number of 1.6 implied that two uranyl arsenate species with U:As ratios of 1:1 and 1:2 formed in nearly equal proportions and that the hydrated uranyl ion was present only as a minor component. The two uranyl arsenate species could not be differentiated spectroscopically, since their U-As distances were equal. A comparison based on DFT modeling indicated for both the 1:1 and the 1:2 species, that the bidentate arsenates were bound to uranium with one of the binding oxygen atoms being protonated. Based on the present spectroscopic study, the two species that will have to be considered in acidic uranium-arsenic-rich solutions are thus UO(2)H(2)AsO(4)(+), and UO(2)(H(2)AsO(4))(2)(0).

An analytical analysis of energy release rate in bonded composite joints in a mode I condition

A complete analytical solution of mode I strain energy release rate, GI, was derived for bonded composite joints based on an augmented double cantilever beam (DCB) model. Good agreement was obtained between current and existing comparable theoretical solutions for this joint with a long adhesive bond. For a short bond length joint, the current solution can greatly reduce the degree of the mathematical singularity encountered in analyses of thick, short beams and avoid it entirely for thin, long beams. A correlation between the current theoretical and associated ASTM solutions was established. A bonded DCB laminate test case was conducted, and good agreement was obtained between the experimental and current theoretical results. Commentary was included regarding the tested critical strain energy release rate and the deduced critical adhesive peel stress.

Short-Range Order and Dynamics in Crystalline α-TeO2

The short-range order and dynamics in crystalline α-TeO2 have been investigated by neutron and X-ray total scattering and by Rietveld refinement of neutron diffraction data. The true lengths of the two bonds in a Te–O–Te bridge are 1.882(1) and 2.117(1) Å, and the high valence, 1.293, of the strong, short bond is balanced by the low valence, 0.686, of the weak, long bond. The root-mean-square (rms) thermal variation, 0.083(1) Å, in the long bond length is nearly twice the rms thermal variation, 0.048(1) Å, in the short bond length because the largest motion of both Te and O atoms is perpendicular to the short bonds. A bond-valence model for the thermal variation in bond lengths, in which both the average and the instantaneous positions of the atoms conform to bond-valence requirements, accounts closely for the observed distribution of Te–O distances in α-TeO2. This has important implications for the interpretation of diffraction experiments on tellurite glasses.

Weaker Bonds with Shorter Bond Lengths

Um dos paradigmas da química prevê que uma ligação mais curta de um dado tipo é sempre a ligação mais forte. Apesar disto funcionar qualitativamente para alguns compostos, não existe em geral prova de que isso seja sempre correto. Neste trabalho, nós discutimos moleculas para as quais ligações longas levam a ligações fortes ao contrário de ligações fracas. Isto é possível introduzindo constantes de força dos modos locais de estiramento como descritores de força de ligação confi áveis. Para as aminas fluoradas NH2 F (1), NHF2 (2), e NF3 (3), o comprimento de ligação NF diminui enquanto que a força da ligação diminui. Efeitos similares são encontrados para ligações envolvendo um elemento pesado com um efeito relativístico distinto. Uma razão para estes resultados será dada.

Mechanical properties of graphyne monolayers: a first-principles study

We investigated the mechanical properties of graphyne monolayers using first-principles calculations based on the Density Functional Theory. Graphyne has a relatively low in-plane Young's modulus (162 N m(-1)) and a large Poisson ratio (0.429) compared to graphene. It can sustain large nonlinear elastic deformations up to an ultimate strain of 0.2 followed by strain softening until failure. The single bond is more vulnerable to rupture than the triple bond and aromatic bond, although it has a shorter bond length (0.19 Å shorter) than the aromatic bond. A rigorous continuum description of the elastic response is formulated by expanding the elastic strain energy density in a Taylor series in strain truncated after the fifth-order term. We obtained a total of fourteen nonzero independent elastic constants which are components of tensors up to the tenth order. Pressure effects on the second-order elastic constants, in-plane Young's modulus, and Poisson ratio are predicted. This study implies that graphyne-based surface acoustic wave sensors and waveguides may be synthesized by introducing precisely controlled local strains on graphyne monolayers.

Competitive hydrogen bonding in aspirin-aspirin and aspirin-leucine interactions

Aspirin-aspirin and aspirin-leucine interactions are studied by the density functional theory (DFT) and high level ab initio calculations with second order Moller-Plesset perturbation theory (MP2). The rotational isomers of aspirin are identified by their relative stability both in gaseous phase and in water using the polarizable continuum method (PCM). Local minima of aspirin monomers in water are found to be all highly populated compared to the gas phase behavior. Homodimers of aspirin form hydrogen bonds with bond energies of 10 kcal/mol. Weak hydrogen bonds utilizing phenyl and methyl groups are also found. The interaction between aspirin and leucine is stronger with relatively short bond lengths compared to homodimeric aspirin interactions. The potential energy surface has several minima with comparable stability. This study shows the significance of diverse bonding schemes, which are important for understanding complete interaction mechanisms of aspirin.