Are 1,5-disubstituted semibullvalenes that have C2v equilibrium geometries necessarily bishomoaromatic?

Unrestricted density functional theory (UB3LYP), CASSCF, and CASPT2 calculations have been employed to compute the relative energies of the C(s) and C(2v) geometries of several 1,5-disubstituted semibullvalenes. Substitution at these positions with R = F, -CH(2)-, or -O- affords semibullvalenes that are predicted to have C(2v) equilibrium geometries. Calculated singlet-triplet energy splittings and the energies of isodesmic reactions are used to assess the amount of bishomoaromatic character at these geometries. The results of these calculations show that employing strain to destabilize the C(s) geometries of semibullvalenes can lead to a significant decrease in the amount of bishomoaromatic stabilization of the C(2v) geometries, due to reduced through-space interaction between the two allyl groups. However, the C(2v) equilibrium geometries of the 1,5-disubstituted semibullvalenes with R = F and -RR- = -O- do benefit from stabilizing through-bond interactions between the two allyl groups. These interactions involve mixing of the bisallyl HOMO with the low-lying C-F or C-O sigma orbital combinations of the same symmetry. In contrast, for -RR- = -CH(2)-, through-bond interactions destabilize the bisallyl HOMO and are predicted to make the ground state of this semibullvalene a triplet.     

Would the pseudocoordination centre method be appropriate to describe the geometries of lanthanide complexes?

The correct prediction of the ground-state geometries of lanthanide complexes is an important step in the development of efficient light conversion molecular devices (LCMD). Considering this, we evaluate here the capability of semiempirical approaches and ab initio effective core potential (ECP) methodology in reproducing the coordination polyhedron geometries of lanthanide complexes. Initially, we compare the facility of two semiempirical approaches: Pseudocoordination centre method (PCC) and Sparkle model. In the first step, we considered only high-quality crystallographic structures and included 633 complexes, and in the last step, we compare the capability of two semiempirical approaches with ab initio/ECP calculations. Because this last methodology was found to be computationally very demanding, we further used a subset containing 91 high-quality crystallographic structures. A total of 91 ab initio full geometry optimizations were performed. Our results suggest that only the semiempirical Sparkle model (hundreds of times faster) present accuracy similar to what can be obtained by present-day ab initio/ECP full geometry optimization calculations on such lanthanide complexes. In addition, it further indicates that the PCC approach has a poor prediction related to the coordination polyhedron geometries of lanthanide complexes.     

X-ray quality geometries of geodesic polyarenes from theoretical calculations: what levels of theory are reliable?

[structure: see text] Computational methods for calculating molecular geometries have not been well calibrated heretofore against X-ray data for bowl-shaped polycyclic aromatic hydrocarbons (PAHs). The analysis presented here capitalizes on a rare opportunity provided by corannulene to account explicitly for molecular distortions from crystal packing forces. Within the error limits of an extensive X-ray data set, B3LYP/6-31G* calculations were found to correctly reproduce all of the experimental bond distances and bond angles. The reliability and shortcomings of geometry calculations at other levels of theory are enumerated.     

Ag (I)–organodiimine coordination complex polymers: structural influences of ligand geometries and charge-compensating oxoanions

Hydrothermal synthesis has been exploited in the preparation of two new materials of the Ag(I)-organodiimine class of materials. By exploiting variations in ligand geometry and tether length and the structural influence of different oxoanions, the inorganic oxides [Ag(dpe)(NO₃)](dpe=1,2-bias(4-pyridyl)ethane) and [Ag₂(2,4′-bpy)₂(SO₄)(H₂O)]·5H₂O(2·5H₂O) were isolated. Compound 1 was prepared in the reaction of Ag(NO₃), dpe, and H₂O in the mole ratio 1:1:500 at 120°C for 24 h, while compound 2 was prepared from Ag₂SO₄, 2,4′-bpy, and H₂O under similar conditions. The structure of 1 is constructed from {Ag(dpe)}_nⁿ⁺ chains linked through η², μ²–NO₃⁻ groups into a two-dimensional network. The structure of 2·5H₂O consists of one-dimensional sinusoidal chains. The Ag(I) sites exhibit two distinct geometries: one is ‘T’-shaped through bonding to two nitrogen donors from two 2,4′-bpy groups and a sulfate oxygen; the second site is also ‘T’-shaped through bonding to two pyridyl nitrogen atoms and an aqua ligand.     

Excited-state molecular geometries of ClO2, O−3, St-3 and TiI4 determined from resonance Raman spectra

Resonance Raman band intensities for the υ₁ν₁ bands of some non-linear triatomic species (ClO₂, O⁻₃, and S^t-₃) and the tetrahedral molecule TiI₄ are analyzed in terms of an A-term scattering regime. It is demonstrated that excited-state molecular geometries can be determined, even in the absence of vibronically structured absorption spectra and excitation profiles, from the intensity distributions of overtone progressions, excited with different laser lines throughout the resonance region. Calculations of the bond length changes accompanying the lowest energy electric-dipole-allowed transitions are shown to be in accord with simple molecular orbital considerations.     

Accuracy of geometries: influence of basis set,exchange–correlation potential,inclusion of core electrons,and relativistic corrections

The geometries of a set of small molecules were optimized using eight different exchange–correlation (xc) potentials in a few different basis sets of Slater-type orbitals, ranging from a minimal basis (I) to a triple-zeta valence basis plus double polarization functions (VII). This enables a comparison of the accuracy of the xc potentials in a certain basis set, which can be related to the accuracies of wavefunction-based methods such as Hartree–Fock and coupled cluster. Four different checks are done on the accuracy by looking at the mean error, standard deviation, mean absolute error and maximum error. It is shown that the mean absolute error decreases with increasing basis set size, and reaches a basis set limit at basis VI. With this basis set, the mean absolute errors of the xc potentials are of the order of 0.7–1.3 pm. This is comparable to the accuracy obtained with CCSD and MP2/MP3 methods, but is still larger than the accuracy of the CCSD(T) method (0.2 pm). The best performing xc potentials are found to be Becke–Perdew, PBE and PW91, which perform as well as the hybrid B3LYP potential. In the second part of this paper, we report the optimization of the geometries of five metallocenes with the same potentials and basis sets, either in a nonrelativistic or a scalar relativistic calculation using the zeroth-order regular approximation approach. For the first-row transition-metal complexes, the relativistic corrections have a negligible effect on the optimized structures, but for ruthenocene they improve the optimized Ru–ring distance by some 1.4–2.2 pm. In the largest basis set used, the absolute mean error is again of the order of 1.0 pm. As the wavefunction-based methods either give a poor performance for metallocenes (Hartree–Fock, MP2), or the size of the system makes a treatment with accurate methods such as CCSD(T) in a reasonable basis set cumbersome, the good performance of density functional theory calculations for these molecules is very promising; even more so as density functional theory is an efficient method that can be used without problems on systems of this size, or larger.     

Coordination geometries and crystal structures of cadmium(II) complexes with a new amino alcohol (NN′O) ligand

The new ligand 2-(2-(2-hydroxyethylamino)ethylamino)cyclohexanol, (HEAC), was prepared under microwave conditions through ring opening of cyclohexene oxide with 2-(2-amino-ethylamino)ethanol. Its cadmium(II) complexes [Cd₂(HEAC)₂(μ-Cl)₂Cl₂] (1) and [Cd(HEAC)₂][CdI₄] (2) were identified by elemental analysis, FT-IR, Raman, ¹H NMR spectroscopies, and single-crystal X-ray diffraction. HEAC formed 1?:?1 M?:?L complexes with cadmium chloride and cadmium iodide. Complex 1 crystallized as a dimer with two asymmetrically bound bridging Cl^? and a terminally coordinated Cl^? on each metal. The geometry around the cadmiums in 1 with four five-membered chelate rings and four Cl^? ligands is distorted octahedral for each Cd(II). The cyclohexanol OH of each ligand forms intramolecular hydrogen bonds. In 2, the coordination numbers for cadmium in [Cd(HEAC)₂]²⁺ and [CdI₄]^2? moieties are six and four, respectively. In [Cd(HEAC)₂]²⁺ each ligand coordinates through two N- and one O-donors, leading to a distorted octahedral geometry. The geometry of [CdI₄]^2? in 2 is slightly distorted tetrahedral. The protonation equilibrium constants of the two secondary amino groups in HEAC, determined by pH-potentiometry, were 6.26 and 9.26, respectively, at 25°C. Stability constants for this ligand with Ni(II), Cu(II), and Zn(II) (1?:?1 M?:?L), determined by glass-electrode potentiometry, were 7.13, 10.50, and 5.42, respectively.     

Synchrotron radiation induced total reflection X-ray fluorescence of low Z elements on Si wafer surfaces at SSRL — comparison of excitation geometries and conditions

The analysis of low Z elements, like Na and Al at ultra trace levels (<10¹⁰ atoms/cm²) on Si wafer surfaces is required by the semiconductor industry. Synchrotron radiation induced total reflection X-ray fluorescence analysis (SR-TXRF) is a promising method to fulfill this task, if a special energy dispersive detector with an ultra thin window is used. Synchrotron radiation is the ideal excitation source for TXRF of low Z elements due to its intense, naturally collimated and linearly polarized radiation with a wide spectral range down to low energies even below 1 keV. TXRF offers some advantages for wafer surface analysis such as non-destructive analysis and mapping capabilities. Experiments have been performed at the Stanford Synchrotron Radiation Lab (SSRL) using Beamline 3-4 (BL 3-4), a bending magnet beamline using white (<3 keV) and monochromatic radiation, as well as Beamline 3-3 (BL 3-3), using a crystal monochromator as well as a multilayer monochromator. A comparison of excitation–detection geometry was performed, using a side-looking detector with a vertically positioned wafer as well as a down-looking detector with a horizontally arranged wafer. The advantages and disadvantages of the various geometrical and excitation conditions are presented and the results compared. Detection limits are in the 100-fg range for Na, as determined with droplet samples on Si wafer surfaces.     

Molecular geometries of H2S···ICF3 and H2O···ICF3 characterised by broadband rotational spectroscopy

The rotational spectra of three isotopologues of H(2)S···ICF(3) and four isotopologues of H(2)O···ICF(3) are measured from 7-18 GHz by chirped-pulse Fourier transform microwave spectroscopy. The rotational constant, B(0), centrifugal distortion constants, D(J) and D(JK), and nuclear quadrupole coupling constant of (127)I, χ(aa)(I), are precisely determined for H(2)S···ICF(3) and H(2)O···ICF(3) by fitting observed transitions to the Hamiltonians appropriate to symmetric tops. The measured rotational constants allow determination of the molecular geometries. The C(2) axis of H(2)O/H(2)S intersects the C(3) axis of the CF(3)I sub-unit at the oxygen atom. The lengths of halogen bonds identified between iodine and sulphur, r(S···I), and iodine and oxygen, r(O···I), are determined to be 3.5589(2) ? and 3.0517(18) ? respectively. The angle, φ, between the local C(2) axis of the H(2)S/H(2)O sub-unit and the C(3) axis of CF(3)I is found to be 93.7(2)° in H(2)S···ICF(3) and 34.4(20)° in H(2)O···ICF(3). The observed symmetric top spectra imply nearly free internal rotation of the C(2) axis of the hydrogen sulphide/water unit about the C(3) axis of CF(3)I in each of these complexes. Additional transitions of H(2)(16)O···ICF(3), D(2)(16)O···ICF(3) and H(2)(18)O···ICF(3) can be assigned only using asymmetric top Hamiltonians, suggesting that the effective rigid-rotor fits employed do not completely represent the internal dynamics of H(2)O···ICF(3).     

Quantum cluster size and solvent polarity effects on the geometries and Mössbauer properties of the active site model for ribonucleotide reductase intermediate X: a density functional theory study

In studying the properties of metalloproteins using ab initio quantum mechanical methods, one has to focus on the calculations on the active site. The bulk protein and solvent environment is often neglected, or is treated as a continuum dielectric medium with a certain dielectric constant. The size of the quantum cluster of the active site chosen for calculations can vary by including only the first-shell ligands which are directly bound to the metal centers, or including also the second-shell residues which are adjacent to and normally have H-bonding interactions with the first-shell ligands, or by including also further hydrogen bonding residues. It is not well understood how the size of the quantum cluster and the value of the dielectric constant chosen for the calculations will influence the calculated properties. In this paper, we have studied three models (A, B, and C) of different sizes for the active site of the ribonucleotide reductase intermediate X, using density functional theory (DFT) OPBE functional with broken-symmetry methodology. Each model is studied in gas-phase and in the conductor-like screening (COSMO) solvation model with different dielectric constants ε = 4, 10, 20, and 80, respectively. All the calculated Fe-ligand geometries, Heisenberg J coupling constants, and the Mössbauer isomer shifts, quadrupole splittings, and the ⁵⁷Fe, ¹H, and ¹⁷O hyperfine tensors are compared. We find that the calculated isomer shifts are very stable. They are virtually unchanged with respect to the size of the cluster and the dielectric constant of the environment. On the other hand, certain Fe-ligand distances are sensitive to both the size of the cluster and the value of ε. ε = 4, which is normally used for the protein environment, appears too small when studying the diiron active site geometry with only the first-shell ligands as seen by comparisons with larger models.     

Density functional analysis of geometries and electronic structures of gold-phosphine clusters. The case of Au4(PR3)42+ and A(u4μ2-I)2(PR3)4

Geometries, ligand binding energies, electronic structure, and excitation spectra are determined for Au(4)(PR(3))(4)(2+) and Au(4)(μ(2)-I)(2)(PR(3))(4) clusters (R = PH(3), PMe(3), and PPh(3)). Density functionals including SVWN5, Xα, OPBE, LC-ωPBE, TPSS, PBE0, CAM-B3LYP, and SAOP are employed with basis sets ranging from LANL2DZ to SDD to TZVP. Metal--metal and metal--ligand bond distances are calculated and compared with experiment. The effect of changing the phosphine ligands is assessed for geometries and excitation spectra. Standard DFT and hybrid ONIOM calculations are employed for geometry optimizations with PPh(3) groups. The electronic structure of the gold--phosphine clusters examined in this work is analyzed in terms of cluster ("superatom") orbitals and d-band orbitals. Transitions out of the d band are significant in the excitation spectra. The use of different basis sets and DFT functionals leads to noticeable variations in the relative intensities of strong transitions, although the overall spectral profile remains qualitatively unchanged. The replacement of PMe(3) with PPh(3) changes the nature of the electronic transitions in the cluster due to low-lying π*-orbitals. To reproduce the experimental geometries of clusters with PPh(3) ligands, computationally less expensive PH(3) or PMe(3) ligands are sufficient for geometry optimizations. However, to predict cluster excitation spectra, the full PPh(3) ligand must be considered.     

A study of the B2 excited state geometries of the metal-metal quadruply bonded compounds Mo2X4(PMe3)4 (X  Cl, Br or I)

The excited state geometries of the metal-metal quadruply bonded compounds Mo₂X₄(PMe₃)₄ (X  Cl, Br or I) have been studied by means of resonance Raman and absorption spectroscopy. A fit of the parameters of a simple theoretical model to the experimental data indicates that the metal-metal bond increases some 10 pm on excitation to the ¹B₂ () state, whereas other geometric changes are small. Furthermore, the phenomenological lifetime factor of the excited state, Γ, is found to be dependent on the vibrational quantum number, ν, of this state.     

Molecular geometries,electronic properties,and vibrational spectroscopic studies of endohedral metallofullerenes TM@C<Subscript>24</Subscript> and TM@C<Subscript>24</Subscript>H<Subscript>12</Subscript> (TM = Cr,Mo, and W)

Molecular geometries, electronic properties, and vibrational spectroscopies of TM@C₂₄ and TM@C₂₄H₁₂ (TM = Cr, Mo, and W) in their different spin configurations have been systematically investigated with the hybrid DFT-(U)B3PW91 functional. The results show that the TM atoms bind over the pentagon ring inside C₂₄ cage, and they move gradually toward the center of C₂₄ cage along with the increasing atomic radii. The most stable Mo@C₂₄H₁₂ and W@C₂₄H₁₂ are in their spin-triplet states. The analyses of dissociation energy and energy gap reveal that TM@C₂₄ (TM = Cr, Mo, and W) and Cr@C₂₄H₁₂ are not only thermodynamically stable, but also considerably stable kinetically. Meanwhile, natural population analyses tell us that the two cages act as electron acceptors, and the transferred charge from the W atom to C₂₄ cage is the largest in the endohedral metallofullerenes. Additionally, the vibrational frequencies and active infrared intensities may be used as evidence to characterize these unknown species.     

Theoretical investigation on the geometries and electronic properties of cesium–silicon CsSi<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 2–12) clusters

The structures, relative stabilities, and electronic properties of pure Si _n and Cs-doped silicon clusters (n = 2–12) are systematically investigated using the density functional theory at the B3LYP level. The optimized structures indicated that the lowest-energy structures of CsSi _n are similar to those of pure Si _n clusters and prefer the 3-dimensional configuration for n = 3–12. The relative stabilities of CsSi _n clusters are analyzed based on the averaged binding energy, fragmentation energy, second-order energy difference, and HOMO–LUMO energy gap. It is found that CsSi₆ and CsSi₉ are the magic clusters, and the doping of Cs atom reduces the chemical stabilities of Si _n frame. The Mulliken population analysis pointed out that the charges in the corresponding CsSi _n clusters always transfer from Cs atom to Si _n host in the range of 0.80–0.91 electron. In addition, the partial density of states, infrared, and Raman spectra is discussed.     

Syntheses and structures of three complexes of formulas [L3Co(μ2-O2P(Bn)2)3CoL'][L"], featuring octahedral and tetrahedral cobalt(II) geometries; variable-temperature magnetic susceptibility measurement and analysis on [(py)3Co(μ2-O2PBn2)3Co(py)][ClO4

The syntheses and structural properties of three dinuclear complexes [L(3)Co(μ(2)-O(2)P(Bn)(2))(3)CoL'][L"] [one ionic L(3) = py(3), L' = py, L" = ClO(4)(-) (1) and two molecular L(3) = py(3), L' = Cl (2) and L(3) = py, μ(2)-NO(3)(-), L' = py (3)] are reported. Complexes feature octahedral Co(II) sites bridged by three dibenzylphosphinate ligands to a tetrahedrally ligated Co(II) site, with the remaining coordination sites occupied by py, nitrato, and Cl ligands. The Co-Co distances are 4.248 ? at 291 K and 4.265 ? at 100 K for 1 and 4.278 and 4.0313(7) ? for 2 and 3, respectively at 100 K. A fit of the low-temperature magnetic susceptibility data was derived for complex 1 with g = 2.25, TIP = 700 × 10(-6) cm(3) mol (-1), λ = -173 cm(-1), κ = 0.93, ν = -3.9, Δ = 630 cm(-1), J = 0.15 cm(-1), and θ = -1.8 resulting in R(χ(M)) = 2.5 × 10(-5) and R(χ(M)T) = 5.8 × 10(-5).