Changes In Bond Angles Research Articles

Metallic ferromagnetism in Ni-doped La0.7Sr0.3CoO3

The structure, magnetization, and electrical transport of perovskite cobaltites La0.7Sr0.3Co1−yNiyO3 have been studied. It is found that the substitution of Ni for Co induces no apparent changes in bond length and angle in the Co(Ni)–O network, and only moderately suppresses the ferromagnetism. Moreover, a retention of the metallic conduction has been observed from y=0 to 0.2, which is in strong contrast to the reported insulating state of the other Co site doped La0.7Sr0.3CoO3. A double-exchange-like interaction between Ni ion and its neighboring Co ion is suggested to explain the experimental results.

Mathematical relationships between bond-bending force fields

Molecular mechanics softwares adopt various set of force field functions. In some cases, reliable data from one set of force field parameters cannot be used in a software that adopts another set of force field. Using mathematical approach, exact relationships between parameters from three bond-bending force fields, namely the (i) harmonic cosine angle, (ii) polynomial series, and (iii) Fourier series, are herein developed. Parameters from these three potential functions are further related to the approximate form, the harmonic angle function, which is valid for small change in chemical bond angle.

Use of software to search for higher symmetry: space group C2.

From a search of the October 2000 release of the Cambridge Structural Database we find coordinate data for approximately 1500 entries under space group No. 5: C2 or, occasionally, A2, I2 or B112. Software designed to detect cases of missed higher symmetry identified 144 entries for detailed inspection. Of these, 50 should, we believe, be revised to space groups of higher symmetry. The most common revision is to space group C2/m, which entails adding a center of inversion and usually results in important changes in bond lengths and angles.

Structural study of two N(4)-substituted thiosemicarbazones prepared from 1-phenyl-1,2-propanedione-2-oxime and their binuclear nickel(II) complexes

The crystal structures of the oxime/thiosemicarbazones 1-phenyl-1-{ N(4)-methyl- and 1-phenyl-1-{ N(4)-ethylthiosemicarbazone}-2-oximepropane, H 2Po4M and H 2Po4E, were found to have the oxime and thiosemicarbazone moieties on opposite sides of the carbon–carbon backbone. Intermolecular hydrogen bonding involves the oxime function forming a symmetrical dimer for both compounds. The structures of the binuclear nickel(II) complexes, [Ni(Po4M)] 2 and [Ni(Po4E)] 2, show that bridging by the oximato N–O results in a centrosymmetric arrangement of the two planar nickel centers in each complex. The coordinated thiosemicarbazonato moieties undergo the expected changes in bond distances and angles compared to H 2Po4M and H 2Po4E.

AM1 andab initio studies on the internal reorganization energy of self-exchange electron transfer reactions of several quinone derivatives

The semiempirical AM1 method, ab initio (HF/3-21G, 6-31G, 6-31G(d), 6-31+G(d)) and DFT (B3LYP/6-31G(d), 6-31+G(d)) methods were used to optimize the geometry of DDQ and its anion radical ⋯ ⋯ Nelsen’s model was used to calculate the internal reorganization energy λi of self-exchange electron transfer (ET) reactions. The calculated λi results of DDQ/DDQ⊸ by AM1 and B3LYP/ 6-31G(d), 6-31+G(d) methods are close to each other and consistent with the reported values; while those from Hartree-Fock methods are too large because of not considering the effect of electron correlation. The structure and ET behavior of MQ0/MQ 0 ⊸ couple were studied by AM1 and DFT (B3LYP/6-31G(d), 6-31+ G(d, p)) methods, and those of MQ0/MQ n ⊸ (n = 1–7) were studied by AM1 method for the first time. The results indicate that the values of the heat of formation of MQn increases with the increasing of the length of the isoamylene substituent chains. It also shows that the length of substituent has little effect on the bond lengths, bond angles of ring A, ring B and the dihedral angles of ring B, but it has considerable effect on the dihedral angles between the plane of ring A and oxygen atoms. The calculated λi results of MQ0/MQ 0 ⊸ and MQn/MQ n ⊸ (n = 1–7) indicate that not only the changes of high frequency vibrations, corresponding to the changes of bond lengths and bond angles, contribute to λi of MQn/MQ n ⊸ (n = 1–7), but also do those of the low frequency vibrations, corresponding to the changes of dihedral angles of MQn and MQ n ⊸ . The contribution from the change of low frequency vibrations between the plane of ring A and oxygen atoms to the λi values of MQn/MQ n ⊸ (n = 1–7) is greater than 1.60 kJ/mol; din addition, the contribution from the changes of the low frequency vibrations of the isoamylene substituent to the λi values of MQ4/MQ 4 ⊸ and MQ6/MQ 6 ⊸ is about 2 kJ/mol.

Solvent effects on ground and excited electronic state structures of p-nitroaniline

Resonance Raman intensities of p-nitroaniline, a prototypical “push–pull” chromophore with a large first hyperpolarizability (β), have been measured in dilute solution in five solvents having a wide range of polarities (cyclohexane, 1,4-dioxane, dichloromethane, acetonitrile, and methanol) at excitation wavelengths spanning the strong near-ultraviolet charge-transfer absorption band. The absolute Raman excitation profiles and absorption spectra are simulated using time-dependent wave packet propagation techniques to determine the excited-state geometry changes along the five or six principal Raman-active vibrations as well as estimates of the solvent reorganization energies. The total vibrational reorganization energy decreases and the solvent reorganization energy increases with increasing solvent polarity in all solvents except methanol, where specific hydrogen-bonding interactions may be important. The dimensionless normal coordinate geometry changes obtained from the resonance Raman analysis are converted to actual bond length and bond angle changes with the aid of normal mode coefficients from a ground-state density functional theory calculation. The geometry changes upon electronic excitation involve predominantly the Cphenyl–Nnitro, N–O, and phenyl C2–C3 bond lengths, with little involvement of the amino group. Nonresonant Raman spectra in 1,4-dioxane, dichloromethane, ethyl acetate, acetone, acetonitrile, and methanol show only a very small solvent dependence of the vibrational frequencies. This suggests that changing the solvent affects the excited state more than the ground state, calling into question two-state models that treat the ground and charge-transfer excited states as linear combinations of neutral and zwitterionic basis states with solvent dependent coefficients.

Theoretical studies of carbocations in ion pairs. Part 7. Formation of ion pairs from 2-fluoropropane and Lewis acids [1–3

High level ab initio MO calculations have identified two complexes of borane with 2-fluoropropane. In the first, the boron atom is above the small C1,C2,C3 angle ( in complex); in the other, the boron atom is outside that angle ( out complex). The ionization to form the 2-propyl cation and the trihydrofluoroborate ion A was followed by lengthening the C–F bond, d, in each complex and reoptimizing all other geometrical parameters. It was concluded that ionization occurred at d=1.8–2.0 A ̊ . The out ionization pathway was of lower energy (1–2 kcal/mol at MP2(FC)/6-31G ∗∗) at al values of d. A third pathway ( top), in which the F–B bond was held perpendicular to the C1,C2,C3 plane, rather than allowed to tilt, was 8–9 kcal/mol higher in energy throughout. Ionization to the tight ion pair did not require a large energy expenditure (19.0 kcal/mol over the isolated reactants at d=2.00 A ̊ , 30.3 kcal/mol at d=2.20 A ̊ ). A medium of dielectric constant 8.93, in SCRF(IPCM)-MP2(FC)/6-31G ∗∗MP2/6-31G ∗∗ calculations, reduced the ionization energy to 14.2 kcal/mol at d=2.20 A ̊ . The dielectric medium also reorders the relative energy of the three orientations to out< top (1.0 kcal/mol) < in (4.5 kcal/mol), at d=2.20 A ̊ . Changes in bond lengths and angles show hyperconjugative assistance to the ionization by the methyl hydrogens anti to the fluorine along all pathways. As the ions separate, this effect decreases and. the interaction with the anion of one of the hydrogens initially syn to the fluorine becomes important. Along the in pathway, rotation of one of the methyl groups occurred along the in pathway at 2.20 Å and elimination at 2.30 Å; along the top pathway, it occurred at 2.30 and 2.40 Å, respectively. Along the out pathway, methyl group rotation brought a hydrogen in each close to the anion at d=2.50 A ̊ and elimination followed at 2.70 Å. The top orientation had not eliminated at distances about 2.6 Å and higher in our previous work. Both the in and out forms were optimized without elimination at d=2.80 A ̊ with tetrafluoroborate ( C) as anion. The calculations predict features of solvolyses, such as transfer of a nucleophile from the backside of the anion (retentive solvolysis), elimination to olefin within the ion pair, and recombination at the backside of the anion (oxygen scrambling faster than racemization of tosylates and carboxylates).

How different can the bond angles be in two conformers?

In our previous studies, a rule was formulated referring to how the internuclear distances and the bond angles in a second conformer differ from those in the most stable one. A test of this rule on 36 molecules (existing as two conformer mixtures) showed that it works well for the internuclear distances but is poor in predicting the bond angle changes. We undertook a systematic analysis of some of the molecules showing the highest angular changes using ab initio methods. It was found that the X–C–Y bond angles in systems like CH2X–YH, where Y=O, S and CH2X–YH2, where Y=N, P (X=CH3, F, Cl) can differ as much as 5.8° in different conformers and the direction of change mostly contradicts the above mentioned rule.

Structural-relaxation-induced bond length and bond angle changes in amorphized Ge

Low-temperature structural relaxation in amorphized Ge has been characterized by extended x-ray-absorption fine-structure spectroscopy and Raman spectroscopy. A relaxation-temperature-dependent decrease in the mean value and asymmetry of the interatomic distance distribution has been shown to accompany the well-documented reduction in bond angle distribution. While the initial, as-implanted state of amorphous Ge was ion-dose dependent, relaxation at 200 \ifmmode^\circ\else\textdegree\fi{}C yielded a common ion-dose-independent interatomic distance distribution. The heat release upon structural relaxation due to reductions in both bond length and bond angle distortion was calculated separately and the former exhibited an ion-dose dependence. The results provide compelling support for the defect annihilation model of structural relaxation and imply that the heat release upon structural relaxation should be implant-condition dependent.

Shear-induced mechanochromism in polydiacetylene monolayers

We use atomic force microscopy to actuate and characterize the nanoscale “mechanochromism” of polydiacetylene monolayers on atomically-flat silicon oxide substrates. We find explicit evidence that the irreversible blue-to-red transformation is caused by shear forces exerted normal to the polydiacetylene polymer backbone. The anisotropic probe-induced transformation is characterized by a significant change in the tilt orientation of the side chains with respect to the surface normal. We discuss preliminary molecular dynamics simulations and electronic structure calculations on twelve-unit polydiacetylene oligomers that allow us to correlate the transformation with bond-angle changes in the conjugated polymer backbone.

Sugar interaction with metal ions. The crystal structure and Raman spectra study of SmCl3–galactitol complex

The crystal structure of 2SmCl3·galactitol·14H2O has been determined. The crystal system is triclinic, space group: P-1. The unit cell dimensions: a=9.683(2) Å, b=10.341(2) Å, c=7.990(2) Å; α=108.01(3)°, β=92.71(3)°, γ=88.42(3)°. Each Sm atom is coordinated to nine oxygen atoms, three from the alditol and six from water molecules, with Sm–O distance from 2.417 to 2.520 Å. The seventh water molecule is hydrogen-bonded by the hydroxy hydrogen on O–3 (O(3)–H(13)⋯O(10), 2.635 Å). After forming complexes the peaks have shifted and the relative intensities have changed in the IR and Raman spectra, which are corresponding to the changes in bond distances and bond angles of the structures. The IR and Raman spectra of Pr–, Nd– and Sm–galactitol complexes are similar, which show that the three metal ions have the same coordination mode.

Deformation of Elastomeric Networks: Relation between Molecular Level Deformation and Classical Statistical Mechanics Models of Rubber Elasticity

In this work a specialized molecular simulation code has been used to provide details of the underlying micromechanisms governing the observed macroscopic behavior of elastomeric materials. In the simulations the polymer microstructure was modeled as a collection of unified atoms interacting by two-body potentials of bonded and non-bonded type. Representative Volume Elements (RVEs) containing a network of 200 molecular chains of 100 bond lengths are constructed. The evolution of the RVEs with uniaxial deformation was studied with molecular dynamics techniques. The simulations enable observation of structural features with deformation including bond lengths and angles as well as chain lengths and angles. The simulations also enable calculation of the macroscopic stress-strain behavior and its decomposition into bonded and non-bonded contributions. The distribution in initial end-to-end chain lengths is consistent with Gaussian statistics treatments of rubber elasticity. It is shown that application of an axial strain of +/ 0.7 (a logarithmic strain measure is used) only causes a change in the average bond angle of /+ 5 degrees indicating the freedom of bonds to sample space at these low-moderate deformations; the same strain causes the average chain angle to change by /+ 20 degrees. Randomly selected individual chains are monitored during deformation; their individual chain lengths and angles are found to evolve in an essentially ane manner consistent with Gaussian statistics treatments of rubber elasticity. The average chain length and angle are found to evolve in a manner consistent with the eight-chain network model of elasticity. Energy quantities are found to remain constant during deformation consistent with the nature of rubber elasticity begin entropic in origin. The stress-strain response is found to have important bonded and non-bonded contributions. The bonded contributions arise from the rotations of the bonds toward the maximum principal stretch axis(es) in tensile(compressive) loading.

Lowest singlet excited state geometries, rotational constants and molecular electrostatic potentials of some substituted benzenes: an ab initio study

Ground and lowest singlet excited state geometries of certain substituted benzenes (fluorobenzene, chlorobenzene, p-difluorobenzene, p-dichlorobenzene, p-fluorochlorobenzene and aniline) were optimized using the ab initio RHF procedure employing the 6-31+G∗ basis set. The calculations were also carried out using the 6-311++G∗∗ basis set for two molecules. Excited states were generated using configuration interaction involving singly excited configuration (CIS). The calculated lowest singlet transition energies of the molecules agree with experimental ones satisfactorily. It is found that our calculations reproduce the ground and excited state rotational constants A, B and C of the molecules obtained from high-resolution spectroscopy quite well. Excited state geometries of the molecules have not been determined experimentally precisely but certain approximate estimates of the changes in bond lengths and bond angles consequent to excitation are available in the literature. There is a satisfactory agreement between these and our calculated changes in ring bond lengths and bond angles of the molecules consequent to excitation. Studies of excited state molecular electrostatic potential (MEP) maps are scarce in the literature. Our study of ground and excited state MEP maps of the molecules has revealed several interesting features some of which, e.g. the ortho, para directing property of the substituents in the ground state, are in agreement with experiment. It is indicated that reactions at the ortho, para positions in the ground state would take place in planes located much above the ring planes and there is an appreciable modification in this respect following excitation of the molecules.

A comparison of crystallographic and NMR data for thieno[2,3‐b:4,5‐b′]dipyridine and its monohydroperchlorate salt

AbstractX‐ray crystallographic studies of thieno[2,3‐b:4,5‐b′]dipyridine (1) and its monohydroperchlorate salt (1a) show that 1 is protonated at N1 in ring A and not at N6 in ring C. In each compound individual rings are planar, but there is a small dihedral angle‐of‐twist between the A and C rings. On going from 1 to 1a the largest changes in bond angles and bond lengths occur in ring A. 1H and l3C nmr spectra of 1 plus the 13C nmr spectrum of 1a are reported.

Structural correlations and conformational preference in edge-sharing binuclear d8 complexes with XR2 bridges. A theoretical study.

The binuclear complexes of d8 transition metal ions of the type [M2(mu-XR2)2L4] (where M = RhI, IrI, NiII, PdII, PtII, or AuIII; X = S, N, P, or As) appear in a variety of molecular conformations in which the coordination planes around the two metal atoms are sometimes coplanar, sometimes bent. For the bent compounds with asymmetric bridges, XR1R2, the substituents adopt different orientations relative to the metal framework and to each other. Ab initio theoretical studies on the different conformers of 30 representative complexes, complemented with a structural database analysis, have allowed the establishment of structural correlations in this family of compounds. The conformational choice results from a delicate balance of different interactions which are qualitatively analyzed, such as the changes in bond angles around the bridging atoms, the existence of weak metal...metal bonding in the bent structures, and steric interactions involving the terminal ligands and the substituents at the bridging atoms.

Structures of photo-produced transient species

An overview of recent advances in the experimental measurements, theoretical interpretations, and practical applications of bond length and bond angle changes that occur after a molecule absorbs one or more photons is presented. “Gentle” changes are those in which the chemical bonds remain intact, but the lengths and angles increase or decrease. The bond length and bond angle changes that occur when a molecule absorbs a photon are measured by using a combination of electronic (emission and absorption) spectroscopy, resonance Raman spectroscopy, and the time-dependent theory of spectroscopy. “Catastrophic” changes are those in which multiple bonds are broken, leading to extensive photofragmentation. Luminescence spectroscopy is used to identify the transient fragments of metal-containing compounds that are precursors for laser assisted chemical vapor deposition.

31P chemical shielding as a function of bond angle: phosphorus chemical shielding surface of phosphinoborane R2PBR'2

The phosphorus chemical shielding surface of phosphinoborane R2PBR'2 has been investigated via molecular orbital theory calculation and experimental measurement of selected derivatives. Ab initio calculations of phosphorus chemical shielding tensors were determined for the phosphinoboranes H2PBH2 and (CH3)2PB(CH3)2. Changes in the angle from planarity, i.e., that between the P-BR'2 plane and the bisector of the RPR angle, are reflected in the orientations and magnitudes of the three principal components of the phosphorus chemical shielding tensor. To determine the validity of the calculated phosphorus chemical shielding surface, three phosphinoborane compounds with different angles from planarity were synthesized and studied by solid-state 31P NMR spectroscopy. The 31P NMR powder patterns provided experimental magnitudes of the principal components of the phosphorus chemical shielding tensor for each compound, which compared well to the calculated predictions; where orientations of these tensors could be determined experimentally, they also agreed well with the calculated results. The combined experimental and theoretical results provide a good description of the effects on changes in bond angle on phosphorus chemical shielding as the molecule is distorted from a planar to folded geometry.Key words: chemical shielding, solid-state NMR, phoshinoborane, ab initio calculations.

A Structural Strategy for Generating Rapid Electron-Transfer Kinetics in Copper(II/I) Systems

Electron-transfer in low molecular weight copper(II/I) systems is generally accompanied by a large reorganization of the inner-coordination sphere. On the basis of recent kinetic studies involving Cu(II/I)-macrocyclic polythiaether complexes, it was hypothesized that forcing Cu(II) out of the macrocyclic cavity (i) decreases the changes in bond angles upon reduction and (ii) obviates any need for donor atom inversion. This should diminish the reorganizational barrier and, thereby, increase the electron self-exchange rate. This hypothesis has now been tested utilizing a somewhat soluble 12-membered macrocyclic tetrathiaether, oxathiane[12]aneS4 (L). Crystal structures of the CuIIL and CuIL complexes confirm that, whereas one Cu−S bond dissociates upon reduction, the remaining bond lengths and angles change only minimally. The free ligand, oxathiane[12]aneS4, C10H18OS4, crystallizes in the orthorhombic space group Pbca with Z = 8, a = 15.211(2) Å, b = 8.5113(9) Å, c = 20.548(3) Å. The CuIIL complex crystallizes as a 5-coordinate monomer with water as the apical ligand: [CuL(OH2)](ClO4)2·H2O, C10H22O11S4Cl2Cu, monoclinic P2(1)/c, Z = 4, a = 15.774(2) Å, b = 8.485(5) Å, c = 16.508(9) Å, β = 112.11(6)°. The CuIL complex crystallizes as a binuclear species: [(CuL)2NCCH3](ClO4)2·NCCH3, C24H42N2O10S8Cl2Cu2, in the triclinic space group P1̄ with Z = 4, a = 12.5917(2) Å, b = 13.0020(3) Å, c = 14.9285(3) Å, α = 68.356(1)°, β = 84.298(1)°, γ = 61.129(1)°. The kinetics of CuII/I(oxathiane[12]aneS4) reacting with four selected counter reagentstwo oxidants and two reductantsyield exceptionally large cross-reaction rate constants. Application of the Marcus cross relation yields calculated self-exchange rate constants ranging from 4 × 105 to 8 × 105 M-1 s-1 (median: 6 × 105 M-1 s-1) for this CuII/IL redox system at 25 °C, μ = 0.10. A comparable result of k11 = (8.4 ± 0.8) × 105 M-1 s-1 has been obtained by NMR line-broadening measurements (at 25 °C, corrected to μ = 0.10). This is the largest self-exchange rate constant ever reported for a low molecular weight Cu(II/I) system. Thus, elimination of donor atom inversion coupled with a constrained inner sphere appears to represent a feasible approach for accelerating electron transfer in Cu(II/I) macrocyclic systems.

UVRR Spectroscopy and Vibrational Analysis of Mercury Thiolate Compounds Resembling d(10) Metal Binding Sites in Proteins.

Raman, ultraviolet resonance Raman (UVRR) and far-IR spectra are reported for the mercury-cysteamine complex, Hg(SCH(2)CH(2)NH(2))(2). Band assignments are made for Hg(SCH(2)CH(2)NH(2))(2), and also for [Hg(SBu(t))(3)](-) and [Hg(SMe)(3)](-) on the basis of ab initio calculations with the effective core potential approximation and also on the basis of comparison with vibrational data of corresponding thiols. The calculations show that geometry-optimized [Hg(SBu(t))(3)](-) and [Hg(SMe)(3)](-) have virtually the same Hg-S bond lengths, but very different nu(s) HgS frequencies, 196 and 268 cm(-)(1), in good agreement with the experimental data. The exceptionally low HgS frequency for [Hg(SBu(t))(3)](-) compared to [Hg(SMe)(3)](-) and to the Hg-MerR protein results from kinematic interactions of the Hg-S stretching and S-C-C bending coordinates when all three substituents at C(alpha) are carbon atoms. For Hg(SCH(2)CH(2)NH(2))(2), the HgS stretching coordinate is distributed over three modes, at 339, 273, and 217 cm(-)(1), all of which exhibit UVRR enhancement. The other contributors to these modes are angle bending and torsional coordinates of the chelate rings. Involvement of the CCN bending coordinates is supported by observed and calculated frequency shifts in D(2)O. The excitation profiles track the main UV absorption band, associated with S-->Hg charge transfer. Enhancement is attributable to the weakening of the Hg-S bonds in the excited state, and probably to changes in the SCC bond angle. Also enhanced, albeit weakly, is the nu(CS) mode at 658 cm(-)(1), reflecting C-S bond shortening in the excited state. The mingling of metal-sulfur and internal ligand coordinates is reminiscent of the mingling seen in RR spectra of type 1 Cu proteins. In both cases the phenomenon may be associated with elevated torsional contributions associated with the rigidity of the ligands.

Density functional calculations of nuclear magnetic shieldings using the zeroth-order regular approximation (ZORA) for relativistic effects: ZORA nuclear magnetic resonance

We present a new relativistic formulation for the calculation of nuclear magnetic resonance (NMR) shielding tensors. The formulation makes use of gauge-including atomic orbitals and is based on density functional theory. The relativistic effects are included by making use of the zeroth-order regular approximation. This formulation has been implemented and the Hg199 NMR shifts of HgMe2, HgMeCN, Hg(CN)2, HgMeCl, HgMeBr, HgMeI, HgCl2, HgBr2, and HgI2 have been calculated using both experimental and optimized geometries. For experimental geometries, good qualitative agreement with experiment is obtained. Quantitatively, the calculated results deviate from experiment on average by 163 ppm, which is approximately 3% of the range of Hg199 NMR. The experimental effects of an electron donating solvent on the mercury shifts have been reproduced with calculations on HgCl2(NH3)2, HgBr2(NH3)2, and HgI2(NH3)2. In addition, it is shown that the mercury NMR shieldings are sensitive to geometry with changes for HgCl2 of approximately 50 ppm for each 0.01 Å change in bond length, and 100 ppm for each 10° change in bond angle.