Changes In Bond Angles Research Articles

Deformation of single-walled carbon nanotubes under large axial strains

The deformations of single-walled carbon nanotubes (SWCNTs) under large axial strains are investigated. The Tersoff–Brenner potential is adopted to describe the interactions between carbon atoms. Results show that the changes of strain energies are dependent on chirality but independent of the tubes' radii. Under large axial tension, abrupt changes of the configurations of SWCNTs may occur when the strains exceed 0.382 for armchair patterns and 0.43 for zigzag patterns. The reason is that the changes of bond lengths and angles lead to corresponding changes of many-body coupling interactions between atoms. Then the tubes reach new equilibrium states. Such abrupt changes of configurations must trigger fracture of CNTs in a dynamic deformation.

A Density Functional Theory Calculation of the Electronic Properties of Several High-Spin and Low-Spin Iron(II) Pyrazolylborate Complexes

Density functional theory has been used to study the electronic spin-state properties of low-spin Fe[HB(pz)3]2, high-spin Fe[HB(3-Mepz)3]2, high-spin Fe[HB(3,5-Me 2pz)3]2, and high-spin Fe[HB(3,4,5-Me 3pz)3]2 complexes that exhibit very different iron(II) electronic spin-sate crossover behaviors with changing temperature and pressure. Excellent agreement is obtained between the experimentally observed Mössbauer-effect quadrupole splittings and isomer shifts of these complexes and those calculated with the B3LYP functional and various different basis sets for both the high-spin and low-spin states of iron(II). The calculations for Fe[HB(pz)3]2 that use the LANL2DZ, 6-31++G(d,p), and 6-311++G(d,p) basis sets for iron all lead to very similar electric field gradients and thus quadrupole splittings. The initial calculations, which were based upon the known X-ray structures, were followed by structural optimization, an optimization that led to small increases in the Fe-N bond distances. Optimization led to at most trivial changes in the intraligand bond distances and angles. The importance of the 3-methyl-H...H-3-methyl nonbonded intramolecular interligand interactions in controlling the minimum Fe-N bond distances and determining the iron(II) spin state both in Fe[HB(3-Mepz)3]2 and in the related methyl-substituted complexes has been identified.

Systematic study on the pressure dependence ofM2AlCphases(M=Ti,V,Cr,Zr,Nb,Mo,Hf,Ta,W)

The compressibility of the nanolaminated ${M}_{2}\mathrm{Al}\mathrm{C}$ phases (space group $P{6}_{3}∕mmc$) with $M=\mathrm{Ti},\mathrm{Zr},\mathrm{Hf}$ [valence electron concentration (VEC) of the $M$ element of 4], V, Nb, Ta $(\mathrm{VEC}=5)$, and Cr, Mo, W $(\mathrm{VEC}=6)$ is systematically studied in the pressure range from $0\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}\ensuremath{\sim}70\phantom{\rule{0.3em}{0ex}}\mathrm{GPa}$ using ab initio calculations. These phases are characterized by interleaving of MC and Al layers. For $\mathrm{VEC}=4$, we observe a larger compressibility along the $c$ axis as compared to the $a$ axis. As the VEC is increased to 5, the compressibility in the $c$ direction decreases and becomes comparable to the compressibility in the $a$ direction, whereas at $\mathrm{VEC}=6$, the compressibility in the $a$ direction is larger than that along the $c$ direction. These results are consistent with recent experimental work. Based on a systematic study of the VEC-induced changes in bond stiffness, bond angle, and bond energy, we conclude that the geometric alteration of the bonding configuration in combination with the increase in $M--\mathrm{C}$ bond stiffness is mainly responsible for the observed compressibility change.

Temperature dependent vibrational modes of glycosidic bond in disaccharide sugars

We studied the temperature dependent vibrational modes of the glycosidic bond in trehalose, sucrose, and maltose at wavenumbers ranging from 1000 to 1200 cm −1. We found that the slope of temperature dependent Raman shifts of the glycosidic bond in trehalose and sucrose changed at temperatures around 120 °C, indicating a bond length or a bond angle (dihedral and torsional angles) change. However, we did not observe any slope change in maltose because the melting temperature of maltose is very close to 120 °C. We also found, at temperatures below 120 °C, that Raman shifts of the vibrational modes of the glycosidic bond in trehalose showed the strongest temperature dependence among the three disaccharides.

Comparisons of Phosphorus Ligation Properties in P(CH2NR)3P

Bicyclic P(CH2NMe)3P was synthesized, and its reactions with MnO2, elemental sulfur, p-toluenesulfonyl azide, BH3.THF, and W(CO)5(THF) were shown to furnish a variety of products in which the PC3 and/or the PN3 phosphorus are oxidized/coordinated. In contrast, reactions of the previously known P(CH2NPh)3P with Mo(0) and Ru(II) precursors were shown to afford products in which only the PC3 phosphorus is coordinated. The contrast in reactivity of P(CH2NR)3P (R = Me, Ph) with the aforementioned reagents is discussed in terms of steric and electronic factors. The new compounds are characterized by analytical and spectroscopic (IR, 1H, 31P, and 13C NMR) methods. The results of crystal and molecular structure X-ray analyses of the previously known compounds P(CH2O)3P and P(CH2NPh)3P and 6 of the 14 new compounds obtained in this investigation are presented. Salient features of these structures and the analysis of the Tolman cone angles calculated from their structural parameters are discussed in terms of the effects of constraint in the bicyclic moieties. Evidence is presented for greater M-P sigma bonding effects on coordination of the PC3 phosphorus of P(CH2NR)3P (R = Me, Ph) than are present in PMe3 analogues of group 6B metal carbonyls. From 1JBP data on the BH3 adducts of P(CH2NMe)3P, it is suggested that the free bases MeC(CH2NMe)3P < P(CH2NMe)3P < (Me2N)3P < P(MeNCH2CH2)3N increase in Lewis basicity at the PN3 phosphorus in the order shown. Substantial differences in 31P chemical shifts in the bicyclic compounds discussed herein relative to their acyclic analogues do not seem to be associated with the relatively small bond angle changes that occur around either the PN3 or the PC3 trivalent phosphorus atoms.

Anharmonicity and tunneling effects in revisited vibrational O(1s) photoelectron spectrum of water gas phase

The authors have revisited the description of the core-hole ionization dynamics of the oxygen atom in water by re-exploiting the high-resolution, vibrationally resolved, XPS photoelectron spectrum of gas phase at the O(1s) edge. The agreement between theory and experiments is mainly controlled by (i) the description of the tunneling behavior near the barrier top (linear H-O-H conformation) of wave functions with high vibrational quanta, and (ii) the relative displacement of the potential-energy minimum of the O(1s) final state with respect to the ground state one. Accurate change in bond angle between the neutral and core-ionized states is essential to account for the Franck-Condon factors. The O(1s) photoelectron spectrum of water is well reproduced by the molecular ab initio calculations based on density functional theory and Franck-Condon factors calculations in a double-well (2 x W) simulation of the bending motion.

Molecular mechanics (MM4) study of amines

The MM4 force field has been extended to include aliphatic amines. About 20 amines have been examined to obtain a set of useful molecular mechanics parameters for this class. The vibrational spectra of seven amines (172 frequencies) calculated by MM4 have an overall rms error of 27 cm(-1), compared with corresponding MM4 value of 24 cm(-1) for alkanes. The rms and signed average errors of the moments of inertia of nine simple amines compared with the experimental data were 0.18% and -0.004%, respectively. The heats of formation of 30 amines were also studied. The MM4 weighted standard deviation is 0.41 kcal/mol, compared with experiment. Electronegativity effects occur in the hydrocarbon portion of an amine from the nitrogen, and are accounted for by including electronegativity induced changes in bond lengths and angles, and induced dipole-dipole interactions in the molecule. Negative hyperconjugation results from the presence of the lone pair of electrons on nitrogen, and leads to the Bohlmann bands in the infrared, and also to strong and unusual geometric changes in the molecules (Bohlmann effect), all of which are fairly well accounted for. The conformational energies in amines appear to be less straightforward than those for most other classes of molecules, apparently because of the Bohlmann effect, and these are probably not yet completely understood. In general, the agreement between the MM4 calculated results and the available data is reasonably good.

Gamma ray interaction with lithium diborate glasses containing transition metals ions

UV–visible spectroscopy of undoped and TM-doped (Ti–Cu) lithium diborate glasses have been measured before and after successive gamma irradiation. In the undoped borate glass, strong charge transfer UV bands are observed at 235 and 280nm which are related mostly to trace iron impurities (Fe3+) ions.In the TM-doped glasses, characteristics absorption bands are obtained due to each specific TM ion in addition to that due to the base glass.Gamma irradiation produced induced bands due either to the intrinsic host borate glass in the UV region at about 210, 230, 280nm and one visible band at 540nm or extrinsic bands which are different according to the added TM ions and initiated by photochemical processes. The rate of induced color centers formation is fast at first and then becomes slower or reaches saturation and some TM ions (V, Cr, Co, Ni, Cu) show retardation or shielding to gamma ray but with varying degrees. Infrared absorption measurements of the undoped and TM-doped glasses are measured to justify the structural groups of the host lithium borate glass and the effects of TM ions on their arrangement.Gamma irradiation causes a decrease in the intensities of the IR bands accompanied by losing sharpness. These features are related to more amorphicity or disorder by irradiation or to the possible changes in bond angle or bond length in the building groups arrangement.

An examination of structural characteristics of phenylacetylene by vibronic and rovibronic simulations of ab initio data

The structural properties of phenylacetylene have been investigated in the S(0)((1)A(1)) neutral ground and S(1)((1)B(2)) and S(2)((1)A(1)) singlet excited states and the D(0)((2)B(1)) cationic state using both rovibronic and multidimensional Franck-Condon simulations from data determined via correlated ab initio methods. Results are compared to experimental and ab initio data reported in the literature. (10,10)-CASSCF and a hybrid CASSCF/SACCI frequency analysis using the cc-pVDZ Dunning basis set have been employed to produce vibronic simulations of REMPI/FES, dispersed fluorescence, TPES and MATI spectra. Calculated rotational constants are used where appropriate to compare to rotationally resolved experimental studies. Whilst the simulations are of generally good quality, it is apparent that the distortion of the ring along the long axis upon electronic excitation is underestimated, resulting in smaller predicted changes in ipso and para CCC bond angles and weaker activities in the 6a and 9a modes compared with experiment. Simulations of one-photon MATI spectra on the other hand, which do not rely on excited state methodologies, compare very well with experiment, suggesting that the neutral and cationic ground state geometries are quite accurate, as are the predicted changes in geometry accompanying ionisation. Simulated rotational and vibrational profiles, as well as other calculated physical data, show good agreement with the numerous experimental and computational studies of phenylacetylene in the literature.

Radiative relaxation and fragmentation dynamics of S 2p-excited hydrogen sulfide

Radiative relaxation of S 2p-excited hydrogen sulfide (H(2)S) is investigated by dispersed ultraviolet and visible fluorescence spectroscopies. We observe distinct changes in the fluorescence spectra as a function of excitation energy. Excitation to Rydberg states below the S 2p ionization threshold yields intense fluorescence from neutral and ionic atomic fragments (H, S(+), and S(2+)). In addition to the atomic emission, fluorescence of the molecular fragment ion HS(+) is preferably found after excitation of the S 2p electron into the unoccupied 6a(1) and 3b(2) orbitals with sigma(*) character. This is interpreted as evidence for ultrafast dissociation of the core-excited molecule prior to electronic relaxation. The rotationally resolved fluorescence spectra of the A (3)Pi-->X (3)Sigma(-) transition are analyzed in terms of the fragmentation dynamics leading to the formation of the excited molecular fragment ion, where changes in bond angle are discussed in terms of the rotational population.

Very Large Changes in Bond Length and Bond Angle in a Heavy Group 14 Element Alkyne Analogue by Modification of a Remote Ligand Substituent

The synthesis and characterization of the compound Me3Si-4-Ar'SnSnAr'-4-SiMe3 (Ar'-4-SiMe3 = C6H2-2,6-(C6H3-2,6-i-Pr2)2-4-SiMe3) shows that it has a Sn-Sn bond length = 3.066(1) A and a Sn-Sn-C bending angle of 99.25(14) degrees . These parameters differ by about 0.4 A and about 26 degrees from those previously reported for the closely related Ar'SnSnAr' (Ar' = C6H3-2,6-(C6H3-2,6-i-Pr2)2). The results show that, in accordance with the theoretical predictions by Nagase and Takagi, very small amounts of energy (ca. 5 kcal mol-1) separate structural isomers of distannynes that have large differences in their bonding parameters.

Stepwise hydration of cellobiose by DFT methods: 1. Conformational and structural changes brought about by the addition of one to four water molecules

Previous density-functional theory (DFT) calculations found that the anti (or “flipped”) form of cellobiose (with the H1 and H4′ hydrogen atoms on opposite sides of the pseudo-plane formed by the sugar rings) is more stable in vacuo than the syn (or “normal”) conformation most often observed in crystalline- and solution-phase experiments. In order to understand the reason for this conformational preference, cellobiose–water complexes were optimized at the B3LYP/6-311++G ∗∗ level of theory. Ten different anhydrous cellobiose structures were used as starting points, and the results of calculations on 30 monohydrates, 20 dihydrates, 12 trihydrates, and 5 tetrahydrates are presented. The syn form of the molecule was stabilized relative to the anti form as more water molecules were added, with the two conformers being approximately equal in stability at the dihydrate level. Addition of more than two water molecules further increased the relative stability of the syn conformer. One reason for the increase in stability of the syn form upon hydration is the ability of that conformational class to better accommodate a water molecule between the two rings. Changes in bond lengths, bond angles, and dihedral angles that occur due to the interactions with water molecules are described in detail. These hydration induced structural changes are largely localized near the water molecule(s), and the effects of the addition of subsequent water molecules can be predicted based upon the structure differences between the monohydrates and the corresponding anhydrous cellobiose conformers.

Single-crystal X-ray diffraction and temperature dependent 57Fe Mossbauer spectroscopy on the hedenbergite-aegirine (Ca,Na)(Fe2+,Fe3+)Si2O6 solid solution

Synthetic samples with different chemical compositions along the hedenbergite–aegirine (CaFe 2+ Si 2 O 6 –NaFe 3+ Si 2 O 6 ) solid-solution series have been investigated by single-crystal X-ray diffraction and 57 Fe Mossbauer spectroscopy. All compounds show C 2 /c symmetry, both at 298 K and at low temperature (100 K). The structural changes within the hedenbergite–aegirine series are dominated by the M1 site while the M2 site plays a minor role. Replacement of Fe 2+ by Fe 3+ increases the polyhedral distortion of the M1 site and causes an increased repulsion between neighboring M1 sites. The changes in M1-site geometry also induce distinct alterations within the kinking state of the tetrahedral chains, but the changes in tetrahedral bond lengths and angles are small. In addition to the single-crystal X-ray diffraction experiments, a large number of synthetic samples were investigated by 57 Fe Mossbauer spectroscopy at 298 K and, for three selected compositions, between 80 and 700 K. Here, substantial line broadening of the Fe 2+ resonance absorption was observed as an aegirine component is substituted. Two different groups of local distortion environments were observed for Fe 2+ within the solid-solution series, which change relative proportions and numeric value of the quadrupole splitting as a function of chemistry and temperature. This line broadening cannot be ascribed to discrete next-nearest-neighbor (NNN) configurations of Ca and Na as has been done in the literature. Above ~250 K, additional resonance absorption appears in the spectra of samples with aegirine components between 20 and 75 mol%. This absorption gains intensity with increasing temperature, while the 57 Fe hyperfine parameters approach values intermediate between Fe 2+ and Fe 3+ . This effect is ascribed to fast electron delocalization between Fe 2+ and Fe 3+ at elevated temperature.

Physical characterization of amorphous GeSe 2 films

AC conductivity, photodarkening and electron spin resonance measurements are carried out on amorphous GeSe 2 films. The AC conductivity is measured as a function of frequency and temperature. The AC conduction mechanism of the studied films is interpreted via single electron transfer between the C − 1( C + 3) and C 0 centers. The photodarkening is induced with He–Ne laser and observed as transmission and reflection changes through 1.02 μm thick film. Both reversible and irreversible processes are detected with these measurements. The reversible process is induced by defects located in energy at the band edge. The presence of these defects is confirmed by the blue shift of the band edge and the restoration of the initial optical gap value by annealing. On the other hand, the irreversible process results from defects situated in energy into the band tails. These defects cause a considerable additional absorption below the band edge and a remarkable decrease in the refractive index. Electron spin resonance experiments are carried out for the as-deposited, irradiated and annealed film. Free spin centers with concentration 1.013×10 15 cm −3 are detected at g=2.0064 for the as-deposited film. These centers are assumed to be intrinsic since their density slightly decreases by laser irradiation. The defects associated with the photodarkening effect are suggested to originate from topological changes in bond length, bond angle and/or bond configuration.

Structures and XPS studies of several 3d–4f cyano-bridged Ln III–Fe III/Co III heterometallic complexes

Characterization and crystal structure determination of 3d–4f cyano-bridged bimetallic assemblies, Ln(DMF) 4(H 2O) 3Co(CN) 6 · H 2O (DMF = N, N′-dimethylformamide, Ln = Tb, Dy, Ho and Er) have been newly carried out. We have observed their isostructural features and gradual decreasing cell constants and corresponding changes of local bond distances and angles around the cyano-bridges in accord with the ionic radii changes due to lanthanoid contraction. In order to elucidate the reasons that only Nd–Fe and Nd–Co complexes can exhibit photo-induced magnetic functions, we have also investigated the electronic properties for several analogous 3d–4f complexes, Ln(DMF) 4(H 2O) 3M(CN) 6 · H 2O (Ln = Ce, Nd, Sm, Gd, Tb, Dy, Ho and Er; M = Co and Fe), by means of X-ray photoelectron spectroscopy (XPS). We found that the characteristic bent features of Nd–N–C bond angles and the slight shift of binding energies of Ln 4d 3/2 peaks in the 3d–4f systems being closed to mixed-valence states might be the reasons for the novel functions.

Pressure dependence of the 3P 0→ 3H 4 and 1D 2→ 3H 4 emission in Pr 3+:YAG

Photoluminescence related to the 3P 0→ 3H 4 and 1D 2→ 3H 4 transitions of Pr 3+ in YAG is measured in the pressure range from ambient to 290 kbar. The Γ 1→ Γ 3 and Γ 1→ Γ 4 transitions show different dependencies on pressure. All pressure shifts are negative and are smaller for the lines of lower energies for the emission from the 3P 0 and 1D 2 states, that were attributed to the Γ 3 and Γ 4 energy crossover in the ground state. To reproduce the energetic structure of the Pr 3+:YAG system and dependencies of the emission energy on pressure we have used the crystal field model and considered separately isotropic compression of the Pr 3+-ligand system and a non-isotropic effect described by changes of the Pr-O bond angles. The main conclusion of our investigation is that, contrary to expectation, the effect of the hydrostatic pressure is not isotropic; it changes the local bond angles of the ion–ligands system.

How H‐Bonding Modifies Molecular Structure and π‐Electron Delocalization in the Ring of Pyridine/Pyridinium Derivatives Involved in H‐Bond Complexation.

Analysis of the experimental geometry of 397 variously substituted pyridine and pyridinium derivatives has shown very little variation of all bond lengths in the ring and substantial changes in the values of α and β angles, being in line with theoretically modeled data (at the B3LYP/6-311+G** level of theory). No dependence of bond lengths and π-electron delocalization in the ring measured by HOMA index on the changes in bond angle at the N-atom is observed. This is at variance with the patterns observed in substituted phenolate/phenol systems involved in H-bonding. Due to significant differences in magnitude of the ipso angle at the nitrogen atom that depend on the location of hydrogen atom in pyridine/pyridinium systems (N, N···H, and N−H), this angle may be used as a valuable indicator of N···H interactions since the X-ray structural analysis does not give a reliable position for the proton.

Stress reduction behavior in metal-incorporated amorphous carbon films: first-principles approach

The stress reduction behavior in metal-incorporated amorphous carbon films was investigated by the first-principle calculation. We calculated the total energy of the system with changes in bond angles between the incorporated metal (Ti, Mo, Cr, W, Ag, Au, Al, Si, etc) and the carbon atoms by using DMOL3computational software package. The four carbon atoms are arranged as a tetrahedron, with a carbon or metal atom at the center. The total energy increased substantially as the bond angle deviated from the equilibrium value when a carbon atom is located at the tetrahedron center. However, with a replacement by a metal atom at the center of the tetrahedron, the increase in the total energy due to the distortion in bond angle was significantly reduced. The pivotal action of the metal atoms dissolved in the carbon matrix would be more significant when noble metals having filled d-shells are incorporated compared to the transition metals having unfilled d-shells. These atoms have a weak and more isotropic bond with carbon atoms as confirmed by the electron density distribution.

Ab initio studies on excited state intramolecular electron transfer in 4‐amino‐N‐methylphthalimide and 3‐amino‐N‐methylphthalimide

AbstractThe molecules 4‐amino‐N‐methylphthalimide (4AMP) and 3‐amino‐N‐methylphthalimide (3AMP) are bichromophoric compounds composed of both electron donors and acceptor groups. They undergo intramolecular electron transfer (ET), and these types of compounds are frequently used to probe microenvironments in proteins, micelles, membranes, polymer, surfaces, etc. Ab initio calculations using restricted Hartree–Fock (RHF), Møller–Plesset second‐order perturbation theory (MP2) and the multi‐configurational self‐consistent field (MCSCF) methods with the 6‐31G** basis set have been performed to characterize the intermediates of the ET process. Analysis of geometrical and electronic parameters, e.g., changes in bond lengths, angles, dihedrals, and charge density, generally used to predict the ET pathway, is not always sufficient to understand the through‐bond intramolecular charge‐transfer (ICT) process. Hence we have attempted to support the predicted ET pathway in a very unique way by analyzing normal modes of vibrations for molecules in both the ground and excited states. Our results predict a planar ICT model that exhibits a conformational change of the amino nitrogen from nearly sp3 in the ground state to approximately sp2 type in the ICT state. A through‐bond ET occurs from the amino group of both molecules to the proximal carbonyl group in 4AMP and to the distant carbonyl group in 3AMP. Besides ET, the proximal carbonyl group in 3AMP also takes part in hydrogen bonding with the same amino group especially in excited state, which may also contribute toward ET. Such a hydrogen bond, which demands a planar amino group, is not observed in ground‐state 3AMP. These results indicate that nonplanar amino group geometry in the vicinity of a conjugated system is favored, rather than the conventional planar geometry, even in the presence of a suitable hydrogen bond acceptor. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

How H-bonding Modifies Molecular Structure and π-Electron Delocalization in the Ring of Pyridine/Pyridinium Derivatives Involved in H-Bond Complexation

[structure: see text] Analysis of the experimental geometry of 397 variously substituted pyridine and pyridinium derivatives has shown very little variation of all bond lengths in the ring and substantial changes in the values of alpha and beta angles, being in line with theoretically modeled data (at the B3LYP/6-311+G level of theory). No dependence of bond lengths and pi-electron delocalization in the ring measured by HOMA index on the changes in bond angle at the N-atom is observed. This is at variance with the patterns observed in substituted phenolate/phenol systems involved in H-bonding. Due to significant differences in magnitude of the ipso angle at the nitrogen atom that depend on the location of hydrogen atom in pyridine/pyridinium systems (N, N...H, and N-H), this angle may be used as a valuable indicator of N...H interactions since the X-ray structural analysis does not give a reliable position for the proton.