Showing papers on "Dihedral angle published in 2011"
TL;DR: In this article, a combined experimental and theoretical study of the electronic transport through single-molecule junctions based on nitrile-terminated biphenyl derivatives is presented.
Abstract: We present a combined experimental and theoretical study of the electronic transport through single-molecule junctions based on nitrile-terminated biphenyl derivatives. Using a scanning tunneling microscope-based break-junction technique, we show that the nitrile-terminated compounds give rise to well-defined peaks in the conductance histograms resulting from the high selectivity of the N-Au binding. Ab initio calculations have revealed that the transport takes place through the tail of the LUMO. Furthermore, we have found both theoretically and experimentally that the conductance of the molecular junctions is roughly proportional to the square of the cosine of the torsion angle between the two benzene rings of the biphenyl core, which demonstrates the robustness of this structure-conductance relationship.
202 citations
TL;DR: Assessment using the 70-molecule van Duijnen and Swart data set clearly showed that the developed models are both accurate and highly transferable and are in fact have smaller errors than the models developed using this particular data set (set E models).
Abstract: In this work, four types of polarizable models have been developed for calculating interactions between atomic charges and induced point dipoles. These include the Applequist, Thole linear, Thole exponential model, and the Thole Tinker-like. The polarizability models have been optimized to reproduce the experimental static molecular polarizabilities obtained from the molecular refraction measurements on a set of 420 molecules reported by Bosque and Sales. We grouped the models into five sets depending on the interaction types, that is, whether the interactions of two atoms that form the bond, bond angle, and dihedral angle are turned off or scaled down. When 1−2 (bonded) and 1−3 (separated by two bonds) interactions are turned off, 1−4 (separated by three bonds) interactions are scaled down, or both, all models including the Applequist model achieved similar performance: the average percentage error (APE) ranges from 1.15 to 1.23%, and the average unsigned error (AUE) ranges from 0.143 to 0.158 A3. When t...
137 citations
TL;DR: Extensive magneto-structural correlations have been developed for the trinuclear complexes and the observed J trend for thetrinuclear complex is similar to that of the dinuclear {Ni-Gd} complex.
Abstract: Theoretical calculations using density functional methods have been performed on two dinuclear {NiII–GdIII} and two trinuclear {NiII–GdIII–NiII} complexes having two and three μ-OR (R = alkyl or aromatic groups) bridging groups. The different magnetic behaviour, having moderately strong ferromagnetic coupling for complexes having two μ-OR groups and weak ferromagnetic coupling for complexes having three μ-OR groups, observed experimentally is very well reproduced by the calculations. Additionally, computation of overlap integrals MO and NBO analysis reveals a clear increase in antiferromagnetic contribution to the net exchange for three μ-OR bridged {Ni–Gd} dimers and also provides several important clues regarding the mechanism of magnetic coupling. Besides, MO and NBO analysis discloses the role of the empty 5d orbitals of the GdIII ion on the mechanism of magnetic coupling. Magneto-structural correlations for Ni–O–Gd bond angles, Ni–O and Gd–O bond distances, and the Ni–O–Gd–O dihedral angle have been developed and compared with the published experimental {Ni–Gd} structures and their J values indicate that the Ni–O–Gd bond angles play a prominent role in these types of complexes. The computation has then been extended to two trinuclear {NiII–GdIII–NiII} complexes and here both the {Ni–Gd} and the {Ni–Ni} interactions have been computed. Our calculations reveal that, for both structures studied, the two {NiGd} interactions are ferromagnetic and are similar in strength. The {Ni–Ni} interaction is antiferromagnetic in nature and our study reveals that its inclusion in fitting the magnetic data is necessary to obtain a reliable set of spin Hamiltonian parameters. Extensive magneto-structural correlations have been developed for the trinuclear complexes and the observed J trend for the trinuclear complex is similar to that of the dinuclear {Ni–Gd} complex. In addition to the structural parameters discussed above, for trinuclear complexes the twist angle between the two Ni–O–Gd planes is also an important parameter which influences the J values.
131 citations
TL;DR: These compounds are the first OFF-ON-OFF type of pH-dependent fluorescent sensors and both the intrinsic fluorescence of these compounds and their fluorescent quenching properties along with the change in the pH value have been found to depend on the steric configuration as well as the linking group between 8-hydroxyquinoline and Bodipy moieties.
Abstract: A series of four novel 8-hydroxyquinoline-substituted boron–dipyrromethene derivatives, namely 4,4-difluoro-8-(5-(8-hydroxyquinoline))-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (1), 4,4-difluoro-8-(5-(8-hydroxyquinoline))-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (2), 4,4-difluoro-8-(5-azastyryl-(8-hydroxyquinoline))-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (3), and 4,4-difluoro-8-(5-azastyryl-(8-hydroxyquinoline))-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (4), have been synthesized and characterized by a series of spectroscopic methods. The molecular structures of 1 and 2 have been determined by single-crystal X-ray diffraction analyses. The two methyl substituents attached at C-1 and C-7 positions of boron–dipyrromethene (Bodipy) in compound 2 was revealed to prevent the free rotation of the 8-hydroxyquinoline (8-HQ) moiety, resulting in an almost vertical 8-HQ-Bodipy configuration of this compound. This is obviously different from those for 1 with the dihedral angle between 8-hydroxy...
102 citations
TL;DR: The strategy introduced here represents a powerful addition to force field optimization approaches by overcoming shortcomings of methods that are solely based on quantum-chemical calculations of small molecules and protein fragments in the gas phase.
Abstract: High quality molecular mechanics force fields of proteins are key for the quantitative interpretation of experimental data and the predictive understanding of protein function based on computer simulations. A strategy is presented for the optimization of protein force fields based on full-length proteins in their native environment that is guided by experimental NMR chemical shifts and residual dipolar couplings (RDCs). An energy-based reweighting approach is applied to a long molecular dynamics trajectory, performed with a parent force field, to efficiently screen a large number of trial force fields. The force field that yields the best agreement with the experimental data is then used as the new parent force field, and the procedure is repeated until no further improvement is obtained. This method is demonstrated for the optimization of the backbone φ,ψ dihedral angle potential of the Amber ff99SB force field using six trial proteins and another 17 proteins for cross-validation using (13)C chemical shifts with and without backbone RDCs. The φ,ψ dihedral angle potential is systematically improved by the inclusion of correlation effects through the addition of up to 24 bivariate Gaussian functions of variable height, width, and tilt angle. The resulting force fields, termed ff99SB_φψ(g24;CS) and ff99SB_φψ(g8;CS,RDC), perform significantly better than their parent force field in terms of both NMR data reproduction and Cartesian coordinate root-mean-square deviations between the MD trajectories and the X-ray crystal structures. The strategy introduced here represents a powerful addition to force field optimization approaches by overcoming shortcomings of methods that are solely based on quantum-chemical calculations of small molecules and protein fragments in the gas phase.
85 citations
TL;DR: In this paper, a set of oxide and chalcogenide tetrahedral glasses is investigated using molecular dynamics simulations, and it is shown that the changes in the Ge composition affect mostly bending around germanium in binary Ge-Se systems, leaving Se-centered bending almost unchanged.
Abstract: A set of oxide and chalcogenide tetrahedral glasses is investigated using molecular dynamics simulations. We show that the changes in the Ge composition affect mostly bending around germanium in binary Ge-Se systems, leaving Se-centered bending almost unchanged. In contrast, the corresponding Se twisting (quantified by the dihedral angle) depends on the Ge composition and is reduced when the system becomes rigid. It is also shown that angles involving the fourth neighbor around Ge is found to change when the system enters the stressed rigid phase. The same analysis reveals that unlike stoichiometric selenides such as GeSe2 and SiSe2, germania and silica display large standard deviations in the bond angle distributions. Within bond-bending constraints theory, this pattern can be interpreted as a manifestation of broken (i.e., ineffective) oxygen bond-bending constraints, whereas the silicon and germanium bending in oxides is found to be similar to the one found in flexible and intermediate Ge-Se systems. Our results establish the atomic-scale foundations of the phenomenological rigidity theory, thereby profoundly extending its significance and impact on the structural description of network glasses.
85 citations
TL;DR: It is shown that the distribution of ϕ/ψ angles for all 87,000 residues in these proteins shows the same dependence on τ as predicted by Ramachandran and colleagues, making clear that steric constraints alone are sufficient to explain the backbone dihedral angle distributions observed in proteins.
Abstract: The pioneering work of Ramachandran and colleagues emphasized the dominance of steric constraints in specifying the structure of polypeptides. The ubiquitous Ramachandran plot of backbone dihedral angles (f and c) defined the allowed regions of conformational space. These predictions were subsequently confirmed in proteins of known structure. Ramachandran and colleagues also investigated the influence of the backbone angle s on the distribution of allowed f/c combinations. The ''bridge region'' (f � 0 and 220 � c � 40) was predicted to be particularly sensitive to the value of s. Here we present an analysis of the distribution of f/c angles in 850 non- homologous proteins whose structures are known to a resolution of 1.7 Aor less and sidechain B- factor less than 30 A ˚ 2 . We show that the distribution of f/c angles for all 87,000 residues in these proteins shows the same dependence on s as predicted by Ramachandran and colleagues. Our results are important because they make clear that steric constraints alone are sufficient to explain the backbone dihedral angle distributions observed in proteins. Contrary to recent suggestions, no additional energetic contributions, such as hydrogen bonding, need be invoked.
82 citations
TL;DR: The demonstrated spectroelectrochemical strategy and the direct correlation of the spectroscopic results with (single) molecular conductance studies may guide the selection and elucidation of functional molecules for potential applications in novel nanodevices.
Abstract: In situ gap-mode Raman spectra were acquired in an electrochemical environment on a single-crystal gold electrode employing a Au(100)|4,4′-biphenyldithiol (BPDT)|Au-NP(55 nm) sandwich assembly. This geometry enabled an investigation of the influence of an applied electrochemical gate field on the conformational changes in nanojunctions, such as the torsion angle (φ) of molecules. A linear correlation between the intensity ratio IC═C/ICring–S and cos2 φ in 4,4′-BPDT-type molecular junctions was established and subsequently utilized to estimate the potential dependence of the torsion angle of the “flexible” molecule M1 at different potentials. The latter decreases as the potential (charge) becomes more negative, resulting in better π–π coupling, which correlates with enhanced junction conductance. The demonstrated spectroelectrochemical strategy and the direct correlation of the spectroscopic results with (single) molecular conductance studies may guide the selection and elucidation of functional molecules ...
77 citations
TL;DR: The decoupling approach outlined herein provides the basis for constructing rigid rod architectures composed of multiple azobenzene photochromes, which display practically quantitative photoswitching properties, a necessary prerequisite to achieve highly efficient transduction of light energy directly into motion.
Abstract: A strategy to optimize the photoswitching efficiency of rigid, linear multiazobenzene constructs is presented. It consists of introducing large dihedral angles between azobenzene moieties linked via aryl–aryl connections in their para positions. Four bisazobenzenes exhibiting different dihedral angles as well as three single azobenzene reference compounds have been synthesized, and their switching behavior has been studied as well as experimentally and theoretically analyzed. As the dihedral angle between the two azobenzene units increases and consequently the electronic conjugation decreases, the photochromic characteristics improve, finally leading to individual azobenzene switches operating independently in the case of the perpendicular ortho,ortho,ortho′,ortho′-tetramethyl biphenyl linker. The electronic decoupling leads to efficient separation of the absorption spectra of the involved switching states and hence by choosing the appropriate irradiation wavelength, an almost quantitative E → Z photoisom...
73 citations
TL;DR: The CH3Shift method of performing structure-based predictions of methyl chemical shifts is presented and an accuracy range is shown that ranges from 0.133 to 0.198 ppm for 1H chemical shifts for Ala, Thr, Val, Leu and Ile methyl groups.
Abstract: Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to extend the scope of chemical shifts for structure determination, we present here the CH3Shift method of performing structure-based predictions of methyl chemical shifts. The terms considered in the predictions take account of ring current, magnetic anisotropy, electric field, rotameric type, and dihedral angle effects, which are considered in conjunction with polynomial functions of interatomic distances. We show that the CH3Shift method achieves an accuracy in the predictions that ranges from 0.133 to 0.198 ppm for 1H chemical shifts for Ala, Thr, Val, Leu and Ile methyl groups. We illustrate the use of the method by assessing the accuracy of side-chain structures in structural ensembles representing the dynamics of proteins.
68 citations
TL;DR: The results verify the plausibility for defining and computing the steric effect in the post-Hartree-Fock level of theory according to the scheme proposed by Liu.
Abstract: On the basis of a density-based quantification of the steric effect [Liu, S. B. J. Chem. Phys.2007, 126, 244103], the origin of the internal rotation barrier between the eclipsed and staggered conformers of ethane is systematically investigated in this work from an information-theoretical point of view by using the Fisher information measure in conjugated spaces. Two kinds of computational approaches are considered in this work: adiabatic (with optimal structure) and vertical (with fixed geometry). The analyses are performed systematically by following, in each case, the conformeric path by changing the dihedral angle from 0 to 180° . This is calculated at the HF, MP2, B3LYP, and CCSD(T) levels of theory and with several basis sets. Selected descriptors of the densities are utilized to support the observations. Our results show that in the adiabatic case the eclipsed conformer possesses a larger steric repulsion than the staggered conformer, but in the vertical cases the staggered conformer retains a larg...
TL;DR: It is concluded that Oi−1 and C′i are linked by a partial covalent bond in α‐ helices, which has important ramifications for the folding and conformational stability of α‐helices in isolation and in proteins.
Abstract: The oxygen of a peptide bond has two lone pairs of electrons. One of these lone pairs is poised to interact with the electron-deficient carbon of the subsequent peptide bond in the chain. Any partial covalency that results from this n→π* interaction should induce pyramidalization of the carbon (C′i) toward the oxygen (Oi−1). We searched for such pyramidalization in 14 peptides that contain both α- and β-amino acid residues and that assume a helical structure. We found that the α-amino acid residues, which adopt the main chain dihedral angles of an α-helix, display dramatic pyramidalization but the β-amino acid residues do not. Thus, we conclude that Oi−1 and C′i are linked by a partial covalent bond in α-helices. This finding has important ramifications for the folding and conformational stability of α-helices in isolation and in proteins.
TL;DR: Using density-functional-based molecular dynamics simulations, comparative studies of the trans-cis isomerizations of azobenzene and bridged azobenzo (B-Ab) 5,6-dihydrodibenzo[c,g][1,2]diazocine induced by nπ* electronic excitation find that the complete isomers have approximately the same time scales.
Abstract: Using density-functional-based molecular dynamics simulations, we have performed comparative studies of the trans-cis isomerizations of azobenzene and bridged azobenzene (B-Ab) 5,6-dihydrodibenzo[c,g][1,2]diazocine induced by nπ* electronic excitation. The quantum yields found in our calculations, 45% for the bridged azobenzene versus 25% for azobenzene, are consistent with the experiment. Both isomerization processes involve two steps: (1) Starting from the trans structure, each molecule moves on its S(1) excited-state potential energy surface, via rotation around the NN bond, to an avoided crossing near the S(1)/S(0) conical intersection, where de-excitation occurs. (2) Subsequently, in the electronic ground state, there is further rotation around the NN bond, accompanied by twisting of the phenyl rings around their CN bonds, until the cis geometry is achieved. Because of its lower symmetry and smaller initial CNNC dihedral angle, the bridged azobenzene has a much shorter lifetime for the S(1) excited state, about 30 fs, as compared to about 400 fs for azobenzene. However, we find that the complete isomerizations have approximately the same time scales. Although the bridging feature in trans-B-Ab does not hinder rotation around the NN bond in step 1, it makes twisting of the two phenyl rings around the CN bonds much slower in step 2.
TL;DR: Two methyl substituents attached at C-1 and C-7 positions of boron-dipyrromethene (Bodipy) moiety in compounds 1-3 were revealed to prevent the free rotation of the benzene moiety, resulting in a molecular configuration with an almost orthogonal dihedral angle between the Bodipy and Benzene moieties.
Abstract: A series of six Bodipy derivatives, namely 4,4-difluoro-8-(4-amidophenyl)-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (1), 4,4-difluoro-8-(4-methylphenyl)-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (2), 4,4-difluoro-8-(4-nitrylphenyl)-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (3), 4,4-difluoro-8-(4-amidophenyl)-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (4), 4,4-difluoro-8-(4-methylphenyl)-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (5), and 4,4-difluoro-8-(4-nitrylphenyl)-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (6) were structurally characterized by single crystal X-ray diffraction analysis. Two methyl substituents attached at C-1 and C-7 positions of boron-dipyrromethene (Bodipy) moiety in compounds 1–3 were revealed to prevent the free rotation of the benzene moiety, resulting in a molecular configuration with an almost orthogonal dihedral angle between the Bodipy and benzene moieties with the dihedral angle in the range of 81.14–88.56°. This is obviously different from that for 4–6 with a free-rotating benzene moiety relative to the Bodipy core due to the lack of two methyl substituents in the latter series of compounds, leading to an enhanced interaction between the Bodipy and benzene moieties for 4–6 in comparison with 1–3. The resulting larger HOMO–LUMO gap for 1–3 than 4–6 results in a blue-shifted absorption band for 1–3 relative to that for 4–6. Comparative studies over their fluorescence properties also disclose the blue-shifted fluorescence emission band and corresponding higher fluorescence quantum yield for 1–3 relative to those of 4–6, revealing the effect of molecular configuration on the spectroscopic properties of Bodipy derivatives. Comparison of the redox behaviors of these two series of Bodipy compounds provides additional support for this point. In addition, the electron-donating/withdrawing property of the para substituent of the benzene moiety was shown to exhibit a slight influence on the electronic absorption and fluorescence emission properties of the Bodipy compounds.
TL;DR: This comprehensive study characterized the amide I and II spectral signatures of the fully extended conformation, which will facilitate the conformational analysis of artificial oligopeptides that contain such structural motifs.
Abstract: We have carried out structural determination of capped Cα,α-diethylglycine (Deg) homopeptides with different chain lengths, Ac-(Deg)n-OtBu (n = 2−5), solvated in CDCl3, and investigated vibrational properties of the amide I and II modes by linear and 2D IR spectroscopy, ONIOM calculations, and molecular dynamics simulations. 2D IR experiments were performed in the amide I region using the rephasing pulse sequence under the double-crossed polarization and the nonrephasing sequence under a new polarization configuration to measure cross-peak patterns in the off-diagonal regions. The 2D IR spectra measured in the amide I and II regions reveal complex couplings between these modes. Model spectral calculations finely reproduced the measured spectral profiles by using vibrational parameters that were very close to the values predicted by the ONIOM method. The agreement led to a conclusion that peptide backbones are fully extended with the dihedral angles (ϕ,ψ) ≈ (±180°,±180°) and that a sequence of intramolecul...
TL;DR: The study indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged and the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends.
Abstract: By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed.
TL;DR: UV-vis and fluorescence titration experiments confirmed the existence of strong π-π interactions between the fullerene Sc(3)N@C(80) and the flexible bisporphyrin dimer with hexyl spacers.
Abstract: We report the synthesis of two cyclic β-pyrrole unsubstituted meso-tetraphenyl bisporphyrins in which the porphyrin units are connected by two 2,3-hexadiynyl-1,6-dioxo or two hexyl-1,6-dioxo spacers, respectively. Both cyclic porphyrin dimers exist in solution as mixtures of two conformational isomers. In the solid state, the receptor with diynyl spacers forms a 1:1 complex with the icosahedral (Ih) isomer of the trimetallic nitride endohedral fullerene Sc3N@C80. In this complex the receptor adopts a scoop-shaped conformation having a dihedral angle of 87.25° between the two porphyrin planes. The hexyl spaced analogue, however, adopts a similar conformation upon encapsulation of one molecule of Sc3N@C80 in a self-assembled dimeric capsule. The capsular complexes pack in columns and render the fullerene units completely isolated. In toluene solution, 1H NMR experiments indicate that the endohedral fullerene Sc3N@C80 is exclusively bound by the expanded isomer of both dimers. UV−vis and fluorescence titrati...
TL;DR: An excited (1)ILCT state has been the origin of emission of the type-I isomers and delocalizations of the photoactive π(diimine) and π-π orbitals of the L(R)(Φ) over the stacked layers shift theΦ(ext) and λ(em) of solids to lower energies than those in frozen glasses.
Abstract: Three types of atropisomeric unsymmetrical diimine complexes, tetrahedral (LRϕ)MX2 (M = Zn, Cd; X = Cl, Br; R = Me, CMe3, OH, OMe, Cl; 1a–k, type-I), tetrahedral (LMe2ϕ)ZnBr2 (2, type-II) and square planar (LOHϕ)PdCl2 (3, type-III) with different photoluminescence properties, have been reported (LRϕ = (E)-4-R-N-(pyridine-2-ylmethylene)aniline; ϕ = dihedral angle between the diimine unit including the pyridine ring and the phenyl ring planes). In crystals, ϕ = 0° for type-I, 90° for type-II and 63° for type-III atropisomers have been confirmed by single crystal X-ray structure determinations of 1c, 1e, 2 and 3·H2O isomers. Optimizations of geometries in methanol have established ϕ = 28–32° for type-I, 90.83° for type-II and 43.44° for type-III isomers. In solids, type-I atropisomers with ϕ = 0, behave as conjugated 14πe systems facilitating π–π stacking and are brightly luminescent at room temperature while type-II and type-III isomers in solid and type-I isomers in solutions are more like non-conjugated 8πe + 6πe systems and non-emissive. Frozen glasses of acetonitrile, methanol and dichloromethane–toluene mixture at 77 K of type-I isomers are emissive and display structured excitation and emission spectra for R = Me, CMe3, OMe species. Excitation and emission maxima of frozen glasses (λex = 320–380 nm; λem = 440–485 nm) are red shifted in the solid (λex = 390–455 nm; λem = 470–550 nm). TD–DFT calculations on 1b, 1d, 1f and stacked (1b)2 isomers and luminescence lifetime measurements have elucidated that an excited 1ILCT state has been the origin of emission of the type-I isomers and delocalizations of the photoactive πdiimine and πdiimine* orbitals of the LRϕ over the stacked layers shift the λext and λem of solids to lower energies than those in frozen glasses. The trends of diimine ligand based electron transfer events of the complexes in DMF have been investigated by cyclic voltammetry at 298 K.
TL;DR: Eight inorganic-organic hybrid compounds with a formula of [R-Bz-1-APy][PbI(3], which have been synthesized and characterized structurally and which emit multi-band luminescence in the 300-650 nm regions under the excitation of ultraviolet light are presented.
Abstract: Eight inorganic–organic hybrid compounds with a formula of [R-Bz-1-APy][PbI3] (R-Bz-1-APy+ = mono-substituted benzylidene-1-aminopyridinium Schiff base derivative; R = m-CN (1), m-CH3 (2), H (3), p-F (4), p-Cl (5), p-Br (6), o-Cl (7), o-Br (8)) have been synthesized and characterized structurally. The common characteristic of the crystal structures of 1–8 is that the inorganic components form straight and face-sharing octahedral [PbI3]∞ chains and the Schiff base cations surround the [PbI3]∞ chains to form molecular stacks. The substituent (R) on the phenyl ring of the Schiff base cation clearly influences the packing structures of 1–8, and the hybrid compound crystallizes in the space groupP63 when R = CN (1) in the meta-position of the phenyl ring, and in a central symmetric space group when R is in the ortho- or para-position of the phenyl ring. The conformation of the Schiff base cation is related to the R position, and the dihedral angle between the phenyl and pyridyl rings increases in the order of para- < meta- < ortho-position substitution of the phenyl ring. The long molecular axis of the Schiff base cation adopts a manner approximately parallel to the straight inorganic [PbI3]∞ chain in the para-substituted hybrid compounds, and perpendicular to the straight inorganic [PbI3]∞ chain in the ortho-substituted hybrid compounds. 1 is second harmonic generation (SHG) active with a comparable response as that of urea and also exhibits ferroelectricity with larger Ps and Pr values; 1–8 emit multi-band luminescence in the 300–650 nm regions under the excitation of ultraviolet light.
TL;DR: The pure rotational spectra of 1,1,1-trifluoro-2-butanone and its four (13)C isotopologues have been studied using the new chirped-pulsed Fourier transform microwave spectrometer at the University of Manitoba in combination with a conventional Balle-Flygare-type instrument.
Abstract: The pure rotational spectra of 1,1,1-trifluoro-2-butanone and its four 13C isotopologues have been studied using the new chirped-pulsed Fourier transform microwave spectrometer at the University of Manitoba in combination with a conventional Balle−Flygare-type instrument. Quantum chemical calculations, at the MP2/6-311++G(d,p) level, were carried out to obtain information about the structure, relative stability, and difference in populations of the three lowest energy conformers corresponding to dihedral angles of 0°, 82.8°, and 119.2° along the carbon backbone. The observed spectra are that of conformer I (dihedral angle 0°), and, based on analysis of the observed splitting, the V3 barrier to internal rotation of the methyl group has been determined to be 9.380(5) kJ mol−1. The spectroscopic constants of the five isotopologues were used to precisely derive the rs and partial r0 geometries of this conformer based on an assumed planar carbon backbone (as supported by the spectra and ab initio calculations).
TL;DR: Synthetic, computational, and spectral studies have been made to reveal the differences between cross-coupling approaches on the C-C bond and C-N bond formation as well as band gaps and energy levels and optical and electrochemical properties for related compounds.
Abstract: A family of novel linear 1,10-phenanthroline-based (A–D–A–D–A) and oligothiophene-based (A–D–D–D–(D)–A) heterocyclic aromatic fluorescence compounds having N-containing imidazole and pyridine tails with effective π-conjugated systems, prepared by the combination of carbon–carbon (C–C) bond and carbon–nitrogen (C–N) bond cross-coupling reactions, is described. They have molecular lengths of more than 2.30 nm in the cases of 4, 6, 9, and 26, various D–A spacers, and certain N-coordination sites (phen, imidazole, and pyridine). X-ray single-crystal structures of 13 compounds reveal a variety of trans and cis configurations with different dihedral angles between adjacent aromatic heterocycles. Synthetic, computational, and spectral studies have been made to reveal the differences between cross-coupling approaches on the C–C bond and C–N bond formation as well as band gaps and energy levels and optical and electrochemical properties for related compounds. The influences of introducing a β-methyl group to the t...
TL;DR: In this paper, the authors investigated the pressure-induced Raman spectral change of 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) using Raman spectroscopy.
Abstract: We have investigated the pressure-induced Raman spectral change of 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) using Raman spectroscopy. The relative Raman intensity at 590 cm−1 of the CH2 rocking band assigned to the gauche conformer of the NCCC dihedral angle of the butyl group in the [bmim]+ cation increases when the pressure-induced liquid-crystalline phase transition occurs, while that at 610 cm−1 assigned to the trans conformer decreases. Our results show that the high-pressure phase transition of [bmim][PF6] causes the increase of the gauche conformer of the [bmim]+ cation.
TL;DR: In this article, a new thiourea derivative, N -(biphenyl-2-thiocarbamoyl)-4-phenylcarboxamide, is synthesized and characterized by elemental analysis, FTIR, NMR and the single crystal X-ray diffraction study.
TL;DR: Ultrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes and are shown by theory and experiment to have a similar correlation time as the anisotropy decay.
Abstract: Ultrafast vibrational spectra of the aqueous oxalate ion in the region of its carboxylate asymmetric stretch modes show novel relaxation processes. Two-dimensional infrared vibrational echo spectra and the vibrational dynamics obtained from them along with measurements of the anisotropy decay provide a picture in which the localization of the oxalate vibrational excitation onto the carboxylate groups occurs in ∼450 fs. Molecular dynamics simulations are used to characterize the vibrational dynamics in terms of dihedral angle motion between the two carboxylate planes and solvation dynamics. The localization of the oxalate vibrational excitation onto the carboxylates is induced by the fluctuations in the carboxylate vibrational frequencies which are shown by theory and experiment to have a similar correlation time as the anisotropy decay.
TL;DR: A reliable and complete vibrational assignment for each of the isotopomers has been achieved for the first time, and these agree very well with the DFT (B3LYP/cc-pVTZ) computations.
Abstract: The infrared and Raman spectra of vapor, liquid, and solid state cyclopentane and its d1, 1,1-d2, 1,1,2,2,3,3-d6, and d10 isotopomers have been recorded and analyzed. The experimental work was complemented by ab initio and density functional theory (DFT) calculations. The computations confirm that the two conformational forms of cyclopentane are the twist (C2) and bent (Cs) structures and that they differ very little in energy, less than about 10 cm–1 (0.1 kJ/mol). The bending angle for the Cs form is 41.5° and the dihedral angle of twisting is 43.2° for the C2 form. A reliable and complete vibrational assignment for each of the isotopomers has been achieved for the first time, and these agree very well with the DFT (B3LYP/cc-pVTZ) computations. The ab initio CCSD/cc-pVTZ calculations predict a barrier to planarity of 1887 cm–1, which is in excellent agreement with the experimental value of 1808 cm–1.
TL;DR: In this paper, the effect of varying the strain rate and dihedral angle of the liquid phase on liquid interconnectivity was investigated for core-mantle differentiation of small planetesimals.
TL;DR: In this article, the effects of torsion speed and temperature on carbon nanotubes torsional properties were investigated and it was shown that the buckling of CNTs is a reversible process in which by unloading the buckled CNT in opposite direction, it returns to its original configuration.
TL;DR: The first single-crystal X-ray diffraction study of tetrafluorinated monosaccharide derivatives is presented and both α- and β-methyl 2,3-dideoxy-2,2,3, 3-tetrafluoro-d-galactopyranoside anomers adopt the (4)C(1) conformation.
TL;DR: The herringbone structure is a representative molecular packing in organic semiconductors, but there are some modifications with largely different dihedral angles ranging from 40 to 130° as discussed by the authors.
Abstract: The herringbone structure is a representative molecular packing in organic semiconductors, but there are some modifications with largely different dihedral angles ranging from 40 to 130°. Dihedral ...
TL;DR: In this article, relaxed iso-potential maps are generated for different conformational states of cellobiose, showing how glycosidic bond dihedral angles vary as different sets of hydroxymethyl rotamers and hydroxyl directions are examined.
Abstract: New cellobiose ϕH/ψH maps are generated using a mixed basis set DFTr method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are created for different conformational states of cellobiose, showing how glycosidic bond dihedral angles vary as different sets of hydroxymethyl rotamers and hydroxyl directions are examined. These maps are generated, fixing the dihedral ϕH and ψH values at ten degree intervals and energy optimizing the remaining geometry using the B3LYP/6-31+G* functional for all atoms except carbon atoms, where the functional B3LYP was used with the mixed basis set, 4-31G. Mapping results are compared between in vacuo structures using the mixed basis set, in vacuo using the full basis set, and those in which the implicit solvent method, COSMO, is included with the mixed basis set. Results show significant changes in position of energy minima with variation in hydroxyl rotamers and with application of solvent. Unique to this study is the mapping of the hydration energy at each ϕH/ψH point on the map using the energy derived at each point by applying COSMO. Using hydration gradients as a guide one observes directional solvent driven changes in the minimum energy positions. Interesting internal coordinate variances are described.