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Showing papers on "Dihedral angle published in 2018"


Journal ArticleDOI
TL;DR: The differences between the introduction of chlorine and fluorine atoms to small-molecule acceptors were deeply investigated and IDIC-4Cl shows the closest π-π stacking distance and the smallest dihedral angle between adjacent molecules to form ideal J-aggregation, which should be beneficial for charge transportation between different connected molecules in this direction.
Abstract: The differences between the introduction of chlorine and fluorine atoms to small-molecule acceptors were deeply investigated. From the single-crystal structures of three molecules, the Cl-substitution intervention into the molecular configuration and packing mainly lies in three aspects as follows: single molecule configuration, one direction of the intermolecular arrangement, and three-dimensional (3D) molecular packing. First, the introduction of the chlorine atom in IDIC-4Cl leads to a more planar molecular configuration than IDIC-4H and IDIC-4F because of the formation of a molecular interlocked network induced by the strong Cl···S intermolecular interactions. Second, IDIC-4Cl shows the closest π-π stacking distance and the smallest dihedral angle (0°) between adjacent molecules to form ideal J-aggregation, which should be beneficial for charge transportation between different connected molecules in this direction. Finally, the interlocked interactions between Cl and S atoms lead to a highly ordered 3D molecular packing, in which the end groups will form an ideal overlapped packing among different molecules, whereas the other two analogues with H or F show less ordered packing of their 1,1-dicyanomethylene-3-indanone ending groups. Organic solar cells based on IDIC-4Cl show the highest power conversion efficiency (PCE) of 9.24%, whereas the PCEs of IDIC-4H- and IDIC-4F-based devices are 4.57 and 7.10%, respectively.

100 citations


Journal ArticleDOI
TL;DR: This study shows a molecular design strategy for controlling the dihedral angle of two carbazole donors linked to a 2,4-diphenyl-1,3,5-triazine acceptor by a phenyl unit and concludes that materials containing two substituted-ortho donors or one -ortho and an adjacent -meta have the smallest energy gaps and the shortest delayed fluorescence lifetimes.
Abstract: This study shows a molecular design strategy for controlling the dihedral angle of two carbazole donors linked to a 2,4-diphenyl-1,3,5-triazine acceptor by a phenyl unit. Using this approach, six thermally activated delayed fluorescence emitters were synthesized with donors placed in various positions around a central phenyl core, and the photophysical relationship between the donor position and its dihedral angle was investigated. We demonstrate that this angle can affect both the strength of the charge transfer state and the conjugation across the entire molecule, effectively changing the singlet–triplet energy gap of the system. We conclude that materials containing two substituted −ortho donors or one −ortho and an adjacent −meta have the smallest energy gaps and the shortest delayed fluorescence lifetimes. On the other hand, emitters with no −ortho substituted donors have larger energy gaps and slow-to-negligible delayed fluorescence. When applying these materials to organic light-emitting diodes, th...

67 citations



Journal ArticleDOI
TL;DR: A core-expanded, pyrrole-fused azacoronene analogue containing two unusual N-doped heptagons and the Hückel aromaticity owing to a peripheral π-conjugation in the dicationic state was concluded from the bond-length alternation and nucleus-independent chemical shift (NICS) and anisotropy of the induced current density (ACID) calculations.
Abstract: A core-expanded, pyrrole-fused azacoronene analogue containing two unusual N-doped heptagons was obtained from commercially available octafluoronaphthalene and 3,4-diethylpyrrole in two steps as a heteroatom-doped nonplanar nanographene. Full fusion with the formation of the tetraazadipleiadiene framework and the longitudinally twisted structure was unambiguously confirmed by single-crystal X-ray diffraction analysis. The edge-to-edge dihedral angle along the acene moiety was 63°. This electron-rich π-system showed four reversible oxidation peaks. Despite the nonplanar structure, the Huckel aromaticity owing to a peripheral π-conjugation in the dicationic state was concluded from the bond-length alternation and nucleus-independent chemical shift (NICS) and anisotropy of the induced current density (ACID) calculations.

62 citations


Journal ArticleDOI
TL;DR: A method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape is introduced and it is shown that ∼89% of the total friction cannot be described as solvent friction and is caused by degrees of freedom that are orthogonal to the dihedral reaction coordinate.
Abstract: The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity; possible explanations for this involve inertial effects or Kramers’ turnover, the finite memory time of friction, and the presence of so-called internal friction. To disentangle these factors, we introduce a method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution that does not scale linearly with water viscosity. At normal water viscosity, the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane’s dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, non-Markovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier-crossing rate of butane. These results not only settle the character of dihedral dynamics in small solvated molecular systems such as butane, they also have important implications for the folding of polymers and proteins.

55 citations


Journal ArticleDOI
TL;DR: In this article, a pyrazole derivative, 3-(benzo[d][1,3]dioxol-5-yl)-5-(3-methylthiophen-2yl)-4,5-dihydro-1H-pyrazole-1-carboxamide was synthesized and characterized by elemental analysis, FT-IR, NMR ( 1 H and 13 C), MS, UV-visible spectra and finally the structure was confirmed by the single crystal X-ray diffraction studies.

54 citations


Journal ArticleDOI
TL;DR: This study presents a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning that outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient and Mean Absolute Error.
Abstract: Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary structure prediction. However, direct angle prediction from sequence alone is challenging. In this article, we present a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning. Tested on a subset of PDB25 and the targets in the latest two Critical Assessment of protein Structure Prediction (CASP), our method outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient (PCC) and Mean Absolute Error (MAE). Our result also shows approximately linear relationship between the real prediction errors and our estimated bounds. That is, the real prediction error can be well approximated by our estimated bounds. Our study provides an alternative and more accurate prediction of dihedral angles, which may facilitate protein structure prediction and functional study.

52 citations


Journal ArticleDOI
TL;DR: In this paper, the (E) −1 −(3, 5 dibromo benzylidene) semicarbazide (35DBBS) has been synthesized and characterized using Fourier-transform infrared (FT-IR), Fourier transform Raman(FT-Raman), 1H and 13C Nuclear magnetic resonance (NMR) spectral analyzes.

43 citations


Journal ArticleDOI
TL;DR: The structure cis-1,3-butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory.
Abstract: The planarity of the second stable conformer of 1,3-butadiene, the archetypal diene for the Diels-Alder reaction in which a planar conjugated diene and a dienophile combine to form a ring, is not established. The most recent high level calculations predicted the species to adopt a twisted, gauche structure owing to steric interactions between the inner terminal hydrogens rather than a planar, cis structure favored by the conjugation of the double bonds. The structure cis-1,3-butadiene is unambiguously confirmed experimentally to indeed be gauche with a substantial dihedral angle of 34°, in excellent agreement with theory. Observation of two tunneling components indicates that the molecule undergoes facile interconversion between two equivalent enantiomeric forms. Comparison of experimentally determined structures for gauche- and trans-butadiene provides an opportunity to examine the effects of conjugation and steric interactions.

42 citations


Journal ArticleDOI
TL;DR: A new time-resolved vibrational analysis unveils the mechanism of an excited state proton shuttle in green fluorescent protein.
Abstract: We simulated an excited state proton transfer in green fluorescent protein by excited state ab initio dynamics, and examined the reaction mechanism in both the time and the frequency domain through a multi resolution wavelet analysis. This original approach allowed us, for the first time, to directly compare the trends of photoactivated vibrations to femtosecond stimulated Raman spectroscopy results, and to give an unequivocal interpretation of the role played by low frequency modes in promoting the reaction. We could attribute the main driving force of the reaction to an important photoinduced softening of the ring-ring orientational motion of the chromophore, thus permitting the tightening of the hydrogen bond network and the opening of the reaction pathway. We also found that both the chromophore (in terms of its inter-ring dihedral angle and phenolic C-O and imidazolinone C-N bond distances) and its pocket (in terms of the inter-molecular oxygen's dihedral angle of the chromophore pocket) relaxations are modulated by low frequency (about 120 cm-1) modes involving the oxygen atoms of the network. This is in agreement with the femtosecond Raman spectroscopy findings in the time-frequency domain. Moreover, the rate in proximity to the Franck Condon region involves a picosecond time scale, with a significant influence from fluctuations of nearby hydrogen bonded residues such as His148. This approach opens a new scenario with ab initio simulations as routinely used tools to understand photoreactivity and the results of advanced time resolved spectroscopy techniques.

37 citations


Journal ArticleDOI
TL;DR: In this article, numerical calculations of textural equilibrium geometries are presented for a space-filling tessellation of grains with a tetrakaidecahedral (truncated octahedral) unit cell.
Abstract: In textural equilibrium, partially molten materials minimize the total surface energy bound up in grain boundaries and grain–melt interfaces. Here, numerical calculations of such textural equilibrium geometries are presented for a space-filling tessellation of grains with a tetrakaidecahedral (truncated octahedral) unit cell. Two parameters determine the nature of the geometries: the porosity and the dihedral angle. A variety of distinct melt topologies occur for different combinations of these two parameters, and the boundaries between different topologies have been determined. For small dihedral angles, wetting of grain boundaries occurs once the porosity has exceeded 11%. An exhaustive account is given of the main properties of the geometries: their energy, pressure, mean curvature, contiguity and areas on cross sections and faces. Their effective permeabilities have been calculated, and demonstrate a transition between a quadratic variation with porosity at low porosities to a cubic variation at high porosities.

Journal ArticleDOI
31 Jan 2018-Polymer
TL;DR: In this paper, the structural differences that arise from different types of curing agents (aliphatic and aromatic) have been estimated using the compressive loading-unloading responses in terms of the energy, stress, and geometric characteristics.

Journal ArticleDOI
TL;DR: In this paper, a new compound, 4-chlorobenzylammonium nitrate, was obtained by a reaction between 4-carbomethyl benzene and nitric acid, and characterized by X-ray diffraction and FT-IR spectroscopy.

Journal ArticleDOI
TL;DR: Human islet amyloid polypeptide (hIAPP) aggregates into fibrils through oligomers that have been postulated to contain α-helices as well as β-sheets.
Abstract: Human islet amyloid polypeptide (hIAPP) aggregates into fibrils through oligomers that have been postulated to contain α-helices as well as β-sheets. We employ a site-specific isotope labeling strategy that is capable of detecting changes in dihedral angles when used in conjunction with 2D IR spectroscopy. The method is analogous to the chemical shift index used in NMR spectroscopy for assigning protein secondary structure. We introduce isotope labels at two neighbouring residues, which results in an increased intensity and positive frequency shift if those residues are α-helical versus a negative frequency shift in β-sheets and turns. The 2D IR dihedral index approach is demonstrated for hIAPP in micelles for which the polypeptide structure is known, using pairs of 13C18O isotope labels L12A13 and L16V17, along with single labeled control experiments. Applying the approach to aggregation experiments performed in buffer, we show that about 27–38% of hIAPP peptides adopt an α-helix secondary structure in the monomeric state at L12A13, prior to aggregation, but not at L16V17 residues. At L16V17, the kinetics are described solely by the monomer and fiber conformations, but at L12A13 the kinetics exhibit a third state that is created by an oligomeric intermediate. Control experiments performed with a single isotope label at A13 exhibit two-state kinetics, indicating that a previously unknown change in dihedral angle occurs at L12A13 as hIAPP transitions from the intermediate to fiber structures. We propose a mechanism for aggregation, in which helices seed oligomer formation via structures analogous to leucine rich repeat proteins.

Journal ArticleDOI
TL;DR: Chemical shifts can be used to predict the conformation of disulfide bonds, greatly improving resolution of solution NMR structures.
Abstract: Cystine residues result from the formation of disulfide bonds between pairs of cysteine residues. This cross linking of the backbone is essential for the structure and activity of peptides and proteins. The conformation of a cystine side chain can be described using five dihedral angles, χ1, χ2, χ3, χ2′, and χ1′, with cystines favouring certain combinations of these angles. 2D NMR spectroscopy is ideally suited for structure determination of disulfide-rich peptides, because of their small size and constrained nature. However, only limited information of the cystine side chain conformation can be determined by NMR spectroscopy, leading to ambiguity in the deduced 3D structures. Resolving accurate structures is important as disulfide-rich peptides have proven to be promising drug candidates in a number of fields, either as bioactive leads or scaffolds. Using a database of NMR chemical shifts combined with crystallographic structures, we have developed a method called DISH that uses support vector machines to predict the dihedral angles of cysteine side chains. It is able to successfully predict χ2 angles with 91% accuracy, and has improved performance over existing prediction methods for χ1 angles, with 87% accuracy. For 81% of cysteine residues, DISH successfully predicted both the χ1 and χ2 angles. By revisiting published solution structures of peptides determined using NMR spectroscopy, we assessed the impact of additional cystine dihedral restraints on the quality of 3D models. DISH improved the resolution and accuracy, highlighting the potential for improving the understanding of structure–activity relationships and rational development of peptide drugs.

Journal ArticleDOI
TL;DR: Two hybrid dyes possessing tetraphenylethylene moieties weakly conjugated with a pyrrolo[3,2- b]pyrrole core have been synthesized and display a weak emission in solution, however, in the solid state a ∼100-fold increase in the fluorescence quantum yield is observed.

Journal ArticleDOI
TL;DR: In this article, a pyrazole derivative, 3-(3methoxyphenyl)-5-(3-methylthiophen-2-yl)-4,5-dihydro-1H-pyrazole-1-carboxamide was synthesized, characterized by NMR, mass spectra, FT-IR, UV-Visible, TG-DTG and finally the three dimensional structure was confirmed by single crystal X-ray diffraction studies.

Journal ArticleDOI
TL;DR: In this paper, two thermally activated delayed fluorescence (TADF) emitters were synthesized and compared to the previously reported molecule 9′-(4,6-diphenyl-1,3,5-triazin-2-yl)phenyl)-9′H-9,3′:6′, 9′,9′-tercarbazole (TCTZ-F), which led to the highest photoluminescence quantum yield (PLQY).
Abstract: Two thermally activated delayed fluorescence (TADF) emitters 9′-(4-(4,6-diphenyl-1,3,5-triazin-2-yl)-2-fluorophenyl)-9′H-9,3′:6′,9′′-tercarbazole (TCTZ-F) and 9′-(4-(4,6-diphenyl-1,3,5-triazin-2-yl)-2,6-difluorophenyl)-9′H-9,3′:6′,9′′-tercarbazole (TCTZ-2F) were synthesized and compared to the previously reported molecule 9′-(4-(4,6-diphenyl-1,3,5-triazin-2-yl)phenyl)-9′H-9,3′:6′,9′′-tercarbazole (TCTZ) to explore the possible effects of the fluorine atom(s) on the molecular conformation, electronic coupling between the donor and acceptor groups, and consequently the photophysical behavior of the emitters. Specifically, the TCTZ-F molecule was calculated to have a smaller dihedral angle than TCTZ-2F and a smaller S1–T1 gap than TCTZ, which led it to have the highest photoluminescence quantum yield (PLQY) among this series of compounds. An OLED fabricated with TCTZ-F as the emitter achieved the highest external quantum efficiencies (22.5%) of this series, indicating that fluorination can play a useful role in TADF emitters.

Journal ArticleDOI
TL;DR: It is shown in this work that non-local correlations of dihedral potentials play a decisive role in the description of the total molecular energy—an effect which is neglected in most state-of-the-art dihedral force fields.
Abstract: Computer simulation increasingly complements experimental efforts to describe nanoscale structure formation. Molecular mechanics simulations and related computational methods fundamentally rely on the accuracy of classical atomistic force fields for the evaluation of inter- and intramolecular energies. One indispensable component of such force fields, in particular for large organic molecules, is the accuracy of molecule-specific dihedral potentials which are the key determinants of molecular flexibility. We show in this work that non-local correlations of dihedral potentials play a decisive role in the description of the total molecular energy—an effect which is neglected in most state-of-the-art dihedral force fields. We furthermore present an efficient machine learning approach to compute intramolecular conformational energies. We demonstrate with the example of α-NPD, a molecule frequently used in organic electronics, that this approach outperforms traditional force fields by decreasing the mean absolute deviations by one order of magnitude to values smaller than 0.37 kcal/mol (16.0 meV) per dihedral angle.

Journal ArticleDOI
TL;DR: In this paper, a series of molecular descriptors derived from empirical force-fields and relate them to single chain conformation characterized by radius of gyration calculated from molecular dynamics simulations are analyzed.

Journal ArticleDOI
TL;DR: In this paper, the photochromic properties of N-salicylideneaminopyridine (SAP) derivatives and their co-crystals were synthesized, and their crystal structures were analyzed to determine the relationship between their structures and photochromics.
Abstract: N-Salicylideneaminopyridine (SAP) is a derivative of the common organic photochromic compound, N-salicylideneaniline (SA), whose crystal changes colors from orange to red upon UV irradiation. Interestingly, the photochromic property of the crystal depends on the crystal structure. In this study, SAP derivatives and their co-crystals were synthesized, and their crystal structures were analyzed to determine the relationship between their structures and photochromic properties. The photochromic property was found to be closely related to the molecular conformation and the packing efficiency in the crystal. In general, crystals with large dihedral angles were photochromic, while those with small dihedral angles were non-photochromic. However, even for crystals with large dihedral angles, small free available spaces in the crystal structure led to non-photochromic properties. This study demonstrates the importance of a combination of structural factors to elucidate the photochromic property of SAP derivatives.

Journal ArticleDOI
TL;DR: In this article, the authors focus on cocrystals of isomeric N-salicylideneaminopyridines with perfluorinated halogen bond donors as coformers.
Abstract: In N-salicylideneaniline derivatives, photochromism occurs by a two-step isomerization mechanism Photochromism has been reported to be closely related to the molecular conformation of the N-salicylideneanilines (described by the dihedral angle Φ) and to the free available space (Vfree) in the crystal In this contribution, we focus on cocrystals of isomeric N-salicylideneaminopyridines with perfluorinated halogen bond donors as coformers The advantage of working with isomers is that they have a similar (if not equal) molecular volume This aspect means that the evaluation and comparison of the free available spaces within cocrystals is not affected by the differences in the molecular volumes of their constituents Cocrystals were synthesized by a one-pot procedure, which allowed concomitant formation of covalent (imine) and noncovalent (halogen) bonds Each cocrystal was characterized by X-ray diffraction, and its photochromism was assessed by UV–vis diffuse reflectance Our results suggest that the Φ/V

Journal ArticleDOI
TL;DR: This grid-based technique can yield 2–6% higher accuracy in predicting angles in the same 5° bin than existing prediction techniques compared and demonstrates the usefulness of predicted probabilities at given angle bins in discrimination of intrinsically disorder regions and in selection of protein models.
Abstract: Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi-Cαi + 1 (θ) and the rotational angle about the Cαi-Cαi + 1 bond (τ). Thus, their accurate prediction is useful for structure prediction and model refinement. Early methods predicted torsion angles in a few discrete bins whereas most recent methods have focused on prediction of angles in real, continuous values. Real value prediction, however, is unable to provide the information on probabilities of predicted angles. Here, we propose to predict angles in fine grids of 5° by using deep learning neural networks. We found that this grid-based technique can yield 2–6% higher accuracy in predicting angles in the same 5° bin than existing prediction techniques compared. We further demonstrate the usefulness of predicted probabilities at given angle bins in discrimination of intrinsically disorder regions and in selection of protein models. The proposed method may be useful for characterizing protein structure and disorder. The method is available at http://sparks-lab.org/server/SPIDER2/ as a part of SPIDER2 package.

Journal ArticleDOI
TL;DR: This study applied ROA spectroscopy to a photoreceptor protein and indicates that a hydrogen out-of-plane ROA band provides a spectroscopic ruler for the out- of-plane distortion of the chromophore that is embedded in a protein environment.
Abstract: Photoactive yellow protein (PYP), from the phototrophic bacterium Halorhodospira halophila, is a small water-soluble photoreceptor protein and contains p-coumaric acid (pCA) as a chromophore. PYP has been an attractive model for studying the physical chemistry of protein active sites. Here, we explore how Raman optical activity (ROA) can be used to extract quantitative information on distortions of the pCA chromophore at the active site in PYP. We use 13C8-pCA to assign an intense signal at 826 cm−1 in the ROA spectrum of PYP to a hydrogen out-of-plane vibration of the ethylenic moiety of the chromophore. Quantum-chemical calculations based on density functional theory demonstrate that the sign of this ROA band reports the direction of the distortion in the dihedral angle about the ethylenic C=C bond, while its amplitude is proportional to the dihedral angle. These results document the ability of ROA to quantify structural deformations of a cofactor molecule embedded in a protein moiety.

Journal ArticleDOI
TL;DR: Among the developed correlations, the Mn-O distance is found to be the most sensitive parameter that switches the sign of the magnetic coupling from negative to positive, which has long been ignored as being too small to be effective.
Abstract: We have synthesised twelve manganese(III) dinuclear complexes, 1–12, in order to understand the origin of magnetic exchange (J) between the metal centres and the magnetic anisotropy (D) of each metal ion using a combined experimental and theoretical approach. All twelve complexes contain the same bridging ligand environment of one μ-oxo and two μ-carboxylato, that helped us to probe how the structural parameters, such as bond distance, bond angle and especially Jahn–Teller dihedral angle affect the magnetic behaviour. Among the twelve complexes, we found ferromagnetic coupling for five and antiferromagnetic coupling for seven. DFT computed the J and ab initio methods computed the D parameter, and are in general agreement with the experimentally determined values. The dihedral angle between the two Jahn–Teller axes of the constituent MnIII ions are found to play a key role in determining the sign of the magnetic coupling. Magneto-structural correlations are developed by varying the Mn–O distance and the Mn–O–Mn angle to understand how the magnetic coupling changes upon these structural changes. Among the developed correlations, the Mn–O distance is found to be the most sensitive parameter that switches the sign of the magnetic coupling from negative to positive. The single-ion zero-field splitting of the MnIII centres is found to be negative for complexes 1–11 and positive for complex 12. However, the zero-field splitting of the S = 4 state for the ferromagnetic coupled dimers is found to be positive, revealing a significant contribution from the exchange anisotropy – a parameter which has long been ignored as being too small to be effective.

Journal ArticleDOI
TL;DR: In this paper, the authors search for possible structures of crystalline poly(3-hexylthiophene) and identify the one that holds a simulated Raman spectrum most approximate to the experimental one of ordered P3HT aggregates in the frozen solvent.
Abstract: Poly(3-hexylthiophene) (P3HT), being a prototypic conjugated polymer, bears a high charge mobility that is sensitive to its packing configuration in the condensed phase. Despite its extensive experimental study with X-ray diffraction, its specified packing structure still remains stymied. This study searched for possible structures of crystalline P3HT and identified the one that holds a simulated Raman spectrum most approximate to the experimental one of ordered P3HT aggregates in the frozen solvent. The spectral correspondence shows that the Raman-active C–C stretch peak exhibits a red shift in frequency, while the C═C stretch peak displays a blue shift as the layer planarity of P3HT is relaxed. Moreover, the C═C peak splits into two when adjacent thiophene rings in the P3HT chain hold a dihedral angle of 22° with respect to each other. This study demonstrates that Raman spectroscopy plus first-principles simulations can serve as a powerful tool to resolve fine structures of molecular crystals.

Journal ArticleDOI
TL;DR: This work produces potential IDP ensembles using an existing database of pair residue φ and ψ angle probabilities chosen from turn, coil, and bend parts of sequences from the Protein Data Bank and shows that the combination of the database and the Markov algorithm yields ensemble that agree very well with the NMR and MD results for the above-listed observables.
Abstract: Intrinsically disordered proteins (IDPs), involved in regulatory pathways and cell signaling, sample a range of conformations Constructing structural ensembles of IDPs is a difficult task for both experiment and simulation In this work, we produce potential IDP ensembles using an existing database of pair residue φ and ψ angle probabilities chosen from turn, coil, and bend parts of sequences from the Protein Data Bank For all residue pair types, a k-means-based discretization is used to create a set of rotamers and their probabilities in this pair Ramachandran space For a given sequence, a Markov-based probabilistic algorithm is used to create Ramachandran space database-Markov ensembles that are converted to Cartesian coordinates of the backbone atoms From these Cartesian coordinates and φ and ψ dihedral angles of a sequence, various observables: the radius of gyration and shape parameters, the distance probability distribution that is related to the small-angle X-ray scattering intensity, atom–atom

Journal ArticleDOI
TL;DR: It was found that BBzC1 with ester groups on 3,3'-positions exhibit an abnormal aggregation-annihilation circular dichroism (AACD) phenomenon, which could be caused by the decrease of the dihedral angle between adjacent benzocoumarin rings in the aggregation state.

Journal ArticleDOI
TL;DR: In this paper, five new quinacridone (QA)-based dyes containing a N-donor moiety have been synthesized for the application of third-order nonlinear optical (NLO) responses.

Journal ArticleDOI
TL;DR: In this paper, the structural phase transitions of PEA2MnCl4 (PEA = phenethylamine) were investigated using temperature dependent single-crystal X-ray diffraction analysis, including the symmetry analysis of the observed space groups.
Abstract: We investigate possible mechanisms to induce electric polarization in layered organic-inorganic hybrids. Specifically, we investigate the structural phase transitions of PEA2MnCl4 (PEA = phenethylamine) using temperature dependent single-crystal X-ray diffraction analysis, including the symmetry analysis of the observed space groups. Our results show that PEA2MnCl4 transforms from a high-temperature centrosymmetric structure with space group I4/mmm to a low-temperature polar Pca21 phase via an intermediate phase with polar space group Aea2. We study the mechanism responsible for the I4/mmm to Aea2 polar phase transition and find that it is different from previously proposed mechanisms in similar systems. The transition is governed by the opening of a small dihedral angle between the phenyl ring planes of two adjacent PEA molecules, which consequently become crystallographically inequivalent in the Aea2 phase. This molecular rotation induces a significant difference in the lengths of the ethylammonium tails of the two molecules, which coordinate the inorganic layer asymmetrically and are consequently involved in different hydrogen bonding patterns. Consequently, the negatively charged chlorine octahedron that coordinates the Mn2+ cation deforms. This deformation moves the Mn2+ off-center along the out-of-plane-axis, contributing to the polar nature of the structure. Notably, the polar axis is out-of-plane with respect to the inorganic sheets. This is in contrast to other layered organic-inorganic hybrids as well as conventional layered perovskites, such as the Aurivillius phases, where in-plane polarization is observed. Our findings add to the understanding of possible mechanisms that can induce ferroelectric behavior in layered organic-inorganic hybrids.