Conformation Of Symmetry Research Articles

Crystal and Molecular Structure and DFT Calculations of the Steroidal Oxime 6E-Hydroximino-androst-4-ene-3,17-dione (C19H25NO3) a Molecule with Antiproliferative Activity

The single crystal X-ray structure of the novel steroid derivative, 6E-hydroximino-androst-4-ene-3,17-dione (C19H25NO3) (code name RB-499), possessing antiproliferative activity against various cell lines is presented. The analysis produced the following results: chemical formula C19H25NO3; Mr = 315.40; crystals are orthorhombic space group P212121 with Z = 4 molecules per unit cell with a = 6.2609(2), b = 12.5711(4), c = 20.0517(4) Å,Vc = 1578.18(7) Å3, crystal density Dc = 1.327 g/cm³. Structure determination was performed by direct methods, Fourier and full-matrix least-squares refinement. Hydrogens were located in the electron density and refined in position with isotropic thermal parameters. The final R-index was 0.0324 for 3140 reflections with I > 2σ and 308 parameters. The Absolute Structure Parameter − 0.07(5) confirms the correct allocation of the absolute configuration. The presence of the double bond C=O at position 3 in Ring A has caused a distortion from the usual chair conformation and created an unusual distorted sofa conformation folded across an approximate m-plane through C(1)–C(4). Ring B is a distorted chair, its conformation being influenced by the presence of the C(6)=N(6)–O(6)H group in position 6. Ring C is a symmetrical chair. Ring D exhibits both a distorted mirror symmetry conformation [influenced by the C(17)=O(17) group] and a distorted twofold conformation. DFT calculations indicated some degree of flexibility in rings A, C and D with ring A showing the greatest variation in torsion angles. The crystal packing is governed by H-bonds involving O(3), O(6) and O(17). DFT calculations of bond distances and angles, optimized at the B3LYP/6–31++G(d,p) level, were in good agreement with the X-ray structure.Graphical Ring A conformations: (a) Experimental and (b) Calculated. The differences in torsion angle values indicate a degree of flexibility in the ring. The ring conformations are shown in Figures (ii) and (iv) respectively (drawn with BIOVIA [12]. Regions A1 and A2 are approximately planar in both, being planar within 0.048 Å and 0.105 Å respectively.

Raman, infrared and NMR spectra, vibrational assignments and quantum mechanical calculations of centrosymmetric 3,6-Dicholoro-1,2,4,5-tetrazine

The Raman spectrum (2000−100 cm−1) of 3,6-Dicholoro-1,2,4,5-tetrazine (DCTZ, C2N4Cl2) in solid phase has been recorded. Moreover, the mid-IR (2000–400 cm−1) and ATR-IR (2000-480 cm−1), 13C (0–200 ppm) and 15N (0–440 ppm) NMR spectra were recorded. Initially, optimization followed by frequency calculations were carried out for DCTZ restricted to Ci and D2h point groups to work out the least energy conformer with real frequencies. DFT(B3LYP) and MP2(full) computations utilizing 6-31G(d) and 6–311++G(d,p) basis sets favor Ci symmetry conformer by 781/598 cm−1 (9.3/7.2 kjmol−1) and 745/698 cm−1 (8.9/8.3 kjmol−1). The simulated spectra are well compiled to the experimentally recorded IR, Raman, 13C and 15N regardless of few coincident vibrational frequencies that belong to D2h symmetry conformer. Thus, we have carried out additional CASTEP solid state optimization for one molecule per unit cell (Ci symmetry) employing Materials Studio using DFT-PBE method. Similar calculations were completed for D2h molecular symmetry for one molecule and repeated molecules per unit cell in which Ci symmetry is favored by 341 cm−1 (4.1 kjmol−1). It is worth mentioning that computations for both Ci and D2h conformers produce real vibrational frequencies. Assisted by normal coordinate analysis, potential energy distributions (PEDs), complete and confident vibrational assignments are provided herein for Ci conformer. The results are conferred herein are compared with comparable molecules whenever applicable.

Ferroelectric aging effects and large recoverable electrostrain in ceria‐doped BaTiO3 ceramics

AbstractFerroelectric aging is a phenomenon that is generally observed in acceptor‐doped ferroelectrics and usually produces a large recoverable electrostrain. In this work, using an oxide ionic conducting material, a Gd‐modified ceria solution (GDC), as a dopant, we find that GDC‐doped BaTiO3 ceramics exhibit ferroelectric aging behaviors at room temperature. These ceramics show double polarization hysteresis (P‐E) loops and sprout‐shaped recoverable strain vs electric field (S‐E) curves. GDC‐doped BT ceramic (3 mol%) produces a large recoverable electrostrain of 0.12% at 3 kV/cm. The large ions of Ce3+ and Gd3+, which have small electronegativity, lead to the high mobility of oxygen vacancies and a rapid symmetry conformation for short range ordering (SC‐SRO) of points defects, which appear as fast aging effects and a large electrostrain in GDC‐doped BT ceramics at room temperature.

Single-Acetylene Linked Porphyrin Nanorings.

The synthesis of ethyne-linked porphyrin nanorings has been achieved by template-directed Sonogashira coupling. The cyclic hexamer and octamer are predicted by density functional theory to adopt low symmetry conformations, due to dihedral twists between neighboring porphyrin units, but their symmetries are effectively D6h and D8h, respectively, in solution by 1H NMR. The fluorescence spectra indicate that the singlet excited states of these nanorings are highly delocalized.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

Leveraging symmetry to predict self-assembly of multiple polymers

Protein self-assembly is fundamental to biological function and disease. Experimentally, the atomic-level structure is difficult to obtain and the assembly mechanism is poorly understood. The large number of possible states accessible to such systems limits computational prediction. Here, I introduce a new computational approach that enforces conformational symmetry, whereby all chains in the system adopt the same conformation. Using this approach on a 2D lattice, a designed multi-chain conformation is found more than four orders of magnitude faster than existing approaches. Furthermore, the free energy landscape can be efficiently computed, showing potential for enabling atomistic prediction of protein self-assembly.

Water-Induced Structural Changes in Crown Ethers from Broadband Rotational Spectroscopy.

The complexes of 12-crown-4 ether (12C4) with water, generated in a supersonic jet, have been studied using broadband Fourier transform microwave spectroscopy. Three 1:1 and one 1:2 clusters have been observed and their structures unambiguously identified through the observation of isotopologue spectra. The structures of the clusters are based on networks of O-H···O and C-H···O hydrogen bonds. The most abundant 1:1 cluster is formed from the most stable S4 symmetry conformer of 12C4, even though it is not the energetically favored water complex. Interestingly, the structures of the most stable water cluster and the other remaining observed 1:1 and 1:2 complexes are formed from the second or the fifth most abundant conformers of 12C4. This shows the existence of a mechanism that changes the conformation of 12C4 so that the host-guest interactions can be maximized, even for a "soft" ligand like water.

Structural polymorphism in poly(3-ethyl-3-phenyl-2-azetidinone)

The structural characterization of chiral nylon-3 derivative, poly (3-ethyl-3-phenyl-2- azetidinone) (PEPA) has been carried out using FTIR, thermal analysis, X-ray diffraction and electron microscopy. X-ray diffraction of power and fiber samples were analyzed together with electron diffraction patterns of single crystals obtained from isothermal crystallization in solution. Two different crystalline forms were found in accordance with DSC traces, FTIR spectra and X-ray diffraction diagrams. Electron microscopy corroborates the morphological and crystallographic differences between both crystalline forms. Molecular modeling was applied to characterize the two crystalline forms, which were related to different conformation and consequent space symmetry into the crystal unit cell.

S1←S0 vibronic spectra and structure of cyclopropanecarboxaldehyde molecule in the S1 lowest excited singlet electronic state

The S1←S0 vibronic spectra of gas-phase absorption at room temperature and fluorescence excitation of jet-cooled cyclopropanecarboxaldehyde (CPCA, c-C3H5CHO)were obtained and analyzed. In addition, the quantum chemical calculation (CASPT2/cc-pVTZ)was carried out for CPCA in the ground (S0) and lowest excited singlet (S1) electronic states. As a result, it was proved that the S1←S0 electronic excitation of the CPCA conformers (syn and anti) causes (after geometrical relaxation) significant structural changes, namely, the carbonyl fragments become non-planar and the cyclopropyl groups rotate around the central C–C bond. As a consequence, the potential energy surface of CPCA in the S1 state has six minima, 1ab, 2ab, and 3ab, corresponding to three pairs of mirror symmetry conformers: a and b. It was shown that vibronic bands of experimental spectra can be assigned to the 2(S1)←syn(S0) electronic transition with the origin at 30,481cm−1. A number of fundamental vibrational frequencies for the 2 conformer of CPCA were assigned. In addition, several inversional energy levels for the 2 conformer were found and the 2a↔2b potential function of inversion was determined. The experimental barrier to inversion and the equilibrium angle between the CH bond and the CCO plane were calculated as 570cm−1 and 28°, respectively.

Anion photoelectron spectroscopy and CCSD(T) calculations of the Cl−⋯N2 complex

The gas phase anion photoelectron spectrum of the Cl−⋯N2 complex is presented, allowing determination of the electron binding energy, and is compared to CCSD(T) calculations. The calculations reveal three stationary points on the neutral complex surface; a linear C∞v and two C2v symmetry geometries. For the anion complex, two geometries are predicted, similar to the C2v symmetry conformations determined for the neutral. Comparing both computational and experimental results with those from previous work we show trends between anion complex stability and electron stabilisation energy and also the neutral complex stability with respect to the polarisability of the halogen.

CADA-computer-aided DaTSCAN analysis.

BackgroundDopamine transporter (DaT) imaging (DaTSCAN) is useful for the differential diagnosis of parkinsonian syndromes. Visual evaluation of DaTSCAN images represents the generally accepted diagnostic method, but it is strongly dependent on the observer’s experience and shows inter- and intra-observer variability. A reliable and automatic method for DaTSCAN evaluation can provide objective quantification; it is desirable for longitudinal studies, and it allows for a better follow-up control. Moreover, it is crucial for an automated method to produce coherent measures related to the severity of motor symptoms.MethodsIn this work, we propose a novel fully automated technique for DaTSCAN analysis that generates quantitative measures based on striatal intensity, shape, symmetry and extent. We tested these measures using a support vector machine (SVM) classifier.ResultsThe proposed measures reached 100 % accuracy in distinguishing between patients with Parkinson’s disease (PD) and control subjects. We also demonstrate the existence of a linear relationship and an exponential trend between pooled structural and functional striatal characteristics and the Unified Parkinson’s disease Rating Scale (UPDRS) motor score.ConclusionsWe present a novel, highly reproducible, user-independent technique for DaTSCAN analysis producing quantitative measures directly connected to striatum uptake and shape. In our method, no a priori assumption is required on the spatial conformation and localization of striatum, and both uptake and symmetry contribute to the index quantification. These measures can reliably support a computer-assisted decision system.Electronic supplementary materialThe online version of this article (doi:10.1186/s40658-016-0140-9) contains supplementary material, which is available to authorized users.

Stoichiometry for α-bungarotoxin block of α7 acetylcholine receptors.

α-Bungarotoxin (α-Btx) binds to the five agonist binding sites on the homopentameric α7-acetylcholine receptor, yet the number of bound α-Btx molecules required to prevent agonist-induced channel opening remains unknown. To determine the stoichiometry for α-Btx blockade, we generate receptors comprised of wild-type and α-Btx-resistant subunits, tag one of the subunit types with conductance mutations to report subunit stoichiometry, and following incubation with α-Btx, monitor opening of individual receptor channels with defined subunit stoichiometry. We find that a single α-Btx-sensitive subunit confers nearly maximal suppression of channel opening, despite four binding sites remaining unoccupied by α-Btx and accessible to the agonist. Given structural evidence that α-Btx locks the agonist binding site in an inactive conformation, we conclude that the dominant mechanism of antagonism is non-competitive, originating from conformational arrest of the binding sites, and that the five α7 subunits are interdependent and maintain conformational symmetry in the open channel state.

Morphology Tailoring of Pt Nanocatalysts for the Oxygen Reduction Reaction: The Paradigm of Pt13

AbstractUnderstanding the relationship between the morphology of Pt nanocatalysts and their catalytic performance towards the oxygen reduction reaction (ORR) is important for their applications as electrocatalysts. In this work, using density functional theory calculations, we investigate structural properties, ORR activity, and CO tolerance of five morphological forms of the Pt13 cluster. Four of these are low‐energy, lower symmetry conformations (Pt13−1 and Pt13−4 have CS symmetry, Pt13−2 and Pt13−3 are of C2v symmetry) and the fifth (Pt13−5) is a higher energy, icosahedral structure. Our results indicate that of the five considered, Pt13−1 and Pt13−2 possesses the best, overall comparable, combination of catalytic characteristics—activity and CO tolerance—relevant to the ORR. Computational characterization of morphology‐dependent catalytic properties of sub‐nano and nanosized particles herein can inform the design and synthesis of nanocatalysts with superior targeted functionalities.

Non-radiative deactivation in phenol-pyridine complex: theoretical study.

Minimum energy structures of the ground and lowest excited states of the phenol (PhOH)-pyridine (Py) hydrogen-bonded complex in the gas phase were determined by ab initio calculations. Photophysical and photochemical features of the complex under Cs symmetry (planar (Pl) and perpendicular (Pe) conformers) and without any symmetry constraints (unconstrained (Un) conformer) were studied with respect to nonradiative decay processes to the ground state. The mechanism involves internal conversion (IC) and intersystem crossing (ISC) along the O-H bond elongation coordinate, where a coupled electron/proton-transfer reaction plays a decisive role in the photophysics of this complex. For the Pl conformer, nonradiative decay proceeds from a locally excited (1)ππ*(LE) minimum over a conical intersection barrier (0.12 eV) to a charge-transfer (CT) minimum, which corresponds to a hydrogen-bonded PhO˙HPy˙ biradical. Near this second minimum, a barrierless conical intersection (1)A'(ππ*(CT))-S0 funnels the electron population from the CT to the ground S0 state, completing the nonradiative deactivation. Calculations performed for the Pe and Un conformers confirmed that the same radiationless mechanism proceeds with no (1)ππ*(LE)/(1)ππ*(CT) conical intersection near the Franck-Condon region. Furthermore, the population of the lowest triplet states via ISC and their contribution to the photophysics of PhOH-Py complex have been discussed. These findings appear to suggest that there is no single dominant path, but rather many distinct paths involving different quenching mechanisms.

Effects of conformational symmetry in conjugated side chains on intermolecular packing of conjugated polymers and photovoltaic properties

Introduction of the symmetric conjugated side chain to the conjugated backbone of the polymer was found to improve both the light-harvesting ability of the polymer and its charge carrier mobility, apparently by increasing the packing between the polymer chains.

The Relationship Between Foot Conformation, Foot Placement and Motion Symmetry in the Equine Hindlimb

Reasons for performing studyThe relationships between hind foot conformation, placement and motion symmetry in the equine hindlimb are poorly defined. Little research has been carried out into the potential interactions between these variables despite the commonality of hindlimb lameness in sports and leisure horses.ObjectivesTo determine hind foot placement and describe the relationships between hind foot conformation, placement and motion symmetry.Study designObservational study.MethodsOverall foot placement of 43 horses was determined from simultaneous orthogonal filming at walk and trot, foot conformation was measured from digital photographs and motion symmetry data was collected using horse mounted inertial sensors.ResultsLeft and right hind foot conformation differed significantly (P = 0.001–0.036). Foot placement was not significantly different between left and right feet, despite these conformational differences. Foot placement was significantly different between walk and trot (P<0.001). Lateral heel landing was the most common landing pattern observed at walk (55.81%) and trot (43.12%). Lateral and lateral toe landings were more common at trot, though relatively uncommon at both gaits. Foot conformation was significantly associated with motion symmetry (P<0.001–0.007) and with placement at trot (P = 0.002–0.005) but not walk.ConclusionsHind feet land preferentially laterally and heel first at both the walk and trot. Foot conformation appeared to be associated with landing patterns at the trot but not walk. Foot conformation was also associated with motion symmetry, although it is difficult to say whether conformation affects symmetry or vice versa. Multiple factors contribute to equine locomotion, foot conformation, landing patterns and the maintenance of orthopaedic health.Ethical animal research: This study was granted approval by the Royal Veterinary College Ethics Committee. Informed consent was obtained from all owners involved. Sources of funding: None. Competing interests: None.

Vibrational spectra, theoretical calculations, and structure of 4-silaspiro(3,3)heptane

Theoretical computations have been carried out for 4-silaspiro(3,3)heptane (SSH) in order to calculate its structure and vibrational spectra. SSH was found to have two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. The puckering and tilting reduce the D2d symmetry to C2. Nonetheless, the vibrational assignments can be done quite well on the basis of D2d symmetry. This is confirmed by the fact that all but the lowest E vibrations show insignificant splitting into A and B modes of C2 symmetry. However, the observed splittings of the lowest frequency modes do confirm the lower conformational symmetry. The calculated infrared and Raman spectra were compared to the experimental spectra collected for the vapor, liquid, and solid states, and the agreement is excellent.

Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

We investigate the wrapping conformations of a single, strongly adsorbed polymer chain on an oppositely charged nano-sphere by employing a reduced (dimensionless) representation of a primitive chain-sphere model. This enables us to determine the global behavior of the chain conformation in a wide range of values for the system parameters including the chain contour length, its linear charge density and persistence length as well as the nano-sphere charge and radius, and also the salt concentration in the bathing solution. The structural behavior of a charged chain-sphere complex can be described in terms of a few distinct conformational symmetry classes separated by continuous or discontinuous transition lines which are determined by means of appropriately defined (order) parameters. Our results can be applied to a wide class of strongly coupled polymer-sphere complexes including, for instance, complexes that comprise a mechanically flexible or semiflexible polymer chain or an extremely short or long chain and, as a special case, include the biologically relevant example of DNA-histone complexes.

Substitution of aqua ligands from alkyldiamine-bridged dinuclear Pt(II) complexes using azole nucleophiles

The rate of substitution of aqua ligands in dinuclear Pt(II) complexes, which are bridged by alkyldiamine linkers of variable chain lengths, and their mononuclear Pt(II) analogues were studied under pseudo-first order conditions as a function of concentration and temperature using azoles. The results indicate that substitution of aqua ligands of the dinuclear Pt(II) complexes occurs simultaneously and increases as the alkyl chain length of the diamine bridge increases. Steric hindrance due to the C2h conformational symmetry, whose influence decreases as the length of alkylamine linker increases, appears to be the dominant factor controlling the reactivity of the dinuclear Pt(II) complexes. Prop, a homologue which has a 1,3-propanediamine bridge and a C2v conformation, shows an unusual high reactivity. Weak sigma donicity due to the α,ω-alkyldiamine bridge is evident when the reactivity of dinuclear species is compared to their mononuclear analogues. Mononuclear Pt(II) complexes are more reactive than the dinuclear Pt(II) complexes with their reactivity increasing with increasing chain length of the alkylamine tail. The nucleophilicity of the azoles decreases in the order Pz > Tz > mPz. This is in accord with the basicity of the coordinating nitrogen donor in the case of Pz and Tz, while a steric hindrance to the approach of 1-methylpyrazole due to the ortho N-methyl substituent on the ring is evident for mPz. The substitution of aqua ligands by azoles remains associatively-activated.

Synthesis, spectroscopic characterization and theoretical calculations of ClF2CC(O)N[dbnd]PCl3 ([chloro(difluor)acetyl]phosphorimidic trichloride)

The synthesis of [chloro(difluor)acetyl]phosphorimidic trichloride (ClF2CC(O)NPCl3), together with a tentative assignment of the vibrational, NMR and mass spectra, are reported. Quantum chemical calculations (MP2 and B3LYP methods with 6-311+G(d) and 6-311+G(2df,p) basis sets) predict three stable conformers in the gas phase (syn, gauche and anti, defined according to the rotation around both the ClCCN and the CCNP dihedral angles). However, only a single C1 symmetry conformer is observed in the liquid phase, possessing the CO double bond in synperiplanar orientation with respect to the PN double bond, and the ClC bond distorted from the plane defined by the CC(O)NP entity. A Natural Bond Orbital (NBO) analysis was carried out for the title compound and related molecules in order to provide an explanation about the electronic properties.