Rotational Conformers Research Articles

High-Resolution Electron Spectroscopy and Rotational Conformers of Group 6 Metal (Cr, Mo, and W) Bis(mesitylene) Sandwich Complexes

Group 6 metal-bis(mesitylene) sandwich complexes are produced by interactions between the laser-vaporized metal atoms and mesitylene vapor in a pulsed molecular beam source, identified by photoionization time-of-flight mass spectrometry, and studied by pulsed-field ionization zero-electron kinetic energy spectroscopy and density functional theory calculations. Although transition metal-bis(arene) sandwich complexes may adopt eclipsed and staggered conformations, the group 6 metal-bis(mesitylene) complexes are determined to be in the eclipsed form. In this form, rotational conformers with methyl group dihedral angles of 0 and 60° are identified for the Cr complex, whereas the 0° rotamer is observed for the Mo and W species. The 0° rotamer is in a C(2v) symmetry with the neutral ground state of (1)A1 and the singly positive charged ion state of (2)A1. The 60° rotamer is in a C(i) symmetry with the neutral ground state of (1)A(g) and the ion state of (2)A(g). Partial conversion of the 60 to 0° rotamer is observed from He to He/Ar supersonic expansion for Cr-bis(mesitylene). The unsuccessful observation of the 60° rotamer for the Mo and W complexes is the result of its complete conversion to the 0° rotamer in both He and He/Ar expansions. The adiabatic ionization energies of the 0° rotamers of the three complexes are in the order of Cr-bis(mesitylene) < W-bis(mesitylene) < Mo-bis(mesitylene), which is different from that of the metal atoms. These metal-bis(mesitylene) complexes have lower ionization energies than the corresponding metal-bis(benzene) and -bis(toluene) species.

On the Regulation and Activation of JAK2: A Novel Hypothetical Model

Janus kinase 2 (JAK2) is a protein tyrosine kinase central to a multitude of cellular processes. Here, a novel model of JAK2 regulation and activation is proposed. In the JAK2 dimer, instead of being auto-inhibited by its own JH2 domain, inhibition comes from the JH2 domain of the partnering JAK2 monomer. Upon ligand binding, the receptor undergoes a conformational rotation that is passed to its dimeric partner. The activation is achieved by the rotation of two JAK2 molecules, which relieves the JH1/JH2 inhibitory interface and brings two JH1 domains in proximity for the subsequent trans-phosphorylation event. This hypothetical model is consistent with most of the currently available experimental evidence and warrants further tests. Based on the proposed model, it is possible to rationalize the differential responses of JAK2 signaling involving various receptors and ligands. The proposed model of JAK2 regulation and activation is poised to suggest potential alternative drug-discovery strategies that could impact a number of relevant diseases.

Synthesis, characterisation, mesomorphic investigation and temperature-dependent Raman study of a novel calamitic liquid crystal: methyl 4-(4′-n-alkoxybenzylideneamino)benzoate

A new series of Schiff base calamitic liquid crystal; methyl 4-(4′-n-alkoxybenzylideneamino)benzoate (MABAB), H2n+1C n OC6H4C(H)=NC6H4COOCH3 (n = 6, 8, 10, 12, 14, 16) has been synthesised and characterised by elemental analyses, Fourier transform infrared spectroscopy (FT-IR), 1H and 13C Nuclear Magnetic Resonance (NMR) spectroscopy. The mesomorphic properties of these compounds were studied by differential scanning calorimetry (DSC) and polarising optical microscopy (POM). All members of the series exhibit enantiotropic smectic A (SmA) mesophase. Temperature-dependent micro-Raman study of one of the members, MABAB-10 has been employed to identify phase transitions and the molecular rearrangement therein. Analysis of Raman marker bands; C–H in-plane bending, C–C stretching of phenyl rings and –C(H)=N– linking group of core confirms the transitions clearly as observed through DSC and POM. An in situ Raman measurement of C–H in-plane bending mode has also been performed to visualise the molecular changes more clearly. The Raman study gives an evidence of induced co-planarity of rings at Cr→SmA phase transition. The density functional theoretical (DFT) optimisation of monomer, dimer and rotational conformer of MABAB-10 also support the induced co-planarity at Cr→SmA phase transition.

Refining the Interpretation of Near‐Infrared Band Shapes in a Polyynediyl Molecular Wire

Spinning to improve (band) shape: A blend of theoretical and experimental work demonstrates that the rotational conformation of mixed-valence complexes influences the low-energy (NIR) transitions in such molecules. Interpretations of the NIR band shapes are presented.

(E)-Ethyl 3-(3,4-dihydroxyphenyl)prop-2-enoate: a natural polymorph extracted fromAristotelia chilensis(Maqui)

The natural title compound, C11H12O4, extracted from the Chilean native tree Aristotelia chilensis (Maqui), is a polymorph of the synthetic E form reported by Xia, Hu & Rao [Acta Cryst. (2004), E60, o913-o914]. Both rotational conformers are identical from a metrical point of view, and only differ in the orientation of the 3,4-dihydroxyphenyl ring with respect to the rest of the molecule, which leads to completely different crystal structure arrangements and packing efficiencies. The reasons behind both reside in the different hydrogen-bonding interactions.

An ab initio analysis of the Diels–Alder reaction between two isoprenes

The concerted and stepwise mechanisms of the isoprene dimerization via Diels–Alder reaction have been studied with MP2 method. The frontier orbital densities can explain the asynchronous character of the concerted transition structures. The first transition states and intermediates of the stepwise reactions were identified and the conformational rotations of the intermediates were investigated for their stability and possibility to form monocyclic adducts. All the stepwise activation energies were about 15–40kJ/mol higher than the concerted pathways and the meta-adduct (sylvestene) of the endo concerted reaction with cis-dienophile had the lowest activation energy, ∼47kJ/mol, in all reaction systems. A novel synchronous transition state was also predicted which suggests an interesting intramolecular rearrangement of the monoterpenoids.

Time passes yet errors remain: Comments on the structure of N10‐formyltetrahydrofolate synthetase

PDB Code(s): 4IOJ, 4IOK, 4IOL, 4IOM

Rethinking the existence of a steady-state Δψ component of the proton motive force across plant thylakoid membranes

Light-driven photosynthetic electron transport is coupled to the movement of protons from the chloroplast stroma to the thylakoid lumen. The resulting proton motive force that is generated is used to drive the conformational rotation of the transmembrane thylakoid ATPase enzyme which converts ADP (adenosine diphosphate) and Pi (inorganic phosphate) into ATP (adenosine triphosphate), the energy currency of the plant cell required for carbon fixation and other metabolic processes. According to Mitchell's chemiosmotic hypothesis, the proton motive force can be parsed into the transmembrane proton gradient (ΔpH) and the electric field gradient (Δψ), which are thermodynamically equivalent. In chloroplasts, the proton motive force has been suggested to be split almost equally between Δψ and ΔpH (Kramer et al., Photosynth Res 60:151-163, 1999). One of the central pieces of evidence for this theory is the existence of a steady-state electrochromic shift (ECS) absorption signal detected ~515nm in plant leaves during illumination. The interpretation of this signal is complicated, however, by a heavily overlapping absorption change ~535nm associated with the formation of photoprotective energy dissipation (qE) during illumination. In this study, we present new evidence that dissects the overlapping contributions of the ECS and qE-related absorption changes in wild-type Arabidopsis leaves using specific inhibitors of the ΔpH (nigericin) and Δψ (valinomycin) and separately using leaves of the Arabidopsis lut2npq1 mutant that lacks qE. In both cases, our data show that no steady-state ECS signal persists in the light longer than ~60s. The consequences of our observations for the suggesting parsing of steady-state thylakoid proton motive force between (ΔpH) and the electric field gradient (Δψ) are discussed.

Structural Mechanism of CCM3 Heterodimerization with GCKIII Kinases

Mutation of CCM3 causes cerebral cavernous malformations of the vasculature, leading to focal neurological deficits, seizures, and hemorrhagic stroke. CCM3 can heterodimerize with GCKIII kinases (MST3, MST4, and STK25) to regulate cardiovascular development. Here, we provide direct experimental evidence to prove that CCM3 heterodimerizes with GCKIII in a manner structurally resembling the CCM3 homodimerization. Structural comparison revealed the mechanism and critical residues that drive CCM3-GCKIII heterodimerization versus homodimerization. A flexible linker was identified for CCM3, which mediates a large-scale conformational rotation of the FAT domain relative to the dimerization domain. The conformational flip over of FAT domain removes steric locking in the CCM3 homodimer and allows its disassembly and subsequent heterodimerization with GCKIII. CCM3 forms a stable complex with MST4 in vivo to promote cell proliferation and migration synergistically in a manner dependent on MST4 kinase activity. Collectively, our work offers a structural basis for further functional study.

Visual detection of tetracycline antibiotics with the turned on fluorescence induced by a metal–organic coordination polymer

Here, a rapid, simple and sensitive method for visual detection of tetracycline antibiotics (TCs) was developed based on the turned on fluorescence induced by a metal–organic coordination polymer of Zn(bix) [bix=1,4-bis(imidazol-1-ylmethyl)benzene]. Tetracycline antibiotics, such as tetracycline hydrochloride (TC), doxycycline hyclate (DC), chlortetracycline hydrochloride (CTC) and oxytetracyline hydrochloride (OTC), showed very weak fluorescence in Tris–HCl buffer of pH 8.68–9.40. However, the fluorescence intensities of these TCs were greatly enhanced in the presence of Zn(bix) and were found to be proportional to the concentrations of TCs. Accordingly, TCs could be quantitatively determined with the detection limits of 12.0, 6.0, 19.0 and 19.0nM for TC, DC, CTC and OTC, respectively. Furthermore, this fluorimetric method was successfully applied to the determination of DC contents in doxycycline hyclate tablets from three factories with satisfactory results compared with the HPLC method. Also, the interaction mechanism between TCs and Zn(bix) was investigated by the absorption spectra, fluorescence spectra and circular dichroism spectra. The results showed that TCs could interact with Zn(bix) to form TCs–Zn(bix) ternary complexes and the turned on fluorescence was mainly ascribed to the restricted conformational rotation of TCs molecules through coordination with Zn(II) from the polymeric networks of Zn(bix).

Open‐chain unsaturated selanyl sulfides: stereochemical structure and stereochemical behavior of their 77Se–1H spin–spin coupling constants

Stereochemical structure of nine Z-2-(vinylsulfanyl)ethenylselanyl organyl sulfides has been investigated by means of experimental measurements and second-order polarization propagator approach calculations of their (1)H-(1)H, (13)C-(1)H, and (77)Se-(1)H spin-spin coupling constants together with a theoretical conformational analysis performed at the MP2/6-311G** level. All nine compounds were shown to adopt the preferable skewed s-cis conformation of their terminal vinylsulfanyl group, whereas the favorable rotational conformations with respect to the internal rotations around the C-S and C-Se bonds of the internal ethenyl group are both skewed s-trans. Stereochemical trends of (77)Se-(1)H spin-spin coupling constants originating in the geometry of their coupling pathways and the selenium lone pair effect were rationalized in terms of the natural J-coupling analysis within the framework of the natural bond orbital approach.

Picosecond Rotational Interconversion Adjacent to a C═O Bond Studied by Two-Dimensional Infrared Spectroscopy

Molecular conformations around the C═O group of carbonyl compounds like ketones and aldehydes play an important role in determining their reaction properties in solutions, including reaction rate, mechanism, steric structure, and chirality of products. Investigating different rotational conformers and their rapid exchange at room temperature will provide information on the rotational barrier and insights into how different rotamers may contribute to fundamental reactions in chemistry. We applied two-dimensional infrared (2D IR) spectroscopy and polarization-dependent IR transient grating technique to the study of 4,4-dimethyl-2-pentanone in CCl(4). Spectroscopic evidence showed that the internal rotation around the single carbon-carbon bond adjacent to the C═O group takes place on a picosecond time scale. DFT calculations suggested the presence of three different rotational conformations, one eclipsed and two staggered forms. Spectral simulation utilized the stochastic Liouville equation with a three-state jump model and incorporated the polarization factors that take into account the different direction of transition dipole moment in the three rotamers. The effects of the intramolecular vibrational energy redistribution process on the waiting time dependence of the 2D absorptive spectra were also included. Through comprehensive simulation of the observed spectral features, the exchange time constants between the three rotamers were determined: 5.4 ps from the eclipsed to staggered forms and 1.7 ps for the reverse direction.

Nonagostic M···H–C Interactions. Synthesis, Characterization, and DFT Study of the Titanium Amide Ti2Cl6[N(t-Bu)2]2

The compound Ti2Cl6[N(t-Bu)2]2 (1) has been synthesized by treating TiCl4 with di(tert-butyl)amine, HN(t-Bu)2. Compound 1 crystallizes in two different polymorphs from pentane, both conforming to the space group P21/n. In both polymorphs, 1 exhibits a close Ti···C contact of 2.634(3) Å between titanium and a γ-methyl group in one of the two tert-butyl groups of the bound amido ligand. Interestingly, the γ-methyl group adopts a rotational conformation that maximizes the Ti···H distances, the shortest of which are 2.36(2) and 2.62(2) Å. Even though the former distance is within the range characteristic of agostic interactions, the rotational orientation of the methyl group suggests that the Ti···H interactions are repulsive rather than attractive. DFT and NBO analysis confirms this supposition: there is no evidence of weakening of the C–H bond closest to the titanium and no evidence of significant overlap of titanium orbitals with the C–H bonding orbitals of the γ-methyl group involved in the close contact. Further evidence that the close contact is repulsive was obtained from a DFT study of a series of related complexes in which the N(t-Bu)2 ligand is replaced with a NR(t-Bu) ligand, where the substituent R not involved in the close contact is Et, Me, or SiMe3. All of these latter substituents, which are sterically smaller than a t-Bu group, enable the amide group to pivot in such a way as to move the tert-butyl group farther from the metal center. The results suggest that the short Ti···C and Ti···H distances seen crystallographically for 1 are actually the result of intraligand and interligand steric repulsions involving the amide substituent not involved in the close contact. The lack of an agostic interaction despite the close contact (and the low electron count of the Ti center) is ascribed to the strong σ- and π-donor properties of the amide and chloride ligands, which raise the energies of the empty orbitals on Ti.

Studies of the solvatochromic emission properties of N-aroylurea derivatives I: Influence of the substitution pattern

The influence of the substituent of the N-aroylurea functionality on the solvatochromic properties of this class of compounds was investigated with eight examples. The absorption spectra of these compounds exhibit the characteristic spectroscopic properties of the corresponding arene fragment and are only slightly dependent on the solvent. In contrast, all investigated aroylurea derivatives exhibit a strong solvatochromism with a good linear correlation between the emission energy and the acceptor numbers (AN) of the solvents; that is, the emission maximum shifts bathochromically (Δλ = 50-93 nm) with increasing AN. Furthermore, in media with increasing viscosity, as established in glycerol or ethanol solutions with decreasing temperature, the emission maxima are significantly shifted to shorter wavelengths and the full width at half maximum (FWHM) changes. All experimental data point to two emitting states, namely the locally excited (LE) state and the charge-transfer (CT) state. Thus, after initial photoexcitation to the LE state an internal charge transfer (ICT) takes place due to the donor-acceptor interplay between the arene unit and the N-acylureido functionality, mainly assisted by the intramolecular hydrogen bond between the terminal NH group and the aryl-substituted carbonyl functionality, hence interconverting the latter to a stronger acceptor. In the polarized CT state the acylurea unit develops a negative charge, which, after solvent relaxation, is stabilized by solvents with high acceptor number. Time-resolved emission spectroscopy revealed additional conformational changes in the excited state. Two emissive species were identified at room temperature, whose lifetimes depend strongly on the chemical environment. In addition, time-resolved emission spectra (TRES) showed red-shifted emission bands at longer delays after the excitation pulse in polar solvents. These findings are rationalized by the presence of two different emitting rotational conformers.

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation–conformation–translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program,RSR, was created, and the programsNUT,HELandDHLwere upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.

Dual Emission from Rhenium(I) Complexes Induced by an Interligand Aromatic Interaction

A series of rhenium(I) diimine complexes cis,trans-[Re(dmb)(CO)(2)(PR(1)R(2)R(3))(PR(4)R(5)R(6))](+) (dmb=4,4'-dimethyl-2,2'-bipyridine, R(n)=phenyl or alkyl), each of which bears two phosphine ligands with various numbers of phenyl groups, has been synthesized by using the photochemical ligand-substitution reaction. Detailed studies of the structural features, not only in the crystal but also in solution, indicate that the number of phenyl groups is a crucial factor in controlling the rotational conformation of the phosphine ligands, which in turn determines the extent of the π-π interaction between the aromatic diimine ligand and the phenyl group(s). The π-π interaction strongly affected both electrochemical and photophysical properties: 1) the oxidation power of the Re complex became stronger, 2) the lifetime of the excited state became longer, and 3) the Stokes shift between the (1) MLCT absorption band and emission from the corresponding (3) MLCT excited state became smaller. In particular, the diphenyl and triphenyl phosphine had much greater influence on the properties than the monophenyl phosphine ligand. Dual emission was observed from the different rotational conformers of the complexes with an intermediate number of phenyl groups in the phosphine ligands.

Hydrogen abstraction from n-butanol by the methyl radical: high level ab initio study of abstraction pathways and the importance of low energy rotational conformers

Hydrogen abstraction reactions by the methyl radical from n-butanol have been investigated at the ROCBS-QB3 level of theory. Reaction energies and product geometries for the most stable conformer of n-butanol (ROH) have been computed, the reaction energies order α < γ < β < δ < OH. The preference for n-butane to favour H-abstraction at C(β) and C(γ) while, in contrast, n-butanol favours radical reactions at the C(α) carbon is rationalised. Transition state (TS) barriers and geometries for the most stable conformer of n-butanol are presented, and discussed with respect to the Hammond postulate. The reaction barriers order as α < OH < γ < β < δ. This relative ordering is not consistent with product radical stability, C-H bond dissociation energies or previous studies using O[combining dot above]H and HO[combining dot above](2) radicals. We provide a molecular orbital based rationalisation for this ordering and answer two related questions: Why is the γ-channel more stable than the β-channel? Why do the two C(γ)-H H-abstraction TS differ in energy? The method and basis set dependence of the TS barriers is investigated. The Boltzmann probability distribution for the n-butanol conformers suggests that low energy conformers are present in approximately equal proportions to the most stable conformer at combustion temperatures where ĊH(3) radicals are present. Thus, the relative significance of the various H-abstraction channels has been assessed for a selection of higher energy conformers (ROH'). Key results include finding that higher energy n-butanol conformers (E(ROH') > E(ROH)) can generate lower energy product radicals, E(ROH') < E(ROH). Moreover, higher energy conformers can also have a globally competitive TS energy for H-abstraction.

Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome

The class II release factor RF3 is a GTPase related to elongation factor EF-G, which catalyzes release of class I release factors RF1 and RF2 from the ribosome after termination of protein synthesis. The 3.3 Å crystal structure of the RF3·GDPNP·ribosome complex provides a high-resolution description of interactions and structural rearrangements that occur when binding of this translational GTPase induces large-scale rotational movements in the ribosome. RF3 induces a 7° rotation of the body and 14° rotation of the head of the 30S ribosomal subunit, and itself undergoes inter- and intradomain conformational rearrangements. We suggest that ordering of critical elements of switch loop I and the P loop, which help to form the GTPase catalytic site, are caused by interactions between the G domain of RF3 and the sarcin-ricin loop of 23S rRNA. The rotational movements in the ribosome induced by RF3, and its distinctly different binding orientation to the sarcin-ricin loop of 23S rRNA, raise interesting implications for the mechanism of action of EF-G in translocation.

Effects of the Heat Treatment on the Mechanical Properties of a Novel Thermotropic Liquid-Crystalline Polymer Fiber

Thermotropic liquid-crystalline polymers (TLCPs) have aroused wide public concern which is attributed to their high strength, stiffness, chemical resistance and perfect dimensional stability as high-performance engineering materials. Vectran heat treated after melt spinning is a representative commercial aromatic copolyester fiber. In this study, a novel TLCP melt-polymerized with 4,4’-diphenyloxide dicarboxylic acid (DODA), 4-acetoxybenzoic acid (ABA), hydroquinone diactate (HQA), 2,6-naphthalene dicarboxylic (NDA) and terephthalic acid (TA) were melt spun into fibers and heat treated to enhance the breaking strength and Young’s modulus. Intermolecular mechanical elements slipped between 120-130 °C and crystallization or the conformational rotations occurred along the extended polymer chain. For this new TLCP fiber, the optimal heat treatment temperature was 260 °C and the suitable heat-treatment time was over 48 hours. The breaking strength, Young’s modulus and breaking elongation of the as-spun fiber were improved from 1.58GPa, 45.21GPa and 1.97% to 3.20GPa, 133.44GPa and 2.42% respectively after heat treatment.

Time resolved spectroscopy of 2-(dimethylamine)fluorene. Solvent effects and photophysical behavior

The effect of different solvents on the fluorescent properties of 2-(dimethylamine)fluorene (DAF) were studied. In aprotic solvents we detected a strongly emissive intramolecular charge transfer (ICT) state that decayed by intersystem crossing to triplet. In proton-accepting solvents DAF exhibits in the excited state an intramolecular proton transfer. An ionized species is postulated, which simultaneously twists to a rotated conformation in the excited state. Thus, the specific solvent interactions supplement but do not replace the twist mechanism and accompany the charge transfer accepted as the prerequisite for twisted intramolecular charged transfer (TICT) state formation.