Showing papers on "Dihedral angle published in 2017"

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

Abstract: The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG-CC-PVTZ basis set). Umbrella sampling was used to determine conformational free energies along the dihedral angles, and these better agree with the population of conformations observed in the protein data bank for the new parameters than for the conventional parameters. Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramers CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters. For the tetramers, the new parameters largely avoid the incorrec...

Spiro Metalla-aromatics of Pd, Pt, and Rh: Synthesis and Characterization

Abstract: Since the concept of aromaticity represents one of the most fundamental principles in chemistry, the search for unprecedented and exciting aromatic systems, therefore, continues to drive research in this area. Herein we report the synthesis and characterization of spiro metalla-aromatics, in which the transition metal (Pd, Pt, or Rh) is the spiro atom, that cross-conjugates two aromatic five-membered metallacycles. These spiro metalla-aromatics tend to take square planar geometries, with the dihedral angle being influenced by the steric repulsion between the α-positioned substituents. Rationalized and classified via both experimental measurements (X-ray structural analysis, NMR spectroscopy, XPS, etc.) and theoretical analysis (DFT calculation, ISE, AICD, NICS, and CMOs), all these fundamental observations extend the concept of aromaticity and organometallic chemistry.

Molecular Engineering of Triphenylamine Based Aggregation Enhanced Emissive Fluorophore: Structure-Dependent Mechanochromism and Self-Reversible Fluorescence Switching

Abstract: Triphenylamine (TPA), a propeller-shaped optoelectronic molecule, has been used to generate stimuli-responsive smart fluorescent organic materials and correlate the effect of subtle structural changes on the molecular packing and mechanochromic fluorescence (MCF). The substituent (OCH3) position in the TPA phenyl ring and acceptors (malononitrile, cyanoacetamide, cyanoacetic acid, ethyl cyanoacetate, and diethylmalonate) strongly influenced the solid state and mechanochromic fluorescence as well as the molecular packing. The structure–property studies revealed that (i) TPA derivatives without the OCH3 substituent exhibit strong fluorescence (Φf = 85% (TCAAD-1, 55% (TDEM)), (ii) higher dihedral angle (τ) between donor (aminophenyl) and acceptor lead to weak/non fluorescent material, (iii) substituent at the ortho position to acceptor increased the dihedral angle (τ = 26.49 (TCAAD-2), τ = 27.14 (TDMM)), and (iv) the increase of alkyl groups produced self-reversible high contrast off-on fluorescence switchin...

PET-based bisBODIPY photosensitizers for highly efficient excited triplet state and singlet oxygen generation: tuning photosensitizing ability by dihedral angles

Abstract: Herein, four covalent BODIPY heterodimers that differ by dihedral angles were shown to be highly efficient excited triplet state (T1) photosensitizers (PSs) for singlet oxygen formation with a quantum yield (ΦΔ) of up to 0.94 as compared to their respective monomers, which had only negligible ΦΔ of ca. 0.060. More interestingly, these PSs generate T1via charge recombination mechanism rather than traditional inter-system crossing. The photosensitizing ability of dimers is easily tuned by either the dihedral angle (between the two linked BODIPYs) or solvent polarity. Laser flash photolysis, time-resolved and steady state fluorescence, quantum chemical calculation, as well as thermodynamic analysis were employed to study the associated photophysical process to reveal the T1 formation mechanism: photo-induced electron transfer (PET) followed by charge recombination. Due to its heavy-atom-free nature, polarity selectivity, high efficiency, and easy tunability, this PET-based PS and its mechanism are very useful in developing new PS for photodynamic therapy of tumors, photobiology, and organic photochemistry.

Accuracy of trajectory surface-hopping methods: Test for a two-dimensional model of the photodissociation of phenol.

Abstract: Trajectory surface hopping (TSH) methods have been widely used for the study of nonadiabatic molecular dynamics. In the present work, the accuracy of two TSH algorithms, Tully’s fewest switching algorithm and an algorithm based on the Landau-Zener formula, has been critically evaluated in comparison with exact nonadiabatic quantum dynamics calculations for a model of the photoinduced hydrogen-atom dissociation reaction in phenol. The model consists of three electronic states (S0, 1ππ*, 1πσ*) and two nuclear degrees of freedom (the OH stretching coordinate and CCOH dihedral angle) and displays two successive conical intersections (1ππ*/1πσ* and 1πσ*/S0). Considering instantaneous photoexcitation from different vibrational levels of the S0 state to the 1ππ* state, we examined the time-dependent electronic population dynamics as well as the branching ratio of the two dissociation channels. The results of fully converged trajectory calculations are compared with the results of exact quantum wave-packet calcul...

Symmetry Breaking in Pyrrolo[3,2-b]pyrroles: Synthesis, Solvatofluorochromism and Two-photon Absorption.

Abstract: Five centrosymmetric and one dipolar pyrrolo[3,2-b]pyrroles, possessing either two or one strongly electron-withdrawing nitro group have been synthesized in a straightforward manner from simple building blocks. For the symmetric compounds, the nitroaryl groups induced spontaneous breaking of inversion symmetry in the excited state, thereby leading to large solvatofluorochromism. To study the origin of this effect, the series employed peripheral structural motifs that control the degree of conjugation via altering of dihedral angle between the 4-nitrophenyl moiety and the electron-rich core. We observed that for compounds with a larger dihedral angle, the fluorescence quantum yield decreased quickly when exposed to even moderately polar solvents. Reducing the dihedral angle (i.e., placing the nitrobenzene moiety in the same plane as the rest of the molecule) moderated the dependence on solvent polarity so that the dye exhibited significant emission, even in THF. To investigate at what stage the symmetry breaking occurs, we measured two-photon absorption (2PA) spectra and 2PA cross-sections (σ2PA) for all six compounds. The 2PA transition profile of the dipolar pyrrolo[3,2-b]pyrrole, followed the corresponding one-photon absorption (1PA) spectrum, which provided an estimate of the change of the permanent electric dipole upon transition, ≈18 D. The nominally symmetric compounds displayed an allowed 2PA transition in the wavelength range of 700–900 nm. The expansion via a triple bond resulted in the largest peak value, σ2PA=770 GM, whereas altering the dihedral angle had no effect other than reducing the peak value two- or even three-fold. In the S0→S1 transition region, the symmetric structures also showed a partial overlap between 2PA and 1PA transitions in the long-wavelength wing of the band, from which a tentative, relatively small dipole moment change, 2–7 D, was deduced, thus suggesting that some small symmetry breaking may be possible in the ground state, even before major symmetry breaking occurs in the excited state.

Stability of a liquid bridge between nonparallel hydrophilic surfaces

Abstract: Formation of liquid bridges between two solid surfaces is frequently observed in industry and nature, e.g. in printing applications. When the two solid surfaces are not parallel (with a dihedral angle ψ between them), an interesting phenomenon emerges: if ψ exceeds a critical angle (denoted as ψc) the bridge is no longer stable, and propels itself toward the cusp of the surfaces. In this work we performed, for the first time, a systematic study on the parameters influencing ψc by combining experimental, theoretical, and numerical investigations. It was shown that ψc is determined by the advancing contact angle (θa) and Contact Angle Hysteresis (CAH) of the surfaces: it increases as θa or CAH increases, and these two parameters have a nonlinear and interdependent influence on ψc. Based on our quantitative results, an empirical equation is presented to predict the critical angle, ψc=f(θa,CAH) in closed analytical form. This equation can be used to calculate ψc for bridges formed by moving down a pre-tilted surface towards a sessile drop on a stationary lower surface, or bridges between initially parallel surfaces which the top surface tilts after bridge formation.

A two-dimensional molecule with a large conjugation degree: synthesis, two-photon absorption and charge transport ability

Abstract: A new molecule, 5,5′-bis(4,6-bis((E)-4-(octyloxy)styryl)pyrimidin-2-yl)-2,2′-bithiophene (OSPB), was designed and synthesized. It contains two D–π–A–π–D (donor–π–acceptor–π–donor) segments with an alkoxy group D and a pyrimidine moiety A, and these two segments are connected through a bithiophene moiety to shape a two-dimensional (2D) multibranched conjugated system. The molecule showed high thermal stability. It demonstrated good solubility in THF with an emission maximum at 470 nm, and excimer emission appeared in poor solvents such as aqueous media showing an obvious red-shift. A two-photon excited fluorescence (TPEF) test revealed that the maximal two-photon absorption (2PA) cross-section of the molecule was 1352 GM, which is comparable with the reported bipyrimidine-based multibranched compounds with a stronger donor. Theoretical calculation suggested that the molecule showed good coplanarity made up by two conjugated segments with a small dihedral angle. The charge transport ability of OSPB was preliminarily studied using an organic thin-film transistor (OTFT) device via a low-cost solution processing technique, and the results demonstrated that it was a p-type semiconductor.

The Influence of Methoxy and Ethoxy Groups on Supramolecular Arrangement of Two Methoxy-chalcones

Abstract: The structures of two methoxylated chalcones, namely (E)-1-(4-methoxyphenyl)-3-(3,4,5-trimethoxyphenyl)prop-2-en-1-one and (E)-3-(4-ethoxyphenyl)-1-(4-methoxyphenyl)prop-2-en-1-one, reveal the effect of the inclusion of the methoxyl and ethoxyl substituents of the conformation on methoxy-chalcone. Structural comparative study between two chalcones was done in this work and some effects on geometric parameters, such as planarity and dihedral angles, were described. In addition, intermolecular interactions responsible for crystalline packaging were investigated by Hirshfeld surfaces and the values of those interactions were analysed by comparing experimental and theoretical models. The molecular stability was expressed in terms of softness and hardness, both obtained from frontier molecular orbitals. Finally, there is a good agreement between calculated and experimental infrared spectrum, which allowed the assignment of the normal vibrational modes.

Conformational isomerism in cyclic peptoids and its specification.

Abstract: Most of the structural studies made on the secondary structure of peptoids describe their geometric attributes in terms of the classic Ramachandran plot (based on the local analysis of ω, ψ, χ, φ dihedral angles). However, little intuitive understanding is available from internal coordinates when stereochemistry is involved. In this contribution we list all the conformationally stable cyclic peptoids reported up to the year 2017 and propose a simple method to define their geometric arrangement in terms of planar chirality. Evidence of conformational isomerism (due to the long average time of single bond rotation) and conformational chirality (induced by the absence of roto-reflection axes) in this promising class of synthetic macrocycles is provided by NMR spectroscopy (using Pirkle's alcohol as chiral solvating agent) and careful evaluation of X-ray crystallographic studies. The full understanding of the oligomeric macrocycles' structural properties and the clear framing of their conformational isomerism in a proper conceptual scheme is fundamental for future application of peptoids in asymmetric synthesis, chiral recognition and supramolecular chemistry.

Dispersion and Halogen-Bonding Interactions: Binding of the Axial Conformers of Monohalo- and (±)-trans-1,2-Dihalocyclohexanes in Enantiopure Alleno-Acetylenic Cages

Abstract: Enantiopure alleno-acetylenic cage (AAC) receptors with a resorcin[4]arene scaffold, from which four homochiral alleno-acetylenes converge to shape a cavity closed by a four-fold OH-hydrogen-bonding array, form a highly ordered porous network in the solid state. They enable the complexation and co-crystallization of otherwise non-crystalline small molecules. This paper analyzes the axial conformers of monohalo- and (±)-trans-1,2-dihalocyclohexanes, bound in the interior cavity of the AACs, on the atomic level in the solid state and in solution, accompanied by accurate calculations. The dihedral angles ϑa,a (X–C(1)–C(2)–X/H) of the axial/diaxial conformers deviate substantially from 180°, down to 144°, accompanied by strong flattening of the ring dihedral angles. Structure optimization of the isolated guest molecules demonstrates that the non-covalent interactions with the host hardly affect the dihedral angles, validating that the host is an ideal means to study the elusive axial/diaxial conformers. X-ray...

Conformation of Ethylene Glycol in the Liquid State: Intra- versus Intermolecular Interactions

Abstract: Ethylene glycol is a typical rotor molecule with the three dihedral angles that allow for a number of possible conformers. The geometry of the molecule in the liquid state brings into sharp focus the competition between intra- and inter-molecular interactions in deciding conformation. Here, we report a conformational analysis of ethylene glycol in the liquid state from ab initio molecular dynamics simulations. Our results highlight the importance of intermolecular hydrogen bonding over intramolecular interactions in the liquid, with the central OCCO linkage adopting both gauche and trans geometries in contrast to the gas phase, wherein only the gauche has been reported. The influence of intermolecular interactions on the conformation of the terminal CCOH moieties is even more striking, with certain regions of conformational space, wherein the ethylene glycol molecule cannot participate with its full complement of intermolecular hydrogen bonds, excluded. The results are in agreement with Raman and NMR spec...

Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins

Abstract: In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles Many of these conformations are excluded due to steric overlaps Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues Since the Ramachandran map essentially focuses on local interactions (residues closer in sequence), out of interest, we have analyzed the dihedral angle preferences of residues that make non-local interactions (residues far away in sequence and closer in space) in the folded structures of proteins The non-local interactions have been grouped into different types such as hydrogen bond, van der Waals interactions between hydrophobic groups, ion pairs (salt bridges), and ππ-stacking interactions The results show the propensity of amino acid residues in proteins forming local and non-local interactions Our results point to the vital role of different types of non-local interactions and their effect on dihedral angles in forming secondary and tertiary structural elements to adopt their native fold

The effect of a highly twisted CC double bond on the electronic structures of 9,9′-bifluorenylidene derivatives in the ground and excited states

Abstract: We synthesized methyl-substituted 9,9′-bifluorenylidene (9,9′-BF) derivatives in which two planar fluorene units are connected through a CC double bond. The CC double bond is twisted owing to the steric crowding between the fluorene units, and by introducing substituents at 1,1′-positions (inner space of 9,9′-BF) it becomes more twisted. Indeed, single crystal X-ray structural analysis and theoretical calculation reveal that the dihedral angle between two fluorene π-planes of a 1,1′-dimethyl-substituted 9,9′-BF is 56°, which is clearly larger than those of pristine 9,9′-BF (42°) and 1-methyl-substituted 9,9′-BF (50°). The twisted conformation of 1,1′-dimethyl-substituted 9,9′-BF facilitates the cis–trans isomerization process which we assessed quantitatively by variable-temperature NMR measurements. The 9,9′-BF derivatives with different numbers of methyl groups also exhibit remarkable changes in optoelectronic properties, primarily because of the change in the twisting angle of the central CC double bond. Theoretical calculation further indicates that the electronic structures of methyl-substituted 9,9′-BF derivatives in the excited states are considerably different from those of pristine 9,9′-BF.

Pressure Tuning Dual Fluorescence of 4-(N,N-Dimethylamino)benzonitrile

Abstract: The intramolecular charge-transfer (ICT) emission band in the dual fluorescence of the 4-(N,N-dimethylamino)benzonitrile (DMABN) molecular crystal exhibits increase in response to compression up to 10 GPa. On the basis of Raman and angle-dispersive X-ray diffraction (ADXRD) experiments combining with computational studies, the mechanism of this phenomenon could be assigned to the change of the intramolecular geometrical conformation, especially for the decrease of the dihedral angle between the dimethylamino (NMe2) and phenyl moieties. Meanwhile the reduction of excited-state energies and the HOMO–LUMO band gap leads to the redshifts of photoluminescence (PL) spectra and the absorption edge, respectively. Competing with the aggregation caused quenching (ACQ) effect, the planarity of molecular conformation and the slight rotation of the NMe2 group under high pressure both could enhance the ICT process, which will contribute to the revelation of the ICT mechanism and designs of new piezochromic luminescent ...

Manipulation of Chain Conformation for Optimum Charge-Transport Pathways in Conjugated Polymers

Abstract: A pair of different diketopyrrolopyrrole-based conjugated polymers (CPs) were designed and synthesized to investigate the effect of chain conformation on their molecular assembly. Conformation management was achieved by the incorporation of different linkers during polymerization. Through the use of computational calculations and UV-vis absorption measurements, the resulting CPs (PDPP-T and PDPP-BT) were found to exhibit partly modulated chain geometry. Grazing incident X-ray diffraction experiments with a two-dimensional detector revealed that PDPP-T having a planar chain conformation exhibited an edge-on type molecular arrangement, which evolved to a face-on type chain assembly when the planar geometry was altered to a slightly twisted one as in PDPP-BT. In addition, it was verified that the directional electric carrier mobility of CPs was critically distinguished by the distinctive chain arrangement in spite of their similar chemical structure. Concentration-dependent absorption measurements could provide an improved understanding of the assembly mechanism of CP chains: the planar conformation of PDPP-T facilitates the formation of preassembled chains in a concentrated solution and further directs the edge-on stacking, while the twisted dihedral angle along the benzothiophene in PDPP-BT prevents chain assembly, resulting in the face-on stacking. Because CP chain conformation is inevitably connected with the generation of preassembled chains, manipulating CP geometry could be an efficient tool for extracting an optimum chain assembly that is connected with the principal charge-transport pathway in CPs.

Tuning the structural and electronic properties of novel thiophene-pyrrole based 1,2,3,4-tetrazine

Abstract: Here, we have studied the structural and optoelectronic behaviour of a series of conjugated heterocyclic polymers. The basic monomer unit of the conjugated polymers contains a backbone of novel thiophene and pyrrole based 1,2,3,4-tetrazine. The other oligomers are designed by substituting the basic monomer unit with different electron-donating and electron-withdrawing groups at the nitrogen and the 3rd C-atom of the pyrrole and the thiophene ring respectively. We have calculated dihedral angles, HOMO-LUMO gaps, excitation energies and oscillator strengths by employing TD-DFT method. Our study reveals that compounds having bulky substituents exhibit larger dihedral angles. This in turn renders an increase in the band gaps (Δ H − L ). Presence of the electron-withdrawing substituents also increases the Δ H − L values of the oligomers. However, the electron-donating groups decrease the Δ H − L values of the oligomers. Therefore, small electron-donating substituents have an overwhelming effect on the optoelectronic properties of the conjugated polymers which in turn makes them interesting materials with good conduction properties for fabrication of optoelectronic devices such as OLEDs, OFETs and solar cells.

A crystalline molecular gyrotop with a biphenylene dirotor and its temperature-dependent birefringence

Abstract: Biphenyl contains a direct bond between two phenyl functional groups, and the dihedral angle between the two phenyl groups has been discussed in terms of electronic and steric stabilization. Facile rotation about the C–C bond between the two phenyl components is expected to occur at high temperatures. Here, we report observations of the rotational dynamics of a biphenylene dirotor in a crystalline state in a novel molecular gyrotop. The structure and rotational dynamics of the rotor exhibit remarkable temperature dependence. In accordance with the amplification of the angular displacement of biphenylene inside a crystal with increasing temperature, the birefringence of the single crystal decreased.

On the significant relativistic heavy atom effect on 13C NMR chemical shifts of β- and γ-carbons in seleno- and telluroketones

Abstract: Unexpectedly large ‘Heavy Atom on Light Atom’ (HALA) effects have been found in 13C NMR (Nuclear Magnetic Resonance) chemical shifts of β- and γ-carbons of seleno- and telluroketones established by means of the high-accuracy calculations of 13C NMR chemical shifts in three representative real-life compounds, 2,2,5,5-tetramethyl-3-cyclopentene-1-selone, selenofenchone and 1,1,3,3-tetramethyl-1,3-dihydro-2H-indene-2-tellurone. The proposed computational scheme consists of the combination of accurately correlated coupled-cluster singles and doubles model approach for the non-relativistic calculations of shielding constants taking into account the solvent, vibrational and relativistic corrections, the latter obtained within the 4-component fully relativistic gauge-including atomic orbitals KT2 approach resulting in a very good agreement of the performed calculations with the experiment. The stereochemical dependence of the ‘long-range’ γ-HALA effect on the dihedral angle has been established in the mo...

Systematic investigation of the excited-state properties of anthracene-dicarboxylic acids

Abstract: We report the photophysical properties of three anthracene-dicarboxylic acids – 1,4-anthracene dicarboxylic acid (1,4-ADCA), 2,6-anthracene dicarboxylic acid (2,6-ADCA) and 9,10-anthracene dicarboxylic acid (9,10-ADCA) – in a series of polar aprotic solvents using steady-state absorption spectroscopy, steady-state emission spectroscopy and time-correlated single photon counting emission lifetime spectroscopy. The addition of carboxylic acid functional groups on the anthracene ring perturbs the electronic transitions oriented along the longitudinal and transverse axes to varying degrees, resulting in differences in the photophysical properties. The three anthracene derivatives exhibit very different excited-state properties in basic solution compared to acidic and neutral solutions. Density functional theory (DFT) calculations reveal that the lowest-energy ground-state structures of both 2,6-ADCA and 1,4-ADCA have dihedral angles between the carboxylic acids and aromatic planes of θ = 0°. For 9,10-ADCA, the same dihedral angle increases to θ = 56.6°. Time-dependent DFT calculations suggest that the carboxyl groups of 1,4-ADCA and 2,6-ADCA remain coplanar with the anthracene ring system in the excited state. In contrast, the calculations reveal significant changes between the ground and excited geometries for 9,10-ADCA as the dihedrals decrease from 56.6° to 27.7° in the first excited state, and puckering of the anthracene moiety of 9,10-ADCA is observed.