Molecular engineering enabling reversible transformation between helical and planar conformations by cyclization of alkynes

Molecular engineering enabling reversible transformation between helical and planar conformations is described herein. Starting from easily available 2-(pyridin-2-yl)anilines and alkynes, a one-pot strategy is set up for the synthesis of aza[4]helicenes via two successive rhodium-catalyzed C–H activation/cyclizations. Helical pyrrolophenanthridiziniums can be transformed into planar conformations through the cleavage of acidic pyrrole N–H, leading to turn-off fluorescence. NMR spectra, single crystal X-ray diffraction and DFT calculations demonstrate that the formation of an intramolecular C–H⋯N hydrogen bond is beneficial to stabilize the pyrrole nitrogen anion of the planar molecule and provide increased planarity. The reversible conformation transformations can be finely adjusted by the electron-donating and -withdrawing groups on the π⁺-fused pyrrole skeleton in the physiological pH range, thus affording an opportunity for pH-controlled intracellular selective fluorescence imaging. Pyrrolophenanthridiziniums show turn-on fluorescence in lysosomes owing to the acidic environment of lysosomes and turn-off fluorescence out of lysosomes, indicating the occurrence of the deprotonation reaction outside lysosomes and the corresponding transformation from helical to planar conformations.

One-pot synthesis of aza[4]helicenes is accomplished through two successive C–H activation/cyclizations, which exhibit on/off fluorescence switching through reversible transformation between helical and planar conformations.     

Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.     

Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

线型和星型平面噻吩类低聚物衍生物分子结构及光电性质研究

运用密度泛函DFT B3LYP／6-31G(d)方法对线型(a)和星型(b)平面噻吩类低聚物衍生物分别进行了几何构型优化,并采用含时密度泛函TD-DFT B3LYP／6-31G(d)方法计算了其紫外吸收光谱．计算结果表明:用TD-DFT．方法计算体系的紫外吸收光谱值与实验数据吻合;通过对噻吩类低聚物衍生物分子几何结构和前线分子轨道能级的分析,并从理论上解释了线型(a)和星型(b)衍生物光谱性质的差异:后者与前者相比较吸收光谱发生红移,这是由于星型结构使其相应HOMO能级升高,电离能(IP)降低,成为很好的电子给体和空穴传输材料．     

Molecular structure of eight-membered cyclic sulfites with two planar fragments

Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2033–2036, September, 1988.     

Molecular structure of hydrazoic acid with hydrogen-bonded tetramers in nearly planar layers

Hydrazoic acid (HN(3))--potentially explosive, highly toxic, and very hygroscopic--is the simplest covalent azide and contains 97.7 wt % nitrogen. Although its molecular structure was established decades ago, its crystal structure has now been solved by X-ray diffraction for the first time. Molecules of HN(3) are connected to each other by hydrogen bonds in nearly planar layers parallel to (001) with stacking sequence A, B, ... The layer distance, at 2.950(1) ?, is shorter than that in 2H-graphite [3.355(2) ?]. The hydrogen bonds N-H···N are of great interest, since the azido group consists of three homonuclear atoms with identical electronegativity, but different formal charges. These hydrogen bonds are bifurcated into moderate ones with ≈2.0 ? and into weak ones with ≈2.6 ?. The moderate ones build up tetramers (HN(3))(4) in a nearly planar net of eight-membered rings. To the best of our knowledge, such a network of tetramers of a simple molecule is unique.     

Molecular conformations and relative stabilities can be as demanding of the electronic structure method as intermolecular calculations

We have performed a variety of high-level electronic structure calculations on two moderately sized organic molecules and found considerable sensitivity of the intramolecular potential energy surface to the method employed. The gas-phase structure of tyrosine-glycine varies qualitatively between B3LYP and MP2 optimizations, producing different close contacts between the tyrosine ring and the glycine moiety. The relative energies of the 2-(acetylamino)benzamide conformations found in its two polymorphs can vary by over 20 kJ mol-1 between MP2 and B3LYP calculations, using the same basis set. It is shown by a novel analysis that the intramolecular equivalent of basis set superposition error competes with the errors in the intramolecular dispersion in causing this sensitivity.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

Low temperature crystal and molecular structure of nitrobenzene

The crystal and molecular structure of nitrobenzene was determined at 103 K by X-ray diffraction, yieldingR=0.034 and a highly precise geometry of the molecule (esds of bond lengths 0.001 Å and bond angles 0.1°). The bond angles in the ring agree very well with additive scheme based on angular substituent parameters. X-X electron density maps support the view that the C-N bond does not exhibit-character, and, hence, the nitro group interacts with the ring mostly by inductive effects.     

Molecular conformations at the cellulose–water interface

¹³C-NMR chemical shifts were measured for C-4 and C-6 in a collection of eight crystalline glucoses and glucosides. The influence of the hydroxymethyl conformation was greater at C-4 than at C-6, with mean chemical shifts for gauche–trans molecules displaced 3.1 ppm (C-4) and 2.5 ppm (C-6) relative to gauche–gauche molecules. This information was used to interpret ¹³C-NMR spectra of crystalline celluloses. Chemical shifts for C-4 in the crystallite cores of celluloses I and II differed by just 0.2 ppm, but the corresponding chemical shifts for well-ordered crystallite surfaces differed by 3.0 ppm. The separation between crystallite-surface signals was attributed to different hydroxymethyl conformations at the cellulose–water interface, i.e., gauche–gauche and gauche–trans on crystallites of cellulose I and cellulose II, respectively. A broad C-4 signal in the spectrum of cellulose II indicated gauche–gauche conformations in disordered cellulose. Chemical shifts for C-6 were consistent with these conformations.     

Molecular structures and conformations: Experiment and theory

Theoretical calculations in combination with experimental gas phase structure research can be performed in two ways. The first is to support and improve experimental analyses by including additional data from theoretical calculations. This is to the advantage of the experiment. The second way is a comparison of geometric structures and conformational properties obtained with different theoretical methods with the experimental result. This comparison indicates which theoretical method or methods are suitable for a specific compound. This approach is to the advantage of the theory. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 123–128, 1998     

Molecular conformations of aminophenylimidazoles exhibiting antiulcer activities

To experimentally clarify a possible stereostructure-activity relationship proposed for H2-receptor antagonists, three 5-aminophenylimidazoles (1, 2 and 3), in which respective amino groups are located on the ortho, meta and para positions of the benzene ring, were synthesized and examined for their conformational characteristics using X-ray diffraction and proton nuclear magnetic resonance (1H-NMR) methods, and for antiulcer activities on rats and H2-receptor antagonist activities in guinea pig. The ortho isomer 1, which preferentially formed an intramolecular N-H (amino)...N (imidazole) hydrogen bond, showed the highest antiulcer activity with half the efficacy of cimetidine. On the other hand, none of 1, 2 and 3 showed significant H2-receptor antagonist activity. Based on these results, the conformational characteristic for the exhibition of antiulcer activity has been discussed.     

Indo study of the angular dependences of isotropic hyperfese interaction constants in the model conformations of the nitrobenzene radical anion

The UHF/INDO calculations of the model conformations of the nitrobenzene radical onion show that rotation of the nitro group relative to the plane of the benzene ring is accompanied by a pyramidal distortion of the group caused by the pseudo-Jahn-Teller effect (vibronic interaction between the ground n and totally symmetric lowest excited σ states). The angular dependences of the¹⁴N,¹³C,¹H, and¹⁷O Isotropic hyperfine interaction constants are analyzed. Experimental ESR data are interpreted for the radical anions of nitrobenzene derivatives with ortho-alkyl groups. Translated fromZhumal Strukturnoi Khimii, Vol. 41, No. 3, pp. 457-467, May-June, 2000.     

Molecular structure design of planar zwitterionic polymer electrode materials for all-organic symmetric batteries

All-organic symmetric lithium-ion batteries (LIBs) show promising prospects in sustainable energy storage systems, due to their environmental friendliness, structural diversity and low cost. Nevertheless, it remains a great challenge to explore suitable electrode materials and achieve excellent battery performance for all-organic symmetric LIBs. Herein, a squaraine-anthraquinone polymer (PSQ) electrode material was designed through rational molecular engineering. The well-designed extended π-conjugated system, donor–acceptor structure, abundant redox-active sites and rational manipulation of weak inter-/intramolecular interactions endow the PSQ electrode with outstanding electrochemical performance. The capacity of the PSQ cathode can be optimized to 311.5 mA h g⁻¹ by in situ carbon-template polymerization. Impressively, PSQ-based all-organic symmetric LIBs displayed high reversible capacity (170.8 mA h g⁻¹ at 50 mA g⁻¹), excellent rate performance (64.9% capacity retention at 4000 mA g⁻¹vs. 50 mA g⁻¹), ultralong cycle life up to 30 000 cycles at 2000 mA g⁻¹ and 97% capacity retention after 2500 cycles at 500 mA g⁻¹, which is one of the best comprehensive battery performances among the all-organic LIBs reported thus far.

A squaraine-linked polymer (PSQ) was applied in all-organic symmetric batteries. Attributed to its well-designed molecular strucuture, PSQ shows excellent electrochemical performance, which is one of the best results among the all-organic LIBs.     

Molecular conformations,hydrodynamics and optics of ladder polymers

Hydrodynamic (diffusion, sedimentation, viscosity), dynamo-optical and electro-optical properties of several ladder polysiloxanes with different substituents in the side groups have been investigated.In accordance with the theories of hydrodynamic properties of worm-like chains, the equilibrium rigidity of the main chain of these macromolecules was evaluated quantitatively. High equilibrium rigidity of ladder polysiloxanes is a direct consequence of the double-chain structure of their molecular chains.Values of reduced birefringence in electrical and mechanical fields in solutions of ladder polysiloxanes increase with molecular weight but tend to a limit, which is characteristic for semirigid macromolecules.Birefringence in an electrical field for solutions of all ladder polymers investigated is by two orders higher than the value of electro-optical effect in polymers with flexible chains and its sign (negative) coincides with that of flow birefringence. In a variable (sinusoidal) field in the region of high frequencies, strong frequency dependence of birefringence is characteristic for all samples. Unique electrooptical properties in constant and variable fields prove that, in contrast to polymers with flexible chains, highly organized orientational long-range order exists in ladder macromolecules, moreover, it is not only an axial order but also a polar one. The occurrence of long-range correlation in the orientation of polar groups and bonds of the molecular chain gives rise to high total moment of the macromolecule, which is responsible for its rotation in an electrical field. The direction of this dipole moment coincides with the long axis of the molecule since the Kerr effect is of the same sign as flow birefringence.     

Molecular dynamics study of 2-nitrophenyl octyl ether and nitrobenzene

The pure organic liquids nitrobenzene (NB) and 2-nitrophenyl octyl ether (NPOE) have been studied by means of molecular dynamics simulations. Both solvents are extremely important in various interfacial processes, mainly connected with ion transfer taking place across the interface with water. Thermodynamic (mass density, enthalpy of vaporization, isothermal compressibility, dipole moment) and dynamic (viscosities and self-diffusion coefficients) properties of both liquids have been calculated and are in very good agreement with the experimental data. In the case of NB, several potentials have been tested and the obtained results compared and discussed. In most cases, the OPLS all-atom potential gives results that are in better agreement with available experimental values. Atomic radial distribution functions, dihedral and angle distributions, as well as dipole-orientation correlation functions are used to probe the structure and interactions of the bulk molecules of both organic solvents. These were seen to be very similar in terms of structure and thermodynamics, but quite distinct in terms of dynamic behavior, with NPOE showing a much slower dynamic response than NB. A simulation study of the simple Cl- and K+ ions dissolved in both solvents has been also undertaken, revealing details about the diffusion and solvation mechanisms of these ions. It was found that in both liquids the positive potassium ion is solvated by the negative end of the molecular dipole, whereas the negative chloride ion is solvated by the positive end of the dipole.     

Molecular conformations of jet-cooled 2-methylindan and 2-phenylindan

The molecular conformations of jet-cooled 2-methylindan (2MI) and 2-phenylindan (2PI) have been studied using resonant-enhanced two-photon ionization spectroscopy in combination with ab initio calculations. Both axial (2MI_ax) and equatorial (2MI_eq) conformers of 2MI have been observed. A 2MI_eq/2MI_ax conformer ratio of 2.3 was estimated at 298 K, leading to the energy difference, \Updelta E = E _{2 \textMI\textax} - E _{2 \textMI\texteq} \Updelta E = E_{{ 2 {\text{MI}}_{\text{ax}} }} - E_{{ 2 {\text{MI}}_{\text{eq}} }} , of 0.49 kcal/mol. Ab initio calculations predicted three stable conformers of 2PI: two equatorial conformers (2PI_eq0 and 2PI_eq90), and one axial conformer (2PI_ax). Only the axial conformer of 2PI (2PI_ax) was experimentally observed. The indan ring of 2PI_ax is slightly more planar than the indan rings of the two equatorial conformers of 2PI because of the intramolecular C_sp2–H/π interactions in 2PI_ax. The equatorial conformers of 2PI relax to the more stable axial conformer because of the high pre-expansion temperature (383 K), and relatively low barrier (1.68 kcal/mol) to axial–equatorial interconversion. The barrier (2.33 kcal/mol) to axial–equatorial interconversion in 2MI is high enough to prevent conformational relaxation at the pre-expansion temperature of 298 K. Intramolecular C–H/π interactions are found to be more important in determining the conformational preference of 2PI than 2MI; this can be attributed to the higher acidity of the C_sp2–H bond than that of C_sp3–H bond.