Synthesis, Crystal Structure and Insecticidal Activity of the Optical Active Neonicotinoid Analogues

Eight novel neonicotinoid analogues 1‐(2‐tetrahydrofurfuryl)‐5‐substituted‐1,3,5‐hexahydrotriazine‐2‐N‐nitroimines 3a – 3h were synthesized, and their structures were characterized by ¹H NMR, IR and elemental analysis. The stereostructure of 3a was determined by the single‐crystal X‐ray analysis, which exhibits a half‐chair conformation and dihedral angle is 49.70°. The preliminary bioassay tests showed that all the title compounds exhibited good insecticide activities against Nilaparvata legen (N. legen).     

Solution Structure of Conomarphin, a Novel Conopeptide Containing D-Amino Acid at pH 5

Conomarphin, a novel conopeptide containing D-amino acid, was identified from the venom of Conus marmoreus and classified into M-superfamily of conotoxin. In this article, we reported the 3D structure of conomarphin at pH 5 determined using 2D ¹H NMR method in aqueous solution. Twenty converged structures of this peptide were obtained based on 205 distance constraints, 8 dihedral angle constraints, and 2 hydrogen bond constraints. The root mean square deviation (RMSD) values of the backbone atoms were (0.074±0.029) nm. The refined structure of conomarphin at pH 5 contains a short 3¹⁰-helix at C-terminal of the peptide. It was also characterized by a loose loop centered at Ala6. Comparison of structural and electrostatic potential between conomarphin at pH 3 and pH 5 were presented. Although the solution structure of conomarphin at pH 5 shared part of the same secondary structure element with the structure of conomarphin at pH 3, it adopted a distinctive backbone conformation with the overall molecule resembling a “flexual arm” when viewed from the front. Structural differences implied that this conopeptide was rather pH sensitive and its bioactivity in vivo might be related to the acidity.     

含有D型氨基酸的新型毒肽——芋螺马芬在pH 5的溶液结构

Conomarphin, a novel conopeptide containing D-amino acid, was identified from the venom of Conus marmoreus and classified into M-superfamily of conotoxin. In this article, we reported the 3D structure of conomarphin at pH 5 determined using 2D 1H NMR method in aqueous solution. Twenty converged structures of this peptide were obtained based on 205 distance constraints, 8 dihedral angle constraints, and 2 hydrogen bond constraints. The root mean square deviation (RMSD) values of the backbone atoms were (0.074依0.029) nm. The refined structure of conomarphin at pH 5 contained a short 310-helix at C-terminal of the peptide. It was also characterized by a loose loop centered at Ala6. Comparison of structural and electrostatic potential between conomarphin at pH 3 and pH 5 were presented. Although the solution structure of conomarphin at pH 5 shared part of the same secondary structure element with the structure of conomarphin at pH 3, it adopted a distinctive backbone conformation with the overall molecule resembling a“flexcual arm”when viewed fromthe front. Structural differences imply that this conopeptide is rather pH sensitive and its bioactivity in vivo might be related to the acidity.     

Highly efficient and stable blue‐light‐emitting binaphthol‐fluorene copolymers: A joint experimental and theoretical study of the main‐chain chirality

In a quest for the main‐chain chiral and highly stable blue‐light‐emitting π‐conjugated polymers, a novel series of soluble conjugated random and alternating copolymers (PF‐BN) derived from fluorene and axially chiral 1,1′‐binaphthol (BINOL) were successfully synthesized by Suzuki coupling polymerization. The polymer structures, optical properties, and their electrochemical properties were investigated by ¹H NMR, TGA/DSC, UV‐Vis absorption, photoluminescence, cyclic voltammetry, circular dichroism spectroscopy, and DFT calculations. The blue‐light‐emitting BINOL‐containing copolymers with proper content of BINOL show highly efficient photoluminescence and ultra highly stable light‐emission with almost unchanged fluorescent spectra after annealing at 200 °C in air for 10 h. The joint experimental and theoretical study of the main‐chain chirality reveals that (1) the chirality of BINOL can be transferred to the polymer backbone, (2) the effective conjugation length is about one BINOL and three fluorenes, (3) the main active chiral block in the copolymers is probably composed by one BINOL with the other two or three fluorenes, and (4) the dihedral angle in the PF‐BN copolymers should be larger than 105°. The incorporation of BINOL into the polyfluorene backbone is an effective way to produce highly efficient and stable blue‐light‐emitting main‐chain chiral conjugated polymer with interesting optoelectronic properties. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3868–3879, 2010     

An axial tert‐butyl group in strained cyclohexene: X‐ray analysis and theoretical calculations of 2‐(2‐tert‐butylcyclohex‐3‐enyl)propan‐2‐ol

The structure of the title compound, C₁₃H₂₄O, (I), shows a sofa conformation of the ring with two pseudo‐axial substituents. The dihedral angle between these substituents is 131.56 (12)°. Calculations using the B3LYP/6‐31G* level of theory show two minima, one corresponding to the crystal structure and the other to a boat conformation of the ring with two equatorial substituents. The energy of this latter conformation is 17.4 kcal mol⁻¹ higher than that of (I). The molecule forms an infinite co‐operative hydrogen‐bonded chain running in the b direction.     

Vibrational analysis of the benzophenone molecule and influence of its conformation on vibrational transitions

IR and Raman spectra of benzophenone and several of its isotopomers (d_5⁻, d_l0⁻, ¹³C- and ¹³Cd₅-benzophenone) are the experimental basis for the normal coordinate analysis. The possibility of determining the conformation of the benzophenone molecule in solution from its vibrational spectrum is considered carefully. The dihedral angle between the central part of the molecule and the phenyl ring has been determined by fitting the calculated to the observed spectra. The final force field for the molecule was obtained for the dihedral angle of 35°.     

3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints

In a wide variety of proteins, insolubility presents a challenge to structural biology, as X-ray crystallography and liquid-state NMR are unsuitable. Indeed, no general approach is available as of today for studying the three-dimensional structures of membrane proteins and protein fibrils. We here demonstrate, at the example of the microcrystalline model protein Crh, how high-resolution 3D structures can be derived from magic-angle spinning solid-state NMR distance restraints for fully labeled protein samples. First, we show that proton-mediated rare-spin correlation spectra, as well as carbon-13 spin diffusion experiments, provide enough short, medium, and long-range structural restraints to obtain high-resolution structures of this 2 x 10.4 kDa dimeric protein. Nevertheless, the large number of 13C/15N spins present in this protein, combined with solid-state NMR line widths of about 0.5-1 ppm, induces substantial ambiguities in resonance assignments, preventing 3D structure determination by using distance restraints uniquely assigned on the basis of their chemical shifts. In the second part, we thus demonstrate that an automated iterative assignment algorithm implemented in a dedicated solid-state NMR version of the program ARIA permits to resolve the majority of ambiguities and to calculate a de novo 3D structure from highly ambiguous solid-state NMR data, using a unique fully labeled protein sample. We present, using distance restraints obtained through the iterative assignment process, as well as dihedral angle restraints predicted from chemical shifts, the 3D structure of the fully labeled Crh dimer refined at a root-mean-square deviation of 1.33 A.     

Pyranosyl-RNA (‘p-RNA’): NMR and Molecular-Dynamics Study of the Duplex Formed by Self-pairing of Ribopyranosyl-(C-G-A-A-T-T-C-G)

The solution structure of the duplex formed by self-pairing of the p-RNA octamer β-D -ribopyranosyl-(2′→4′)-(CGAATTCG) was studied by NMR techniques and, independently, by molecular-dynamics calculations. The resonances of all non-exchanging protons, H-bearing C-atoms, P-atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling constants and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qualitative conformational analysis. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles β and ? in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better interstrand stacking and lessen unfavorable interactions in the backbone. The average base-pair axis forms an angle of ca. 40° with the backbone. The resulting interstrand π-π stacking between either two purines, or a purine and a pyrimidine, but not between two pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps molecular-dynamics (MD) calculation with the AMBER force field resulted in an average structure of the same conformation type as derived by NMR. For the backbone torsion angle ?, dynamically averaged coupling constants from the MD calculation agree well with the experimental values, but for the angle β, a systematic difference of ca. 25° remains. The two base pairs at the ends of the duplex are calculated to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR.     

Structure elucidation,complete NMR assignment and PM5 theoretical studies of new hydroxy‐aminoalkyl‐α,β‐unsaturated derivatives of the macrolide antibiotic josamycin

Four new hydroxy‐aminoalkyl derivatives of α,β‐unsaturated macrolide‐josamycin (2–5) have been synthesised and their structures have been studied by means of ¹H and ¹³C NMR and FT‐IR methods. Complete assignment of resonances in the ¹H and ¹³C NMR spectra has been made on the basis of ¹H? ¹³C HSQC, ¹H? ¹³C HMBC, ¹H? ¹H COSY, ¹H? ¹H NOESY 2D experiments. Spectroscopic data indicated that for the derivatives 3 and 4 some equilibrium between two different structures exists in contrast to derivatives 2 and 5. The lowest‐energy structures of the new derivatives of josamycin have been calculated and visualised by PM5 method at semi‐empirical level of theory, taking into account the NMR and FT‐IR data. The most significant differences between the structures of josamycin and its newly synthesised derivatives' were found in the conformation of the macrolide aglycone part and in the mutual orientation of the 4‐O‐isovalerylmycarosylmycaminose moiety relative to the aglycone part. PM5 semi‐empirical calculations indicated that the structures of the new macrolide derivatives are stabilised by rather weak intramolecular hydrogen bonds in agreement with spectroscopic data. Antimicrobial properties of the new derivatives 2–5 as well as those having an acetate group at C‐3 (6 and 7) were determined and compared to that of the parent macrolide antibiotic josamycin (1). Copyright © 2010 John Wiley & Sons, Ltd.     

N-methylated cyclic pentaalanine peptides as template structures

The N-methylation of cyclic peptides can be used to modify the activity and/or selectivity of biologically active peptides. As N-methylation introduces different flexibility and lipophilicity, it can also improve the bioavailability (the ADMET profile). To search for conformationally constrained cyclic peptides, a library of 30 different N-methylated peptides with the basic sequence cyclo(-D-Ala-L-Ala4-) was synthesized. Based on the NMR analysis, seven of these peptides exhibited single conformations (>98%). The structural features of these peptides were determined by a combination of NMR and distance geometry and then further refined by molecular dynamics simulations in an explicit DMSO solvent box. The structures provided from these efforts can now serve as templates for the rational design of cyclic pentapeptides with a distinct backbone conformation or for "spatial screening" to explore the bioactive conformation of medically important peptide systems.     

From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

An improved scheme to help in the prediction of protein structure is presented. This procedure generates improved starting conformations of a protein suitable for energy minimization. Trivariate gaussian distribution functions for the π, ψ, and χ¹ dihedral angles have been derived, using conformational data from high resolution protein structures selected from the Protein Data Bank (PDB). These trivariate probability functions generate initial values for the π, ψ, and χ¹ dihedral angles which reflect the experimental values found in the PDB. These starting structures speed the search of the conformational space by focusing the search mainly in the regions of native proteins. The efficiency of the new trivariate probability distributions is demonstrated by comparing the results for the α-class polypeptide fragment, the mutant Antennapedia (C39 → S) homeodomain (2HOA), with those from two reference probability functions. The first reference probability function is a uniform or flat probability function and the second is a bivariate probability function for π and ψ. The trivariate gaussian probability functions are shown to search the conformational space more efficiently than the other two probability functions. The trivariate gaussian probability functions are also tested on the binding domain of Streptococcal protein G (2GB1), an α/β class protein. Since presently available energy functions are not accurate enough to identify the most native-like energy-minimized structures, three selection criteria were used to identify a native-like structure with a 1.90-Å rmsd from the NMR structure as the best structure for the Antennapedia fragment. Each individual selection criterion (ECEPP/3 energy, ECEPP/3 energy-plus-free energy of hydration, or a knowledge-based mean field method) was unable to identify a native-like structure, but simultaneous application of more than one selection criterion resulted in a successful identification of a native-like structure for the Antennapedia fragment. In addition to these tests, structure predictions are made for the Antennapedia polypeptide, using a Pattern Recognition-based Importance-Sampling Minimization (PRISM) procedure to predict the backbone conformational state of the mutant Antennapedia homeodomain. The ten most probable backbone conformational state predictions were used with the trivariate and bivariate gaussian dihedral angle probability distributions to generate starting structures (i.e., dihedral angles) suitable for energy minimization. The final energy-minimized structures show that neither the trivariate nor the bivariate gaussian probability distributions are able to overcome the inaccuracies in the backbone conformational state predictions to produce a native-like structure. Until highly accurate predictions of the backbone conformational states become available, application of these dihedral angle probability distributions must be limited to problems, such as homology modeling, in which only a limited portion of the backbone (e.g., surface loops) must be explored. © 1996 John Wiley & Sons, Inc.     

The molecular structure of tetrathiofulvalene-13C (TTF) from proton magnetic resonance studies using nematic solvents

The molecular structure of TTF dissolved in nematic liquid crystalline solvents has been determined from the proton magnetic resonance including couplings due to ¹³C in natural abundance. The molecule is puckered in a boat conformation with the SCHCHS planes making a dihedral angle of 13 ± 2° with the S₂C  CS₂ plane. The other structural parameters obtained are r_CH = 1.085 ± 0.014 Å and the angel CCH = 123.7 ± 1.5°.     

Note: Helix or No Helix of β‐Peptides Containing β3hAla(αF) Residues?

A remote ⁴J(F,H) coupling (F? C(α)? C(O)? N? H) of up to 4.2 Hz in α‐fluoro amides with antiperiplanar arrangement of the C? F and the C?O bonds (dihedral angle F? C? C?O ca. 180°) confirms that previous NMR determinations, using the XPLOR‐NIH procedure, of the secondary structures of β‐peptides containing β³hAla(αF) and β³hAla(αF₂) residues were correct. In contrast, molecular‐dynamics (MD) simulations, using the GROMOS program with the 45A3 force field, led to an incorrect conclusion about the relative stability of secondary structures of these β‐peptides. The problems encountered in NMR analyses and computations of the structures of backbone‐F‐substituted peptides are briefly discussed.     

Dihedral angle study in Hesperidin using NMR Spectroscopy

Hesperidin is flavonoid molecule found in citrus fruits (Citrus reticulata), especially difficult to extract, classify and characterize. Present work is to study the unresolved relative configuration of Hesperidin through the dihedral angle, coupling constant and different NMR techniques. The Karplus equation and its modifications have been originated from the valence bond theory and associated with dihedral angle and coupling constant. The result data set of calculated dihedral angle can probe significant method to assign the virtual configuration of natural products and also resolved stereochemistry of Hesperidin at C‐2 position in. Copyright © 2016 John Wiley & Sons, Ltd.     

Synthesis and Solvent Effects on the Conformation of Hymenistatin 1

The cyclic octapeptide cyclo(-Pro-Pro-Tyr-Val-ProLeu-Ile-Ile-) ( 1 ), isolated from the Hymeniacidon sponge, was synthesized and examined conformationally using NMR and molecular-dynamics simulations. Most structural parameters of synthetic 1 are in accord with those reported for the isolated material. Our study indicates some small but significant differences in the assignment of the ¹H- and ¹³C-NMR resonances from those of the natural material. The Conformation was determind in both CHCl3 and DMSO using ¹H-NMR and molecular-dynamics simulations. Both NOE's and coupling constants were used as experimental restraints during the simulations which utilized explicitly the same solvent as in the NMR study. The differences in the interaction of the solvent with 1 were examined, providing insight into the observed differenced in conformation. The dominant conformation contains a ßVIa turn about Ile⁸-Tyr³ including a Pro¹-Pro² cis-peptide bond and a ßI or ßII turn about Val⁴-Ile⁷ in CHCl₃ and DMSO, respectively.     

Predicting 15N amide chemical shifts in proteins. I. An additive model for the backbone contribution

Because proteins adopt unique structures, chemically identical nuclei in proteins exhibit different chemical shifts. Amide ¹⁵N chemical shifts have been shown to vary over 20 ppm. The cause of these chemical shift inequivalencies is the different intra‐ and intermolecular interactions that individual nuclei experience at different locations in the protein structure. These chemical shift inequivalencies can be described as structural shifts, the difference between the actual chemical shift and the random coil chemical shift. As a first step toward the prediction of these amide ¹⁵N structural shifts, calculations have been carried out on acetyl‐glycine‐methyl amide to examine how a neighboring peptide group influences the amide ¹⁵N structural shifts. The ϕ,ψ dihedral angle space is completely surveyed, while all other geometrical variables are held fixed, to isolate the effect of the backbone conformation. Similar calculations for a limited number of conformations of acetyl‐glycine‐glycine‐methyl amide were carried out, where the effects of the two terminal peptide groups on the central amide ¹⁵N structural shift are examined. It is shown that the effect of the two adjacent groups can be accurately modeled by combining their individual effects additively. This provides a quite simple method to predict the backbone influence on amide ¹⁵N structural shifts in proteins. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 366–372, 2001     

NMR Solution Structure of the Duplex Formed by Self‐Pairing of α‐L‐Arabinopyranosyl‐(4′2′)‐(CGAATTCG)

The solution structure of the duplex formed by α‐L ‐arabinopyranosyl‐(4′→2′)‐(CGAATTCG) was studied by NMR. The resonances of all H‐, P‐ and most C‐atoms could be assigned. Dihedral angles and distance estimates derived from coupling constants and NOESY spectra were used as restraints in a simulated annealing calculation, which generated a well‐defined bundle of structures for the six innermost nucleotide pairs. The essential features of the resulting structures are an antiparallel, Watson Crick‐paired duplex with a strong backbone inclination of ca. −50° and, therefore, predominant interstrand base stacking. The very similar inclination and rise parameters of arabinopyranosyl‐(4′→2′)‐oligonucleotides and p‐RNA explain why these two pentapyranosyl isomers are able to cross‐pair.     

两个新颖的联环十二烷衍生物的合成及结构表征

2-（2＇-Oxo-3＇-oximidocyclododecyl） cyclododecanone （1） and 2-（1＇-hydroxylcyclododecyl） cyclododecanone （2） were synthesized and characterized. The conformation analysis was carried out based on the NMR, molecular mechanics calculation and X-ray diffraction. The conformation of two cyclododecyl moieties of both 1 and 2 was found to be the [3333]-2-one or [3333] square conformation both in the crystal state and the solution. The dihedral angle between carbonyl and the oxime double bond of the ring B is 180°in the crystal of 1. The protons or hydroxyl group of carbon atoms to link the two cyclododecyl moieties of 1 and 2 constitute dihedral angles of 174°in the crystal, and 175°in the solution, and the C-C 6 bond between two cyclododecyl moieties can not freely rotate in the solid state and the solution. In addition, compound 2 was the first example of a-comer-anti-monosubstituted cyclododecanone. synthesis     

2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil,a cyclouridine nucleoside with a C4′‐endo furanosyl conformation

2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil, C₁₃H₁₄N₂O₇, was obtained by refluxing 2′,3′‐O‐(methoxymethylene)uridine in acetic anhydride. The structure exhibits a nearly perfect C4′‐endo (⁴E) conformation. The best four‐atom plane of the five‐membered furanose ring is O—C—C—C, involving the C atoms of the fused five‐membered oxazolidine ring, and the torsion angle is only −0.4 (2)°. The oxazolidine ring is essentially coplanar with the six‐membered uracil ring [r.m.s. deviation = 0.012 (5) Å and dihedral angle = −3.2 (3)°]. The conformation at the exocyclic C—C bond is gauche–trans which is stabilized by various C—H...π and C—O...π interactions.