scholarly journals 1H- and 13C-n.m.r. studies of the antitumour antibiotic luzopeptin. Resonance assignments, conformation and flexibility in solution

1988 ◽  
Vol 256 (1) ◽  
pp. 271-278 ◽  
Author(s):  
M S Searle ◽  
J G Hall ◽  
P G Wakelin
Keyword(s):  
Hydrogen Bonds ◽  
Nuclear Overhauser Effect ◽  
Resonance Assignments ◽  
Carbonyl Oxygen ◽  
Correlation Spectroscopy ◽  
Spin Lattice Relaxation ◽  
Double Quantum ◽  
Two Dimensional ◽  
Relaxation Data ◽  
Oxygen Atoms

The depsipeptide DNA-intercalating antibiotic luzopeptin was studied in solution by n.m.r. methods. Two-dimensional 1H double-quantum-filtered correlation spectroscopy (DQF-COSY) and nuclear-Overhauser-effect spectroscopy (NOESY) confirm the primary structure and twofold symmetry of luzopeptin and provide details of its three-dimensional conformation in solution. Trans-annular hydrogen bonds between the glycine NH groups and carbonyl oxygen atoms have been identified in the crystalline state [Arnold & Clardy (1981) J. Am. Chem. Soc. 103, 1243-1244], and are important in maintaining an antiparallel beta-sheet conformation. The n.m.r. data indicate that the glycine NH protons are appreciably shielded from the solvent molecules, which suggests that these hydrogen bonds are maintained in solution. The orientation of the quinoline chromophores is defined by two-dimensional NOE cross-peaks that position the N-methyl group of the L-beta-hydroxyvaline residue close in space to both the quinoline H-8 and serine NH proton. This pattern of NOEs is in accord both with the chromophore configuration found in the crystal and one where the quinoline rings are aligned in a parallel manner at right-angles to the depsipeptide ring. The n.m.r. data are consistent with a hydrogen bond between the quinoline hydroxy groups and the quinoline carbonyl oxygen atoms. The pyridazine acetylmethyl groups give NOEs to the C(alpha)H groups of the beta-hydroxy-N-methylvaline residues, showing that the acetyl groups, for at least some of the time, stretch over the depsipeptide ring, occluding one face of the molecule. Both of the latter features are also found in the crystal structure. Resonances in the 13C-n.m.r. spectrum of luzopeptin have been assigned by transferring 1H assignments to their covalently bonded carbon atoms via a heteronuclear shift-correlation experiment (HETCOR). The measurement of spin-lattice relaxation times and 1H-13C NOEs at specific sites in the molecule has led us to conclude that segmental motions within the depsipeptide ring are restricted and that the 13C relaxation data for luzopeptin's protonated carbon atoms are adequately described by isotropic tumbling in solution. Furthermore, relaxation data for the carbon atoms of the quinoline chromophores show that these rings exhibit similar motion to the depsipeptide ring and are not rotating rapidly with respect to it. Taken together all the data imply that luzopeptin is fairly rigid in solution, on the time scale of molecular tumbling, and has, or can readily attain, a staple-like structure suitable for bisintercalation.(ABSTRACT TRUNCATED AT 400 WORDS)

scholarly journals Different Molecular Interaction between Collagen and α- or β-Chitin in Mechanically Improved Electrospun Composite

Marine Drugs ◽  
2019 ◽  
Vol 17 (6) ◽  
pp. 318 ◽  
Author(s):  
Hyunwoo Moon ◽  
Seunghwan Choy ◽  
Yeonju Park ◽  
Young Mee Jung ◽  
Jun Mo Koo ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Tensile Strength ◽  
Regenerative Medicine ◽  
Hydrogen Bonds ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
Molecular Hydrogen ◽  
Correlation Spectroscopy ◽  
Two Dimensional ◽  
Secondary Interaction

Although collagens from vertebrates are mainly used in regenerative medicine, the most elusive issue in the collagen-based biomedical scaffolds is its insufficient mechanical strength. To solve this problem, electrospun collagen composites with chitins were prepared and molecular interactions which are the cause of the mechanical improvement in the composites were investigated by two-dimensional correlation spectroscopy (2DCOS). The electrospun collagen is composed of two kinds of polymorphs, α- and β-chitin, showing different mechanical enhancement and molecular interactions due to different inherent configurations in the crystal structure, resulting in solvent and polymer susceptibility. The collagen/α-chitin has two distinctive phases in the composite, but β-chitin composite has a relatively homogeneous phase. The β-chitin composite showed better tensile strength with ~41% and ~14% higher strength compared to collagen and α-chitin composites, respectively, due to a favorable secondary interaction, i.e., inter- rather than intra-molecular hydrogen bonds. The revealed molecular interaction indicates that β-chitin prefers to form inter-molecular hydrogen bonds with collagen by rearranging their uncrumpled crystalline regions, unlike α-chitin.

Two-Dimensional Infrared Spectroscopy and Principal Component Analysis Studies on a New Azobenzene Derivative Supramolecular System Based on Hydrogen Bonds

2003 ◽  
Vol 57 (8) ◽  
pp. 933-942 ◽  
Author(s):  
Yuqing Wu ◽  
Ya-Qiong Hao ◽  
Min Li ◽  
Chaowei Guo ◽  
Yukihiro Ozaki
Keyword(s):  
Principal Component Analysis ◽  
Hydrogen Bonds ◽  
Supramolecular Assembly ◽  
Principal Component ◽  
Correlation Spectroscopy ◽  
Supramolecular System ◽  
Two Dimensional ◽  
Temperature Dependent ◽  
2D Correlation Spectroscopy ◽  
2D Correlation Analysis

Infrared (IR) spectra of a supramolecular assembly with an azobenzene derivative and intermolecular hydrogen bonds have been measured in the temperature range from 30 to 200 °C to investigate heat-induced structural changes and thermal stability. Principal component analysis (PCA) and two kinds of two-dimensional (2D) correlation spectroscopy, variable–variable (VV) 2D and sample–sample (SS) 2D spectroscopy, have been employed to analyze the observed temperature-dependent spectral variations. The PCA and SS 2D correlation analyses have demonstrated that the complete decoupling of hydrogen bonds in the supramolecular assembly occurs between 110 and 115 °C, which is in good agreement with the results of a differential scanning calorimetry (DSC) study for the heating process. The PCA of the IR spectra in the region of 3600–3100 cm−1 has illustrated that there are at least four principal components for the different NH2 and CONH species in the present supramolecular system. The VV 2D correlation spectroscopy study has provided information about the structure and strength of hydrogen bonds of NH2 and CONH groups and their temperature-dependent variations. The different species of hydrogen-bonded NH2 and CONH groups in the supramolecular system can be clarified by the VV 2D correlation analysis. The VV 2D correlation analysis has also revealed the specific order of the temperature-induced changes in the hydrogen bonds of NH2 and CONH groups.

Bindung von Metall-Ionen an Dipeptide: Struktur von Thallium(I)-(3-benzyl-6-carboxylatomethyl-2,5-diketopiperazin) / Binding of Metal Ions by Dipeptides: Structure of Thallium(I) 3-Benzyl-6-carboxylatomethyl-2,5-diketopiperazine

1992 ◽  
Vol 47 (7) ◽  
pp. 952-956
Author(s):  
P. Mikulcik ◽  
P. Bissinger ◽  
J. Riede ◽  
H. Schmidbaur
Keyword(s):  
Solid State ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Carbonyl Oxygen ◽  
State Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystalline Product ◽  
Oxygen Atoms

Ester cleavage of aspartame (L-α-aspartyl-L-phenylalanine methylester) (1), by equimolar quantities of thallium ethoxide is accompanied by intramolecular cyclisation to give thallium 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine (2). The solid state structure of the crystalline product was determined by single-crystal X-ray diffraction analysis. The cations were found to form four short and four elongated contacts to seven oxygen atoms and one nitrogen atom of a total of six neighbouring 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine anions. There are inter-anionic hydrogen bonds only between the imino groups and the carbonyl oxygen atoms (O3, O4), featuring a pattern similar to that found for cytosine-guanosine contacts in DNA.

scholarly journals Conformation and dynamics of the deoxyribose rings of a (nogalamycin)2–d (5′-GCATGC)2 complex studied in solution by 1H-n.m.r. spectroscopy

1990 ◽  
Vol 269 (2) ◽  
pp. 341-346 ◽  
Author(s):  
M S Searle ◽  
L P Wakelin
Keyword(s):  
Base Pair ◽  
Dynamic Equilibrium ◽  
Graphical Analysis ◽  
Correlation Spectroscopy ◽  
Coupling Constants ◽  
Double Quantum ◽  
Two Dimensional ◽  
Coherence Transfer ◽  
Data Set ◽  
Base Pair Stacking

The conformation and dynamics of the deoxyribose rings of a (nogalamycin)2-d(5′-GCATGC)2 complex have been determined from an analysis of 1H-1H vicinal coupling constants and sums of coupling constants (J1′-2′,J1′-2″,epsilon 1′, epsilon 2′ and epsilon 2″) measured from one-dimensional n.m.r. spectra and from H-1′-H-2′ and H-1′-H-2″ cross-peaks in high-resolution phase-sensitive two-dimensional correlation spectroscopy (COSY) and double-quantum-filtered correlation spectroscopy (DQF-COSY) experiments. The value of J3′-4′ has also been estimated from the magnitude of H-3′-H-4′ cross-peaks in DQF-COSY spectra and H-1′-H-4′ coherence transfer cross-peaks in two-dimensional homonuclear Hartman-Hahn spectroscopy (HOHAHA) spectra. The data were analysed, in terms of a dynamic equilibrium between North (C-3′-endo) and South (C-2′-endo) conformers, by using the graphical-analysis methods described by Rinkel & Altona [(1987) J. Biomol. Struct. Dyn. 4,621-649]. The data reveal that the sugars of the 2C-5G and 3A-4T base-pairs, which form the drug-intercalation site, have strikingly different properties. The deoxyribose rings of the 2C-5G base-pair are best described in terms of an equilibrium heavily weighted in favour of the C-2′-endo geometry (greater than 95% ‘S’), with a phase angle, P, lying in the range 170-175 degrees and amplitude of pucker between 35 and 40 degrees, as typically found for B-DNA. For the deoxyribose rings of the 3A-4T base-pair, however, the analysis shows that, for 3A, the C-2′-endo and C3′-endo conformers are equally populated, whereas a more limited data set for the 4T nucleotide restricts the equilibrium to within 65-75% C-2′-endo. The deoxyribose rings of the 1G-6C base-pair have populations of 70-80% C-2′-endo, typical of nucleotides at the ends of a duplex. Although drug-base-pair stacking interactions are an important determinant of the enhanced duplex stability of the complex [Searle, Hall, Denny, & Wakelin (1988) Biochemistry 27, 4340-4349], the current findings make it clear that the same interactions can be associated with considerable variations in the degree of local structural dynamics at the level of the sugar puckers.

Structural characterization, by two-dimensional NMR spectroscopy and fast-atom-bombardment mass spectrometry, of a highly acylated trirhamnoside from Mezzettialeptopoda (Annonaceae)

1990 ◽  
Vol 68 (7) ◽  
pp. 1044-1050 ◽  
Author(s):  
Donald A. Powell ◽  
William S. York ◽  
Herman van Halbeek ◽  
Joseph T. Etse ◽  
Alexander I. Gray ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Fast Atom Bombardment ◽  
Multiple Bond ◽  
Stem Bark ◽  
Correlation Spectroscopy ◽  
Double Quantum ◽  
Two Dimensional ◽  
Complex Carbohydrate ◽  
Heteronuclear Multiple Bond Correlation

The structure of Mezzettiaside 3, a highly acylated trisaccharide obtained from the stem bark of Mezzettialeptopoda, was determined by a combination of double-quantum-filtered {1H,1H} correlation spectroscopy, two-dimensional homonuclear Hartmann–Hahn, and 1H-detected {1H,13C} one-bond and multiple-bond shift correlation nuclear magnetic resonance experiments, in conjunction with fast-atom-bombardment mass spectrometry. Mezzettiaside 3 was found to be the α-(n-octyl)glycoside of 3,4-di-O-acetyl-L-rhamnopyranosyl-α(1 → 3)-2,4-di-O-acetyl-L-rhamnopyranosyl-α(1 → 3)-4-O-hexanoyl-L-rhamnopyranose. The heteronuclear multiple-bond correlation NMR technique proved to be invaluable in establishing the location of the O-acyl groups in this complex carbohydrate. Keywords: oligosaccharide, HMBC, HMQC, HOHAHA, FAB-MS.

scholarly journals Hydrogen Bonds between Acidic Protons from Alkynes (C–H···O) and Amides (N–H···O) and Carbonyl Oxygen Atoms as Acceptor Partners

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Pierre Baillargeon ◽  
Tommy Lussier ◽  
Yves L. Dory
Keyword(s):  
Dipole Moment ◽  
Hydrogen Bonds ◽  
Electric Dipole Moment ◽  
Electric Dipole ◽  
Title Compound ◽  
Carbonyl Oxygen ◽  
The Other ◽  
Orthorhombic System ◽  
Space Group ◽  
Oxygen Atoms

Crystals of tert-butyl (2S)-2-(prop-2-yn-1-ylcarbamoyl)pyrrolidine-1-carboxylate (Boc-L-Pro-NHCH2CCH) have been obtained. The title compound crystallizes easily as sharp needles in orthorhombic system, space group P 21 21 21 with a = 9.2890(2), b = 9.7292(2), c = 15.7918(4) Å, V = 1427.18(6) Å3, and Z = 4. The main feature of the structure is the orientation of the carbamate and amide. Their dipoles add up and the molecule displays an electric dipole moment of 5.61 D from B3LYP/6-31G(d) calculations. The antiparallel H bonding of amides and the alignment of dipoles induce columnar stacking (the dipole moment along the columnar a axis is 4.46 D for each molecule). The other components across the other axes are, therefore weaker, (3.17 D and 1.23 D along the b and c axes, resp.). The resulting anisotropic columns pack side by side, in an antiparallel fashion mostly by (alkyne) CH···O=C (carbamate) interactions.

Potential of Generalised Two-Dimensional Correlation Spectroscopy in the near Infrared Region

1996 ◽  
Vol 4 (1) ◽  
pp. 85-99 ◽  
Author(s):  
Yukihiro Ozaki ◽  
Isao Noda
Keyword(s):  
Near Infrared ◽  
Infrared Region ◽  
Carbonyl Oxygen ◽  
Correlation Spectroscopy ◽  
Pure Liquid ◽  
Two Dimensional ◽  
Temperature Dependent ◽  
Thermally Induced ◽  
Correlation Spectrum ◽  
Nylon 12

This review demonstrates the potential of generalised two-dimensional (2D) correlation spectroscopy in the near infrared (NIR) region. Three examples of generalised 2D NIR correlation analysis, which are all concerned with the temperature-dependent spectral variations of self-associated molecules, are discussed in this paper. The first example presents the 2D correlation approach to the analysis of a set of NIR spectra of oleyl alcohol in the pure liquid state under temperature changes. The 2D NIR analysis enhances the spectral resolution and simplifies the spectra with overlapped bands. For example, it was found that a band at 7090 cm−1, arising from the first overtone of an OH stretching mode of the monomeric alcohol, consists of two bands due to the rotational isomerism of the free OH group. The second example deals with the temperature-dependent NIR spectral changes of N-methylacetamide (NMA). The close-up view of 2D NIR correlation spectra of NMA, obtained at narrow spectral and temperature windows, enabled us to propose not only band assignments in the 6800–6050 cm−1 region, where the first overtones of stretching modes of free, free-end and hydrogen-bonded NH groups were expected to appear, but also a detailed mechanistic picture of the thermally-induced dissociation of NMA for each temperature range. A 2D NIR study of premelting behaviour and hydrogen bonds of Nylon 12 is discussed as the third example. The asynchronous 2D NIR correlation spectrum of Nylon 12 obtained from 30 to 150°C in the 6900–6100 cm−1 region indicated that the amide group with a free carbonyl oxygen appears first and then the unassociated free amide and amide with free NH follow as the temperature is increased. The asynchronous spectrum in the 6000–5500 cm−1 region, where the first overtones of the CH2 stretching modes are expected to appear, suggested that a substantial amount of disordered or dissociated components start appearing before the disappearance of more ordered components. It seemed that they appear as the premelting precursors (or even possibly as the indirect cause) to the precipitous decrease of the ordered components associated with the melting of Nylon 12 occurring at a much higher temperature.

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