Secondary Structures in a Freeze-Dried Lignite Humic Acid Fraction Caused by Hydrogen-Bonding of Acidic Protons with Aromatic Rings

2016 ◽  
Vol 50 (4) ◽  
pp. 1663-1669 ◽  
Author(s):  
Xiaoyan Cao ◽  
Marios Drosos ◽  
Jerry A. Leenheer ◽  
Jingdong Mao
Keyword(s):  
Hydrogen Bonding ◽  
Humic Acid ◽  
Secondary Structures ◽  
Acid Fraction ◽  
Aromatic Rings ◽  
Freeze Dried ◽  
Lignite Humic Acid

scholarly journals Characterization of Ultrafiltration-Fractionated Humic Acid Derived from Chinese Weathered Coal by Spectroscopic Techniques

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2030
Author(s):  
Shuiqin Zhang ◽  
Liang Yuan ◽  
Yanting Li ◽  
Bingqiang Zhao
Keyword(s):  
Molecular Weight ◽  
Humic Acid ◽  
Atomic Ratio ◽  
Raw Material ◽  
Spectroscopic Techniques ◽  
Acid Fraction ◽  
Aromatic Rings ◽  
Xps Spectra ◽  
Weathered Coal ◽  
Degree Of Aromaticity

Weathered coal is a widely used raw material of farm-oriented humic acid in China, while the high heterogeneity impedes its sufficient utilization. In this study, we fractionated the humic acid derived from Chinese weathered coal by ultrafiltration, and three fractions with the molecular range of ≥100 kDa, 10–100 kDa, ≤10 kDa were obtained. Subsequently, the chemical and spectral properties of the fractions were characterized by elemental analysis, potentiometric titration, Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and X-ray photoelectron (XPS) and other spectroscopy. The results showed that more than 60% of humic acid by weight was concentrated in the molecular range higher than 100 kDa, while only 3.25% was assigned to that with molecular weight lower than 10 kDa. The humic acid fraction with molecular weight higher than 100 kDa showed more carbon content, lower H/C atomic ratio, while higher E4/E6 ratio, more aromatic structure in FTIR, 13C NMR, and XPS spectra, indicating a higher degree of aromaticity and stronger hydrophobicity. Conversely, there were more carboxyl groups and aliphatic structures, while fewer condensed aromatic rings for the humic acid fraction with molecular weight less than 100 kDa. These differences provide a baseline for the better utilization of weathered coal.

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Polymers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 2074
Author(s):  
Sara Tabandeh ◽  
Cristina Elisabeth Lemus ◽  
Lorraine Leon
Keyword(s):  
Hydrogen Bonding ◽  
Phase Separation ◽  
Liquid Phase ◽  
Charge Density ◽  
Secondary Structures ◽  
Liquid Phase Separation ◽  
Polyelectrolyte Complexes ◽  
Π Interactions ◽  
Liquid Liquid Phase Separation

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.

Structural and spectroscopic studies of transition metal nitrite complexes. V. Crystal structures and spectra of trans-Tetrakis(pyridine)dinitritonickel(II)-pyridine (1/2), trans-Tetrakis(4-methylpyridine)dinitritonickel(II) and trans-Tetrakis(pyrazole)-dinitritonickel(II)

1981 ◽  
Vol 34 (10) ◽  
pp. 2095 ◽  
Author(s):  
AJ Finney ◽  
MA Hitchman ◽  
CL Raston ◽  
GL Rowbottom ◽  
BW Skelton ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Transition Metal ◽  
Crystal Structures ◽  
Electronic Spectra ◽  
Spectroscopic Studies ◽  
Molecular Structures ◽  
Aromatic Rings ◽  
Paddle Wheel ◽  
Crystal And Molecular Structures ◽  
Infrared Frequencies

The crystal and molecular structures of the compounds [Ni(py)4(ONO)2],2py, [Ni(γmpy),(ONO)2] and [Ni(prz)4(ONO)2] are reported.�All three are trans nitrito complexes, the pyridine (py) compound containing two pyridine molecules of solvation. The aromatic rings in the first two complexes adopt 'paddle wheel' conformations with pitch angles varying between 40 and 70�. The nitrite ions are positioned so as to minimize repulsive interactions with the amines, and it seems likely that these groups bond through oxygen rather than nitrogen because this allows a lesser degree of interligand steric interference. The amine rings in [Ni(prz)4(ONO)2] are orthogonal to the plane containing the nickel and coordinated pyrazole nitrogen atoms; the nitrito groups are disordered between two inequivalent positions, each of which involves hydrogen bonding with the pyrazole NH groups. The nitrite infrared frequencies are similar to those observed for other nickel(II) nitrito complexes except that the antisymmetric NO stretching mode of one of the groups in the pyrazole complex is much lower in energy than expected, being in the range normally associated with a nitrogen-bonded or chelated nitrite group. It is suggested that this deviation may be caused by the hydrogen bonding in the complex. The electronic spectra of the compounds yield 10Dq values of 9100 and 8500 cm-1 for the nitrite ligands in [Ni(py)4(ONO)2] and Ni(prz)4(ONO)2], respectively, placing the nitrito group towards the weaker end of the spectro-chemical series.

HUMUS FRACTION RATIOS AS A MEANS OF DISCRIMINATING BETWEEN HORIZON TYPES

1980 ◽  
Vol 60 (2) ◽  
pp. 219-229 ◽  
Author(s):  
L. E. LOWE
Keyword(s):  
Organic Matter ◽  
Humic Acid ◽  
Carbon Content ◽  
Fulvic Acid ◽  
Soil Classification ◽  
Acid Fraction ◽  
Humus Fraction ◽  
Wide Range ◽  
Fraction Distribution

Humus fraction distribution in a wide range of horizon samples was examined by measuring carbon content in humic acid (Ch), in fulvic acid (Cf) and in the strongly colored polyphenolic component of the fulvic acid fraction (Ca). Fraction distribution was described by the ratios Ch/Cf and Ca/Cf. It was concluded that humus fraction ratios were related to horizon types as used in the Canadian System of Soil Classification, and were effective in discriminating between certain horizon types, particularly between Luvisolic Bt and Podzolic Bf. The results also suggested that humus fraction ratios may be effective in separating distinct sub-populations within Ah horizons and Bf horizons in general, based on qualitative differences in organic matter present. Aspects of the role of humus fractions in soil genesis are discussed.

scholarly journals Binding of proton and iron to lignite humic acid size-fractions in aqueous matrix

2018 ◽  
Vol 254 ◽  
pp. 241-247 ◽  
Author(s):  
Zinnat A. Begum ◽  
Ismail M.M. Rahman ◽  
Yousuke Tate ◽  
Toshiharu Ichijo ◽  
Hiroshi Hasegawa
Keyword(s):  
Humic Acid ◽  
Size Fractions ◽  
Lignite Humic Acid
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