scholarly journals Binding Strength and Hydrogen Bond Numbers between COVID-19 RBD and HVR of Antibody

Crystals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 997
Author(s):  
Ryan Taoran Wang ◽  
Alex Fan Xu ◽  
Qi Zhou ◽  
Tinglu Song ◽  
Kelvin J. Xu ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Temperature Dependence ◽  
Hypervariable Region ◽  
Bond Number ◽  
Genomic Sequencing ◽  
Physical Chemical ◽  
Virus Interaction ◽  
Antibody Interactions ◽  
Serum Testing

The global battle against the COVID-19 pandemic relies strongly on the human defense of antibody, which is assumed to bind the antigen’s receptor binding domain (RBD) with its hypervariable region (HVR). Due to the similarity to other viruses such as SARS, however, our understanding of the antibody-virus interaction has been largely limited to the genomic sequencing, which poses serious challenges to containment and rapid serum testing. Based on the physical/chemical nature of the interaction, infrared spectroscopy was employed to reveal the binding disparity, the real cause of the antibody-virus specificity at the molecular level, which is inconceivable to be investigated otherwise. Temperature dependence was discovered in the absorption value from the 1550 cm−1 absorption band, attributed to the hydrogen bonds by carboxyl/amino groups, binding the SARS-CoV-2 spike protein and closely resembled SARS-CoV-2 or SARS-CoV-1 antibodies. The infrared absorption intensity, associated with the number of hydrogen bonds, was found to increase sharply between 27 °C and 31 °C, with the relative absorbance matching the hydrogen bonding numbers of the two antibody types (19 vs. 12) at 37 °C. Meanwhile, the ratio of bonds at 27 °C, calculated by thermodynamic exponentials, produces at least 5% inaccuracy. Beyond genomic sequencing, the temperature dependence, as well as the bond number match at 37 °C between relative absorbance and the hydrogen bonding numbers of the two antibody types, is not only of clinical significance in particular but also as a sample for the physical/chemical understanding of vaccine–antibody interactions in general.

scholarly journals Binding strength and hydrogen bond numbers between Covid-19 RBD and HVR of antibody

2020 ◽  
Author(s):  
Ryan Taoran Wang ◽  
Alex Fan Xu ◽  
Qi Zhou ◽  
Tinglu Song ◽  
Kelvin J. Xu ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Temperature Dependence ◽  
Hypervariable Region ◽  
Bond Number ◽  
Genomic Sequencing ◽  
Physical Chemical ◽  
Virus Interaction ◽  
Antibody Interactions ◽  
Serum Testing

AbstractThe global battle against the Covid-19 pandemic relies strongly on the human defence of antibody, which is assumed to bind the antigen’s Receptor Binding Domain with its Hypervariable Region. Due to the similarity to other viruses such as SARS, however, our understanding of the antibody-virus interaction has been largely limited to the genomic sequencing, which poses serious challenges to the containment, vaccine exploration and rapid serum testing. Based on the physical/chemical nature of the interaction, infrared spectroscopy was employed to reveal the binding disparity, when unusual temperature dependence was discovered from the 1550cm-1 absorption band, attributed to the hydrogen bonds by carboxyl/amino groups, binding the SARS-CoV-2 spike protein and closely resembled SARS-CoV-2 or SARS-CoV-1 antibodies. The infrared absorption intensity, associated with the number of hydrogen bonds, was found to increase sharply between 27°C and 31°C, with the relative absorbance matches at 37°C the hydrogen bonding numbers of the two antibody types (19 vs 12). Meanwhile the ratio of bonds at 27°C, calculated by thermodynamic exponentials rather than by the layman’s guess, produces at least 5% inaccuracy. As a result, the specificity of the SARS-CoV-2 antibody will be more conclusive beyond 31°C, instead of at the usual room temperature of 20°C - 25°C, when the vaccine research and antibody diagnosis would likely be undermined. Beyond genomic sequencing, the temperature dependence, as well as the bond number match at 37°C between relative absorbance and the hydrogen bonding numbers of the two antibody types, are not only of clinical significance in particular, but also of a sample for the physical/chemical understanding of the vaccine-antibody interactions in general.

SPECTROSCOPIC STUDIES OF ALCOHOLS: VI. INTRAMOLECULAR HYDROGEN BONDS IN ETHANOLAMINE AND ITS O- AND N-METHYL DERIVATIVES

1965 ◽  
Vol 43 (11) ◽  
pp. 2970-2977 ◽  
Author(s):  
P. J. Krueger ◽  
H. D. Mettee
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Temperature Dependence ◽  
Spectroscopic Studies ◽  
Intramolecular Hydrogen Bonds ◽  
Distinct Band ◽  
Conformational Equilibria ◽  
Methyl Derivatives ◽  
Intramolecular Hydrogen

The competitive intramolecular [Formula: see text] hydrogen bonding in ethanolamine and N-methylethanolamine has been studied in dilute C2Cl4 solution by means of the temperature dependence of the fundamental OH and NH stretching bands. Of the three conformers identified for each of these compounds, the least stable shows a distinct band which is assigned to a "terminal" OH group involved in an intramolecular [Formula: see text] hydrogen bond. Enthalpy differences between conformers are reported and discussed, and compared with those found for the conformational equilibria in 2-methoxyethylamine and N,N-dimethyl-ethanolamine.

scholarly journals Hydrogen Bonds: Raman Spectroscopic Study

2021 ◽  
Vol 22 (10) ◽  
pp. 5380
Author(s):  
Boris A. Kolesov
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Spectroscopic Study ◽  
Raman Spectra ◽  
Temperature Region ◽  
Vibrational Frequency ◽  
Chemical Compounds ◽  
Raman Spectroscopic ◽  
Raman Spectroscopic Study ◽  
Proton Dynamics

The work outlines general ideas on how the frequency and the intensity of proton vibrations of X–H×××Y hydrogen bonding are formed as the bond evolves from weak to maximally strong bonding. For this purpose, the Raman spectra of different chemical compounds with moderate, strong, and extremely strong hydrogen bonds were obtained in the temperature region of 5 K–300 K. The dependence of the proton vibrational frequency is schematically presented as a function of the rigidity of O-H×××O bonding. The problems of proton dynamics on tautomeric O–H···O bonds are considered. A brief description of the N–H···O and C–H···Y hydrogen bonds is given.

Hydrogen bonding and its temperature dependence in vinyl chloride-vinyl acetate-vinyl alcohol terpolymer: A study using the IR absorption technique

1990 ◽  
Vol 192 (1) ◽  
pp. 157-162 ◽  
Author(s):  
V.S. Panwar ◽  
Ramadhar Singh ◽  
P.C. Mehendru ◽  
N.P. Gupta
Keyword(s):  
Hydrogen Bonding ◽  
Temperature Dependence ◽  
Vinyl Acetate ◽  
Vinyl Chloride ◽  
Vinyl Alcohol ◽  
Ir Absorption ◽  
Absorption Technique

2-Hydroxy-3-methoxybenzaldehyde (pyridinium-4-ylcarbonyl)hydrazone chloride hemihydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o2043-o2044 ◽  
Author(s):  
Shao-Wen Chen ◽  
Han-Dong Yin ◽  
Da-Qi Wang ◽  
Xia Kong ◽  
Xiao-Fang Chen
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Compound C

The crystal structure of the title compound, C14H14ClN3O3 +·Cl−·0.5H2O, exhibits O—H...O, C—H...O, C—H...Cl, N—H...Cl and O—H...Cl hydrogen bonds. The chloride anions participate in extensive hydrogen bonding with the aminium cations and link molecules through multiple N—H+...Cl− interactions.

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

scholarly journals Two New Polyiodides in the 4,4´-Bipyridinium Diiodide/Iodine System

2012 ◽  
Vol 67 (1) ◽  
pp. 5-10
Author(s):  
Guido J. Reiss ◽  
Martin van Megen
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Complex I ◽  
The Other ◽  
Cyclic Dimer ◽  
Water Molecules ◽  
Spectroscopic Methods ◽  
Halogen Bonds ◽  
One Dimensional ◽  
Hydroiodic Acid

The reaction of bipyridine with hydroiodic acid in the presence of iodine gave two new polyiodide-containing salts best described as 4,4´-bipyridinium bis(triiodide), C10H10N2[I3]2, 1, and bis(4,4´-bipyridinium) diiodide bis(triiodide) tris(diiodine) solvate dihydrate, (C10H10N2)2I2[I3]2 · 3 I2 ·2H2O, 2. Both compounds have been structurally characterized by crystallographic and spectroscopic methods (Raman and IR). Compound 1 is composed of I3 − anions forming one-dimensional polymers connected by interionic halogen bonds. These chains run along [101] with one crystallographically independent triiodide anion aligned and the other triiodide anion perpendicular to the chain direction. There are no classical hydrogen bonds present in 1. The structure of 2 consists of a complex I144− anion, 4,4´-bipyridinium dications and hydrogen-bonded water molecules in the ratio of 1 : 2 : 2. The I144− polyiodide anion is best described as an adduct of two iodide and two triiodide anions and three diiodine molecules. Two 4,4´-bipyridinium cations and two water molecules form a cyclic dimer through N-H· · ·O hydrogen bonds. Only weak hydrogen bonding is found between these cyclic dimers and the polyiodide anions.

Quantum Cluster Equilibrium Theory of Liquids:  Temperature Dependence of Hydrogen Bonding in LiquidN-Methylacetamide Studied by IR Spectra

1998 ◽  
Vol 102 (46) ◽  
pp. 9312-9318 ◽  
Author(s):  
R. Ludwig ◽  
O. Reis ◽  
R. Winter ◽  
F. Weinhold ◽  
T. C. Farrar
Keyword(s):  
Hydrogen Bonding ◽  
Ir Spectra ◽  
Temperature Dependence ◽  
Equilibrium Theory ◽  
Theory Of Liquids ◽  
Quantum Cluster
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