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Related Concept Videos

Hydrogen Bonds00:26

Hydrogen Bonds

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Hydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.
Hydrogen Bonds Control the World!
Because hydrogen has very weak electronegativity when it binds with a strongly electronegative atom, such as oxygen or nitrogen, electrons in the bond are unequally shared....
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Hydrogen Bonds01:04

Hydrogen Bonds

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A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...
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Preparation and Reactions of Sulfides02:26

Preparation and Reactions of Sulfides

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Sulfides are the sulfur analog of ethers, just as thiols are the sulfur analog of alcohol. Like ethers, sulfides also consist of two hydrocarbon groups bonded to the central sulfur atom. Depending upon the type of groups present, sulfides can be symmetrical or asymmetrical. Symmetrical sulfides can be prepared via an SN2 reaction between 2 equivalents of an alkyl halide and one equivalent of sodium sulfide.
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Structure and Nomenclature of Thiols and Sulfides02:17

Structure and Nomenclature of Thiols and Sulfides

5.8K
Thiols and sulfides are sulfur analogs of alcohols and ethers, respectively, where the sulfur atom takes the place of the oxygen atom. Thus, thiols are generally represented as RSH, where R is an alkyl substituent and —SH is the functional group. On the other hand, in sulfides, the central sulfur atom is bonded to two hydrocarbon groups on either side. Depending upon the type of group, sulfides can be either symmetrical or asymmetrical. Both thiols and sulfides display a bent geometry,...
5.8K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
15.2K

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A detailed analysis of the spin-crossover reaction of H<sub>2</sub>S binding to heme and the six-coordinated FeP(Im)-HS<sup>-</sup> porphyrin complex.

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A Sensitive Visual Method for the Detection of Hydrogen Sulfide Producing Bacteria
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Modeling the hydrogen sulfide binding to heme.

B D Ostojić1, P Schwerdtfeger2, D S Đorđević1

  • 1Center of Excellence in Environmental Chemistry and Engineering, Institute for Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade 11000, Serbia.

Journal of Inorganic Biochemistry
|April 30, 2018
PubMed
Summary

Hydrogen sulfide binding to heme models was studied using advanced computational methods. Results indicate reversible binding, crucial for understanding its role in biochemical reactions.

Keywords:
Coupled cluster theoryDensity functional theoryElectronic statesH(2)S bindingHemeImidazole

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Area of Science:

  • Computational chemistry
  • Biochemistry
  • Quantum chemistry

Background:

  • Hydrogen sulfide (H₂S) plays vital roles in biological systems.
  • Heme proteins are critical in various biological processes.
  • Understanding H₂S interaction with heme is essential for biochemical insights.

Purpose of the Study:

  • To investigate the binding mechanism of hydrogen sulfide to a model heme compound.
  • To determine the energy landscape and binding affinity of the FeP(Im)-H₂S complex.
  • To explore the implications of binding reversibility in biochemical contexts.

Main Methods:

  • Coupled-cluster singles-doubles with perturbative triples (CCSD(T)) calculations.
  • Density functional theory (DFT) for relaxed potential energy curves.
  • Modeling the heme compound as FeP(Im) (Iron porphyrin-imidazole).

Main Results:

  • The FeP(Im)-H₂S aduct exhibits a binding energy of 13.7 kcal/mol at the CCSD(T) level.
  • DFT calculations revealed a "double spin-crossover" reaction during binding.
  • Long-distance van der Waals minima were found near the ground state energy.

Conclusions:

  • The calculated binding energy and proximity to dissociation suggest reversible H₂S adsorption/desorption.
  • This reversibility is significant for the function of H₂S in biochemical reactions.
  • The study provides a detailed molecular-level understanding of H₂S-heme interactions.