Tuning the Interaction Energy of Hydrogen Bonds: The Effect of the Substituent

Vitamin D protective effects result from its role as a nuclear transcription factor that regulates cell growth, differentiation, and a wide range of cellular mechanisms crucial to the development and progression of cancer.[1] Many academic investigators and pharmaceutical companies try to develop calcitriol analogs that exhibit equal or even increased anti-proliferative activity while exhibiting a reduced tendency to cause hypercalcemia. Analysis of 24 Vitamin D analogs bearing similar molecular structures with a complex of a Vitamin D Receptor (VDR) enabled the design of new agonists (TB1, TB2, TB3 and TB4). Undertaken approach was to minimize the electrostatic interaction energies available after the reconstruction of charge density with the aid of the pseudoatom databank (UBDB[2]). Comprehensive studies revealed 29 residues crucial for agonist binding. Trp286, which is specific to VDR among the representatives of the Nuclear Receptor Family, plays the crucial role of positioning the ligand forming dispersive interactions, mostly C-H...π, with an average strength of -4 kcal mol-1. The ligand binding pocket is primarily composed of hydrophobic residues, however there are 6 hydrogen bonds characteristic for all the ligands. They electrostatic interaction energies strongly contribute to the total interaction energy, with an average strength of -8, -19, -11 and -12 kcal mol-1 for hydrogen bonds to Ser237, Arg274, Ser278 and Tyr143. The aliphatic chain of the Vitamin D analogs adopt an extended conformation and the 25-hydroxyl group is hydrogen bonded to His305 and His397 with electrostatic interaction energies of -13 and -11 kcal mol-1. The geometries of complexes of the proposed ligand with VDR were obtained by the docking procedure implemented in Autodock4.3[3]. New agonsits form all mentioned before interactions with VDR. The final results of electrostatic interaction energy for TB1 and TB2 are -153 and -120 kcal mol-1, and this results are the smallest among all studied Vitamin D analogs.

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Hydrogen bond simulation in molecular crystals of tyrosine

Butlerov Communications ◽

10.37952/roi-jbc-01/19-58-6-73 ◽

2019 ◽

Vol 58 (6) ◽

pp. 73-77

Author(s):

Tatiana G. Volkova ◽

◽

Irina O. Talanova ◽

Keyword(s):

Amino Acids ◽

Hydrogen Bond ◽

Hydrogen Bonds ◽

Interaction Energy ◽

Biologically Active ◽

Model Systems ◽

Significant Difference ◽

Molecular Associate ◽

Order Of Magnitude ◽

Chemical Simulation

The problem of the study of hydrogen bonds in biomolecules and living systems is important. Among the drugs, doctors emphasize substances of natural origin involved in metabolic processes. Such compounds include amino acids, peptides, vitamins, enzymes, macro- and microelements, and other biologically active substances, many of which are capable of forming hydrogen bonds. Amino acids and their derivatives are drugs of metabolic pharmacotherapy, characterized by low toxicity and severity of side effects. They also have virtually no allergenic effect, which makes them promising for the creation of drugs or their modifications. The instability of the hydrogen bond can significantly affect the state of pharmaceutical drug containing, for example, amino acids, during their storage, transportation or technological processing. One of the methods for studying the nature and determining the strength of hydrogen bonds is quantum chemical simulation. The calculation of the interaction energy in the studied molecular associate and its decomposition have been carried out according to Morocuma’s method (HF/6-31G (PC GAMESS). The evaluation of such energy components as electrostatic, exchange repulsion, polarization, charge transfer, mixing is given. The main contribution to the interaction energy comes from the electrostatic component. All the studied models have the same distribution of the components of the interaction energy in order of magnitude. Significant difference in the interaction energy in two model systems was noted, that could be explained by different geometry of hydrogen bonds. The comparison of received data made it possible to conclude that there are three types of hydrogen bonds in the molecular tyrosine crystal, which differ from each other in energy and geometry.

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Molecular Dynamics Simulation in the Interlayer of Mixed-Layer Clays Due to Hydration and Swelling Mechanism

Crystals ◽

10.3390/cryst11060586 ◽

2021 ◽

Vol 11 (6) ◽

pp. 586

Author(s):

Yu Yang ◽

Sanjeev Adhikari ◽

Guoyuan Xu

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bonds ◽

Interaction Energy ◽

Mixed Layer ◽

Bound Water ◽

Swelling Behavior ◽

Dynamics Simulation ◽

Basal Spacing ◽

Water Interaction ◽

Swelling Mechanism

The swelling behavior of clay minerals is widely known for its importance in soil and environmental sciences and its detrimental effects in engineering fields. Although more than 70 percent of all clays are of mixed-layer types, the vast majority of the previous experiments and simulations are focused on pure clays, which cause the swelling mechanism of the widespread mixed-layer clay (MLC) and its role in soils are little understood, especially the most common illite-montmorillonite (I-M) mixed-layer clay (MLC). This paper reports on a molecular dynamics (MD) study of the differences in swelling behavior between I-M MLCs containing K+ and Na+ and Na-montmorillonite (MMT). It captures the evolution of quantitative properties such as basal spacing d, interaction energy, and many hydrogen bonds in the clay interlayer, increasing hydration for the first time through the scripts. It is found that MLCs have smaller swellings than Na-MMT due to the asymmetric interlayer charges and mixed counterions in the I-M interlayer. However, in terms of the interaction energy for the in-depth reason of swelling, it is found that the clay-clay interaction energy and the clay-ion interaction energy drop, while the clay-water interaction energy increases with increasing hydration. In addition, the attractive interaction of clay-bound water seriously promotes swelling, and it is mainly composed of Coulomb interaction and Van der Waals interaction. The higher the K+ concentration, the more noticeable these phenomena are. Besides, it is also reported that the number and distribution mechanism of hydrogen bonds in MLCs are very different from that of pure clay. This work provides insight into the molecular mechanism for initial swelling and clay-bound water interaction in widespread MLCs. This will help to decipher its specific role in soils and minimize clay swelling.

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A Thermodynamic Study of Methane Hydrates Formation In Glass Beads

ASEAN Journal of Chemical Engineering ◽

10.22146/ajche.49670 ◽

2016 ◽

Vol 16 (1) ◽

pp. 15

Author(s):

Tintin Mutiara ◽

Budhijanto Budhijanto ◽

I Made Bendiyasa ◽

Imam Prasetyo

Keyword(s):

Hydrogen Bonds ◽

Gas Hydrates ◽

Methane Hydrate ◽

Hydrate Formation ◽

Glass Beads ◽

Water Molecules ◽

Equilibrium Pressure ◽

Natural Gas Hydrates ◽

System Pressure ◽

Energy Of Hydrogen Bonds

Natural gas hydrates are non-stoichiometry compounds, in which the molecules of gas are trapped in crystalline cells consisting of water molecules retained by energy of hydrogen bonds. The experiments of Methane hydrate formation are performed at constant temperature in a reactor filled with various sizes of glass beads and water. Methane gas was fed into the reactor at various initial pressures. Equilibrium condition was reached when the system pressure did not change. The experimental results showed that the size of the glass beads gave very small effect on the equilibrium pressure of methane hydrate formation, so the effect could be neglected. In this study, the equation of Langmuir constant was Ci,CH4=(1/RT)exp[A+(B/T)] with the values of A and B for small cages were 6.8465 and 18.0342. The values of A and B for large cages were 7.7598 and 18.0361

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