Behavior of interaction energy and intramolecular bond stretch in linear and bifurcated hydrogen bonds

1993 ◽  
Vol 48 (S20) ◽  
pp. 181-190 ◽  
Author(s):  
Xiaofeng Duan ◽  
Steve Scheiner
Keyword(s):  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Bond Stretch

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

2011 ◽  
Vol 115 (45) ◽  
pp. 12561-12571 ◽  
Author(s):  
Ignasi Mata ◽  
Elies Molins ◽  
Ibon Alkorta ◽  
Enrique Espinosa
Keyword(s):  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Energy Of Hydrogen Bonds

scholarly journals New Ligands and New Insights for Vitamin D Receptor from Charge Density

2014 ◽  
Vol 70 (a1) ◽  
pp. C966-C966
Author(s):  
Maura Malińska ◽  
Andrzej Kutner ◽  
Krzysztof Woźniak
Keyword(s):  
Vitamin D ◽  
Hydrogen Bonds ◽  
Charge Density ◽  
Interaction Energy ◽  
Vitamin D Receptor ◽  
Electrostatic Interaction ◽  
Interaction Energies ◽  
Average Strength ◽  
Vitamin D Analogs ◽  
Wide Range

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.

scholarly journals Hydrogen bond simulation in molecular crystals of tyrosine

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.

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

Crystals ◽  
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.

scholarly journals Double-Layer Capacitances Caused by Ion–Solvent Interaction in the Form of Langmuir-Typed Concentration Dependence

Electrochem ◽  
2021 ◽  
Vol 2 (4) ◽  
pp. 631-642
Author(s):  
Koichi Jeremiah Aoki ◽  
Ridong He ◽  
Jingyuan Chen
Keyword(s):  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Double Layer ◽  
Salt Concentration ◽  
Linear Relation ◽  
Platinum Electrode ◽  
Solvent Interaction ◽  
Solution Interface ◽  
Mechanic Calculation ◽  
Water Dipole

Variations of the double layer capacitances (DLCs) at a platinum electrode with concentrations and kinds of salts in aqueous solutions were examined in the context of facilitating orientation of solvent dipoles. With an increase in ionic concentrations, the DLCs increased by ca. a half and then kept constant at concentrations over 1 mol dm−3. This increase was classically explained in terms of the Gouy–Chapman (GC) equation combined with the Stern model. Unfortunately, measured DLCs were neither satisfied with the Stern model nor the GC theory. Our model suggests that salts destroy hydrogen bonds at the electrode–solution interface to orient water dipoles toward the external electric field. A degree of the orientation depends on the interaction energy between the salt ion and a water dipole. The statistical mechanic calculation allowed us to derive an equation for the DLC as a function of salt concentration and the interaction energy. The equation took the Langmuir-type in the relation with the concentration. The interaction energy was obtained for eight kinds of salts. The energy showed a linear relation with the interaction energy of ion–solvent for viscosity, called the B-coefficient.

scholarly journals Modeling of hydrogen bonds in molecular alanine crystals

2020 ◽  
Vol 62 (4) ◽  
pp. 57-61
Author(s):  
Tatiana G. Volkova ◽  
◽  
Aygul N. Shajayewa ◽  
Irina O. Talanova ◽  
◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Model Systems ◽  
Polymorphic Transformations ◽  
Chemical Modeling ◽  
Covalent Interaction ◽  
Significant Difference ◽  
The Difference ◽  
Distribution Of Components ◽  
Energy Components

The study of hydrogen bonds (H-bonds) in biomolecules and living systems is currently one of the most urgent tasks. Changes in the structure of molecular crystals associated with h-bond instability may affect the state of drugs due to uncontrolled polymorphic transformations. Quantum chemical modeling is one of the methods for studying the nature and determining the strength of hydrogen bonds. The interaction energy in molecular alanine crystals and its decomposition were calculated using the Morokuma method (HF/6-31G (PC GAMESS)). The estimation of such energy components as electrostatic, repulsion exchange, polarization, charge transfer, and mixing is given. It is shown that for four model systems, the electrostatic component makes the main contribution to the interaction energy, and the trend of distribution of components  Е by values is the same for them. For the two model systems, there is a significant difference from the others both in the amount of interaction energy and in the distribution of individual energy components. The difference in the interaction energy and in the values of its components indicates a difference in the nature of hydrogen bonds in the studied associate. In four models, the H-bond system is the result of electrostatic interaction (Ees and Ect are respectively equal to -41.0 and -6.84 kcal/mol), and in two-the proportion of covalent interaction is significantly greater (Ees = -7.94 kcal/mol and Ect = -3.92 kcal/mol). The comparison of data allows us to conclude that there are three types of hydrogen bonds in the molecular crystal of alanine that differ from each other in energy characteristics.

Carbonyl–Carbonyl Interactions can be Competitive with Hydrogen Bonds

1998 ◽  
Vol 54 (3) ◽  
pp. 320-329 ◽  
Author(s):  
F. H. Allen ◽  
C. A. Baalham ◽  
J. P. M. Lommerse ◽  
P. R. Raithby
Keyword(s):  
Hydrogen Bonds ◽  
Ab Initio ◽  
Interaction Energy ◽  
Molecular Orbital ◽  
Crystallographic Data ◽  
Basis Sets ◽  
Attractive Interaction ◽  
Molecular Orbital Calculations ◽  
Dimer Model ◽  
Intermolecular Perturbation Theory

The geometries and attractive energies of carbonyl–carbonyl interactions have been investigated using crystallographic data and ab initio molecular-orbital calculations. Analysis of crystallographic data for 9049 carbon-substituted >C=O groups shows that 1328 (15%) form contacts with other >C=O groups, in which d(C...O) < 3.6 Å. Three common interaction motifs are observed in crystal structures: (a) a slightly sheared antiparallel motif (650 instances) involving a pair of short C...O interactions, together with (b) a perpendicular motif (116 instances) and (c) a highly sheared parallel motif (130 instances), which both involve a single short C...O interaction. Together, these motifs account for 945 (71%) of the observed interactions. Ab-initio-based molecular-orbital calculations (6-31G** basis sets), using intermolecular perturbation theory (IMPT) applied to a bis-propanone dimer model, yield an attractive interaction energy of −22.3 kJ mol−1 for a perfect rectangular antiparallel dimer having both d(C...O) = 3.02 Å and attractive energies < −20 kJ mol−1 over the d(C...O) range 2.92–3.32 Å. These energies are comparable to those of medium-strength hydrogen bonds. The IMPT calculations indicate a slight shearing of the antiparallel motif with increasing d(C...O). For the perpendicular motif, IMPT yields an attractive interaction energy of −7.6 kJ mol−1, comparable in strength to a C—H...O hydrogen bond and with the single d(C...O) again at 3.02 Å.

scholarly journals On the Relationship between Hydrogen Bond Strength and the Formation Energy in Resonance-Assisted Hydrogen Bonds

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4196
Author(s):  
José Manuel Guevara-Vela ◽  
Miguel Gallegos ◽  
Mónica A. Valentín-Rodríguez ◽  
Aurora Costales ◽  
Tomás Rocha-Rinza ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Interaction Energy ◽  
Formation Energy ◽  
Function Analysis ◽  
Computational Cost ◽  
Intramolecular Interactions ◽  
Hydrogen Bond Interaction ◽  
Wave Function Analysis ◽  
The Relationship

Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely −F, −Cl, −Br, −CF3, −N(CH3)2, −OCH3, −NHCOCH3 on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the π skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions.

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