Molecular modelling of cation–π interactions

Lamoureux, Guillaume; Orabi, Esam A.

doi:10.1080/08927022.2012.696640

Cited by 25 publications

(54 citation statements)

References 207 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…47,48 In light of the overall good performance of the models, it should be noted that, while the ion−ammonia model is adjusted to reproduce the properties of the ion− ammonia dimer, the ion−water, 39 ammonia−ammonia, 44 and ammonia−water 44 models have not been further adjusted. This suggests that the models can be reliably used to investigate properties of the ion solvated in liquid and aqueous ammonia solutions.…”

Section: Journal Of Chemical Theory and Computationmentioning

confidence: 99%

Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia

Orabi

Lamoureux

2013

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

A polarizable potential model for M(+)-NH3 interactions (M(+) = Li(+), Na(+), K(+), Rb(+), Cs(+)) is optimized based on the ab initio properties of the ion-ammonia dimers calculated at the MP2 level of theory. The optimized model reproduces the ab initio binding energies of M(+)(NH3)n (n = 2-4) and M(+)(NH3)n(H2O)m (n, m = 1-3 and n + m ≤ 4) clusters and gives relative solvation free energies in liquid ammonia in good agreement with experimental data, without further adjustments. It also reproduces binding cooperativity in ion-ammonia and ion-ammonia-water clusters. The model is used in molecular dynamics simulations of isolated ions in liquid ammonia and in aqueous ammonia solutions with various ammonia molar fractions (0.0 ≤ xNH3 ≤ 1.0). Simulations in liquid ammonia show coordination numbers of 4.0 for Li(+), 5.3 for Na(+), 6.1 for K(+), 6.7 for Rb(+), and 7.7 for Cs(+), in very good agreement with available experimental results. Simulations of ions in aqueous ammonia show preferential solvation by water in their first solvation shells and preferential solvation by ammonia in their second shells. Potentials of mean force are calculated between each ion and NH3 in liquid water, and between each ion and H2O in liquid ammonia. The results suggest that, in liquid water, Li(+) and Na(+) bind NH3 in their second solvation shells only, while Cs(+) binds NH3 in its first solvation shell only (K(+) and Rb(+) ions show only weak affinity for NH3 in water). In liquid ammonia, the ions bind H2O in their first solvation shells with an affinity following the trend Li(+) > Na(+) > K(+) ≈ Rb(+) > Cs(+).

show abstract

Section: Journal Of Chemical Theory and Computationmentioning

confidence: 99%

Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia

Orabi

Lamoureux

2013

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Competing solute‐solvent interactions weaken the affinity between solute molecules in solution . For example, the salt bridge formed between acetate and methylammonium has a binding energy of −2.2 kcal mol −1 in water vs. −125.5 kcal mol −1 in the gas phase, and the affinity of monovalent cations (Li + , Na + , K + , and NH 4 + ) for benzene decreases from a maximum of −35 kcal mol −1 in the gas phase to a maximum of −1.4 kcal mol −1 in water …”

Section: Resultsmentioning

confidence: 99%

“…The ten lowest energy points from each PEC provide a total of 20 points ( k ) for optimization of each model. The coordinates of the complexes are fixed at their ab initio values and the LJ parameters are optimized to minimize χ 2 for the selected points ( k ) on the PEC:

true χ^{2} = \sum_{k} {(E_{k}^{CP} - E_{k}^{MM})}^{2} .

…”

Section: Methodsmentioning

confidence: 99%

“…Except for the interaction of H 2 O with imidazolium and 4‐methylimidazolium, the default CHARMM36 FF yields binding energies and PECs for the complexes that are in poor agreement with the ab initio MP2 values (Section 3.1). FF calibration involves optimization of pair‐specific LJ parameters (introduced via the NBFIX facility of CHARMM) with the ab initio PECs as targets . Two different PECs are used for each pair to ensure that the optimized FFs perform well for various binding conformations.…”

Section: Methodsmentioning

confidence: 99%

“…The CHARMM FF underestimates the binding energy of MeSH‐benzene calculated at the MP2/6‐311G(2d,p) level and corrected for BSSE, while the CHARMM, AMBER, OPLS, and MM3 FFs underestimate the equilibrium S‐ring‐centroid distance in H 2 S‐benzene and overestimate the binding energy (with the exception of MM3) of the complex . These studies highlight the need for FF calibration in studying S‐aromatic interactions, adding to the fact that FF calibration is important for interactions involving ions . Here, we calibrate the CHARMM36 FF for the S‐aromatic‐ion, the H 2 O‐aromatic‐ion, and S‐H 2 O interactions based on the potential energy curve (PEC) calculated for each complex at the MP2(full)/6‐311++G(d,p) level and corrected for BSSE.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Sulfur‐Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer

Orabi

English

2016

Israel Journal of Chemistry

Self Cite

View full text Add to dashboard Cite

Cys and Met interactions with aromatic residues stabilize proteins and also may alter their redox properties. We establish here how ionization of the aromatic groups may influence such interactions. Specifically, ab initio quantum mechanical calculations at the MP2(full)/6‐311++G(d,p) level of theory are performed on the gas‐phase complexes of hydrogen sulfide, methanethiol (MeSH), and dimethyl sulfide (Me2S), with the imidazolium and phenolate ions and their 4‐methylated forms. The S‐ligands bind the aromatic ions more tightly than the neutral species, preferentially edge‐on to imidazolium and en‐face to phenolate. Charge transfer occurs within the complexes, which will impact the redox properties of the interacting moieties. The CHARMM36 force field, calibrated using potential energy curves generated at the same level of theory, yields affinities (kcal mol−1) in water of −4.3 and −3.1 for MeSH‐ and Me2S‐imidazolium, and −2.9 and −2.1 for the phenolate complexes. En‐face binding is preferred in water, with an equilibrium S‐ring‐centroid separation of ∼4 Å, which increases to > 5 Å in Me2S‐phenolate. Their high gas‐phase and aqueous stability suggests that S‐aromatic‐ion complexes are an important determinant of protein behavior. Since the uncalibrated CHARMM36 force field predicts very weak S‐aromatic‐ion binding in water (−0.3 to −0.6 kcal mol−1) and in the gas phase, the optimized parameters should be used to obtain a reliable description of these interactions in proteins.

show abstract

Cation–π Interactions in Graphene‐Containing Systems for Water Treatment and Beyond

2020

View full text Add to dashboard Cite

was also recognized. [2] In addition to these forces, one intriguing noncovalent interaction: cation-π interaction, has emerged as an intermolecular force of great significance in chemistry, biology, and materials science. [3] The cation-π interactions basically refers to the interplay between cations and the π electron cloud of an aromatic system. It plays a great role in biological systems for molecular recognition, protein-protein interactions, and the maintenance of macromolecular structures. It also occurs in protein-ligand interactions and protein-DNA complexes. In structural biology, the positively charged amino acids interact with aromatic amino acids, which contribute to the formation of complex protein structures. The amide NHs are in close contact with the aromatic ring of another amino acid in the protein crystal structures. [4] The cation-π interactions are of great importance to protein stability. There is at least one intermolecular cation-π interaction in half of proteins and one third of homodimers, [5] making significant contributions to the tertiary and quaternary protein structures caused by protein folding. In addition, metallic cations, such as Na + , K + , Cu 2+ , Fe 2+ , Ca 2+ , exist in many enzymes. Their interactions with the π systems in protein structures cannot be ignored. In molecular neurobiology, many studies have proved that receptors bind the neurotransmitters through cation-π interactions. [6] The cation-π interaction is electrostatic in nature because the major contributions arise from the electrostatic attractions between cations and the quadrupole moment of the aromatics. [7] As a result, the strength of cation-π interactions can be the strongest among the noncovalent interactions, several times greater than others. It can also be regulated to be weak, depending on the type of cations and the nature of the π system. The adjustability of cation-π interaction offers a potential strategy to modify the neighboring environment where it is involved.Graphene, a 2D carbon network, with carbon atoms jointed together in a hexagonal honeycomb matrix, can be taken as a novel aromatic macromolecule from certain points of view. The unique structure endows it with excellent physicochemical, electronic, optical, thermal, and mechanical properties, leading to its potential applications in broad fields. [8] The interplay between cations and the delocalized polarizable π electrons of graphene, would alter the intrinsic characteristics of graphene-based structures and impart influences on the performance of graphene-based devices.Cation-π interactions are common in nature, especially in organisms. Their profound influences in chemistry, physics, and biology have been continuously investigated since they were discovered in 1981. However, the importance of cation-π interactions in materials science, regarding carbonaceous nanomaterials, has just been realized. The interplay between cations and delocalized polarizable π electrons of graphene would bring about significant changes to the intrinsic...

show abstract

Molecular modelling of cation–π interactions

Cited by 25 publications

References 207 publications

Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia

Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia

Sulfur‐Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer

Cation–π Interactions in Graphene‐Containing Systems for Water Treatment and Beyond

Contact Info

Product

Resources

About