Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

Yan, Xiufen; Jiang, Nan; Ma, Jing

doi:10.1007/s11426-009-0273-y

Cited by 4 publications

(2 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The general idea in the explicit polarizable model is that, the partial charges of a molecule were not fixed but were changeable in response to the local condition represented with background point charges 40 – 42 . In contrast, the partial charge in the implicit polarizable model was fixed, but the parameterization was carried out to take the surrounding environment into consideration by using the continuum medium model, and ensemble average of the trajectory (obtained from MD simulations by using conventional force field) was used to account for the redistribution of molecular dipole (Supplementary Schemes 1 and 2).…”

Section: Computational Detailsmentioning

confidence: 99%

Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane

Zhu

et al. 2017

Sci Rep

Self Cite

View full text Add to dashboard Cite

Partition and transportation of drug in the plasma membrane of a mammalian cell are the prerequisite for its function on target protein. Therefore, comprehensive understanding of the physicochemical properties and mechanism behind these complex phenomena is crucial in pharmaceutical research. By using the state-of-art molecular simulations with polarization effect implicitly or explicitly included, we studied the permeation behavior of 2-aminoethoxydiphenyl borate (2-APB), a broad-spectrum modulator for a number of membrane proteins. We showed that the protonation state and therefore the polarity of the drug is critical for its partition, and that the drug is likely to switch between different protonation states along its permeation pathway. By changing the degrees of freedom, protonation further affects the thermodynamic of the permeation pathway of 2-APB, leading to different entropic contributions. A survey on 54 analog structures with similar backbone to 2-APB showed that delicate balance between entropy and polarity plays an important role in drugs’ potency.

show abstract

Section: Computational Detailsmentioning

confidence: 99%

Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane

Zhu

et al. 2017

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Treating the polarization effect using variable electrostatic parameters has been validated in many systems, such as the energy and structure prediction of charged species, , solvent effects on conformational changes, ,− charge-transport properties of metal phthalocyanines and analogues, understanding of optical changes ,,− and molecular behaviors ,, under different stimulus, and so on. For example, in the situation of aqueous solution, cooperative HB and long-range electrostatic together with polarization interactions play key roles in understanding the photostability and photoreaction of nucleobases .…”

Section: Polarization and Entropy Effects In Log P Predictionsmentioning

confidence: 99%

Treating Polarization Effects in Charged and Polar Bio-Molecules Through Variable Electrostatic Parameters

Zhu

et al. 2023

J. Chem. Theory Comput.

Self Cite

View full text Add to dashboard Cite

Polarization plays important roles in charged and hydrogen bonding containing systems. Much effort ranging from the construction of physics-based models to quantum mechanism (QM)-based and machine learning (ML)-assisted models have been devoted to incorporating the polarization effect into the conventional force fields at different levels, such as atomic and coarse grained (CG). The application of polarizable force fields or polarization models was limited by two aspects, namely, computational cost and transferability. Different from physics-based models, no predetermining parameters were required in the QM-based approaches. Taking advantage of both the accuracy of QM calculations and efficiency of molecular mechanism (MM) and ML, polarization effects could be treated more efficiently while maintaining the QM accuracy. The computational cost could be reduced with variable electrostatic parameters, such as the charge, dipole, and electronic dielectric constant with the help of linear scaling fragmentation-based QM calculations and ML models. Polarization and entropy effects on the prediction of partition coefficient of druglike molecules are demonstrated by using both explicit or implicit all-atom molecular dynamics simulations and machine learning-assisted models. Directions and challenges for future development are also envisioned.

show abstract

Can a Proton be Encapsulated in Tetraamido/Diamino Quaternized Macrocycles in Aqueous Solution and Electric Field?

Jiang¹,

Ma²

2011

ChemPhysChem

Self Cite

View full text Add to dashboard Cite

The proton-binding behavior of solvated tetraamido/diamino quaternized macrocyclic compounds with rigid phenyl and flexible phenyl bridges in the absence or presence of an external electric field is investigated by molecular dynamics simulation. The proton can be held through H-bonding interactions with the two carbonyl oxygen atoms in macrocycles containing rigid (phenyl) and flexible (propyl) bridges. The solute-solvent H-bonding interactions cause the macrocyclic backbones to twist to different extents, depending on the different bridges. The macrocycle with the rigid phenyl linkages folds into a cuplike shape due to π-π interaction, while the propyl analogue still maintains the ellipsoidal ringlike shape with just a slight distortion. The potential energy required for proton transfer is larger in the phenyl-containing macrocycle than in the compound with propyl units. When an external electric field with a strength of 2.5 V nm(-1) is exerted along the carbonyl oxygen atoms, a difference in proton encircling is exhibited for macrocycles with rigid and flexible bridges. In contrast to encapsulation of a proton in the propyl analogue, the intermolecular solute-solvent H-bonding and intramolecular π-π stacking between the two rigid phenyl spacers leads to loss of the proton from the highly distorted cuplike macrocycle with phenyl bridges. The competition between intra- and intermolecular interactions governs the behavior of proton encircling in macrocycles.

show abstract

Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

Cited by 4 publications

References 33 publications

Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane

Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane

Treating Polarization Effects in Charged and Polar Bio-Molecules Through Variable Electrostatic Parameters

Can a Proton be Encapsulated in Tetraamido/Diamino Quaternized Macrocycles in Aqueous Solution and Electric Field?

Contact Info

Product

Resources

About