Advertisement

Topics

Infinite dilution activity coefficients as constraints for force field parameterization and method development.

08:00 EDT 2nd April 2019 | BioPortfolio

Summary of "Infinite dilution activity coefficients as constraints for force field parameterization and method development."

Molecular simulations see widespread use in calculating various physical properties of interest, with a key goal being predictive molecular design. These simulations, including molecular dynamics (MD) simulations, begin with a underlying energy model or force field and then, based on this model, use simulations to compute properties of interest. However, one of the most significant challenges in molecular dynamics and modeling studies is ensuring that the force field is a good enough approximation of the underlying physics that computed quantities can be used to reproduce experimental properties with the desired level of accuracy. Parameterization of force fields depend on various experimental properties including as much of the chemistry of interest as possible. Physicochemical properties measurable in a relatively straightforward manner are particularly interesting for developers. Such properties can be measured for a relatively diverse chemical set and used to expand the parameterization dataset as needed. Here, we examine infinite dilution activity coefficients (IDACs) which are experimental quantities that can play this role. We retrieved 237 empirical IDACs from NIST's ThermoML, a database of measured thermodynamic properties, and we estimated the corresponding values using solvation free energy calculations. We found that calculated IDAC values correlate strongly with experiment. Specifically, the natural logarithm of calculated and experimental IDAC values shows a Pearson correlation coefficient of 0.85+/-0.02. The calculated IDAC values allow us to identify strengths and potential weaknesses of force field parameters for specific functional groups in solutes and solvents, suggesting these may be a valuable source of data for force field parameterization, capturing some of the same type of information as hydration and solvation free energies and thus potentially providing a useful new source of experimental data.

Affiliation

Journal Details

This article was published in the following journal.

Name: Journal of chemical theory and computation
ISSN: 1549-9626
Pages:

Links

DeepDyve research library

PubMed Articles [17835 Associated PubMed Articles listed on BioPortfolio]

Ab initio derived force fields for Zeolitic Imidazolate Frameworks: MOF-FF for ZIFs.

In this paper we parameterized in a consistent way a new force field for a range of different zeolitic imidazolate framework systems (ZIF-8, IF-8(H), ZIF-8(Br) and ZIF-8(Cl)), extending the MOF-FF par...

Determination of gas-liquid partition coefficients of several organic solutes in trihexyl (tetradecyl) phosphonium dicyanamide using capillary gas chromatography columns.

We report here gas-liquid partition constants and activity coefficients for thirty-seven volatile organic solutes in ionic liquid trihexyl(tetradecyl)phosphonium dicyanamide measured by gas-liquid chr...

Force field parameterization from the Hirshfeld molecular electronic density.

The Hirshfeld charges are linearly increased to reproduce the experimental dielectric constant of 10 polar solvents having values between 13 (pyridine) and 182 (N-methylformamide). The OPLS/AA force f...

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.

Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chemical space by addressing limitations in chemotype transferabil...

Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Forcefield and Parametrization of Au-S Bonds.

The interaction of amino acids with metal electrodes plays a crucial role in bioelectrochemistry and the emerging field of bionanoelectronics. Here we present benchmark calculations of the adsorption ...

Clinical Trials [4717 Associated Clinical Trials listed on BioPortfolio]

Comparison of Post- and Pre-dilutional Hemodiafiltration in Hemodialysis Patients

Hemodiafiltration (HDF) is a choice of treatment modalities for patients with end-stage renal disease. Hemodiafiltration, combining diffusion and convection, may increase removal of large ...

The Effect of BMI on Hand Grip Force in Healthy Adults

This study will be conducted to investigate the effect of BMI on hand grip force in healthy subjects. The participants in this study will be 90 healthy subjects with right dominant lower l...

Fibromyalgia and Specific Physical Activity

Fibromyalgia is a common, expensive and controversial condition, one of whose origins would be central nervous system sensitization to pain. Usual treatment consists of multimodal care in...

Evaluation of Handheld Colonoscopy Force Monitor by Expert Endoscopists in the Performance of Colonoscopy

The purpose of this study is to evaluate a handheld Colonoscopy Force Monitor(CFM™), a push-pull force and torque measuring device, that grips the shaft of the colonoscope and wirelessly...

N-Force Screws Augmented With N-Force Blue in Hip Fractures

The objective of this prospective study is to confirm safety and performance of N-Force Screws augmented with N-Force Blue applied in intracapsular proximal femur fracture treatment.

Medical and Biotech [MESH] Definitions

The rotational force about an axis that is equal to the product of a force times the distance from the axis where the force is applied.

Condition in which no acceleration, whether due to gravity or any other force, can be detected by an observer within a system. It also means the absence of weight or the absence of the force of gravity acting on a body. Microgravity, gravitational force between 0 and 10 -6 g, is included here. (From NASA Thesaurus, 1988)

The measurement of infection-blocking titer of ANTISERA by testing a series of dilutions for a given virus-antiserum interaction end-point, which is generally the dilution at which tissue cultures inoculated with the serum-virus mixtures demonstrate cytopathology (CPE) or the dilution at which 50% of test animals injected with serum-virus mixtures show infectivity (ID50) or die (LD50).

Method of measuring the bactericidal activity contained in a patient's serum as a result of antimicrobial therapy. It is used to monitor the therapy in BACTERIAL ENDOCARDITIS; OSTEOMYELITIS and other serious bacterial infections. As commonly performed, the test is a variation of the broth dilution test. This test needs to be distinguished from testing of the naturally occurring BLOOD BACTERICIDAL ACTIVITY.

The force applied by the masticatory muscles in dental occlusion.

Advertisement
Quick Search
Advertisement
Advertisement

 


DeepDyve research library

Searches Linking to this Article