A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: ...

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within t...

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

There is a special reason for reviewing this book at this time: it is the 50th edition of a compendium that is known and used frequently in most chemical and physical laboratories in many parts of the world. Surely, a publication that has been published for 56 years, withstanding the vagaries of science in this century, must have had something to offer. There is another reason: while the book is a standard fixture in most chemical and physical laboratories, including those in medical centers, it is not as frequently seen in the laboratories of physician's offices (those either in solo or group practice). I believe that the Handbook can be useful in those laboratories. One of the reasons, among others, is that the various basic items of information it offers may be helpful in new tests, either physical or chemical, which are continuously being published. The basic information may relate

Handbook of Chemistry and Physics

The Stability of Cyclodextrin Complexes in Solution.

저작근 근전도에 관한 정상교합자와 ii급 부정교합자의 비교 연구

The dipole potential of phospholipid membranes and methods for its detection.

Influence of Anions and Cations on the Dipole Potential of Phosphatidylcholine Vesicles: A Basis for the Hofmeister Effect

Publisher Summary This chapter provides an overview of the inclusion complexes of cyclomalto-oligosaccharides (cyclodextrins). Inclusion complexes are chemical species consisting of two or more associated molecules in which one of the molecules—the “host”—forms or possesses a cavity into which it can admit a “guest” molecule, resulting in a stable association without formation of any covalent bonds. Secondary forces are alone responsible for the maintenance of the integrity of all inclusion complexes. One of the most important properties of the cyclodextrins is their ability to form complexes with a variety of organic and inorganic compounds. 1 H-Nuclear magnetic resonance (NMR) spectroscopy provided the first direct evidence of inclusion within the cyclodextrin cavity in solution. Using aromatic “guest” molecules, it was found that, on the addition of the guest, the resonances of the hydrogen atoms of the cyclodextrin situated on the inside of the cavity were shifted significantly upfield due to shielding by the aromatic guest. This chapter discusses determination of the structure of the cyclodextrins, and formation of the cyclodextrins from starch. It provides details about formation of inclusion complexes, detection of complex formation, and thermodynamics of complex formation. Kinetics of complex formation is also explained in the chapter.

Inclusion Complexes of the Cyclomalto-Oligosaccharides (Cyclodextrins)

Optical detection of membrane dipole potential: avoidance of fluidity and dye-induced effects.

https://www.cell.com/biophysj/pdf/S0006-3495(06)72586-3.pdf

Ronald J. Clarke

Papers

The dipole potential of phospholipid membranes and methods for its detection.

Influence of Anions and Cations on the Dipole Potential of Phosphatidylcholine Vesicles: A Basis for the Hofmeister Effect

Inclusion Complexes of the Cyclomalto-Oligosaccharides (Cyclodextrins)

Optical detection of membrane dipole potential: avoidance of fluidity and dye-induced effects.

Cholesterol effect on the dipole potential of lipid membranes.