Generation of OPLS-like charges from molecular electrostatic potential using restraints

A new method for generating atom-centered charges for use in condensed phase computer simulations is presented, which is based on a restrained electrostatic potential (RESP) procedure. Charges are calculated from a least-squares fit to the quantum mechanical electrostatic potential with a restraint applied to reduce their magnitude. The restraint developed here offers advantages over that used in RESP. The magnitude of the restraint is optimized to yield charges as close to the equivalent OPLS values as possible while still reproducing the molecule's electrostatic potential. A cross-validation analysis is used to show that the restraint is insensitive to the selection of OPLS molecules from which it is derived. Thus, with this method, OPLS-like charges may be produced from the electrostatic potential for atom types not in the OPLS force field. In addition, the restraint is shown to reduce the conformational dependence of the charges. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 483–498, 1999     

Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters

Partition coefficients quantify a molecule’s distribution between two immiscible liquid phases. While there are many methods to compute them, there is not yet a method based on the free energy of each system in terms of energy and entropy, where entropy depends on the probability distribution of all quantum states of the system. Here we test a method in this class called Energy Entropy Multiscale Cell Correlation (EE-MCC) for the calculation of octanol–water logP values for 22 N-acyl sulfonamides in the SAMPL7 Physical Properties Challenge (Statistical Assessment of the Modelling of Proteins and Ligands). EE-MCC logP values have a mean error of 1.8 logP units versus experiment and a standard error of the mean of 1.0 logP units for three separate calculations. These errors are primarily due to getting sufficiently converged energies to give accurate differences of large numbers, particularly for the large-molecule solvent octanol. However, this is also an issue for entropy, and approximations in the force field and MCC theory also contribute to the error. Unique to MCC is that it explains the entropy contributions over all the degrees of freedom of all molecules in the system. A gain in orientational entropy of water is the main favourable entropic contribution, supported by small gains in solute vibrational and orientational entropy but offset by unfavourable changes in the orientational entropy of octanol, the vibrational entropy of both solvents, and the positional and conformational entropy of the solute.

     

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy–entropy (EE) method to calculate the host–guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host–guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol^?1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.

     

Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation

Our previous molecular dynamics simulation (10 ns) of mouse acetylcholinesterase (EC 3.1.1.7) revealed complex fluctuation of the enzyme active site gorge. Now we report a 5-ns simulation of acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to the gorge entrance of acetylcholinesterase with excellent complementarity and many polar and hydrophobic interactions. In this simulation of the protein-protein complex, where fasciculin 2 appears to sterically block access of ligands to the gorge, again we observe a two-peaked probability distribution of the gorge width. When fasciculin is present, the gorge width distribution is altered such that the gorge is more likely to be narrow. Moreover, there are large increases in the opening of alternative passages, namely, the side door (near Thr 75) and the back door (near Tyr 449). Finally, the catalytic triad arrangement in the acetylcholinesterase active site is disrupted with fasciculin bound. These data support that, in addition to the steric obstruction seen in the crystal structure, fasciculin may inhibit acetylcholinesterase by combined allosteric and dynamical means. Additional data from these simulations can be found at http://mccammon.ucsd.edu/.     

A host-guest optical sensor for aliphatic amines based on lipophilic cyclodextrin

A host-guest optical sensor for the determination of aliphatic amines as exemplified by octylamine is proposed. It is based on the reversible fluorescence enhancement of heptakis(2,6-di-O-isobutyl)-β-cyclodextrin(DOB-β-CD) hosting tetraphenylporphyrin (TPP) immobilized in poly(vinyl chloride) (PVC) membrane by aliphatic amine extracted from aqueous phase into membrane phase. The optimum membrane contained 1.15 wt % TPP, 6.15 wt % DOB-β-CD as sensing reagent and other membrane materials. The fluorescence enhancement of the membrane resulted from the formation of a stable three-component complex among DOB-β-CD, TPP, and aliphatic amines. With the optimum conditions described, the fluorescence response of the sensor to octylamine shows a good correlation with the theoretically derived equation in the range 1.0 × 10^–6 to 8.0 × 10^–4 mol/L. The response characteristics including reversibility, response time, reproducibility and lifetime and selectivity of this optical device are also discussed in detail. This sensor has also been applied for the determination of octylamine in water samples containing interferents with satisfactory recovery. Received: 21 November 1999 / Revised: 10 January 2000 / Accepted: 15 January 2000     

Long-range hydrogen-bond structure in aqueous solutions and the vapor-water interface

There is a considerable disagreement about the extent to which solutes perturb water structure. On the one hand, studies that analyse structure directly only show local structuring in a solute's first and possibly second hydration shells. On the other hand, thermodynamic and kinetic data imply indirectly that structuring occurs much further away. Here, the hydrogen-bond structure of water around halide anions, alkali cations, noble-gas solutes, and at the vapor-water interface is examined using molecular dynamics simulations. In addition to the expected perturbation in the first hydration shell, deviations from bulk behavior are observed at longer range in the rest of the simulation box. In particular, at the longer range, there is an excess of acceptors around halide anions, an excess of donors around alkali cations, weakly enhanced tetrahedrality and an oscillating excess and deficiency of donors and acceptors around noble-gas solutes, and enhanced tetrahedrality at the vapor-water interface. The structuring compensates for the short-range perturbation in water-water hydrogen bonds induced by the solute. Rather than being confined close to the solute, it is spread over as many water molecules as possible, presumably to minimize the perturbation to each water molecule.