𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Conformational stability and flexibility of the ala dipeptide in free space and water: Monte Carlo computer simulation studies

✍ Scribed by G. Ravishanker; M. Mezei; D. L. Beveridge

Publisher
John Wiley and Sons
Year
1986
Tongue
English
Weight
401 KB
Volume
7
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

determinations of the intramolecular thermodynamics of the Ala dipeptide in the C7, Cs, C X ~, and PI1 conformations are reported. The calculations are carried out in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of the atomic displacements. The free energy of transition from C7 to Cs, ( Y R , and PI1 are found to be endergonic and dominated by the intrinsic energy of disrupting the intramolecular hydrogen bond in the C7 conformation. These results are combined with previous estimates of the free energy of hydration of the Ala dipeptide in water computed from liquid state Monte Carlo simulations using the probability ratio method. The net free energy of C7, aR , and PII are found to be similar, and it is thus reasonable to expect that all three forms are thermally populated at ambient temperature. The intermolecular carbonyl-water hydrogen bond in CS, CXR , and PII competes successfully with the intramolecular N -H * . * 0 -C interaction in C7.

📜 SIMILAR VOLUMES

AB INITIO MO AND MONTE CARLO SIMULATION
AB INITIO MO AND MONTE CARLO SIMULATION STUDY ON THE CONFORMATION OF L-ALANINE ZWITTERION IN AQUEOUS SOLUTION
✍ Osamu Kikuchi; Toshio Watanabe; Yasushi Ogawa; Hideto Takase; Ohgi Takahashi 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 190 KB 👁 2 views

The conformation of the L-alanine zwitterion (ALAZ) in aqueous solution was examined by an ab initio MO method including the solvent effect with the generalized Born (GB) equation. The geometry optimization with the 6-31++G\* basis set gave the (, ) = (80, 8) conformation as the most stable conforma

Hydrodynamic study of flexibility in imm
Hydrodynamic study of flexibility in immunoglobulin igG1 using Brownian dynamics and the Monte Carlo simulations of a simple model
✍ F. G. Díaz; A. Iniesta; J. García De La Torre 📂 Article 📅 1990 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 563 KB

## Abstract A simple bead model is proposed for the antibody molecule immunoglobulin IgG1. The partial flexibility of the hinge is represented by a quadratic potential associated to the angles between arms. Conformational and hydrodynamic properties are calculated using Monte Carlo (rigid‐body) and

A Monte Carlo simulation of free energy
A Monte Carlo simulation of free energy relationships for the electron transfer reaction between Fe+ and Fe2+ in water
✍ Angels González-Lafont; José M. Lluch; Antonio Oliva; Juan Bertrán 📂 Article 📅 1991 🏛 John Wiley and Sons 🌐 English ⚖ 555 KB

A free energy barrier AF+ = 174.2 kJ/mol for the self-exchange electron transfer reaction model Fe+/Fe2+ in water has been calculated by combining Monte Carlo simulations and the statistical perturbation theory. We have shown that, even for those electron transfer reactions that present a very high

DFT study and Monte Carlo simulation on
DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water
✍ Ying Xue; Chan Kyung Kim; Yong Guo; Dai Qian Xie; Guo Sen Yan 📂 Article 📅 2005 🏛 John Wiley and Sons 🌐 English ⚖ 553 KB

## Abstract Density functional theory (DFT) and Monte Carlo (MC) simulation with free energy perturbation (FEP) techniques have been used to study the tautomeric proton transfer reaction of 2‐amino‐2‐oxazoline, 2‐amino‐2‐thiazoline, and 2‐amino‐2‐imidazoline in the gas phase and in water. Two react