✦ LIBER ✦

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

✍ Scribed by Alessandra Villa; Alan E. Mark

Publisher: John Wiley and Sons
Year: 2002
Tongue: English
Weight: 102 KB
Volume: 23
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.10052

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations using molecular dynamics simulations. The calculations show that while the force field reproduces the experimental solvation free energies of nonpolar analogs with reasonable accuracy the solvation free energies of polar analogs in water are systematically overestimated (too positive). The dependence of the calculated free energies on the atomic partial charges was also studied. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 548–553, 2002; DOI 10.1002/jcc.10052

📜 SIMILAR VOLUMES

Electrostatic solvation free energy of a

Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water

✍ Bin Lin; B. Montgomery Pettitt 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 303 KB

## Abstract Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson‐Boltzmann (PB), and linear response approximation (LRA)

Calculation of the water–cyclohexane tra

Calculation of the water–cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field

✍ Justin L. MacCallum; D. Peter Tieleman 📂 Article 📅 2003 🏛 John Wiley and Sons 🌐 English ⚖ 98 KB

## Abstract We calculated the free energy of solvation of the neutral analogs of 18 amino acid side‐chains (not including glycine and proline) using the OPLS all‐atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average u

Multicanonical Monte Carlo calculation o

Multicanonical Monte Carlo calculation of the free-energy map of the base–amino acid interaction

✍ Kenji Sayano; Hidetoshi Kono; M. Michael Gromiha; Akinori Sarai 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 385 KB 👁 2 views

An Efficient Method for the Synthesis of

An Efficient Method for the Synthesis of Enantiopure ω-Amino Acids with Proteinogenic Side Chain.

✍ Caterina Noula; Vassilios Loukas; George Kokotos 📂 Article 📅 2003 🏛 John Wiley and Sons ⚖ 206 KB 👁 1 views

Effect of side chains on the conformatio

Effect of side chains on the conformational energy and rotational strength of n–π* transition for some α-helical poly-α-amino acids

✍ John N. Vournakis; Johnson F. Yan; Harold A. Scheraga 📂 Article 📅 1969 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 59 KB 👁 1 views

On page 1533, in the last term of eq. (2), (alm[O) should be (alml0). On page 1538, in line 3 of the Results section, R,,\* should be Rn,\*; in the next line, RB should also be Rn,\*, and the first "in" should be "is.

ChemInform Abstract: Two Novel Amino Aci

ChemInform Abstract: Two Novel Amino Acid Derivatives Containing Side-Chain Thioamides for the Synthesis of Photoactivatable Peptides.

✍ P. SINGH; C. R. HURRELL; J. B. C. FINDLAY; C. W. G. FISHWICK 📂 Article 📅 2010 🏛 John Wiley and Sons ⚖ 28 KB 👁 2 views

Two Novel Amino Acid Derivatives Containing Side-Chain Thioamides for the Synthesis of Photoactivatable Peptides. -An efficient method to obtain novel amino acid derivatives (V), which can be introduced into peptides by solid-phase standard procedures, is described. -