Journal of Computational Chemistry

Henchman, Richard H.; Essex, Jonathan W.

doi: 10.1002/(SICI)1096-987X(19990415)20:5<499::AID-JCC3>3.0.CO;2-Jpmid: N/A

To determine the reliability of the restrained electrostatic potential derived (REPD) charge method described in a companion article, the free energies of hydration of 22 simple organic molecules were calculated using free energy perturbations and linear response theory. Of the four charge sets examined using the free energy perturbation method, REPD/6–31+G* charges gave the closest agreement with the experiment, followed by conventional EPD charges derived at the 6–31G* level. The average absolute error for the former was 2.9 kJ mol−1 and for the latter was 3.5 kJ mol−1. The linear response method was then used to predict free energies of hydration based on the average van der Waals and electrostatic solute‐solvent energies obtained from Monte Carlo computer simulations and solvent accessible surface areas. Use of the three parameter relationship gave a good agreement with the experiment. However, a number of simpler fitting functions were also examined and found to be only marginally less reliable. A careful statistical analysis of the linear response method is therefore needed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 499–510, 1999

Santamaria, R.; Charro, E.; Zacarías, A.; Castro, M.

doi: 10.1002/(SICI)1096-987X(19990415)20:5<511::AID-JCC4>3.0.CO;2-8pmid: N/A

The vibrational spectra of the nucleic acid bases adenine, thymine, guanine, and cytosine are calculated in the frame of density functional theory (DFT). In particular we use the Kohn–Sham scheme with gradient corrections for exchange and correlation to determine normal modes, frequencies, and intensities. The DFT results are found to be in good agreement with the experiment. Our computations provide assignments for IR, Raman, and neutron inelastic scattering spectroscopies; yield characteristic vibrational fingerprints of each compound for its identification in larger systems; and show general vibrational trends of nucleic acids. The Kohn–Sham scheme is further applied to obtain the spectra of the Watson–Crick pairs adenine‐thymine and guanine‐cytosine. A large number of monomeric vibrations are recognized in dimers; characteristic vibrations of pairs, which are mainly attributed to hydrogen bridges, are quantified according to changes in normal modes and frequency shifts. Binding and zero‐point vibrational energies are analyzed to establish the stability of the complexes and discuss the quality of the energetic calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 511–530, 1999

Smondyrev, Alexander M.; Berkowitz, Max L.

doi: 10.1002/(SICI)1096-987X(19990415)20:5<531::AID-JCC5>3.0.CO;2-3pmid: N/A

We refined the united atom field for the simulations of phospholipid membranes. To validate this potential we performed 1000‐ps constant pressure simulation of a dipalmitoylphosphatidicholine (DPPC) bilayer at T=50° C. The average area per head group (61.6±0.6) Å2 obtained in our simulation agrees well with the measured one of (62.9±1.3) Å2. The calculated SCD order parameters for the Sn‐2 hydrocarbon tail also display a good agreement with the experiment. The conformations of head groups in our simulations of the liquid crystal phase are different than the ones observed in the crystal structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20, 531–545, 1999

Sun, Ying‐Chieh; Yang, Shu‐Fen; Hwang, I‐Lung; Wu, Tzu‐Hsien

doi: 10.1002/(SICI)1096-987X(19990415)20:5<546::AID-JCC6>3.0.CO;2-Lpmid: N/A

Molecular dynamics simulation of a small, basic, all β‐sheet cardiotoxin, CTX II, from Taiwan cobra venom, with proper treatment of long‐range electrostatic interactions, was carried out to examine the backbone mobility of CTX II in solution and aid in interpretation of order parameters of CαH bonds obtained from NMR experiments based on the Lipari–Szabo theory. The calculated order parameters of CαH bonds and B‐factors of CTX II in solution were compared with NMR‐derived backbone order parameters and the crystal structure data, respectively. An overall qualitative agreement was obtained and, quantitatively, the calculated values and experimental results of many residues were also in good agreement. The discrepancies between the results computed herein and the experimental values, physical bases, and plausible biological functions are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 546–562, 1999