QM/MM Model Study on Properties and Structure of Some Antibiotics in Gas Phase: Comparison of Energy and NMR Chemical Shift

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M. Monajjemi^1*, M. Heshmata², and H. H. Haeria³

¹Science and Research Branch, Islamic Azad University, P.O. Box: 14515-775, Tehran, Iran; E-mail: m_Monajjemi@yahoo.com

²Islamshahr Branch, Islamic Azad University Tehran, Iran

³Tehran Shargh Branch (ghyamdasht), Islamic Azad University, Tehran, Iran

^* To whom correspondence should be addressed.

Received January 9, 2005; Revision received April 18, 2005

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The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.

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KEY WORDS: quantum mechanics, molecular mechanics, ab initio calculations, antibiotics

DOI: 10.1134/S0006297906130190

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