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WIREs Comput Mol Sci
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Noncovalent interactions in biochemistry

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Abstract Noncovalent interactions are known to play a key role in biochemistry. The knowledge of stabilization (relative) energies and their components is very important for understanding the nature of these interactions. Accurate and benchmark data on interaction (relative) energies and structures can be obtained from coupled‐cluster with single and double and perturbative triple excitations [CCSD(T)] calculations with extended basis of atomic orbitals or even at the complete basis set limit. These methods cannot be, however, used for systems larger than about 50 atoms. In this contribution, the applicability and performance of various recently introduced wavefunction and density functional methods are examined in detail. It is shown that a very good performance by some of these methods is obtained only by introducing empirical parameters fitted mostly to CCSD(T) benchmark data. Among the methods described, special attention is paid to two techniques. First, the symmetry‐adapted perturbation technique that allows obtaining not only accurate values of total interaction energies but also their components. Results of these calculations reveal a key role of dispersion energy in stabilizing the structures of biomolecular systems. Second, the semiempirical quantum chemical parameterized model 6 method (PM6) augmented by empirical terms describing the dispersion and H‐bonding energies. The method is suitable for much extended systems having several thousands of atoms and can be thus used, e.g., in the drug design. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 3‐17 DOI: 10.1002/wcms.8 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics

Potential energy curves for the benzene ··· water complex using several different methods. CCSD(T) = MP2/CBS + ΔCCSD(T)/aDZ, MP2.5 = MP2/CBS + ΔMP2.5/aDZ, DFT–SAPT = DFT–SAPT/aTZ, SCS‐MI = SCS(MI)–MP2/cc‐pVTZ, DFT‐D = DFT‐D/TPSS/LP, M06–2X = DFT/M06–2X/6–311+G(2df,2pd).

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DNA dodecamers from molecular dynamics (MD) simulations with (left) and without (right) dispersion contributions.

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Potential energy curves for the propane dimer using several different methods.

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Potential energy curves for the benzene ··· cytosine complex using several different methods.

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Structure and Mechanism > Computational Biochemistry and Biophysics

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