Calculation of strong and weak interactions in TDA1 and RangDP52 by the kernel energy method

Abstract

Using the Kernel Energy Method we apply ab initio quantum mechanics to study the relative importance of weak and strong interactions (including hydrogen bonds) in the crystal structures of the title compounds TDA1 and RangDP52. Perhaps contrary to widespread belief, in these compounds the weak interaction energies, because of their large number and cooperativity, can be significant to the binding energetics of the crystal, and thus also to its other properties.CH-O bonds ͉ cooperativity of bonds ͉ cysteine macrocycles ͉ NH-CO bonds ͉ NH-S T he topic of weak interactions (including hydrogen bonds) is of increasing general interest because in large numbers and cooperativity they can be important to molecular properties. Desiraju and Steiner (1) discuss this aspect of weak hydrogen bonds and have published a collection of structures in which these bonds participate. The understanding of these weak interactions will likely be useful in future designs of complex selforganizing structures. It has been noted that cooperativity among weak interactions allows them to contribute effectively to tighten molecular packing in crystals to an extent beyond that associated with ordinary van der Waals forces. This can affect the thermal and electronic properties of molecules, including electron mobility, and physical properties such as hardness, melting point, and crystal stability (1-4). Because it is of increasing interest to recognize the significant and sometimes subtle effects on molecular properties caused by weak interactions, we have undertaken a quantum mechanical study of their energetics in crystals of 2 molecules that may stand as examples in addition to the compounds discussed by Desiraju and Steiner. These areIn the molecules to be studied the crystal structures and atomic coordinates are known (2, 3). This information is used to obtain the atomic coordinates of the near-neighbor molecules in the crystal to which they are related by operations of space group symmetry. In particular, it is the interaction energy between neighboring molecules of the crystal that is the object of our study. We wish to calculate the interaction energy between full neighboring molecules, and having that value, to calculate the components of such interactions that are contributed by the various ''pieces'' of the molecules through their strong and weak hydrogen bonds. Thus, the relative importance of the weak and strong hydrogen bonds would be an outcome of the study.Since the molecules to be studied may be thought of as having a variety of pieces, each contributing to the various strong and weak interactions, a natural method of quantum calculation from 1995 is that of kernel density matrices (5-7), which has evolved more recently to the Kernel Energy Method (KEM) of Quantum Crystallography (8)(9)(10)(11)(12)(13)(14). In the KEM, the results of X-ray crystallography are combined with those of quantum mechanics. It is assumed that the crystal structure is known for a molecule under study. With known atomic coordinates, the molecule is math...

Protoribosome by quantum kernel energy method

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Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

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Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

“…A number of low scaling quantum‐mechanical (QM) approaches have been developed for calculating large systems, including linear scaling QM methods and fragmentation approaches . One can also use semiempirical methods and hybrid QM and molecular mechanics approaches.…”

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