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A theory of entropic bonding.

ABSTRACT: Entropy alone can self-assemble hard nanoparticles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Molecular simulation is a powerful tool used extensively to study the self-assembly of ordered phases from disordered fluid phases of atoms, molecules, or nanoparticles. However, it is not yet possible to predict colloidal crystal structures a priori from particle shape as we can for atomic crystals from electronic valency. Here, we present such a first-principles theory. By calculating and minimizing excluded volume within the framework of statistical mechanics, we describe the directional entropic forces that collectively emerge between hard shapes, in familiar terms used to describe chemical bonds. We validate our theory by demonstrating that it predicts thermodynamically preferred structures for four families of hard polyhedra that match, in every instance, previous simulation results. The success of this first-principles approach to entropic colloidal crystal structure prediction furthers fundamental understanding of both entropically driven crystallization and conceptual pictures of bonding in matter.

SUBMITTER: Vo T

PROVIDER: S-EPMC8795519 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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A theory of entropic bonding.

Vo Thi T Glotzer Sharon C SC

Proceedings of the National Academy of Sciences of the United States of America 20220101 4

Entropy alone can self-assemble hard nanoparticles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Molecular simulation is a powerful tool used extensively to study the self-assembly of ordered phases from disordered fluid phases of atoms, molecules, or nanoparticles. However, it is not yet possible to predict colloidal crystal structures a priori from particle shape as we can for atomic crystals f ...[more]

PMID: 35042813

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Project description:We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A is ~28% of that of T-A, and most of this interaction does not arise from the F···HN interaction, but rather from the CH···N interaction. The nucleobase analogue shows no inherent selectivity for adenine over other bases, and L-A pairing energies are slightly weaker than for F-A. Overall, the results are consistent with a small favorable noncovalent interaction of F with A offset by a large desolvation cost for the polar partner. We discuss the findings in light of recent structural studies and of DNA replication experiments involving these analogues.

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A theory of entropic bonding.

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A theory of entropic bonding.

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