Weak noncovalent interactions

Over the past decade, there have been numerous books and arti-cles reviewing ab initio and density functional theory (DFT) computations of hydrogen bonding and other weak noncovalent interactions. In fact, the very first chapter of this entire review series examines basis sets for noncovalent interactions between atoms and/or molecules, while a chapter in the second volume reviews ab initio methods for hydrogen bonding. Three thematic issues of Chemical Reviews have been dedicated to van der Waals interactions (Vol. 88, No. 6, 1988 Vol. 94, No. 7, 1994 and Vol. 100, No. 11, 2000). Two articles in the centennial issue of the Journal of Physical Chemistry discuss weakly bound clusters and solvation. It is also worth noting that 7i-type stacking interactions are very topical at the moment and are the subject not only of a separate chapter in this volume of Reviews in Computational Chemistry but also of a special issue of Physical Chemistry Chemical Physics (Vol. 10, No. 19, 2008). 

This chapter is intended to serve two very distinct purposes. Readers new to the subject matter will find a fairly thorough introduction to reliable electronic structure computations for weakly bound clusters (including a step-by-step tutorial). For more experienced readers, this chapter also reviews many of the significant advances made in the field since the turn of the twenty-first century, particularly current state-of-the-art benchmark studies. This work also offers some valuable perspective and will attempt to illustrate the importance of balancing what is possible with what is practical. 

Defining the scope of a chapter for Reviews in Computational Chemistry on clusters of molecules (and/or atoms) held together by hydrogen bonding. 

London dispersion forces, and/or similar interactions is not a simple task. Chemical bonding, whether noncovalent, covalent, ionic, or metallic, covers a broad, continuous spectrum of electronic interactions and energies. Consequently, the classification of a bond or interaction (e.g., double versus triple or covalent versus noncovalent ) is sometimes open to interpretation. As a result, there is no unique criterion or set of criteria that can be used to define weak interactions or noncovalent interactions. In the second volume of this review series, Scheiner already notes this issue and highlighted the difficulties associated with defining the hydrogen bond. Here, matters are even more complicated because other weak interactions are also considered. 

Although a wide variety of theoretical methods is available to study weak noncovalent interactions such as hydrogen bonding or dispersion forces between molecules (and/or atoms), this chapter focuses on size consistent electronic structure techniques likely to be employed by researchers new to the field of computational chemistry. Not stuprisingly, the list of popular electronic structure techniques includes the self-consistent field (SCF) Hartree-Fock method as well as popular implementations of density functional theory (DFT). However, correlated wave function theory (WFT) methods are often required to obtain accmate structures and energetics for weakly bound clusters, and the most useful of these WFT techniques tend to be based on many-body perturbation theory (MBPT) (specifically, Moller-Plesset perturbation theory), quadratic configuration interaction (QCI) theory, and coupled-cluster (CC) theory. 

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The prerequisite for templating is the presence of weak noncovalent interactions between the hydrophilic micelle interface and the precursor, so that the total interfacial energies of the resulting composite are lowered. Too strong interactions, as for example strong electrostatic ones, can lead to the... 

Here, the concept of linkage implies only that each intermolecular noncovalent bond is sufficiently large compared with kTto withstand ambient thermal collisions. Thus, for near-standard-state conditions (where kT 0.6kcal mol-1), even weak noncovalent interactions of 1-2 kcal mol-1 may be adequate to yield supramolecular complexes with stable equilibrium populations, thereby becoming true constituent units of the phase of lowest free energy. 

If the utilization of weak noncovalent interactions leading to molecular aggregations is a general principle in supramolecular chemistry, and periodicity is a general prerequisite in the crystalline state, then periodically distributed noncovalent interactions constitute the basis of molecular crystal engineering [1]. In other words, molecular crystal engineering can be considered as supramolecular solid-state chemistry, again based on weak noncovalent interactions. 

Application of the new but already widely employed MS technique of ESI readily allowed the detection of weak noncovalent interactions of antitumor drug-DNA complexes <1999RCM2489, 2002CC556> ESI data were used to derive a semi-quantitative estimate of the relative stability of the DNA complexes formed with 1,3-dithiane analogs. 

Numerous weak, noncovalent interactions decisively influence the folding of macromolecules such as proteins and nucleic acids. The most stable macromolecular conformations are those in which hydrogen bonding is maximized within the molecule and between the molecule and the solvent, and in which hydrophobic moieties cluster in the interior of the molecule away from the aqueous solvent. 

Thus, aside from the covalently polymerized a-chain itself, the majority of protein structure is determined by weak, noncovalent interactions that potentially can be disturbed by environmental changes. It is for this reason that protein structure can be easily disrupted or denatured by fluctuations in pH or temperature or by substances that can alter the structure of water, such as detergents or chaotropes. 

The key to controlling multiscale self-assembly is based on (i) the existence of previous individual components (ii) the weak-noncovalent-interactions between them and (iii) the dynamic formation of multiple suprastructures of which the most favored is that which minimizes its energy by a maximum number of interactions between individual components [48]. For this reason, the ultimate structure is predefined by various parameters of the initial components such as functionality, surface chemistry, shape, and size. 

The folding of a protein into a compact structure is accompanied by a large decrease in conformational entropy (disorder) of the protein, which is thermodynamically unfavorable. The native, folded conformation is maintained by a large number of weak, noncovalent interactions that act cooperatively to offset the unfavorable reduction in entropy. These noncovalent interactions include hydrogen bonds, and electrostatic, hydrophobic, and van der Waals interactions. These interactions ensure that the folded protein is (often just marginally) more stable than the unfolded form. 

Beyond covalent connections within protein and lipid molecules, weak noncovalent interactions between large molecules govern properties of cellular structure and interfadal adhesion in biology. These bonds and structures have limited lifetimes and so will fail under any level of force if pulled on for the right length of time. As such, the strength of interaction is the level of force most likely to disrupt a bond on a particular time scale. 

The three-dimensional structures of DNA, RNA, and proteins are determined by weak noncovalent interactions, principally hydrogen bonds and hydrophobic interactions. The free energies of these interactions are not much greater than the energy of thermal motion at room temperature, so that at elevated temperatures the structures of these molecules are disrupted. A macromolecule in a disrupted state is said to be denatured the ordered state, which is presumably that originally present in nature, is called the native state. A transition from the native to the denatured state is called denaturation. When double-stranded (native) DNA is heated, the bonding forces between the strands are disrupted and the two DNA strands separate thus, completely denatured DNA is single stranded. 

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