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

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.

Kernel energy method applied to vesicular stomatitis virus nucleoprotein.

The kernel energy method (KEM) is applied to the vesicular stomatitis virus (VSV) nucleoprotein (PDB ID code 2QVJ). The calculations employ atomic coordinates from the crystal structure at 2.8-A resolution, except for the hydrogen atoms, whose positions were modeled by using the computer program HYPERCHEM.

Calculated interactions of a nitro group with aromatic rings of crystalline picryl bromide.

Several crystalline polymorphs have been discovered for picryl bromide. Among the several forces that control the formation of such polymorphs are the interactions among the nitro groups and phenyl rings of those crystals. Although there are >300 structures to be found in the Cambridge Structural Database displaying the nitro-phenyl interaction, nonetheless this interesting, and apparently important, interaction, seems not to have been discussed within any of the papers reporting the structures.

The kernel energy method of quantum mechanical approximation carried to fourth-order terms.

It is now possible to calculate the ab initio quantum mechanics of very large biological molecules. Two things lead to this perspective, namely, (i) the advances of parallel supercomputers, and (ii) the discovery of a quantum formalism called quantum crystallography and the use of quantum kernels, a method that is well suited for parallel computation. The kernel energy method (KEM) carried to second order has been used to calculate the quantum mechanical ab initio molecular energy of peptides, protein (insulin and collagen), DNA, and RNA and the interaction of drugs with their biochemical molecular targets.

The OH-anion acting as an acid.

In the crystalline state, the OH- anion is shown to be capable of acting as a base or as an acid with respect to waters of crystallization to which it is linked by hydrogen bonds. We examined the OH- anion in three crystalline samples and studied its behavior using quantum mechanics. Four quantum mechanical approximations were employed (HF, B3LYP, SVWN, and MP2) to obtain the relative stability of isomers of the H3O2- molecule in the three crystals considered.

The structures of cyclic dihydronium cations.

Recent experimental discoveries have revealed the existence of hitherto unexpected cyclic hydronium di-cations trapped within crystal structures. The molecular formulas are (H(14)O(6))(2+), present as two isomers, four- and six-member cyclic structures, and (H(18)O(8))(2+), an eight-member cyclic structure. As these unprecedented hydronium species are stabilized by the crystal structures in which they are captured, the question arises whether they could be stable as independent species as, for example, in solution or gas phase.

Kernel Energy Method: The Interaction Energy of the Collagen Triple Helix.

There is a rapid growth in computational difficulty with the number of atoms when quantum mechanics is applied to the study of biological molecules. This difficulty may be alleviated in two different ways. One is the advance of parallel supercomputers.

Drug target interaction energies by the kernel energy method in aminoglycoside drugs and ribosomal A site RNA targets.

It is possible to use the full power of ab initio quantum mechanics in application to the interaction of drugs and their molecular targets. This idea had barely been realized until recently, because of the well known growth in computational difficulty of the use of quantum mechanics, with the number of atoms in the molecule to be studied. Because the biochemical molecules of medicinal chemistry are so often large, containing thousands or even tens of thousands of atoms, the computational difficulty of the full quantum problem had been prohibitive.

The transition state for formation of the peptide bond in the ribosome.

Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation.

The Kernel Energy Method: application to a tRNA.

The Kernel Energy Method (KEM) may be used to calculate quantum mechanical molecular energy by the use of several model chemistries. Simplification is obtained by mathematically breaking a large molecule into smaller parts, called kernels. The full molecule is reassembled from calculations carried out on the kernels.

Kernel energy method: application to DNA.

The kernel energy method (KEM) has been used in three recent papers (1-3) to calculate the quantum mechanical ab inito molecular energy of peptides and the protein insulin. It was found to have good accuracy. The computational difficulty of representing a molecule increases only modestly with the number of atoms.

Kernel energy method: application to insulin.

In two recent articles a method has been described for calculating the total energy of large molecules. The method is called the kernel energy method (KEM) and requires knowledge of the crystal structure of interest. Calculations are simplified by adopting the approximation that a full molecule could be represented by smaller kernels of atoms.

Form factors for core electrons useful for the application of quantum crystallography (QCr) to organic molecules.

Form factors are calculated for the core electrons of the first-row atoms B, C, N, O and F. The form factors are presented in an analytical form, as appears in International Tables for X-ray Crystallography [Ibers & Hamilton (1974), Vol. IV, pp.