Atomic Coordinates

Aside from the conventions mentioned for the cell choice, further rules have been developed to achieve standardized descriptions of crystal structures [36], They should be followed to assure a systematic and comparable documentation of the data and to facilitate the inclusion in databases. However, contraventions of the standards are rather frequent, not only from negligence or ignorance of the rules, but often for compelling reasons, for example when the relationships between different structures are to be pointed out. 

Specification of the lattice parameters and the positions of all atoms contained in the unit cell is sufficient to characterize all essential aspects of a crystal structure. A unit cell can only contain an integral number of atoms. When stating the contents of the cell one refers to the chemical formula, i. e. the number of formula units per unit cell is given this number is usually termed Z. How the atoms are to be counted is shown in Fig. 2.7. 

The way to count the contents of a unit cell for the example of the face-centered unit cell of NaCl 8 Cl- ions in 8 vertices, each of which belongs to 8 adjacent cells makes 8/8 = 1 6 Cl- ions in the centers of 6 faces belonging to two adjacent cells each makes 6/2 = 3. 12 Na+ ions in the centers of 12 edges belonging to 4 cells each makes 12/4 = 3 1 Na+ ion in the cube center, belonging only to this cell. Total 4 Na+ and 4 Cl-ions or four formula units of NaCl (Z = 4). 

Commonly, only the atomic coordinates for the atoms in one asymmetric unit are listed. Atoms that can be generated from these by symmetry operations are not listed. Which symmetry operations are to be applied is revealed by stating the space group (cf Section 3.3). When the lattice parameters, the space group, and the atomic coordinates are known, all structural details can be deduced. In particular, all interatomic distances and angles can be calculated. 

The following formula can be used to calculate the distance d between two atoms from the lattice parameters and atomic coordinates  

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In this section, we concentrate on the relationship between diffraction pattern and surface lattice [5], In direct analogy with the tln-ee-dimensional bulk case, the surface lattice is defined by two vectors a and b parallel to the surface (defined already above), subtended by an angle y a and b together specify one unit cell, as illustrated in figure B1.21.4. Withm that unit cell atoms are arranged according to a basis, which is the list of atomic coordinates within drat unit cell we need not know these positions for the purposes of this discussion. Note that this unit cell can be viewed as being infinitely deep in the third dimension (perpendicular to the surface), so as to include all atoms below the surface to arbitrary depth. 

Since H=K. + V, the canonical ensemble partition fiinction factorizes into ideal gas and excess parts, and as a consequence most averages of interest may be split into corresponding ideal and excess components, which sum to give the total. In MC simulations, we frequently calculate just the excess or configurational parts in this case, y consists just of the atomic coordinates, not the momenta, and the appropriate expressions are obtained from equation b3.3.2 by replacing fby the potential energy V. The ideal gas contributions are usually easily calculated from exact... 

Statistical mechanics may be used to derive practical microscopic fomuilae for themiodynamic quantities. A well-known example is tire virial expression for the pressure, easily derived by scaling the atomic coordinates in the canonical ensemble partition fiinction... 

Often a degree of freedom moves very slowly for example, a heavy-atom coordinate. In that case, a plausible approach is to use a sudden approximation, i.e. fix that coordinate and do reduced dimensionality quantum-dynamics simulations on the remaining coordinates. A connnon application of this teclmique, in a three-dimensional case, is to fix the angle of approach to the target [120. 121] (see figure B3.4.14). 

X is a matrix whose elements Xu give the mass-weighted internal displacements of each atomic coordinate i from its average position at a given time step t. N is the total number of integration steps. 

Fig. 1. Nonbonded force evaluation may be distributed among processors according to atomic coordinates, as in spatial decomposition (left), or according to the indices of the interacting atoms, as in force-matrix decomposition (right). Shades of gray indicate processors to which interactions are assigned.

Fig. 4. In NAMD 2 forces are calculated not by force objects owned by individual patches, but rather by independent compute objects which depend on one or more patches for atomic coordinates. As suggested by shading in this illustration, a compute object need not reside on the same node as the patches upon which it depends.

Moving responsibility for the force computation away from the patches required a move away from pure message-driven execution to dependency-driven execution in which patches control the data (atomic coordinates) needed for compute objects to execute. A compute object, upon creation, registers this dependency with those patches from which it needs data. The patch then triggers force calculation by notifying its dependent compute objects when the next timestep s data is available. Once a compute object has received notification from all of the patches it depends on, it is placed in a prioritized queue for eventual execution. 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

Coordinate atomic coordinate data MODEL, AEOM, SIC ATOM... 

The HETATM records (Figure 2-115) represent atomic coordinates for atoms within non-.standard grotips (water molecules and atoms presented in HET... 

Figure 2-114. Atomic coordinate data section of the analy2ed PD B file.

Additional features determine properties such as interatomic distances, bond angles, and dihedral angles from atomic coordinates. Animations of computed vibrational modes from quantum chemistry packages arc also included. http //fiourceforge.nei/projecl /j mol/... 

The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

The problem of perception complete structures is related to the problem of their representation, for which the basic requirements are to represent as much as possible the functionality of the structure, to be unique, and to allow the restoration of the structure. Various approaches have been devised to this end. They comprise the use of molecular formulas, molecular weights, trade and/or trivial names, various line notations, registry numbers, constitutional diagrams 2D representations), atom coordinates (2D or 3D representations), topological indices, hash codes, and others (see Chapter 2). 

A force field does not consist only of a mathematical eiqjression that describes the energy of a molecule with respect to the atomic coordinates. The second integral part is the parameter set itself. Two different force fields may share the same functional form, but use a completely different parameterization. On the other hand, different functional forms may lead to almost the same results, depending on the parameters. This comparison shows that force fields are empirical there is no "correct form. Because some functional forms give better results than others, most of the implementations within the various available software packages (academic and commercial) are very similar. 

However, it is common practice to sample an isothermal isobaric ensemble NPT, constant pressure and constant temperature), which normally reflects standard laboratory conditions well. Similarly to temperature control, the system is coupled to an external bath with the desired target pressure Pq. By rescaling the dimensions of the periodic box and the atomic coordinates by the factor // at each integration step At according to Eq. (46), the volume of the box and the forces of the solvent molecules acting on the box walls are adjusted. 

For each combination of atoms i.j, k, and I, c is defined by Eq. (29), where X , y,. and Zj are the coordinates of atom j in Cartesian space defined in such a way that atom i is at position (0, 0, 0), atomj lies on the positive side of the x-axis, and atom k lies on the xy-plaiic and has a positive y-coordinate. On the right-hand side of Eq. (29), the numerator represents the volume of a rectangular prism with edges % , y ., and Zi, while the denominator is proportional to the surface of the same solid. If X . y ., or 2 has a very small absolute value, the set of four atoms is deviating only slightly from an achiral situation. This is reflected in c, which would then take a small absolute value the value of c is conformation-dependent because it is a function of the 3D atomic coordinates. 

Ch aracteri/e a poten tial en ergy m in im u m. A geom etry optim i-zalioti results in a new structure at a m in itn urn. You can examine atomic coordinates and energy of this slruetiire. 

View the contour map m several planes to see the general Torm of the distiibiiiioii. As long as you don t alter the molecular coordinates, you don t need to repeat th e wave function calculation. Use the left mouse button and the IlyperChem Rotation or Translation tools (or Tool icons ) to change the view of amolecnle without changing its atomic coordinates. 

It can be readily confirmed thaf by decreases as the number of bonds N increases and/or llieir length (r ) decreases. This relationship between the bond strength and the number of neighbours provides a useful way to rationalise the structure of solids. Thus the high coordination of metals suggests that it is more effective for them to form more bonds, even though each individual bond is weakened as a consequence. Materials such as silicon achieve the balance for an infermediate number of neighbours and molecular solids have the smallest atomic coordination numbers. 

The most straightforward fype of lattice minimisation is performed at constant volume, where the dimensions of the basic imit cell do not change. A more advanced type of calculation is one performed at constant pressure, in which case there are forces on both the atoms and the unit cell as a whole. The lattice vectors are considered as additional variables along with the atomic coordinates. The laws of elasticify describe the behaviour of a material when... 

The diagonal elements of are the eigenvalues of G and the columns of V are i eigenvectors. The atomic coordinates can be derived from the metric matrix by rewritir... 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

There are a number of different ways that the molecular graph can be conununicated between the computer and the end-user. One common representation is the connection table, of which there are various flavours, but most provide information about the atoms present in the molecule and their connectivity. The most basic connection tables simply indicate the atomic number of each atom and which atoms form each bond others may include information about the atom hybridisation state and the bond order. Hydrogens may be included or they may be imphed. In addition, information about the atomic coordinates (for the standard two-dimensional chemical drawing or for the three-dimensional conformation) can be included. The connection table for acetic acid in one of the most popular formats, the Molecular Design mol format [Dalby et al. 1992], is shown in Figure 12.3. 

Gasteiger J, C Rudolph and J Sadowski 1990. Automatic Generation of 3D Atomic Coordinates fo Organic Molecules. Tetrahedron Computer Methodology 3 537-547. 

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