Cartesian coordinates, calculations

The second common type of operationally defined structure is the so-called substitution or rt structure.10 The structural parameter is said to be an rs parameter whenever it has been obtained from Cartesian coordinates calculated from changes in moments of inertia that occur on isotopic substitution at the atoms involved by using Kraitchman s equations.9 In contrast to r0 structures, rs structures are very nearly isotopically consistent. Nonetheless, isotope effects can cause difficulties as discussed by Schwendeman. Watson12 has recently shown that to first-order in perturbation theory a moment of inertia calculated entirely from substitution coordinates is approximately the average of the effective and equilibrium moments of inertia. However, this relation does not extend to the structural parameters themselves, except for a diatomic molecule or a very few special cases of polyatomics. In fact, one drawback of rs structures is their lack of a well-defined relation to other types of structural parameters in spite of the well-defined way in which they are determined. It is occasionally stated in the literature that r, parameters approximate re parameters, but this cannot be true in general. For example, for a linear molecule Watson12 has shown that to first order ... 

To generalize what we have just done to reactive and inelastic scattering, one needs to calculate numerically integrated trajectories for motions in many degrees of freedom. This is most convenient to develop in space-fixed Cartesian coordinates. In this case, the classical equations of motion (Hamilton s equations) are given... 

This section deals with the transfonnation of coordinates and forces [U, 47] between different coordinate systems. In particular, we will consider the transfonnation between Cartesian coordinates, in which the geometry is ultimately specified and the forces are calculated, and internal coordmates which allow efficient optimization. 

Single surface calculations with a vector potential in the adiabatic representation and two surface calculations in the diabatic representation with or without shifting the conical intersection from the origin are performed using Cartesian coordinates. As in the asymptotic region the two coordinates of the model represent a translational and a vibrational mode, respectively, the initial wave function for the ground state can be represented as. 

After transforming to Cartesian coordinates, the position and velocities must be corrected for anharmonicities in the potential surface so that the desired energy is obtained. This procedure can be used, for example, to include the effects of zero-point energy into a classical calculation. 

Figure 6, Equi-nonadiabatic coupling lines for the terms ri2(r,v) and r23(r,y) as calculated for the C2H molecule for a fixed C—C distauce, that is, rcc — 1-35 A. (a) Equi-non-adiabaric coupling term lines for the ri2(r,y). (b) Equi-non-adiabatic coupling term lines for X23(r,y). The Cartesian coordinates (x,y) are related to (q, 9) as follows x — qcosO] y —, sin9, where q and 9 are measured with respect to the midpoint between the two carbons.

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

A descriptor for the 3D arrangement of atoms in a molceulc can be derived in a similar manner. The Cartesian coordinates of the atoms in a molecule can be calculated by semi-empirical quantum mechanical or molecular mechanics (force field) methods, For larger data sets, fast 3D structure generators are available that combine data- and rule-driven methods to calculate Cartesian coordinates from the connection table of a molecule (e.g., CORINA [10]). 

Th c Newton-Raph son block dingotial method is a second order optim izer. It calculates both the first and second derivatives of potential energy with respect to Cartesian coordinates. I hese derivatives provide information ahont both the slope and curvature of lh e poten tial en ergy surface, Un like a full Newton -Raph son method, the block diagonal algorilh m calculates the second derivative matrix for one atom at a lime, avoiding the second derivatives with respect to two atoms. 

An N-atom molecular system may he described by dX Cartesian coordinates. Six independent coordinates (five for linear molecules, three fora single atom) describe translation and rotation of the system as a whole. The remaining coordinates describe the nioleciiUir configuration and the internal structure. Whether you use molecular mechanics, quantum mechanics, or a specific computational method (AMBER, CXDO. etc.), yon can ask for the energy of the system at a specified configuration. This is called a single poin t calculation. ... 

It is always possible to convert internal to Cartesian coordinates and vice versa. However, one coordinate system is usually preferred for a given application. Internal coordinates can usefully describe the relationship between the atoms in a single molecule, but Cartesian coordinates may be more appropriate when describing a collection of discrete molecules. Internal coordinates are commonly used as input to quantum mechanics programs, whereas calculations using molecular mechanics are usually done in Cartesian coordinates. The total number of coordinates that must be specified in the internal coordinate system is six fewer... 

We next solve the secular equation F — I = 0 to obtain the eigenvalues and eigenvectors o the matrix F. This step is usually performed using matrix diagonalisation, as outlined ii Section 1.10.3. If the Hessian is defined in terms of Cartesian coordinates then six of thes( eigenvalues will be zero as they correspond to translational and rotational motion of th( entire system. The frequency of each normal mode is then calculated from the eigenvalue using the relationship ... 

The program uses two ASCII input files for the SCF and properties stages of the calculation. There is a text output file as well as a number of binary or ASCII data files that can be created. The geometry is entered in fractional coordinates for periodic dimensions and Cartesian coordinates for nonperiodic dimensions. The user must specify the symmetry of the system. The input geometry must be oriented according to the symmetry axes and only the symmetry-unique atoms are listed. Some aspects of the input are cumbersome, such as the basis set specification. However, the input format is documented in detail. 

AMPAC can also be run from a shell or queue system using an ASCII input file. The input file format is easy to use. It consists of a molecular structure defined either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. 

The molecular structure input requires atom types to be assigned, which are not the same from one force field to the next. The input also includes a list of bonds in the molecule. There is not a module to automatically assign atom types. Most of the modules use a Cartesian coordinate molecular structure, except for a few that work with torsional space. The same keyword file is read by all the executables. A little bit of input is obtained by the program either interactively or from an ASCII file piped to standard input, which makes for a somewhat cryptic input file. This system of common input files and the user choosing which executables to run give TINKER the ability to run very sophisticated simulations while keeping the input required for simple calculations fairly minimal within the limitations mentioned here. 

Cartesian coordinates system for locating points in space based on three coordinates, which are usually given the symbols x, y, z or i, j, k CBS (complete basis set) an ah initio method CC (coupled cluster) a correlated ah initio method CFF (consistent force field) a class of molecular mechanics force fields CFMM (continuous fast multipole method) a method for fast DFT calculations on large molecules... 

A vibrations calculation is the first step of a vibrational analysis. It involves the time consuming step of evaluating the Hessian matrix (the second derivatives of the energy with respect to atomic Cartesian coordinates) and diagonalizing it to determine normal modes and harmonic frequencies. For the SCFmethods the Hessian matrix is evaluated by finite difference of analytic gradients, so the time required quickly grows with system size. 

Covariances between the Cartesian coordinates can also be calculated using... 

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