Cartesian coordinates potential

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. 

The forces in a protein molecule are modeled by the gradient of the potential energy V(s, x) in dependence on a vector s encoding the amino acid sequence of the molecule and a vector x containing the Cartesian coordinates of all essential atoms of a molecule. In an equilibrium state x, the forces (s, x) vanish, so x is stationary and for stability reasons we must have a local minimizer. The most stable equilibrium state of a molecule is usually the... 

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. 

To carry out ageometry optimization (minimi/atioiT), IlyperCh em starts with a set of Cartesian coordinates for a molecule and tries to find anew set of coordinates with a minimum potential energy. Yon should appreciate that the potential energy surface is very complex, even for a molecule containing only a few dihedral an gles. 

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. 

Molecular Mechanic use an aiialyLical, dil fereiiliable, aiui relatively simple potential energy function, -(R). for describing the inieraciions between a set of atoms specified by their Cartesian coordinates R. 

Enter Cartesian Coordinate Eile Name cbu2.xyz Enter Potential Parameter File Name mm3... 

For a potential energy V and Cartesian coordinates rj, the optimized coordinates satisfy this equation ... 

The steepest descent method is a first order minimizer. It uses the first derivative of the potential energy with respect to the Cartesian coordinates. The method moves down the steepest slope of the interatomic forces on the potential energy surface. The descent is accomplished by adding an increment to the coordinates in the direction of the negative gradient of the potential energy, or the force. 

The function W(X) is called the potential of mean force (PMF). The fundamental concept of the PMF was first introduced by Kirkwood [4] to describe the average structure of liquids. It is a simple matter to show that the gradient of W(X) in Cartesian coordinates is related to the average force. 

Free energy calculations rely on the following thermodynamic perturbation theory [6-8]. Consider a system A described by the energy function = 17 + T. 17 = 17 (r ) is the potential energy, which depends on the coordinates = (Fi, r, , r ), and T is the kinetic energy, which (in a Cartesian coordinate system) depends on the velocities v. For concreteness, the system could be made up of a biomolecule in solution. We limit ourselves (mostly) to a classical mechanical description for simplicity and reasons of space. In the canonical thermodynamic ensemble (constant N, volume V, temperature T), the classical partition function Z is proportional to the configurational integral Q, which in a Cartesian coordinate system is... 

The entries in the table are arranged in order of increasing reaction coordinate or distance along the reaction path (the reaction coordinate is a composite variable spanning all of the degrees of freedom of the potential energy surface). The energy and optimized variable values are listed for each point (in this case, as Cartesian coordinates). The first and last entries correspond to the final points on each side of the reaction path. 

Suppose that our potential function U is now a function of many p) variables. They could be bond lengths, bond angles, dihedral angles or the Cartesian coordinates of each atom in a molecule. I will write these variables x, X2, , Xp and so... 

It should be clear from our discussion of potential energy surfaces that we have to examine the gradient of the electron density and the matrix of second derivatives, in order to make progress. The gradient of the electron density P(r) is, in Cartesian coordinates,... 

Figure 14. Classical trajectories for the H + H2(v = l,j = 0) reaction representing a 1-TS (a-d) and a 2-TS reaction path (e-h). Both trajectories lead to H2(v = 2,/ = 5,k = 0) products and the same scattering angle, 0 = 50°. (a-c) 1-TS trajectory in Cartesian coordinates. The positions of the atoms (Ha, solid circles Hb, open circles He, dotted circles) are plotted at constant time intervals of 4.1 fs on top of snapshots of the potential energy surface in a space-fixed frame centered at the reactant HbHc molecule. The location of the conical intersection is indicated by crosses (x). (d) 1-TS trajectory in hyperspherical coordinates (cf. Fig. 1) showing the different H - - H2 arrangements (open diamonds) at the same time intervals as panels (a-c) the potential energy contours are for a fixed hyperradius of p = 4.0 a.u. (e-h) As above for the 2-TS trajectory. Note that the 1-TS trajectory is deflected to the nearside (deflection angle 0 = +50°), whereas the 2-TS trajectory proceeds via an insertion mechanism and is deflected to the farside (0 = —50°).

Equations (56) and (57) give six constrains and define the BF-system uniquely. The internal coordinates qk(k = 1,2, , 21) are introduced so that the functions satisfy these equations at any qk- In the present calculations, 6 Cartesian coordinates (xi9,X29,xi8,Xn,X2i,X3i) from the triangle Og — H9 — Oi and 15 Cartesian coordinates of 5 atoms C2,C4,Ce,H3,Hy are taken. These 21 coordinates are denoted as qk- Their explicit numeration is immaterial. Equations (56) and (57) enable us to express the rest of the Cartesian coordinates (x39,X28,X38,r5) in terms of qk. With this definition, x, ( i, ,..., 21) are just linear functions of qk, which is convenient for constructing the metric tensor. Note also that the symmetry of the potential is easily established in terms of these internal coordinates. This naturally reduces the numerical effort to one-half. Constmction of the Hamiltonian for zero total angular momentum J = 0) is now straightforward. First, let us consider the metric. 

The electrons at the Mossbauer atom and the surrounding charges on the ligands cause an electric potential V(r) at the nucleus (located at r = (0,0,0). The negative value of the first derivative of the potential represents the electric field, E = — VV, which has three components in Cartesian coordinates, E (3V73x, dVIdy, dVIdz). 

The classical harmonic oscillator in one dimension was illustrated in Seetfon 5.2.2 by the simple pendulum. Hooke s law was employed in the fSfin / = —kx where / is the force acting on the mass and k is the force constant The force can also be expressed as the negative gradient of a scalar potential function, V(jc) = for the problem in one dimension [Eq. (4-88)]. Similarly, the three-dimensional harmonic oscillator in Cartesian coordinates can be represented by the potential function... 

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