Potential energy surface scans

In Gaussian, potential energy surface scans are automated. Here is a sample input file fora simple potential energy surface scan  

This input file requests a potential energy surface scan for CH by including the Scan keyword in the route section. The variables section of the molecule specification uses an expanded format  

When only one parameter follows a variable name, that variable is held fixed throughout the entire scan. When all three parameters are included, that variable will be allowed to vary during the scan. Its initial value will be set to initial-value this value will increase by increment-size at each of number-of-points subsequent points. 

When only one variable is allowed to vary, the scan begins at the stnicture where the specified variable is equal to initial-value. At each subsequent point, increment-size is added to the current value for the variable. The process is repeated until number-of-points additional points have been completed. 

When more than one variable is allowed to vary, then all possible combinations of their values will be included. For example, the following variable definitions will result in a total of 20 scan points  

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The results of a potential energy surface scan appear following this heading within Gaussian output ... 

We ll look at examples of potential energy surface scan calculations in Exercise 8.2. 

In this exercise, you will explore the bond rupture process by performing a potential energy surface scan. Run potential energy surface scans for these molecules, gradually increasing one of the C-H bond lengths, using the specified model chemistries ... 

FIGURE 13.2 Potential energy surface scan at (A) BPE0/6-3H-G and (B) MP2/6-3H-G levels of theory of benzene-chlorine system in plane perpendicular to the benzene ring passing through opposite carbons atoms of benzene. 

LH also examined the carbonyl substitution reaction by phosphine. The approximate transition states as well as the barriers were determined by relaxed potential energy surface scans, that is, optimizing a system L MX Y (where X is the entering... 

A potential energy surface scan allows you to explore a r ion of a potential energy surface. A normal scan calculation performs a series of single point energy calculations at various structures, thereby sampling points on the potential energy surface. When you request a scan, you specify the variable(s) in the molecular structure which are to vary and the range of values which they should take on. 

Structure optimization of the reactants, products, and some transition states was performed by the Bemy geometry optimization algorithm without symmetry constraints [ 12]. In cases where identification of transition states was rather complicated, the relaxed potential energy surface scan and/or the combined synchronous transit-guided quasi-Newton (STQN) method was employed [13]. 

An input file for carrying out this potential energy surface scan in the Gaussian programs is included in the CD accompanying this text, along with a Matlab plot file of the surface shown in Fig. 3, which can be loaded into Matlab and then rotated and manipulated. 

Jensen has carried out detailed studies on the dissociation of phosphine from metathesis precatalysts, using BLYP-D-CP (with Grimme s dispersion corrections and counterpoise correction, to reduce basis set superposition error). This functional was selected after a brief benchmarking study. Relaxed potential energy surface scans were carried out, where the ruthenium-phosphorus distances in complexes 3 and 8 were stepped in increments (Figure 2.33). Maxima were observed at c. 4 A, which were used to obtain optimized structures for transition states with Ru-P distances of 3.95 A (for 3) and 3.97 A (for 8), and concomitant benzylidene rotation. Weakly bound complexes resulted from dissociation, with Ru-P distances of 5-7 A. Notably, there existed a significant difference in energy between the dissociation transition state and the infinitely separated products (c. 15—16 kcal mol ), and therefore the association of phosphine is not barrierless. 

Mesoscopic parameters, such as the full-diffusion tensor and potential V, are usually determined phenomenologically or from complementary approaches. For instance, dissipative properties described by the diffusion tensor can be obtained on the basis of hydrodynamic modeling (see below). The internal potential can be evaluated as a potential energy surface scan over the torsional angle 6. For small molecules this operation can be easily conducted at the DFT level, while for big molecules such as proteins, mixed quantum mechanical/molecular mechanics (QM/MM) methodologies can be employed. 

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