Intermediate structures

The bond orders obtained from Mayer s formula often seem intuitively reasonable, as illustrated in Table 2.6 for some simple molecules. The method has also been used to compute the bond orders for intermediate structures in reactions of the form H -1- XH HX -1- H and X I- XH -H H (X = F, Cl, Br). The results suggested that bond orders were a useful way to describe the similarity of the transition structure to the reactants or to the products. Moreover, the bond orders were approximately conserved along the reaction pathway. 

You can retrieve an intermediate structure from the output log file manually. Alternatively, you may use the Geom=(Check,Step=n) keyword to retrieve the structure corresponding to step n from a checkpoint file. 

There may be more than one TS connecting two minima. As many of the interpolation methods start off by assuming a linear reaction coordinate between the reactant and product, the user needs to guide the initial search (for example by adding different intermediate structures) to find more than one TS. 

The mechanism of the Hurd-Mori reaction has been discussed extensively in the review by Stanetty. The mechanism of the reaction was initially postulated by Hurd-Mori based on the isolation of intermediate 10. This intermediate was shown to transform into the desired thiadiazole upon heating in ethanol, either with or without acid. The reaction was thought to proceed via the four-membered intermediate 11, which would release the volatile ethylformate as a by-product. In 1995, Kobori and co-workers were able to isolate and determine crystallographically a very similar intermediate structure to 10 in their mechanistic studies of the reaction. ... 

The fulminate ion, CNO-, probably has a structure intermediate between C N O and C N 6 for since these two bond types have the same bond angles and term symbols ( 2), they can form intermediate structures lying anywhere between the two extremes. Which extreme is the more closely approached could be determined from a study of the bond angles in un-ionized fulminate molecules, such as AgCNO or ONCHgCNO, for the first structure would lead to an angle of 125° between the CNO axis and the metal-carbon bond, the second to an angle of 180°. 

There are two types of intermediate structures which need consideration for benzaurin, involving respectively a negatively charged carbon atom (for example, the structure... 

HOMO Amplitudes, Quasi-Intermediate Structures, and Mode Selectivities... 

Intermediates are intermediate structures in going from the starting material to the prodnct. They do not live for very long, and it is rare that you can isolate one and store it in a bottle, but they do exist for very short periods of time. Their structures are often critical in understanding the next step of the reaction. Going back to the analogy, if I saw the picture of you without your hat on, and I knew how cold it was on that mountain, then I would have been able to predict that you put on a hat right after the picture was taken. I would have known this because I would have been able to immediately identify an uncomfortable situation, and I could have predicted what resolution must have taken place to alleviate the problem. The same is true of intermediates. If we can look at an intermediate and determine which part of the intermediate is unstable, and we also know what options are available to alleviate the instability, then we can predict the products of the reaction based on an analysis of the intermediate. That s why they are so important. 

Multiple pathways leading to the same product channel can also be observed in a reaction when there are a sufficient number of identical atoms, thereby allowing different intermediate structures to yield the same products. In these cases, the mechanisms in the two pathways are often quite similar, but involve differing positions of identical atoms on the reactants. The different pathways often involve formation of ring intermediates in which the rings have different sizes. A simple example of this class is the photodissociation of vinyl chloride [9]... 

Structure, then the time-resolved photoelectron spectra [20, 21] could reveal signatures of two different intermediate structures, representing two different pathways on the PES. Transient absorption spectroscopy and other femtosecond time-resolved techniques may also be applicable to this problem. 

Number of points of convergence = Number of branches attached to main reduced tree consisting of vertices representing all intermediate structures and final product structure along root of tree. 

Reduced synthesis tree diagrams for the Sheehan plan for penicillin are shown in Figure 4.56 and their metrics summary is shown in Table 4.24. The two plans differ in an extra racemization step between the two intermediate structures shown. The a-isomer is the... 

A simple example serves to illnstrate the similarities between a reaction mechanism with a conventional intermediate and a reaction mechanism with a conical intersection. Consider Scheme 9.2 for the photochemical di-tt-methane rearrangement. Chemical intnition snggests two possible key intermediate structures, II and III. Computations conhrm that, for the singlet photochemical di-Jt-methane rearrangement, structure III is a conical intersection that divides the excited-state branch of the reaction coordinate from the ground state branch. In contrast, structure II is a conventional biradical intermediate for the triplet reaction. 

It has also been shown by 31P n.m.r., that pseudorotation of the oxyphosphoranes (4) and (5) involves intermediate structures with a diequatorial disposition of the dioxaphospholene ring, thus violating the ring-strain rule16. 

In the case of the intermediates, the calculated potential and free energies for the first three paths follow the same trend as for the TS. However, a big difference is observed with respect to path D. This energy difference is due to the fact that in the case of the first three paths, the MM environment of the intermediate structure was more relaxed for the calculations than that of path D. This relaxation in the environment resulted in the big energy differences for both the potential and free energy barriers of path D with respect to the other paths. 

Figure 3-8. Superposition of intermediate structures (active site) for all 4 paths. Path A red, path B blue, path C grey, path D yellow...

Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED (2003) Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures. Proc Natl Acad Sci USA 100 12111-12116... 

Fig. 11. Top molecular orbital energies for precursor, structure C (broken lines) and for bridged intermediate, structure D (full lines). Bottom bridging energy (AE) for N =0 (full line) and N = 1 (broken line), where N is the number of electrons transferred from the carbon residue to the platinum. The energies are plotted as functions of the 7rC3-to-platinum overlap integral (S). The energy unit 0 [ is the absolute value of the exchange integral between a pair of p1 orbitals in benzene. For structures C and D, cf. reaction (7). After J. R. Anderson and N. R. Avery, J. Calal. 7, 315 (1967).

The kinetics and mechanisms of the C —> G transition in a concentrated solution of PS-fr-PI in the PS-selective solvent di-n-butyl phthalate was studied [137,149]. An epitaxially transformation of the shear-oriented C phase to G, as previously established in melts [13,50,150], was observed. For shallow quenches into G, the transition proceeds directly by a nucleation and growth process. For deeper quenches, a metastable intermediate structure appears, with scattering and rheological features consistent with the hexag-onally perforated layer (PL) state. The C -> G transition follows the same pathways, and at approximately the same rates, even when the initial C phase is not shear-oriented. 

However, a PS-fo-PI/PI blend shows direct L G transitions without appearance of the PL phase. The L microdomain is more favourable than the PL phase since the volume fraction of the PI block component and the symmetry of microdomains is increased by the addition of PI homopolymer. Hence, the PL phase may not be formed as an intermediate structure if relatively high molecular weight PI homopolymer is added. The latter is not able to effectively fill the corners of the Wigner-Seitz cells in consequence packing frustration cannot be released and the PL phase is not favoured [152]. In contrast, the addition of low molecular weight PI homopolymer to the minor component of the PL phase reduces the packing frustration imposed on the block copolymers and stabilizes it [153]. Hence, transition from the PL to the G phase indicates an epitaxial relationship between the two structures, while the direct transition between L and G yields a polydomain structure indicative of epitaxial mismatches in domain orientations [152]. 

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