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9

You can do that. For example, a Google Image search for "cisplatin structure" suggests that although the hashed + wedged depiction is more common, the four plain bonds depiction is also in regular use. For more detail on what's "acceptable" or not, refer to: Graphical representation of stereochemical configuration (IUPAC Recommendations ...


6

Since we're comparing: molden has a zmat builder and a force field (amber) implemented. You can start with the obvious choices of getting a structure from a database, or generating a starting structure with Open Babel, or simply click it together. The result will come to something like this (I admit this is even less prettier than VMD, but you can use some ...


5

Another nice free (but limited in function) tool for this job is NIH PubChem's viewer: The computed distance (not clearly visible in the figure) is $\pu{6.10 Å}$ The structure is also from PubChem: https://pubchem.ncbi.nlm.nih.gov/compound/Tropolone#section=3D-Conformer You can alternately process the coordinates with a tool such as Matlab/Octave: data=[-2....


7

A quick way to do this would be to enter the molecule in name in the search form on ChemSpider (maintained by the UK Royal Society of Chemistry). Select the 3D representation by hitting the 3D button. In the JSMol window, you can select an atom by double clicking it. To get the largest atom-to-atom distance, I've selected the hydroxyl hydrogen. By moving the ...


12

You wanted to measure the distance "across tropolone" but you didn't specify from where to where. The distance from a remote hydrogen to each of the oxygens and to the hydroxyl hydrogen are shown below. You can do the measurements you want yourself here: http://ursula.chem.yale.edu/~chem220/chem220js/STUDYAIDS/ESPotential/ESPmisc2.html


11

According to ChemDoodle's ruler tool, this molecule is probably about 5.35 Angstroms across. I'm a little annoyed that the font doesn't seem to have a proper Angstrom symbol. The symbol is part of the symbol selection widget, but doesn't get used by the ruler tool. Oh well, still cheaper than ChemDraw. EDIT: The angstrom symbol issue is font related. If I ...


1

According to (1) and (2), the values in your table would be as follows (all values in Å): $$\begin{array}{c c c} & \ce{PF4Cl} & \ce{PF3Cl2} \\ \ce{P-F_{eq}} & 1.541 & 1.546 \\ \ce{P-Cl_{eq}} & 1.999 & 2.004 \\ \end{array}$$ we have $x < y$ and $a < b$, which means that (b) is the correct answer According to Bent's rule: atomic ...


1

You have calculated correctly for parts $\bf{a}$ and $\bf{b}$. However, to answer part $\bf{c}$, you need to use the given plot, the interception and slope of which can be calculated as follows: The slope is $\tan \alpha = - \frac{1}{K_d}$: $$\tan \alpha = \frac{1-0.2}{0.1-0.8} = -1.14 \ \Rightarrow \ \therefore \ \frac{1}{K_d} = 1.14$$ According to the ...


5

The RKR method determines the classical turning points $r_{\pm}$ of the potential energy based on knowing experimentally determined spectroscopic constants. ( Rydberg, 1931, Z. Physik. v73,376, Klein, 1932 Z. Physik. v76, 226, Rees Proc. Phys. Soc.(Lond.) 1947, v59, 998.) The energy equation takes the usual form. Parameters all in cm$^{-1}$, distances in m, ...


2

Bond angle is largely governed by the location of electron cloud with regard to atoms in a molecule. In dichlorine monoxide, the electron cloud is more spread out between oxygen and chlorine while in the water molecule it’s much closer to the oxygen atom. Therefore, the net bond paid-bond pair repulsion is higher in dichlorine monoxide than in water, while ...


1

From the abstract of the 2019 Nature article outlining the success of AlphaFold: Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force4 that can ...


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