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15

The justification is simple and comes from a very fundamental law of thermodynamics: Internal energy is a complete differential form and is independent of intermediate states and only depends on start and final states: $$\Delta U = U_{2} - U_{1}$$ In your case: $U_{2} = E_{AB}$ and $U_{1} = E_{A} + E_{B}$ and if $\Delta U$ or binding energy $E_{\text{... 14 If I want to break a Li$_2$molecule (i.e. remove atom A from atom B), one way to do it is by shining a laser on it such that the frequency ($\nu$) or energy ($h\nu$) corresponds to the difference between the energy at$v=0$(if the molecule starts in the ground state) and the dissociation asymptote in this picture (generated based on [1,2]): I think the ... 12 The binding energy is defined in terms of the relaxed structures: it is the minimum energy required to disassemble a system of particles into separate parts. Mathematically$E_{\rm bind} = E(A)+E(B)-E(AB)$where$E(A)$and$E(B)$are the energies of subsystems$A$and$B$, and$E(AB)$is the energy of the compound system. Relaxing the structures of$A$and$...

12

You can analyze your docking results in two ways. First way is looking for the score function your program uses. For some score functions, lower value indicates better interactions and for others, higher values indicate better interactions. Also,, look for the decomposition of the score. Normally, the score is composed by different type of interaction/...

10

As Susi notes, the rearrangements of the $\ce{A}$ and $\ce{B}$ fragments are a part of the binding process, and so it is natural to include this "rearrangement energy" into the overall binding energy. Starting with the fragments in the complex geometry would artificially increase the binding energy, as it would destabilize the initial fragments. ...

9

In general, a system composed of $K$ interacting subsystems have a potential energy at a specific configuration of its parts. For instance, a system of $M$ nuclei and $N$ electrons can be separated into interacting subsystems with internal geometries, having $\{\mathbf{R}_A\}$ as nuclear positions for subsystem $A$ with $N_A$ electrons, $\{\mathbf{R}_B\}$ ...

8

A more approximate but sometimes easier approach than the one of Nike Dattani might be to calculate an artificial reaction coordinate of separating the two systems. This can be done manually or by employing some accelerated MD technique, e.g. metadynamics. The latter would even allow you to map the free energy along this path and thereby give you an estimate ...

7

Docking results can be analyzed in a number of ways by looking at various geometric parameters, such as a distances, angles and dihedrals. These are then typically compared against "ideal" values, such as a those at the transition state. Graphs typically contain a parameter on each axis with the results and ideal points plotted. Interactions can mean various ...

7

The model you are describing corresponds to a Wannier-Mott exciton and the binding energy is approximated by: $$\tag{1} E_{\mathrm{B}}=\frac{\mu}{\epsilon^2_{\infty}}R,$$ where $\mu$ is the reduced mass of the electron and hole, $\epsilon_{\infty}$ is the high frequency dielectric constant, and $R$ is the Rydberg constant. You can in principle construct ...

6

One way these calculations are performed is using MD and implicit solvent calculations. The general procedure for these simulations are: Perform simulations and get frames Perform implicit solvent calculations on the complex, receptor, and ligand Calculate docking energy from the three individual components Generally there is not an additional ...

6

The short answer is: yes you need to sample the whole reaction coordinate if you want accurate free energy values. If you are simply interested in qualitative behaviour, then you might (key word being might) get away with fewer windows (but they still need to be distributed fairly uniformly), but I would only recommend this for a dry/test run and never for a ...

6

As mentioned by @Camps in the comments, the Zn reference used in the paper is almost certainly that of an isolated Zn atom in the gas phase. If I understand correctly from briefly scanning the paper, the source of Zn in the device (as viewed from the graphene-coated separator) will be Zn2+ ions dissolved in the electrolyte - not quite the same thing as Zn in ...

3

Unfortunately, these appear to be the same quantity (a somewhat disappointing answer). They only differ in units, you can convert between the atomwise and area based units by simply calculating the area per atom in the cell. This is commonly seen for surface energies as well. You can see it reported either way in literature. Interestingly, we never really ...

2

Absolutely not. You only need that your input structure geometry is ok (no atomic clash, all valence ok, etc ). Using DFT or Molecular Dynamics to optimize the geometry pre docking is a waste of time. The justification to that is that every docking software will generate/search for a population of conformers, so, each conformer will be out of optimal ...

2

A good way to proceed is to use a control in your experiment as with modelling experiment in general. You can, for example, use the co-crystalized ligand or a well-know inhibitor (something experimentally established with IC50 value for example) of your protein of interest. The values obtained with that ligand in your docking/MMGBSA calculations will serve ...

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