16 votes

How reactivity of a organic molecule depends upon HOMO and LUMO

The HOMO-LUMO gap is only weakly correlated with the reactivity of the molecule. Many sources, however, only point out the correlation between the HOMO-LUMO gap and reactivity, but fail to point out ...
wzkchem5's user avatar
  • 9,621
14 votes
Accepted

How does one compute the boiling point of a liquid made of a particular molecule?

I would like to start off by saying this is first and foremost a thermodynamic problem. Secondly, and as a result of thermodynamics, refer to Gibbs Phase Rule which says \begin{equation} F = C - P + 2 ...
B. Kelly's user avatar
  • 4,366
13 votes

What thermodynamic data is collected in order to build a CALPHAD model?

I concur with the answer by Alone programmer, but his answer only gives half the story. The coefficients or the model parameters come into the picture later and are actually obtained by optimization ...
Achintya Patra's user avatar
12 votes
Accepted

What are the ways to ensure thermodynamic stability of a DFT modelled new structure?

This is a tricky question and there is a whole area of research dedicated to solving it. The definition of the thermodynamically stable phase of a system is that occupying the global minimum of the ...
ProfM's user avatar
  • 11k
11 votes

What thermodynamic data is collected in order to build a CALPHAD model?

Basically you need to find $L_{ij}^{m}$ coefficients in the Redlich-Kister polynomials from DFT calculations, related to temperature as: $$L_{ij}^{m} = a_{ij}^{m} + b_{ij}^{m} T + c_{ij}^{m} T \ln(T) ...
Mithridates the Great's user avatar
10 votes

Are there any MD packages that do proper free energy sampling in the NPT ensemble?

It is straightforward to show that in a typical $NPT$ setting the Zwanzig equation still only depends on the energy difference and not on the volume (here I define $H$ to be the Hamiltonian of each ...
Godzilla's user avatar
  • 1,918
10 votes

Flying ice cube effect in molecular dynamics?

High frequency in this case is 'particles move all independently, with different directions and speed', and low frequency means 'particles can be represented as gradually changing field of speed and ...
Surprised Seagull's user avatar
10 votes
Accepted

Can the dehydrogenation energy be negative?

Because the hydrogenation release has a barrier (activation energy) that is not too low. The fact that the dehydrogenation energy of $\ce{H3N-BH3}$ is negative does prove that it will eventually ...
wzkchem5's user avatar
  • 9,621
9 votes

Flying ice cube effect in molecular dynamics?

The flying ice cube effect is when the kinetic energy leaks into the translations and rotations. In a constant energy simulation (NVE) this must come at the expense of vibrations, which has the effect ...
Cody Aldaz's user avatar
  • 8,017
9 votes
Accepted

Why is specific heat not zero at absolute zero?

You are correct that this is due to not including quantum effects. Ref 1 in your figure is the paper cited below. In this paper, they explicitly mention that $C_v$ calculated using the cell-cluster ...
Tyberius's user avatar
  • 15.5k
8 votes

Selection of appropriate Langevin damping parameter for MD of solid metal

I know it's a boring thing to say, but: It depends on what you want to do. The way I use Langevin thermostats, is to ensure good equipartitioning in my setup, so that I don't have any local hotspots ...
Kristof Bal's user avatar
  • 1,331
8 votes
Accepted

Is there any reason not to sum the kinetic and potential energy from an NPT simulation to get internal energy?

Energy in an NPT simulation is not conserved, but (once equilibrated), it will fluctuate around an average value, and that average value has meaning. That is the ensemble average for your NPT and is a ...
B. Kelly's user avatar
  • 4,366
8 votes
Accepted

For ergodicity, what is the significance of the R value and slope?

Short introduction to ergodicity Ergodicity is when the time-average equals the ensemble-average. A process is ergodic if the time-average "converges in the square mean" to the ensemble ...
I have no free time anymore's user avatar
7 votes
Accepted

What contributes to the total enthalpy of a system?

Thermochemistry (for a single molecule, e.g., ideal gas) depends on the Temperature. At T=0K thermochemistry is kind to us. At T = 0K $U = G = H$. This is because H = U + PV, which for an ideal gas ...
B. Kelly's user avatar
  • 4,366
7 votes

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

The answer to how much information are we losing by considering a temperature-independent forcefield in such systems? is, to a first approximation, none. The reason is that the statement ...
Shern Ren Tee's user avatar
7 votes
Accepted

Effect of temperature on Forcefield parameters in classical molecular dynamics simulations

I have reasonable experience with the parameterization and MD simulations of molecules with CHARMM FF, which is one of the temperature-agnostic FF. I will try to answer the questions, but please note ...
Hemanth Haridas's user avatar
6 votes

What thermodynamic data is collected in order to build a CALPHAD model?

As a retired professor in Computational Thermodynamics I am happy that young students try to use the Calphad methods to understand materials. However, to model a phase using Calphad there are some ...
Bo Sundman's user avatar
6 votes

For a Thermo-Calc database, is it possible to view the equation/parameters of the Gibbs free energy models?

I am not sure about TC-Python but in console mode, you can access the Gibbs energy equations directly using the Gibbs Energy System (GES) module. In case you need the details about a particular phase ...
Achintya Patra's user avatar
6 votes
Accepted

If a molecule's theoretical formation energy is positive, can it still be synthesized?

The theoretical formation energy is a little ambiguous here, depending on the way you calculate it. Is it a 0 K calculation (for example using DFT)? or have you already accounted for the entropic ...
Tara Mishra's user avatar
6 votes
Accepted

Is it possible to analytically solve for a particular phase region of a CALPHAD database? (instead of guessing and checking)

if you had access to the database equations for a given alloy system, could you analytically solve (and thus solve quickly) for the conditions (i.e., temperatures and compositions) that would produce ...
Brandon Bocklund's user avatar
6 votes
Accepted

How are diffusion coefficients calculated?

There are several different methods to calculate diffusion coefficients depending on the problem and some nuances to consider. Mean square displacement The most common way to calculate diffusion ...
WaterMolecule's user avatar
5 votes
Accepted

Should I add vdW interaction to estimate chemical potential of metallic elements?

Short version If the $\text{LiCoO}_2$ is computed with van der Waals included, so should everything else. Long version This seems more of a thermodynamics question than a simulations question given ...
Andrey Poletayev's user avatar
5 votes

Thermo-calc: Calculate precipitation driving force by parallel tangent construction

Thermo-Calc's DGM is the normalized parallel tangent driving force per mole of components. To be able to compute the driving force of a phase, it must be set to &...
Brandon Bocklund's user avatar
5 votes
Accepted

High accuracy energy methods, are they worth it?

High accuracy energy methods, are they worth it? They are absolutely worth it for many types of studies, but not worth it for other types of studies. It depends on precisely what the aim of your ...
I have no free time anymore's user avatar
5 votes
Accepted

How to get order constitution data for single equilibrium calculation in Thermo-Calc's TC Python module?

I don't have access to TC-Python, so I can't offer advice on how to use the API specifically. This is more of a workaround than a direct way to get Thermo-Calc to tell you whether the phase is ordered ...
Brandon Bocklund's user avatar
4 votes

What are the methods for calculating solvation effects in free energies and how do they compare?

Just throwing a couple of ideas out there: (i) Perform a free energy perturbation or potential of mean force calculation as available in typical classical MD setups. For known salt systems in water, ...
gogo's user avatar
  • 1,247
4 votes

How to calculate t-zero temperature using Thermo-Calc- Python (TCPython) for multiple alloys?

I have faced a similar issue and it seems that something happens while calling calculate(). I think it may be because when you use the same single equilibrium calculation for determining the Gibbs ...
Achintya Patra's user avatar
4 votes
Accepted

COSMO Model and Electric Potential on the Surface of the Cavity Inside Perfect Conductor

First of all, the method used in chemical engineering for calculating chemical potential and similar quantities (actitvity coefficients) for solutes in solutions/mixtures is called COSMO-RS and not ...
Uwe's user avatar
  • 196
4 votes
Accepted

Excited determinants, electronic partition function and thermochemistry calculation

"This works for organic molecules, but what happens when the excited states are closer in energy to the ground state, for example in open-shell molecules or in atoms?" If there's excited ...
I have no free time anymore's user avatar
4 votes

How are diffusion coefficients calculated?

I decided to make my comment an answer... Diffusion coefficients are simple to calculate in molecular dynamics. GROMACS has built in software specifically for this calculation. GROMACS diffusion ...
B. Kelly's user avatar
  • 4,366

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