**1. What is AQUA-MER aqueous speciation database? **

*AQUA-MER* is the first online resource that realizes multi-scale modeling of Hg biogeochemistry in the environmental water systems.
It has four modules, a speciation calculator for mesoscale modeling, a computational chemistry toolkit for atomic-scale and quantum-scale modeling,
a calculated stability constants database and an experimental measured stability constants database,
which includes **solvation free energies (ΔG _{solv})** and

**proton disassociation constants (p**of low molecular weight organic/inorganic compounds in aqueous solution, and

*K*_{a})**stability constants (log**of these compounds interacting with Hg.

*K*)**2. What can I do with AQUA-MER? **

With *AQUA-MER* you can perform multi-scale modeling of Hg biogeochemistry studies,
such as speciation calculation, conformational search for small molecules, ΔG_{solv} calculation, p*K*_{a} calculation,
and log *K* calculation, etc.

**3. Can I use AQUA-MER to study other metals, such as Cd Pd Co etc? **

Yes, you can use *AQUA-MER* to perform biogeochemistry study of other metals.
However, since *AQUA-MER* has been optimized against Hg biogeochemistry studies, you need to provide your own log *K* data
to study these metals. If you don't have the experimental data of the metal you want to study, you can use our
Computational Chemistry Toolkit to calculate them.

**4. Can I perform the calculations online? **

Yes and no. For speciation calculations and conformational search calculations, you can use our server to perform the calculations online.
But for ΔG_{solv} calculation, p*K*_{a} calculation, and log *K* calculation,
which require quantum mechanics (QM) calculations, such as density functional theory (DFT), we only generate input files for you.
You have to perform these calculations with your own computers.

**5. Can I use my own data for speciation calculations? **

Sure. During construction of the virtual solution, if no parameters can be found in *AQUA-MER*,
you will be promoted the options to add your own data or to calculate the required constants with our computational chemistry toolkit.
Please look at **HERE** for more details.

**6. Which algorithms are available for conformational search? **

Currently, three different methods are available on *AQUA-MER*. They are Random sampling with MM optimization,
Random sampling with QM optimization, and MD simulation with replica exchange sampling.
Please look at **HERE** for more details.

**7. Which QM software should I use to perform ΔG _{solv}, pK_{a}, and log K calculations? **

We recommend using Gaussian 09/16. That's because the parameters and validation calculations were performed with Gaussian 09.
Since it is commercial software, if you don't have a license, you can also use NWChem instead. *AQUA-MER* can generate
input files for both of them.

**8. Which solvation model should I use to perform ΔG _{solv}, pK_{a}, and log K calculations? **

We recommend using SMD_{sSAS} (SMD with a scaled solvent-accessible surface) model, which is an optimized SMD solvation model.
*AQUA-MER* uses this technique as a default for ΔG_{solv}, p*K*_{a}, and log *K* calculations.
For more details of this model, please refer to Dr. Peng Lian and Dr. Deepa Devarajan's papers at the citation part of this FAQ.

**9. Can I contribute data to AQUA-MER? **

Sure. You are welcome to do that! Please contact **Dr. Peng Lian** lianp@ornl.gov for data contribution and bug report.

**10. Who is behind AQUA-MER? **

*AQUA-MER* is run and devised by the Center for Molecular Biophysics (CMB) of the University of
Tennessee/Oak Ridge National Laboratory (UT/ORNL). It is supported by an award from the Subsurface Biogeochemical Research (SBR)
Program of the Biological and Environmental Research arm of the Office of Science of the U.S. Department of Energy (DOE).

**11. Any step-by-step guide on how to use AQUA-MER? **

Sure. The supporting information of our JCC paper is a good start. You can find if from Here.

**12. How can I cite AQUA-MER? **

1) Peng Lian, Luanjing Guo, Deepa Devarajan, Jerry M. Parks, Scott L. Painter, Scott C. Brooks, and Jeremy C. Smith. The *AQUA-MER* Databases and Aqueous Speciation Server: A Web Resource for Multiscale Modeling of Mercury Speciation. (2019) *Journal of Computational Chemistry*. DOI: 10.1002/jcc.26081

The technical papers on accurate calculation of ΔG_{solv}, p*K*_{a}, and log *K* are listed as bellow,

2) Peng Lian, Ryne C. Johnston, Jerry M. Parks, Jeremy C. Smith. Quantum Chemical Calculation of p*K*_{a}s of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution. (2018) *The Journal of Physical Chemistry A*. 122 (17), pp 4366–4374. DOI: 10.1021/acs.jpca.8b01751

3) Deepa Devarajan, Peng Lian, Scoot C. Brooks, Jerry M. Parks, Jeremy C. Smith. Quantum Chemical Approach for Calculating Stability Constants of Mercury Complexes. (2018) *ACS Earth and Space Chemistry*. DOI: 10.1021/acsearthspacechem.8b00102