Science topics: ChemistryChemo-informatics
Science topic
Chemo-informatics - Science topic
Chemo-informatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry.
Questions related to Chemo-informatics
Hi all,
I'm a master student working with computational molecular fragmentation and docking.
I did a virtual screening using autodock vina of some thousends of molecules, and I'm wondering if there's a solution to fragment the molecules based on the interactions observed on the docking poses. In the end I want obtain the smiles of the fragment, the AA the fragment is interacting and the type of interaction.
Is there any methods to do this?
I handle large amounts of data on chemical substances. There is unique information for each chemical, but there is repetitive information that is required to be prepared and processed.
I do not have much knowledge of coding, automated functions in Excel, or even AI tools for these matters. I only know one Macro feature in Excel but that is all I know. The pace and amount of data is just increasing over the months. So, I wonder where to start leveraging existing tools that I can use for such tasks.
Which package do you use in R for general chemoinformatics, like handling molecular formulas, computing weights and mass to charge ratios, maybe even handling adducts etc.? Ideally something well maintained and with little dependencies.
Hi all,
I'm a master student working with computational molecular fragmentation and docking.
I did a virtual screening using autodock vina of some thousends of molecules, and I'm wondering if there's a solution to fragment the molecules based on the interactions observed on the docking poses. In the end I want obtain the smiles of the fragment, the AA the fragment is interacting and the type of interaction.
Is there any methods to do this?
Its my very first attempt when I am learning chemoinformatics while I am working on gromacs there is a warning sign if anybody can provide me with guidance will be great.
The warning states this : WARNING: Empty diagonal for a 3-dimensional periodic box

Hello all
When I was filtering a chemical database for virtual screening using open babel software, I got this error message few times "Fail to set stereochemistry as unable to find available bond".
Herein, I have two questions:
1. Is it a limitation of open babel or a problem with the database preparation work? Any suggestions to solve this issue?
2. If this issue happens to a molecule that already passed the filter criterion (being < 400 Da), does the molecule got written to the output file?
Thnx
I want to understand what is the significance of fukui functions and in what way it helps in predicting the vibrational structure of a molecule. kindly help me in this regard.
Hi everyone! I'm trying to work on the acquisition of the Raman Spectra of a leaf section using Confocal Raman Spectroscopy. The samples to be used are pure, dried, and powdered leaf samples. I am going to use a 785 nm laser source.
However, the only thing I get was a spectra with no peaks or it is strongly masked by fluorescence. Do you have any tricks/sample preparations to avoid the fluorescence because I'm afraid that it covers the raman signal or enhance the Raman Signal because the compounds might have a relatively weak Raman Signal compare to the background signal and the fluorescence? Are there any sample preparations that can be done without the use of water or an immersion objective like the use of solid matrices which can be mixed with the sample? Thank you.
we didn't find any specific TLR7 specific antagonist . maximum are dual antagonist of TLR7 and TLR9 antagonist. Is there any specificity on the protein active site? what was the reason for that?
I am interested in software, databases and web servers in the field of chemoinformatics or pharmacoinformatics . We are trying to collect and maintain these resources at our web site http://crdd.osdd.net/ . Your information will be useful for us as well as for scientific community as we in process of developing repository of freeware in above fields.
Recently, Researcher using Bioinformatics and Chemoinformatics for Drug development for covid-19, what are the limitations of in computational analysis vs. experimental?
Basically I want to know what Bragg reflexes I can access with my goniometer.
I'm trying to generate CGR and in order to do so I want to use the Marvin Sketch auto mapper function on a bunch of reactions, stored as reaction smarts. But in order to use the auto mapper function from Marvin sketch I have to pass the reactions as rxn files or as a RDF file.
I am performing a molecular dynamics simulation from CRBN protein (PDB ID: 4tz4), which contain a ZN binding site composed of four cysteines. The main goal is understanding the chemical and biological changes in the Zn binding site from this protein when Cys391-to-Arg (C391R) substitution occur. For this, we performed the geometry optimization of the complex of four cysteines and Zn using DFT calculations on Gaussian 16 suite. Then, we put the coordinates obtained through DFT on the PDB format, and we will perform molecular dynamics simulation to obtain results in the perspective of the whole protein.
Now, I am using Gromacs to perform the MD simulation, but there is an error on my simulation during the NVT stabilization. This is the error message:
"Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
^Mstep 0
WARNING: Listed nonbonded interaction between particles 4204 and 4221
at distance 4.402 which is larger than the table limit 2.029 nm.
This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason."
I am thinking about the reason for this error, and this could be because the force field which I am using to perform the simulation (amber03), but I am not sure about that. It is proper to mention that the atoms in which there is the error are the C of the residues (Lys324 and Gly325) which are between two of the Cys that form the Zn binding site.
Please, can anyone help me with this issue? Thank you very much
I am deciding whether to buy a license for Dragon (https://chm.kode-solutions.net/products_dragon.php), but I wanted to check if there are any free alternatives that compute most of these features. I have used Mordred (https://github.com/mordred-descriptor/mordred) and PaDEL, but these only provide a small subset of those available in Dragon, and haven't been as valuable for predictive modeling. Is there anything free (and preferably open source) that provides anything close to the coverage of Dragon?
#chemoinformatics #computational #chemistry #qsar
I have to calculate the molecular descriptor using freeware. Which software is best for calculating the molecular descriptor? Or does anyone have a license for any software(paid)? Please help me out.
While going through various articles, I found the common practice of selecting a particular chain over others if a protein is in multimeric form. In this regard, I have the following questions
1) Is there any rule regarding which chain should be kept and which one should be deleted.
2) Since we mimic biological molecule in docking study to find the binding mode then how far it is valid to select only particular chain of the protein. Moreover, what if we took the whole protein pdb for docking study?
Hi there !
I'm loking for a tools that is able calculate a similarity score for each term of 2 list name and give me the top 10 similarity score he found. For exemple
List 1 :
(-)-epigallocatechin
(+)-catechin
(pyro)catechol sulfate
3',4'-Dimethoxyphenylacetic acid
List 2 :
3',3'-Dimethoxy-phenylacetic acid
catechin
(epi)gallocatechin
catechol sulfate
Results
(-)-epigallocatechin VS (epi)gallocatechin - Score = 0.9 (very similar)
(-)-epigallocatechin VS (+)-catechin - Score = 0.5
(+)-catechin VS catechin - Score = 0.9
etc etc ...
Thanks a lot for your great help.
I have a large set of molecules and I'd like to assess its diversity in terms of molecular structure, assuming I'm designing a screening library. My question is not what tools to use, but rather how should I interpret the results?
Let's say I choose clustering. How many clusters indicate a diverse library?
"Modern Approaches in Drug Discovery" suggests comparing Morgan fingerprints against Tanimoto distance matrix with multidimensional scaling applied, among others. But what will it get me?
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I would like to decide whether a given internal coordinate (angle or dihedral angle) is totally symmetric, i.e., E(y1,y2,...,yi+delta,y[3N-5/6])=E(y1,y2,...,yi-delta,y[3N-5/6]) for any delta, where E is the total electronic energy, y1,y2,...,y[3N-5/6] are the internal coordinates, and yi is the selected coordinate. Is there any chance to prove that yi is totally symmetric by using only the molecular structure?
We are working on computational aspect of target screening for effective diagnostic. We are combining systems pharmacogenomics, chemoinformatics, systems biology, graph theory, structural biology aspects majorly. More focused towards interdisciplinary approaches. If you are interested to be a part of project and contribute to scientific community through our approach, you are most welcome.
I am training machine learning models to predict the binding affinity of small molecules against a protein receptor. During the training set preparation I remove very small and very big moelcules, as they are more likely to binding non-specifically to the receptor and abolish its funtion. Currently, I use z-score thresholds (-2.5 for the very small and 2.5 for the very big molecules). However, the z-score depends each time on the distribution of MW in the available data and hence I believe that actual MW lower and upper thresholds would be more accurate. According to your experience, what should be these MW thresholds?
PS: please don't point me to Lipinski's rule of 5 (180 to 500) or some related rule. When training a machine learning model on known data you have to be more "generous" otherwise you will discard lots of precious experimental data.
Hi there,
I have about ~1 million compounds to cluster. While calculating the fingerprints were relatively fast using Canvas on a desktop computer, I found clustering (by K-Means) very slow. For example, clustering them into 128 clusters took ~10 hrs, and I wonder if this would increase exponentially as I increase the number of clusters.
So are there alternative/faster methods to cluster a library of compounds into arbitrary number of clusters?
Thanks!
Today, there is a huge body of scientific data that can probably solve all the problems of mankind. However, even a group of scientists can not physically analyze this Big Data. In addition, people are subjective in judgment and often do not notice the negative consequences of some innovation...
So scientists inevitably set local goals. Can the Artificial Intelligence setting "absolute" goals for the scientific community?
My aim is to cluster a set of molecules coming from a virtual screening (in the order of thousands of compounds). I want to cluster them by chemical similarity using hierarchical clustering. The distance metric used is the Tanimoto index. Ideally, I want to identify a limited number of clusters (10-30) that can be conveniently represented by the molecule corresponding to the centroid of each cluster.
My problem is that the results of hierarchical clustering seem to be strongly dependent on the linkage algorithm chosen. The optimal number of clusters predicted (in terms of Kelley criterion) seem to vary a lot according to different algorithms tested. Eventually, I am afraid that the results of my clustering will depend too strongly on the linkage algorithm chosen.
Is there a way to perform clustering without this kind of bias? Can consensus clustering help removing this problem? If so, is there any software that performs consensus clustering on molecular libraries?
how Can I do williams plot for showing applicability domain for QSAR model?
I synthesized some novel heterocycles which shows a particular in-vitro bioactivity. After this, I decided to go for its docking study. Synthesized heterocycles are in the racemic mixture; also the in-vitro bioactivity is assessed by using a racemic mixture. My question is, for docking purpose is it necessary to use each and every individual from the racemic mixture one by one or the individual single isomer structure (among its racemic mixture) after energy minimization is sufficient? Out of this which method is correct?
(For energy minimization I used ChemDraw program)
I have one drug candidate in diastereomeric mixture. Is it possible to identify the number of isomers in diastereomeric mixture by using the second derivative calculations and Gaussian curve fitting analysis of DTG (Differential Thermogravimetric analysis) curve by using OriginPro 8 software?
MINEQL is a powerful and easy-to-use chemical equilibrium modeling system that can be used to perform calculations on low temperature (0-50oC), low to moderate ionic strength (<0.5 M) aqueous systems.
MINEQL is a data driven program, so you do NO programming. In the simplest scenario, you create systems by selecting chemical components from a menu, scan the thermodynamic database and run the calculation.
However, MINEQL also provides tools to allow you to take control of your reaction data, create a personal thermodynamic database, perform synthetic titrations and automatically process mutiple samples (such as field data).
Dear Friends,
The high quality electronic version of a very nice book namely "Exploring Chemistry with Electronic Structure Methods, Third Edition" is extremely requested. Can anyone help me to reach to this book in a free of charge manner?
Thanks for your help.
Saeed
I am trying to create the topology files for my input protein which contains zinc and calcium ions. The OPLS forcefield in gromacs does not contain the parameters for these metals and I could not find it in the forcefield files as well. I have made a search on internet but I could not find a solution. Any ideas ?
What are the steps to do MM potential energy surface scan for an organic molecule using Gromacs?
i have got the values of all the parameters A, B, Bo, S, E, L and V of a organic compound using an online portal. I also got to know what each parameter means. but i am not able to interpret my result. For eg. B of my compound is 0.88...so what does it mean? Is there some acceptable range of the parameters for good drug molecules?
I want to calculate the frontier electron density (FED) for each atom in the molecule, so I need to extract the Homo and Lumo values for each atom not for the whole system. can anyone guide me how to extract these data from the output file?
I'm a structural biologist and because of that I have not much experience with software that is able to model inorganic compounds like polyoxometalate clusters. I have an old version of Diamond but I'm wondering if there are more intuitive software packages available.
Hi, I’m a PhD, who is beginning to learn about molecular modeling. I work with enzymes and for prepare it, I use the application PDB2PQR of Chimera and this software offer 6 forcefields:
- PARSE (default) - PARameters for Solvation Energy
- AMBER - AMBER ff99.
- SWANSON - AMBER ff99 charges with optimized radii.
- CHARMM - CHARMM27.
- PEOEPB - a version of Gasteiger-Marsili Partial Equalization of Orbital Electronegativities, optimized for Poisson-Boltzmann calculations.
- TYL06 - a Poisson-Boltzmann-optimized force field.
I read some about them and I think that PARSE could be a good option but I don’t know if another forcefield could be better than it. I would be very grateful if anyone could help me with this question. Thank you all for your anticipated response.
My molecule is too big for ATP ou PRODRG server. I wanna to prepare files for DM at GROMACS but a can't create this topology file for my enzyme.
I'm looking for a tool that can give how many methyl groups, hydroxyl groups etc. are in a compound from it's SMILES, SDF or MOL2 format.
Hello, I need to predict the mass spectrum of a molecule to compare it with the mass spectrum obtained experimentally, if anyone knows a program or web server that gives me this option I would appreciate it a lot
Thanks
I have done virtual screening of a database containing around 3.5 K ligands. Best five ligands were sorted out by considering the binding affinity with the protein. All five showed binding affinity around -14, but after optimization in PM6 or DFT in Gaussian 09, it decreases to around -8.
Is there a way to choose the site where we want to place the grid box using the command line?
When creating the grid parameter file in ADT, in the graphical interface, you go to Grid ---> Grid Box --> Center. Then you have to chose to center the grid box in either: 1) Pick an atom 2) Center on ligand 3) Center on macromolecule 4) On a named atom. Therefore, it is possible to chose to center the grid box in the ligand.
My question is how can you do it (chose the position of the grid box) with the command line? Is there a script that I could use? There is no option in the grid parameter file. I have more than 10000 compounds and it would take me a really big amount of time to do it graphically. Then, I would like to automatate the process. Is there a way that I can do it?
I am going to do rescoring which means that the grid will not be in the same place of the ligand automatically.
Hi,
I am looking for free databases (like ZINC database) of compounds from which I can choose ligands for docking.
The electronic state of the initial guess is 1-A.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
Integral accuracy reduced to 1.0D-05 until final iterations.
Problem detected with inexpensive integrals.
Switching to full accuracy and repeating last cycle.
Spurious integrated density or basis function:
NE= 228 NElCor= 0 El error=5.13D-01 rel=1.49D-03 Tolerance=1.00D-03
Shell 101 absolute error=2.76D-04 Tolerance=1.20D-02
Shell 71 signed error=1.90D-04 Tolerance=1.00D-01
Inaccurate quadrature in CalDSu.
Error termination via Lnk1e in /opt/apps/gaussian09/g09l/g09/l502.exe at Wed Oct 12 18:51:23 2016.
Job cpu time: 0 days 5 hours 33 minutes 22.6 seconds.
File lengths (MBytes): RWF= 447 Int= 0 D2E= 0 Chk= 10 Scr= 1
I am beginner for gromacs simulation package, I used it for organic compounds. But unable to understand how to deal with inorganic compounds and what about the force field and solvent we can use.
In pubchem, i found the pKa of DMF is -0.3. However it is a strong base, which means its pKa value should be high (>16).
Working on my PhD im using a catalysis that offers the creation of alkylamines with full stereoselective controle. To put this to use im looking for bioactive structure that might be accesible through the synthesis. SciFinder, Reaxys and so on gave either huge or none results, while the Merck index doesnt offer full potential as free user. Im looking for platforms or tools that might help.
I've been using Glide for docking. I got some data for docking score and Gscore, but i dont really understand what they mean....and so I cannot choose the best ligand.
Could anyone help me please?
i successfully done the protein ligand complex simulation on NAMD with Generalized born implicit solvent model on 20ps timescales. and it is smoothly done.
but after loading the .DCD and .PSF file on VMD nothing is shown on screen.
can any one tell me where is the problem?
i upload the dcd and psf files heres.
Hi!
I was wondering if you can suggest program/script for linux or not, that can calculate the interactions between Ligand and protein from a pdb file. When I'm saying interactions i mean, h-bonds, aromatic interactions, hydrophobic bonds etc.
I found IChem on the internet, but it seems that it doesn't work properly. I couldn't even run it.
Thanks
Actually, I am submitting the job into the Polyrate 8.0 software for my reactants and products to calculate the rate coefficients for a particular reaction.
But, in the output, I am getting some non-zero imaginary frequencies. In principle, for reactants and products, there should not be any negative frequency(NImag=0). I have made sure that my inputs are correct including the Z-matrix too for the reactants and products.
I am unable to understand as to why this is happening. Can somebody please help me with this?
I am also attaching the i/p files for your reference.
The files "r1.dat" and "r1.71" are the i/p files for Polyrate. And, the file "esp.fu82" is the Gaussian o/p file from the Polyrate software.
recently,I met the difficulty on material studio.
The two pdb files has similar contains,but display differcently.
the files has been attached.
Why the structure display pink bonds and atoms in material studio?
and how to adjust the file of hem.pdb ?
we should pay attention of what is the key point of pdb file when we constructing it.
Thank you very much in advance.


I have done molecular docking on water solvated model of hERG open and close model and from final poses build GRIND model and prediction power is comparatively very low from the model I have obtained from vacuum docking poses
It was always a challenging problem to describe the electrostatics of proteins. Over last few years there has been a significant effort, and considerable progress was seen in this area. Most of those efforts are concentrated on applying continuum electrostatics, such as Poisson−Boltzmann (PB) or molecular dynamics simulations approaches. Though the accuracy level of those prediction methods are encouraging but most methods require a significant computational effort with impractical calculation times. In this light, I'm interested if any one could explain me regarding a relatively fast calculating methods with good accuracy. Thanks in advance for your time and consideration.
I have carried out MD simulations about membrane channel. In the process of MD simulations, the upper leaflet and the lower leaflet were separated as shown in figure 1. I tried to center the two leaflet together and used PBC wrap command in VMD "pbc wrap -centersel "resname PAP" -center com -compound res -all", PAP is the name of the fixed channel in the membrane. The two leaflets were together as shown in figure 2. When I evaluated the thickness of the membrane, something weird happened. The thickness of the membrane experiences great fluctuations from the time the two leaflets was taken apart. I guess there is something wrong in the treatment of PBC but I don't know how to tackle this problem.


In machine learning approaches many researchers are taking different reference values to classify molecules as actives and inactives?
Let's say we want to generate conformers of ligands prior to docking them rigidly.
Is there a formula, like a function of the number of rotatable bonds, to decide how many conformers (maximum) to generate for a given molecule ?
I write in executable line AOMix : "molecule.out fragments.txt FO"
but after run, I can't find EDA in output.
I think it doesn't diagnose the fragments.
i made a thickness of transmembrane of 100 * 100 on vmd. but can we reduce the thickness of the transmembrane on vmd ?
In order to digitize smells, one would need a device that can recognize individual smells as binary inputs/outputs and then form the molecules required to create the smell. I would love to hear some ideas on this.
I know the definition (Maximum E-state of an atom in the molecule), but I don't understand how we get a number.
I have a problem calculate 3d descriptors using Chemopy(as Python modele).
Usually this function working normally, but sometimes occur same error...(Input file is same!!)
I added the image file that captured error messege.
l wonder why ouccur this problem .....
plz reply to me...
I am new to REMD simulations. I have performed REMD simulation on a short peptide in AMBER12. I need to calculate the acceptance ratios for all the replicas. Can anybody explain how and where to get this information in amber output files?
Hello
I want to model interaction between C60 and few some chemical compounds in a box with water. Can anybody suggest me any software tool (except gromacs) for such kind of work ?
I would be very grateful for that.
I'm looking for a database that contains generic synthetic reaction. Most databases I found only hold reactions for specific molecules. I'm interested in a somewhat more generic representation, or a hierarchical classification of reactions in a synthetic context (i.e. not enzymatic reactions).
Since I would like to process these reactions in an chemoinformatics context, the database should offer a machine readable download, e.g. RXN or Reaction- SMILES/-SMARTS/SMIRKS, with atom mapping.
Dear all:
I think from NBO calculation after running in Gaussian we can obtain Mullikan electrical charge for each atoms ,then we can compare this charge in TS with reactant ,but I don't know How we can calculate CT for all transition state structure?
Thanks in advance
Is there any way to find the IC50 values if we do not have the experimentally performed data?
Does anyone know how to consider the intra-molecular basis set superposition error of conformers for a molecule if I use Gaussian 09?
I am trying to get the Raman spectra of solutions with very low concentrations of amino acids 1mM-6 mM. However, I can not see their peaks because they are masked by the fluorescence of the solutions, which also prevents me from using long exposure times. I have no idea what is the source of this fluorescence because my buffer is 25 mM in Tris-HCl and 150 mM in NaCl (pH=7.2). Also, I always wash my cuvettes with soap and nitric acid before using them. Does anyone have any tips on how to decrease the fluorescence? By the way, I am using a 514 nm laser source.
I get convergence problems when I use the following input:
$contrl scftyp=rhf dfttyp=b3lyp tddft=excite
maxit=200 runtyp=energy icharg=-1 mult=1 $end
$tddft nstate=3 mult=1 iroot=1 tammd=.false. $end
$SYSTEM MWORDS=2400 MEMDDI=1600 $END
$SCF diis=.f. soscf=.f. NPREO(1)=0,-1,1,9999 $end
$FMOPRP NCVSCF(1)=2 mconv(4)=65 MAXIT=1000 IREST=2 $end
$guess guess=huckel $end
$basis gbasis=N31 ngauss=6 $end
$data cobalt compound
I have a crystal structure of azopyridine molecule linked to another (different) molecule by hydrogen bond. It is well known that azopyridine molecule shows trans to cis isomerization when exposed to UV (365 nm). Crystalline sample of this hydrogen bonded system becomes amorphous when it is exposed to UV (365 nm). We predict that the intermolecular hydrogen bond is breaking upon UV exposure. Could anybody explain how this effect can be reliably simulated in gaussian09?
Also, some of such photo-isomerization processes are reversible. How can one predict this reversibility computationally?
The AlogP parameterisation that I'd like an implementation of is defined in this J. Phys. Chem. paper from 1998: http://pubs.acs.org/doi/pdf/10.1021/jp980230o
Thanks in advance!