I am new to computational chemistry and my project now involves the use DFT calculations to find my products transition state/intermediate. The reaction involves a hydride shift followed by cyclisation to get to the final product. I am trying to find the best protecting group for my nitrogen atom and will be looking at several different protecting groups. Do you have a suggestions of literature and test files I could use to get my head around these calculations? Any advice would be much appreciated!

Many Thanks

]]>Add virtual bond connecting atoms H12 and H9 Dist= 3.27D+00.

Error parsing secondary structure:

QPErr — A syntax error was detected in the input line.

gua_inta.wfn

‘

Last state= “Top”

TCursr= 104 LCursr= 0

Error termination via Lnk1e in C:\G09W\l101.exe at Sat Jul 04 10:50:05 2020.

Job cpu time: 0 days 0 hours 0 minutes 0.0 seconds.

File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1

I have used the input below,

%chk=C:\Users\Soumyadeep Saha\Documents\gua_inta.chk

# opt freq b3lyp/6-31g density=current geom=connectivity counterpoise=2 out=wfn

gua_inta

0 1 0 1 0 1 0 1 0 1

C(PDBName=C,ResName=UNL,ResNum=1,Fragment=1) 0 -5.75200000 2.63500000 -0.45700000 H

N(PDBName=N,ResName=UNL,ResNum=1,Fragment=1) 0 -5.05200000 3.80600000 -0.09700000 H

N(PDBName=N,ResName=UNL,ResNum=1,Fragment=1) 0 -5.03300000 1.52100000 0.01000000 H

H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -4.00500000 1.53100000 0.03200000 H

H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -5.46900000 0.68300000 0.37400000 H

N(PDBName=N,ResName=UNL,ResNum=1,Fragment=1) 0 -7.01900000 2.64200000 0.16600000 H

H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -7.86300000 2.41400000 -0.35000000 H

H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -7.15900000 2.98700000 1.10900000 H

H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -4.14500000 3.96400000 -0.44500000 H

O(PDBName=O,ResName=HOH,ResNum=2,Fragment=2) 0 -2.36200000 2.74400000 0.03800000 L

H(PDBName=H,ResName=HOH,ResNum=0,Fragment=2) 0 -1.39200000 2.74400000 0.03800000 L

H(PDBName=H,ResName=HOH,ResNum=0,Fragment=2) 0 -2.68600000 3.10200000 -0.80400000 L

1 2 1.0 3 1.0 6 1.0

2 9 1.0

3 4 1.0 5 1.0

4

5

6 7 1.0 8 1.0

7

8

9

10 11 1.0 12 1.0

11

12

gua_inta.wfn

]]>I want to do BSSE correction of H3O+(H2O)4 system, So for this, I am giving keyword conterpoise=5, But getting error.

Can you please tell me what keyword I should use or how to do BSSE calculation of H3O+(H2O)4 system.

Thank you

]]>I am trying to calculate the Spin Orbit Coupling (SOC) of some molecules.

I calculated the absorption and emission wavelength in singlet state

Could you help me, how to calculate SOC from S1 (or S2… ) to T1 (or T2…) transition states.

Please tell me the method and process.

Thank you very much

]]>Dear Jack,

Have you tried re-orienting the molecule? Try making your Cs or C2 axis lie over the z-axis and use the cartesian frame of reference to define your symmetry operations, e.g. place the atoms which are supposed to be on the sigma-v plane on the xz plane and so on.

Gaussian tries to re-orient the molecule to get advantage of the symmetry but it’s better to help it.

I hope this helps!

]]>I don’t use Psi4, sorry. Maybe try Chimera or VMD, those are free. Chemcraft is my favorite but GaussView is just very easy to use and I’m getting lazier by the minute.

I hope this helps

]]>Hola Edgardo,

Thanks for bringing ORCA to our attention, I should break some old habits and work other pieces of software I just need more time.

Yes, you can work it with open shell systems but you have to consider alpha and beta spin densities separately, beware of the occupation numbers.

I hope this helps!

]]>Hola Pablo

It sounds right, I mean in the end there is nothing that prevents you from adding several NTO cubes into one and in the end each molecular orbital is the linear combination of other orbitals. I may be forgetting something here but I think there isn’t any fundamental prohibition to perform this linear combination (I’m assuming your weighing coefficients are the relative occupations). The only thing that would be fundamentally wrong would be to sum hole and particle NTOs

Gracias por leernos!

]]>Molekel 4.3 is already deprecated. I fixed the broken link but if you cannot download it from this blog anymore then I’m afraid I don’t have it (https://joaquinbarroso.com/tag/download-molekel/).

Sorry.

Hello Kiana

So the “D 1 1.00” means one single d function without scaling (or more precisely with a scaling factor of 1.00) is used. If two gaussian functions were to be used for this d orbital then the line would look like “D 2 1.00”

The following line are exponents and coefficients for the construction of this function, each gaussian function has the form c*exp{-zr^2} where c is the coefficient 0.800000 and the exponent is z = 1.000000

You may also some times have something like:

SP 2 1.0

number1,1 number1,2 number1,3

number2,1 number 2,2 number2,3

Where SP means the same exponents are used for S and P functions, hence number1,1 is the exponent and number1,2 and number1,3 are the coefficients for the first (of the 2 in SP 2 1.00) gaussian function used to construct this orbital.

It’s straightforward once you get the hang of it but I’ll admit it took me a while to get it down back in the old days. 🙂

I hope this helps