Quantum Chemistry - Science topic

I am expecting a broad range of views from fundamental research to manufacturing units. I will be more than happy if these suggestions use full to setup a small scale manufacturing startup( mostly table top unit) in semiconductor sector.

There are currently two mainstreams in science. One of them is hydrogels. A huge number of articles have appeared about smart hydrogels, their properties and applications. Hydrogels are made up of two components, polymers and water. However, in articles about hydrogels, water is almost never mentioned. As if it is not in the gels.

The second mainstream in water science is the nuclear quantum effect. It defines the special properties of water compared to other liquids. Therefore, nature has chosen water as the building block of its hydrogels.

The problem of understanding and cognition lies in the fact that polymers and water communicate with each other at the level of quantum mechanics: proton tunneling, zero point energy of water and polymer, quantum and thermal fluctuations.

Science requires the unification of these areas. It is desirable to unite specialists from these two areas to write a review article. Please write to me if the specialists have such a desire.

I want to calculate PECD spectra and in order to do so I require calculated electron density in terms of symmetry adopted spherical harmonic basis functions. How should I do that?

Calculating the temperature in the average number of Bosons in the following states:

A. 5

B. 0.5

C. 0.05

is it possible to calculate photoelectron Circular dichroism (PECD) using quantum chemistry?

Dear Orca users,

I'm new to ORCA... I want to perform a relaxed PES scan rotating 5 diedra angles 360º of many molecules.

I read in the manual that I should add in the input file the diedra angles as follow: D atoms1-4 = initial value, final value, n steps. I used to work with Gaussian, where the same calculation need the atoms, number of steps and how much degrees each step will rotate... My question is I always have to include the initial/final angle values or is there something simpler to create the input file? i.e., can I create the input file without have to obtain the initial diedra angles of each molecule?

Thanks for your time and help.

Using Gaussian software, how can I draw Fukui functions (f-, f0, f+)?

DFT Simulation,

Quantum chemistry,

Gaussian,

I would like to calculate the vertical ionization energy of a molecule using Gaussian16. And which is the best method to do it?

Crystal violet lactone in acidic condition (opened ring) is deep blue-purple color, resulting from the absorbance around 600 nm. Why is it not emitting fluorescence from this excitation (FL > 600 nm).

So far, only FL around blue-green (~500 nm) with blue light (420 nm) excitation was ever reported.

The green fluorescence could be resulted from the leuco form (closed ring) or the Sn -> S0.

But what happened to the 600 nm excitation?

Could it be excited state induced rotation of one of the rings leading to non-radiative relaxation?

Or anti-kasha, due to some vibronic coupling dissipating the S1?

If it's from rotation, does it mean in viscous or solid environment, >600 nm FL could be detected?

I am optimizing a W2O6 cluster with Gaussian09. But, the final geometry is nonsense, with the atoms collapsing into one another.

here is the input file

# opt b3lyp extrabasis

Title Card Required

0 1

W -2.35410995 0.25419377 -0.18979809

O -4.18555807 -0.10300014 -0.78963998

O -1.14901309 -1.29104889 -0.15021650

O -1.21400618 1.22822045 -1.45195316

O -2.62576349 1.13971563 1.53752799

W 0.11052123 -0.18873487 -1.17005821

O 1.71676340 0.35930291 -0.18962938

O 0.84723163 -1.00746272 -2.79133625

O 0

6-31G

****

W 0

LANL2DZ

****

File 721 does not exist

File 722 does not exist

S(n) -> S(n+1) and S(n+1) -> S(n)

Dear all,

I am trying to calculate the first 6 excited states (singlets and triplets) of a molecule using CIS and CISD module in GAMESS. The implementation of CIS in the Gamess input file is easy and I obtain the results. However, I am unable to find a keyword in the manual that will allow me to calculate the singlets and triplets with CISD. It will be really helpful if you can kindly help me with the input file that allows singlet and triplet excited states. Below I mention what I am using for the CIS module.

$contrl nprint=-5 ispher=1 cityp=cis maxit=200

scftyp=rhf $end

$system timlim=5700 mwords=1000 $end

$scf SOSCF=.FALSE. DIIS=.TRUE. DIRSCF=.TRUE. DAMP=.TRUE. $end

$cis nstate=6 dgaprx=.FALSE. NDAVIT=50 iroot=1 $end

$basis gbasis=KTZVP $end

$guess guess=huckel $end

$data

Methylene...CI... Cnv 2 Carbon 6.0 Hydrogen 1.0 0.0 0.82884 0.7079 $END

Dear collegues!

Now I am working with newly discovered cytochromes and trying to put heme with Fe2+ inside it using QMMM methods to optimize its geometry. Nevertheless, it turned out to be very hard to reach SCF convergence even for heme not in protein environment, but just itself with only two aminoacids - deprotonated CYS that coordinates iron and GLU which is covalently bound to one of heme tails (i did not forget to delete the corresponding hydrogen). I am using DFT/B3LYP/6-31G** level of theory (no particular reason why, just because this pack usually works), charge -3 and multiplicity 1. Geometry is a bit distorted, but I took it from pdb database (for one of cytochromes it is a native conformation), so I do not think it is a reason.

And you know... ORCA is dealing with it, but really by a finger's breadth, slowly, using its TRAH converger, with many warnings about negative diagonal hessian elements (this warnings disappear upon reaching convergence point) and negative HOMO-LUMO gap (in the end it is not negative, but small, +-0.3 eV or 0.01 hartree).

If so will be continued, I would not be able to run qmmm dynamics and I am not sure NWChem will be able to converge SCF as far as its algorithms are slower and weaker than ORCA's.

I have no idea what is going wrong and would be pleased by any advices. I attach input and output also.

Thanks in advance!

Do you consider yourself a real scientist in your field?

As for me, I don't because I don't know the answer of many basic questions in solid-state physics. For instance, from what's the energy origin of orbitalizing electrons? Is is the thermal energy at T>0 or some sort of quantum energy or both? What's exactly the group velocity of orbitalizing electronic waves and its relation to the ground state energy and thermal energy near T=0. I know there exist so many formal definitions of all the above terms! But is the exact relation between them? In particular, the quasi-free electrons in the conduction band (at T>0) what is exactly the nature of their (so-called) velocity in equilibrium, in the inter-collisional paths (between successive scattering with atoms )? Is is just their thermal velocity? or combination of this thermal velocity with some sort of quantum energy?

I need to store molecular geometries in redundant internal coordinates (RICs) and have so far been able to get all of the information I need aside from what the d.o.f.s correspond to. I presume that the "Redundant internal coordinate indices" hold this information but I cannot find information on them anywhere in Gaussian documentation or other forums, etc. It doesn't seem to be a connectivity matrix, but the numbers clearly correspond to each atom and it is not clear to me from analyzing the geometry visually either. I would really like to avoid having to write and validate code from scratch to backtrack this information from cartesian coordinates or pulling connectivity from a different output file format.

I have attached an example of the formchk file output from Gaussian optimization and frequency analysis for a basic case (methanol) but here is the crucial information for easy viewing:

Atomic numbers I N= 6

6 1 1 1 8 1

...

...

Redundant internal dimensions I N= 4

15 5 7 3

Redundant internal coordinate indices I N= 60

1 2 0 0 1 3

0 0 1 4 0 0

1 5 0 0 5 6

0 0 2 1 3 0

2 1 4 0 2 1

5 0 3 1 4 0

3 1 5 0 4 1

5 0 1 5 6 0

2 1 5 6 3 1

5 6 4 1 5 6

Redundant internal coordinates R N= 15

2.06335755E+00 2.07679249E+00 2.07679461E+00 2.73743812E+00 1.83354933E+00

1.90516186E+00 1.90518195E+00 1.84167462E+00 1.91434964E+00 1.94775283E+00

1.94775582E+00 1.96310537E+00 -3.14097002E+00 -1.07379153E+00 1.07501112E+00

Thank you for any and all insight!

Hey, I have been looking for it a lot. Are there sigma + - constants for meta substitution?

And also I couldn't find the sigma * constants.

I have just started using ORCA and was following a YouTube tutorial series by Dr. S. Kishor => https://www.youtube.com/playlist?list=PLJIwRG-f5Gjd95jUG4cGjfSxs2gQfQAza

I'm using ORCA 5.0.3 on windows 10 with an i5 9400 processor and 500 GB A2000 Kingston RAM. In the 16th video of the series, I was introduced to IR frequencies calculation with geometry optimization with the following input -

# avogadro generated ORCA input file

# Basic Mode

# GeomOpt + Freq for Acetone

! RHF OPT FREQ 6-311++G**

* xyz 0 1

C -3.50986 2.85550 -0.14979

C -2.02053 3.03306 -0.02862

H -3.77767 1.82632 0.10157

H -3.82355 3.06176 -1.17685

H -4.01762 3.55239 0.52151

C -1.41776 2.78670 1.32795

H -1.61034 1.75505 1.63245

H -1.85017 3.48112 2.05247

H -0.33688 2.94710 1.28593

O -1.32971 3.36340 -0.99127

*

Now, when I'm opening the output file (.out) using Avogadro 1.2.0, the molecule was loading, but the frequencies were not loading. I checked the output file, and they were there but were not coming in Avogadro (should render automatically while opening the output file). I opened the Vibration toolbar from the settings of Avogadro to find they were not loaded. Can anyone help me how to view the IR frequencies generated from ORCA in Avogadro or other software?

N.B. - I found a discussion in the ORCA forum about OfakeG which can convert the ORCA output file into a Gaussian output file and I used that to covert as I have institutional access to Gaussian and GaussView (https://orcaforum.kofo.mpg.de/viewtopic.php?f=8&t=5018&p=21189&hilit=OfakeG#p21189). I followed the documentation but I was unable to convert the file type. I got an error saying the application couldn't find the file.

1) Output File

2) Screenshot of Avogadro window

3) Screenshot of OfakeG application window

I learned from somewhere that ORCA is the most popular free and open-source computational quantum chemistry software developed by Frank Neese and others. Now, being a language enthusiast, I want to go through the package's source code. But I couldn't find that in GitHub or GitLab. The ORCAQuantumChemistry GitHub organization has only one repository with a collection of 'compound scripts' for use with the ORCA quantum chemistry software. Searching on Google also couldn't give me a result. Can anyone help me by providing the link to the source code?

I am using MP2/cc-pVDZ, MP2/cc-pVTZ, MP2/cc-pVQZ, QCISD/cc-pVDZ and QCISD/cc-pVTZ theories to calculate SPE of C2H4N4O4, but frequently met Error l502, that is likely to be caused by SCF convergence failure. Increasing the SCF cycle from default 128 to 512 doesn't help.

I understand that changing the convergence way to quadratically convergent SCF procedure (scf=qc or xqc) can solve my problem, and indeed it works. But it would influence the energy calculation results, making them obviously different from those obtained via normal SCF convergence way, and it will also increase the T1 Diagnostic of QCISD methods over an unacceptable value (eg. bigger than 0.05).

Part log files for your information

-----------------------------------------------------------------------------------------------

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

Rare condition: small coef for last iteration: 0.000D+00

>>>>>>>>>> Convergence criterion not met.

SCF Done: E(UHF) = -670.314163564 A.U. after 513 cycles

NFock=128 Conv=0.11D-03 -V/T= 2.0006

<Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 0.9099 S= 0.5770

<L.S>= 0.000000000000E+00

Annihilation of the first spin contaminant:

S**2 before annihilation 0.9099, after 0.7656

Convergence failure -- run terminated.

Error termination via Lnk1e in /app1/centos6.3/gnu/apps/gaussian/g16a6/g16/l502.exe at Mon May 30 16:51:42 2022.

-----------------------------------------------------------------------------------------------

I appreciate your kind help.

Hi to everyone! I would like to know if there is a way to "calibrate" DFT calculations without relying on experimental data.

I'm trying to validate some calculations of complex ion formation constants, considering 1,3-diamino-2-propanol as the ligand (NN' and NO) and Cd2+, Fe2+/Fe3+, Pb2+, Zn2+ as metal centers. I performed geometry optimizations+frequency calculation using:

- Gaussian09 as software.

- DFT theory with 6-31g++(d,p) for ligand's atoms and def2tzvp for metals (pseudopotentials for Cd and Pb)

- PCM for water as solvent.

-The final formation constant calculations was performed using Gaussian thermochemistry output.

Thank you in advance!

Hello,

I am using ORCA Ab initio method for my work. I got an below error:

[file orca_main/run.cpp, line 11467]: Cannot open input file: be.out

Can anyone suggest to me how to fix this error.

Thank you.

While using keyword Pop=ESP in the input file for running g09, the job gets terminated showing an error message. It happens only when the molecule has potassium atom in it. The error message is "GetVDW: no radius for atom 77 atomic number 19"

I am running a DFT-D3 geometry optimization with ORCA5.0 of a condensed system (a portion of a pdb file; no metal ions).

What I did? - I assumed it to be a closed-shell system but applied UKS treatment (!UKS) lest the system, in fact, turned out to be open-shell.

What I fear? - What could, or worse - WOULD, go wrong with mismatched keywords, i.e., applying !UKS with closed-shell systems OR !RKS with open-shell systems?

I have a problem running ADC2 excitation spectrum in Orca 5.0.3. The job finishes successfully, but the output contains no uv-vis spectrum. I use a typical input like

! KDIIS NOSOSCF ADC2 def2-SVP def2-SVP/C TightSCF

%mdci

nroots 6

end

Please, help me!

Reading some of David Deutsch's books convinced me that the multiverse is key to understanding quantum mechanics. Molecules are objects in the multiverse - can we use this knowledge to teach Hartree-Fock, Configuration Interaction, etc.? My hunch would be that using the multiverse consistently and from the beginning (instead of treating it as a possible "interpretation", to be tacked on at the end) would make quantum chemistry simpler to teach, instead of more difficult, if done right. I have not seen anything like this, though.

I would like to calculate the energy of a system when you can have the occupation number of a specific orbitals always at 1 (only 1 electrons all the time).

With gaussian I can select or discard some specific configurations but it is not really adapt to my problem.

Does someone know a software that could do it?

A beam of identical particles sent in a Stern-Gerlach equipment splits in four parts. What is the maximum value of m_l+m_s for these particles?

m_l is the magnetic Quantum Number & m_s is the spin Quantum Number.

In Becke's B3LYP hybrid functional, Fock exchange is being mixed with Slater LSDA exchange (and then plus gradient correction), plus correlation expressions. But what LSDA exchange parametrization is used?

So which LSDA parametrization is used nowadays in B3LYP? Did people stick to the VWN version from Becke's initial paper or did they switch to the more modern PW version as Becke probably did? Or do different implementations in program packages use different versions?

Dear all,

I did the optimization and frequency for a system in which contains C,N and H atoms using the following keywords in the input file:

# opt freq=raman b3lyp/6-31g(d,p) pop=full gfinput gfprint iop(6/7=3).

From this calculation, I got 1 imaginary frequency and the calculation was terminated normally. So, I assume that probably this is the transition state. Then I want to include the diffuse function in the basis set then I repeat the same calculation using the following keywords,

# opt freq=raman b3lyp/6-31+g(d,p) pop=full gfinput gfprint iop(6/7=3)

From the latter, I got the following error,

Inaccurate quadrature in CalDSu.

Error termination via Lnk1e in /soft/G09_RevC01/g09/l1002.exe

I already tried the suggestions from the link below but, still got the same error.

As I understand this related to the integration method and the initial guess wave function used in Gaussian09 (by the default is Harris, CMIIW). Does anyone know how to solve this problem? Any explanations or suggestions are welcomed.

Thank you.

I need to calculate BSSE.

I got the following error message.

QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.

#HF/6-31G(D) COUNTERPOISE=2

'

Last state="GCL"

TCursr= 910 LCursr= 13

Error termination via Lnk1e in C:\G98W\l1.exe.

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

File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1

Herewith I have attached my input file and output file.

Could you please anyone help me to rectify this error.

Thanks

I am checking the interaction between two molecules, but when I am trying to optimise, the bonds are breaking, and the original structures are deforming. I want to optimise while retaining their initial structure. There must be a command like geom=connectivity to do such things. Please help.

What is the best free program to calculate quantum-chemical molecular descriptors, such as the total electronic energy, energies of the highest occupied and lowest unoccupied molecular orbital, and absolute electronegativity? And, for thermodynamic descriptors, like, standard Gibbs free energy and enthalpy?

For the COOP function I get a message that indicates the program cannot find my Group.txt file even though I have systematically placed a copy in every folder within the Gaussum directory. Can you tell me how I can create the Group.txt file. I have attached the Gaussian output file also below. Secondly, I like to know that, from the DOS image in gausssum, how can I understand one peak is belongs to which orbital state. I also like to know how I draw the DOS in origin from the Gausssum?

Dear all,

Some help understanding this GAMESS-US output file would be appreciated. I am well versed in GAUSSIAN and ORCA, but unfortunately, with no license for GAUSSIAN and a strict requirement that I need to use GAMESS-US (required to parameterise the Amber force field), I'm having to understand the cryptic output of GAMESS-US extremely quickly.

Firstly, I optimised the electronic structure of my system with:

$SYSTEM MEMDDI=400 MWORDS=200 $END

$CONTRL MAXIT=200 SCFTYP=RHF DFTTYP=B3LYP RUNTYP=OPTIMIZE ICHARG=-2 MULT=1 $END

$STATPT NSTEP=50000 OPTTOL=0.01 $END

$SCF DAMP=.T. SOSCF=.F. DIIS=.T. $END

$BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END

........

This produced an equilibrated geometry that I am happy with. However, when I try performing a Hessian calculation (see attached output log file), I get the cryptic message:

FT ANALYTIC HESSIAN PRESENTLY HAS 5 RESTRICTIONS:

$CONTRL: SCFTYP MUST BE EITHER RHF OR UHF

$CONTRL: POINT GROUP SYMMETRY NOT ALLOWED, SET NOSYM=1

$SCF: AO INTEGRAL DIRECT: SET DIRSCF=.TRUE.

$CPHF: AO INTEGRAL DRIVEN: SET CPHF=AO

AND THE FUNCTIONAL MUST NOT BE OF META-GGA TYPE.

ALTERNATIVELY, CHOOSE SEMI-NUMERICAL DIFFERENTIATION,

$FORCE: METHOD=SEMINUM

PLEASE FIX ERROR(S) AND TRY AGAIN.

EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT 11:37:47 31-JUL-2021

580000 WORDS OF DYNAMIC MEMORY USED

CPU 0: STEP CPU TIME= 0.00 TOTAL CPU TIME= 0.1 ( 0.0 MIN)

TOTAL WALL CLOCK TIME= 0.1 SECONDS, CPU UTILIZATION IS 100.00%

This is very important: I have 6 calculations to perform. So far, calculations #1 and #2 (containing zinc) have worked and their input is the same as the inputs that are failing.

Help and suggestions are most welcome.

Dear all,

I no longer have a Gaussian license so I've moved over to GAMESS. I have a set of GAMESS input (inp) files automatically generated whilst running AMBER's MCPB.py metal-binding process.

I've never used GAMESS before and I only intend on using it to calculate the HESSIAN for Molecular Dynamics force field parameterisation of metals. I'm seeing an error based on the .inp file automatically generated with AmberTools21.

I would be very grateful for any suggestions on why the input file format is causing an error. Note: there are NO blank lines in the input files except after the fine $END at the bottom of the file. The appearance here is due to the terrible/rubbish TextBox in ResearchGate.

=============================================================

=============================================================

This is the error:

*** ERROR!

This is the input:

I need to improve my DFT calculation energies for Metal ligand complex by forcing the program to rearrange the molecular orbital vectors. But I am stuck with finding a correct order of energy orbitals. Any thoughts about MO swapping ???

I have done some Transition state calculations on UB3LYP/cc-pVTZ level of theory and verified from IRC calculations too. Now i am trying same transition states calculations on CBS-QB3 level of theory but getting an error every time. Any suggestions to overcome this problem ?

While strong catenation is almost exclusively reserved for C, some transition and post-transition elements can oftentimes take part in delocalized electron systems and ring systems. But does the two come together, that is, is there any known aromatic compound that has two adjacent transitional/post-transitional elements in aromatic ring as heteroatoms? If Yes or No, then Why?

Suppose for a 5-valency element, there are two mutually perpendicular pi-orbitals (along with a sigma molecular orbital) that make a triple bond between two atoms, remaining two valency "hands" are used up for taking part in two mutually perpendicular aromatic ring system. Keeping in mind instability of benzyne and ONC (Octanitrocubane), would that structure be chemically stable and permissible by quantum chemistry? If yes, then what kind of novel properties can be expected from the compound and what would be the stability of it? What would the most suitable element for this purpose?

Attached with it is a Lewis structure of a tentative complex of X metal. Note, the two aromatic structures are not coplanar, rather they are orthogonal

im looking for a diy at home (home lab) molecular magnet in a chemical suspension that is stable at room temperatures and cheap

benzene C-C bond length is 1.39 angstrom, graphene 1.42 angstrom, so like an inscribed circle in a perfect hexagon, anything narrower than 1.20 or 1.229 angstrom diameter would suppose to pass through it. H, He, as well as most 2nd and 3rd row post-transition elements at periodic table have radius (ionic, covalent, atomic).But atoms are not solid, and the upper and lower (or front and back) delocalized electron cloud would act as potential barrier (not necessarily purely coulombic). However in quantum mechanical realm, especially lighter elements can more easily quantum-tunnel. Have there been any comprehensive review on selective atomic/molecular species sieving with PAH/ Graphene sheets? please let me know

I have been running some S1 (excited state) optimization calculations of imine based compounds in g16/q-chem, and normally the -C=N- double bonds tend to bend to dihedral angle ~90 deg. This is normal to me and probably how imine trans-cis photoisomerization occured.

When I extended the conjugation (by adding -CH2=CH2- moiety), I found the -C=N- are no longer bending in S1 optimization, even I manually bend them (They bend back to planar!!).

Is the enhanced "conjugation energy stabilization" to blame?

I have been running excited state (Mostly TD) geometry optimization in Gaussian or Q-chem. Most of my compounds have exclusive HOMO -> LUMO (amplitude^2 ~ 1) at excitation state 1 (B3LYP). But when it comes to CAM-B3LYP, many transitions comprised 1 excitation state, usually I can still identify the state I want for optimization.

The thing is, during optimization, let's say state 3, the excited states crossed. So in the half-way of optimization, previous state 3 could become state 2, and I ended up optimizing a different state 3, which was previously state 2. Then the new state 3 was not the state I am interested in (comprised different linearly combined transitions)

Is there any commands that I can try to keep the running "locked to" to specific transitions?

Dear Quantum Chemistry experts,

I am trying to run a GAMESS calculation with an external basis. The purpose is to simply test the input format with the basis set information added to $Data section in the input file. Below you can find an example of H2O molecule that I am trying to run it with the 3-21G basis set supplied from the EMSL repository. I have already managed to solve this test calculation with an input card of the 3-21G basis set read from the $BASIS control statement. Would be really helpful if anyone can correct the error in the input file as I constantly get an error.

=============================================

$CONTRL SCFTYP=MCSCF MPLEVL=2 COORD=UNIQUE $END

$SYSTEM timlim=5700 mwords=1000 $end

$GUESS GUESS=HUCKEL $END

$DET NCORE=1 NACT=6 NELS=8 $END

$MCQDPT NSTATE=1 ISTSYM=1 REFWGT=.TRUE. $END

$DATA

WATER...3-21G BASIS...FORS-MCSCF...

Cnv 2

OXYGEN 8.0 0.0 0.0 0.0

HYDROGEN 1.0 0.0 0.7572157 0.5865358

OXYGEN

S 3

1 0.3220370000E+03 0.5923939339E-01

2 0.4843080000E+02 0.3514999608E+00

3 0.1042060000E+02 0.7076579210E+00

L 2

1 0.7402940000E+01 -0.4044535832E+00 0.2445861070E+00

2 0.1576200000E+01 0.1221561761E+01 0.8539553735E+00

L 1

1 0.3736840000E+00 0.1000000000E+01 0.1000000000E+01

HYDROGEN

S 2

1 0.5447178000E+01 0.1562849787E+00

2 0.8245472400E+00 0.9046908767E+00

S 1

1 0.1831915800E+00 1.0000000

$END

=========================================================

I thank you in advance for time and consideration.

Regards

Hi everyone

I'm planning to do a potential energy surface scan over a specific bond for a doubly ionized Methyl Chloride (CH3Cl2+ over C-Cl bond) using Gaussian 16 (UNIX-based operating system), my question is, how to extract the energy at each point from the output file and how to specify the bond that we want to do the scan over, in the code,

the code I initially used is shown here: (I feel there should be a line specifying the CCl bond)

%chk=CCl.chk

%mem=9GB

%NProcShared=4

#scan td=(nstates=6) wb97xd/aug-cc-pvtz

CH3Cl neutral GS syn

2 1

C

H 1 B1

H 1 B2 2 A1

H 1 B3 3 A2 2 0.0

Cl 1 B4 4 A3 3 0.0

B1=1.07011

B2=1.19035

B3=1.19148

B4=1.72691

A1=94.56838

A2=69.00098

A3=52.79175

The Hartree–Fock (HF) method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system in a stationary state. Why does the Hartree-Fock require the Molecular Orbitals to be orthogonal to each other?

Dear All,

I struggle with determining the most optimal multiplicity of small metal oxide nanoclusters, e.g. Fe2O3 or Al2O3. For instance, here they say https://pubs.rsc.org/en/content/articlepdf/2014/cp/c4cp02099e that singlet state is the most stable one as there are formaly Fe3+ and Fe2+ cations with total spin number of S=-5/2 and S=2, respectively. However, I don't really understand how this sign is determined. Is it plausible to do it a priori, i.e. not through trials and errors?

In case of Al2O3, the triplet state, i.e. with two unpaired electron is somehow more stable than singlet one. I don't really understand how it is possible for the Al3+ cations. Al belongs to block p, so after the valence electrons transfer to oxygen atoms all molecular should be closed as far as I'm concered. However, I checked and in fact the triplet state is more stable.

I would like to understand how I can determine the optimal multiplicity because I have a whole series of metal oxides and I'm not happy with doing it by trials and errors.

Thank you for all suggestions.

Recently I had this problem: to calculate in Gaussian the energy of a hydrogen bond between methyl acetate and heavy water. Am I right that i need to calculate the corresponding thermodynamic quantities for the two systems shown on the slide, taking into account the solvation effects. In addition, I recently have started taking the first steps in quantum chemistry and dont know what is right way to compose an input file (not clear how to add heavy water to the SCRF list and some other aspects).thank you in advance.

It is well known that for a closed shell (all electrons are paired up) molecule, the HOMO-LUMO gap is related to its stability. However, I often see that the same argument is used for open-shell systems (Unrestricted calculation). In such a case, the authors consider energies of both alpha and beta spin orbitals, and the orbital with the highest energy is considered as SOMO. Similarly, the LUMO is decided among both alpha and beta, and the respective gap is considered as the SOMO-LUMO gap. Next, the authors discuss the stability of the system based on that value.

However, to the best of my understanding, for an unrestricted calculation, three SOMO-LUMO gaps can be calculated (1) Gap between alpha spin HOMO and alpha spin LUMO (2) Gap between beta spin HOMO and beta spin LUMO, and (3). The method I mentioned above (considering both alpha and beta).

So, my questions are the following,

a) Is it technically correct to relate stability with the SOMO-LUMO gap calculated by method 3 for an open-shell system? Is it even possible to draw such a relation? How correct are such value and such correlation? If yes, then is there any reason why we are ignoring the other two gaps?

b) Are the gaps obtained by an unrestricted calculation have any practical significance at all (As argued here: https://joaquinbarroso.com/2018/09/27/the-homo-lumo-gap-in-open-shell-calculations-meaningful-or-meaningless/)

Any insightful response will be welcome. Thank you in advance.

I read a review paper on СOVID. See the file. There is nothing about the

role of water in the process of infection and treatment from СOVID. How does a virus receive information from a cell that it can be attacked? How orders are transmitted in a cell about the beginning and end of complex processes of synthesis of biological molecules. Meanwhile, the role of water as a matrix of these processes is very great. Using the simplest models of the hydrophobic process, we have shown that in the water of the body, which is responsible for the hydrophobic interaction, there should be a large contribution of the water zero point energy (ZPE). A simple ZPE model is a harmonic oscillator whose energy is quantized. ZPE is a quantum phenomenon. The presence of ZPE in the body can be easily checked by the isotope effect. If there is a ZPE contribution in the cell water, then there must be an isotope effect.

To do this, you need to do the following experiment. To a certain concentration, humans and mice tolerate D2O well. It is necessary to select this concentration and compare the infection with COVID without the addition of D2O and with H2O.

I have not found any such research. If someone has such opportunities, I will consult in detail.

(The image is taken from wikipedia https://en.wikipedia.org/wiki/Periodic_table_(crystal_structure) ,

and I claim no originality of creating the image)

The reason of the following structures are given in wikipedia, with some exceptions, at room temperature.

If all of these can be explained in terms of electronic configuration , then a significant electronic-to-crystal structure interrelation in simpler terms can be obtained.

(and possibly, ratio of metallic bandgap or Fermi energy etc. like energy parameters and average electron K.E at room temperature, then I think the correlation would be stronger. Perhaps, if one replaces spherical model of a metallic atom with its feasible 3D dirctional variation of outermost electron shell geometry, the the correlation is likely to be even stronger)

Can anyone recommend some any software/models available that can predict substance reactivities and the reaction yield under a specific set of reaction conditions process and proposing pathways to synthesize target molecules from a complex mixture?

I am stuck between Quantum mechanics and General relativity. The mind consuming scientific humor ranging from continuous and deterministic to probabilistic seems with no end. I would appreciate anyone for the words which can help me understand at least a bit, with relevance.

Thank you,

Regards,

Ayaz

For a little background, I'm interested in dabbling more into computational chemistry since I had it as a course last year for my MSc. We used Quantum Espresso back then and that's what I plan to use. My intention is just for some light DFT calculations in general for surface catalysis or with nanotubes, mostly periodic based. Planning to build a system and was wondering if the processor and RAM are enough for my purposes, which will be an 8 core Ryzen 7 3700X and 32GB, respectively. Are these enough for light to medium intensity calculations in terms of time taken for calculations to run?

I would like to calculate the reaction kinetics using gaussian. The reactants are two molecules that form amide bond and resultant is polyamide.

What would be the transition state in this reaction?

I am trying to calculate the enthalpy of formation for an organic ion(ex: Carbamate), but i can only find the method quantum chemistry, and the result can't be satisfied.

is there other method exist? contribution of group?

I have been thinking about a material that was made 6 months ago, which is a tetramethylsiloxane linked to a thiazolidinedione and finally to a naphthalene, but I can't find the original paper (if someone can find it please tell me) but that material had a time of duration of 2 hours until the bond of thiazolidinedione to naphthalene is broken and the material is no longer hard but I know it is an isomeration but the bond does not know why it occurred, could someone tell me that defines the time of the bond in molecular switches or is there any related role please?

I was looking under what conditions gold can bind to carbon under room temperature conditions,but I have the question of what defines the stability of a link when high electric currents are applied? How to calculate a nanowire that will conduct high voltage with a carbon-gold bond in the chain

(Probing the nature of gold–carbon bonding in gold–alkynyl complexes nature)

Could someone tell me that it defines magnetism at the quantum level, that is, quantitatively molecular magnets that make them attractive or repellent (I am not referring to electron density and geometric or folding optimization methods) but to the interaction of spins? that according to some texts that I have read have a pauli exclusion principle when they enter an organometallic complex

Dear HPC-guys,

my lab has about 20k euro to buy a small cluster for CFD and quantum chemistry.

We are thinking about buying two servers:

2xXeon 6240

2x32GB

DDR4 Raid Perc H740P

HDD 2x240Gb SSD

Is this a good idea? What do you think?

Why shape of an orbital calculated by solving schrodinger's equation on hydrogen atom is closely followed by other atoms, even when net force on an individual electron is no longer central and inverse-square ?(I am using classical terminology). If it is not, how much is the difference? please provide links for graphical depiction of shape (NOT SIZE) difference between hydrogen atom and other atom orbital.

The hydrogen spectral lines are organized in various series. Lyman series are the lines corresponding to transitions targeting the ground state.

Most pictures dealing with hydrogen spectra and available in the web are recordings dealing with extraterrestrial hydrogen sitting in celestial entities. Otherwise they are illustrations obtained not from experimental recordings, but from the well known Rydberg formula.

Of interest for the undersigned are pictures of Lyman series as recorded in laboratory observations of hydrogen atoms, with the atoms sitting in the laboratory itself. Not extraterrestrial hydrogen, nor molecules H2, even if the molecules are sitting nearby.

Presumably such recordings would have required ultraviolet sensitive CCDs, UV photographic plates, or similars. Particularly relevant would be careful raw recordings of Lyman series that INCLUDE THE ALPHA-LINE at 1216 Å.

Experimental remarks about the Lyman alpha-line, difficulties to observe it ---if any---, line width, line broadening, etc., and difficult-to-explain anomalies, are of particular concern. So far Web searching has not been successful.

I would appreciate any link or suggestions as to how to obtain the pictures and experimentally based information of the kind explained above.

Most cordially,

Daniel Crespin

We know that for Spin-¹/₂ particles, we can find the Creation and Annihilation operators from the Spin operators by using Jordan–Wigner transformation and also for Spin-1 particles, we can utilise Holstein-Primakoff transformations for mapping bosonic Creation and Annihilation operators to the Spin operators. But suppose if we need to find the same relationship for Spin-³/₂ or Spin-2 particles or other higher spin particles, then how can we approach to it?

I will be highly grateful if someone kindly clarifies my doubt.

Hello,

I am building a database of simulated properties for chemicals. However, before starting, I was wondering if there is any research available on the efficiency of parallelisation of the ORCA quantum chemistry package. I am especially interested in the sweet spot of cores.

Thanks,

Julian

Hello, I have trouble with transitional state calculation in gaussian 16 program. I started with the first frequency calculation with cartesian coordination and it ends up normally. the input command and ended output massage of first frequency as followed:

#frequency input:

%int=TS2

%d2e=TS2

%skr=TS2

%Nosave

%chk=TS2

%rwf=TS2

%cpu=4

#n b3lyp/def2svp empiricaldispersion=gd3bj freq

****def2svp****

0 1

(cartesian coordination)

#frequency output ended massage :

00001280,-0.00010827,-0.00000806,-0.00006098,0.00000975,-0.00001458,0.

00000041,-0.00000047,0.00001420,-0.00002694,-0.00012206,-0.00001580,-0

.00002062\\\@

LENDING MONEY TO FRIENDS CAUSES THEM TO LOSE THEIR MEMORIES.

-- PETER'S THEORY OF RECIPROCAL INHIBITION OF FISCAL RECALL

Job cpu time: 0 days 4 hours 37 minutes 37.7 seconds.

Elapsed time: 0 days 7 hours 37 minutes 9.2 seconds.

File lengths (MBytes): RWF= 390 Int= 0 D2E= 0 Chk= 27 Scr= 1319

Normal termination of Gaussian 16 at Fri Oct 16 07:40:04 2020.

However, when continues with transitional state geometry search, l301.exe error occurs with hint massage "unrecognized in LdAtmC" at the end of output file. it really baffle me because all the geometry and wavefunction detail are continued from checkpoint file. The geometry optimization command and selected output file massage as followed:

#geometry optimization input:

%int=TS2

%d2e=TS2

%skr=TS2

%Nosave

%chk=TS2

%rwf=TS2

%cpu=4

#n b3lyp/def2svp empiricaldispersion=gd3bj

opt=(redundant,ts,readfc,loose,recalcfc=5,Z-matrix,noeigentest,nolinear,nrscale,notrust)

nosym guess=read freq geom=check

****def2svp****

0 1

(end)

#geometry optimization output ended massage :

(Omited)

Input orientation:

---------------------------------------------------------------------

Center Atomic Atomic Coordinates (Angstroms)

Number Number Type X Y Z

---------------------------------------------------------------------

1 13 131003 -1.739946 0.561761 -0.155305

2 6 61000 -1.067005 2.357661 0.197053

3 8 81003 -0.165297 1.177915 -0.550000

4 6 61003 -2.572009 -1.131958 -1.230006

5 6 61003 -2.060566 -1.648024 -2.541631

6 6 61003 -3.597962 -0.140638 -1.015148

(Omited)

Rotational constants (GHZ): 0.3499893 0.1370911 0.1269179

Standard basis: def2SVP (5D, 7F)

IAtTyp= 131003 unrecognized in LdAtmC.

Error termination via Lnk1e in /pkg/gaussian/g16/g16/l301.exe at Fri Oct 16 11:14:35 2020.

Job cpu time: 0 days 0 hours 0 minutes 0.4 seconds.

Elapsed time: 0 days 0 hours 0 minutes 0.8 seconds.

File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 27 Scr= 1

Can some nice person who has experience solving this kind of problem teach me how to solve it? Thank you in advance.