From owner-chemistry@ccl.net Mon Dec 9 02:33:01 2024 From: "Grigoriy Zhurko reg_zhurko[#]chemcraftprog.com" To: CCL Subject: CCL: Atomic masses used in Orca for computing vibrational frequencies Message-Id: <-55277-241209022753-23789-HRxY9pjg/TgAAVR7I/5mHg*o*server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 9 Dec 2024 10:27:41 +0300 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko===chemcraftprog.com] > This is the standard atomic weight. An interval is given because the value depends on the origin of the material. > From the ORCA manual at https://www.faccts.de/docs/orca/6.0/manual/contents/typical/frequencies.html > It is clear that ORCA uses atomic weights to calculate the hessian. But this can be changed afterwards using the orca_vib routine. Or during the calculation with the !Mass2016 keywords, that commands Orca to use the isotopic masses of the most abundant isotopes. I performed an Orca computation with !Mass2016 keyword. It indeed prints the masses of most abundant isotopes (12.0 for C, 1.00783 for H, etc). However the frequencies computed by Orca and my program do not match. I found that Orca in this case uses the mass 12.0004364861161 for C. For calculating this value, I computed a C4 molecule and divided a frequency produced by my program by the one printed by Orca. I remember that Orca uses some QRRHO approach instead of RRHO; firstly I thought that this is applied only for computing the entropy, but maybe for the frequencies computations too? Also, I have one more question for all: would you find useful if Chemcraft computes the vibrational spectrum for each variant of isotopes distribution in the molecule, and averages them and shows at a singe graph (like in the computations of mass spectra)? I see that e.g. for Cl the isotope Cl37 produces different frequencies than Cl35, and its percentage is rather high - 25%. Grigoriy. From owner-chemistry@ccl.net Mon Dec 9 10:35:00 2024 From: "Jean-Pierre DJUKIC djukic_-_unistra.fr" To: CCL Subject: CCL: Atomic masses used in Orca for computing vibrational frequencies Message-Id: <-55278-241209042550-25580-k9oUdBF9+feIxPVVn/3jrA|server.ccl.net> X-Original-From: Jean-Pierre DJUKIC Content-Language: fr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 9 Dec 2024 10:25:32 +0100 MIME-Version: 1.0 Sent to CCL by: Jean-Pierre DJUKIC [djukic ~~ unistra.fr] Please, preserve this academic diffusion list from propaganda and neoMacarthyism or start your own witchhunt elsewhere. Thank you. Le 07/12/2024 à 18:35, mikka.qc mikka.qc---proton.me a écrit : > Dear colleagues, > > I'm asking everyone to be strong and not engage or collaborate with > associates of Russian entities. The Russian government, as their > founder, is causing a lot of problems right now. They're invading > Ukraine and attacking civilian infrastructure. Plus, they've used > _chemical_ weapons like Novichok around the world. Also, Russia has > been disrupting undersea internet cables in Europe, which threatens > how we all communicate globally. These actions show they don't care > about international laws, rules or human rights. > The international community has rightly banned cooperation with Russia > for such reasons. > Working with them goes against our values and helps a regime that's > hurting the global community. > > > Best, > Mika Rossi > Aalto University > From owner-chemistry@ccl.net Mon Dec 9 11:10:00 2024 From: "=?utf-8?B?TWFyaXVzeiBSYWRvxYQ=?= mariusz.radon- -uj.edu.pl" To: CCL Subject: CCL: Atomic masses used in Orca for computing vibrational frequencies Message-Id: <-55279-241209074031-3690-wOqHRelrpQaR0etPX1ZVlg++server.ccl.net> X-Original-From: =?utf-8?B?TWFyaXVzeiBSYWRvxYQ=?= Content-ID: Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 9 Dec 2024 12:40:15 +0000 MIME-Version: 1.0 Sent to CCL by: =?utf-8?B?TWFyaXVzeiBSYWRvxYQ=?= [mariusz.radon]^[uj.edu.pl] Dear Grigoriy: > On 9 Dec 2024, at 08:27, Grigoriy Zhurko reg_zhurko[#]chemcraftprog.com wrote: > Sent to CCL by: Grigoriy Zhurko [reg_zhurko===chemcraftprog.com] >> This is the standard atomic weight. An interval is given because the value depends on the origin of the material. > >> From the ORCA manual at https://www.faccts.de/docs/orca/6.0/manual/contents/typical/frequencies.html >> It is clear that ORCA uses atomic weights to calculate the hessian. But this can be changed afterwards using the orca_vib routine. Or during the calculation with the !Mass2016 keywords, that commands Orca to use the isotopic masses of the most abundant isotopes. > > I performed an Orca computation with !Mass2016 keyword. It indeed prints the masses of most abundant isotopes (12.0 for C, 1.00783 for H, etc). However the frequencies computed by Orca and my program do not match. I found that Orca in this case uses the mass 12.0004364861161 for C. For calculating this value, I computed a C4 molecule and divided a frequency produced by my program by the one printed by Orca. > I remember that Orca uses some QRRHO approach instead of RRHO; firstly I thought that this is applied only for computing the entropy, but maybe for the frequencies computations too? I doubt it can have anything to do with the QRRHO approach. As you wrote, this should only affect the computation of entropy (and maybe other thermodynamics functions). I wonder if the deviations you observe might be related to whether or not the translations and rotations are projected out before computing the frequencies. Different program may adopt slightly different algorithms at this stage, possibly explaining these discrepancies. In such a case, the discrepancies would be molecule-dependent and perhaps even frequency-dependent within a given molecule. Are they? Is the C-12 “effective mass” of 12.00044 amu that you obtained from Orca by “reverse-engineering" identical for (a) different normal modes of the same molecule? (b) different carbon-only molecules, like C2, C3, C4? Perhaps you are well aware of this, but let me add the following: It looks like that you are interested in tiny effects, which are often overlooked by most people, partly for the reason that these effects or related discrepancies would be irrelevant in most (if not all) practical applications due to other sources of larger errors in computed frequencies, such as: (a) inaccurate computation of the harmonic force constant, (b) anharmonicity effects being neglected or inaccurately modeled, (c) fundamentally inexact separation of rotations and vibrations. Also, when concerning isotopically averaged masses, their uncertainties are also relatively large, e.g., for C which you discussed before, the uncertainty of the standard atomic weight is 0.002 amu (12.0116−12.0096) due to uncertainties of the individual isotopes’ abundances (atomic masses of the C-12 and C-13 isotopes are very accurately known). The uncertainty of the isotopically averaged mass is more important effect than including or neglecting the electrons’ masses (for C: 0.0003 amu). > Also, I have one more question for all: would you find useful if Chemcraft computes the vibrational spectrum for each variant of isotopes distribution in the molecule, and averages them and shows at a singe graph (like in the computations of mass spectra)? I see that e.g. for Cl the isotope Cl37 produces different frequencies than Cl35, and its percentage is rather high - 25%. > Grigoriy. I do not use Chemcraft myself, but the strategy you described is definitely a good approach to tackle the problem of isotope mixtures (better than using isotopically averaged mass to compute a single set of frequencies). Such a feature would be useful for some people in specific applications, but I guess that in mainstream applications there exist other far more importance sources of errors in theory (inaccurate hessian and anharmonicity neglected, neglect of the environmental effects) and the experimental band are usually too broad to ever bother about such “subtleties”. The same holds true about the computation of statistical thermodynamics corrections based on the RRHO (or QRRHO) model, which is a crude approximation in some molecules. Best regards, Mariusz Radon -- Mariusz Radon, Ph.D., D.Sc. Associate Professor Faculty of Chemistry, Jagiellonian University Address: Gronostajowa 2, 30-387 Krakow, Poland Room C1-06, Phone: 48-12-686-24-89 E-mail: mradon|*|chemia.uj.edu.pl (mariusz.radon|*|uj.edu.pl) Web: https://tungsten.ch.uj.edu.pl/~mradon ORCID: https://orcid.org/0000-0002-1901-8521