From owner-chemistry@ccl.net Wed Feb 23 14:29:00 2022 From: "Andrew DeYoung andrewdaviddeyoung()gmail.com" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54598-220223134908-6771-bS09GApKLr5tyScd7VRSaw#server.ccl.net> X-Original-From: Andrew DeYoung Content-Type: multipart/alternative; boundary="00000000000050f18705d8b3ebe7" Date: Wed, 23 Feb 2022 13:48:51 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung]^[gmail.com] --00000000000050f18705d8b3ebe7 Content-Type: text/plain; charset="UTF-8" Hi, Could you please help me to understand the "double slash" notation that I see in quantum chemical literature? The notation is: method/basis set//method/basis set What is the convention -- if any -- for the order of the calculations, (a) or (b)? (a) Is the calculation before the "//" performed first, while the calculation after the "//" is performed second? In other words, "do this [left], then that [right]"? (b) Or is it the other way around, meaning that the left-hand calculation is performed ON the output of the right-hand calculation? In other words, somewhat like an operator acting on a wave function; "do this [left] on the output of that [right]." Below are two examples from the literature. I try to reason through the notation based on these examples: (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, 984-1010 ( https://doi.org/10.1002/jcc.540160807 ). In this paper, ab initio calculations were performed to determine torsional parameters for organic molecules and ions. From the abstract, "The rotational energy profiles were obtained at the HF/6-31G*//HF/6-31G*." In certain cases, they also used MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I think this means an initial, unconstrained geometry optimization of the entire molecule/ion was performed first, followed by a geometry optimization at each selected, constrained value of the torsional angle. In the case of MP2//RHF, then, is MP2 used for the initial optimization and RHF for the scan? Because RHF is less expensive, I think, that would probably make sense. Based on this, I would say that MP2//RHF means that MP2 is performed first and RHF is performed second; in other words, the "double slash" notation is read from left to right. So interpretation (a) above is correct. (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( https://doi.org/10.1021/ja010534f ). In this paper, the free energy of solvation, DeltaG_s, is calculated using an implementation of the polarizable conductor model (CPCM) -- see the third page (p. 7316) of this paper. Near the top left-hand side of that page, it says, "The CPCM calculations were performed as SPCs (single-point calculations) using the 6-31G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six systems." Based on that description, the HF geometry optimization was performed first and the CPCM single-point calculation was performed second. So, if my reasoning from example (1) above is correct (i.e., interpretation (a) above), I'd expect the "double slash" notation in the paper to be HF//CPCM. But, in fact, it's not. In the Results section near the bottom of the left-hand side of the third page (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted S1, S2, and S3 [in Table 1]." This, I think, implies that interpretation (b) above is correct. The strange thing, though, is that at the bottom of Table 1 on the fourth page [p. 7317], the definitions of S1, S2, and S3 are different from those stated in the text, by an "extra" "HF" to the left of the "//"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)." It's entirely possible, then, that there is no set convention for "double slash notation" in quantum chemistry (or that I'm misinterpreting these papers). Could anyone shed some light on this, since I'm not a quantum chemist? Thanks so much for any insight you can provide, Andrew Andrew DeYoung, PhD Carnegie Mellon University --00000000000050f18705d8b3ebe7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

Could you please help me to underst= and the "double slash" notation that I see in quantum chemical li= terature?=C2=A0 The notation is:=C2=A0

method/basi= s set//method/basis set

What is the convention -- = if any -- for the order of the calculations,=C2=A0(a) or (b)?=C2=A0=C2=A0

(a) Is the calculation before the "//" pe= rformed first, while the calculation after the "//" is performed = second?=C2=A0 In other words, "do this [left], then that [right]"= ?

(b) Or is it the other way around,=C2=A0meaning = that the left-hand calculation is performed ON the output of the right-hand= calculation?=C2=A0 In other words, somewhat like an operator acting on a w= ave function; "do this [left] on the output of that [right]."

Below are two examples from the literature.=C2=A0 I t= ry to reason through the notation based on these examples:

(1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 1= 6, 984-1010 (=C2=A0https://doi.org/10.1002/jcc.540160807 ).=C2=A0 In this pape= r, ab initio calculations=C2=A0were performed to determine torsional parame= ters for organic molecules and ions.=C2=A0 From the abstract, "The rot= ational energy profiles were obtained at the HF/6-31G*//HF/6-31G*."=C2= =A0 In certain cases, they also used MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//= MP2/6-31G*.=C2=A0 I think this means an initial, unconstrained geometry opt= imization of the entire molecule/ion was performed first, followed by a geo= metry optimization at each selected, constrained value of the torsional ang= le.=C2=A0 In the case of MP2//RHF, then, is MP2 used for the initial optimi= zation and RHF for the scan?=C2=A0 Because RHF is less expensive, I think, = that would probably make sense.=C2=A0 Based on this, I would say that MP2//= RHF means that MP2 is performed first and RHF is performed second; in other= words, the "double slash" notation is read from left to right.= =C2=A0 So interpretation (a) above is correct.

(2)= Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 (=C2=A0https://doi.org/10.1021/ja010534f ).=C2=A0 In this paper, the free energy of solvation, DeltaG_s, is calcul= ated using an implementation of the polarizable conductor model (CPCM) -- s= ee the third page (p. 7316) of this paper.=C2=A0 Near the top left-hand sid= e of that page, it says, "The CPCM calculations were performed as SPCs= (single-point calculations) using the 6-31G(d) and 6-31+G(d) basis sets on= the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six systems.&q= uot;=C2=A0 Based on that description, the HF geometry optimization was perf= ormed first and the CPCM single-point calculation was performed second.=C2= =A0 So, if my reasoning from example (1) above is correct (i.e., interpreta= tion=C2=A0(a) above), I'd expect the "double slash" notation = in the paper to be HF//CPCM.=C2=A0 But, in fact, it's not.=C2=A0 In the= Results section near the bottom of the left-hand side of the third page (p= . 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), CPCM/6-31+G(d= )//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted S1, S2, and S3= [in Table 1]."=C2=A0 This, I think, implies that interpretation=C2=A0= (b) above is correct.=C2=A0 The strange thing, though, is that at the botto= m of Table 1 on the fourth page [p. 7317], the definitions of S1, S2, and S= 3 are different from those stated in the text, by an "extra" &quo= t;HF" to the left of the "//"; there, they state, "S1: = CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: CPCM= /HF/6-31+G(d)//HF/6-31+G(d)."



--00000000000050f18705d8b3ebe7-- From owner-chemistry@ccl.net Wed Feb 23 15:57:00 2022 From: "Frank Jensen frj!^!chem.au.dk" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54599-220223155537-14894-w2VHyip38H3es961d9Inrw|a|server.ccl.net> X-Original-From: Frank Jensen Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_AM8PR01MB80282D446FC73CA48A1B10299C3C9AM8PR01MB8028eurp_" Date: Wed, 23 Feb 2022 20:55:23 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj\a/chem.au.dk] --_000_AM8PR01MB80282D446FC73CA48A1B10299C3C9AM8PR01MB8028eurp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 VGhpcyBQb3BsZSBub3RhdGlvbiBpbmRpY2F0ZXMgdGhhdCB0aGUgbW9sZWN1bGFyIHN0cnVjdHVy ZSBpcyBvcHRpbWl6ZWQgKHRvIGEgc3RhdGlvbmFyeSBwb2ludCwgbWluaW11bSBvciBzYWRkbGUg cG9pbnQpIHdpdGggdGhlIGNvbWJpbmF0aW9uIG9mIG1ldGhvZCBhbmQgYmFzaXMgc2V0IHRvIHRo ZSByaWdodCBvZiB0aGUgLy8NClN1YnNlcXVlbnRseSB0aGUgZW5lcmd5IGlzIGNhbGN1bGF0ZWQg 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[marcel.swart:_:gmail.com] --Apple-Mail-984DEA06-7097-4CFA-BBF0-6AE41D7F6F9E Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable A single point energy calculation was done with method mA and basis bA, on g= eometry that was optimized with method mB and basis bB: mA/bA//mB/bB Marcel Swart FRSC FYAE MAE, Prof. Dr. ICREA Research Professor at University of Girona Director of Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi Univ. Girona, Campus Montilivi (Ci=C3=A8ncies) c/ Maria Aur=C3=A8lia Capmany i Farn=C3=A9s, 69 17003 Girona, Spain www.marcelswart.eu marcel.swart%%gmail.com vCard addressbook://www.marcelswart.eu/MSwart.vcf > On 23 Feb 2022, at 21:57, Andrew DeYoung andrewdaviddeyoung()gmail.com wrote: >=20 > =EF=BB=BF > Hi, >=20 > Could you please help me to understand the "double slash" notation that I s= ee in quantum chemical literature? The notation is:=20 >=20 > method/basis set//method/basis set >=20 > What is the convention -- if any -- for the order of the calculations, (a)= or (b)? =20 >=20 > (a) Is the calculation before the "//" performed first, while the calculat= ion after the "//" is performed second? In other words, "do this [left], th= en that [right]"? >=20 > (b) Or is it the other way around, meaning that the left-hand calculation i= s performed ON the output of the right-hand calculation? In other words, so= mewhat like an operator acting on a wave function; "do this [left] on the ou= tput of that [right]." >=20 > Below are two examples from the literature. I try to reason through the n= otation based on these examples: >=20 > (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, 984-1= 010 ( https://doi.org/10.1002/jcc.540160807 ). In this paper, ab initio cal= culations were performed to determine torsional parameters for organic molec= ules and ions. =46rom the abstract, "The rotational energy profiles were ob= tained at the HF/6-31G*//HF/6-31G*." In certain cases, they also used MP2/6= -31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I think this means an initial,= unconstrained geometry optimization of the entire molecule/ion was performe= d first, followed by a geometry optimization at each selected, constrained v= alue of the torsional angle. In the case of MP2//RHF, then, is MP2 used for= the initial optimization and RHF for the scan? Because RHF is less expensi= ve, I think, that would probably make sense. Based on this, I would say tha= t MP2//RHF means that MP2 is performed first and RHF is performed second; in= other words, the "double slash" notation is read from left to right. So in= terpretation (a) above is correct. >=20 > (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( https://d= oi.org/10.1021/ja010534f ). In this paper, the free energy of solvation, De= ltaG_s, is calculated using an implementation of the polarizable conductor m= odel (CPCM) -- see the third page (p. 7316) of this paper. Near the top lef= t-hand side of that page, it says, "The CPCM calculations were performed as S= PCs (single-point calculations) using the 6-31G(d) and 6-31+G(d) basis sets o= n the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six systems." = Based on that description, the HF geometry optimization was performed first= and the CPCM single-point calculation was performed second. So, if my reas= oning from example (1) above is correct (i.e., interpretation (a) above), I'= d expect the "double slash" notation in the paper to be HF//CPCM. But, in f= act, it's not. In the Results section near the bottom of the left-hand side= of the third page (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d)= , CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted S= 1, S2, and S3 [in Table 1]." This, I think, implies that interpretation (b)= above is correct. The strange thing, though, is that at the bottom of Tabl= e 1 on the fourth page [p. 7317], the definitions of S1, S2, and S3 are diff= erent from those stated in the text, by an "extra" "HF" to the left of the "= //"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/6-31= +G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)." >=20 > It's entirely possible, then, that there is no set convention for "double s= lash notation" in quantum chemistry (or that I'm misinterpreting these paper= s). Could anyone shed some light on this, since I'm not a quantum chemist? >=20 > Thanks so much for any insight you can provide, > Andrew >=20 > Andrew DeYoung, PhD > Carnegie Mellon University --Apple-Mail-984DEA06-7097-4CFA-BBF0-6AE41D7F6F9E Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable A single point energy calculation was done w= ith method mA and basis bA, on geometry that was optimized with method mB an= d basis bB:

mA/bA//mB/bB


Marcel Swart&n= bsp;FRSC FYAE MAE, Prof. Dr.
I= CREA Research Professor at University of Girona
Director of Institut de Qu=C3=ADmica Computacional i Cat=C3= =A0lisi

Univ. Girona, Campus Montilivi (Ci=C3=A8ncies= )
c/ Maria Aur=C3=A8lia Capmany i&= nbsp;17003 Girona, Spain

www.ma= rcelswart.eu
marcel.swart%%gmail.com
<= div class=3D"" style=3D"font-variant-ligatures: normal; font-variant-positio= n: normal; font-variant-numeric: normal; font-variant-alternates: normal; fo= nt-variant-east-asian: normal; word-wrap: break-word; -webkit-nbsp-mode: spa= ce; line-break: after-white-space;">
vCard
addressbook://www.marcelsw= art.eu/MSwart.vcf

=

On 23 Feb 2022, a= t 21:57, Andrew DeYoung andrewdaviddeyoung()gmail.com <owner-chemistry%%cc= l.net> wrote:

=EF=BB=BF
Hi,

Could you please h= elp me to understand the "double slash" notation that I see in quantum chemi= cal literature?  The notation is: 

method= /basis set//method/basis set

What is the convention= -- if any -- for the order of the calculations, (a) or (b)?  = ;

(a) Is the calculation before the "//" performed f= irst, while the calculation after the "//" is performed second?  In oth= er words, "do this [left], then that [right]"?

(b) O= r is it the other way around, meaning that the left-hand calculation is= performed ON the output of the right-hand calculation?  In other words= , somewhat like an operator acting on a wave function; "do this [left] on th= e output of that [right]."

Below are two examples f= rom the literature.  I try to reason through the notation based on thes= e examples:

(1) Maxwell, Tirado-Rives, and Jorgense= n. J. Comput. Chem. 1995, 16, 984-1010 ( https://doi.org/10.1002/jcc.540160807<= /a> ).  In this paper, ab initio calculations were performed to de= termine torsional parameters for organic molecules and ions.  =46rom th= e abstract, "The rotational energy profiles were obtained at the HF/6-31G*//= HF/6-31G*."  In certain cases, they also used MP2/6-31G*//RHF/6-31G* or= MP2/6-31G*//MP2/6-31G*.  I think this means an initial, unconstrained g= eometry optimization of the entire molecule/ion was performed first, followe= d by a geometry optimization at each selected, constrained value of the tors= ional angle.  In the case of MP2//RHF, then, is MP2 used for the initia= l optimization and RHF for the scan?  Because RHF is less expensive, I t= hink, that would probably make sense.  Based on this, I would say that M= P2//RHF means that MP2 is performed first and RHF is performed second; in ot= her words, the "double slash" notation is read from left to right.  So i= nterpretation (a) above is correct.

(2) Liptak and S= hields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( https://doi.org/10.1021/ja010534f ).  In th= is paper, the free energy of solvation, DeltaG_s, is calculated using an imp= lementation of the polarizable conductor model (CPCM) -- see the third page (= p. 7316) of this paper.  Near the top left-hand side of that page, it s= ays, "The CPCM calculations were performed as SPCs (single-point calculation= s) using the 6-31G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-3= 1+G(d) geometries for each of the six systems."  Based on that descript= ion, the HF geometry optimization was performed first and the CPCM single-po= int calculation was performed second.  So, if my reasoning from example= (1) above is correct (i.e., interpretation (a) above), I'd expect the "= double slash" notation in the paper to be HF//CPCM.  But, in fact, it's= not.  In the Results section near the bottom of the left-hand side of t= he third page (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), CPC= M/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted S1, S= 2, and S3 [in Table 1]."  This, I think, implies that interpretation&nb= sp;(b) above is correct.  The strange thing, though, is that at the bot= tom of Table 1 on the fourth page [p. 7317], the definitions of S1, S2, and S= 3 are different from those stated in the text, by an "extra" "HF" to the lef= t of the "//"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CP= CM/HF/6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)."

It's entirely possible, then, that there is no set conventi= on for "double slash notation" in quantum chemistry (or that I'm misinterpre= ting these papers).  Could anyone shed some light on this, since I'm no= t a quantum chemist?

Thanks so much for any insight= you can provide,
Andrew

Andrew DeYoung, P= hD
Carnegie Mellon University
= --Apple-Mail-984DEA06-7097-4CFA-BBF0-6AE41D7F6F9E-- From owner-chemistry@ccl.net Wed Feb 23 17:07:01 2022 From: "Eric Patterson eric.patterson-*-stonybrook.edu" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54601-220223161528-24578-BQi/b3kuMDxR9NvKKt1zxA(_)server.ccl.net> X-Original-From: Eric Patterson Content-Type: multipart/alternative; boundary="Apple-Mail=_AA665AD5-A14B-43B6-AC01-C057597E2F06" Date: Wed, 23 Feb 2022 16:15:21 -0500 Mime-Version: 1.0 (Mac OS X Mail 15.0 \(3693.40.0.1.81\)) Sent to CCL by: Eric Patterson [eric.patterson_._stonybrook.edu] --Apple-Mail=_AA665AD5-A14B-43B6-AC01-C057597E2F06 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi Andrew, The convention is energy-at-this-level//optimization-at-this level. MP2/6-31G(d)//HF/6-31G(d) means MP2/6-31G(d) single-point energy on = HF/6-31G(d) optimized geometries. Cheers, Eric > On Feb 23, 2022, at 1:48 PM, Andrew DeYoung = andrewdaviddeyoung()gmail.com wrote: >=20 > Hi, >=20 > Could you please help me to understand the "double slash" notation = that I see in quantum chemical literature? The notation is:=20 >=20 > method/basis set//method/basis set >=20 > What is the convention -- if any -- for the order of the calculations, = (a) or (b)? =20 >=20 > (a) Is the calculation before the "//" performed first, while the = calculation after the "//" is performed second? In other words, "do = this [left], then that [right]"? >=20 > (b) Or is it the other way around, meaning that the left-hand = calculation is performed ON the output of the right-hand calculation? = In other words, somewhat like an operator acting on a wave function; "do = this [left] on the output of that [right]." >=20 > Below are two examples from the literature. I try to reason through = the notation based on these examples: >=20 > (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, = 984-1010 ( https://doi.org/10.1002/jcc.540160807 = ). In this paper, ab initio = calculations were performed to determine torsional parameters for = organic molecules and ions. =46rom the abstract, "The rotational energy = profiles were obtained at the HF/6-31G*//HF/6-31G*." In certain cases, = they also used MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I = think this means an initial, unconstrained geometry optimization of the = entire molecule/ion was performed first, followed by a geometry = optimization at each selected, constrained value of the torsional angle. = In the case of MP2//RHF, then, is MP2 used for the initial optimization = and RHF for the scan? Because RHF is less expensive, I think, that = would probably make sense. Based on this, I would say that MP2//RHF = means that MP2 is performed first and RHF is performed second; in other = words, the "double slash" notation is read from left to right. So = interpretation (a) above is correct. >=20 > (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( = https://doi.org/10.1021/ja010534f ). = In this paper, the free energy of solvation, DeltaG_s, is calculated = using an implementation of the polarizable conductor model (CPCM) -- see = the third page (p. 7316) of this paper. Near the top left-hand side of = that page, it says, "The CPCM calculations were performed as SPCs = (single-point calculations) using the 6-31G(d) and 6-31+G(d) basis sets = on the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six = systems." Based on that description, the HF geometry optimization was = performed first and the CPCM single-point calculation was performed = second. So, if my reasoning from example (1) above is correct (i.e., = interpretation (a) above), I'd expect the "double slash" notation in the = paper to be HF//CPCM. But, in fact, it's not. In the Results section = near the bottom of the left-hand side of the third page (p. 7316), the = authors state, "CPCM/6-31G(d)//HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), = and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted S1, S2, and S3 [in Table = 1]." This, I think, implies that interpretation (b) above is correct. = The strange thing, though, is that at the bottom of Table 1 on the = fourth page [p. 7317], the definitions of S1, S2, and S3 are different = > from those stated in the text, by an "extra" "HF" to the left of the = "//"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: = CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)." >=20 > It's entirely possible, then, that there is no set convention for = "double slash notation" in quantum chemistry (or that I'm = misinterpreting these papers). Could anyone shed some light on this, = since I'm not a quantum chemist? >=20 > Thanks so much for any insight you can provide, > Andrew >=20 > Andrew DeYoung, PhD > Carnegie Mellon University --Apple-Mail=_AA665AD5-A14B-43B6-AC01-C057597E2F06 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Hi = Andrew,

The = convention is energy-at-this-level//optimization-at-this = level.

MP2/6-31G(d)//HF/6-31G(d) means MP2/6-31G(d) single-point = energy on HF/6-31G(d) optimized geometries.

Cheers,
Eric

=

On Feb 23, 2022, at 1:48 PM, Andrew DeYoung = andrewdaviddeyoung()gmail.com = <owner-chemistry:-:ccl.net> wrote:

Hi,

Could = you please help me to understand the "double slash" notation that I see = in quantum chemical literature?  The notation is: 

method/basis = set//method/basis set

What is the convention -- if any -- for the order of the = calculations, (a) or (b)?  

(a) Is the calculation before the "//" = performed first, while the calculation after the "//" is performed = second?  In other words, "do this [left], then that = [right]"?

(b) = Or is it the other way around, meaning that the left-hand = calculation is performed ON the output of the right-hand = calculation?  In other words, somewhat like an operator acting on a = wave function; "do this [left] on the output of that [right]."

Below are two examples = > from the literature.  I try to reason through the notation based on = these examples:

(1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. = 1995, 16, 984-1010 ( https://doi.org/10.1002/jcc.540160807 ).  In this = paper, ab initio calculations were performed to determine torsional = parameters for organic molecules and ions.  =46rom the abstract, = "The rotational energy profiles were obtained at the = HF/6-31G*//HF/6-31G*."  In certain cases, they also used = MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*.  I think this = means an initial, unconstrained geometry optimization of the entire = molecule/ion was performed first, followed by a geometry optimization at = each selected, constrained value of the torsional angle.  In the = case of MP2//RHF, then, is MP2 used for the initial optimization and RHF = for the scan?  Because RHF is less expensive, I think, that would = probably make sense.  Based on this, I would say that MP2//RHF = means that MP2 is performed first and RHF is performed second; in other = words, the "double slash" notation is read from left to right.  So = interpretation (a) above is correct.

(2) Liptak and Shields, J. Am. Chem. = Soc. 2001, 123, 7314-7319 ( https://doi.org/10.1021/ja010534f ).  In this paper, = the free energy of solvation, DeltaG_s, is calculated using an = implementation of the polarizable conductor model (CPCM) -- see the = third page (p. 7316) of this paper.  Near the top left-hand side of = that page, it says, "The CPCM calculations were performed as SPCs = (single-point calculations) using the 6-31G(d) and 6-31+G(d) basis sets = on the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six = systems."  Based on that description, the HF geometry optimization = was performed first and the CPCM single-point calculation was performed = second.  So, if my reasoning from example (1) above is correct = (i.e., interpretation (a) above), I'd expect the "double slash" = notation in the paper to be HF//CPCM.  But, in fact, it's = not.  In the Results section near the bottom of the left-hand side = of the third page (p. 7316), the authors state, = "CPCM/6-31G(d)//HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), and = CPCM/6-31+G(d)//HF/6-31+G(d) are denoted S1, S2, and S3 [in Table = 1]."  This, I think, implies that interpretation (b) above is = correct.  The strange thing, though, is that at the bottom of Table = 1 on the fourth page [p. 7317], the definitions of S1, S2, and S3 are = different from those stated in the text, by an "extra" "HF" to the left = of the "//"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: = CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: = CPCM/HF/6-31+G(d)//HF/6-31+G(d)."

It's entirely possible, then, that = there is no set convention for "double slash notation" in quantum = chemistry (or that I'm misinterpreting these papers).  Could anyone = shed some light on this, since I'm not a quantum chemist?

Thanks so much for any = insight you can provide,
Andrew

Andrew DeYoung, = PhD
Carnegie Mellon University

= --Apple-Mail=_AA665AD5-A14B-43B6-AC01-C057597E2F06-- From owner-chemistry@ccl.net Wed Feb 23 17:41:00 2022 From: "dipankar roy theodip _ gmail.com" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54602-220223162227-27224-v5B1TeLk40DyAuqWPw6+SA() server.ccl.net> X-Original-From: dipankar roy Content-Type: multipart/alternative; boundary="00000000000097a6d905d8b60ffc" Date: Wed, 23 Feb 2022 14:22:09 -0700 MIME-Version: 1.0 Sent to CCL by: dipankar roy [theodip-*-gmail.com] --00000000000097a6d905d8b60ffc Content-Type: text/plain; charset="UTF-8" Hi, You are right. The general idea is the left hand part of the calculation is done one the optimized geometry from the right hand side operation. It is generally meant to refer to a single point calculation done using the theory mentioned in the left hand side. If the level of theory is the same for the geometry optimization and subsequent single point calculation, then the theory is not mentioned in the left hand side (except additional/nature of the calculation). If the single point theory is different from the theory used for geometry optimization (RHS) then the whole theory/method is written. In example 2, all calculations, optimizations and subsequent single point solvation energy ones, were done using HF level. I hope this helps. best, Dipankar ----------------------------------- Dipankar Roy *PhD* On Wed, Feb 23, 2022 at 1:57 PM Andrew DeYoung andrewdaviddeyoung()gmail.com wrote: > Hi, > > Could you please help me to understand the "double slash" notation that I > see in quantum chemical literature? The notation is: > > method/basis set//method/basis set > > What is the convention -- if any -- for the order of the calculations, (a) > or (b)? > > (a) Is the calculation before the "//" performed first, while the > calculation after the "//" is performed second? In other words, "do this > [left], then that [right]"? > > (b) Or is it the other way around, meaning that the left-hand calculation > is performed ON the output of the right-hand calculation? In other words, > somewhat like an operator acting on a wave function; "do this [left] on the > output of that [right]." > > Below are two examples from the literature. I try to reason through the > notation based on these examples: > > (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, > 984-1010 ( https://doi.org/10.1002/jcc.540160807 ). In this paper, ab > initio calculations were performed to determine torsional parameters for > organic molecules and ions. From the abstract, "The rotational energy > profiles were obtained at the HF/6-31G*//HF/6-31G*." In certain cases, > they also used MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I think > this means an initial, unconstrained geometry optimization of the entire > molecule/ion was performed first, followed by a geometry optimization at > each selected, constrained value of the torsional angle. In the case of > MP2//RHF, then, is MP2 used for the initial optimization and RHF for the > scan? Because RHF is less expensive, I think, that would probably make > sense. Based on this, I would say that MP2//RHF means that MP2 is > performed first and RHF is performed second; in other words, the "double > slash" notation is read from left to right. So interpretation (a) above is > correct. > > (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( > https://doi.org/10.1021/ja010534f ). In this paper, the free energy of > solvation, DeltaG_s, is calculated using an implementation of the > polarizable conductor model (CPCM) -- see the third page (p. 7316) of this > paper. Near the top left-hand side of that page, it says, "The CPCM > calculations were performed as SPCs (single-point calculations) using the > 6-31G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-31+G(d) > geometries for each of the six systems." Based on that description, the HF > geometry optimization was performed first and the CPCM single-point > calculation was performed second. So, if my reasoning from example (1) > above is correct (i.e., interpretation (a) above), I'd expect the "double > slash" notation in the paper to be HF//CPCM. But, in fact, it's not. In > the Results section near the bottom of the left-hand side of the third page > (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), > CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted > S1, S2, and S3 [in Table 1]." This, I think, implies that > interpretation (b) above is correct. The strange thing, though, is that at > the bottom of Table 1 on the fourth page [p. 7317], the definitions of S1, > S2, and S3 are different from those stated in the text, by an "extra" "HF" > to the left of the "//"; there, they state, "S1: > CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: > CPCM/HF/6-31+G(d)//HF/6-31+G(d)." > > It's entirely possible, then, that there is no set convention for "double > slash notation" in quantum chemistry (or that I'm misinterpreting these > papers). Could anyone shed some light on this, since I'm not a quantum > chemist? > > Thanks so much for any insight you can provide, > Andrew > > Andrew DeYoung, PhD > Carnegie Mellon University > --00000000000097a6d905d8b60ffc Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
You are right. The general idea is the = left hand part of the calculation is done one the optimized geometry from t= he right hand side operation. It is generally meant to refer to a single po= int calculation done using the theory mentioned in the left hand side. If t= he level of theory is the same for the geometry optimization and subsequent= single point calculation, then the theory is not mentioned in the left han= d side (except additional/nature of the calculation). If the single point t= heory is different from the theory used for geometry optimization (RHS) the= n the whole theory/method is written.

In example 2= , all calculations, optimizations and subsequent single point solvation ene= rgy ones, were done using HF level.
I hope this helps.
<= div>
best,
Dipankar

-----------------------------------
Dipankar Roy= =C2=A0 =C2=A0PhD


<= /div>

On Wed, Feb 23, 2022 at 1:57 PM Andrew DeYoung andrewdaviddeyoung()gmail.com <owner-chemistry*o*ccl.net> wrote:
Hi,

= Could you please help me to understand the "double slash" notatio= n that I see in quantum chemical literature?=C2=A0 The notation is:=C2=A0

method/basis set//method/basis set

What is the convention -- if any -- for the order of the calculati= ons,=C2=A0(a) or (b)?=C2=A0=C2=A0

(a) Is the calcu= lation before the "//" performed first, while the calculation aft= er the "//" is performed second?=C2=A0 In other words, "do t= his [left], then that [right]"?

(b) Or is it = the other way around,=C2=A0meaning that the left-hand calculation is perfor= med ON the output of the right-hand calculation?=C2=A0 In other words, some= what like an operator acting on a wave function; "do this [left] on th= e output of that [right]."

Below are two exam= ples from the literature.=C2=A0 I try to reason through the notation based = on these examples:

(1) Maxwell, Tirado-Rives, and = Jorgensen. J. Comput. Chem. 1995, 16, 984-1010 (=C2=A0https://doi.org/10.1002/jcc.= 540160807 ).=C2=A0 In this paper, ab initio calculations=C2=A0were perf= ormed to determine torsional parameters for organic molecules and ions.=C2= =A0 From the abstract, "The rotational energy profiles were obtained a= t the HF/6-31G*//HF/6-31G*."=C2=A0 In certain cases, they also used MP= 2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*.=C2=A0 I think this means an= initial, unconstrained geometry optimization of the entire molecule/ion wa= s performed first, followed by a geometry optimization at each selected, co= nstrained value of the torsional angle.=C2=A0 In the case of MP2//RHF, then= , is MP2 used for the initial optimization and RHF for the scan?=C2=A0 Beca= use RHF is less expensive, I think, that would probably make sense.=C2=A0 B= ased on this, I would say that MP2//RHF means that MP2 is performed first a= nd RHF is performed second; in other words, the "double slash" no= tation is read from left to right.=C2=A0 So interpretation (a) above is cor= rect.

(2) Liptak and Shields, J. Am. Chem. Soc. 20= 01, 123, 7314-7319 (=C2=A0https://doi.org/10.1021/ja010534f ).=C2=A0 In this paper= , the free energy of solvation, DeltaG_s, is calculated using an implementa= tion of the polarizable conductor model (CPCM) -- see the third page (p. 73= 16) of this paper.=C2=A0 Near the top left-hand side of that page, it says,= "The CPCM calculations were performed as SPCs (single-point calculati= ons) using the 6-31G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/= 6-31+G(d) geometries for each of the six systems."=C2=A0 Based on that= description, the HF geometry optimization was performed first and the CPCM= single-point calculation was performed second.=C2=A0 So, if my reasoning f= rom example (1) above is correct (i.e., interpretation=C2=A0(a) above), I&#= 39;d expect the "double slash" notation in the paper to be HF//CP= CM.=C2=A0 But, in fact, it's not.=C2=A0 In the Results section near the= bottom of the left-hand side of the third page (p. 7316), the authors stat= e, "CPCM/6-31G(d)//HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/= 6-31+G(d)//HF/6-31+G(d) are denoted S1, S2, and S3 [in Table 1]."=C2= =A0 This, I think, implies that interpretation=C2=A0(b) above is correct.= =C2=A0 The strange thing, though, is that at the bottom of Table 1 on the f= ourth page [p. 7317], the definitions of S1, S2, and S3 are different from = those stated in the text, by an "extra" "HF" to the lef= t of the "//"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/= 6-31G(d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-3= 1+G(d)."

It's entirely possible, then, th= at there is no set convention for "double slash notation" in quan= tum chemistry (or that I'm misinterpreting these papers).=C2=A0 Could a= nyone shed some light on this, since I'm not a quantum chemist?

Thanks so much for any insight you can provide,
Andrew

Andrew DeYoung, PhD
Carnegie Mel= lon University
--00000000000097a6d905d8b60ffc-- From owner-chemistry@ccl.net Wed Feb 23 18:17:01 2022 From: "Tobias Kramer tobias.kraemer _ mu.ie" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54603-220223161607-24960-GatJaWRxiRtQjRjcXaK60Q---server.ccl.net> X-Original-From: "Tobias Kramer" Date: Wed, 23 Feb 2022 16:16:05 -0500 Sent to CCL by: "Tobias Kramer" [tobias.kraemer(!)mu.ie] Dear Andrew, The notation generally refers to a single point calculation (level of theory before //) performed on the optimised geometry from another level of theory (after the //). So, MP2/6-31G*//RHF/6-31G* would mean that a single point energy (or property) calculation was performed at the MP2 level with a 6-31G* basis set, using the geometry obtained from an optimisation with RHF/6-31G*. I think some of the examples you have mentioned in your post might just have typos in them, which has caused some confusion. I think something like CPCM/HF/6-31G(d)//HF/6-31G(d) is correct, whilst CPCM/6-31G(d)//HF/6-31G(d) would be missing the level of theory (here HF) in the first part. CPCM just indicates that a salvation model was employed, but does not tell you which electronic structure method was used in combination with it. Hope this helps. Tobias > "Andrew DeYoung andrewdaviddeyoung()gmail.com" wrote: > > Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung]^[gmail.com] > --00000000000050f18705d8b3ebe7 > Content-Type: text/plain; charset="UTF-8" > > Hi, > > Could you please help me to understand the "double slash" notation that I > see in quantum chemical literature? The notation is: > > method/basis set//method/basis set > > What is the convention -- if any -- for the order of the calculations, (a) > or (b)? > > (a) Is the calculation before the "//" performed first, while the > calculation after the "//" is performed second? In other words, "do this > [left], then that [right]"? > > (b) Or is it the other way around, meaning that the left-hand calculation > is performed ON the output of the right-hand calculation? In other words, > somewhat like an operator acting on a wave function; "do this [left] on the > output of that [right]." > > Below are two examples from the literature. I try to reason through the > notation based on these examples: > > (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, > 984-1010 ( https://doi.org/10.1002/jcc.540160807 ). In this paper, ab > initio calculations were performed to determine torsional parameters for > organic molecules and ions. From the abstract, "The rotational energy > profiles were obtained at the HF/6-31G*//HF/6-31G*." In certain cases, > they also used MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I think > this means an initial, unconstrained geometry optimization of the entire > molecule/ion was performed first, followed by a geometry optimization at > each selected, constrained value of the torsional angle. In the case of > MP2//RHF, then, is MP2 used for the initial optimization and RHF for the > scan? Because RHF is less expensive, I think, that would probably make > sense. Based on this, I would say that MP2//RHF means that MP2 is > performed first and RHF is performed second; in other words, the "double > slash" notation is read from left to right. So interpretation (a) above is > correct. > > (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( > https://doi.org/10.1021/ja010534f ). In this paper, the free energy of > solvation, DeltaG_s, is calculated using an implementation of the > polarizable conductor model (CPCM) -- see the third page (p. 7316) of this > paper. Near the top left-hand side of that page, it says, "The CPCM > calculations were performed as SPCs (single-point calculations) using the > 6-31G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-31+G(d) > geometries for each of the six systems." Based on that description, the HF > geometry optimization was performed first and the CPCM single-point > calculation was performed second. So, if my reasoning from example (1) > above is correct (i.e., interpretation (a) above), I'd expect the "double > slash" notation in the paper to be HF//CPCM. But, in fact, it's not. In > the Results section near the bottom of the left-hand side of the third page > (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), > CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted > S1, S2, and S3 [in Table 1]." This, I think, implies that > interpretation (b) above is correct. The strange thing, though, is that at > the bottom of Table 1 on the fourth page [p. 7317], the definitions of S1, > S2, and S3 are different from those stated in the text, by an "extra" "HF" > to the left of the "//"; there, they state, "S1: > CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: > CPCM/HF/6-31+G(d)//HF/6-31+G(d)." > > It's entirely possible, then, that there is no set convention for "double > slash notation" in quantum chemistry (or that I'm misinterpreting these > papers). Could anyone shed some light on this, since I'm not a quantum > chemist? > > Thanks so much for any insight you can provide, > Andrew > > Andrew DeYoung, PhD > Carnegie Mellon University From owner-chemistry@ccl.net Wed Feb 23 18:52:00 2022 From: "Rassolov, Vitaly RASSOLOV.###.mailbox.sc.edu" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54604-220223170749-23622-pnhNFH78MBahL8PQMyJ3aA###server.ccl.net> X-Original-From: "Rassolov, Vitaly" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_SA1PR19MB5152DBE88FC3069A84761652EB3C9SA1PR19MB5152namp_" Date: Wed, 23 Feb 2022 22:07:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Rassolov, Vitaly" [RASSOLOV a mailbox.sc.edu] --_000_SA1PR19MB5152DBE88FC3069A84761652EB3C9SA1PR19MB5152namp_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Double slash separates the single point calculation (i.e. how the energy is= obtained) from the geometry optimization (how the geometry is obtained). = The order is: SP//Opt ________________________________ Vitaly Rassolov Department of Chemistry and Biochemistry University of South Carolina 631 Sumter St, Columbia SC 29208 https://sc.edu/study/colleges_schools/chemistry_and_biochemistry/our_people= /directory/rassolov_vitaly.php ________________________________ > From: owner-chemistry+rassolov=3D=3Dmail.chem.sc.edu*o*ccl.net on behalf of Andrew DeYoung andr= ewdaviddeyoung()gmail.com Sent: Wednesday, February 23, 2022 1:48 PM To: Rassolov, Vitaly Subject: CCL: Double slash notation in quantum chemistry Hi, Could you please help me to understand the "double slash" notation that I s= ee in quantum chemical literature? The notation is: method/basis set//method/basis set What is the convention -- if any -- for the order of the calculations, (a) = or (b)? (a) Is the calculation before the "//" performed first, while the calculati= on after the "//" is performed second? In other words, "do this [left], th= en that [right]"? (b) Or is it the other way around, meaning that the left-hand calculation i= s performed ON the output of the right-hand calculation? In other words, s= omewhat like an operator acting on a wave function; "do this [left] on the = output of that [right]." Below are two examples from the literature. I try to reason through the no= tation based on these examples: (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, 984-10= 10 ( https://doi.org/10.1002/jcc.540160807 ). In this paper, ab initio cal= culations were performed to determine torsional parameters for organic mole= cules and ions. From the abstract, "The rotational energy profiles were ob= tained at the HF/6-31G*//HF/6-31G*." In certain cases, they also used MP2/= 6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I think this means an initia= l, unconstrained geometry optimization of the entire molecule/ion was perfo= rmed first, followed by a geometry optimization at each selected, constrain= ed value of the torsional angle. In the case of MP2//RHF, then, is MP2 use= d for the initial optimization and RHF for the scan? Because RHF is less e= xpensive, I think, that would probably make sense. Based on this, I would = say that MP2//RHF means that MP2 is performed first and RHF is performed se= cond; in other words, the "double slash" notation is read from left to righ= t. So interpretation (a) above is correct. (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( https://do= i.org/10.1021/ja010534f ). In this paper, the free energy of solvation, De= ltaG_s, is calculated using an implementation of the polarizable conductor = model (CPCM) -- see the third page (p. 7316) of this paper. Near the top l= eft-hand side of that page, it says, "The CPCM calculations were performed = as SPCs (single-point calculations) using the 6-31G(d) and 6-31+G(d) basis = sets on the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six sys= tems." Based on that description, the HF geometry optimization was perform= ed first and the CPCM single-point calculation was performed second. So, i= f my reasoning from example (1) above is correct (i.e., interpretation (a) = above), I'd expect the "double slash" notation in the paper to be HF//CPCM.= But, in fact, it's not. In the Results section near the bottom of the le= ft-hand side of the third page (p. 7316), the authors state, "CPCM/6-31G(d)= //HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d= ) are denoted S1, S2, and S3 [in Table 1]." This, I think, implies that in= terpretation (b) above is correct. The strange thing, though, is that at t= he bottom of Table 1 on the fourth page [p. 7317], the definitions of S1, S= 2, and S3 are different from those stated in the text, by an "extra" "HF" t= o the left of the "//"; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(= d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)= ." It's entirely possible, then, that there is no set convention for "double s= lash notation" in quantum chemistry (or that I'm misinterpreting these pape= rs). Could anyone shed some light on this, since I'm not a quantum chemist= ? Thanks so much for any insight you can provide, Andrew Andrew DeYoung, PhD Carnegie Mellon University --_000_SA1PR19MB5152DBE88FC3069A84761652EB3C9SA1PR19MB5152namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Double slash separates the single point calculation (i.e. how the energy is= obtained) from the geometry optimization (how the geometry is obtained).&n= bsp; The order is:  SP//Opt

Vitaly Rassolov
Department of Chemistry and Biochemistry
University of South Carolina
631 Sumter St, Columbia SC 29208
https://sc.edu/study/colleges_sc= hools/chemistry_and_biochemistry/our_people/directory/rassolov_vitaly.php
From: owner-chemistry+rasso= lov=3D=3Dmail.chem.sc.edu*o*ccl.net <owner-chemistry+rassolov=3D=3Dmail.ch= em.sc.edu*o*ccl.net> on behalf of Andrew DeYoung andrewdaviddeyoung()gmail= .com <owner-chemistry*o*ccl.net>
Sent: Wednesday, February 23, 2022 1:48 PM
To: Rassolov, Vitaly <RASSOLOV*o*mailbox.sc.edu>
Subject: CCL: Double slash notation in quantum chemistry
 
Hi,

Could you please help me to understand the "double slash" no= tation that I see in quantum chemical literature?  The notation is:&nb= sp;

method/basis set//method/basis set

What is the convention -- if any -- for the order of the calculations,=  (a) or (b)?  

(a) Is the calculation before the "//" performed first, whil= e the calculation after the "//" is performed second?  In ot= her words, "do this [left], then that [right]"?

(b) Or is it the other way around, meaning that the left-hand cal= culation is performed ON the output of the right-hand calculation?  In= other words, somewhat like an operator acting on a wave function; "do= this [left] on the output of that [right]."

Below are two examples from the literature.  I try to reason thro= ugh the notation based on these examples:

(1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, 9= 84-1010 ( https://doi.org/10.1002/jcc.540160807 ).  In this paper, a= b initio calculations were performed to determine torsional parameters for organic molecules and ions.  From the abstra= ct, "The rotational energy profiles were obtained at the HF/6-31G*//HF= /6-31G*."  In certain cases, they also used MP2/6-31G*//RHF/6-31G= * or MP2/6-31G*//MP2/6-31G*.  I think this means an initial, unconstrained geometry optimization of the entire molecule/ion wa= s performed first, followed by a geometry optimization at each selected, co= nstrained value of the torsional angle.  In the case of MP2//RHF, then= , is MP2 used for the initial optimization and RHF for the scan?  Because RHF is less expensive, I think, that w= ould probably make sense.  Based on this, I would say that MP2//RHF me= ans that MP2 is performed first and RHF is performed second; in other words= , the "double slash" notation is read from left to right.  So interpretation (a) above is correct.

(2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( = https://doi.org/10.1021/ja010= 534f ).  In this paper, the free energy of solvation, DeltaG_s, is= calculated using an implementation of the polarizable conductor model (CPCM) -- see the third page (p. 7316) of this paper. = ; Near the top left-hand side of that page, it says, "The CPCM calcula= tions were performed as SPCs (single-point calculations) using the 6-31G(d)= and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-31+G(d) geometries for each of the six systems."  Based= on that description, the HF geometry optimization was performed first and = the CPCM single-point calculation was performed second.  So, if my rea= soning from example (1) above is correct (i.e., interpretation (a) above), I'd expect the "double slash" no= tation in the paper to be HF//CPCM.  But, in fact, it's not.  In = the Results section near the bottom of the left-hand side of the third page= (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted = S1, S2, and S3 [in Table 1]."  This, I think, implies that interp= retation (b) above is correct.  The strange thing, though, is tha= t at the bottom of Table 1 on the fourth page [p. 7317], the definitions of S1, S2, and S3 are different from those stated in the t= ext, by an "extra" "HF" to the left of the "//&quo= t;; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF= /6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)."

It's entirely possible, then, that there is no set convention for &quo= t;double slash notation" in quantum chemistry (or that I'm misinterpre= ting these papers).  Could anyone shed some light on this, since I'm n= ot a quantum chemist?

Thanks so much for any insight you can provide,
Andrew

Andrew DeYoung, PhD
Carnegie Mellon University
--_000_SA1PR19MB5152DBE88FC3069A84761652EB3C9SA1PR19MB5152namp_-- From owner-chemistry@ccl.net Wed Feb 23 19:26:01 2022 From: "Victor Rosas Garcia rosas.victor\a/gmail.com" To: CCL Subject: CCL: Double slash notation in quantum chemistry Message-Id: <-54605-220223165801-15981-cMh5Dnl/mxA5sWclSAnSxQ]~[server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary="000000000000d2b8b305d8b68eed" Date: Wed, 23 Feb 2022 15:57:44 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor-,-gmail.com] --000000000000d2b8b305d8b68eed Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Andrew, Usually, the level of theory at the right of the "//" indicates the level used for a geometry optimization, and that at the left is for another level used for a single point. For example, I would read MP2/6-31G(d)//HF/3-21G as "single point energy at the MP2/6-31G(d) level calculated on a geometry optimized at the HF/3-21G level". As for the CPCM/HF/6-31G(d)//HF/6-31G(d) example, I would read it as: "CPCM single point energy at the HF/6-31G(d) level, done on a geometry optimized at the HF/6-31G(d) level of theory". The geometry optimization was done in the gas phase, without solvent effect. So, in both cases the calculation specified at the right side of the "//" was done first. Just my 2 cents. Victor El mi=C3=A9, 23 feb 2022 a las 15:06, Andrew DeYoung andrewdaviddeyoung() gmail.com () escribi=C3=B3: > Hi, > > Could you please help me to understand the "double slash" notation that I > see in quantum chemical literature? The notation is: > > method/basis set//method/basis set > > What is the convention -- if any -- for the order of the calculations, (a= ) > or (b)? > > (a) Is the calculation before the "//" performed first, while the > calculation after the "//" is performed second? In other words, "do this > [left], then that [right]"? > > (b) Or is it the other way around, meaning that the left-hand calculation > is performed ON the output of the right-hand calculation? In other words= , > somewhat like an operator acting on a wave function; "do this [left] on t= he > output of that [right]." > > Below are two examples from the literature. I try to reason through the > notation based on these examples: > > (1) Maxwell, Tirado-Rives, and Jorgensen. J. Comput. Chem. 1995, 16, > 984-1010 ( https://doi.org/10.1002/jcc.540160807 ). In this paper, ab > initio calculations were performed to determine torsional parameters for > organic molecules and ions. From the abstract, "The rotational energy > profiles were obtained at the HF/6-31G*//HF/6-31G*." In certain cases, > they also used MP2/6-31G*//RHF/6-31G* or MP2/6-31G*//MP2/6-31G*. I think > this means an initial, unconstrained geometry optimization of the entire > molecule/ion was performed first, followed by a geometry optimization at > each selected, constrained value of the torsional angle. In the case of > MP2//RHF, then, is MP2 used for the initial optimization and RHF for the > scan? Because RHF is less expensive, I think, that would probably make > sense. Based on this, I would say that MP2//RHF means that MP2 is > performed first and RHF is performed second; in other words, the "double > slash" notation is read from left to right. So interpretation (a) above = is > correct. > > (2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 ( > https://doi.org/10.1021/ja010534f ). In this paper, the free energy of > solvation, DeltaG_s, is calculated using an implementation of the > polarizable conductor model (CPCM) -- see the third page (p. 7316) of thi= s > paper. Near the top left-hand side of that page, it says, "The CPCM > calculations were performed as SPCs (single-point calculations) using the > 6-31G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-31+G(d) > geometries for each of the six systems." Based on that description, the = HF > geometry optimization was performed first and the CPCM single-point > calculation was performed second. So, if my reasoning from example (1) > above is correct (i.e., interpretation (a) above), I'd expect the "double > slash" notation in the paper to be HF//CPCM. But, in fact, it's not. In > the Results section near the bottom of the left-hand side of the third pa= ge > (p. 7316), the authors state, "CPCM/6-31G(d)//HF/6-31G(d), > CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31+G(d) are denoted > S1, S2, and S3 [in Table 1]." This, I think, implies that > interpretation (b) above is correct. The strange thing, though, is that = at > the bottom of Table 1 on the fourth page [p. 7317], the definitions of S1= , > S2, and S3 are different from those stated in the text, by an "extra" "HF= " > to the left of the "//"; there, they state, "S1: > CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/6-31+G(d)//HF/6-31G(d). S3: > CPCM/HF/6-31+G(d)//HF/6-31+G(d)." > > It's entirely possible, then, that there is no set convention for "double > slash notation" in quantum chemistry (or that I'm misinterpreting these > papers). Could anyone shed some light on this, since I'm not a quantum > chemist? > > Thanks so much for any insight you can provide, > Andrew > > Andrew DeYoung, PhD > Carnegie Mellon University > --000000000000d2b8b305d8b68eed Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Andrew,

Usually, the l= evel of theory at the right of the "//" indicates the level used = for a geometry optimization, and that at the left is for another level used= for a single point.=C2=A0 For example, I would read MP2/6-31G(d)//HF/3-21G= as "single point energy at the MP2/6-31G(d) level calculated on a geo= metry optimized at the HF/3-21G level".

As fo= r the CPCM/HF/6-31G(d)//HF/6-31G(d) example, I would read it as: "CPCM= single point energy at the HF/6-31G(d) level, done on a geometry optimized= at the HF/6-31G(d) level of theory".=C2=A0 The geometry optimization = was done in the gas phase, without solvent effect.=C2=A0
So, in both cases the calculation specified at the right side o= f the "//" was done first.

Just my 2 cen= ts.

Victor

El mi=C3=A9, 23 feb 2022 a las= 15:06, Andrew DeYoung andrewdaviddeyoung()gma= il.com (<owner-chemistry]_[= ccl.net>) escribi=C3=B3:
Hi,

Could you please he= lp me to understand the "double slash" notation that I see in qua= ntum chemical literature?=C2=A0 The notation is:=C2=A0

=
method/basis set//method/basis set

What is th= e convention -- if any -- for the order of the calculations,=C2=A0(a) or (b= )?=C2=A0=C2=A0

(a) Is the calculation before the &= quot;//" performed first, while the calculation after the "//&quo= t; is performed second?=C2=A0 In other words, "do this [left], then th= at [right]"?

(b) Or is it the other way aroun= d,=C2=A0meaning that the left-hand calculation is performed ON the output o= f the right-hand calculation?=C2=A0 In other words, somewhat like an operat= or acting on a wave function; "do this [left] on the output of that [r= ight]."

Below are two examples from the liter= ature.=C2=A0 I try to reason through the notation based on these examples:<= /div>

(1) Maxwell, Tirado-Rives, and Jorgensen. J. Compu= t. Chem. 1995, 16, 984-1010 (=C2=A0https://doi.org/10.1002/jcc.540160807 ).=C2= =A0 In this paper, ab initio calculations=C2=A0were performed to determine = torsional parameters for organic molecules and ions.=C2=A0 From the abstrac= t, "The rotational energy profiles were obtained at the HF/6-31G*//HF/= 6-31G*."=C2=A0 In certain cases, they also used MP2/6-31G*//RHF/6-31G*= or MP2/6-31G*//MP2/6-31G*.=C2=A0 I think this means an initial, unconstrai= ned geometry optimization of the entire molecule/ion was performed first, f= ollowed by a geometry optimization at each selected, constrained value of t= he torsional angle.=C2=A0 In the case of MP2//RHF, then, is MP2 used for th= e initial optimization and RHF for the scan?=C2=A0 Because RHF is less expe= nsive, I think, that would probably make sense.=C2=A0 Based on this, I woul= d say that MP2//RHF means that MP2 is performed first and RHF is performed = second; in other words, the "double slash" notation is read from = left to right.=C2=A0 So interpretation (a) above is correct.

=
(2) Liptak and Shields, J. Am. Chem. Soc. 2001, 123, 7314-7319 (= =C2=A0https= ://doi.org/10.1021/ja010534f ).=C2=A0 In this paper, the free energy of= solvation, DeltaG_s, is calculated using an implementation of the polariza= ble conductor model (CPCM) -- see the third page (p. 7316) of this paper.= =C2=A0 Near the top left-hand side of that page, it says, "The CPCM ca= lculations were performed as SPCs (single-point calculations) using the 6-3= 1G(d) and 6-31+G(d) basis sets on the HF/6-31G(d) and HF/6-31+G(d) geometri= es for each of the six systems."=C2=A0 Based on that description, the = HF geometry optimization was performed first and the CPCM single-point calc= ulation was performed second.=C2=A0 So, if my reasoning from example (1) ab= ove is correct (i.e., interpretation=C2=A0(a) above), I'd expect the &q= uot;double slash" notation in the paper to be HF//CPCM.=C2=A0 But, in = fact, it's not.=C2=A0 In the Results section near the bottom of the lef= t-hand side of the third page (p. 7316), the authors state, "CPCM/6-31= G(d)//HF/6-31G(d), CPCM/6-31+G(d)//HF/6-31G(d), and CPCM/6-31+G(d)//HF/6-31= +G(d) are denoted S1, S2, and S3 [in Table 1]."=C2=A0 This, I think, i= mplies that interpretation=C2=A0(b) above is correct.=C2=A0 The strange thi= ng, though, is that at the bottom of Table 1 on the fourth page [p. 7317], = the definitions of S1, S2, and S3 are different from those stated in the te= xt, by an "extra" "HF" to the left of the "//"= ;; there, they state, "S1: CPCM/HF/6-31G(d)//HF/6-31G(d). S2: CPCM/HF/= 6-31+G(d)//HF/6-31G(d). S3: CPCM/HF/6-31+G(d)//HF/6-31+G(d)."

It's entirely possible, then, that there is no set con= vention for "double slash notation" in quantum chemistry (or that= I'm misinterpreting these papers).=C2=A0 Could anyone shed some light = on this, since I'm not a quantum chemist?

Than= ks so much for any insight you can provide,
Andrew

=
Andrew DeYoung, PhD
Carnegie Mellon University
--000000000000d2b8b305d8b68eed-- From owner-chemistry@ccl.net Wed Feb 23 20:01:00 2022 From: "Alexander Sokolov sokolov.8^osu.edu" To: CCL Subject: CCL: Symposium Quantum Chemistry: Current and Future Frontiers, ACS Fall Message-Id: <-54606-220223173835-15082-FewUht2v7ZwC/PcAzCdp3A^-^server.ccl.net> X-Original-From: "Alexander Sokolov" Date: Wed, 23 Feb 2022 17:38:34 -0500 Sent to CCL by: "Alexander Sokolov" [sokolov.8/./osu.edu] Colleagues, We are organizing a PHYS division symposium: Quantum Chemistry: Current and Future Frontiers, at the ACS National Meeting in Chicago, IL, to be held on August 2125, 2022. This symposium aims to bring together a diverse community of theoretical chemists to discuss recent advances in quantum chemistry, current challenges, and prospects for future developments. The program of this symposium will consist of eight half-day sessions and will be divided into four frontier themes: 1. Strong electron correlation 2. Excited states and spectroscopy 3. Quantum chemistry in condensed phases 4. Emerging approaches (e.g., quantum computing, machine learning) The program of the symposium will feature presentations from ~40 invited speakers and more than 30 contributed talks. Abstract submission is now open and will close on March 14, 2022. We welcome contributions from postdocs and senior graduate students. Please submit your abstract here: https://callforabstracts.acs.org/acsfall2022/PHYS We hope to see you in Chicago this Fall! Best regards, Francesco Evangelista Alexander Sokolov