From owner-chemistry@ccl.net Thu Apr 26 09:25:00 2007 From: "Fedor t.goumans~!~ucl.ac.uk" To: CCL Subject: CCL:G: large imaginary frequency in coronene when diffuse functions are used Message-Id: <-34139-070426054934-7969-bEKZMB89/3og0oBRdadsuQ/./server.ccl.net> X-Original-From: Fedor Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 26 Apr 2007 10:06:11 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor [t.goumans() ucl.ac.uk] Dear CCl-ers, When the frequencies are calculated with diffuse functions (6-31+G*) for coronene there is a large imaginary frequency corresponding to a puckering motion of the atoms in the inner ring, although it does not appear to be a first order saddle point. I have tried to understand what gives rise to this puzzling feature, so I have tried several things: * The large imaginary frequency arises for HF, DFT (pw91) as well as for hybrid DFT (B3LYP,B97-1,MPWB1K). Its magnitude is between 700 and 400 imaginary wavenumbers. * The wavefunction is stable to all the perturbations that are considered with gaussian's Stable keyword. * The imaginary frequency is observed for both G03 and GAMESS-UK. * Symmetry-lowering gives higher-energy structures (nosymm, c2v, c2). * Intrinsic reaction coordinate following likewise gives rise to higher-energy structures. * Numerical frequencies also give 1 imaginary frequency. From this calculation, it is seen that all displacements are higher in energy than the starting point, the optimised coronene. This gives reason to belief that the D6H structure is indeed a minimum and not a first-order saddle point. * A split basis set (6-31+G* on the central ring, 6-31G* on the peripheral rings) either with 6 d-functions or 5 d-functions also gives 1 imaginary frequency. With a triple-zeta basis set, however, no imaginary frequency is observed. It appears that this imaginary frequency arises from the use of diffuse functions only. I think that it may be related to the near-linear dependency of the basis. Has anybody observed similar behaviour, or have a better idea where this apparent superfluous imaginary frequency may come from? Thanks for any help, kind regards, Fedor Goumans From owner-chemistry@ccl.net Thu Apr 26 12:23:01 2007 From: "Cory Pye cpye]-[crux.smu.ca" To: CCL Subject: CCL:G: large imaginary frequency in coronene when diffuse functions are used Message-Id: <-34140-070426121557-31073-Ii1/JNW9XCKJtAQwiGP20A+*+server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 26 Apr 2007 13:15:27 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye^_^crux.smu.ca] Hello Fedor, Another possibility is that there does indeed exist a lower energy minimum. You have already mentioned that you tried lowering the symmetry (C1,C2v,C2). If the structure is stuck on the saddle, then you would need to supply a displacement downhill. Other possibilities are: D6, C6h,C6v, D3h, D3d, D2h, D3, C3v, C3h, S6, D2, C2h, Cs, or Ci but I would need to know the irreducible representation of the imaginary mode to suggest something. If the imaginary mode is of A1g symmetry, chances are it's a theory problem. If it is some other symmetry, then there might exist a lower-energy minima. If you want, send me the Gaussian output file with the frequencies in it and I can take a look. -Cory On Thu, 26 Apr 2007, Fedor t.goumans~!~ucl.ac.uk wrote: > > Sent to CCL by: Fedor [t.goumans() ucl.ac.uk] > Dear CCl-ers, > > When the frequencies are calculated with diffuse functions (6-31+G*) for > coronene there is a large imaginary frequency corresponding to a puckering > motion of the atoms in the inner ring, although it does not appear to be a > first order saddle point. > > I have tried to understand what gives rise to this puzzling feature, so I have > tried several things: > > * The large imaginary frequency arises for HF, DFT (pw91) as well as for hybrid > DFT (B3LYP,B97-1,MPWB1K). Its magnitude is between 700 and 400 imaginary > wavenumbers. > * The wavefunction is stable to all the perturbations that are considered with > gaussian's Stable keyword. > * The imaginary frequency is observed for both G03 and GAMESS-UK. > * Symmetry-lowering gives higher-energy structures (nosymm, c2v, c2). > * Intrinsic reaction coordinate following likewise gives rise to higher-energy > structures. > * Numerical frequencies also give 1 imaginary frequency. From this calculation, > it is seen that all displacements are higher in energy than the starting point, > the optimised coronene. This gives reason to belief that the D6H structure is > indeed a minimum and not a first-order saddle point. > * A split basis set (6-31+G* on the central ring, 6-31G* on the peripheral > rings) either with 6 d-functions or 5 d-functions also gives 1 imaginary > frequency. With a triple-zeta basis set, however, no imaginary frequency is > observed. > > It appears that this imaginary frequency arises from the use of diffuse > functions only. I think that it may be related to the near-linear dependency of > the basis. > Has anybody observed similar behaviour, or have a better idea where this > apparent superfluous imaginary frequency may come from? > > Thanks for any help, > kind regards, > > Fedor Goumans ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye*|*crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Thu Apr 26 13:06:00 2007 From: "Bachrach, Steven STEVEN.BACHRACH_._Trinity.edu" To: CCL Subject: CCL:G: large imaginary frequency in coronene when diffuse functions are used Message-Id: <-34141-070426125355-14006-lh9FDXCUFRGoU9H75lzgPA|,|server.ccl.net> X-Original-From: "Bachrach, Steven" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 26 Apr 2007 11:20:18 -0500 MIME-Version: 1.0 Sent to CCL by: "Bachrach, Steven" [STEVEN.BACHRACH],[Trinity.edu] This might be an artifact related to problems associated with optimizing the structure of benzene itself - where some "popular methods" also find an imaginary frequency associated with the planar structure. See: Moran, D.; Simmonett, A. C.; Leach, F. E.; Allen, W. D.; Schleyer, P. v. R.; Schaefer, H. F., III J. Am. Chem. Soc. 2006, 128, 9342-9343, DOI: 10.1021/ja0630285 Steve -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 1 Trinity Place San Antonio, TX 78212 steven.bachrach * trinity.edu -----Original Message----- > From: owner-chemistry * ccl.net [mailto:owner-chemistry * ccl.net] Sent: Thursday, April 26, 2007 4:06 AM To: Bachrach, Steven Subject: CCL:G: large imaginary frequency in coronene when diffuse functions are used Sent to CCL by: Fedor [t.goumans() ucl.ac.uk] Dear CCl-ers, When the frequencies are calculated with diffuse functions (6-31+G*) for coronene there is a large imaginary frequency corresponding to a puckering motion of the atoms in the inner ring, although it does not appear to be a first order saddle point. I have tried to understand what gives rise to this puzzling feature, so I have tried several things: * The large imaginary frequency arises for HF, DFT (pw91) as well as for hybrid DFT (B3LYP,B97-1,MPWB1K). Its magnitude is between 700 and 400 imaginary wavenumbers. * The wavefunction is stable to all the perturbations that are considered with gaussian's Stable keyword. * The imaginary frequency is observed for both G03 and GAMESS-UK. * Symmetry-lowering gives higher-energy structures (nosymm, c2v, c2). * Intrinsic reaction coordinate following likewise gives rise to higher-energy structures. * Numerical frequencies also give 1 imaginary frequency. From this calculation, it is seen that all displacements are higher in energy than the starting point, the optimised coronene. This gives reason to belief that the D6H structure is indeed a minimum and not a first-order saddle point. * A split basis set (6-31+G* on the central ring, 6-31G* on the peripheral rings) either with 6 d-functions or 5 d-functions also gives 1 imaginary frequency. With a triple-zeta basis set, however, no imaginary frequency is observed. It appears that this imaginary frequency arises from the use of diffuse functions only. I think that it may be related to the near-linear dependency of the basis. Has anybody observed similar behaviour, or have a better idea where this apparent superfluous imaginary frequency may come from? Thanks for any help, kind regards, Fedor Goumanshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Apr 26 13:40:00 2007 From: "errol lewars elewars=trentu.ca" To: CCL Subject: CCL:G: large imaginary frequency in coronene when diffuse functions are used Message-Id: <-34142-070426110051-23735-cgIPmmfnc+Fc+zA9DbKefg*server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 26 Apr 2007 11:00:33 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars()trentu.ca] 2007 April 27 This surprising phenomenon has been noted: D. Moran et al., J Am Chem Soc., 2006, 128(9), 9342. With MP2/6-311+G(d), planar benzene is said to give imaginary freqs! See the ref for suggestions as to the cause. E. Lewars =========== Fedor t.goumans~!~ucl.ac.uk wrote: >Sent to CCL by: Fedor [t.goumans() ucl.ac.uk] >Dear CCl-ers, > >When the frequencies are calculated with diffuse functions (6-31+G*) for >coronene there is a large imaginary frequency corresponding to a puckering >motion of the atoms in the inner ring, although it does not appear to be a >first order saddle point. > >I have tried to understand what gives rise to this puzzling feature, so I have >tried several things: > >* The large imaginary frequency arises for HF, DFT (pw91) as well as for hybrid >DFT (B3LYP,B97-1,MPWB1K). Its magnitude is between 700 and 400 imaginary >wavenumbers. >* The wavefunction is stable to all the perturbations that are considered with >gaussian's Stable keyword. >* The imaginary frequency is observed for both G03 and GAMESS-UK. >* Symmetry-lowering gives higher-energy structures (nosymm, c2v, c2). >* Intrinsic reaction coordinate following likewise gives rise to higher-energy >structures. >* Numerical frequencies also give 1 imaginary frequency. From this calculation, >it is seen that all displacements are higher in energy than the starting point, >the optimised coronene. This gives reason to belief that the D6H structure is >indeed a minimum and not a first-order saddle point. >* A split basis set (6-31+G* on the central ring, 6-31G* on the peripheral >rings) either with 6 d-functions or 5 d-functions also gives 1 imaginary >frequency. With a triple-zeta basis set, however, no imaginary frequency is >observed. > >It appears that this imaginary frequency arises from the use of diffuse >functions only. I think that it may be related to the near-linear dependency of >the basis. >Has anybody observed similar behaviour, or have a better idea where this >apparent superfluous imaginary frequency may come from? > >Thanks for any help, >kind regards, > >Fedor Goumans> > > > > From owner-chemistry@ccl.net Thu Apr 26 14:16:00 2007 From: "Rudolph J Magyar rjmagyar+*+nist.gov" To: CCL Subject: CCL:G: G03 cubman Message-Id: <-34143-070426112343-26119-zYvsLASn9misyiBgm1YzRw*server.ccl.net> X-Original-From: "Rudolph J Magyar" Date: Thu, 26 Apr 2007 11:23:38 -0400 Sent to CCL by: "Rudolph J Magyar" [rjmagyar..:..nist.gov] Hi, I am trying to use cubman to subtract two g03 density cube files. The trouble is that one cube file has more atoms than the other, and I get an eof error. Has any one seen this? Is there an easy fix? Thanks, Rudy From owner-chemistry@ccl.net Thu Apr 26 14:50:00 2007 From: "Aurora Clark auclark_+_wsu.edu" To: CCL Subject: CCL: Northwest Regional ACS Meeting - Special Symposium - Deadline May 7 Message-Id: <-34144-070426135132-20286-K0H6fmH09svLzZmAjboa7w*server.ccl.net> X-Original-From: "Aurora Clark" Date: Thu, 26 Apr 2007 13:51:29 -0400 Sent to CCL by: "Aurora Clark" [auclark__wsu.edu] Symposium: The Chemistry of Advanced Nuclear Systems Co-organizers: Aurora Clark (WSU) and Wibe de Jong (PNNL) Symposium Abstract: The northwest is a hotbed of research geared towards understanding the fundamental chemistry and behavior of actinide and lanthanide elements as it pertains to the design and implementation of the next generation of nuclear energy systems and environmental remediation. This research area encompasses scientists from both academia and national laboratories, including (but not limited to) Washington State University, the University of Idaho, Pacific Northwest National Laboratory, and Idaho National Laboratory. Given current trends in federal funding, the formation of the Global Nuclear Energy Partnership, and the anticipated construction of several new nuclear reactors in the US, researchers in the northwest are poised to take center stage in what will be a national effort to tackle the major scientific challenges associated with advanced nuclear systems. These include: 1) mastering the chemistry and physics of actinides and actinide-bearing materials, 2) developing multiscale descriptions of material properties in complex materials under potentially extreme conditions, and 3) understanding and designing new molecular systems to gain control of chemical selectivity during processing. The proposed symposium will provide a forum for computational and experimental researchers from these and other institutions to share their progress on these issues, foster collaborative relationships, and address future areas of interest. There will be 4 umbrella topics, one for each half-day session: Session I: Environmental actinide chemistry Session II: Theoretical modeling and simulation Session III: Separations Session IV: Fuels and waste forms Contributed presentations by researchers and students are welcome at this symposium, and can be submitted through either the AASPD or NORM websites. The Pacific Division of the AAAS website is http://www.sou.edu/aaaspd/2007Boise/Index.html and abstracts may be submitted through http://acs.confex.com/acs/norm07/aaas/papers/index.cgi The abstract deadline for AAAS is April 30. Submission via the Norwest Regional Division of the ACS website may be done through http://northwestchemistry.org/Norm_2007/ (note: at the time of this email, the symposia is not listed on the Technical Program, but is listed on the abstract submission page). The abstract deadline for NORM is May 7. From owner-chemistry@ccl.net Thu Apr 26 15:25:01 2007 From: "cwannere^_^chem.uga.edu" To: CCL Subject: CCL:G: large imaginary frequency in coronene when diffuse Message-Id: <-34145-070426133016-3991-CKS0VqUfz2aLyMMKMN6vvw-#-server.ccl.net> X-Original-From: cwannere,+,chem.uga.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 26 Apr 2007 12:57:47 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: cwannere[*]chem.uga.edu Dear Dr. Goumans, Prof. Schleyer's response to your mail is attached below. Best wishes, Chait Dear Dr. Goumans Our paper may answer your question: Popular Theoretical Methods Predict Benzene and Arenes To Be Nonplanar. D. Moran, A. C. Simmonett, F. E. Leach III, W. D. Allen, P. v. R. Schleyer, H. F.Schaefer III J. Am. Chem. Soc. 2006, 128(29), 9342-9343. Please let us know what you find out. Sincerely, Paul Schleyer > > Sent to CCL by: Fedor [t.goumans() ucl.ac.uk] > Dear CCl-ers, > > When the frequencies are calculated with diffuse functions (6-31+G*) for > coronene there is a large imaginary frequency corresponding to a puckering > motion of the atoms in the inner ring, although it does not appear to be a > first order saddle point. > > I have tried to understand what gives rise to this puzzling feature, so I > have > tried several things: > > * The large imaginary frequency arises for HF, DFT (pw91) as well as for > hybrid > DFT (B3LYP,B97-1,MPWB1K). Its magnitude is between 700 and 400 imaginary > wavenumbers. > * The wavefunction is stable to all the perturbations that are considered > with > gaussian's Stable keyword. > * The imaginary frequency is observed for both G03 and GAMESS-UK. > * Symmetry-lowering gives higher-energy structures (nosymm, c2v, c2). > * Intrinsic reaction coordinate following likewise gives rise to > higher-energy > structures. > * Numerical frequencies also give 1 imaginary frequency. From this > calculation, > it is seen that all displacements are higher in energy than the starting > point, > the optimised coronene. This gives reason to belief that the D6H structure > is > indeed a minimum and not a first-order saddle point. > * A split basis set (6-31+G* on the central ring, 6-31G* on the peripheral > rings) either with 6 d-functions or 5 d-functions also gives 1 imaginary > frequency. With a triple-zeta basis set, however, no imaginary frequency > is > observed. > > It appears that this imaginary frequency arises from the use of diffuse > functions only. I think that it may be related to the near-linear > dependency of > the basis. > Has anybody observed similar behaviour, or have a better idea where this > apparent superfluous imaginary frequency may come from? > > Thanks for any help, > kind regards, > > Fedor Goumans> > > > From owner-chemistry@ccl.net Thu Apr 26 16:13:00 2007 From: "Sriraj Srinivasan ss537\a/drexel.edu" To: CCL Subject: CCL: Vibrational frequencies with RHF and R-B3LYP Message-Id: <-34146-070426142642-13446-dU4v/JvhPDj1PmjBUn2A3A:+:server.ccl.net> X-Original-From: "Sriraj Srinivasan" Date: Thu, 26 Apr 2007 14:26:38 -0400 Sent to CCL by: "Sriraj Srinivasan" [ss537]-[drexel.edu] Hi, I have been trying to obtain the vibrational frequency of a particular ethylene geometry, i encountered the following scenario By performing my Hessian calculations with only RHF i obtained one negative frequency, and when i did the same with R-B3LYP i got 3 negative frequencies. I was wondering if anyone could tell me why this has happened, and which of the results do i consider to be correct. I performed all my geometry optimizations with R-B3LYP. Thanks, Sriraj From owner-chemistry@ccl.net Thu Apr 26 16:47:01 2007 From: "Steve Williams willsd%a%appstate.edu" To: CCL Subject: CCL:G: large imaginary frequency in coronene when diffuse functions are used Message-Id: <-34147-070426151336-13658-E4KLh9dbzytx+5RfeBYifw++server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 Apr 2007 15:03:50 -0400 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd^^^appstate.edu] This reminded me... I have seen this before with benzene as well, as part of a study on Raman intensites: MP2 with large Pople basis sets (6-311+G(3df,2p)) gives imaginary frequency for out of plane motion of alternate C atoms (a B1g mode if C2' axes contain C atoms and C2" bisect the carbon-carbon bonds). See Theor. Chem. Acc. (2007) 117:283-290. Steve Williams errol lewars elewars=trentu.ca wrote: > > Sent to CCL by: errol lewars [elewars()trentu.ca] > 2007 April 27 > > This surprising phenomenon has been noted: D. Moran et al., J Am Chem > Soc., 2006, 128(9), 9342. With MP2/6-311+G(d), planar benzene is said > to give imaginary freqs! See the ref for suggestions as to the cause. > > E. Lewars > =========== > > > > Fedor t.goumans~!~ucl.ac.uk wrote: > >> Sent to CCL by: Fedor [t.goumans() ucl.ac.uk] >> Dear CCl-ers, >> >> When the frequencies are calculated with diffuse functions (6-31+G*) for >> coronene there is a large imaginary frequency corresponding to a >> puckering >> motion of the atoms in the inner ring, although it does not appear to >> be a >> first order saddle point. >> >> I have tried to understand what gives rise to this puzzling feature, >> so I have >> tried several things: >> >> * The large imaginary frequency arises for HF, DFT (pw91) as well as >> for hybrid >> DFT (B3LYP,B97-1,MPWB1K). Its magnitude is between 700 and 400 imaginary >> wavenumbers. >> * The wavefunction is stable to all the perturbations that are >> considered with >> gaussian's Stable keyword. >> * The imaginary frequency is observed for both G03 and GAMESS-UK. >> * Symmetry-lowering gives higher-energy structures (nosymm, c2v, c2). >> * Intrinsic reaction coordinate following likewise gives rise to >> higher-energy >> structures. >> * Numerical frequencies also give 1 imaginary frequency. From this >> calculation, >> it is seen that all displacements are higher in energy than the >> starting point, >> the optimised coronene. This gives reason to belief that the D6H >> structure is >> indeed a minimum and not a first-order saddle point. >> * A split basis set (6-31+G* on the central ring, 6-31G* on the >> peripheral >> rings) either with 6 d-functions or 5 d-functions also gives 1 imaginary >> frequency. With a triple-zeta basis set, however, no imaginary >> frequency is >> observed. >> >> It appears that this imaginary frequency arises from the use of diffuse >> functions only. I think that it may be related to the near-linear >> dependency of >> the basis. >> Has anybody observed similar behaviour, or have a better idea where this >> apparent superfluous imaginary frequency may come from? >> >> Thanks for any help, >> kind regards, >> >> Fedor Goumanshttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Thu Apr 26 17:49:01 2007 From: "errol lewars elewars:-:trentu.ca" To: CCL Subject: CCL: Vibrational frequencies with RHF and R-B3LYP Message-Id: <-34148-070426173447-9277-4lyz0IBpZeA9BL59XgYnyQ:+:server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 Apr 2007 17:34:27 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars*_*trentu.ca] 2007 April 26 I'm not sure what you mean by "a particular ethylene geometry" (a particular alkene?), but: I assume each of these frequency jobs was done with the same method/basis (e.g. HF/3-21G, or B3LYP/6-31G*, etc.) as was used for the geometry opt, and that the freqs refer to a stationary point structure; otherwise it's not valid. There is no reason why two different method/basis calcs (I'll call this "different methods") have to give the same number of imaginary ("negative") frequencies for a stationary point. It depends on how the energy of the PES changes with geometry near the stationary point, i.e. on the qualitative nature of the curvature around the point, which does not have to be the same for different methods, altho' at high levels one would expect agreement. This is not usually a problem for "normal" molecules like water, vitamin B12, etc., but for exotic species different methods may well give different numbers of imag freqs. That's why it's often necessary to go to high-level methods to decide with some confidence if such a molecule can exist (= really has no imag freqs). Relevant are the recent CCL postings on planar aromatics (e.g. coronene, benzene) and diffuse functions, and A. I. Boldyrev et al., J Comp Chem, 1992, 9, 1066. E. Lewars === Sriraj Srinivasan ss537a/drexel.edu wrote: >Sent to CCL by: "Sriraj Srinivasan" [ss537]-[drexel.edu] >Hi, > >I have been trying to obtain the vibrational frequency of a particular ethylene geometry, i encountered the following scenario > > By performing my Hessian calculations with only RHF i obtained one negative frequency, and when i did the same with R-B3LYP i got 3 negative frequencies. > >I was wondering if anyone could tell me why this has happened, and which of the results do i consider to be correct. I performed all my geometry optimizations with R-B3LYP. > >Thanks, > >Sriraj> > > > >