From owner-chemistry@ccl.net Mon Oct 12 05:56:01 2015 From: "Oellien, Frank frank.oellien * abbvie.com" To: CCL Subject: CCL: 11. Germ Conf Chemoinformatics - Program available / Registration open / Moonlight Session Message-Id: <-51812-151012055338-20374-LsIH1fyhEAZQHOwO/iPUmg .. server.ccl.net> X-Original-From: "Oellien, Frank" Content-Language: de-DE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 12 Oct 2015 09:52:17 +0000 MIME-Version: 1.0 Sent to CCL by: "Oellien, Frank" [frank.oellien- -abbvie.com] Dear Colleagues, The scientific program of the 11. German Conference on Chemoinformatics (GCC2015) is online. https://www.gdch.de/fileadmin/downloads/Veranstaltungen/Tagungen/2015_Tagungen/GCC_2015/GCC_Programm_2015.pdf You can still register for this international event via our conference web page: www.gdch.de/gcc2015 To enhance and support the networking and scientific exchange between young scientists, we will organize a Moonlight session. All PhD students attending at the GCC2015 can participate at this specific session. Each student should introduce his work shortly by a very small (max. 5 minutes) presentation. Scientific work is discussed with other PhD students. To leverage this event we would like to reward each contribution (most probably with several free drinks). So get connected! Best regards, Frank FRANK OELLIEN, PHD LabHead Cheminformatics and Modeling Computer-Aided Drug Design (CADD) / Medicinal Chemistry AbbVie Deutschland GmbH & Co KG Neuroscience Discovery Knollstr. 67061 Ludwigshafen OFFICE +49 621-589-4683 FAX +49 621-589-63449 EMAIL frank.oellien{:}abbvie.com abbvie.com | Follow us: This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________ Sitz der Gesellschaft: Wiesbaden - Registergericht: AG Wiesbaden HRA 9790 Persönlich haftende Gesellschafterin: AbbVie Komplementär GmbH Sitz der persönlich haftenden Gesellschafterin: Wiesbaden - Registergericht: AG Wiesbaden HRB 26371 Geschäftsführer: Dr. Patrick Horber, Dr. Friedrich Richter, William J. Chase Vorsitzende des Aufsichtsrats: Dr. Azita Saleki-Gerhardt This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. Diese Kommunikation kann Informationen enthalten, die geheim, vertraulich oder hinsichtlich der Offenlegung beschränkt sind. Wenn Sie nicht der beabsichtigte Empfänger sind, nehmen Sie bitte zur Kenntnis, dass jede Weitergabe, Verteilung, Verwendung oder Vervielfältigung dieser. Kommunikation strikt untersagt ist. Jeder, der diese Nachricht fehlerhaft erhält, sollte den Sender unverzüglich telefonisch oder durch Rücksendung der E-Mail benachrichtigen und diese von seinem oder ihrem Computer löschen. From owner-chemistry@ccl.net Mon Oct 12 07:08:01 2015 From: "Susi Lehtola susi.lehtola*_*alumni.helsinki.fi" To: CCL Subject: CCL: values of imaginary Message-Id: <-51813-151012052711-17980-9e1j42dolrVHLqT7g6PSSQ(_)server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Mon, 12 Oct 2015 02:26:47 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola,alumni.helsinki.fi] On 10/11/2015 08:08 AM, Partha Sengupta anapspsmo * gmail.com wrote: > Friends, I am calculating the imaginary frequency of a loosely bound > transition state with a number of weak hydrogen bonds. The system > containing 55 atoms including Carbon, hydrogen, nitrogen and oxygen atoms. > The structure have 6 hydrogen bonds covering O-H..O, O-H..N. The negative > frequency is only 68 cm-1. > Is it correct from theoretical consideration? You aren't specifying the method you use. If you use DFT, the numerical integration of the exchange-correlation potential can produce spurious negative frequencies if a big enough grid isn't used. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola#%#alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Oct 12 13:12:00 2015 From: "Theodore S. Dibble tsdibble/./esf.edu" To: CCL Subject: CCL:G: values of imaginary Message-Id: <-51814-151012122518-32536-9uyTKHvY3WMOF07rWY6eDg~~server.ccl.net> X-Original-From: "Theodore S. Dibble" Date: Mon, 12 Oct 2015 12:25:17 -0400 Sent to CCL by: "Theodore S. Dibble" [tsdibble.:.esf.edu] To expand on the point below, you may need to reoptimize the geometry with a finer grid and then recomputed the frequencies with a finer grid. Note that in GAUSSIAN, there are separate keywords for the grid of the optimization (INT) and frequency (CPHF). The Minnesota functionals seems to require finer grids than some other functionals. To the previous point, an imaginary frequency of 68/cm seems more characteristic of the transition state for a torsional motion than a chemical reaction. It sounds like you need to calculate the intrinsic reaction coordinate to determine what reactant and product correspond to the TS you have found. Theodore S. Dibble Professor and Associate Chair Chemistry Department SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 315-470-6596 315-470-6856 (fax) http://www.esf.edu/faculty/dibble > "Susi Lehtola susi.lehtola*_*alumni.helsinki.fi" wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola,alumni.helsinki.fi] > On 10/11/2015 08:08 AM, Partha Sengupta anapspsmo * gmail.com wrote: > > Friends, I am calculating the imaginary frequency of a loosely bound > > transition state with a number of weak hydrogen bonds. The system > > containing 55 atoms including Carbon, hydrogen, nitrogen and oxygen atoms. > > The structure have 6 hydrogen bonds covering O-H..O, O-H..N. The negative > > frequency is only 68 cm-1. > > Is it correct from theoretical consideration? > > You aren't specifying the method you use. If you use DFT, the numerical > integration of the exchange-correlation potential can produce spurious > negative frequencies if a big enough grid isn't used. > -- > ----------------------------------------------------------------------- > Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow > susi.lehtola#%#alumni.helsinki.fi Lawrence Berkeley National Laboratory > http://www.helsinki.fi/~jzlehtol USA > ----------------------------------------------------------------------- > > From owner-chemistry@ccl.net Mon Oct 12 13:46:00 2015 From: "Yingbin Ge yingbin.ge]*[gmail.com" To: CCL Subject: CCL: values of imaginary Message-Id: <-51815-151012134503-13801-yFjtoxUQvQ4weFa8XU9W8A . server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=001a1139cf462d97e00521ebe302 Date: Mon, 12 Oct 2015 10:44:55 -0700 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge_-_gmail.com] --001a1139cf462d97e00521ebe302 Content-Type: text/plain; charset=UTF-8 Dear Partha, To know for sure, you may run an intrinsic reaction coordinate (IRC) or minimum energy path (MEP) calculation starting from the structure with the small negative frequency, You've got the correct TS if your IRC/MEP calculation ends up with desired reactant and product. Sincerely, Yingbin On Sun, Oct 11, 2015 at 8:08 AM, Partha Sengupta anapspsmo * gmail.com < owner-chemistry*_*ccl.net> wrote: > Friends, I am calculating the imaginary frequency of a loosely bound > transition state with a number of weak hydrogen bonds. The system > containing 55 atoms including Carbon, hydrogen, nitrogen and oxygen atoms. > The structure have 6 hydrogen bonds covering O-H..O, O-H..N. The negative > frequency is only 68 cm-1. > Is it correct from theoretical consideration? > Partha > > -- > > > *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, > Burdwan* > --001a1139cf462d97e00521ebe302 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Partha,
To know for sure, you may = run an intrinsic reaction coordinate (IRC) or minimum energy path (MEP) cal= culation starting from the structure with the small negative frequency,
=
You've got the correct TS if your IRC/MEP calculation ends u= p with desired reactant and product.
Sincerely, Yingbin
<= div class=3D"gmail_extra">
On Sun, Oct 11, 20= 15 at 8:08 AM, Partha Sengupta anapspsmo * gma= il.com <owner-chemistry*_*ccl.net> wrote:
Friends, I am calculatin= g the imaginary frequency of a loosely bound=C2=A0 transition state=C2=A0 w= ith a number of weak hydrogen bonds. The system containing 55 atoms includi= ng Carbon, hydrogen, nitrogen and oxygen atoms. The structure have 6 hydrog= en bonds covering O-H..O, O-H..N. The negative frequency is only 68 cm-1.
Is it correct from theoretical consideration?
Partha

--
Dr. Partha Sarathi Sengupta
Associate P= rofessor
Vivekananda Mahavidyalaya, Burdwan

--001a1139cf462d97e00521ebe302--