From owner-chemistry@ccl.net Wed Jan 8 01:08:00 2014 From: "David Sherrill sherrill*o*gatech.edu" To: CCL Subject: CCL: Georgia Tech Summer Theory REU Program Message-Id: <-49525-140107180934-26218-MIEw7ym/++UUcCjG3mnKpQ:server.ccl.net> X-Original-From: "David Sherrill" Date: Tue, 7 Jan 2014 18:09:32 -0500 Sent to CCL by: "David Sherrill" [sherrill:+:gatech.edu] Georgia Tech will host its annual Summer Theory Program as part of its NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 19 to July 25 and is open to students who will be in their junior or senior years during the next academic year. Theory students will work with Professors David Sherrill, Rigoberto Hernandez, Jean-Luc Bredas, or Angelo Bongiorno in the areas of electronic structure theory, nonequilibrium dynamics, electronic properties of materials, or condensed-matter simulations. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $4500, a travel allowance, and housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html and http://ww2.chemistry.gatech.edu/reu/ Participants supported by the NSF must be US citizens or permanent residents of the US. The deadline for applications is February 15, 2014. Early applications are encouraged. From owner-chemistry@ccl.net Wed Jan 8 01:51:00 2014 From: "partha kundu partha1kundu+/-gmail.com" To: CCL Subject: CCL:G: SCF energy Message-Id: <-49526-140108014932-10576-9PRp6emWPp1CAbvUpSKCKg-x-server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=485b3970d68ad1e29e04ef6fe403 Date: Wed, 8 Jan 2014 12:18:46 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu^_^gmail.com] --485b3970d68ad1e29e04ef6fe403 Content-Type: text/plain; charset=ISO-8859-1 Dear All, In my case my interest was to calculate the Raman spectrum of some complex with different protonation state. And I saw one of the state to match more closely with experiment. Since Raman is sensitive to the protonation state, I believe that this is what the real situation is. This is also supported by MALDI data. I did all the calculation on a single molecule in a gas phase. For the deprotonated species, I did not include H+ in my model. Is it a correct approach? Regards. Partha On Tue, Jan 7, 2014 at 10:35 PM, Brian Skinn brian.skinn a gmail.com < owner-chemistry[*]ccl.net> wrote: > Partha, > > No, the energy of the proton is not zero -- if nothing else, it > contributes some additional nuclear-nuclear repulsion to the total energy. > It also provides a center onto which some electron density can shift, which > will influence the calculated energy -- perhaps negligibly, perhaps not. > > Are you performing your simulations on the isolated structures, or with > surrounding solvent molecules? In the gas phase, or with a PCM/COSMO > solvation model? The question, "which structure is more stable?" means > different things in different situations, and getting a good answer to the > question you're interested in depends critically on running the proper > simulations. > > > Best regards, > Brian > > > > On Tue, Jan 7, 2014 at 10:49 AM, partha kundu partha1kundu%gmail.com < > owner-chemistry**ccl.net> wrote: > >> Dear Dave Close, >> Since its an electronic energy calculation, the energy of a proton should >> be zero, right? I also had a similar question and got the answer from >> Gaussian help. >> Regards. >> >> Partha >> >> On Tue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu < >> owner-chemistry__ccl.net> wrote: >> >>> >>> Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu] >>> I'm not sure if I can answer your question with the information >>> provided. The difference in energy you provided is roughly the energy of a >>> proton. You don 't tell us the molecule you are studying. All you say >>> is "two different structure in acidic or neutral conditions"? What is the >>> difference is these structures? Has one structure lost a proton? If so, >>> how are you accounting for this in making the comparison between the two >>> structures? >>> Regards, Dave Close. >>> >>> -----Original Message----- >>> > From: owner-chemistry+closed==etsu.edu*_*ccl.net [mailto: >>> owner-chemistry+closed==etsu.edu*_*ccl.net] On Behalf Of mahnaz gh >>> mahnaz271163%a%yahoo.com >>> Sent: Monday, January 06, 2014 2:11 PM >>> To: Close, David M. >>> Subject: CCL: SCF energy >>> >>> >>> Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I have >>> a molecule which have two different structure in acidic or neutral >>> conditions. In order to determine which of them is the more stable >>> structure, I used the SCF done term, the values is as follows: SCF done 1 = >>> -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me >>> and tell which of them is the more stable one and is the difference enough >>> to distinguish between the structures? >>> Regardshttp:// >>> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>>> E-mail to subscribers: CHEMISTRY__ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use>>> >>> >>> >> > --485b3970d68ad1e29e04ef6fe403 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,
In my case my interest was to= calculate the Raman spectrum of some complex=A0 with different protonation= state. And I saw one of the state to match more closely with experiment. S= ince Raman is sensitive to the protonation state, I believe that this is wh= at the real situation is. This is also supported by MALDI data. I did all t= he calculation on a single molecule in a gas phase. For the deprotonated sp= ecies, I did not include H+ in my model. Is it a correct approach?
Regards.

Partha



On Tue, Jan 7, 2014 at 10:35 PM, Brian S= kinn brian.skinn a gmail.com <owner-chemistry[*]ccl.net> wr= ote:
Partha,
<= br>
No, the energy of the proton is not zero -- if nothing else, it co= ntributes some additional nuclear-nuclear repulsion to the total energy.=A0= It also provides a center onto which some electron density can shift, whic= h will influence the calculated energy -- perhaps negligibly, perhaps not.<= br>
Are you performing your simulations on the isolated structures, o= r with surrounding solvent molecules?=A0 In the gas phase, or with a PCM/CO= SMO solvation model?=A0 The question, "which structure is= more stable?" means different things in different situations, and get= ting a good answer to the question you're interested in depends critica= lly on running the proper simulations.


Best regards,
Brian



On Tue, Jan 7, 2014 at 10:49 AM, partha kundu = partha1kundu%gmail.com <= span dir=3D"ltr"><owner-chemistry**ccl.net> wrote:
Dear Dave Close,<= br>
Since its an electronic energy calculation, the energy of a proton= should be zero, right? I also had a similar question and got the answer fr= om Gaussian help.
Regards.

Partha

On T= ue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu <owner-chemistry__cc= l.net> wrote:

Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu]
=A0 I'm not sure if I can answer your question with the information pro= vided. =A0The difference in energy you provided is roughly the energy of a = proton. You don 't tell us the molecule you are studying. = =A0All you say is "two different structure in acidic or neutral condit= ions"? =A0What is the difference is these structures? =A0Has one struc= ture lost a proton? If so, how are you accounting for this in making the co= mparison between the two structures?
=A0 Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu*_*ccl= .net [mailto:owner-chemistry+closed=3D=3Detsu.edu*_*ccl.net<= /a>] On Behalf Of mahnaz gh mahnaz271163%a%yahoo.com
Sent: Monday, January 06, 2014 2:11 PM
To: Close, David M.
Subject: CCL: SCF energy


Sent to CCL by: "mahnaz =A0gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule whic= h have two different structure in acidic or neutral conditions. In order to= determine which of them is the more stable structure, I used the SCF done = term, the values is as follows: SCF done 1 =3D -1330.29275098 and SCF done = 2 =3D -1330.76227822. Could you please help me and tell which of them is th= e more stable one and is the difference enough to distinguish between the s= tructures?
Regardshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net= /chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


-=3D This is automatically added to each message by the mailing script =3D-=
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--485b3970d68ad1e29e04ef6fe403-- From owner-chemistry@ccl.net Wed Jan 8 09:13:00 2014 From: "Brian Skinn brian.skinn_-_gmail.com" To: CCL Subject: CCL:G: SCF energy Message-Id: <-49527-140108091150-17328-tj+775NnS7/RvPy7U9iqNg,server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=bcaec53d5ee18532e404ef7612de Date: Wed, 8 Jan 2014 09:11:22 -0500 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [brian.skinn]^[gmail.com] --bcaec53d5ee18532e404ef7612de Content-Type: text/plain; charset=ISO-8859-1 Partha, It sounds like what you're really trying to determine is the acidity constant of your species -- that is, if you can calculate the pKa, you can tell whether it will be mostly protonated or deprotontated in the solution you've analyzed experimentally. Is this the case? I think you're at the start of the right path, but unfortunately, to my best understanding, gas-phase SCF energies on isolated species tend to be an unreliable predictor of solvated equilibrium. If nothing else, you need to calculate the thermochemistry of both species and compare the change in free energy, not just the change in electronic (SCF) energy. You'll definitely want to read the literature extensively on these types of calculations. (As it happens, estimating equilibrium constants of metal-ligand complexes from first-principles is something I'm interested in myself, but am still learning about & so I can't help directly very much.) After a quick Google search, I actually turned up a reference I hadn't come across before, which may be a helpful introduction: http://dasher.wustl.edu/chem478/reading/annrepcompchem-6-113-10.pdf These are a few specific examples of approaches taken for calculating pK values: http://dx.doi.org/10.1088/0953-8984/22/28/284116 http://dx.doi.org/10.1039/b312518c http://dx.doi.org/10.1134/S003602360702026X Good luck, Brian On Wed, Jan 8, 2014 at 1:48 AM, partha kundu partha1kundu+/-gmail.com < owner-chemistry]|[ccl.net> wrote: > Dear All, > In my case my interest was to calculate the Raman spectrum of some > complex with different protonation state. And I saw one of the state to > match more closely with experiment. Since Raman is sensitive to the > protonation state, I believe that this is what the real situation is. This > is also supported by MALDI data. I did all the calculation on a single > molecule in a gas phase. For the deprotonated species, I did not include H+ > in my model. Is it a correct approach? > Regards. > > Partha > > > > On Tue, Jan 7, 2014 at 10:35 PM, Brian Skinn brian.skinn a gmail.com < > owner-chemistry|ccl.net> wrote: > >> Partha, >> >> No, the energy of the proton is not zero -- if nothing else, it >> contributes some additional nuclear-nuclear repulsion to the total energy. >> It also provides a center onto which some electron density can shift, which >> will influence the calculated energy -- perhaps negligibly, perhaps not. >> >> Are you performing your simulations on the isolated structures, or with >> surrounding solvent molecules? In the gas phase, or with a PCM/COSMO >> solvation model? The question, "which structure is more stable?" means >> different things in different situations, and getting a good answer to the >> question you're interested in depends critically on running the proper >> simulations. >> >> >> Best regards, >> Brian >> >> >> >> On Tue, Jan 7, 2014 at 10:49 AM, partha kundu partha1kundu%gmail.com < >> owner-chemistry**ccl.net> wrote: >> >>> Dear Dave Close, >>> Since its an electronic energy calculation, the energy of a proton >>> should be zero, right? I also had a similar question and got the answer >>> from Gaussian help. >>> Regards. >>> >>> Partha >>> >>> On Tue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu < >>> owner-chemistry__ccl.net> wrote: >>> >>>> >>>> Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu] >>>> I'm not sure if I can answer your question with the information >>>> provided. The difference in energy you provided is roughly the energy of a >>>> proton. You don 't tell us the molecule you are studying. All you say >>>> is "two different structure in acidic or neutral conditions"? What is the >>>> difference is these structures? Has one structure lost a proton? If so, >>>> how are you accounting for this in making the comparison between the two >>>> structures? >>>> Regards, Dave Close. >>>> >>>> -----Original Message----- >>>> > From: owner-chemistry+closed==etsu.edu*_*ccl.net [mailto: >>>> owner-chemistry+closed==etsu.edu*_*ccl.net] On Behalf Of mahnaz gh >>>> mahnaz271163%a%yahoo.com >>>> Sent: Monday, January 06, 2014 2:11 PM >>>> To: Close, David M. >>>> Subject: CCL: SCF energy >>>> >>>> >>>> Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I >>>> have a molecule which have two different structure in acidic or neutral >>>> conditions. In order to determine which of them is the more stable >>>> structure, I used the SCF done term, the values is as follows: SCF done 1 = >>>> -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me >>>> and tell which of them is the more stable one and is the difference enough >>>> to distinguish between the structures? >>>> Regardshttp:// >>>> www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>>>> E-mail to subscribers: CHEMISTRY__ccl.net or use:>>>> >>>> E-mail to administrators: CHEMISTRY-REQUEST__ccl.net or use>>>> >>>> >>>> >>> >> > --bcaec53d5ee18532e404ef7612de Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Partha,

It sounds li= ke what you're really trying to determine is the acidity constant of yo= ur species -- that is, if you can calculate the pKa, you can tell whether i= t will be mostly protonated or deprotontated in the solution you've ana= lyzed experimentally.=A0 Is this the case?

I think you're at the start of the right path, but unfortunately, t= o my best understanding, gas-phase SCF energies on isolated species tend to= be an unreliable predictor of solvated equilibrium.=A0 If nothing else, yo= u need to calculate the thermochemistry of both species and compare the cha= nge in free energy, not just the change in electronic (SCF) energy.=A0 You&= #39;ll definitely want to read the literature extensively on these types of= calculations.=A0 (As it happens, estimating equilibrium constants of metal= -ligand complexes from first-principles is something I'm interested in = myself, but am still learning about & so I can't help directly very= much.)

After a quick Google search, I actually turned up a reference I h= adn't come across before, which may be a helpful introduction: ht= tp://dasher.wustl.edu/chem478/reading/annrepcompchem-6-113-10.pdf

These are a few specific examples of approaches taken for calcula= ting pK values:


Good luck,
Brian



On Wed, Jan 8, 20= 14 at 1:48 AM, partha kundu partha1kundu+/-gma= il.com <owner-chemistry]|[ccl.net> wrote:
Dear All,
In my case my interest was to calculate the Raman spectrum of some comple= x=A0 with different protonation state. And I saw one of the state to match = more closely with experiment. Since Raman is sensitive to the protonation s= tate, I believe that this is what the real situation is. This is also suppo= rted by MALDI data. I did all the calculation on a single molecule in a gas= phase. For the deprotonated species, I did not include H+ in my model. Is = it a correct approach?
Regards.

Partha



On Tue, Jan 7, 2014 at 10:35 PM, Brian S= kinn brian.skinn a gmail.com <owner-chemistry|ccl= .net> wrote:
Partha,
<= br>
No, the energy of the proton is not zero -- if nothing else, it co= ntributes some additional nuclear-nuclear repulsion to the total energy.=A0= It also provides a center onto which some electron density can shift, whic= h will influence the calculated energy -- perhaps negligibly, perhaps not.<= br>
Are you performing your simulations on the isolated structures, o= r with surrounding solvent molecules?=A0 In the gas phase, or with a PCM/CO= SMO solvation model?=A0 The question, "which structure is= more stable?" means different things in different situations, and get= ting a good answer to the question you're interested in depends critica= lly on running the proper simulations.


Best regards,
Brian



On Tue, Jan 7, 2014 at 10:49= AM, partha kundu partha1kundu%gmail.com <owner-chemistry**ccl.ne= t> wrote:
Dear Dave Close,<= br>
Since its an electronic energy calculation, the energy of a proton= should be zero, right? I also had a similar question and got the answer fr= om Gaussian help.
Regards.

Partha

On T= ue, Jan 7, 2014 at 8:06 PM, Close, David M. CLOSED%a%mail.etsu.edu <owner-chemistry__cc= l.net> wrote:

Sent to CCL by: "Close, David M." [CLOSED^^^mail.etsu.edu]
=A0 I'm not sure if I can answer your question with the information pro= vided. =A0The difference in energy you provided is roughly the energy of a = proton. You don 't tell us the molecule you are studying. = =A0All you say is "two different structure in acidic or neutral condit= ions"? =A0What is the difference is these structures? =A0Has one struc= ture lost a proton? If so, how are you accounting for this in making the co= mparison between the two structures?
=A0 Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed=3D=3Detsu.edu*_*ccl= .net [mailto:owner-chemistry+closed=3D=3Detsu.edu*_*ccl.net<= /a>] On Behalf Of mahnaz gh mahnaz271163%a%yahoo.com
Sent: Monday, January 06, 2014 2:11 PM
To: Close, David M.
Subject: CCL: SCF energy


Sent to CCL by: "mahnaz =A0gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule whic= h have two different structure in acidic or neutral conditions. In order to= determine which of them is the more stable structure, I used the SCF done = term, the values is as follows: SCF done 1 =3D -1330.29275098 and SCF done = 2 =3D -1330.76227822. Could you please help me and tell which of them is th= e more stable one and is the difference enough to distinguish between the s= tructures?
Regardshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net= /chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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--bcaec53d5ee18532e404ef7612de-- From owner-chemistry@ccl.net Wed Jan 8 12:59:00 2014 From: "Eric Schwegler schwegler1:llnl.gov" To: CCL Subject: CCL: 2014 CCMS Summer Institute at Lawrence Livermore National Lab Message-Id: <-49528-140108113936-25468-V3CkL/1HyMQaUzGFjmGeMQ*_*server.ccl.net> X-Original-From: "Eric Schwegler" Date: Wed, 8 Jan 2014 11:39:34 -0500 Sent to CCL by: "Eric Schwegler" [schwegler1(!)llnl.gov] We are pleased to announce the 2014 Computational Chemistry and Material Science (CCMS) Summer Institute: Mesoscale Materials and Chemistry, which will take place from June 9 - August 15, 2014 at Lawrence Livermore National Laboratory (LLNL). The goal of the Summer Institute is to provide graduate students with the opportunity to work directly with LLNL researchers on the development and application of cutting edge methods in computational materials science and chemistry and other related areas. The 2014 CCMS Summer Institute will have a special focus on "Mesoscale Materials and Chemistry" to reflect the ever increasing interest and enormous research opportunities in mesoscale phenomena, where classical, nanoscale and quantum science meet. Each student will spend ten weeks at LLNL as a guest of an LLNL host scientist working on a computational project in the host's area of expertise. In addition, leading researchers from universities and national labs will give a series of mini-courses for the students. These courses will cover state-of-the-art and emerging computational methods in materials science and chemistry. Travel funds and a generous stipend will be provided to the participants. In order to be considered, prospective participants will need to fill out an application form that can be found at the following website: www.llnl.gov/ccms The application deadline is February 16, 2014. We would greatly appreciate it if you could bring this announcement to the attention of graduate students that you feel would benefit from the experience of hands-on research in computational chemistry and materials science, working with leading researchers at a national laboratory. Additional details about the summer institute can be found on the website listed above. Vincenzo Lordi (lordi2/./llnl.gov) Eric Schwegler (schwegler1/./llnl.gov) From owner-chemistry@ccl.net Wed Jan 8 14:01:00 2014 From: "Joy Ku joyku{:}stanford.edu" To: CCL Subject: CCL: Webinar: OpenMM - Accelerating and Customizing MD Simulations on GPUs Message-Id: <-49529-140108135934-15670-8VrmebTgOpDvoyUwVQCynQ _ server.ccl.net> X-Original-From: "Joy Ku" Date: Wed, 8 Jan 2014 13:59:33 -0500 Sent to CCL by: "Joy Ku" [joyku{}stanford.edu] Please join us on January 16th for a webinar presented by Professor Vijay Pande, a pioneer in the field of protein folding and the author of Folding[a]Home. Learn about OpenMM, the computational engine behind the Folding[a]Home distributed computing system, and hear how others have leveraged its high-performance on GPUs and its custom classes and extreme flexibility to accelerate research in areas such as free energy calculations, protein folding, and protein conformational change. This webinar is planned for January 16th 2014 at 9.00 AM Pacific Time. Register at: http://bit.ly/OpenMM About Prof. Vijay Pande: Professor Pande received his PhD from MIT. He is currently a Professor of chemistry, structural biology and computer science at Stanford University. He is the director of Stanfords BioPhysics Program, founder and director of the Folding[a]Home project, and a co-PI of the Simbios National Center for Physics-Based Simulations of Biological Structures.