From owner-chemistry@ccl.net Mon May 9 10:27:01 2016 From: "Hachmann, Johannes hachmann%%buffalo.edu" To: CCL Subject: CCL: Data Mining and Machine Learning in Molecular Sciences at AIChE Message-Id: <-52185-160509095022-28602-QofQim3UPIZjXOW0WqDedw**server.ccl.net> X-Original-From: "Hachmann, Johannes" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 9 May 2016 13:50:16 +0000 MIME-Version: 1.0 Sent to CCL by: "Hachmann, Johannes" [hachmann(0)buffalo.edu] A quick reminder that today is the deadline for the submission to the AIChE CoMSEF session on "Data Mining and Machine Learning in Molecular Sciences" at the 2016 AIChE Annual Meeting in San Francisco. Best regards, Johannes Hachmann > -----Original Message----- > From: owner-chemistry+hachmann==buffalo.edu=-=ccl.net [mailto:owner- > chemistry+hachmann==buffalo.edu=-=ccl.net] On Behalf Of Johannes Hachmann > hachmann_+_buffalo.edu > Sent: 18 April, 2016 23:06 > To: Hachmann, Johannes > Subject: CCL: Data Mining and Machine Learning in Molecular Sciences at > AIChE > > > Sent to CCL by: "Johannes Hachmann" [hachmann(~)buffalo.edu] > Dear Colleagues, > > We are writing today to let you know that we will again be running the > CoMSEF technical session "Data Mining and Machine Learning in Molecular > Sciences" at the 2016 AIChE Annual Meeting in San Francisco (Nov 13-18). > > Last year's inaugural edition proved to be exceedingly popular and well- > attended, indicative of a critical groundswell of excitement and interest within > the ChemE community for data-driven methods and applications in the > physical, chemical, materials, and life sciences. We are also delighted to > announce that this year's session will be anchored by two invited talks from > Yannis Kevrekidis (Princeton) and Kristin Persson (Lawrence Berkeley National > Lab). > > We are currently soliciting abstracts for contributed talks, and if you or your > students are interested in presenting in this session we would be excited to > receive your submission through the online application portal. The scope of the > session is intentionally broad, concerning the generic applications of data > mining and machine learning for property prediction, molecular understanding, > and rational design. Details of the session scope and instructions for abstract > submission are provided below. The submission deadline is Monday, May 9. > > We look forward to seeing you in San Francisco! > > Kind Regards, > > Andrew Ferguson (University of Illinois, alf[]illinois.edu) > Johannes Hachmann (University at Buffalo, hachmann[]buffalo.edu) > > --- > > Data Mining and Machine Learning in Molecular Sciences > > https://aiche.confex.com/aiche/2016/webprogrampreliminary/Session32684.ht > ml > > Computational approaches to correlate, analyze, and understand large and > complex data sets are playing increasingly important roles in the physical, > chemical, and life sciences. This session solicits submissions pertaining to > methodological advances and applications of data mining and machine learning > methods, with particular emphasis on data-driven modeling and property > prediction, statistical inference, big data, and informatics. Topics of interest > include: algorithm development, inverse engineering, chemical property > prediction, genomics/proteomics/metabolomics, (virtual) high-throughput > screening, rational design, accelerated simulation, biomolecular folding, > reaction networks, and quantum chemistry. > > 1. Go to https://aiche.confex.com/aiche/2016/cfp.cgi > 2. Click on the blue drop down for "Computational Molecular Science and > Engineering Forum", and click "Begin a Submission" > 3. Select "21004 Data Mining and Machine Learning in Molecular Sciences and > then click Save and Continue". > > > ----------------------------------------------------------------------------------------- > Dr. Johannes Hachmann > Assistant Professor > University at Buffalo, The State University of New York > Department of Chemical and Biological Engineering (CBE) > New York State Center of Excellence in Materials Informatics (CMI) > Computational and Data-Enabled Science and Engineering Program (CDSE) > 612 Furnas Hall > Buffalo, NY 14260 > www.cbe.buffalo.edu/hachmann > http://hachmannlab.cbe.buffalo.edu > -----------------------------------------------------------------------------------------> From owner-chemistry@ccl.net Mon May 9 11:02:00 2016 From: "Debopreeti Mukherjee debopreeti91 ~ gmail.com" To: CCL Subject: CCL: TD-DFT calculations performed for simulation of peptide CD spectrum Message-Id: <-52186-160509103656-1664-ZJRwhxFR3RiONkS4qUwa5w%server.ccl.net> X-Original-From: "Debopreeti Mukherjee" Date: Mon, 9 May 2016 10:36:55 -0400 Sent to CCL by: "Debopreeti Mukherjee" [debopreeti91(-)gmail.com] Hello, I am trying to simulate the CD spectrum of a peptide using TD-DFT. In my peptide, I expect to see an excitonic coupling band arising as a result of interactions between two aromatic amino acids (seen from experiment). In order to calculate the rotational strength of this band, I need to construct a Hamiltonian based on dipole-dipole interactions between the aromatic amino acid residues, diagonalize it and then use the eigen vector components. I would also need the transition dipole moment values corresponding to each aromatic chromophore. I ran a TD-DFT calculation (no solvent model, counterpoise for two aromatic fragments; according to the paper - http://onlinelibrary.wiley.com/doi/10.1002/chir.20792/full) and then tried to use Matlab to construct the matrices. However, I am confused regarding the rotational strength units and the values also seem way off. If anyone has done these kind of calculations before, can you please help me? Thank you so much. Regards, Debopreeti Mukherjee Email id: debopreeti91#,#gmail.com From owner-chemistry@ccl.net Mon May 9 11:59:01 2016 From: "zborowsk zborowsk]|[chemia.uj.edu.pl" To: CCL Subject: CCL: About phosphorus-carbon double bond vibrational-frequency(ies) Message-Id: <-52187-160509105831-9297-n1ywajIocoI99flmOSqqKw(_)server.ccl.net> X-Original-From: zborowsk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 09 May 2016 16:58:19 +0200 MIME-Version: 1.0 Sent to CCL by: zborowsk [zborowsk:+:chemia.uj.edu.pl] Daniel, > If > you're lucky, there won't be too many vibrational nodes with > frequencies in your range, and you can pick out the C=P stretch from > watching the animation. it looks you are not lucky, because you said you cannot find the C+P stretching band by vibrational modes animation. > If you are unlucky, there will be several other vibrational nodes > with similar frequencies, and every one of those modes will be a > mixed > mode that has only some C=P stretching character. This is probably your case. The C=P stretching is probably coupled with other internal coordinates and should be detected in several modes. You have to perform the Potential Energy Distribution analysis in order to detect in which vibrational bands the C=P is involved. regards