Dear Dr. Tamulis,

Going public in science and asking for collaborations is a very good initia= tive. Although I may not be of any help to you, I fully wish you good luck = with your research.

With best regards,

Raghu

Dr. Raghunathan Ramakrishnan

Research Associate

University of Basel

Basel CH-4056

Switzerland.

On Wed, May 14, 2014 at 5:33 AM, Arvydas Tamulis tamulis9(!)gmail.com <owner-chemistry() ccl.net> wrote:

Dear Colleagues,
Would you please to cooperate with me in quantum chemical calculations of supramolecule containing of 717 atoms (C, N, O, H).

1) Needs to optimize geometry by using, for example, DFT method B97d and the 6-31G(d) basis set in the G09RevB.01 program package.
2) Later needs to calculate absorption spectrum a= nd HOMO-m/LUMO+n (where m and n=3D20), for example, by<= font face=3D"Nimbus Roman No9 L, Times New Roman, serif"> Turbomole program package TD-DFT PBE0 method with the def-TZVP basis set.

3) Finally, needs to calculate electron charge density transfer in 30 excited states using Turbomole = package.

I will prepare all input files for potential colleagues who wish to collaborate.

I will analy= ze the calculation results and write the joint article similar to our already published:
Tamulis A, Grigalavicius M, Baltrusa=
itis J (2013) Phenomenon of quantum entanglement in a s=
ystem composed of
two minimal protocells. Orig Life Evol=
 Biosph 43:49-66.
With best regards,

Arvydas Tamulis

http://www.it= pa.lt/~tamulis/

--047d7b10ca5579a99904f95cbed8-- From owner-chemistry@ccl.net Wed May 14 11:02:01 2014 From: "Roscioni O.M. omr(a)soton.ac.uk" To: CCL Subject: CCL:G: Asking for cooperation in quantum calculations Message-Id: <-50083-140514105207-15397-kFgVQjZa/HX42UV6Bb+Y/w]-[server.ccl.net> X-Original-From: "Roscioni O.M." Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 14 May 2014 14:51:18 +0000 MIME-Version: 1.0 Sent to CCL by: "Roscioni O.M." [omr%%soton.ac.uk] Dear Arvydas, if you have a collaboration with someone in Italy, you can apply for computing time through the Italian Super Computing Resource Allocation system: http://www.hpc.cineca.it/services/iscra Both Gaussian and Turbomole programs are available for use. Similar calls exist on other HPC centres across Europe. Best wishes, Otello M. Roscioni ________________________________________ > From: owner-chemistry+omr==soton.ac.uk[*]ccl.net [owner-chemistry+omr==soton.ac.uk[*]ccl.net] on behalf of Arvydas Tamulis tamulis9(!)gmail.com [owner-chemistry[*]ccl.net] Sent: 14 May 2014 04:33 To: Roscioni O.M. Subject: CCL: Asking for cooperation in quantum calculations Dear Colleagues, Would you please to cooperate with me in quantum chemical calculations of supramolecule containing of 717 atoms (C, N, O, H). 1) Needs to optimize geometry by using, for example, DFT method B97d and the 6-31G(d) basis set in the G09RevB.01 program package. 2) Later needs to calculate absorption spectrum and HOMO-m/LUMO+n (where m and n=20), for example, by Turbomole program package TD-DFT PBE0 method with the def-TZVP basis set. 3) Finally, needs to calculate electron charge density transfer in 30 excited states using Turbomole package. I will prepare all input files for potential colleagues who wish to collaborate. I will analyze the calculation results and write the joint article similar to our already published: Tamulis A, Grigalavicius M, Baltrusaitis J (2013) Phenomenon of quantum entanglement in a system composed of two minimal protocells. Orig Life Evol Biosph 43:49-66. With best regards, Arvydas Tamulis http://www.itpa.lt/~tamulis/ From owner-chemistry@ccl.net Wed May 14 13:05:00 2014 From: "Jesse Gordon jesse.gordon%dotmatics.com" To: CCL Subject: CCL: Dotmatics User Group Meeting Message-Id: <-50084-140514124701-25556-t4E7NG0UGectuXcJsNJWcQ%a%server.ccl.net> X-Original-From: Jesse Gordon Content-Type: multipart/alternative; boundary=001a1134a56e625eb904f95eede3 Date: Wed, 14 May 2014 12:47:04 -0400 MIME-Version: 1.0 Sent to CCL by: Jesse Gordon [jesse.gordon a dotmatics.com] --001a1134a56e625eb904f95eede3 Content-Type: text/plain; charset=US-ASCII Dotmatics Days: User Group Meeting for chemoinformatics and bioinformatics researchers * June 5, 2014 - Dotmatics Day - East Coast: Museum of Science, Boston, USA Join us at the Science Museum for the first of two events where you will have the opportunity to network with industry peers and hear from our user community about how Dotmatics' solutions have improved the way that data can be queried, handled, managed and analysed. Visit the Event Website below for more information and to secure your place. Agenda below. http://www.dotmatics.com/dotmatics-day-east-coast-2014/ * June 12, 2014 - Dotmatics Day - West Coast: Embassy Suites San Francisco Airport, South San Francisco, USA Once again the speaker line up will be packed with industry leaders who will share their ideas on the interrogation and analysis of data via the Dotmatics Platform. Visit the Event Website below for more information and to secure your place. Agenda below. http://www.dotmatics.com/dotmatics-day-west-coast-2014/ * September 15, 2014 to September 16, 2014 - Dotmatics European User Group Meeting 2014 Join us in the English countryside on 15th and 16th September for two days dedicated to Informatics and Science! The scientific community will come together to discuss and present solutions on data management, visualization, and externalized collaboration. Visit the Event website for more information and to register your attendance. http://www.dotmatics.com/dotmatics-european-user-group-meeting-2014/ * June 5, 2014 - Dotmatics Day - East Coast: Selected speakers * Dr. Paul Johnston, University of Pittsburgh, "Prosecution of a STAT3 Nuclear Localization HCS Campaign" * Dr. Andrew Griffin, NeoMED Institute, "Collaborating in the Cloud: A Scientist's perspective" * Dr. Ryan MacArthur, National Center for Advancing Translational Science, NIH, "Multimode qHTS: What you couldn't learn from traditional visualization tools" * Dr. Jonathan Weiss, Vertex: V[o,e]rtex: Continued integration of Vortex into the Vertex Medicinal Chemistry Workflow * Dr. Martin Mense, Cystic Fibrosis Foundation Therapeutics, "Big Pharma-Like Informatics on a Start-up Budget" * June 12, 2014 - Dotmatics Day - West Coast: Selected speakers * Mark Kenney, Gilead Sciences: "Dotmatics Browser as a Standardized Interface for External Data" * Dr. Alex Borchers, CHDI Foundation, "Implementation of Studies Notebook ELN as a process flow solution" * Dr. Matt Stahl, OpenEye, "Empowering chemists to utilize 3D information within Vortex for lead discovery" * Dr. Yichin Liu, Genentech, "Streamlining mass spec data analysis of complex antibody-drug conjugates" * Dr. Steve Zicha, AstraZeneca, "Enabling real-time data sharing in R&D collaborations" Contact: hayleigh.popplewell(-)dotmatics.com, +44 (0)1279 654 123, +1 855 808 8332 -- This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. Dotmatics Limited screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. Dotmatics Limited accepts no liability for any damage caused by any virus transmitted by this electronic mail. Dotmatics Limited is registered in England & Wales No. 5614524 with offices at The Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --001a1134a56e625eb904f95eede3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dotmatics Days: User Group Meeting for chemoinformatics and bioinformati= cs researchers

=C2=A0

* June 5, 2014 - Dotmatics Day - = East Coast: Museum of Science, Boston, USA

Join us at the Science Mu= seum for the first of two events where you will have the opportunity to net= work with industry peers and hear from our user community about how Dotmati= cs' solutions have improved the way that data can be queried, handled, = managed and analysed. Visit the Event Website below for more information an= d to secure your place. Agenda below.

http://www.dotmatics.com/dotmati= cs-day-east-coast-2014/

=C2=A0

* June 12, 2014 - Dotmatics Day -= West Coast: Embassy Suites San Francisco Airport, South San Francisco, USA=

Once again the speaker li= ne up will be packed with industry leaders who will share their ideas on th= e interrogation and analysis of data via the Dotmatics Platform. Visit the = Event Website below for more information and to secure your place. Agenda b= elow.

http://www.dotmatics.com/dotmati= cs-day-west-coast-2014/

=C2=A0

* September 15, 2014 to September= 16, 2014 - Dotmatics European User Group Meeting 2014

Join us in the English co= untryside on 15th and 16th September for two days dedicated to Informatics = and Science! The scientific community will come together to discuss and pre= sent solutions on data management, visualization, and externalized collabor= ation. Visit the Event website for more information and to register your at= tendance.

http://www.dotmatic= s.com/dotmatics-european-user-group-meeting-2014/

=C2=A0

* June 5, 2014 - Dotmatics Day - = East Coast: Selected speakers

* Dr. Paul Johnston, Univ= ersity of Pittsburgh, =E2=80=9CProsecution of a STAT3 Nuclear Localization = HCS Campaign=E2=80=9D

* Dr. Andrew Griffin, Neo= MED Institute, "Collaborating in the Cloud: A Scientist's perspect= ive"

* Dr. Ryan MacArthur, Nat= ional Center for Advancing Translational Science, NIH, "Multimode qHTS= : What you couldn't learn from traditional visualization tools"

* Dr. Jonathan Weiss, Ver= tex: V[o,e]rtex: Continued integration of Vortex into the Vertex Medicinal = Chemistry Workflow

* Dr. Martin Mense, Cysti= c Fibrosis Foundation Therapeutics, "Big Pharma-Like Informatics on a = Start-up Budget"

=C2=A0

* June 12, 2014 - Dotmatics Day -= West Coast: Selected speakers

* Mark Kenney, Gilead Sci= ences: "Dotmatics Browser as a Standardized Interface for External Dat= a"

* Dr. Alex Borchers, CHDI= Foundation, "Implementation of Studies Notebook ELN as a process flow= solution"

* Dr. Matt Stahl, OpenEye= , "Empowering chemists to utilize 3D information within Vortex for lea= d discovery"

* Dr. Yichin Liu, Genente= ch, "Streamlining mass spec data analysis of complex antibody-drug con= jugates"

* Dr. Steve Zicha, AstraZ= eneca, "Enabling real-time data sharing in R&D collaborations"= ;

=C2=A0

Contact: hayleigh.popplewell(-)dotmatics.com, +44 (0)= 1279 654 123, +1 855 808 8332

This electronic mail and its attachments are intended sole= ly for the person(s) to whom they are addressed and contain information whi= ch is=C2=A0 confidential or otherwise protected from disclosure, except for= the purpose for which they are intended. Dissemination, distribution, or r= eproduction by anyone other than the intended recipients is prohibited and = may be illegal. If you are not an intended recipient, please immediately in= form the sender and return the electronic mail and its attachments and dest= roy any copies which may be in your possession. Dotmatics Limited screens e= lectronic mails for viruses but does not warrant that this electronic mail = is free of any viruses. Dotmatics Limited accepts no liability for any dama= ge caused by any virus transmitted by this electronic mail. Dotmatics Limit= ed is=C2=A0 registered in England & Wales No. 5614524 with offices at T= he Old Monastery,=C2=A0 Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --001a1134a56e625eb904f95eede3-- From owner-chemistry@ccl.net Wed May 14 17:54:00 2014 From: "Raul Alvarez ralvarez:chemcomp.com" To: CCL Subject: CCL: Drug Discovery: FINAL AGENDA - UGM & Conference , Montreal, June 16-20 Message-Id: <-50085-140514162308-17646-TJjCMeq95SrxTDE3rSAUpg]-[server.ccl.net> X-Original-From: "Raul Alvarez" Date: Wed, 14 May 2014 16:23:07 -0400 Sent to CCL by: "Raul Alvarez" [ralvarez,,chemcomp.com] The final agenda for the North American UGM & Conference 2014 is now available. A fantastic group of speakers are participating! The meeting is a 5-day event consisting of workshops, scientific presentations, a poster session, as well as social activities including receptions, dinners and group activities. Please find related details below. More information, including abstracts, is available on our website at http://www.chemcomp.com/UGM-2014-North_America.htm. Deadline for poster submission is May 15, 2014. Registration fees are waived for all attendees presenting an accepted poster. UGM & Conference 2014 W Montreal Hotel, Montreal, Canada >> Workshops: June 16-18 | Presentations: June 18-20 ======================================================= DAY 1 Monday, June 16 Workshops ======================================================= 13:30-17:00 Basic Scientific Vector Language in MOE 13:30-17:00 Designing Inhibitors with MOE Structure-Based Drug Design Tools 13:30-17:00 Q&A - Open Discussions ======================================================= DAY 2 Tuesday, June 17 Workshops ======================================================= 09:00-12:00 Advanced Scientific Vector Language in MOE 09:00-12:00 Scaffold Replacement and Fragment Based Drug Design 09:00-12:00 Protein Sequence Alignments and Homology Models ------------------------------------------------------ 13:30-17:00 Small Molecule Virtual Screening and Analysis 13:30-17:00 Analyzing and Rationalizing Protein-Protein Interactions 13:30-17:00 Q&A - Open Discussions ------------------------------------------------------ 18:30 Poster Session & Opening Reception ======================================================= DAY 3 Wednesday, June 18 Workshops (am) & Talks (pm) ======================================================= 09:00-12:00 Pharmacophore Modeling for Drug Design 09:00-12:00 Computer-Aided Biologics Design and Protein Engineering 09:00-12:00 Designing Inhibitors with MOE Structure-Based Drug Design Tools ------------------------------------------------------ 12:00 Lunch Break ------------------------------------------------------ 13:15 Opening Remarks 13:20 FEP-Guided Lead Optimization W. Jorgensen, Sterling Professor of Chemistry, Yale University 13:50 Characterization of ligand-bound conformations with QM-MM methods: Application to prolyl hydroxylase enzymes A. Crespo, Associate Principal Scientist, Merck 14:20 Plumbing the Depths of Entropy and Enthalpy in Molecular Recognition M. Gilson, Professor, UCSD 14:50 Water in structure based drug design: An elephant in the room J. Truchon, Senior Research Scientist, Vertex ------------------------------------------------------ 15:20 Afternoon Break ------------------------------------------------------ 15:50 Designed Molecular Hybrids as Anticancer Agents J. Gleason, Professor, McGill University 16:20 Pharmacophore modeling, structural optimization and biological studies of phosphatidylinositol 3-kinase inhibitors H. Zhong, Associate Professor of Chemistry, University of Nebraska at Omaha 16:50 Structure- and property-based discovery of a tetrahydroindazole series of potent and selective ITK inhibitors J. Burch, Chemistry Team Leader, Genentech ------------------------------------------------------ 18:30 Conference cocktail : Dinner ======================================================= DAY 4 Thursday, June 19 Talks ======================================================= 08:30 Integrating Design, Analysis, and Visualization into the Phenotoypic Drug Discovery Workflow G. McGaughey, Research Fellow II, Vertex Pharmaceuticals 09:00 Selectivity prediction: where are we now? C. Gao, Computational Chemist, Eli Lilly 09:30 Organizing 3D Project Data for Structure-Based Drug Design in MOE H. Feldman, Principal Scientist, Chemical Computing Group ------------------------------------------------------ 10:00 Morning Break ------------------------------------------------------ 10:30 Defining small-molecule similarity and diversity using high-dimensional cellular assay data P. Clemons, Director, Chemical Biology Research, Broad Institute 11:00 Autonomous Model Construction and Idea Capture: GBTs Computational Platform M. Lardy, Senior Scientist II, Global Blood Therapeutics 11:30 20 aos no es nada: modeling the unmodelable or a journey through dogma and doctrine J. Duca, Head, Computer-Aided Drug Discovery, Novartis ------------------------------------------------------ 12:00 Lunch Break ------------------------------------------------------ 13:30 Assessing drugability of gram negative bacterial (G-) targets or other target classes that require specific ligand properties V. Polyakov, Senior Investigator I, Novartis 14:00 A Hinge-hopping Approach to the Design of Kinase Inhibitors through Mining of Crystal Structure Database L. Xing, Senior Principal Scientist, Pfizer 14:30 Simulating conformational change of kinases and GPCRs on the millisecond timescale in all-atom detail with Markov State Models and large-scale cloud computing V. Pande, Professor, Stanford University ------------------------------------------------------ 15:00 Afternoon Break ------------------------------------------------------ 15:30 Walking Tour Activities: Old Montreal, Le Plateau & Chinatown 18:30 Cruise Celebration on board the Cavalier Maxim ======================================================= DAY 5 Friday, June 20 Talks ======================================================= 09:00 Second Antibody Modeling Assessment (AMA II) J. Almagro, Senior Director, CTI-Boston, Pfizer 09:30 Talk Title TBA J. Luo, Associate Sci. Director, Janssen R&D 10:00 Creating Focused Libraries for Protein Engineering C. Corbeil, Research Scientist, Chemical Computing Group ------------------------------------------------------ 10:30 Morning Break ------------------------------------------------------ 11:00 Why People Believe Weird Things Special guest lecture, featuring Dr. Michael Shermer Ever wonder why people believe in UFOs and alien abductions, mind-reading and psychics who talk to the dead, reincarnation and life after death, out-of-body and near-death experiences, conspiracy theories and government coverups, not to mention Intelligent Design creationism and the pernicious myth that the Holocaust never happened? Dr. Michael Shermer, the Founding Publisher of Skeptic magazine and a monthly columnist for Scientific American, is a genuine myth-buster, a relentless crusader against junk science, bad science, voodoo science, pathological science, pseudoscience, and plain old nonsense. Based on his bestselling books Why People Believe Weird Things and The Believing Brain, Dr. Shermers lecture is filled with humor, insight, illusions, and personal anecdotes about his excursions with those on the fringes, as he presents his theory for how the brain forms beliefs. His talk is an entertaining wake-up call that has become a wildly popular presentation and is similar to his two TED talks, which have been viewed by over 5 million people. ------------------------------------------------------ 12:00 Lunch Break ------------------------------------------------------ 14:00 Talk Title TBA S. Rowland, Associate Scientific Fellow, Millennium Pharmaceuticals 14:30 In Silico Evaluation of Chemical Tractability Ami Lakdawala Shah, Group Leader, GlaxoSmithKline 15:00 Talk Title TBA D. Ryan, Senior Director, Discovery Technologies, Cubist Pharmaceuticals 15:30 Closing Remarks ------------------------------------------------------ 15:45 Closing Wine & Cheese reception : Ristorante OTTO ======================================================= Posters: We are accepting abstracts please include your poster details with you registration. Registration fees are waived for all attendees presenting an accepted poster - Deadline: May 15, 2014. ------------------------------------------------------ Registration and fees: $ 300 USD if registered by April 7, 2014 - $ 400 USD thereafter. Registration fees give attendees full access to all workshop sessions, presentations, meals and receptions. Registration fees are waived for all attendees presenting an accepted poster. ------------------------------------------------------ Important dates: Workshops: June 16-18 Poster session & opening cocktail: June 17 (18:30) Scientific presentations: June 18-20 Closing reception: June 20 (15:45) ------------------------------------------------------ Venue: W Montreal Hotel http://www.wmontrealhotel.com/ 901 Square Victoria, Montral, QC H2Z 1R1 ================================================================== It is a special meeting as we are also celebrating our 20th anniversary. We look forward to seeing you in Montreal this coming June! From owner-chemistry@ccl.net Wed May 14 19:02:00 2014 From: "fatima serag fatimaserag()hotmail.com" To: CCL Subject: CCL: urgent clarifications required Message-Id: <-50086-140514185711-21639-mHhZ81fx1BepI80WDFk49w*server.ccl.net> X-Original-From: "fatima serag" Date: Wed, 14 May 2014 18:57:09 -0400 Sent to CCL by: "fatima serag" [fatimaserag-$-hotmail.com] Dear CCL members/ Material studio, CASTEP developers/ Experts of quantum chemistry. could you support by providing/explaining the calculations procedures using material studio, CASTEP code to calculate: electron or hole effective mass of a metal oxide semiconductor electron o hole injection rate density of the semiconductor bond nature/type (ionic or covalent) thanks.........fatoma