From grzybek@athena.chemie.uni-erlangen.de Fri Jun 27 02:48:17 1997 Received: from athena.chemie.uni-erlangen.de for grzybek@athena.chemie.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id CAA08559; Fri, 27 Jun 1997 02:46:40 -0400 (EDT) Received: from localhost by athena.chemie.uni-erlangen.de via SMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI.AUTO) id IAA01765; Fri, 27 Jun 1997 08:46:36 +0200 Date: Fri, 27 Jun 1997 08:46:36 +0200 (MDT) From: Stefan Grzybek To: "Hr. Dr. S. Shapiro" cc: chemistry@www.ccl.net Subject: Re: CCL:van der Waals radii for amino acids In-Reply-To: <1.5.4.32.19970624140118.00668464@highdent.zzmk.unizh.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 24 Jun 1997, Hr. Dr. S. Shapiro wrote: > Dear Colleagues; > > For a calculation I wish to perform, I require the van der Waals > radii of each of the atoms (including hydrogen) in the 20 common amino > acids. If anyone can recommend a published source of this information (or > if anyone should happen to have this information as an e-mailable file), > I would appreciate hearing from you. > > Thanks in advance to all responders. > > Sincerely, > > S. Shapiro > toukie@zui.unizh.ch > You could try to derive the van der Waals radii from any of the forcefields used in molecular dynamics calculations of proteins, as for example CHARMM, AMBER, DISCOVER. All of them have parameters for the Lennard Jones Potential and these can be converted to atomic radii by a simple transformation. Sincerely yours, S. Gryzbek --- | Dr. Stefan Grzybek email: grzybek@ruf.uni-freiburg.de | | grzybek@athena.chemie.uni-erlangen.de | | http://athena.chemie.uni-erlangen.de/~grzybek | | Universitaet Freiburg, Institut fuer Biologie II, Biochemie | | der Pflanzen, Schaenzlestr. 1, D-79104 Freiburg, Germany | | Voice: +49 +761 203-2703 or -2796, Fax: +49 +761 203-2601 | From rolf@immunologie.Charite.HU-Berlin.DE Fri Jun 27 03:48:16 1997 Received: from Charite.HU-Berlin.DE for rolf@immunologie.Charite.HU-Berlin.DE by www.ccl.net (8.8.3/950822.1) id DAA08907; Fri, 27 Jun 1997 03:45:23 -0400 (EDT) Received: by Charite.HU-Berlin.DE from immunologie.Charite.HU-Berlin.DE with smtp (Smail3.1.28.1 [@@]) id m0whVgJ-00065qC; Fri, 27 Jun 97 09:42 MESZ Received: by immunologie.Charite.HU-Berlin.DE (Smail3.1.28.1 [@@]) id m0whVib-0001DoC; Fri, 27 Jun 97 09:45 MDT From: "Dr. Rolf-Dietrich Stigler" Message-Id: <9706270945.ZM20874@venus.Immunologie.Charite.HU-Berlin.DE> Date: Fri, 27 Jun 1997 09:45:21 -0600 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: CCL:Problem in GRASP Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii In-Reply-To: huixiao hong <" huixiao"@helix.nih.gov> "CCL:Problem in GRASP" (Jun 23, 3:52pm) Hi, try to display the surfaces both of the protein AND the ligand. Then UNDISPLAY the surface of the ligand. I think, you then get the picture (information) you want. Hope this helps. -- Rolf-Dietrich Stigler ===================================================== Dr. Rolf-Dietrich Stigler Tel. +49 30 2802 6224 Inst.f. Med.Immunologie Fax +49 30 2802 6460 Universitaetsklinikum Charite Schumannstr 20-21 D-10098 Berlin, Germany e-mail: rolf@immunologie.charite.hu-berlin.de ===================================================== From Jeffrey.Gosper@brunel.ac.uk Fri Jun 27 03:59:02 1997 Received: from himiko.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id DAA08894; Fri, 27 Jun 1997 03:42:15 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by himiko.brunel.ac.uk with SMTP-BRUNEL (PP); Fri, 27 Jun 1997 08:41:51 +0100 Date: Fri, 27 Jun 1997 08:41:49 BST From: Jeffrey J Gosper Subject: Re: CCL:Want a program ot visualize electronic density contour. To: yubofan Original-To:  PP-Warning: Parse error in original version of preceding To line cc: chemistry Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Tue, 24 Jun 1997 22:06:53 +0800  wrote: > From:  > Date: Tue, 24 Jun 1997 22:06:53 +0800 > Subject: CCL:Want a program ot visualize electronic density contour. > To: chemistry > > > > Hi, ccl'er, > > > I do some calculations on my PC by G94W. I want ot visualize the electric > density contour. Which program can this job? A small one is preferred. > > > Re_View3, a Windows program, has the ability to visualize the results obtained using G94 cube calculations. Although Re_View3 is still being developed this functionality has already be built in. If your interested in finding out more information about Re_View3 see http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view3.htm We have just put up a WWW explaining cube calculations as well see: http://www.brunel.ac.uk/depts/chem/g94_cube.htm Please contact me for more information on how to obtain Re_View3. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From support@mathtrek.com Fri Jun 27 09:48:23 1997 Received: from granite.sentex.net for support@mathtrek.com by www.ccl.net (8.8.3/950822.1) id JAA10520; Fri, 27 Jun 1997 09:15:37 -0400 (EDT) Received: from p29a.lithium.sentex.ca (p29a.lithium.sentex.ca [207.245.212.190]) by granite.sentex.net (8.8.5/8.6.9) with SMTP id JAA14711; Fri, 27 Jun 1997 09:23:28 -0400 (EDT) Message-Id: <3.0.16.19970627091309.084770cc@mathtrek.com> X-Sender: mathtrek@mathtrek.com X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Fri, 27 Jun 1997 09:13:12 -0400 To: Adnan Hazar , CCL From: "W. R. Smith" Subject: Re: CCL:Info on heats of vaporization Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 12:44 PM 6/26/97 +1000, Adnan Hazar wrote: > >Dear CCL colleagues, > >I have a question on behalf of a research colleague. Does anyone have the >following information on heats of vaporization of the following aldehydes: > > Octanal > Nonanal > Dodecanal > Heats of vaporization: \DeltaH = A*(1-Tr)^B where DeltaH = heat of vaporization in J/mol, Tr = T/T_c (reduced temperature). 1-nonanal 1-octanal 1-dodecanal A 7.2500E+07 6.6950E+07 8.3180E+07 B 3.7550E-01 3.6760E-01 3.4800E-01 Tc 640K 621K 685K Source: DIPPR pure component data compilation, 1989 (AIChE) -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From genghis@darkwing.uoregon.edu Fri Jun 27 10:48:18 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id KAA10989; Fri, 27 Jun 1997 10:27:33 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.6/8.8.6) with SMTP id HAA08544; Fri, 27 Jun 1997 07:25:54 -0700 (PDT) Date: Fri, 27 Jun 1997 07:25:54 -0700 (PDT) From: Dale Andrew Braden To: "Hr. Dr. S. Shapiro" cc: chemistry@www.ccl.net Subject: Re: CCL:van der Waals radii for amino acids In-Reply-To: <1.5.4.32.19970624140118.00668464@highdent.zzmk.unizh.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dr. Shapiro, Whenever I am forced to use VDW radii, I use Huheey's Inorganic Chemistry textbook, which has lots of tables for this kind of thing. The latest edition (3rd?) is quite recent. Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From genghis@darkwing.uoregon.edu Fri Jun 27 10:56:14 1997 Received: from darkwing.uoregon.edu for genghis@darkwing.uoregon.edu by www.ccl.net (8.8.3/950822.1) id KAA10906; Fri, 27 Jun 1997 10:21:39 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.8.6/8.8.6) with SMTP id HAA08237; Fri, 27 Jun 1997 07:21:10 -0700 (PDT) Date: Fri, 27 Jun 1997 07:21:09 -0700 (PDT) From: Dale Andrew Braden To: "Hr. Dr. S. Shapiro" cc: chemistry@www.ccl.net Subject: Re: CCL:Hydrogen bonding to acetylenes? In-Reply-To: <1.5.4.32.19970622145515.00663d20@highdent.zzmk.unizh.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dr. Shapiro, I don't have an exact reference, but look up the name Thomas Steiner, especially in the author indices for Chemical Communications. He has done some work with hydrogen bonding and acetylenes. Also see the book "Hydrogen Bonding in Biological Structures" by G.A. Jeffrey and W. Saenger; Springer-Verlag 1991 for more references. Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu From buyong@ibmnla.chem.uga.edu Fri Jun 27 11:03:56 1997 Received: from dns1.uga.edu for buyong@ibmnla.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id JAA10741; Fri, 27 Jun 1997 09:50:34 -0400 (EDT) From: Received: from ibmnla.chem.uga.edu (ibmnla.chem.uga.edu [128.192.5.8]) by dns1.uga.edu (8.8.5/8.8.3) with SMTP id JAA10662; Fri, 27 Jun 1997 09:50:38 -0400 Received: from localhost by ibmnla.chem.uga.edu (AIX 3.2/UCB 5.64/4.03) id AA14143; Fri, 27 Jun 1997 09:50:21 -0400 Date: Fri, 27 Jun 1997 09:50:20 -0400 (EDT) To: ·ΆΣύ#¨ Cc: chemistry@www.ccl.net Subject: Re: CCL:Why does G94W's SCF option make errors? In-Reply-To: <199706241509.XAA14782@gm-email.guomai.sh.cn> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE 1. This is not a SCF calculation, it is at BLYP (DFT) level. 2. Are you sure that molecular geometryies are identical? =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D On Tue, 24 Jun 1997, =B7=B6=D3=FD#=A8 wrote: >=20 > Hi, ccl'ers, >=20 >=20 > I calculated a molecule with 3 Phenyls. I use BLYP/3-21G**. This time, I > try "restart", a SCF option that I didn't use before. I kill the job afte= r > L502.exe had been running 4 cycles, then I put "restart" after "SCF=3D". = I > ran the calculation again. L502.exe did 2 cycles and the result was gotte= n. > Again I did the job from the very original start. After 6 cycles had been > done, another result was gotten. I list them below: >=20 > :With SCF=3D(save, restart) > Convergence on energy, delta-E=3D1.12D-05 > SCF Done: E(RB-LYP) =3D -692.644057005 A.U. after 2 cycles > Convg =3D 0.2054D-03 -V/T =3D 2.0090 > S**2 =3D 0.0000 > KE=3D 6.864357999909D+02 PE=3D-3.864671343753D+03 EE=3D 1.355127785196D+= 03 >=20 > :With SCF=3Dsave > SCF Done: E(RB-LYP) =3D -692.644408415 A.U. after 6 cycles > Convg =3D 0.4070D-05 -V/T =3D 2.0094 > S**2 =3D 0.0000 > KE=3D 6.861718246427D+02 PE=3D-3.864945652472D+03 EE=3D 1.355665717853D+= 03 >=20 >=20 > Why do they have error I think it considerable great? >=20 >=20 > Thanks a lot >=20 > Y. FAN >=20 >=20 >=20 >=20 >=20 > --- > Administrivia: This message is automatically appended by the mail explode= r: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordin= ator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net= 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html=20 > --- >=20 >=20 From bruno@antas.agraria.uniss.it Fri Jun 27 11:48:21 1997 Received: from ssmain.uniss.it for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id LAA11462; Fri, 27 Jun 1997 11:08:45 -0400 (EDT) Received: from antas.agraria.uniss.it by ssmain.uniss.it with SMTP (1.39.111.2/16.2) id AA222254100; Fri, 27 Jun 1997 17:08:20 +0200 Date: Fri, 27 Jun 1997 17:08:21 +0100 (NFT) From: "Dr. Bruno Manunza" To: "Hr. Dr. S. Shapiro" Cc: chemistry@www.ccl.net, toukie@zui.unizh.ch Subject: Re: CCL:MOLZYME? In-Reply-To: <1.5.4.32.19970622144043.0066676c@highdent.zzmk.unizh.ch> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 22 Jun 1997, Hr. Dr. S. Shapiro wrote: > > > Dear Colleagues; > > Has anyone ever heard of a programme called (someting like) MOLZYME? > I've heard that this is a modified version of MOPAC which is supposed to be > able to handle macromolecules, but I've been unable to find out anything > about it. > > Thanks in advance to all responders. > > > Sincerely, > > S. Shapiro > toukie@zui.unizh.ch > Dear Dr Shapiro, the correct spelling is MOZYME, you may have a look to its page at: http://iti2.net/jstewart/mozdesc.htm Regards Bruno Dr Bruno Manunza DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From nobes@fecit.co.uk Fri Jun 27 11:50:15 1997 Received: from fecit-gate.fecit.co.uk for nobes@fecit.co.uk by www.ccl.net (8.8.3/950822.1) id LAA11488; Fri, 27 Jun 1997 11:10:29 -0400 (EDT) Received: by fecit-gate.fecit.co.uk; id RAA15674; Fri, 27 Jun 1997 17:09:13 +0100 (BST) Received: from suisei.fecit.co.uk(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V3.1.1) id xma015672; Fri, 27 Jun 97 17:09:11 +0100 Received: (from nobes@localhost) by suisei.fecit.co.uk (8.6.9/8.6.9) id QAA11011 for chemistry@www.ccl.net; Fri, 27 Jun 1997 16:12:49 +0100 From: Ross Nobes Message-Id: <199706271512.QAA11011@suisei.fecit.co.uk> Subject: Re: CCL:MOLZYME? To: toukie@zui.unizh.ch (Hr. Dr. S. Shapiro) Date: Fri, 27 Jun 1997 08:13:53 +0100 (BST) Cc: chemistry@ccl.net In-Reply-To: <1.5.4.32.19970622144043.0066676c@highdent.zzmk.unizh.ch> from "Hr. Dr. S. Shapiro" at Jun 22, 97 04:40:43 pm X-Mailer: ELM [version 2.4 PL25] Content-Type: text Sender: nobes@fecit.co.uk Hr. Dr. S. Shapiro writes: > > Has anyone ever heard of a programme called (someting like) MOLZYME? > I've heard that this is a modified version of MOPAC which is supposed to be > able to handle macromolecules, but I've been unable to find out anything > about it. > MOZYME is a semiempirical molecular orbital program written by James J.P. Stewart and marketed through Fujitsu. It uses localized molecular orbitals to overcome the N^3 diagonalization bottleneck of conventional programs like MOPAC. It is aimed at small proteins and enzymes of up to about 20,000 atoms. You can get further information about MOZYME at the following URL: http://iti2.net:80/jstewart/mozdesc.htm Regards, Ross Nobes -- +---------------------------------------------------------------------+ | Dr Ross Nobes | | Research Manager | | Fujitsu European Centre for Information Technology | | 2 Longwalk Road Phone: +44 (0)468 684 335 | | Stockley Park Fax: +44 (0)181 606 4422 | | Uxbridge UB11 1AB, UK E-mail: nobes@fecit.co.uk | +---------------------------------------------------------------------+ From pt@chem.postech.ac.kr Fri Jun 27 13:48:21 1997 Received: from chem.postech.ac.kr for pt@chem.postech.ac.kr by www.ccl.net (8.8.3/950822.1) id NAA13234; Fri, 27 Jun 1997 13:12:25 -0400 (EDT) Received: (from pt@localhost) by chem.postech.ac.kr (8.6.12H1/8.6.12) id RAA00974 for chemistry@www.ccl.net; Fri, 27 Jun 1997 17:13:27 GMT From: P Tarakeshwar Message-Id: <199706271713.RAA00974@chem.postech.ac.kr> Subject: Grid Superposition Error!! To: chemistry@www.ccl.net Date: Sat, 28 Jun 1997 02:13:27 +0900 (KST) X-Mailer: ELM [version 2.4 PL25-h4.1] Content-Type: text Hi! Could someone tell me on how binding energies are corrected for grid superposition errors (different from bsse) in dft calculations? Thanks in advance, pt From dsmith@CTCnet.Net Fri Jun 27 13:52:27 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id NAA13248; Fri, 27 Jun 1997 13:13:42 -0400 (EDT) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id NAA10933; Fri, 27 Jun 1997 13:07:09 -0400 Message-Id: <3.0.1.32.19970627125942.009b6960@pop.dasgroup.com> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) X-Priority: 1 (Highest) Date: Fri, 27 Jun 1997 12:59:42 -0400 To: CHEMISTRY@www.ccl.net From: "Douglas A. Smith Ph.D." Subject: modeling surfactants Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I have a number of general questions about modeling of surfactants and chemical species composed of surfactants. What force fields are best for this type of modeling? Which have been validated against experimental results? What types of information is one generally after in doing, for example, an MD simulation of one or more surfactants? Are there any recent and useful review articles on this topic? Please feel free to respond either to CCL or directly to me. I prefer the former, as it always tends to generate useful and often fruitful discussions. Thanks in advance. Doug -- Dr. Douglas A. Smith, President and CEO | voice: (814) 255-7859 The DASGroup, Inc. | fax: (814) 255-3517 1732 Lyter Drive, 2nd Floor | email: dsmith@dasgroup.com Johnstown, PA 15905 | WWW: http://www.dasgroup.com Contract R&D specialists in modeling, simulation, synthesis and risk assessment for chemistry, materials science, and biotechnology. From D.van.der.Spoel@chem.rug.nl Fri Jun 27 14:48:21 1997 Received: from mailhost.rug.nl for D.van.der.Spoel@chem.rug.nl by www.ccl.net (8.8.3/950822.1) id OAA13860; Fri, 27 Jun 1997 14:45:07 -0400 (EDT) From: Received: from rugch4.chem.rug.nl by mailhost with SMTP (XT-PP) with ESMTP; Fri, 27 Jun 1997 20:45:40 +0200 Received: from rugmd2 by rugch4.chem.rug.nl (UAA26196); Fri, 27 Jun 1997 20:45:07 +0200 (DST) Received: (from spoel@localhost) by rugmd2 (950413.SGI.8.6.12/950213.SGI.AUTOCF) id UAA05693 for CHEMISTRY@www.ccl.net; Fri, 27 Jun 1997 20:47:34 +0200 Message-Id: <199706271847.UAA05693@rugmd2> Subject: Surfactant simulations To: CHEMISTRY@www.ccl.net Date: Fri, 27 Jun 1997 20:47:34 +0200 (DST) Reply-To: D.van.der.Spoel@chem.rug.nl X-Mailer: ELM [version 2.4 PL25] Content-Type: text Douglas A. Smith Ph.D. writes: : :I have a number of general questions about modeling of surfactants and :chemical species composed of surfactants. : :What force fields are best for this type of modeling? Which have been :validated against experimental results? : :What types of information is one generally after in doing, for example, an :MD simulation of one or more surfactants? : :Are there any recent and useful review articles on this topic? : Cehck out the articles by Van Buuren and Berendsen: @Article{Buuren93b, author = "A. R. van Buuren and S. J. Marrink and H. J. C. Berendsen", title = "A Molecular Dynamics Study of the Decane/Water Interface", journal = J. Phys. Chem., year = "1993", volume = "97", pages = "9206--9212", } @Article{Buuren94c, author = "A. R. van Buuren and H. J. C. Berendsen", title = "Molecular dynamics simulations of carbohydrate based surfactants in surfactant/water/oil systems", journal = "Langmuir", year = "1994", volume = "10", pages = "1703--1713", } @Article{Buuren95a, author = "Aldert R. van Buuren and Siewert Jan Marrink and Herman J. C. Berendsen", title = "Characterisation of aqueous interfaces with different hydrophobicities by molecular dynamics", journal = "{\em Colloids and Surfaces. A: Physicochemical and Engineering Aspects}", volume = "102", year = "1995", pages = "143--158", } @Article{Buuren95b, author = "Aldert R. van Buuren and Jacob de Vlieg and Herman J. C. Berendsen", title = "Structural Properties of 1,2-Diacyl-{\em sn}-glycerol in Bulk and at the Water Interface by Molecular Dynamics", journal = Langmuir, year = "1995", volume = "11", pages = "2957--2965", } Cosurfactants Lower Surface Tension of the Diglyceride/Water Interface: A Molecular Dynamics Study Aldert R. van Buuren, D. Peter Tieleman, Jacob de Vlieg and Herman J.C. Berendsen Langmuir Vol. 12 1996, pp 2570-2579 Groeten, David. ________________________________________________________________________ Dr. Ir. David van der Spoel Dept. of Biophysical Chemistry s-mail: Nijenborgh 4, 9747 AG Groningen, The Netherlands. e-mail: spoel@chem.rug.nl www: http://rugmd0.chem.rug.nl/~spoel phone: 31-50-3634327 fax: 31-50-3634800 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From amasunov@email.gc.cuny.edu Fri Jun 27 15:48:35 1997 Received: from gaudi.gc.cuny.edu for amasunov@email.gc.cuny.edu by www.ccl.net (8.8.3/950822.1) id PAA14220; Fri, 27 Jun 1997 15:40:29 -0400 (EDT) Received: from broadway.gc.cuny.edu (broadway.gc.cuny.edu) by GAUDI.GC.CUNY.EDU (PMDF V5.0-6 #18284) id <01IKKM7X9TS0005AWJ@GAUDI.GC.CUNY.EDU> for chemistry@www.ccl.net; Fri, 27 Jun 1997 15:40:24 -0400 (EDT) Received: from localhost (amasunov@localhost) by broadway.gc.cuny.edu (8.8.5/ankDU-96) with SMTP id PAA08504 for ; Fri, 27 Jun 1997 15:40:23 -0400 (EDT) Date: Fri, 27 Jun 1997 15:40:23 -0400 (EDT) From: Artem Masunov Subject: RE: Hydrogen bonding to acetylenes? (fwd) X-Sender: amasunov@broadway.gc.cuny.edu To: Computational Chemistry List Reply-to: Artem Masunov Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear Dr. Shapiro, We did AM1 calculations on X-Ph-C#C-H...OH2: A.Masunov, J.J. Dannenberg, J.Mol.Structure 371 (1996) 17-19 Ab initio calculations on water and NR3 are in progress. If you have specific system or experimental results in mind, please let me know. There was also a poster on HCCH...O=C< in Atlanta this month. Contact Boris Galabov For exp. results on HCCH...NH3,OH2 see JCP 1984, 80, 1423 JCP 1984, 81, 3847 Hope this helps, Artem > __ _________ > / \ / _ _ \ Artem.Masunov@hunter.cuny.edu > / \\ \\ \\ \ Chemistry Department, Hunter College > / /\ \\ \\ \\ \ City University of New York > / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 > /__/\__/\__\\__\\__\\__\ Tel: (212) 772-5751, Fax: (212) 772-5332 > \__\/ \/__//__//__//__/ Bpr: 91-777-333-91, that is (917) 773-3391 > > I know you believe you understand what you think I said, but I am not > sure you realize that what you heard is not what I meant. (Gaussian92) From rvenable@deimos.cber.nih.gov Fri Jun 27 15:51:05 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id OAA13939; Fri, 27 Jun 1997 14:58:10 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA207047310; Fri, 27 Jun 1997 14:48:30 -0400 Date: Fri, 27 Jun 1997 14:48:30 -0400 (EDT) From: Rick Venable To: "Douglas A. Smith Ph.D." Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:modeling surfactants In-Reply-To: <3.0.1.32.19970627125942.009b6960@pop.dasgroup.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 27 Jun 1997, Douglas A. Smith Ph.D. wrote: > I have a number of general questions about modeling of surfactants and > chemical species composed of surfactants. > What force fields are best for this type of modeling? Which have been > validated against experimental results? > What types of information is one generally after in doing, for example, an > MD simulation of one or more surfactants? > Are there any recent and useful review articles on this topic? Our lab and others have published simulations of lipid bilayers and monolayers; there are also publications on micelle systems. Lipids have been simulated with AMBER, CHARMM and GROMOS force fields, and give similar results in terms of general agreement with experimental data, such as the lattice D spacing for multilayers. Other properties have also been studied, such as carbon-deuterium order parameters (measured via NMR), but the relaxation times for some parts of the lipid molecules (e.g. the headgroup) is so slow that the MD timescale doesn't produce statistically significant sampling. Authors to search for (independently): Pastor, RW Klein, ML Tobias, D Berendsen, HJC Merz, K I think most of the above have published reviews in the past few years. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) From alper@lisa.moldyn.com Fri Jun 27 16:48:27 1997 Received: from photon.com for alper@lisa.moldyn.com by www.ccl.net (8.8.3/950822.1) id QAA14681; Fri, 27 Jun 1997 16:28:47 -0400 (EDT) Received: from worf.moldyn.com ([172.16.2.22]) by gateway.photon.com with SMTP id <5930-2>; Fri, 27 Jun 1997 13:16:13 -0700 Received: from lisa.moldyn.com by worf.moldyn.com via ESMTP (950413.SGI.8.6.12/950213.SGI.AUTOCF) for <@worf.moldyn.com:CHEMISTRY@www.ccl.net> id QAA17944; Fri, 27 Jun 1997 16:28:56 -0400 Received: by lisa.moldyn.com (940816.SGI.8.6.9/940406.SGI.AUTO) id QAA28033; Fri, 27 Jun 1997 16:28:54 -0400 From: alper@lisa.moldyn.com (Howard Alper) Message-Id: <199706272028.QAA28033@lisa.moldyn.com> Subject: Modeling surfactants To: CHEMISTRY@www.ccl.net Date: Fri, 27 Jun 1997 13:28:51 -0700 Cc: alper@lisa.moldyn.com (Howard Alper) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi, Terry Stouch and associates at Bristol-Myers Squibb have also published extensively on the modeling of phospholipid monolayers and bilayers. The work was done using DISCOVER, and its associated CVFF forcefield. Quantities that have been calculated, and shown good agreement with experiment are: Electron density, bilayer thickness, fraction of gauche conformers in the lipid hydrcarbon chains, and hydrocarbon chain order parameters (these are obtainable from nanosecond simulations). The diffusion of small nonpolar solutes and drug analogs in phospholipid membranes has also been studied, and experimental results for both the diffusion coefficients and their variation with position (of the solute) in the membrane have been reproduced; the mechanism of solute diffusion through membranes has also been elucidated. Some references are: Lipid Parameters: T. R. Stouch, K.B. Ward, A. Altieri, and A. T. Hagler, J. Comp. Chem. 12, 1033 (1991). Simulations of Monolayers and Bilayers: T. R. Stouch, Mol. Sim. 10, 335 (1993). H. E. Alper, D. Bassolino-Klimas, and T. R. Stouch, J. Chem. Phys. 98, 9798 (1993) H. E. Alper, D. Bassolino-Klimas, and T. R. Stouch, J. Chem. Phys. 99, 5547 (1993) Simulations of Solute Diffusion Through Membranes: D. Bassolino-Klimas, H. E. Alper, and T. R. Stouch, Biochemistry 32, 12624 (1993) D. Bassolino-Klimas, H. E. Alper, and T. R. Stouch, J. Am. Chem. Soc. 117, 4118 (1995) H. E. Alper and T. R. Stouch, J. Phys. Chem. 99, 5724 (1995) D. Bassolino-Klimas, H. E. Alper, and T. R. Stouch, Drug Design and Discovery 13 135 (1996) Howard Alper -- Dr. Howard Alper Moldyn Inc. 955 Massachusetts Avenue Fifth Floor Cambridge, MA 02139-3180 617-354-3124 x19 email: alper@moldyn.com - helping molecules find happiness for over a 10th of a century. ATTENTION: May 1997. At present, Moldyn is experiencing problems in the receiving of email from certain addresses/sites. If your email to me bounces after you've tried reply, or direct email to alper@moldyn.com, try emailing to alper@photon.com . Thank you for your patience in this matter. From XIENING@MEENA.CC.UREGINA.CA Fri Jun 27 17:48:23 1997 Received: from veena.cc.uregina.ca for XIENING@MEENA.CC.UREGINA.CA by www.ccl.net (8.8.3/950822.1) id RAA15316; Fri, 27 Jun 1997 17:41:49 -0400 (EDT) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-8 #20153) id <01IKKM5G0EASAFUNR6@meena.cc.uregina.ca> for chemistry@www.ccl.net; Fri, 27 Jun 1997 15:41:36 CST Date: Fri, 27 Jun 1997 15:41:36 -0600 (CST) From: "XIE, NING" Subject: first ionization energy To: chemistry@www.ccl.net Message-id: <01IKKM5G0EAUAFUNR6@meena.cc.uregina.ca> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Hi, there, Is there anybody out there would please tell me how to get the first ionization energy from the Gaussian result? Is it half of the HOMO energy? Thank you diana