From owner-chemistry@ccl.net Mon Apr 16 05:31:02 2007 From: "Greg Sandala sandala::chem.usyd.edu.au" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34050-070416045943-23109-8qW4va+Oe/qbU1MzDUodJw:+:server.ccl.net> X-Original-From: "Greg Sandala" Date: Mon, 16 Apr 2007 04:59:38 -0400 Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] Hi everyone, This is a general question about crystal structures: How likely it is for an oxygen atom to be mistaken for a nitrogen atom and vice versa (so there are two possible H-bonding arrangements) in, say, an acetamide side chain of a protein? Thanks, Greg From owner-chemistry@ccl.net Mon Apr 16 08:01:01 2007 From: "Noko Phala nokophala-,-aim.com" To: CCL Subject: CCL: molecular orbital analysis Message-Id: <-34051-070416033406-14288-oaST1ZfkIX5ERrKFo8gb9g#%#server.ccl.net> X-Original-From: "Noko Phala" Content-Language: i-default Content-Type: multipart/alternative; boundary="EPOC32-gD,2'bxkgYv39-SNMR_zKdQtb,pQ-JSSvKbCtMNJPdwr1X'V" Date: Mon, 16 Apr 2007 09:33:15 +0200 MIME-Version: 1.0 Sent to CCL by: "Noko Phala" [nokophala{}aim.com] --EPOC32-gD,2'bxkgYv39-SNMR_zKdQtb,pQ-JSSvKbCtMNJPdwr1X'V Content-Type: text/plain; charset=UTF-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi, I can immediately think of two influences on bond lengths(simplified): 1)The degree of filling of antibonding orbitals,the less the filling,the sho= rter the bond 2)atomic sizes,larger atoms are further apart than small ones Of course things can sometimes be more complex.. Regards Noko Phala _____ Original message _____ Subject: CCL: molecular orbital analysis Author: "may abdelghani may01dz=3Dyahoo.fr" Date: 15th April 2007 9:25:1=20 Dear CCLers How I can explain, using the molecular orbital analysis, why this bond in=20= this molecule, is shorten (or longer) than that in the other molecule=C2=85 Thank you very much in advance =20 --------------------------------- D=C3=A9couvrez une nouvelle fa=C3=A7on d'obtenir des r=C3=A9ponses =C3=A0 t= outes vos questions ! Profitez des connaissances, des opinions et des exp= =C3=A9riences des internautes sur Yahoo! Questions/R=C3=A9ponses. --EPOC32-gD,2'bxkgYv39-SNMR_zKdQtb,pQ-JSSvKbCtMNJPdwr1X'V Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDMuMiBGaW5hbC8vRU4i Pgo8SFRNTD4gCjxIRUFEPiAKPFRJVExFPkNvbnZlcnRlZCBmcm9tIFJpY2ggVGV4dDwvVElU TEU+CjxNRVRBIEhUVFAtRVFVSVY9IkNvbnRlbnQtVHlwZSIgQ09OVEVOVD0idGV4dC9odG1s OyBjaGFyc2V0PVVURi04Ij48TUVUQSBOQU1FPSJnZW5lcmF0b3IiIENPTlRFTlQ9InJ0Mmh0 bWwgY29udmVydGVyIj4KPC9IRUFEPiAKPEJPRFkgQkdDT0xPUj0iI2ZmZmZmZiIgVEVYVD0i IzAwMDAwMCI+CjxESVYgQUxJR049TEVGVD5IaSw8L0RJVj4gCjxESVYgQUxJR049TEVGVD5J IGNhbiBpbW1lZGlhdGVseSB0aGluayBvZiB0d28gaW5mbHVlbmNlcyBvbiBib25kIGxlbmd0 aHMoc2ltcGxpZmllZCk6PC9ESVY+IAo8RElWIEFMSUdOPUxFRlQ+MSlUaGUgZGVncmVlIG9m IGZpbGxpbmcgb2YgYW50aWJvbmRpbmcgb3JiaXRhbHMsdGhlIGxlc3MgdGhlIGZpbGxpbmcs dGhlIHNob3J0ZXIgdGhlIGJvbmQ8L0RJVj4gCjxESVYgQUxJR049TEVGVD4yKWF0b21pYyBz aXplcyxsYXJnZXIgYXRvbXMgYXJlIGZ1cnRoZXIgYXBhcnQgdGhhbiBzbWFsbCBvbmVzPC9E SVY+IAo8RElWIEFMSUdOPUxFRlQ+Jm5ic3A7PC9ESVY+PERJViBBTElHTj1MRUZUPk9mIGNv dXJzZSB0aGluZ3MgY2FuIHNvbWV0aW1lcyBiZSBtb3JlIGNvbXBsZXguLjwvRElWPiAKPERJ ViBBTElHTj1MRUZUPiZuYnNwOzwvRElWPjxESVYgQUxJR049TEVGVD5SZWdhcmRzPC9ESVY+ IAo8RElWIEFMSUdOPUxFRlQ+Tm9rbyBQaGFsYTwvRElWPiAKPERJViBBTElHTj1MRUZUPl9f X19fIE9yaWdpbmFsIG1lc3NhZ2UgX19fX188L0RJVj4gCjxESVYgQUxJR049TEVGVD5TdWJq ZWN0OiBDQ0w6IG1vbGVjdWxhciBvcmJpdGFsIGFuYWx5c2lzPC9ESVY+IAo8RElWIEFMSUdO PUxFRlQ+QXV0aG9yOiAibWF5IGFiZGVsZ2hhbmkgbWF5MDFkej15YWhvby5mciIgJmx0O293 bmVyLWNoZW1pc3RyeUBjY2wubmV0Jmd0OzwvRElWPiAKPERJViBBTElHTj1MRUZUPkRhdGU6 ICAxNXRoIEFwcmlsIDIwMDcgOToyNToxIDwvRElWPiAKPERJViBBTElHTj1MRUZUPiZuYnNw OzwvRElWPjxESVYgQUxJR049TEVGVD5EZWFyIENDTGVyczxCUj4gIEhvdyBJIGNhbiBleHBs YWluLCB1c2luZyB0aGUgbW9sZWN1bGFyIG9yYml0YWwgYW5hbHlzaXMsIHdoeSB0aGlzIGJv bmQgaW4gdGhpcyBtb2xlY3VsZSwgaXMgc2hvcnRlbiAob3IgbG9uZ2VyKSB0aGFuIHRoYXQg aW4gdGhlIG90aGVyIG1vbGVjdWxlwoU8QlI+ICBUaGFuayB5b3UgdmVyeSBtdWNoIGluIGFk dmFuY2U8QlI+PEJSPiAgICAgICAgICAgICA8QlI+LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tPEJSPiBEw6ljb3V2cmV6IHVuZSBub3V2ZWxsZSBmYcOnb24gZCdvYnRlbmly IGRlcyByw6lwb25zZXMgw6AgdG91dGVzIHZvcyBxdWVzdGlvbnMgISBQcm9maXRleiBkZXMg Y29ubmFpc3NhbmNlcywgZGVzIG9waW5pb25zIGV0IGRlcyBleHDDqXJpZW5jZXMgZGVzIGlu dGVybmF1dGVzIHN1ciBZYWhvbyEgUXVlc3Rpb25zL1LDqXBvbnNlcy48QlI+PC9ESVY+IAo8 L0JPRFk+CjwvSFRNTD4gCg== --EPOC32-gD,2'bxkgYv39-SNMR_zKdQtb,pQ-JSSvKbCtMNJPdwr1X'V-- From owner-chemistry@ccl.net Mon Apr 16 08:39:01 2007 From: "Close, David M. CLOSED=mail.etsu.edu" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34052-070416081247-6380-JlOA4M4wJZnnt4F7XuOKdg]~[server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Apr 2007 08:12:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED~!~mail.etsu.edu] Greg: You have to be more specific. There are indeed such cases. In older papers, where structures were determined by estimating intensities on 5 layers of film, such mistakes were made. So what structure are you talking about? If you are interested, the first solution of 1-MeThymine had a planar structure. 70% of the molecules were oriented one way, and 30% were flipped over. The difference being a carbon interchanged with a nitrogen. Regards, Dave Close -----Original Message----- > From: owner-chemistry##ccl.net [mailto:owner-chemistry##ccl.net] Sent: Monday, April 16, 2007 5:00 AM To: Close, David M. Subject: CCL: Accuracy of crystal structures Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] Hi everyone, This is a general question about crystal structures: How likely it is for an oxygen atom to be mistaken for a nitrogen atom and vice versa (so there are two possible H-bonding arrangements) in, say, an acetamide side chain of a protein? Thanks, Greghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Apr 16 09:12:01 2007 From: "FyD fyd a q4md-forcefieldtools.org" To: CCL Subject: CCL:G: Release of the R.E.D.-III tools Message-Id: <-34053-070415070830-16095-8BGWz6bLCrYazSdRpU+21A,+,server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 15 Apr 2007 12:15:23 +0200 MIME-Version: 1.0 Sent to CCL by: FyD [fyd^^^q4md-forcefieldtools.org] April, 15th, 2007. Dear All, We are pleased to announce the release of the program RESP ESP charge Derive version III (or R.E.D. III) and its related tools (Ante_R.E.D. and X R.E.D. III) available .. http://q4md-forcefieldtools.org/RED/. With the R.E.D. version I, highly reproducible RESP and ESP charge values (+/- 0.0001 e) can be derived by controlling the molecular orientation of the optimized geometry of a single conformation of a single molecule whichever the QM program or initial structure choice is. A new charge derivation procedure has been developed based on multi-orientation RESP or ESP fit. The use of multiple molecular orientations in the fitting process is supposed to limit the charge uncertainty induced when using a single orientation. With the R.E.D. version II, the use of multiple conformations of a single molecule in the fitting procedure has been implemented allowing for the derivation of charge values of high quality (i. e. more general; needed in molecular dynamics simulation). Multi-conformation and multi-orientation RESP or ESP fit can be performed together or independently for structures containing chemical elements of the periodic table up to Z = 35 (Bromine) according to the user's choice. With the R.E.D. version III, the control of charge constraints for atoms and groups of atoms in a molecule or a set of molecules (intra-molecule charge constraint) or between two molecules (inter-molecule charge constraint and inter-molecular charge equivalencing) has been developed allowing for the derivation of the RESP and ESP atom charge values for molecule fragments and sets of molecules. Thus, fitting procedures involving multiple molecules, and for each molecule, multiple conformations, and for each conformation, multiple orientations, can now be automatically carried out. Finally, eight different charge derivation procedures using different MEP computation algorithms (Connolly surface and CHELPG algorithms) and different fitting procedures (with or without hyperbolic restraints) are now available. Potentially, an infinite number of approaches can be developed by simply changing a few words in the R.E.D. III source code. Such procedures can be used in simulations based on AMBER, CHARMM, OPLS and GLYCAM force fields. Once the R.E.D. execution has correctly completed, the charge values are available in Tripos mol2 file(s) which can be considered as precursors of AMBER OFF and CHARMM RFT or PSF force field libraries. R.E.D. makes the development of the 'RESP' and 'ESP' charges a straightforward, simple and highly reliable procedure. R.E.D. is an interface to the GAMESS-US (available .. http://www.msg.ameslab.gov/GAMESS/) or Gaussian (available .. http://www.gaussian.com/) program and RESP program (available .. http://amber.scripps.edu/Questions/resp.html). R.E.D. III is now fully compatible with GAMESS-US, PC-GAMESS (http://classic.chem.msu.su/gran/gamess/) and Gaussian 1994, 1998 and 2003 versions. R.E.D. III is distributed with two other programs: - X R.E.D. is a graphical user-friendly interface, which has been developed to graphically execute R.E.D. and modify R.E.D. variables. - Ante_R.E.D. is a program useful for preparing R.E.D. III inputs, and in particular the "P2N" files. The P2N file format is a new file format introduced with R.E.D. III. It derives from the PDB file format, and corresponds to the PDB file format to whom one has added a second column of atom names. R.E.D. III, Ante_R.E.D., and X R.E.D. III constitute the R.E.D. III tools. R.E.D. (versions 1, 2 and 3) and Ante_R.E.D. have been written with the "Perl" programming language (See also the O'REILLY web site), while X R.E.D. has been developed using the "tcl/tk" programming language. "Perl" and "tcl/tk" are interpreted programming languages, meaning that the programs written with these languages do not need to be compiled. This makes R.E.D., Ante_R.E.D. and X R.E.D. simple to use, highly flexible and portable. They have been tested on PC-LINUX and SGI-IRIX workstations, and should work on all other UNIX platforms. The R.E.D. III tools are not "FREE" programs (i. e. in the sense of "freedom"; see the GNU web site http://www.gnu.org/philosophy/philosophy.html for a clear definition). They are provided at no cost for ACADEMIC users involved in NON-PROFIT RESEARCH after signing a license. A 3000.00 Euros fee is demanded to INDUSTRIAL/COMMERCIAL users and to ACADEMIC users involved in PROFIT-RESEARCH for the use of the R.E.D. III tools. The PI (Principal Investigator or Director) of a laboratory has to be registered as a R.E.D. III user to be authorized to download the R.E.D. III tools. During the registration procedure, the laboratory PI has to select a license among the four different licenses available: (1) License for Academic user & Non-profit research - User from north & south America, (2) License for Academic user & Non-profit research - User from Europe & the rest of the world, (3) License for Profit research (academic & non-academic user) - User > from north & south America, (4) License for Profit research (academic & non-academic user) - User > from Europe & the rest of the world. Please, see the Register section from the R.E.D. home page to register, and display these licenses. Two Tutorials available .. http://q4md-forcefieldtools.org/Tutorial/ have been written. The first one presents different RESP charge derivation approaches using the Ante_R.E.D. and R.E.D. III programs. The second one describes the R.E.DD.B. database. Many examples and choices made are described, and whole data generated from R.E.D. III runs are available for download. Examples of RESP and ESP charge derivation performed using the R.E.D. III program are available in the RESP ESP charge DDataBase: * RESP atomic charges for 10 solvent molecules based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-46" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-46/). * RESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and the HF/6-31G* theory level: Project "W-47" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-47/). * ESP atomic charges for 10 solvent molecules based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-48" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-48/). * ESP atomic charges for 10 solvent molecules based on the CHELPG algorithm and the HF/6-31G* theory level: Project "W-49" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-49/). * RESP atomic charges for the 4 DNA and RNA nucleosides based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "W-69" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-69/) and project "W-74" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-74/). * RESP atomic charges for the 4 DNA and RNA nucleosides based on the CHELPG algorithm and the HF/6-31G* theory level (following a strategy similar to that applied in the GLYCAM 2004 force field): Project "W-73" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-73/) and project "W-78" (available .. http://q4md-forcefieldtools.org/REDDB/up/W-78/). * RESP atomic charges for the central, (+)NH3-terminal, (-)OOC-terminal, NH2-terminal and HOOC-terminal fragments of the dimethylalanine amino acid based on the Connolly surface algorithm and the HF/6-31G* theory level: Project "F-3" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-3/), project "F-7" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-7/), project "F-11" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-11/), project "F-15" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-15/) and project "F-19" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-19/), respectively. * RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA: Project "F-45" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-45/) with a LEaP script (available .. http://q4md-forcefieldtools.org/REDDB/up/F-45/script1.ff) to convert the library precursors (Tripos format) into OFF files. * RESP atomic charges based on the CHELPG algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular DNA (following a strategy similar to that applied in the GLYCAM 2004 force field): Project "F-49" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-49/) * Same as project F-45, but the phosphate is located at the O3' position instead of the O5' one: Project "F-50" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-50/). * RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for the 16 components of a force field topology database useful for modeling regular RNA: Project "F-51" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-51/) with a LEaP script (available .. http://q4md-forcefieldtools.org/REDDB/up/F-51/script1.ff) to convert the library precursors (Tripos format) into OFF files (up to Project "F-56" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-56/ for other RNA force field topology databases). * Unusual nucleotide projects: Project "F-57" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-57/, Project "F-58" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-58/ and Project "F-51" (available .. http://q4md-forcefieldtools.org/REDDB/up/F-59/). More projects are obviously available in R.E.DD.B.; see the download section of R.E.DD.B. regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ From owner-chemistry@ccl.net Mon Apr 16 09:45:03 2007 From: "Phil Hultin hultin^^cc.umanitoba.ca" To: CCL Subject: CCL: molecular orbital analysis Message-Id: <-34054-070416094007-352-GlsgmZP61MsfsHAvndXyEw!A!server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B1_01C78002.CD2607A0" Date: Mon, 16 Apr 2007 08:39:39 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin!A!cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_00B1_01C78002.CD2607A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable There is actually a kind of =93chicken-and-egg=94 issue here: is the = bond longer/shorter because of orbital influences, or do we observe different orbital populations because changing nuclear separations alter = electronic energies? =20 We had a big discussion on CCL a while back about the =93reality=94 of = orbitals, and I DON=92T want to re-ignite that. However, whenever we are talking = about molecular structure we should think about what it means to =93explain=94 something. My view is that molecular orbital theory can = =93rationalize=94 experimental observations and that this is in one sense an = =93explanation=94 but I would hesitate before implying causation. =20 There is also the question of whether =93bonds=94 should be regarded as = physical entities at all, but =85 =20 Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin : cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin =20 _____ =20 > From: owner-chemistry : ccl.net [mailto:owner-chemistry : ccl.net]=20 Sent: April 16, 2007 2:33 AM To: Hultin, Philip G. Subject: CCL: molecular orbital analysis =20 Hi, I can immediately think of two influences on bond lengths(simplified): 1)The degree of filling of antibonding orbitals,the less the filling,the shorter the bond 2)atomic sizes,larger atoms are further apart than small ones =20 Of course things can sometimes be more complex.. =20 Regards Noko Phala _____ Original message _____ Subject: CCL: molecular orbital analysis Author: "may abdelghani may01dz=3Dyahoo.fr" Date: 15th April 2007 9:25:1=20 =20 Dear CCLers How I can explain, using the molecular orbital analysis, why this bond = in this molecule, is shorten (or longer) than that in the other molecule=85 Thank you very much in advance --------------------------------- D=E9couvrez une nouvelle fa=E7on d'obtenir des r=E9ponses =E0 toutes vos = questions ! Profitez des connaissances, des opinions et des exp=E9riences des = internautes sur Yahoo! Questions/R=E9ponses. ------=_NextPart_000_00B1_01C78002.CD2607A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Converted from Rich Text

There is actually a kind of = “chicken-and-egg” issue here: is the bond longer/shorter because of orbital influences, or = do we observe different orbital populations because changing nuclear = separations alter electronic energies?

 

We had a big discussion on CCL a = while back about the “reality” of orbitals, and I DON’T want = to re-ignite that. =A0However, whenever we are talking about molecular = structure we should think about what it means to “explain” something. = =A0My view is that molecular orbital theory can “rationalize” = experimental observations and that this is in one sense an “explanation” = but I would hesitate before implying causation.

 

There is also the question of = whether “bonds” should be regarded as physical entities at all, but = …

 

Dr. Philip G. = Hultin

Professor of = Chemistry,

University of = Manitoba

Winnipeg, MB

R3T 2N2

hultin : cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

From: owner-chemistry : ccl.net [mailto:owner-chemistry : ccl.net]
Sent: April 16, 2007 2:33 = AM
To: Hultin, Philip G. =
Subject: CCL: molecular = orbital analysis

 

Hi,

I can immediately think of two influences on = bond lengths(simplified):

1)The degree of filling of antibonding = orbitals,the less the filling,the shorter the bond

2)atomic sizes,larger atoms are further apart = than small ones

 

Of course things can sometimes be more = complex..

 

Regards

Noko Phala

_____ Original message = _____

Subject: CCL: molecular orbital = analysis

Author: "may abdelghani = may01dz=3Dyahoo.fr" <owner-chemistry : ccl.net>

Date: 15th April 2007 9:25:1 =

 

Dear CCLers
How I can explain, using the molecular orbital analysis, why this bond = in this molecule, is shorten (or longer) than that in the other molecule=85
Thank you very much in advance


---------------------------------
D=E9couvrez une nouvelle fa=E7on d'obtenir des r=E9ponses =E0 toutes vos = questions ! Profitez des connaissances, des opinions et des exp=E9riences des = internautes sur Yahoo! Questions/R=E9ponses.

------=_NextPart_000_00B1_01C78002.CD2607A0-- From owner-chemistry@ccl.net Mon Apr 16 10:22:00 2007 From: "Luis Simon luissimonrubio{=}hotmail.com" To: CCL Subject: CCL: DMSO frictional coefficient Message-Id: <-34055-070416100613-22713-tMzFEfjrpd8pX5/cyyFrpg+*+server.ccl.net> X-Original-From: "Luis Simon" Date: Mon, 16 Apr 2007 10:06:09 -0400 Sent to CCL by: "Luis Simon" [luissimonrubio.[-].hotmail.com] Can anyone tell me where can be found or how can it be calculated the DMSO-DMSO frictional coefficient for stochastic MD simulations? Thanks in advanced: Luis From owner-chemistry@ccl.net Mon Apr 16 10:55:02 2007 From: "Phil Hultin hultin * cc.umanitoba.ca" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34056-070416094250-2470-R0KHU4pzMwOlgk/OYlGfDA{:}server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 16 Apr 2007 08:42:33 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin#%#cc.umanitoba.ca] It is very likely for an O and an NH group to be ambiguous, but of course in peptides most of the NH groups will be identifiable because they are between two carbons. In an acetamide group I would not expect much ambiguity just on structural grounds. You find considerable ambiguity in asparagine, where the sidechain O and NH2 groups can be difficult to distinguish. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin[-]cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry[-]ccl.net [mailto:owner-chemistry[-]ccl.net] Sent: April 16, 2007 4:00 AM To: Hultin, Philip G. Subject: CCL: Accuracy of crystal structures Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] Hi everyone, This is a general question about crystal structures: How likely it is for an oxygen atom to be mistaken for a nitrogen atom and vice versa (so there are two possible H-bonding arrangements) in, say, an acetamide side chain of a protein? Thanks, Greghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Apr 16 11:31:01 2007 From: "Zuccotto, Fabio Nervianoms Fabio.Zuccotto++nervianoms.com" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34057-070416091328-10404-JreSi3nAslcdyDEdyKto3A#server.ccl.net> X-Original-From: "Zuccotto, Fabio [Nervianoms]" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 16 Apr 2007 14:22:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Zuccotto, Fabio [Nervianoms]" [Fabio.Zuccotto,,nervianoms.com] Hello Greg, crystallographers used to says that at normal resolution (about 2.0A) it is almost impossible to differentiate between C,N and O atoms. That is because what you get from Xrays experiments is the electron density map and the number of electrons in the three atom types is very similar (12, 14, 16). Other atoms like say Sulphur have more electrons and are bigger so are more easily recognizable. The situation might be different for resolutions less than 1A where you can see H atoms as well. If you can see Hs it is clearly possible to differentiate NH2 from O. Given that it is only possible to know the position of the atoms rather than the atom type normally the protein structures are built starting from the sequence information. In the case of amide normally the atom type is assigned in a way that allows the optimization of the Hbond pattern around the group. In other cases it is assigned in a pretty much random way. If you think that in your system swapping O with N would lead to a better Hb patter you are probably right in doing so. But it would be interesting to hear from another crystallographer if any one around. Regards Fabio ********************************************************** Fabio Zuccotto - PhD Molecular Modelling and Design - Chemistry - Oncology Nerviano Medical Sciences Viale L. Pasteur 10 - Nerviano 20014 (Milano) Italy Tel. +390331581103 -----Original Message----- > From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] Sent: Monday, April 16, 2007 11:00 AM To: Zuccotto, Fabio [Nervianoms] Subject: CCL: Accuracy of crystal structures Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] Hi everyone, This is a general question about crystal structures: How likely it is for an oxygen atom to be mistaken for a nitrogen atom and vice versa (so there are two possible H-bonding arrangements) in, say, an acetamide side chain of a protein? Thanks, Greghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Apr 16 12:05:01 2007 From: "Kalju Kahn kalju(_)chem.ucsb.edu" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34058-070416114713-6070-x5iIhITaPHWx/apxg83acA]-[server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 16 Apr 2007 08:46:23 -0700 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju*|*chem.ucsb.edu] An interesting recent example of such an ambiguity was the structure of 22nd genetically encoded amino acid, pyrrolysine. The 1.55 Ang resolution X-ray structure was not sufficient to distinguish between -OH, -NH2, or -CH3. Only later high-resolution mass-spectral analysis of tryptic fragments revealed the group to be -CH3. Please see http://pubs.acs.org/cen/topstory/8021/8021notw1.html and http://www.jbc.org/cgi/content/abstract/280/44/36962 for details Kalju > > Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] > Hi everyone, > > This is a general question about crystal structures: How likely it is for an > oxygen atom to be mistaken > for a nitrogen atom and vice versa (so there are two possible H-bonding > arrangements) in, say, an > acetamide side chain of a protein? > > Thanks, > Greghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/ chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Mon Apr 16 12:55:01 2007 From: "Elaine Meng meng..cgl.ucsf.edu" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34059-070416124504-14158-CHX/7O48sygNDgN7PGo5Bg^_^server.ccl.net> X-Original-From: "Elaine Meng" Date: Mon, 16 Apr 2007 12:45:01 -0400 Sent to CCL by: "Elaine Meng" [meng*cgl.ucsf.edu] Hi Greg, In this paper from the Richardson group, 100 high-quality protein crystal structures (0.9-1.7 A resolution) were examined for asparagine and glutamine sidechain flips: Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol. 1999 Jan 29;285(4):1735-47 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=9917408&query_hl=3&itool=pubmed_docsum The authors found about 20% of those side chains needed to be flipped, based on local hydrogen bonding patterns and steric clashes. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng_+_cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Mon Apr 16 13:34:01 2007 From: "Dominic Ryan dominic.ryan a comcast.net" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34060-070416125717-21292-WH5Ot1LEgx23bcA5RJ0LNw###server.ccl.net> X-Original-From: "Dominic Ryan" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Apr 2007 12:28:49 -0400 MIME-Version: 1.0 Sent to CCL by: "Dominic Ryan" [dominic.ryan|*|comcast.net] The more structures you look at the more examples you find of this rotational ambiguity. Other cases of 180 rotations include histidines and glutamines and even threonines. Unless one has an ultra high resolution structure of 1A or better no difference in density is visible for N or O or C. The local network of possible hydrogen bonding partners, including reliable waters, needs to be evaluated when making these assignments. I have found Mike Word's program REDUCE to be a very helpful starting point for checking all those questions. (See http://kinemage.biochem.duke.edu/software/index.php) You will find other useful information at that site as well. Dominic Ryan DRI > -----Original Message----- > From: owner-chemistry||ccl.net [mailto:owner-chemistry||ccl.net] > Sent: Monday, April 16, 2007 9:43 AM > To: Ryan, M Dominic > Subject: CCL: Accuracy of crystal structures > > > Sent to CCL by: "Phil Hultin" [hultin#%#cc.umanitoba.ca] > It is very likely for an O and an NH group to be ambiguous, but of course in > peptides most of the NH groups will be identifiable because they are between > two carbons. In an acetamide group I would not expect much ambiguity just > on structural grounds. > > You find considerable ambiguity in asparagine, where the sidechain O and NH2 > groups can be difficult to distinguish. > > Dr. Philip G. Hultin > > Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin-x-cc.umanitoba.ca > > http://umanitoba.ca/chemistry/people/hultin > > > -----Original Message----- > > From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] > Sent: April 16, 2007 4:00 AM > To: Hultin, Philip G. > Subject: CCL: Accuracy of crystal structures > > > Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] > Hi everyone, > > This is a general question about crystal structures: How likely it is for an > oxygen atom to be mistaken > for a nitrogen atom and vice versa (so there are two possible H-bonding > arrangements) in, say, an > acetamide side chain of a protein? > > Thanks, > Greghttp://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://w ww.c > cl.net/spammers.txt> From owner-chemistry@ccl.net Mon Apr 16 14:46:00 2007 From: "Michael Brunsteiner micb++uic.edu" To: CCL Subject: CCL: Accuracy of crystal structures Message-Id: <-34061-070416143820-15785-jsMWQUARX4KjRfKWsLgCNQ]|[server.ccl.net> X-Original-From: Michael Brunsteiner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 Apr 2007 13:29:23 -0500 MIME-Version: 1.0 Sent to CCL by: Michael Brunsteiner [micb*uic.edu] > -----Original Message----- >> From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] > Sent: April 16, 2007 4:00 AM > To: Hultin, Philip G. > Subject: CCL: Accuracy of crystal structures > > > Sent to CCL by: "Greg Sandala" [sandala^chem.usyd.edu.au] > Hi everyone, > > This is a general question about crystal structures: How likely it is for an > oxygen atom to be mistaken > for a nitrogen atom and vice versa (so there are two possible H-bonding > arrangements) in, say, an > acetamide side chain of a protein? you might want to have a look at: https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php and the refs cited there... michael From owner-chemistry@ccl.net Mon Apr 16 16:11:01 2007 From: "Yogesh Sabnis ysabnis{:}yahoo.com" To: CCL Subject: CCL: predicting photostable molecules Message-Id: <-34062-070416155545-14869-3FGNnPUlwe5pwOlFssdnsQ- -server.ccl.net> X-Original-From: Yogesh Sabnis Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 16 Apr 2007 09:37:50 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Yogesh Sabnis [ysabnis:_:yahoo.com] Hi, I am looking into predicting molecules as photostable or photolabile. I was wondering if there is any software out there that predicts if molecules are photostable or photolabile. Anyone knows any interesting articles on predicting potostable molecules from physchem properties. Thank you. Kind regards, Yogesh =================================== Dr. Yogesh Sabnis 1/14, Priory Courtyard, Priory Road, Ramsgate, Kent CT11 9PW UK __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Mon Apr 16 16:49:00 2007 From: "Conley, Michael mconley=-=leadscope.com" To: CCL Subject: CCL: Leadscope Announces Availability of Prediction Software and FDA SAR-Ready Genetox Database Message-Id: <-34063-070416153222-8346-IvAJbr+Q0jbpCp5LDjYSvA,,server.ccl.net> X-Original-From: "Conley, Michael" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 16 Apr 2007 14:59:37 -0400 MIME-Version: 1.0 Sent to CCL by: "Conley, Michael" [mconley-*-leadscope.com] Columbus, Ohio April 16, 2007 - Leadscope announces the availability of the Leadscope Predictive Data Miner software (model building) and the FDA SAR-Ready Genetox Database. The Predictive Data Miner is powerful OECD compliant software for predicting toxicity or biological activity. Scientists can transparently build customized training sets, add knowledge, and develop models. Once a model is applied to a structure or series of structures the domain of applicability of each is tested and graphically depicted. The FDA SAR-Ready Genetox database is the first in a series of SAR-ready databases to be constructed by Leadscope and the U.S. Food & Drug Administration under their Cooperative Research & Development Agreement (CRADA). This database contains 2,241 compounds with greater than 16,000 test results. All structures and test calls have been verified for accuracy while both structures and data have been balanced to facilitate model training set selection. Toxicity endpoints include bacterial mutagenesis, in vitro chromosome aberration and in vivo micronucleus. Loftus Lucas, Leadscope's CEO, said, "The combination of SAR-ready data and the model building capability allows scientists to easily build and apply transparent Genetox models." The Predictive Data Miner is not black box software. Data, algorithms, domain of applicability, and results are all fully transparent to meet OECD requirements. To view a pre-recorded demonstration of the Predictive Data Miner or the FDA SAR-Ready Genetox database, visit www.leadscope.com/demos. To receive further information on these new products or to request an on-line demonstration with a Leadscope scientist contact info{}leadscope.com. Regards, Michael Conley Leadscope, Inc. 1393 Dublin Road Columbus, Ohio 43215 614-675-3768 614-675-3732 fax mconley{}leadscope.com www.leadscope.com