From chemistry-request@ccl.net Sun Feb 6 01:05:55 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.192]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1665sCx000974 for ; Sun, 6 Feb 2005 01:05:54 -0500 Received: by wproxy.gmail.com with SMTP id 71so791889wri for ; Sat, 05 Feb 2005 22:05:54 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:references; b=sbKXrQVIzQFSZtD+iv8hfbGbu5rZw90b0QGNlQuSrMAZ+tj6r5e6TaYYFMAgdP6NT5t4EQompNCPWS7MYqf7S8AJWzLekmcvlyP3WQiKXk60HA+BSnPf1cBCDQmN/zwp6tUM92xYm1IPBz1WMTAsqHp5+kx7D/Oov13z3IL2JP8= Received: by 10.54.22.2 with SMTP id 2mr81255wrv; Sat, 05 Feb 2005 21:05:54 -0800 (PST) Received: by 10.54.40.15 with HTTP; Sat, 5 Feb 2005 21:05:54 -0800 (PST) Message-ID: <2205580d05020521053c6865a4*at*mail.gmail.com> Date: Sun, 6 Feb 2005 00:05:54 -0500 From: Dave Rogers Reply-To: Dave Rogers To: chemistry*at*ccl.net Subject: CCL: Re: Required list of CDK2 inhibitors In-Reply-To: <000201c5010c$21a935e0$6666a8c0*at*agi.com> Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit References: <000201c5010c$21a935e0$6666a8c0*at*agi.com> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Did anyone reply to this message? Whenever I see something like this, it kind of irks me. If you want really this kind of thing, you should go and look for it yourself. This is the kind of information and type of problem private industry should be working to solve -- for its own benefit and possible income. Also, I am a grad. student, which means that I not financially well-off; and seeing that there are people out there (making more than me) who are actively using the goodwill of academia makes me very unlikely to publish any software that I stayed up countless nights programming (and debugging and validating) until 3am. The counter-argument is, of course, that what I don't publish others will have to labor to re-invent. I think that this list should have an active discussion about means available to develop software (for public use) that will not leave you without royalties to supplement Social Security (when I will ineveitably be unable to read hi-res fonts anymore). Sincerely, David Rogers Department of Chemistry University of Cincinnati Cincinnati, Ohio On Sun, 23 Jan 2005 10:56:46 +0530, Raju Vishwanathan wrote: > Dear CCL.NETMembers > > I would like to have a list compounds which inhibits CDK2 receptor protein. > Currently we are in the initial process of studying this group of > inhibitors. > > Thanking you in advance. > Warm Regards, > Raju Vishwanathan > Sr. Consultant > SysArris Software > # 120 A, Elephant Rock Road, > III Block, Jayanagar,( Opp to HSBC ATM ). > Bangalore-560011 > India. > Tel. No. 91-80-26654965,26655052,26642690, > Fax No. 91-80-26650374 > <> > The information in this message is conf dential and may be legally > privileged. It is intended solely for the addressee. Access to this message > by anyone else is unauthorised. If you are not the intended recipient, any > disclosure, copying, or distribution of the message, or any action or > omission taken by you in reliance on it, is prohibited and may be unlawful. > Please immediately contact the sender if you have received this message in > error.Thank you. > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow*at*nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > From chemistry-request@ccl.net Sun Feb 6 01:08:43 2005 Received: from web51302.mail.yahoo.com (web51302.mail.yahoo.com [206.190.38.168]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j1668fCx002518 for ; Sun, 6 Feb 2005 01:08:41 -0500 Received: (qmail 7832 invoked by uid 60001); 6 Feb 2005 06:08:40 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=ZYeV1n68NOhJ58rBAASr67hzB9lh5eVHs/2ebp4sjoWk3mTJpTOKNCqIRpvEJ/TQ++QOeaUKlQ2LFsWILewls6nGDZauM91JvKdWlRZOotQJLP9Js5c2mrCp1MQwmK7pMhz9PDRG7m2nU6LG9NPags4bueeMFIxu/pfM1ZKqZyA= ; Message-ID: <20050206060840.7830.qmail.-at-.web51302.mail.yahoo.com> Received: from [24.152.169.115] by web51302.mail.yahoo.com via HTTP; Sat, 05 Feb 2005 22:08:40 PST Date: Sat, 5 Feb 2005 22:08:40 -0800 (PST) From: Sengen Sun Subject: CCL: orbitals and reality To: chemistry.-at-.ccl.net In-Reply-To: <20050201194525.75692.qmail.-at-.web51308.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The trajectories or orbits of classical objects have well-defined physical meaning, and even a toddler could well understand them. Their physical meaning is decided by physical reality independant of any mathematical equations. I would say they are experimentally observable (like force field) although we cannot take a snapshot of them. It is also fine to me if you say they are not. It is of no point to argue for which way you say it. But it is not acceptable to say that electrons and nuclei are not observables! In contrast, WFs disappear like ghosts outside our mathemtical schemes! In fact, the 1954 Nobel prize was awarded partially to Born for his interpretation that WFs have no physical meaning. It is also the official interpretation in our textbooks that orbitals are not observables and have no physical meaning. It could not be more clear as shown by Spanget-Larsen's posting on Jan 20, 05. Alan Shusterman, Eric Scerri, many others, and I are not creating any new interpretation. We are just defending the well-established theory after deep thinking for many years and after several years public discussion. Dr. Hultin is speculating whether some physical properties of electronic structure can lead to some information of WFs. This is surely possible for H. However, such an activity distinguishes from any experimental observation, as it is conducted in reference to the pictures in your mind. It is not based on any physical interacting relationship. WFs are not experimental observable whatever, simply because they are not the choice of the nature but humans. The choices of the nature are electrons, their motion (or density distribution), and the space they occupy. The reverse construction of WFs for multielectron systems would be extremely hard and is impossible to me (or I am not quite sure). Here I do share with Dr. N Sukumar's concern with . What I am sure is that the Nature papers did not produce any relevant information for possible mathematical construction of WFs. I see myself to be technique-specific. We must be very careful to reject any competitive experiements. However, what they did is implicit assumptions after assumptions without logical connections. I agree well on the two points by Lou Noodleman on Jan. 24. It is sure that single WFs carry the information of physical reality, even though they are human-formulated. That is why they are so useful. It is also true that virtual orbitals carry physical information one way or the other. WFs are just a mathematical tool to dismantle the reality and to wrap up the pieces in order to carry them through our math procedures. They are just for human convenience and cannot be understood until we reach our destination where we can re-assemble them together to make sense in the reality. I must again emphasize that the electronic structure of a quantum system cannot function physically according to WFs in chemical reactions. To my best knowledge, I am the first person who explicitly states so in the public, although this point was implied in several occassions by Dewar, Bader, et. al. I also wish to emphasize that chemistry is not about orbitals but electron density and its reorganization as nuclei change their positions. The third important point is that chemical reactivity is decided by the easiness of electronic reorganization. These three points are very valuable in teaching and in scientific research, as recognized by two CCL friends recently. I have to say honestly that the authors of the Nature papers and some people blindly supporting them are scientifically naive on this particular issue and need to re-study or re-think of QM. There are no physical entities or physical properties directly associated with WFs! --- Eric Scerri wrote: > On Saturday, January 29, 2005, at 12:46 AM, > konrad.hinsen [a] laposte.net > wrote: > > That's my view as well and I have had the same > sense of bewilderment > > reading the recent discussion. For me the question > is not if orbitals > > are "real" but if they are useful in understanding > molecules. But the > > same comment applies to electrons and nuclei. > > -- > > Konrad Hinsen > > ------- > > Many useful things are unobservable! > > The question was indeed whether one can observe an > orbital. > I don't think anybody really doubts the usefulness > of the concept. > Another problem is what an extent there is that orbitals are useful in understanding molecules. They cannot be used in such a way that scientists in the same field do not understand each other (e.g., on the mechanism of a dipolar addition, JPC A 2001, 105, 10943; 10946; 10947). This is not just an occassional problem. Many claims of explanation based on orbitals in the literature turned out to be non-understandable. In fact, Dr. Scerri stated in a published paper: . I can support such a statement by giving many examples. The claims of orbital observation are just one of them. --- Valentina VETERE wrote: > Sorry I'm still in trouble here..can you please make > me understand why an > electron can not be localized in a HOMO. Is the > reason that outside the > orbital picture there is a probability different > from zero to found the > electron or are you thinking about a > multiconfigurational nature for the > atoms? > The uncertainty of a single electron in a multi-electron system is not limited to a single orbital. This point is well established and documented in many textbooks. You may read some textbooks. I would recommend Bader's note on web: http://www.chemistry.mcmaster.ca/esam/ Sengen __________________________________ Do you Yahoo!? All your favorites on one personal page Try My Yahoo! http://my.yahoo.com From chemistry-request@ccl.net Sun Feb 6 01:33:07 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.194]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j166X6Cx009539 for ; Sun, 6 Feb 2005 01:33:06 -0500 Received: by wproxy.gmail.com with SMTP id 71so793354wri for ; Sat, 05 Feb 2005 22:33:06 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:references; b=RbDYgasw7yp1+l+CHlB2AXX0+IbrJoU1d5LyhCTSH8MufSmisSNhBgwhH4e5eH0xBw9au5uqPtHeDapgMSHtBKph0Msz1CAQB1eKQEmjjTWTTWXUM7Nf4HWzaguT35hg+sYhfytq2H7Do4lkEkEZOGmiLcbs3IV7jhgHY0+DzuY= Received: by 10.54.22.38 with SMTP id 38mr163270wrv; Sat, 05 Feb 2005 22:33:06 -0800 (PST) Received: by 10.54.40.15 with HTTP; Sat, 5 Feb 2005 22:33:06 -0800 (PST) Message-ID: <2205580d050205223355305cfe.-at-.mail.gmail.com> Date: Sun, 6 Feb 2005 01:33:06 -0500 From: Dave Rogers Reply-To: Dave Rogers To: chemistry.-at-.ccl.net Subject: Re: CCL: Re: Required list of CDK2 inhibitors In-Reply-To: <2205580d05020521053c6865a4.-at-.mail.gmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit References: <000201c5010c$21a935e0$6666a8c0.-at-.agi.com> <2205580d05020521053c6865a4.-at-.mail.gmail.com> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I should add to my remarks the fact that they are my own opinions and (possibly) have no bearing on reality. It is impossible to neglect the politics, and this will no doubt bear heavily on any discussion of code publishing. Anyway, what I mean to say is that it is late, and what I have written in no way reflects the views of any entity other than myself. I also believe firmly that private industry is essential in the development of new technologies and in driving the basic research that in the end leads to more private industries (which are beneficial to society). Thus, we are hopelessly stuck in reality and cannot utilize a fixed-reference-frame Born-Oppenheimer approximation when it comes to politics. What this comes down to is that the intentions of private industry are, in the end perfectly legitimate; and that such communication is necessary and should have an equally legitimate channel of communication whereby everyone involved can benefit. ~ David Rogers On Sun, 6 Feb 2005 00:05:54 -0500, Dave Rogers wrote: > > Whenever I see something like this, it kind of irks me. If you want > really this kind of thing, you should go and look for it yourself. > This is the kind of information and type of problem private industry > should be working to solve -- for its own benefit and possible income. > > Also, I am a grad. student, which means that I not financially > well-off; and seeing that there are people out there (making more than > me) who are actively using the goodwill of academia makes me very > unlikely to publish any software that I stayed up countless nights > programming (and debugging and validating) until 3am. The > counter-argument is, of course, that what I don't publish others will > have to labor to re-invent. > > I think that this list should have an active discussion about means > available to develop software (for public use) that will not leave you > without royalties to supplement Social Security (when I will > ineveitably be unable to read hi-res fonts anymore). > > Sincerely, > David Rogers > Department of Chemistry > University of Cincinnati > Cincinnati, Ohio