From owner-chemistry@ccl.net Wed Feb 20 04:31:01 2013 From: "Ramon Crehuet rcsqtc..iqac.csic.es" To: CCL Subject: CCL: How to make public a short code Message-Id: <-48267-130220042807-18317-dWCGBnZuHzYd13yVFqurZQ(0)server.ccl.net> X-Original-From: "Ramon Crehuet" Date: Wed, 20 Feb 2013 04:28:05 -0500 Sent to CCL by: "Ramon Crehuet" [rcsqtc-,-iqac.csic.es] Dear CCLers, In our group we have written a short python code that I would like to make public. We're preparing a communication where I wanted to put a link to the code. But I still don't know how to offer it. At first I thought to put it in the group web page, but then I thought a software repository would be better. And then I realized I didn't know the pros and cons of sourceforge, github, google code... The information in the wikipedia is extensive, but I couldn't grasp the strengths of each repository. Based on your experience, and taking into account that this project only comprises a python script, some examples and software instructions, what would you recommend me? Thanks in advance, Ramon From owner-chemistry@ccl.net Wed Feb 20 05:06:01 2013 From: "uekstrom:_:gmail.com uekstrom:_:gmail.com" To: CCL Subject: CCL: How to make public a short code Message-Id: <-48268-130220044909-25831-cIJXanajna8XTEPZRTYTjQ ~ server.ccl.net> X-Original-From: "uekstrom#gmail.com" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 20 Feb 2013 10:49:02 +0100 MIME-Version: 1.0 Sent to CCL by: "uekstrom^gmail.com" [uekstrom^gmail.com] Dear Ramon, In order to use googlecode or the free version of github your code must be released under an open source license, as defined by the OSI (http://opensource.org/licenses/category). If you do that you can pick either google code or github. Sourceforge was good ten years ago but it now so overloaded with advertisement that I cannot recommend it. Github is probably the best choice if you intend to grow the project a lot and need "private" repositories. I have some small projects on googlecode and it serves me fine. Regards, Ulf Ekström From owner-chemistry@ccl.net Wed Feb 20 08:24:00 2013 From: "A. Candian alessandra.candian[a]gmail.com" To: CCL Subject: CCL:G: GAUSSIAN stops just after reading # line Message-Id: <-48269-130220050458-19853-NXA9G7+g21r37EX7yu6DxQ|server.ccl.net> X-Original-From: "A. Candian" Date: Wed, 20 Feb 2013 05:04:57 -0500 Sent to CCL by: "A. Candian" [alessandra.candian#%#gmail.com] Hello, I am having trouble with GAUSSIAN 03. I prepared a .com file to do geometry optimisation and anharmonicity analysis, but the program stops just after reading the # line without leaving a comment and/or error message on the .log file or the job.sh.eNUMBER file example of .log ... #p B3LYP/6-31+G** SCF(NoVarAcc) OPT(gdiis,tight) int(grid=150770) cphf (grid=sg1) freq(noraman,anharmonic) test ---------------------------------------------------------------------- 1/7=10,14=-1,18=20,19=11,26=3,38=1,80=1/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=111,11=2,16=1,25=1,30=1,74=-5,75=150770/1,2,3; 4//1; 5/5=2,38=1,96=1/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/14=-1,18=20,19=11,80=1/3(1); 99/8=1000/99; 2/9=110/2; 3/5=1,6=6,7=111,11=2,16=1,25=1,30=1,74=-5,75=150770/1,2,3; 4/5=5,16=3/1; 5/5=2,38=1,96=1/2; 7//1,2,3,16; 1/14=-1,18=20,19=11,80=1/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/8=1000,9=1/99; Leave Link 1 at Wed Feb 20 10:49:23 2013, MaxMem= 1342177280 cpu: 0.8 I have enough experience with Gaussian to be sure that my input file is correct. I have also tried to create one with GABEDIT and I still have the problem. Any suggestion? Thanks in advance! Alessandra alessandra.candian]=[gmail.com From owner-chemistry@ccl.net Wed Feb 20 10:20:00 2013 From: "Daniel Jana dfjana*gmail.com" To: CCL Subject: CCL:G: cubegen utility in Gaussian Message-Id: <-48270-130220101302-20668-Tstdanudpsw4nN3dfAn4kw**server.ccl.net> X-Original-From: Daniel Jana Content-Type: multipart/alternative; boundary=20cf3074b5a49c252504d62964c8 Date: Wed, 20 Feb 2013 16:12:56 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana^^gmail.com] --20cf3074b5a49c252504d62964c8 Content-Type: text/plain; charset=ISO-8859-1 Hello, A cube is just a special case of a rectangular parallelepiped. X0, Y0, Z0 do represent the origin of the cube (e.g. -3.0 -3.0 -3.0). And then you use the: X1, Y1, Z1; X2, Y2, Z2; X3, Y3, Z3 to define the increments from that point. If you choose N1=N2=N3 and then X1=Y2=Z3 and all others X, Y and Z equal to 0 you should have a cube. So, with the above example and if I didn't do any mistake, if you use N1=N2=N3=12 and X1=Y2=Z3=0.5 you should have a cube from -3.0 -3.0 -3.0 to 3.0 3.0 3.0. Hope this helps, Daniel On 19 February 2013 21:29, Pieremanuele Canepa canepap#%#wfu.edu < owner-chemistry]|[ccl.net> wrote: > Dear All, > > is there a way to force cubegen to spit a cube file that looks like a > cube, rather than a rectangle? > > I read the page http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm at > the point attached below. > However I don't understand what x0, y0 and Z0 really represent. Do these > coordinate represent the > the origin of the rectangle lattice? is not clear what these numbers are. > > A value of *-1* says to read the cube specification > from the input > stream, according to the following format: > *IFlag, X*0, *Y*0, *Z*0 *Output unit number and initial point.**N*1 > , *X*1, *Y*1, *Z*1*Number of points and step-size in the X-direction.**N*2 > , *X*2, *Y*2, *Z*2*Number of points and step-size in the Y-direction.**N*3 > , *X*3, *Y*3, *Z*3*Number of points and step-size in the Z-direction.** > IFlag* is the output unit number. If *IFlag* is less than 0, then a > formatted file will be produced; otherwise, an unformatted file will be > written. > > If *N*1<0 the input cube coordinates are assumed to be in Bohr, > otherwise, they are interpreted as Angstroms. |*N*1| is used as the > number of X-direction points in any case; *N*2 and *N*3 specify the > number of points in the Y and Z directions, respectively. Note that the > three axes are used exactly as specified; they are not orthogonalized, so > the grid need not be rectangular. > > The value *-5* says to read in an arbitrary list of points from standard > input. If you enter this input by hand, terminate the input with an > end-of-file (i.e., *Ctrl-D* under Unix). Alternatively, you can redirect > standard input to a file containing the list of points (do not place a > blank line or *Ctrl-D* at the end of the file). > > > Thanks, Piero > _____________________________________ > > Pieremanuele (Piero) Canepa PhD > > Wake Forest University, Department of Physics > Winston-Salem, NC 27109 (USA) > t: + 001 (336) 758 4222 > c: +001 (336) 602 6045 > f: + 001 (336) 758 6142 > skype: pieremanuele > _____________________________________ > > --20cf3074b5a49c252504d62964c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello,

A cube is just a special case of a rectangular parallelepiped= .
X0, Y0, Z0 do represent the origin of the cube (e.g. -3.0 -3.0 -3.0).<= br>And then you use the:
X1, Y1, Z1; X2, Y2, Z2; X3, Y3, Z3 to define th= e increments from that point.
If you choose N1=3DN2=3DN3 and then X1=3DY2=3DZ3 and all others X, Y and Z = equal to 0 you should have a cube.

So, with the above example and if= I didn't do any mistake, if you use N1=3DN2=3DN3=3D12 and X1=3DY2=3DZ3= =3D0.5 you should have a cube from -3.0 -3.0 -3.0 to 3.0 3.0 3.0.

Hope this helps,
Daniel

On 19 Febr= uary 2013 21:29, Pieremanuele Canepa canepap#%#w= fu.edu <owner-chemistry]|[ccl.net> wrote:
Dear All= ,=A0

is there a way to force cubegen to spit a cube file= that looks like a cube, rather than a rectangle? =A0

I read the page =A0http://www.gaussian.com/g_tech/= g_ur/u_cubegen.htm =A0at the point attached below.=A0
However= I don't understand what x0, y0 and Z0 really represent. Do these coord= inate represent the=A0
the origin of the rectangle lattice? is not clear what these numbers a= re.=A0

A value of=A0-1=A0says to read the cu= be specification > from the input stream, according to the following for= mat:

IFlag, X0,=A0Y0,= =A0Z<= sub>0 =A0=A0=A0=A0=A0=A0=A0=A0Output unit number and initial point.
N1,=A0X1,=A0Y1= ,=A0Z= 1 Number of points and step-size in the X-directi= on.
N2,=A0<= font face=3D"Times New Roman, Times, serif" size=3D"3">X= 2,=A0Y= 2,=A0Z2 Number of points and step-size in the Y-directi= on.
N3,=A0<= font face=3D"Times New Roman, Times, serif" size=3D"3">X= 3,=A0Y= 3,=A0Z3 Number of points and step-size in the Z-directi= on.
IFlag=A0is the output unit number. If=A0IFlag=A0is less than 0, then a forma= tted file will be produced; otherwise, an unformatted file will be written.= =A0

If=A0N1<0 the input cube coordinates = are assumed to be in Bohr, otherwise, they are interpreted as Angstroms. |<= /span>N1| is used as the number of X-direction points in any= case;=A0N2=A0and=A0<= i>N3=A0specif= y the number of points in the Y and Z directions, respectively. Note that t= he three axes are used exactly as specified; they are not orthogonalized, s= o the grid need not be rectangular.=A0

The value=A0-5=A0says to read in an arbitrary list of poin= ts from standard input. If you enter this input by hand, terminate the inpu= t with an end-of-file (i.e.,=A0Ctrl-D=A0under Unix). Alternatively, y= ou can redirect standard input to a file containing the list of points (do = not place a blank line or=A0Ctrl-D=A0at the end of the file).=


Thanks, Piero=A0
_____________________________________
Pieremanuele (Piero) Canepa PhD=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0

Wake Forest University,=A0Department of Physics
Winston-= Salem, NC 27109 (USA) =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0
t: + 001 (336) 758 4222
c: +001 (336) 602 6045
f: + 001 (336= ) 758 6142
skype: pieremanuele
_____________________________________<= /div>


--20cf3074b5a49c252504d62964c8-- From owner-chemistry@ccl.net Wed Feb 20 10:54:00 2013 From: "Sanjay Bharathwaj computationalchemist_._gmail.com" To: CCL Subject: CCL: Comparing Compounds Message-Id: <-48271-130220103812-27695-yAZ15DO9HVRTaDJO3ylpfg*server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=f46d0442811c66f2ef04d629bed7 Date: Wed, 20 Feb 2013 16:38:03 +0100 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist(~)gmail.com] --f46d0442811c66f2ef04d629bed7 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I have four compounds (say for example A2B, A3B, A4B2, A6B5). I would like to know, how one can explain by computational methods, which of these is more stable. (You can't compare the total energy because of different composition) Is calculating enthalpy of formation for each of these species is a good idea? If so, can any one suggest me how should obtain this value for each species. Any help would be more appreciable. Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --f46d0442811c66f2ef04d629bed7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

I have four compounds (say for example A2B, A3B, A4B= 2, A6B5).

I would like to know, how one can explai= n by computational methods,
which of these is more stable.
(You can't compare the total energy because of different compositi= on)

Is calculating enthalpy of formation for each = of these species is a good idea?
If so, can any one suggest me ho= w should obtain this value for each species.=A0

Any help would be more appreciable.

Sanjay



--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Insti= tute of Technology,
India.
--f46d0442811c66f2ef04d629bed7-- From owner-chemistry@ccl.net Wed Feb 20 12:02:00 2013 From: "Phil Hasnip phil.hasnip_._york.ac.uk" To: CCL Subject: CCL: Comparing Compounds Message-Id: <-48272-130220115903-17917-3Bjxq7+2oPwdyOjhL1hcBA : server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary=047d7bdc1272b0138b04d62adf73 Date: Wed, 20 Feb 2013 16:58:56 +0000 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip^-^york.ac.uk] --047d7bdc1272b0138b04d62adf73 Content-Type: text/plain; charset=ISO-8859-1 Dear Sanjay, You need to look at the energy per atom, e.g. E(A6B5)/11 or E(A4B2)/6, for all the possible structures and stoichiometries of interest, plot them as energy/atom against stoichiometry (% of B for example) and then construct the convex hull. You would usually compute pure A and pure B as well, and then the convex hull construction takes you from pure A through all the various stable stoichiometries to pure B. Compounds whose energy/atom lies on the convex hull are stable, others are not (they would prefer to decompose into the two stable phases that bracket them on the convex hull). This approach does ignore interface effects, so may break down for nanomaterials where the interface and strain energies can be a large proportion of a system's energy. Of course you also need to think about what you mean by "energy", whether that should be internal energy, enthalpy or another free energy etc. and naturally this will also depend on your method of energy calculation. I usually find DFT with PBE is reasonable for most solid-state systems. All the best, Phil Hasnip On 20 February 2013 15:38, Sanjay Bharathwaj computationalchemist_._ gmail.com wrote: > Dear All, > > I have four compounds (say for example A2B, A3B, A4B2, A6B5). > > I would like to know, how one can explain by computational methods, > which of these is more stable. > (You can't compare the total energy because of different composition) > > Is calculating enthalpy of formation for each of these species is a good > idea? > If so, can any one suggest me how should obtain this value for each > species. > > Any help would be more appreciable. > > Sanjay > > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. > -- ----------------------------------------------------------------------------- Dr Phil Hasnip Email: phil.hasnip_._york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 324624 York YO10 5DD --047d7bdc1272b0138b04d62adf73 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sanjay,

You need to look = at the energy=20 per atom, e.g. E(A6B5)/11 or E(A4B2)/6, for all the possible structures=20 and stoichiometries of interest, plot them as energy/atom against stoichiom= etry (% of B for example) and then construct the convex hull. You=20 would usually compute pure A and pure B as well, and then the convex=20 hull construction takes you from pure A through all the various stable=20 stoichiometries to pure B. Compounds whose energy/atom lies on the=20 convex hull are stable, others are not (they would prefer to decompose=20 into the two stable phases that bracket them on the convex hull). This=20 approach does ignore interface effects, so may break down for=20 nanomaterials where the interface and strain energies can be a large=20 proportion of a system's energy.

Of course you also need to think about what you mean by=20 "energy", whether that should be internal energy, enthalpy or ano= ther=20 free energy etc. and naturally this will also depend on your method of=20 energy calculation. I usually find DFT with PBE is reasonable for most=20 solid-state systems.

All the best,

Phil Hasnip
=

On 20 February 2013 15:38, Sanjay Bharat= hwaj computationalchemist_._gmail.com <owner-chemistry_._ccl.net> wrote:
Dear All,

I have four compounds= (say for example A2B, A3B, A4B2, A6B5).

I would l= ike to know, how one can explain by computational methods,
which of these is more stable.
(You can't compare the total energy because of different compositi= on)

Is calculating enthalpy of formation for each = of these species is a good idea?
If so, can any one suggest me ho= w should obtain this value for each species.=A0

Any help would be more appreciable.

Sanjay

<= /div>



--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technology,
India.



--
-----------------------= ------------------------------------------------------
Dr Phil Hasnip = =A0 =A0 =A0 =A0 =A0 =A0Email: phil.hasnip_._york.ac.uk
Dept of Physics
University of York =A0 =A0 =A0 =A0Tel: =A0+44 (0)1904 32= 4624
York YO10 5DD
--047d7bdc1272b0138b04d62adf73-- From owner-chemistry@ccl.net Wed Feb 20 12:37:00 2013 From: "Cina Foroutan-Nejad canyslopus]|[yahoo.co.uk" To: CCL Subject: CCL: Comparing Compounds Message-Id: <-48273-130220120259-20058-vNSa7DCgudEa2QpaN1J7LQ::server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="-361436947-681145300-1361379771=:29328" Date: Wed, 20 Feb 2013 17:02:51 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus#%#yahoo.co.uk] ---361436947-681145300-1361379771=:29328 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sanjay,=0A=0AYour question is quite general! The term stability has be= en misused by many in my view! You should specify the stability in more det= ails. We can generally speak about two types of stability (if we confine ou= rselves to Born-Oppenheimer approximation); a) thermodynamic stability and = b)kinetic stability.=0AIf any of your compounds is a local minimum on its P= ES so they are thermodynamically stable. Now, the question is their kinetic= stability. To define kinetic stability you need to elaborate more. Scannin= g the PES is a good job but usually this is not enough! Many molecules like= lots of metallic clusters are stable in vacuum but they react immediately = when they meet each other or other molecules. For getting an insight toward= this case you may read this paper and the subsequent comments by reviewers= particularly G. Frenking comments: Angew Chem Int Ed 2008, 47, 7164. For a= n example in which kinetic stability is thoroughly studied see this paper: = JPCA, 2008, 112, 10365.=0AAnother issue regarding stability is the thermody= namic conditions.=A0 A molecule could be unstable in atmospheric pressure b= ut quite stable in high pressure. However, as far as I can guess, you are t= alking about normal thermodynamic conditions. (?)=0AYou may wish to measure= the stability of your molecule in a particular reaction, e.g. reaction wit= h water. In this case you should study the reaction of your molecules with = water and measure the reaction barrier toward that particular reaction. =0A= Beside, there are lots of stability indicators like hardness, HOMO-LUMO gap= s, etc. which are used generally by chemists. If you are lucky enough one o= f conceptual DFT guys may explain more about that in CCL.=0AIn a nut shell,= estimation of kinetic stability is not a simple task usually! Your molecul= e(s) might be stable in certain conditions but react madly in another condi= tion.=0A=0ARegards,=0ACina=0A=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= =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=0ACina Foroutan-Nejad, PhD=0Ahttp://muni.academia.edu/CinaForoutanNejad= =0A=0A=0A=0A=0A________________________________=0A From: Sanjay Bharathwaj = computationalchemist_._gmail.com =0ATo: "Foroutan-= Nejad, Cina " =0ASent: Wednesday, 20 Febru= ary 2013, 16:38=0ASubject: CCL: Comparing Compounds=0A =0A=0ADear All,=0A= =0A=0AI have four compounds (say for example A2B, A3B, A4B2, A6B5).=0A=0AI = would like to know, how one can explain by computational methods,=0Awhich o= f these is more stable.=0A(You can't compare the total energy because of di= fferent composition)=0A=0AIs calculating enthalpy of formation for each of = these species is a good idea?=0AIf so, can any one suggest me how should ob= tain this value for each species.=A0=0A=0AAny help would be more appreciabl= e.=0A=0ASanjay=0A=0A=0A=0A=0A-- =0ARegards,=0ADr. Sanjay Bharathwaj Kumar,= =0ADharmendra Institute of Technology,=0AIndia. ---361436947-681145300-1361379771=:29328 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sanjay,
Your question is quite general! The term stability has been misused by man= y in my view! You should specify the stability in more details. We can gene= rally speak about two types of stability (if we confine ourselves to Born-O= ppenheimer approximation); a) thermodynamic stability and b)kinetic stabili= ty.
If any of your compounds is a local minimum on its PES so they are t= hermodynamically stable. Now, the question is their kinetic stability. To d= efine kinetic stability you need to elaborate more. Scanning the PES is a g= ood job but usually this is not enough! Many molecules like lots of metalli= c clusters are stable in vacuum but they react immediately when they meet e= ach other or other molecules. For getting an insight toward this case you m= ay read this paper and the subsequent comments by reviewers particularly G. Frenking comments: Angew Chem Int Ed 2008, 47, 7164. For a= n example in which kinetic stability is thoroughly studied see this paper: = JPCA, 2008, 112, 10365.
Another issue regarding stability is the thermod= ynamic conditions.  A molecule could be unstable in atmospheric pressu= re but quite stable in high pressure. However, as far as I can guess, you a= re talking about normal thermodynamic conditions. (?)
You may wish to me= asure the stability of your molecule in a particular reaction, e.g. reactio= n with water. In this case you should study the reaction of your molecules = with water and measure the reaction barrier toward that particular reaction= .
Beside, there are lots of stability indicators like hardness, HOMO-LU= MO gaps, etc. which are used generally by chemists. If you are lucky enough= one of conceptual DFT guys may explain more about that in CCL.
In a nut= shell, estimation of kinetic stability is not a simple task usually! Your molecule(s) might be stable in certain conditions but react = madly in another condition.

Regards,
Cina
=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=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
Cina Foroutan-Nejad, PhD
http://muni.a= cademia.edu/CinaForoutanNejad


From:= Sanjay Bharathwaj computationalchemist_._gmail.com <owner-chemistry=-=ccl= .net>
To: "Foroutan= -Nejad, Cina " <canyslopus=-=yahoo.co.uk>
Sent: Wednesday, 20 February 2013, 16:38=
Subject: CCL: Comparing Compounds
Dear All,

I have four compounds (say= for example A2B, A3B, A4B2, A6B5).

I would like t= o know, how one can explain by computational methods,
which of th= ese is more stable.
=0A
(You can't compare the total energy becaus= e of different composition)

Is calculating enthalp= y of formation for each of these species is a good idea?
If so, c= an any one suggest me how should obtain this value for each species. <= /div>=0A

Any help would be more appreciable.
<= br>
Sanjay




--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmend= ra Institute of Technology,
=0AIndia.=0A
=0A


---361436947-681145300-1361379771=:29328-- From owner-chemistry@ccl.net Wed Feb 20 13:12:00 2013 From: "Jean-Pierre DJUKIC djukic() unistra.fr" To: CCL Subject: CCL: Comparing Compounds Message-Id: <-48274-130220115003-13504-SESJElj9hfEjHMejwvoi2A()server.ccl.net> X-Original-From: Jean-Pierre DJUKIC Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 20 Feb 2013 17:49:50 +0100 MIME-Version: 1.0 Sent to CCL by: Jean-Pierre DJUKIC [djukic|unistra.fr] Sanjay, Behind the term "stability" there is a lot of underlying issues: -kinetic stability, which implies that one knows how some species among others in a complex mixture can convert into something else, i.e by what mechanism, with what activation barrier, etc... -thermodynamic stability, which implies thermodynamic reversibility between considered species, for example in the process of their (competing) formation. and "persistence", a notion that merges kinetic and thermodynamic stability in a very environment-dependent way: some species are persistent, but not intrinsically "stable", a variation of some environmental parameters may lead to their disappearance or to their proliferation/accumulation. I would suggest you first to clear up the whole problem by having a look at the thermodynamics of your system: are these species competing each other, is their formation a competitive process ? Is the process leading to their formation reversible or not, fully , partly ? What is experiment telling you ? Are they decomposing or evolving into each other or into something else, are some of them not evolving spontaneously ? Things can get very complicated, it depends a lot on how good one is at understanding experimentally the system in question. Once you have answered these questions, then you may adapt your computational approach and chose the criteria, the observables that will characterize the system in the best way. Hope this helps... Jean-Pierre Le 20/02/2013 16:38, Sanjay Bharathwaj computationalchemist_._gmail.com a écrit : > Dear All, > > I have four compounds (say for example A2B, A3B, A4B2, A6B5). > > I would like to know, how one can explain by computational methods, > which of these is more stable. > (You can't compare the total energy because of different composition) > > Is calculating enthalpy of formation for each of these species is a good > idea? > If so, can any one suggest me how should obtain this value for each > species. > > Any help would be more appreciable. > > Sanjay > > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. From owner-chemistry@ccl.net Wed Feb 20 13:47:00 2013 From: "Errol Lewars elewars-.-trentu.ca" To: CCL Subject: CCL: Comparing Compounds Message-Id: <-48275-130220122212-30873-ZGzAr9KFCM6A7pw5+4lSQQ!A!server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 20 Feb 2013 12:22:15 -0500 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars(-)trentu.ca] 2013 Feb 20 "which of these is more stable". "Stable" could mean thermodynamically stable or kinetically stable. The stability that interests you depends on the reason these compounds interest you. If you are trying to develop a new propellant or explosive, you want it to be thermodynamically unstable and kinetically stable. The thermodynamic stability of X is reflects the energy difference between X and its reaction products, e.g. between TNT and the stoichiometric CO2, N2, etc. products. This is straightforward to calculate, and reliable if you know, or guessed right, the reaction products. Taking this into account judiciously, enthalpy of formation can provide an indication of thermodynamic stability. Kinetic stability is much harder to calculate. You need to calculate the decomposition barrier, which is not simple to do accurately. The voluminous literature on calculations of nitrogen polymers Nx (X greater than 2) gives some guide to attempts to assess the kinetic stability of compounds which are undoubtedly thermodynamically highly unstable. Four of maybe 500 references to this are 1) H. Zhou et al, Computational and Theoretical Chemistry, 2013, 1005, 68-74 2) F-L Liu, F. Yang, L-X Zhang, Theochem, 2010, 950, 98-99 3) S. Jasper et al, J Phys Chem A, 2011, 115(42), 11915-11918. 4) J. Thomas, K. Fairman, D. L. Strout, J Phys Chem A, 2011, 114(41), 1144-1146. [D. L. Strout has published a great deal on this]. E. Lewars == Sanjay Bharathwaj computationalchemist_._gmail.com wrote: > Dear All, > > I have four compounds (say for example A2B, A3B, A4B2, A6B5). > > I would like to know, how one can explain by computational methods, > which of these is more stable. > (You can't compare the total energy because of different composition) > > Is calculating enthalpy of formation for each of these species is a > good idea? > If so, can any one suggest me how should obtain this value for each > species. > > Any help would be more appreciable. > > Sanjay > > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. From owner-chemistry@ccl.net Wed Feb 20 16:51:00 2013 From: "Chemist MM nanochemistmm^-^gmail.com" To: CCL Subject: CCL: How to draw anatase cluster with Gaussview? Message-Id: <-48276-130220161753-26752-zd5Ei9k+Niz3MufhMLxLzg{=}server.ccl.net> X-Original-From: Chemist MM Content-Type: multipart/alternative; boundary=14dae934107712c91d04d62e7d2c Date: Thu, 21 Feb 2013 00:17:42 +0300 MIME-Version: 1.0 Sent to CCL by: Chemist MM [nanochemistmm-#-gmail.com] --14dae934107712c91d04d62e7d2c Content-Type: text/plain; charset=ISO-8859-1 Dear CCLers, Iam new user and am working recently in application of computional chemistry on nanotechnology, and i will be highly appreciated if any one kindly guide me to know how to draw anatase cluster with Gaussview?, as it doesnot mentioned in details in researches. Thanks alot for your appreciated and kind support Regards --14dae934107712c91d04d62e7d2c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCLers,
Iam new user and am working recently in application of computional che= mistry on nanotechnology, and i will be highly appreciated if any one kindl= y guide me to know how to draw anatase cluster with Gaussview?, as it doesn= ot mentioned=A0in details in researches.
Thanks alot for your appreciated and kind support
Regards
--14dae934107712c91d04d62e7d2c-- From owner-chemistry@ccl.net Wed Feb 20 17:26:00 2013 From: "Chemist MM nanochemistmm-.-gmail.com" To: CCL Subject: CCL: How to draw anatase cluster with Gaussview? Message-Id: <-48277-130220162506-27159-ukWNFQhoqDNVhaM7hzydHQ*server.ccl.net> X-Original-From: Chemist MM Content-Type: multipart/alternative; boundary=f46d043c7d3a15e64e04d62e97f3 Date: Thu, 21 Feb 2013 00:24:58 +0300 MIME-Version: 1.0 Sent to CCL by: Chemist MM [nanochemistmm(_)gmail.com] --f46d043c7d3a15e64e04d62e97f3 Content-Type: text/plain; charset=ISO-8859-1 Dear CCLers, Iam new user and am working recently in application of computional chemistry on nanotechnology, and i will be highly appreciated if any one kindly guide me to know how to draw anatase cluster with Gaussview?, as it doesnot mentioned in details in researches. Thanks alot for your appreciated and kind support Regards --f46d043c7d3a15e64e04d62e97f3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCLers,
Iam new user and am working recently in application of computional che= mistry on nanotechnology, and i will be highly appreciated if any one kindl= y guide me to know how to draw anatase cluster with Gaussview?, as it doesn= ot mentioned=A0in details in researches.
Thanks alot for your appreciated and kind support
Regards

--f46d043c7d3a15e64e04d62e97f3-- From owner-chemistry@ccl.net Wed Feb 20 18:36:00 2013 From: "Devang Sachdev dsachdev^_^nvidia.com" To: CCL Subject: CCL: Applications for a Computational Chemistry Appliance Message-Id: <-48278-130220160106-17548-9G+LJVIq3x8SDafclTy2jQ * server.ccl.net> X-Original-From: "Devang Sachdev" Date: Wed, 20 Feb 2013 16:01:05 -0500 Sent to CCL by: "Devang Sachdev" [dsachdev::nvidia.com] Hi Today computational chemists have to work with off-the-shelf server nodes or workstations and customizing them with applications that are needed for their research. What if there was an appliance that came with preconfigured hardware (processors, memory, networking, storage, etc), OS, management tools and commonly used computational chemistry applications. So the question is whether this would be useful to the computational chemists and what kind of applications would you like to see on such an appliance? You can reply privately to me if you like. Thanks Devang Sachdev NVIDIA From owner-chemistry@ccl.net Wed Feb 20 20:12:00 2013 From: "Pieremanuele C. canepap[a]wfu.edu" To: CCL Subject: CCL: about cube files generated by gaussian Message-Id: <-48279-130220201133-11700-UGHowgqKglTiwrZ6nR4SDg() server.ccl.net> X-Original-From: "Pieremanuele C." Content-Type: multipart/alternative; boundary="Apple-Mail=_45B142BA-45FA-4B03-B423-E7428350C9A6" Date: Wed, 20 Feb 2013 20:11:25 -0500 Mime-Version: 1.0 (Mac OS X Mail 6.2 \(1499\)) Sent to CCL by: "Pieremanuele C." [canepap(-)wfu.edu] --Apple-Mail=_45B142BA-45FA-4B03-B423-E7428350C9A6 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear all,=20 I'm doing some test calculation on Ar. I'm using fairly large and good = quality Aldrich QZVP basis-set. =20 Now after a full SCF calculation with any method HF, CI I generate a = charge density cube, selecting the appropriate Density as show below=20 #P CISD/QZVP SCF=3DTight fchk Density=3DCI =20 CISD 2/20/2012 Ar atom =20 0 1 AR 0 0.000000000 0.0000000000 0.0000000000 when I generate a cube file out of my chk file with cubegen and I try to = look at some properties with cubman I get something like this=20 Input file titles: CISD 2/20/2012 Ar atom density=3DCI Electron density from Total CI Density SumAP=3D 8.0556141776 SumAN=3D 0.0000000000 SumA=3D = 8.0556141776 CAMax=3D 27.6457000000 XYZ=3D -0.0000300000 -0.0000300000 = -0.0000300000 CAMin=3D 0.0000000000 = XYZ=3D-9999.0000000000-9999.0000000000-9999.0000000000 DipAE=3D -0.0000423721 0.0000046364 0.0000017619 DipAN=3D 0.0000000000 0.0000000000 0.0000000000 DipA=3D -0.0000423721 0.0000046364 0.0000017619 my question is: what's SumAP? is perhaps the integrated density? If = yes would expect it to be 18? Am'I missing something there?=20 Thanks for your help, Piero=20 ______________________________________ Pieremanuele (Piero) Canepa PhD Wake Forest University, Department of Physics Winston-Salem, NC 27109 (USA) t: +001 (336) 758 4222 c: +001 (336) 602 6045 f: +001 (336) 758 6142 Skype: pieremanuele=20 --Apple-Mail=_45B142BA-45FA-4B03-B423-E7428350C9A6 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Dear = all, 

I'm doing some test calculation on Ar. I'm = using fairly large and good quality Aldrich = QZVP basis-set.  
Now after a full SCF = calculation with any method HF, CI I generate a charge density cube, = selecting the appropriate Density
as show = below 

#P CISD/QZVP SCF=3DTight fchk = Density=3DCI
 
CISD 2/20/2012 Ar = atom
 
 0  1
 AR =     0   0.000000000   0.0000000000   = 0.0000000000


when I = generate a cube file out of my chk file with cubegen and I try to look = at some properties with cubman I get something like = this 

Input file = titles:
 CISD 2/20/2012 Ar atom = density=3DCI
 Electron density from Total CI = Density

 SumAP=3D   =  8.0556141776 SumAN=3D    0.0000000000 SumA=3D   =  8.0556141776
 CAMax=3D   27.6457000000 XYZ=3D =   -0.0000300000   -0.0000300000   = -0.0000300000
 CAMin=3D    0.0000000000 = XYZ=3D-9999.0000000000-9999.0000000000-9999.0000000000

 DipAE=3D   -0.0000423721    0.0000046364 =    0.0000017619
 DipAN=3D   =  0.0000000000    0.0000000000   =  0.0000000000
 DipA=3D    -0.0000423721 =    0.0000046364   =  0.0000017619


my question = is: what's  SumAP? is perhaps  the integrated density? If yes = would expect it to be 18? Am'I missing something = there? 

Thanks for your = help,
Piero 
______________________________________

Pie= remanuele (Piero) Canepa PhD

Wake Forest University, Department = of Physics
Winston-Salem, NC 27109 (USA)
t:  +001 (336) 758 = 4222
c: +001 (336) 602 6045
f:  +001 (336) 758 6142
Skype: = pieremanuele 

= --Apple-Mail=_45B142BA-45FA-4B03-B423-E7428350C9A6--