Subject: Re: CCL:calculate the angle

From: [email-masked] (colvin michael e)
Date: Mon, 26 Feb 1996 14:29:03 -0800

Recently [email-masked] (Pornthep Sompornpisut) asked:

>I will appreciate if anyone know of any programs that can measure the angle
>between the planes? 

You are probably looking for something that has a nice GUI for selecting
the atoms, but if you just want a program to calculate the angles, 
here's a tiny C code I wrote sometime back to do this.  It just reads sets
of six cartesian points, three each per plane, and prints out the angle.
Nota bene: To the best of my knowledge it works, but of course I offer
no guarantees to its accuracy, reliability, suitability, etc. etc..., so
definitely check this against a hand-calculated result.

                                               --Mike Colvin
                                                 [email-masked]

=============================================================
/* Routine to calculate the angle between two planes */

#include <math.h>
#include <stdio.h>

typedef struct {
	double x;
	double y;
	double z;
	} point;
	
int main(void);
point cross(point, point);
double dot(point, point);

main()
{
    point a1,a2,a3,b1,b2,b3;
    point va1,va2,vb1,vb2, crossa, crossb;
    double dotab, angle;
	
    while(1)
    {
        if (scanf("%lf %lf %lf",&a1.x,&a1.y,&a1.z)==EOF)
            exit(0);
        scanf("%lf %lf %lf",&a2.x,&a2.y,&a2.z);
        scanf("%lf %lf %lf",&a3.x,&a3.y,&a3.z);
        scanf("%lf %lf %lf",&b1.x,&b1.y,&b1.z);
        scanf("%lf %lf %lf",&b2.x,&b2.y,&b2.z);
        scanf("%lf %lf %lf",&b3.x,&b3.y,&b3.z);
		
        /* calculate direction vectors */
        va1.x=a2.x-a1.x; va1.y=a2.y-a1.y; va1.z=a2.z-a1.z;
        va2.x=a3.x-a1.x; va2.y=a3.y-a1.y; va2.z=a3.z-a1.z;
        vb1.x=b2.x-b1.x; vb1.y=b2.y-b1.y; vb1.z=b2.z-b1.z;
        vb2.x=b3.x-b1.x; vb2.y=b3.y-b1.y; vb2.z=b3.z-b1.z;
		
        /* calculate cross products */
        crossa=cross(va1,va2);
        crossb=cross(vb1,vb2);
		
        dotab=dot(crossa,crossb);
        dotab/=sqrt(dot(crossa,crossa));
        dotab/=sqrt(dot(crossb,crossb));
		
        angle=acos(dotab)*180/3.1415926535;
		
        printf(" Angle = %lf\n",angle);
    }
}

point cross(point a, point b)
{
	point value;
	
	value.x=a.y*b.z-a.z*b.y;
	value.y=a.z*b.x-a.x*b.z;
	value.z=a.x*b.y-a.y*b.x;
	
	return value;
}

double dot(point a, point b)
{
	return a.x*b.x+a.y*b.y+a.z*b.z;
}
=============================================================

>From [email-masked] Sat Feb 24 13:54 EST 1996
From: Albeiro Alonso Restrepo Cossio <[email-masked]>
To: [email-masked]
cc: [email-masked]
Subject: CCL: Summary, Trivial question 
Date: Sat, 24 Feb 96 13:54:32 -0500
Content-Length: 10620
Status: RO

Dear CCL subscribers,

Many thanks to all of you who spent some of your time in answering my question 
about the biggest system optimized ab initio methodologies ad the biggest water 
cluster optimized with simulated annealing; here is my summary.

Albeiro Restrepo.

********************************************************************************
From: [email-masked] (cachau)

Hola Albeiro,

	Vi tu pregunta en el CCL y me arriesgo a darte mi opinion. Creo que
tendras serias dificultades en encontrar una respuesta a tu pregunta. La 
razon es que necesitas una definicion operativa de "mas grande". Si te fijas
en "numero de atomos" puedes elejir una pequenya base y de este modo puedes
calcular moleculas muy grandes. Si en cambio prefieres usar como parametro el
numero de bases, entonces te encuentras con que hay sistemas diatomicos que
se han tratado con muchos cientos de bases y con bases de simetria mas alta
que g lo que es inconcebible de usar para una molecula de interes biologico,
de modo que siguiendo este criterio llegarias a la conclusion de que una
molecula diatomica con algun atomo pesado seria tal vez el sistema mas grande
nunca tratado a nivel HF. Entonces, ni el numero de bases ni el numero de 
atomos constituyen tu definicion. Por si esto no fuera ya complejo, luego
tienes que incorporar el problema de optimizacion: HF sin optimizar
es un problema, optimizada la estructura es un orden de magnitud mas grande
como problema, y si llegas a caracterizar la geometria (calcular su Hessiano) 
es un orden de magnitud mas alto aun. En la complejidad del problema, como
incluyes la simetria?. Hay ENORMES complejos con piridinas resueltos con 
bases enormes pero con simetria altisima. Que "tamanyo" le asignarias al
complejo?. Que tan grande te resulta un buckyball?. 60 atomos o 5 + simetria?.
Y luego tienes los calculos 'a la Clementi (posiblemente en mi criterio los
mas grandes nunca hechos en biomoleculas) en su famoso "Star" system. El 
usaba bases muy grandes, pero usaba una "base asociada" a largas distancias
de modo que se ahorraba de calcular un numero altisimo de integrales de este 
modo, como medirias la complejidad en este caso?.

En fin, que no te he resuelto tu pregunta, sorry, pero creo que necesitas 
darle una pulida a tu definicion si quieres que la respuesta sea "meaningful".

********************************************************************************
From: Kris Van Alsenoy <[email-masked]>

Dear Albeiro,

In response to your question concerning molecular clusters, I would 
like to mention the following papers :

Anik Peeters, C. van Alsenoy, A.T.H. lenstra, H.J. Geise,
Int. J. Quant. Chem., Vol. 46, 73-80 (1993)

C. Van Alsenoy, Anik Peeters,
J. Mol. Struct., Vol. 286, 19-34 (1993)

Anik Peeters, C. Van Alsenoy, A.T.H. Lenstra, H.J. Geise,
J. Mol. Strcut., Vol. 304, 101-107 (1994)

Anik Peeters, C, Van Alsenoy, A.T.H. Lenstra, H.J. Geise,
J. Chem. Phys., Vol. 103, 6608-6616 (1995)

In thes epapers we studied a number of molecules using a cluster approach.
Is this what you were looking for ?

Sincely,

  kris van alsenoy
  [email-masked]

********************************************************************************
From: "E. Lewars" <[email-masked]>

Albeiro Restrepo asked about the biggest systems that have been studied by
ab initio, and the reliability of the results. I don't claim that these are the
biggest anyone has looked at, but they are at the high end of ab initio jobs:

(1) MP2(FC)/6-311G** (312 basis funtions) on  C6H5-C:::C-C6H5: S. Saebo and
    J. Almlof et al, THEOCHEM 59, 361 (1989).
(2) MP2/6-31G* optimizations on porphyrins, ca 20 heavy atoms. At the MP2 level,
    unlike the HF, the known, dampened bond alternation characteristic of these
    aromatic systems is evident. _Long_ calc's. See L. Paquette et al, ca. 1995
    (J Am Chem Soc?).
(3) For a short, very useful review of work on ab initio etc calc's and their
    reliability, see I. N. Levine, _Quantum Chemistry_, 4th Ed., Prentice Hall,
    1991, Chapters 15, 16, 17.

  Errol Lewars

********************************************************************************
From: Artem Masunov <[email-masked]>

Dear Albeiro Restrepo,
	We did HF optimization of some supermolecular clusters containing
up to 80 atoms. They are not published yet. 
	If you find bigger system being optimized, please let me know.
Regards,
Artem

> Does someone in the list have information about the bigest system succesfully
> optimized by any ab initio methodology and about its reliability? 

      __   _________ 
     /  \ /  _   _  \   Artem Masunov - [email-masked]
    /    \\  \\  \\  \       Chemistry Department, Hunter College
   /  /\  \\  \\  \\  \          City University of New York
  /  ____  \\  \\  \\  \     695 Park Avenue, New York, NY 10021
 /__/\__/\__\\__\\__\\__\ Tel: (212) 725-0317, Fax: (212) 772-5332
 \__\/  \/__//__//__//__/
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: Artem Masunov <[email-masked]>

On Mon, 19 Feb 1996, Albeiro Alonso Restrepo Cossio wrote:

> Does your group have any intention of publishing that results?

Yes, mixed hexamer of melamine-barbituric acid will be reported on 
ACS meeting this spring, urea decamers were reported on ACA meeting last 
summer (see abstract on WWW):
http://www.cisti.nrc.ca/programs/ACA95/M/a429.html

Papers will be submitted to one of ACS journals in a few month.

Regards,
Artem

********************************************************************************
From: "Dr. James Brown" <[email-masked]>

On Feb 19, 12:17pm, E. Lewars wrote:
> Subject: CCL:BIG AB INITIO JOBS

> (1) MP2(FC)/6-311G** (312 basis funtions) on  C6H5-C:::C-C6H5: S. Saebo and
>     J. Almlof et al, THEOCHEM 59, 361 (1989).

A study of glucose by us in JACS coming out soon had 348 basis functions.
 Another on glucose conformers by Truhlar and coworkers to be published in
Carbohydrate Research included 624 basis functions.  As far as
reliability...it's difficult to tell since there's not much data on glucose in
the gas phase.

James

********************************************************************************
From: Artem Masunov <[email-masked]>

Dear Albeiro Restrepo,
Since CCLers started to count basis functions, I can tell, that urea 
decamer had 840 basis functions (D95**). Mixed hexamer had 
918 basis functions (D95*) and will be presented at Symposium 
Semiempirical methods: Do they have a future? 
in New Orlean (March 1996) by Prof. J.J.Dannenberg.
 Artem

********************************************************************************
From: Kris Van Alsenoy <[email-masked]>

Dear Albeiro,

I forgot to mention a study on sugars using TZV & TZVP -basisets :

C. Van Alsenoy, A.D. French, M. Cao, S.Q. Newton, L. Sch"afer,
JACS, Vol. 116, 9590-9595 (1994)

sincerly,
   kris

On Mon, 19 Feb 1996, Albeiro Alonso Restrepo Cossio wrote:

********************************************************************************
From: [email-masked] (Juha Muilu)

Hi,

I have done some ab initio calculations on  ZnS clusters up to 

Zn240S240 (1200 basis functions & 6000 primitive functions). 

The calculations are made possible using translational 

properties of finite clusters. What comes to reliability I 

must say that the models are rather academic....

For more information: 

http://www.chem.joensuu.fi/people/juha_muilu/Research/zns_clusters.html
Also from Surf.Science during this year, I hope.

----
 Juha Muilu
 Department of Chemistry,University of Joensuu,P.O. Box 111
 80101 Joensuu,FINLAND/Email:[email-masked],Phone:358-73-1513312,
 Fax:358-73-1513390,http://www.chem.joensuu.fi/people/juha_muilu

********************************************************************************
From: Stuart Watson <[email-masked]>

Hi,

Our current record is performing molecular dynamics on 6700 Na atoms,
using an "Order-N" DFT method (for the initial article see M. Pearson et
al, J. Phys. Cond. Matter, 5, 3321 (1993). The method is only really
applicable to systems with delocalised electrons (ie metals), and reproduces
Kohn-Sham results for alkali metals.

This system was run on a Cray T3D (timing on 128nodes 9s electronic, 
1200 ionic - thats the benefit of an Order-N method), and it is feasible
to probably quadruple the no. of atoms (as the memory requirements, as
well as the time scales linearly).

Stuart Watson

##########################################################################
#  Stuart Watson                    #  Life is like a box of chocolates, #
#  [email-masked]         #  it gets all squishy when dropped  #
#  http://physchem.ox.ac.uk/~stuart #  from a great height.              #
##########################################################################
********************************************************************************
From: Bryan Marten <[email-masked]>
Zhang and Friesner recently reported Self Consistent Reaction Field (QM
solute surrounded by continuum dielectric solvent requiring several
converged HF wavefunctions) calculations at the HF/6-31G** level for
bacteriochlorophyll and bacteriopheophytin on an IBM RS/6000 workstation
using the electronic structure program PSGVB in JPC 99 16479 1995.
Those were in the 880-890 basis function range on molecules with C1 (no)
symmetry and are believed to be the largest SCRF ab inito calculations
to date.  The authors use the SCRF calculations to compute redox
potentials in DMF, compare to experiment, and report qualitative
agreement for relative redox energies.
-- 
				Dr. Bryan Marten
				Ciba Pharmaceuticals
				[email-masked]

********************************************************************************
From: "Schiffer, Heinz, Dr." <[email-masked]>

Sometime ago someone asked for references to large ab initio calculations ( 
sorry, but I forgot who it was ). I just got a copy of a paper of Gustavo 
Scuseria at Rice University in Houston who did a Hartree-Fock geometry 
optimization within icosahedral symmetry for a fullerene with 540 atoms and 
with 2700 basis functions on a single IBM RS6000 workstation. The program he 
used was TURBOMOLE  from Ahlrichs' group in Karlsruhe.

********************************************************************************

>From [email-masked] Mon Feb 26 05:07 EST 1996
Date: Mon, 26 Feb 1996 11:04:27 +0100 (CET)
From: Jan Kazimirski <[email-masked]>
To: [email-masked]
Subject: Question: calc. of PED (potential energy distrib.) 
Content-Length: 556
Status: RO

Dear Netters

One of my friends (not subscribed to CCL - yet(:-()) asked me to
send his question to the list. The question is:

 "Can you recommend any program (commercial or academic) which
  calculates PED (potential energy distribution) based on
  Gaussian 94 - calculated vibrational normal modes?"

We both (me and my friend) would be grateful for any information.
Thanks in advance.
                                 
                                           Jan Kazimirski
                                  e-mail: [email-masked]

>From [email-masked] Mon Feb 26 18:06 EST 1996
Date: Tue, 27 Feb 1996 08:06:11 +0900
To: [email-masked]
From: [email-masked] (Eiji Osawa)
Subject: WATOC96 2nd circular
Return-Receipt-To: [email-masked]
Content-Length: 751
Status: R

To the list members of Japan, Taiwan, Korea, China and other Asian countries:
        I have a stock of the 2nd circular for WATOC96, World Congress of
Comutational Chemists, to be held in Jerusalem, Israel, July 7 to 12, 1996.
Deadline of abstract is April 15, 1996. Those who are interested should
send me e-mail for a copy or take a look at its homepage,
http://www.ch.ic.ac.uk/watoc/watoc_israel.html. Eiji Osawa
/*************************************************
*  Eiji Osawa
*  Department of Knowledge-based Information Engineering
*  Toyohashi University of Technology
*  Aichi 441, Japan
*  Phone: x-81-532-47-0111(ex. 853)
*  FAX: x-81-532-48-5588
*  E-mail: [email-masked]
*************************************************/

>From [email-masked] Fri Feb 23 11:38 EST 1996
Date: Fri, 23 Feb 96 11:50:38 -0500
From: [email-masked] (Joel Polowin)
To: [email-masked], [email-masked]
Subject: Re:  CCL:Dipole-Dipole Interaction in Dynamics
Content-Length: 885
Status: RO

> Date: 21 Feb 1996 07:18:07 GMT
> From: [email-masked]
> 
>    Is there a Molecular Dynamics Package which incorporates dipole-dipole
> interaction in the electrostatic computation?.
> I would appreciate any input in this regard.

Any package that does molecular dynamics with an MM2-derived force field
should include interactions of bond dipoles.  (HyperChem does; please
contact me for details.)  I don't know of any that explicitly include
effects of molecular dipoles, but I'm not sure if that's what you were
asking about.

Joel

------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked] 

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
WWW: http://www.hyper.com/

>From [email-masked] Mon Feb 26 13:29 EST 1996
Date: 26 Feb 1996 12:19:12 GMT
From: "MSBEA01.SUBRAPS" <[email-masked]>
Subject: Summary : Dipole-Dipole Interaction in D
To: [email-masked]
Comment: MEMO 1996/02/26 12:26
Content-Length: 4790
Status: R

----------------------------------------------------------------------
THIS MAIL MESSAGE IS FROM THE INTERNET AND MAY HAVE BEEN READ, COPIED,
OR MODIFIED BY USERS OTHER THAN INTENDED RECIPIENTS.
----------------------------------------------------------------------

Dear CCL members,

  A while ago I posted a query on dipole-dipole interactions , the following
is a summary of responses that I received.

Thanking you all for your time

 --Mani--

Dr. P. S. Subramanian
Fuels and Lubrication Division
Texaco Inc.
P. O. Box 509
Beacon, NY 12508
email: [email-masked]
vmail: 914-838-7561

Response 1.

You have a very strange header above your mail. It sounds almost as if
you expect your mail to be tainted by the filth of the transport through
internet :-)
What does it mean?

It was this text that aroused my curiosity, i don't know of any MD packages
that do dipole-dipole interaction. Maybe Gromos does it, it seems to be
quite advanced.

Greetings,
Frits Daalmans

Frits Daalmans
OIO Conformational Analysis
Gorlaeus Laboratoria
Leiden, The Netherlands
E-mail: [email-masked]
Tel: [+31] (0)71-5274505

Response 2.

Dear Dr. P. S. Subramanian

Could you summarize responses for your querry on CCL ?
Grzegorz Bakalarski
ICM Warsaw University

Response 3.

Hi Mani,

To my knowledge only MM3 incorporates such a entity. It uses bond dipoles
for such a purpose. Everyone else uses point charges (monopole
approximation)
to reproduce these properties.

If you have a good reason to need the electrostatics (which is probably
why you asked the net...) and cannot use a bond dipole scheme, then I
would strongly suggest that you perform ab initio calculations, say at
the HF/6-31G(d,p) level (or 6-31+G(d,p) if you have anions) and compute
the monopole charges from a fit of the electrostatic potential. This
method reproduces the molecular dipole moment pretty well; I'm not so
sure about the molecular quadrupole moment, though. Use of Mulliken and
Natural Bond Order methods is not recommended for this purpose. Be
sure that you use a large enough basis set to suitably reproduce the
electron density of the systems you are interested in.

(As an aside, I stumbled upon this many years ago in grad school by trying
to
use Mulliken-based charges to reproduce the dipole moments in simple
lipids. I failed miserably. In my thinking during that time, I was sure
that I could reproduce the molecular dipole from point charges--after
all, we all learned it could be done in our fields courses. But of course
I was not aware that Mulliken population analysis was not based on
trying to reproduce the molecular dipole. It took me a while to realize
that it was the method, not the idea, that was at fault.)

Hope this helps,

Craig

 --
 ----------------------------------+-----------------------------------------
Papernet:  Craig W. Burkhart      |  *** GO TRIBE!! *** WORLD SERIES '96 ***
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           Akron, OH   44305      | 1995 American League Champion
Mouthnet:  216.796.3163           |
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Internet:  [email-masked] | TSN Fireman of the Year - Jose Mesa
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WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO! WAHOO!
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Response 4.

Any package that does molecular dynamics with an MM2-derived force field
should include interactions of bond dipoles.  (HyperChem does; please
contact me for details.)  I don't know of any that explicitly include
effects of molecular dipoles, but I'm not sure if that's what you were
asking about.

Joel

 ------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked]

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
WWW: http://www.hyper.com/

Response 5

Orient 3.2 by Anthony Stone of Cambridge University calculates all sorts of
things using electrostatic expansions i.e., charges, dipoles, quadrupoles
etc.  The new version has basic molecular dynamics in it.  If you want a
copy you'll have to Email him directly on [email-masked] and explain who
you are and why you want to use it.

Darren Andrews.

University of Manchester,
Department of Chemistry,
Oxford road,
Manchester.
M13 9PL.

[email-masked]
PGP: 512/A971A9

Tel: 0161 275  4699.
Fax: 0161 275 4598.

>From [email-masked] Sat Feb 24 18:44 EST 1996
From: <[email-masked]>
Subject: Summary of [W(CO)3(Cp)Cl]
To: [email-masked]
Date: Sun, 25 Feb 1996 00:44:37 +0100 (MET)
Cc: [email-masked]
Content-Length: 1672
Status: RO

I posted last year:

*************************************************************************

Dear CCL users,

A friend of mine who hasn't got a proper access to internet is seeking
information about [W(CO)3(Cp)Cl] (Cp= Cyclopentadienyl).
(I hope I got that right)

He'd like to know something about the use of that substance,
spectroscopic data or anything else.

As I am NOT subscribed to the CCL, please send a copy of
your answer to me, that is:

 [email-masked]

Thank you very much in advance

***************************************************************************

These are the responses that I got from CCL-users:

1. [email-masked]: (Timothy K. Firman)

        for info, see:
        C.Bueno,M.R.Churchill
        Inorg.Chem., 20, 2197,1981

        Which contains a crystal structure.

2. [email-masked] (Dr. John Lohrenz):

        Try the library!

3. [email-masked]:

        J. Lee, M.G. Humphrey, D.C.R. Hockless, B.W. Skelton, and A.H. White
         "Mixed Metal Cluster Chemistry.  Site-Selective Reactions of
         CpWIr3(CO)11 with PPh3 and Bidentate Phosphines;
        X-ray Crystal Structures of
        CpWIr3(m-dppe)(m-CO)3(CO)6, CpWIr3(m-dppm)(m-CO)3(CO)6 and
        CpWIr3(m-dppa)(m-CO)3(CO)6."
        Organometallics, 12 (9), 3468-3473 (1993).

Some literature my friend found during his lab:
        Hoffmann, N.W., Inorganic Chimica Acta, 88 (1984) 59-61
        Piper, T.S., Wilkinson G., J. Inorg. Nucl. Chem., 3 (1956) 104
        Coffey C. E., Inorg. Nucl. Chem., 3 (1956) 104
        here you use W(CO)3(Cp)Cl as an educt.

Thank you very much for your valuable hints.