Subject: Summary: cavity sizes in crowns

From: "Dmitry E. Dmitriev" <[email-masked]>
Date: Mon, 20 Feb 95 19:19:31 +0300

Dear Netters:
  
   Several days ago, I posted a question on calculating cavity sizes
 in crown ethers.
 Many thanks to all responders.
   Special thanks to Patrick Bultinck for his kindly answer with many 
references.
   Dmitry

 Original message was:
----------------------------------------------------------
Dear Netters!

 I'm looking for references to algorithms or programs which are used to 
calculate cavity sizes in crown ethers. Also, I would like to know about 
molecular modelling packages, which can be estimate this parameter. 

Thanks in advance.
Dmitry

============================================================================
 Dmitry E. Dmitriev,                 ** E-mail:  [email-masked]
 NMR Centre     Moscow               **          *****************
 N.D. Zelinsky Inst. of Org. Chem.,  ** tel   :  7 (095) 135 90 94
 Russian Academy of Sciences         ** fax   :  7 (095) 135 53 28    
============================================================================
****************************************************************************
James Crabbe  <[email-masked]> wrote:

DeskTop Molecular Modeller is a modeling program for PCs that calculates 
distances, volumes and areas.  It should be appropriate for what you 
describe.  It is available from Oxford University Press for about 250 
pounds stirling.  Contact Mrs. Janet Caldwell, Oxford Electronic 
Publishing, Oxford University Press, Walton Street, Oxford OX2 6DP for 
details.  Telephone : +44 865 56767.

James Crabbe.
****************************************************************************

David White  <[email-masked]> wrote:

Have you considered using solid angles?  (White, D; Taverner, B.C.; Leach,
P.G.L.; Coville, N.J.  J. Comput. Chem. 14 (1993) 1042).  If so, I
have a program which can be used to calculate solid angles and from 
those data you can deduce the cavity size.

I think R D Hancock has done some work in this area.  You may want to do
and author search on him.

David White 
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Patrick Bultinck  <[email-masked]> wrote:

About all quantum chemical packages will do, off course you will first
have to work in into the field of Quantum Chemistry of Macrocyclic Chemistry.
These are some references to articles in which programs of all sort were
used to do the calculations. May I ask to PLEASE send a summary of ALL
answers you received since I've been working in QCMC bussiness for 1.5
years now, and will be for about 3 years to come !

Attatched to this letter you will find the following : a list of
references arranged as follows :

Number in my DBase, "Abbreviation in my DB", "Authors",
"Title", "Journal", "Volume and year", "Issue (*=3Dnot relevant)", "Class
(theory, calculation, or experiment)", "Specific (e.g. ab initio, MMx)",
"Keywords (e.g. name of compound)".

25,"ADA92","K.R. Adam    L.F. Lindoy","Computer modelling of 
Metal-Containing Macrocyclic Ligand Systems-the Present and the Future",
"BOOK : Crown Compounds toward future applications","1992",
"ISBN 1-56081-024-6   (anorg. 2336 en 2321)","69-79","Theory","ab initio
semi-empirical","crown-complex"

54,"HAY93","B.P. Hay","Methods for molecular mechanics modeling of
coordination compounds","COORDINATION CHEMISTRY REVIEW","1993 (126)","*",
"177-236","Theory","Molecular mechanics","bidentate-complex
crown-complex"

56,"HAN90","R.D. Hancock","Molecular mechanics calculations and Metal Ion
 recognition","ACCOUNTS OF CHEMICAL RESEARCH","1990 (23)","*","253-257",
"Calculation","Molecular mechanics","crown-complex"

57,"REN93","R. Rencsok    T.A. Kaplan    J.F. Harrison","Electronic
structure of Li(9-crown-3)2 : A molecule with a Rydberg-type ground state",
"JOURNAL OF CHEMICAL PHYSICS","1993 (98)","12","9758-9764",
"Calculation","ab initio","crown-complex"

58,"WAR69","L.G. Warner      D.H. Busch","The stereoisomers of a Macrocyclic
 Nickel (II) Complex containing six asymmetric centers. Factors determining
 the stabilities of configurations and conformations","JOURNAL OF THE 
AMERICAL CHEMICAL SOCIETY","1969 (91)","15","4092-4101","Calculation",
"molecular mechanics","crown-complex"

65,"ROD78","L.J. Rodriguez    G.W. Liesegang   M.M Farrow    N. Purdie 
   E.M. Eyring","Kinetic studies of complexation of divalent Strontium,
 Barium, Lead and mercury cations by aqueous 15-crown-5 and 18-crown-6",
"JOURNAL OF PHYSICAL CHEMISTRY","1978 (82)","6","647-650","Experiment",
"kinetics","crown-complex"

66,"LAM80","J.D. Lamb   R.M. Tzatt   C.S. Swain   J.J. Christensen",
"A systematic study of the effect of macrocycle ring size and donor atom
 type on the log K, DH, and TDS of reactions at 25=A1C in methanol of
 mono- and divalent cations with crown ethers","JOURNAL OF THE AMERICAN
 CHEMICAL SOCIETY","1980 (102)","2","475-479","Experiment","thermodynamics",
"crown-complex"

67,"HAN85","S.V. Hannongbua    B.M Rode","Quantum-chemical investigations
 on the interaction of alkaline-Earth-Metal ions with Macrocyclic 
Compounds","INORGANIC CHEMISTRY","1985 (24)","*","2577-2580","Calculation",
"ab initio","crown-complex"

276,"THO94","M.A. Thompson     E.D. Glendening    D. Feller","The nature of
K+/crown ether interactions: a hybrid quantum chemical mechanical-molecular
 mechanical study.","JOURNAL OF PHYSICAL CHEMISTRY","98 (1994)","*",
"10465-10476","Calculation","ab initio      molecular mechanics",
"crown-complex"

280,"GLE94","E.D. Glendening     D. Feller        M.A. Thompson",
"An ab initio investigation of the structure and alkali metal cation
 selectivity of 18-crown-6","JOURNAL OF THE AMERICAN CHEMICAL SOCIETY",
"116 (1994)","*","10657-10669","Calculation","ab initio","crown 
  crown-complex"

285,"HAM88","T.W. Hambley","Steric contributions to the thermodynamics of 
electron transfer in Cobalt(III) Haxammine complexes","INORGNANIC CHEMISTRY"
"27 (1988)","*","2496-2501","Calculation","Molecular Mechanics",
"ethylenediamine-complex    1,3-propanediamine-complex    crown-complex"

288,"THO84","V.J. Th=9Am     J.C.A. Boeyens     G.J. McDougall    
R.D. Hancock","Origin of the high ligand fiels strength and macrocyclic
 enthalpy of nitrogen-donor macrocycles.","JOURNAL OF THE AMERICAN CHEMICAL
 SOCIETY","106 (1984)","*","3198-3207","Calculation","Molecular Mechanics",
"crown-complex"

289,"SEI91","E.T. Seidl     H.F. Schaefer III","A new configuration of 
12-crown-4","JOURNAL OF PHYSICAL CHEMISTRY","95 (1991)","*","3589-3590",
"Calculation","Ab initio","12-crown-4    crown"

I forgot a reference, and even one of the most interesting for you !

L.P. Trigub, S.V. Krutius and Y.A. Kruglyak, "A package of programs for 
theoretical conformational analysis of macrocyclic molecules", Journal of 
Structural Chemistry, Vol. ? (1984), page 642

The authors are Russian, or at least from somewhere in the former USSR !

I think I could come up with their address...

Patrick

|-----------------------------------------------------------------------|
|     C-C                       Patrick Bultinck                        |
|    /   \                      Dept. Inorganic & Physical Chemistry    |
| C-O     O-C                   Section Quantum Chemistry               |
| |         |                   University of Ghent                     |
| C-O     O-C                   Krijgslaan 281 (S-3)                    |
|    \   /                      9000 Gent                               |
|     C-C                       Belgium                                 |
|                               Tel. Int'l code/32/9/264.44.44          |
| Macrocycles                   Fax. Int'l code/32/9/264.49.83          |
| Quantum Chemical              E-mail : [email-masked]     |
| Calculations                                                          |     
|-----------------------------------------------------------------------|

============================================================================
 Dmitry E. Dmitriev,                 ** E-mail:  [email-masked]
 NMR Centre     Moscow               **          *****************
 N.D. Zelinsky Inst. of Org. Chem.,  ** tel   :  7 (095) 135 90 94
 Russian Academy of Sciences         ** fax   :  7 (095) 135 53 28    
============================================================================