Subject: Summary: H-bonds

From: JING KONG <[email-masked]>
Date: Mon, 14 Mar 1994 12:30:13 -0400

Dear netters,

	Here is the summary of the responses I got for my query about the 
bond lengths and directionalities of h-bonds. Personally, I found Konrad
Koehler's list is helpful. For ab initio studies, Dr. Scheiner has some good
reviews.  But I have not checked through all the references yet.

	Here is my new question: how to access to Cambridge Crystallographic
Data Base and Brookhaven Data Base?

	Thank you all who responsed!

Jing
Dalhousie

------Cut here-------------------

From:	IN%"[email-masked]"  "MA NGAI LING IDA" 10-MAR-1994 23:11:50.82
To:	IN%"[email-masked]"
CC:	
Subj:	RE: CCL:H-bonds

Check out papers by Janet Del Bene.  I think she has done quite
a few H-bond compounds.

Ida


From:	IN%"[email-masked]"  "Dave Winkler" 11-MAR-1994 00:35:53.54
To:	IN%"[email-masked]"  "JING KONG"
CC:	
Subj:	RE: CCL:H-bonds

The best way is to search the Cambridge Crystallographic database (>100,000 
compounds) for all hydrogen-bonded structures.

Cheers,

Dave
__________________________________________________________________________

   Dr. David A. Winkler                        Voice: 61-3-542-2244      
   Principal Research Scientist                Fax:   61-3-543-8160      
   CSIRO Division of Chemicals and Polymers
   Private Bag 10       
   Clayton, Australia.

   "Life is what happens to you while you're making other plans"


From:	IN%"[email-masked]"  "Frank Jensen" 11-MAR-1994 02:56:35.38
To:	IN%"[email-masked]"
CC:	
Subj:	h-bond

	Check one of the very recent issues of JACS (marts 1994).
There is an analysis of H-bonds, I can't remember the authors
names.
	Frank

From:	IN%"[email-masked]" 11-MAR-1994 03:25:07.58
To:	IN%"[email-masked]"
CC:	
Subj:	RE: CCL:H-bonds

Take a look at the book:
Hydrogen bonding in biological structures,
by G. Jeffrey and W. Saenger (1991 or 1992)
(Springer-Verlag I think)

Tom Simonson


From:	IN%"[email-masked]" 11-MAR-1994 04:58:16.63

try

The geometry of the N-H...O=C H-bond,part 3, H-bond distances and angles
R. Taylor, O. Kennard, W. Versichell
Acta Cryst. (1984) B40 280-288

This is a good reference as it looked at many structures from the cambridge
crystal database.

Keith Trollope.

From:	IN%"[email-masked]" 11-MAR-1994 06:38:54.22

In the first vol. of Reviews in Computational Chemistry is a artical on H-bonds
derived from CSD x-ray structural database.

I hadn`t the reference but the editors anonnce the vol.4 briefly on this list.
The publischer was Springer and they editors Bloyd and Lipkowitz. (If i spell
the name incorrect, sorry.

I hope it helps

Joerg R.P. Heuer

Inst. fuer Pharmazie    
[email-masked]


From:	IN%"[email-masked]"  "Konrad, IRBM Chemistry, +39-6-91093606" 11-MAR-1994 07:59:28.77

    Here are some references mainly dealing with geometries and energetics of
protein-water and protein-ligand hydrogen bonding interactions.  I hope you 
find them useful.

(1) Boobbyer, D. N.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. New
    hydrogen-bond potentials for use in determining energetically favorable
    binding sites on molecules of known structure.  J. Med. Chem.   1989, 32,
    1083-94. 
(2) Ippolito, J. A.; Alexander, R. S.; Christianson, D. W. Hydrogen bond
    stereochemistry in protein structure and function.  J. Mol. Biol.   1990,
    215, 457-71. 
(3) Murray-Rust, P.; Glusker, J. P. Directional hydrogen bonding to sp2 and
    sp3-hybridized oxygen atoms and its relevance to ligand-macromolecular
    interactions.  J. Am. Chem. Soc.   1984, 106, 1018-1025.
(4) Thanki, N.; Thornton, J. M.; Goodfellow, J. M. Distributions of water around
    amino acid residues in proteins.  J. Mol. Biol.   1988, 202, 637-57.
(5) Tintelnot, M.; Andrews, P. Geometries of functional group interactions in
    enzyme-ligand complexes:  guides for receptor modelling.  J.
    Comput.-Aided Molec. Des.   1989, 3, 67-84. 
(6) Vedani, A.; Dunitz, J. D. Lone-pair directionality in H-bond potential    
    functions for molecular mechanics calculations.  J. Am. Chem. Soc.   1985,
    107,7653-7658. 
(7) Vedani, A.; Hutha, D. W. An algorithm for the systematic solvation of
    proteins based on the directionality of hydrogen bonds.  J. Am. Chem. Soc.
    1990, 112, 4759-4767.
(8) Vedani, A.; Huhta, D. W. A new force field for modeling metalloproteins.  J.
    Am. Chem. Soc.   1991, 113, 5860-5862.

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From:	IN%"[email-masked]" 11-MAR-1994 09:38:41.74
I did an extensive analysis of hydrogen bonds in crystal structures and
observed in MD simulations of liquid methanol. Relevant publications are:

* P.F.W. Stouten & J. Kroon, "Hydrogen Bonds in Concreto and in Computro,"
  J. Mol. Struct. 177 (1988) 467-475.
* P.F.W. Stouten, B.P. van Eijck & J. Kroon, "Hydrogen Bonds in Concreto
  and in Computro: The Sequel," J. Mol. Struct. 243 (1991) 61-87.

Please give me your physical address if you want reprints.

Cheers, Pieter.

Pieter Stouten, Senior Research Scientist    ||
Computer Aided Drug Design Group             ||
The Du Pont Merck Pharmaceutical Company     ||    Adventures get spoiled
P.O. Box 80353, Wilmington, DE 19880-0353    ||   by being reduced to data
Phone: +1 (302) 695 3515                     ||             --
ARA/Fax: +1 (302) 695 4324                   ||        Poul Anderson
E-mail: [email-masked]      ||
Internet Shogi Server: kzinti                ||


From:	IN%"[email-masked]"  "Mr Andrew D Allen" 11-MAR-1994 10:41:44.21

Try looking through th brookhaven database, for protein structures which have 
explicitly noted hydrogen bonds.

The ftp site is pdb.pdb.bnl.gov.

Andy.

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From:	IN%"[email-masked]" 11-MAR-1994 11:53:29.31

Publications discussing/listing H-bond-lengths and directions (among others):
(1) Jeffrey, G.A.; Saenger, W.  Hydrogen Bonding in Biological Structures,
    Springer, Berlin Heidelberg, 1991.

(2) Murray-Rust, P.; Glusker, J.P.  Directional Hydrogen Bonding to sp2- and
    sp3-Hybridized Oxygen Atoms and Its Relevance to Ligand-Macromolecule
    Interactions,  JACS 106 (1984), 1018-1025.

(3) Chakrabarti, P.  Anion binding sites in protein structures,
    J. Mol. Biol. 234 (1993), 463-482.

(4) Steiner, T.; Saenger, W.  Geometry of the Carbon-Hydrogen....Oxygen Hydrogen
    Bonds in Carbohydrate Crystal Structures. Analysis of Neutron Diffraction Data.
    JACS 114 (1992), 10146-10154.

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 Marc C. Nicklaus                        Lab. of Medicinal Chemistry
 e-mail: [email-masked]               National Cancer Institute, NIH
 Phone:  (301) 402-3111                  Bldg 37, Rm 5B29
 Fax:    (301) 496-5839                  Bethesda, MD 20892
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From:	IN%"[email-masked]" 11-MAR-1994 13:43:24.74
To:	IN%"[email-masked]"
CC:	
Subj:	H-bond

Hi, Jing,

  For theoretical work, please check J. Comput. Chem. 1992, 13, 1151-1169.
For experimental data, please check the references cited in this paper.

       Yajun Zheng

From:	IN%"[email-masked]"  "Uwe Claus Kreis" 11-MAR-1994 15:39:22.01

A search of (HYDROGEN + BOND + STRUCTURE) gave 84 hits in UnCover.
You might want to check out the following:

----------------------------------------------------UnCover--------------------
AUTHOR(s):       Gilli, Paola.  
                 Bertolasi, Valerio.  
                 Ferretti, Valeria.  
TITLE(s):        Covalent Nature of the Strong Homonuclear Hydrogen Bond.
                   Study of the O--H--O System by Crystal Structure
                   Correlation Methods.                                       

           In:   Journal of the american chemical society.  
                 FEB 09 1994 v 116 n 3  
         Page:   909  
----------------------------------------------------UnCover--------------------
AUTHOR(s):       Wade, Rebecca C.  
                 Clark, Kevin J.  
                 Goodford, Peter J.  
TITLE(s):        Further Development of Hydrogen Bond Functions for Use in
                   Determining Energetically Favorable Binding Sites on
                   Molecules of Known Structure. 1. Ligand Probe Groups with
                   the Ability To Form Two Hydrogen Bonds.                    

           In:   Journal of medicinal chemistry.  
                 JAN 08 1993 v 36 n 1  
         Page:   140  
TITLE(s):        Further Development of Hydrogen Bond Functions for Use in
                   Determining Energetically Favorable Binding Sites on
                   Molecules of Known Structure. 2. Ligand Probe Groups with
                   the Ability To Form More Than Two Hydrogen Bonds.          

           In:   Journal of medicinal chemistry.  
                 JAN 08 1993 v 36 n 1  
         Page:   148  
----------------------------------------------------UnCover--------------------
AUTHOR(s):       Mortimer, M.  
                 Moore, E.A.  
                 Healy, A.  
TITLE(s):        A comparison of ab initio, NMR and diffraction results for
                   a strong OHF hydrogen bond.                                

           In:   Journal of molecular structure.  
                 AUG 15 1992 v 271 n 1 / 2  
         Page:   149  
----------------------------------------------------UnCover--------------------
AUTHOR(s):       Plass, M.  
                 Kolbe, A.  
TITLE(s):        Conformational influence on hydrogen bond.  

           In:   Journal of molecular structure.  
                 MAR 01 1992 v 267  
         Page:   21  
----------------------------------------------------UnCover--------------------
AUTHOR(s):       Legon, A. C.  
                 Millen, D. J.  
TITLE(s):        The nature of the hydrogen bond to water in the gas phase. 

           In:   Chemical society reviews.  
                 MAR 01 1992 v 21 n 1  
         Page:   71-78  
----------------------------------------------------UnCover--------------------
AUTHOR(s):       Feil, D.  
TITLE(s):        The electron density distribution in the hydrogen bond. A
                   quantum chemical and crystallographic study.               

           In:   Journal of molecular structure.  
                 SEP 15 1990 v 237  
         Page:   33  

-----
A. Vedani compiled a lot of structural information about H-bonds.
I'm not sure where and whether he published that, but check:
A. Vedani, D.W. Huhta, S.P. Jacober, JACS 111 (1989) 4075.

-----
Hope this helps.
Cheers,
        Uwe

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From:	IN%"[email-masked]" 11-MAR-1994 19:39:30.59

i saw your query about h-bonds over the theoretical chem bulletin board. 
there are probably numerous reviews of h-bonds around.  i know of one that
i myself wrote not too long ago.
S. Scheiner,
	"Ab Initio Studies of Hydrogen Bonding" in Theoretical Models of Chemical
Bonding, Ed. Z. B. Maksic, Springer-Verlag, Berlin, Part 4, 1991, pp.
171-227.
While not encyclopedic, it does cover a fairly wide range of different
H-bonds, at least as far as ab initio calculations go.
  another review is;
S. Scheiner, 	"Calculating the Properties of Hydrogen Bonds by Ab Initio
Methods" in Reviews in Computational Chemistry, Eds. D. Boyd and K.
Lipkowitz, VCH Publishers, New York, 1991, pp. 165-218.
this one is less encyclopedic but talks more about how to do such
calculations and what one might expect from the results.
  if you have trouble finding these in your library, i would be happy to
mail you a copy.
-----
Steve Scheiner, Professor
[email-masked]
Dept. of Chemistry & Biochemistry
MailCode 4409
Southern Illinois University 
Carbondale, IL 62901-4409 
ph: 618/453-6476  fax: 618/453-6408


From:	IN%"[email-masked]"  "MARTIN%CMDA" 12-MAR-1994 12:36:22.49

We summarized a lot in a paper we wrote using such information.

However, there are some nice reviews by the folks from Cambridge Structural
Database & from protein crystallographers.  Let me see if I can get
the references now...

Murray-Rust, P. Glusker, J. P. J. Am. Chem. Soc. 106 (1984) 
1018.

Taylor, R., Kennard, O. Acc. Chem. Res. 17 (1984) 320.

Boobbyer, D. N. A., Goodford, P. J., McWhinnie, P. M., Wade,  
R. C.  J. Med. Chem., 32 (1989) 1083.

Vedani, A., Dunitz, J. D. J. Am. Chem. Soc. 107 (1985) 7653.

Jeffrey, G. A., Saenger, W. Hydrogen Bonding in Biological 
Structures. Springer-Verlag, Berlin 1991

Let me know if you find better ones.

Yvonne Martin