Subject: Summary:H-bonds

From: Patrick Bultinck <[email-masked]>
Date: Fri, 19 Aug 1994 10:30:48 +0200 (MET DST)

Here is the summary of the answers I got to my question on H-bond 
strenghts. It seems to me that the practice of determining H-bond 
energetics will still remain on the arbitrary side, for a while...

Thanks to everybody who shared an opinion, experience, references etc. !!

************************MY ORIGINAL MESSAGE*********************************** 

Netters,

Do any of you know of some theoretical definition or ab initio study of 
intramolecular hydrogen bonding. (the "intra" is important)
I have looked up books like "The hydrogen bond" (Pimentel and McClellan),
"Valence" (Coulson) and some recent books on quantum chemistry. The trouble 
is that I do not know of any definition that would allow me to calculate 
the strenghts of intramolecular H-bonds without having to make somewhat 
arbitrary comparisons to other conformers or molecules etc. (I'm working 
on disubstituted ethanes for which there are experimental values for the 
H-bonding strength...)

Thank you very much, and if enough interest exists a summary of answers 
will be posted !!

Patrick

*******************************THE ANSWERS********************************

>Do any of you know of some theoretical definition or ab initio study of
>intramolecular hydrogen bonding. (the "intra" is important)

        I have seen two recent ab initio studies in JACS (1994) that should
be of interest:  Cramer-Truhlar, page 3892 (glycol) and Hagler et al, page
3904 (inositols).

        Per-Ola Norrby

 *  *****   Notice!  New Email address *****
 *
 *  Per-Ola Norrby
 *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
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Dear Patrick, 
Definition of hydrogen bond energy in case of intramolecular hydrogen 
bond is not so clear like in for intermolecular complex. However, you 
can calculate it as the difference in energy between the closed 
conformation (with H-bond) and the so-called "open" conformation in 
which e.g.A-X-H is rotated (to prevent hydrogen bond formation). 
I can recommend a few useful references: 
1) M.J.Frisch, H.F.Scheiner, H.F.Schaefer III, J.Chem.Phys., 
   82 (1985) 4194 
2) Z.Latajka, S.Scheiner, J.Phys.Chem., 96 (1992) 9764 
3) M.A.Rios, J.Rodriguez, J.Comput.Chem., 13 (1992) 860. 
Hope this helps. 

Zdzislaw Latajka 

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

 Professor Zdzislaw Latajka 

 Address valid untill August 31, 1994:

 Laboratoire de Chimie Theorique 
 Universite de Nancy I 
 B.P.239, 54506 Vandoeuvre-les-Nancy Cedex, France 
 e-mail: [email-masked] 

 Address  from September 1, 1994:

 Institute of Chemistry 
 University of Wroclaw 
 F.Joliot-Curie 14 
 50-383 Wroclaw, Poland 
 e-mail: [email-masked] 

	Hi Patrick, we are working w. a couple of diasteroisomers that presents 
two conformational configuration. In 3 of 4 possible conformations, we've 
observed a strong interaction between OH. 

	In fact, we've not found any sistematic way of caracterizing 
intramolecular H-bund, so we've just adopted the concepts invloved in 
the definition of intermolecular H-bound, e.g., H---O distance and H---O-X 
angle.

	If you other msgs, please sumarizy them for me.

	Regards, Marcelo

&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
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Instituto de Quimica - UNICAMP  &
C.P. 6154 CEP: 13081-970        &
Campinas, S.P. , Brazil         &
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Steve Scheiner wrote an excellent introduction and review about the topic of
computing the properties of hydrogen bonds.  His examples are primarily
inter-molecular, however.  Still there are loads of references.  See Reviews in
Computational Chemistry, Volume 2, chapter 5, 1991.
_______________________________________________________________________________

Hydrogen bonding is defined based on bond angle, and bond length from x-ray
studies. You could compute the energy minimum from several structures, and 
take a mean to use an "energy comparison".

There were some advanced studies on H-bonding, using Morokuma's energy 
partioning scheme. These are not practical though for what you want to do.
They only tell what percentage is electrostaic, and polarizable.

Hope it helps.

Ray
[email-masked]

 Subject:  intramol H-bonding
saw your request for info about intramolecular H-bonding on the CCL net.  i
wrote a review article recently that had a section dealing with such bonds.
 although the review focused on proton transfers, you will find some
relevant data on the nature of the H-bonds, along with the original
references.  the review article  was published in Advances in Biophysical
Chemistry, 1993, JAI Press, pp 119-159.
-----
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

Subject:      Locating Hydrogen-Bonds

Probably the only method which will locate H-bonds for you in a syste-
matic manner in *any* molecular environment is the bond-critical-point
analysis from Bader's "Theory of Atoms in Molecules".

Two papers were published on this subject, both in the journal,
'Molecular Physics', 1988.  Authors M. T. Carroll and R. F. W. Bader.

The examples shown were all of "intERmolecular" H-bonds (in weakly
bound systems) but there is no reason why the approach cannot be taken
for intra-molecular 'bonds'.  All you would need is an 'ab initio' ".wfn"
file (punched from Gaussian/Cadpac) and Bader's programs.

There may well already be examples of intramolecular H-bonds found
this way, in the literature, so it's probably worth a search.

Richard Bone

__________________________________________________________
 
 Richard G. A. Bone, PhD.
 Computational Chemist
 Terrapin Technologies, Inc.
 South San Francisco
 USA
 
 E-mail  [email-masked]

The book, "Modeling the Hydrogen Bond" based on the ACS Symposium  of the
same name at Chicago several meetings ago. I edited the book, and it contains
many chapters on ab initio, DFT, semiempirical and other techniques applied
to modeling hydrogen bonding in various systems including small molecules,
biomolecules, polymers and more.

The book is due out in several weeks. Contact ACS Books for more information.

Doug

Douglas A. Smith			voice:  (419)537-2116
Associate Professor			fax:    (419)537-4033
Department of Chemistry			email:  [email-masked]
 and 
Center for Drug Design and Development
The University of Toledo
Toledo, OH  43606-3390

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+-------------------------------------------------------------------+

Subject:      Intramolecular H-bonds: more refs

Further to the message I posted last week:

3 papers which address specifically the location and analysis of
intramolecular interactions involving Hydrogen:

J. Cioslowski, S. T. Mixon and W. D. Edwards, 
   J. Am. Chem. Soc., 113, 1083, (1991)

J. Cioslowski and S. T. Mixon,  ibid, 114,  (1992)

J. Cioslowski and S. T. Mixon,  Can. J. Chem., 70, 443,  (1992)

All employ Bader's Theory of Atoms in Molecules

Richard Bone

__________________________________________________________
 
 Richard G. A. Bone, PhD.
 Computational Chemist
 Terrapin Technologies, Inc.
 South San Francisco
 USA
 
 E-mail  [email-masked]

***************************RELEVANT MESSAGE**********************************

BOOK ANNOUNCEMENT - available in 6-8 weeks

ACS Symposium Series 569

MODELING THE HYDROGEN BOND

Douglas A. Smith, Editor
ISBN 0-8412-2981-3

This book was developed from a symposium sponsored by the Division of 
Computers in Chemistry at the 206th National Meeting of the American
Chemical Society, Chicago, IL (USA), August 22-27, 1993.

Stop by the ACS Books booth at the Washington ACS meeting to find out 
more information or to order. Approximate price $80.

TABLE OF CONTENTS

1.  A BRIEF HISTORY OF THE HYDROGEN BOND
	Douglas A. Smith

Solvent and Molecular Electrostatic Potential Effects

2.  COMPUTATION OF INTERMOLECULAR INTERACTIONS WITH A COMBINDED QUANTUM 
    MECHANICAL AND CLASSICAL APPROACH
	Jiali Gao

3.  INCLUSION OF EXPLICIT SOLVENT MOLECULES IN A SELF-CONSISTENT-REACTION 
    FIELD MODEL OF SOLVATION
	T. A. Keith and M. J. Frisch

4.  EFFECT OF HYDROGEN BONDING ON MOLECULAR ELECTROSTATIC POTENTIAL
	M. Dominic Ryan

5.  COMPETING INTRA- AND INTERMOLECULAR HYDROGEN BONDS FOR ORGANIC SOLUTES IN 
    AQUEOUS SOLUTION
	Peter I. Nagy, Graham J. Durant, Douglas A. Smith

Theoretical Methods and Graphical Analysis

6.  ENERGETICS AND STRUCTURE IN MODEL NEUTRAL, ANIONIC, AND CATIONIC HYDROGEN-
    BONDED COMPLEXES: COMBINED AB INITIO SCF/MP2 SUPERMOLECUALR, DENSITY
    FUNCTIONAL, AND MOLECULAR MECHANICS INVESTIGATION
	Nohad Gresh, Martin Leboeuf, Dennis Salahub

7.  SAM1: GENERAL DESCRIPTION AND PERFORMANCE EVALUATION FOR HYDROGEN
    BONDS
	Andrew J. Holder and Earl M. Evleth

8.  SEARCH FOR ANALYTICAL FUNCTIONS TO SIMULATE PROTON TRANSFERS IN
    HYDROGEN BONDS
	Steve Scheiner and Xiaofeng Duan

9.  EFFECTIVE FRAGMENT METHOD FOR MODEING INTERMOLECULAR HYDROGEN-BONDING 
    EFFECTS ON QUANTUM MECHANICAL CALCULATIONS
	Jan H. Jensen, Paul N. Day, Mark S. Gordon, Harold Basch, Drora Cohen,
	DAvid R. Barmer, Morris Kraus, and Walter J. Stevens

10. MODELING THE HYDROGEN BOND WITH TRANSFERABLE ATOM EQUIVALENTS
	Curt M. Breneman, Marlon Rhem, Tracy R. Thompson and Mei Hsu Dung

11. ANALYSIS OF HYDROGEN BONDING AND STABILITY OF PROTEIN SECONDARY STRUCTURES 
    IN MOLECULAR DYNAMICS SIMULATION
	S. Vijayakumar, S. Vishveshwara, G. Ravishanker, and D. L. Beveridge

12. UNUSUAL CROSS-STRAND HYDROGEN BONDS IN OLIGOPURINE-OLIGOPYRIMIDINE 
    DUPLEXES: COMPUTER GRAPHICS PRESENTATIONS OF HYDROGEN BONDS IN DNA 
    MOLECULAR DYNAMICS
	Masayuki Shibata and Theresa Julia Zielinski

13. STRIPS: AN ALGORITHM FOR GENERATING TWO-DIMENSIONAL HYDROGE-BOND TOPOLOGY
    DIAGRAMS FOR PROTEINS
	G. Ravishanker, S. Vijayakumar, and D. L. Beveridge

Applications to Molecules and Polymers

14. ROLE OF SPECIFIC INTERMOLECULAR INTERACTIONS IN MODULATING SPECTROSCOPIC
    PROPERTIES OF PHOTOREACTIVE COMPOUNDS BOUND TO PROTEINS
	Marshall G. Cory, Jr., Nigel G. J. Richarsds, and Micheal C. Zerner

15. COMPARISONS OF HYDROGEN BONDING IN SMALL CARBOHYDRATE MOLECULES BY
    DIFFRACTION AND MM3(92) CALCULATIONS
	A. D. French and D. P. Miller

16. ROLE OF NONBONDED INTERACTIONS IN DETERMINING SOLUTION CONFORMATIONS
    OF OLIGOSACCHARIDES
	Robert J. Woods, Bert Fraser-Reid, Raymond A. Dwek, and Christopher
	J. Edge

17. MODELING HYDROGEN BOND ENERGIES IN PSEUDOLADDER POLYMERS BASED ON THE 
    POLYBENZOBISAZOLE BACKBONE
	S. Trohalaki, A. T. Yeates, and D. S. Dudis

18. BOROHYDRIDES AS NOVEL HYDROGEN-BOND ACCEPTORS
	M. A. Zottola, L. G. Pederson, P. Singh, and B. Ramsay-Shaw

***************************THAT'S ALL FOLKS********************************