Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Matthew Merski]

We should also be aware that there is a formal IUPAC definition of hydrogen
bonds as well, although its not really optimized for protein
crystallography.

https://www.iupac.org/publications/pac/pdf/2011/pdf/8308x1637.pdf

Matthew Merski
Univ. of Warsaw

On Thu, Sep 20, 2018 at 5:28 PM Mark Wilson  wrote:

> Just to put a finer point on some of this, the Lennard-Jones (6-12)
> potential is short-range, containing an attractive component arising from
> London dispersion forces (quantum mechanical induced dipole-induced dipole
> interactions) that decay as 1/r^6 and a repulsive component arising from
> the Pauli exclusion principle that rises as 1/r^12.  The minimum of this
> potential for a given homoatomic interaction vs. interatomic distance
> corresponds to the van der Waals radius for that atom.  Also, while
> hydrogen bonds are predominantly electrostatic, it is worth noting that
> there are some unresolved issues with the exact physical nature of these
> interactions, particularly at short donor-acceptor distances.
> Best regards,
> Mark
>
> Mark A. Wilson
> Associate Professor
> Department of Biochemistry/Redox Biology Center
> University of Nebraska
> N118 Beadle Center
> 1901 Vine Street
> Lincoln, NE 68588
> (402) 472-3626
> mwilso...@unl.edu
>
>
>
>
>
> On 9/20/18, 10:13 AM, "CCP4 bulletin board on behalf of Daniel M. Himmel,
> Ph. D." 
> wrote:
>
> >Hello again.  I just want to add that hydrogen bonds by convention are
> >usually
> >considered to be a type of electrostatic interaction (please see the
> >review by
> >E. N. Baker in the International Tables of Crystallography Volume F,
> >second edition,
> >p. 721) and are generally grouped with other "short range" electrostatic
> >interactions
> >along with dipole-dipole, dipole-ionic, and ionic-ionic interactions.
> >This is by
> >contrast to long term interactions that are approximated by the Lennard
> >Jones potential,
> >which includes van der Waals forces.  My understanding is that van der
> >Waals forces
> >result from weak overall attractions between the protons in the nucleus
> >of one atom
> >and the electron cloud of another atom and therefore increase as the
> >atomic number
> >of the atoms increase.
> >
> >
> >-Daniel
> >
> >
> >
> >
> >On Thu, Sep 20, 2018 at 10:04 AM Daniel M. Himmel, Ph. D.
> > wrote:
> >
> >
> >Stefano is correct that hydrophobic interactions are chiefly entropically
> >driven.  Thank you for your
> >input, Stefano.  I disagree with Matthew, however.  It is true that van
> >der Waals forces are always
> >present and therefore form a small contribution to even hydrogen bonds.
> >However, since the major contributions
> >to hydrogen bonds are various types of electronic components, it is proper
> >to group hydrogen bonds with electrostatic interactions.  When using
> >computational
> >software, one must look under the hood (or read the user manual) to see
> >how different
> >force components are being grouped for calculations.
> >
> >
> >I would say to Sheila that, when you write up your analysis, just be sure
> >to define how you are
> >using terms such as "electrostatic" or else specifically list the
> >individual types of interatomic
> >attractive forces that you are surveying  (which I know you prefer to
> >avoid).
> >
> >
> >If any computational chemists are following this discussion, perhaps you
> >can pipe in and
> >share your perspective and expertise.
> >
> >
> >-Daniel
> >
> >
> >
> >
> >On Wed, Sep 19, 2018 at 3:51 PM Sheila Boreiko
> > wrote:
> >
> >
> >Interesting discussion is coming out of this question. I thank all that
> >have provided input.
> >
> >
> >Let me go a bit further concerning Daniel's considerations. What
> >other dipole interaction might be distinctively ascribed by programs out
> >of hydrogen bonds (and of course, they use to describe salt bridges in
> >addition, as an ionic interaction)? Possibly
> > difficult for programs that use only atom positions, distances and
> >angles (excluding the question of pH dependence, let us suppose neutral
> >pH)?
> >
> >I might here be specific with program PISA, which lists Hydrogen
> >Bonds and Salt Bridges. They seem to use these bonds to estimate a Gibbs
> >energy for the formation of the interface.
> >
> >
> >Sheila
> >
> >
> >
> >
> >De: Danie

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Mark Wilson]

Just to put a finer point on some of this, the Lennard-Jones (6-12)
potential is short-range, containing an attractive component arising from
London dispersion forces (quantum mechanical induced dipole-induced dipole
interactions) that decay as 1/r^6 and a repulsive component arising from
the Pauli exclusion principle that rises as 1/r^12.  The minimum of this
potential for a given homoatomic interaction vs. interatomic distance
corresponds to the van der Waals radius for that atom.  Also, while
hydrogen bonds are predominantly electrostatic, it is worth noting that
there are some unresolved issues with the exact physical nature of these
interactions, particularly at short donor-acceptor distances.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu 





On 9/20/18, 10:13 AM, "CCP4 bulletin board on behalf of Daniel M. Himmel,
Ph. D."  wrote:

>Hello again.  I just want to add that hydrogen bonds by convention are
>usually
>considered to be a type of electrostatic interaction (please see the
>review by
>E. N. Baker in the International Tables of Crystallography Volume F,
>second edition, 
>p. 721) and are generally grouped with other "short range" electrostatic
>interactions
>along with dipole-dipole, dipole-ionic, and ionic-ionic interactions.
>This is by
>contrast to long term interactions that are approximated by the Lennard
>Jones potential, 
>which includes van der Waals forces.  My understanding is that van der
>Waals forces
>result from weak overall attractions between the protons in the nucleus
>of one atom
>and the electron cloud of another atom and therefore increase as the
>atomic number
>of the atoms increase.
>
>
>-Daniel
>
>
>
>
>On Thu, Sep 20, 2018 at 10:04 AM Daniel M. Himmel, Ph. D.
> wrote:
>
>
>Stefano is correct that hydrophobic interactions are chiefly entropically
>driven.  Thank you for your
>input, Stefano.  I disagree with Matthew, however.  It is true that van
>der Waals forces are always
>present and therefore form a small contribution to even hydrogen bonds.
>However, since the major contributions
>to hydrogen bonds are various types of electronic components, it is proper
>to group hydrogen bonds with electrostatic interactions.  When using
>computational
>software, one must look under the hood (or read the user manual) to see
>how different
>force components are being grouped for calculations.
>
>
>I would say to Sheila that, when you write up your analysis, just be sure
>to define how you are
>using terms such as "electrostatic" or else specifically list the
>individual types of interatomic
>attractive forces that you are surveying  (which I know you prefer to
>avoid).  
>
>
>If any computational chemists are following this discussion, perhaps you
>can pipe in and
>share your perspective and expertise.
>
>
>-Daniel
>
>
>
>
>On Wed, Sep 19, 2018 at 3:51 PM Sheila Boreiko
> wrote:
>
>
>Interesting discussion is coming out of this question. I thank all that
>have provided input.
>
>
>Let me go a bit further concerning Daniel's considerations. What
>other dipole interaction might be distinctively ascribed by programs out
>of hydrogen bonds (and of course, they use to describe salt bridges in
>addition, as an ionic interaction)? Possibly
> difficult for programs that use only atom positions, distances and
>angles (excluding the question of pH dependence, let us suppose neutral
>pH)?
>
>I might here be specific with program PISA, which lists Hydrogen
>Bonds and Salt Bridges. They seem to use these bonds to estimate a Gibbs
>energy for the formation of the interface.
>
>
>Sheila
>
>
>
>
>De: Daniel M. Himmel, Ph. D. 
>Enviado: terça-feira, 18 de setembro de 2018 15:10
>Para: sheila_bore...@hotmail.com
>Cc: CCP4BB@jiscmail.ac.uk
>Assunto: Re: [ccp4bb] collective term for hydrogen bonds and salt bridges
>
>Sorry.  I may have been unclear.  H-bonds are actually a subset of dipole
>interactions.
>
>
>On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D.
>
> wrote:
>
>
>By the way, distinguishing between dipole and ionic (salt bridge)
>interactions could
>be a slippery slope, because which one you have sometimes depends on the
>protonation 
>state of the protein(s), which is pH dependent.
>
>
>-Daniel
>
>
>
>
>On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D.
>
> wrote:
>
>
>
>
>
>
>Sheila,
>
>
>Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) i

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Daniel M. Himmel, Ph. D.]

Hello again.  I just want to add that hydrogen bonds by convention are
usually
considered to be a type of electrostatic interaction (please see the review
by
E. N. Baker in the International Tables of Crystallography Volume F, second
edition,
p. 721) and are generally grouped with other "short range" electrostatic
interactions
along with dipole-dipole, dipole-ionic, and ionic-ionic interactions.  This
is by
contrast to long term interactions that are approximated by the Lennard
Jones potential,
which includes van der Waals forces.  My understanding is that van der
Waals forces
result from weak overall attractions between the protons in the nucleus of
one atom
and the electron cloud of another atom and therefore increase as the atomic
number
of the atoms increase.

-Daniel


On Thu, Sep 20, 2018 at 10:04 AM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

> Stefano is correct that hydrophobic interactions are chiefly entropically
> driven.  Thank you for your
> input, Stefano.  I disagree with Matthew, however.  It is true that van
> der Waals forces are always
> present and therefore form a small contribution to even hydrogen bonds.
> However, since the major contributions
> to hydrogen bonds are various types of electronic components, it is proper
> to group hydrogen bonds with electrostatic interactions.  When using
> computational
> software, one must look under the hood (or read the user manual) to see
> how different
> force components are being grouped for calculations.
>
> I would say to Sheila that, when you write up your analysis, just be sure
> to define how you are
> using terms such as "electrostatic" or else specifically list the
> individual types of interatomic
> attractive forces that you are surveying  (which I know you prefer to
> avoid).
>
> If any computational chemists are following this discussion, perhaps you
> can pipe in and
> share your perspective and expertise.
>
> -Daniel
>
>
> On Wed, Sep 19, 2018 at 3:51 PM Sheila Boreiko 
> wrote:
>
>> Interesting discussion is coming out of this question. I thank all that
>> have provided input.
>>
>>
>> Let me go a bit further concerning Daniel's considerations. What
>> other dipole interaction might be distinctively ascribed by programs out of
>> hydrogen bonds (and of course, they use to describe salt bridges in
>> addition, as an ionic interaction)? Possibly difficult for programs that
>> use only atom positions, distances and angles (excluding the question of pH
>> dependence, let us suppose neutral pH)?
>>
>> I might here be specific with program PISA, which lists Hydrogen
>> Bonds and Salt Bridges. They seem to use these bonds to estimate a Gibbs
>> energy for the formation of the interface.
>>
>>
>> Sheila
>>
>>
>>
>> ------
>> *De:* Daniel M. Himmel, Ph. D. 
>> *Enviado:* terça-feira, 18 de setembro de 2018 15:10
>> *Para:* sheila_bore...@hotmail.com
>> *Cc:* CCP4BB@jiscmail.ac.uk
>> *Assunto:* Re: [ccp4bb] collective term for hydrogen bonds and salt
>> bridges
>>
>> Sorry.  I may have been unclear.  H-bonds are actually a subset of dipole
>> interactions.
>>
>> On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. <
>> danielmhim...@gmail.com> wrote:
>>
>> By the way, distinguishing between dipole and ionic (salt bridge)
>> interactions could
>> be a slippery slope, because which one you have sometimes depends on the
>> protonation
>> state of the protein(s), which is pH dependent.
>>
>> -Daniel
>>
>>
>> On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. <
>> danielmhim...@gmail.com> wrote:
>>
>>
>>
>> Sheila,
>>
>> Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions
>> are often collectively called
>> electrostatic interactions.  Note that dipole interactions involve
>> partial charges.  If you want to exclude
>> dipole interactions, you have say so specifically in your manuscript.
>> Non-bonded interactions include
>> both electrostatic and van der Waals contacts (where hydrophobic
>> interactions result from van der Waals
>> forces in an aqueous environment).  Water can also interact with dipoles
>> (partial charges), so it would
>> NOT be correct to use the term "hydrophilic" if you were excluding
>> dipolar interactions.
>>
>> -Daniel
>>
>>
>> On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko <
>> sheila_bore...@hotmail.com> wrote:
>>
>> Dear all,
>>
>>  I had some literature searc

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Daniel M. Himmel, Ph. D.]

Stefano is correct that hydrophobic interactions are chiefly entropically
driven.  Thank you for your
input, Stefano.  I disagree with Matthew, however.  It is true that van der
Waals forces are always
present and therefore form a small contribution to even hydrogen bonds.
However, since the major contributions
to hydrogen bonds are various types of electronic components, it is proper
to group hydrogen bonds with electrostatic interactions.  When using
computational
software, one must look under the hood (or read the user manual) to see how
different
force components are being grouped for calculations.

I would say to Sheila that, when you write up your analysis, just be sure
to define how you are
using terms such as "electrostatic" or else specifically list the
individual types of interatomic
attractive forces that you are surveying  (which I know you prefer to
avoid).

If any computational chemists are following this discussion, perhaps you
can pipe in and
share your perspective and expertise.

-Daniel


On Wed, Sep 19, 2018 at 3:51 PM Sheila Boreiko 
wrote:

> Interesting discussion is coming out of this question. I thank all that
> have provided input.
>
>
> Let me go a bit further concerning Daniel's considerations. What other
> dipole interaction might be distinctively ascribed by programs out of
> hydrogen bonds (and of course, they use to describe salt bridges in
> addition, as an ionic interaction)? Possibly difficult for programs that
> use only atom positions, distances and angles (excluding the question of pH
> dependence, let us suppose neutral pH)?
>
> I might here be specific with program PISA, which lists Hydrogen Bonds
> and Salt Bridges. They seem to use these bonds to estimate a Gibbs energy
> for the formation of the interface.
>
>
> Sheila
>
>
>
> --
> *De:* Daniel M. Himmel, Ph. D. 
> *Enviado:* terça-feira, 18 de setembro de 2018 15:10
> *Para:* sheila_bore...@hotmail.com
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Assunto:* Re: [ccp4bb] collective term for hydrogen bonds and salt
> bridges
>
> Sorry.  I may have been unclear.  H-bonds are actually a subset of dipole
> interactions.
>
> On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. <
> danielmhim...@gmail.com> wrote:
>
> By the way, distinguishing between dipole and ionic (salt bridge)
> interactions could
> be a slippery slope, because which one you have sometimes depends on the
> protonation
> state of the protein(s), which is pH dependent.
>
> -Daniel
>
>
> On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. <
> danielmhim...@gmail.com> wrote:
>
>
>
> Sheila,
>
> Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions
> are often collectively called
> electrostatic interactions.  Note that dipole interactions involve partial
> charges.  If you want to exclude
> dipole interactions, you have say so specifically in your manuscript.
> Non-bonded interactions include
> both electrostatic and van der Waals contacts (where hydrophobic
> interactions result from van der Waals
> forces in an aqueous environment).  Water can also interact with dipoles
> (partial charges), so it would
> NOT be correct to use the term "hydrophilic" if you were excluding dipolar
> interactions.
>
> -Daniel
>
>
> On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko 
> wrote:
>
> Dear all,
>
>  I had some literature search, but could not find clearly. Would there
> be an appropriate term to call the sum of hydrogen bonds (HB) and salt
> bridges (SB)? What about "hydrophilic interactions" or "polar
> interactions"? I am analyzing the different number of theses interactions
> in different monomers of my protein, as a totality I wanted to cite
> (compare) the number of HB + SB, yet I think to specify them separately
> could take out some focus of the discussion.
>
>  Thank you,
>
>
> Sheila
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Sheila Boreiko]

Interesting discussion is coming out of this question. I thank all that have 
provided input.


Let me go a bit further concerning Daniel's considerations. What other 
dipole interaction might be distinctively ascribed by programs out of hydrogen 
bonds (and of course, they use to describe salt bridges in addition, as an 
ionic interaction)? Possibly difficult for programs that use only atom 
positions, distances and angles (excluding the question of pH dependence, let 
us suppose neutral pH)?

I might here be specific with program PISA, which lists Hydrogen Bonds and 
Salt Bridges. They seem to use these bonds to estimate a Gibbs energy for the 
formation of the interface.


Sheila




De: Daniel M. Himmel, Ph. D. 
Enviado: terça-feira, 18 de setembro de 2018 15:10
Para: sheila_bore...@hotmail.com
Cc: CCP4BB@jiscmail.ac.uk
Assunto: Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

Sorry.  I may have been unclear.  H-bonds are actually a subset of dipole 
interactions.

On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. 
mailto:danielmhim...@gmail.com>> wrote:
By the way, distinguishing between dipole and ionic (salt bridge) interactions 
could
be a slippery slope, because which one you have sometimes depends on the 
protonation
state of the protein(s), which is pH dependent.

-Daniel


On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. 
mailto:danielmhim...@gmail.com>> wrote:


Sheila,

Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions are 
often collectively called
electrostatic interactions.  Note that dipole interactions involve partial 
charges.  If you want to exclude
dipole interactions, you have say so specifically in your manuscript.  
Non-bonded interactions include
both electrostatic and van der Waals contacts (where hydrophobic interactions 
result from van der Waals
forces in an aqueous environment).  Water can also interact with dipoles 
(partial charges), so it would
NOT be correct to use the term "hydrophilic" if you were excluding dipolar 
interactions.

-Daniel


On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko 
mailto:sheila_bore...@hotmail.com>> wrote:

Dear all,


 I had some literature search, but could not find clearly. Would there be 
an appropriate term to call the sum of hydrogen bonds (HB) and salt bridges 
(SB)? What about "hydrophilic interactions" or "polar interactions"? I am 
analyzing the different number of theses interactions in different monomers of 
my protein, as a totality I wanted to cite (compare) the number of HB + SB, yet 
I think to specify them separately could take out some focus of the discussion.

 Thank you,

Sheila



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Stefano Trapani]

 

Sorry, I did not realised that. 
(I should have changed subject of the original post) 

Yes, we are not saying different things. 

Stefano 

Le 2018-09-19 17:06, Frank von Delft a écrit : 

> Okay. The original poster asked about hydrogen bonds and electrostatic 
> interactions. That's what I was referring to when I mentioned "enthalpic 
> interactions". 
> 
> And I think you're saying the same thing - which is cool.
> 
> On 19/09/2018 15:06, Stefano Trapani wrote:
>> Hi Frank > > I mean that, in my opinion, the term "enthalpic interaction" is 
>> not > appropriate to describe the hydrophobic effect, since the latter is > 
>> mainly driven by changes in the (system) entropy, not enthalpy. > > Table1 
>> of the cited paper reports the thermodynamic functions for > transferring 
>> some nonpolar solutes from a few organic solvents to > water. The author 
>> says that: "The data collected in Table 1 clearly > show that the 
>> thermodynamic barrier to the solution process is > entropic rather than 
>> enthalpic". > > Also, after a brief description of two theoretical models 
>> (the > cavity-based model and the clathrate cage model) the author states: > 
>> "It is important to point out that both the cavity-based model and > the 
>> clathrate cage model rest upon the fact that the hydrophobic > effect is 
>> entropy, not enthalpy driven. The models differ only in how > they explain 
>> the source of the entropy loss." > > Best > > Stefano > > > > Le 2018-09-19 
>> 14:41, Frank von Delft a écrit :
>> >> Hi Stefano - could you elaborate? >> >> Certainly the medicinal chemists 
>> >> go on a great deal about how >> deltaH balances deltaS and how it's 
>> >> bloody hard to know what is >> what even when you try to measure it. 
>> >> Which is what that abstract >> also goes on about. >> >> >> >> On 
>> >> 19/09/2018 10:54, Stefano Trapani wrote: >>> >>> Le 2018-09-19 11:59, 
>> >> Frank von Delft a écrit : >>> >>> I believe medicinal chemists do indeed 
>> >> talk about "enthalpic >>> interactions". Frank >>> >>> Not a good choice 
>> >> either (à mon avis ...) >>> >>> >>> >>> >>> >>> The Real Reason Why Oil 
>> >> and Water Don't Mix >>> >>> Todd P. Silverstein Journal of Chemical 
>> >> Education *1998* /75/ >>> (1), 116 >>> >>> DOI: 10.1021/ed075p116 >>> >>> 
>> >> https://pubs.acs.org/doi/abs/10.1021/ed075p116 [1] >>> >>> >>> Stefano 
>> >> >>> >>> >>> >>> On 19/09/2018 10:40, Stefano Trapani wrote: >>> >>> Le 
>> >> 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : >>> >>> (where 
>> >> hydrophobic interactions result from van der Waals forces >>> in an
aqueous environment). >>> >>> Hi >>> >>> I am not sure that, if one is to give 
a concise definition of >>> hydrophobic "interactions", this would be a 
convenient one, >>> because it may lead someone to identify vdW forces as the 
main >>> factor that maintains apolar aggregated molecules together in >>> 
aqueous environment. I have seen many students (and PhD's) >>> believing to the 
equality: hydrophobic 'forces'=vdW forces (and >>> not understanding, for 
example, that the side chains of a Ser and >>> an Ile can also establish vdW 
interactions). >>> >>> It is true that apolar groups that aggregate establish 
van der >>> Waals interactions (like any molecule in contact with another >>> 
one) but these microscopic (real) forces are not (as far as I >>> know) the 
main reason of aggregation in aqueous environment. >>> >>> The hydrophobic 
effect seem to be of a mainly entropic nature >>> (and it has much more to do 
with hydrogen bonds than van der >>> Waals forces): >>> >>>
https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [2] >>> >>> 
https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [3] >>> >>> 
Being mainly of an entropic nature, hydrophobic "contacts" are >>> not the 
direct result of real microscopic "forces" that act >>> between apolar groups. 
The terms "forces" and "interactions" in >>> widely used expressions like 
"hydrophobic forces" and >>> "hydrophobic interactions" are somehow misleading. 
>>> >>> Best >>> >>> --- Stefano Trapani >>> >>> Maître de Conférences >>> 
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [4] >>> 
>>> -
 Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 >>> 
 MONTPELLIER Cedex, France >>> >>> Tel : +33 (0)4 67 41 77 29 Fax : +33 
 (0)4 67 41 79 13 >>> - Université de 
 Montpellier >>> CNRS UMR 5048 INSERM UMR 1054 >>> 
 - >>> >>> >>> -- This message has been 
 scanned for viruses and dangerous >>> content by *MailScanner* 
  [5], and is >>> believed to be clean. 
 - >>> >>> To unsubscribe from the CCP4BB list, 
 click the following link: >>> 
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 [6] >>> >>> 
 >>> >>> -- This message has been scanned 

Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Frank von Delft]

Okay.  The original poster asked about hydrogen bonds and electrostatic 
interactions.  That's what I was referring to when I mentioned 
"enthalpic interactions".


And I think you're saying the same thing - which is cool.

On 19/09/2018 15:06, Stefano Trapani wrote:
Hi Frank  > > I mean that, in my opinion, the term "enthalpic interaction" is 
not > appropriate to describe the hydrophobic effect, since the latter 
is > mainly driven by changes in the (system) entropy, not enthalpy. > > 
Table1 of the cited paper reports the thermodynamic functions for > 
transferring some nonpolar solutes from a few organic solvents to > 
water. The author says that: "The data collected in Table 1 clearly > 
show that the thermodynamic barrier to the solution process is > 
entropic rather than enthalpic". > > Also, after a brief description of 
two theoretical models (the > cavity-based model and the clathrate cage 
model) the author states: > "It is important to point out that both the 
cavity-based model and > the clathrate cage model rest upon the fact 
that the hydrophobic > effect is entropy, not enthalpy driven. The 
models differ only in how > they explain the source of the entropy 
loss." > > Best > > Stefano > > > > Le 2018-09-19 14:41, Frank von Delft 
a écrit : >> >> Hi Stefano - could you elaborate? >> >> Certainly the 
medicinal chemists go on a great deal about how >> deltaH balances 
deltaS and how it's bloody hard to know what is >> what even when you 
try to measure it. Which is what that abstract >> also goes on about. >> 
>> >> >> On 19/09/2018 10:54, Stefano Trapani wrote: >>> >>> Le 
2018-09-19 11:59, Frank von Delft a écrit : >>> >>> I believe medicinal 
chemists do indeed talk about "enthalpic >>> interactions". Frank >>> 
>>> Not a good choice either (à mon avis ...) >>> >>> >>> >>> >>> >>> 
The Real Reason Why Oil and Water Don't Mix >>> >>> Todd P. Silverstein 
Journal of Chemical Education *1998* /75/ >>> (1), 116 >>> >>> DOI: 
10.1021/ed075p116 >>> >>> https://pubs.acs.org/doi/abs/10.1021/ed075p116 
>>> >>> >>> Stefano >>> >>> >>> >>> On 19/09/2018 10:40, Stefano 
Trapani wrote: >>> >>> Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a 
écrit : >>> >>> (where hydrophobic interactions result from van der 
Waals forces >>> in an aqueous environment). >>> >>> Hi >>> >>> I am not 
sure that, if one is to give a concise definition of >>> hydrophobic 
"interactions", this would be a convenient one, >>> because it may lead 
someone to identify vdW forces as the main >>> factor that maintains 
apolar aggregated molecules together in >>> aqueous environment. I have 
seen many students (and PhD's) >>> believing to the equality: 
hydrophobic 'forces'=vdW forces (and >>> not understanding, for example, 
that the side chains of a Ser and >>> an Ile can also establish vdW 
interactions). >>> >>> It is true that apolar groups that aggregate 
establish van der >>> Waals interactions (like any molecule in contact 
with another >>> one) but these microscopic (real) forces are not (as 
far as I >>> know) the main reason of aggregation in aqueous 
environment. >>> >>> The hydrophobic effect seem to be of a mainly 
entropic nature >>> (and it has much more to do with hydrogen bonds than 
van der >>> Waals forces): >>> >>> 
https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause >>> >>> 
https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force >>> >>> 
Being mainly of an entropic nature, hydrophobic "contacts" are >>> not 
the direct result of real microscopic "forces" that act >>> between 
apolar groups. The terms "forces" and "interactions" in >>> widely used 
expressions like "hydrophobic forces" and >>> "hydrophobic interactions" 
are somehow misleading. >>> >>> Best >>> >>> --- Stefano Trapani >>> >>> 
Maître de Conférences >>> 
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani >>> 
>>> -
Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090  >>> MONTPELLIER Cedex, France >>> >>> Tel : +33 (0)4 67 41 77 29 Fax : 
+33 (0)4 67 41 79 13 >>> - 
Université de Montpellier >>> CNRS UMR 5048 INSERM UMR 1054 >>> 
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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Stefano Trapani]

 

Hi Frank

I mean that, in my opinion, the term "enthalpic interaction" is not
appropriate to describe the hydrophobic effect, since the latter is
mainly driven by changes in the (system) entropy, not enthalpy.

Table1 of the cited paper reports the thermodynamic functions for
transferring some nonpolar solutes from a few organic solvents to water.
The author says that: "The data collected in Table 1 clearly show that
the thermodynamic barrier to the solution process is entropic rather
than enthalpic".

Also, after a brief description of two theoretical models (the
cavity-based model and the clathrate cage model) the author states: "It
is important to point out that both the cavity-based model and the
clathrate cage model rest upon the fact that the hydrophobic effect is
entropy, not enthalpy driven. The models differ only in how they explain
the source of the entropy loss."

Best

Stefano

Le 2018-09-19 14:41, Frank von Delft a écrit :

> Hi Stefano - could you elaborate? 
> 
> Certainly the medicinal chemists go on a great deal about how deltaH balances 
> deltaS and how it's bloody hard to know what is what even when you try to 
> measure it. Which is what that abstract also goes on about. 
> 
> On 19/09/2018 10:54, Stefano Trapani wrote: 
> 
> Le 2018-09-19 11:59, Frank von Delft a écrit : 
> 
> I believe medicinal chemists do indeed talk about "enthalpic interactions". 
> Frank 
> 
> Not a good choice either (à mon avis ...) 
> 
>  
> 
> THE REAL REASON WHY OIL AND WATER DON'T MIX
> 
> Todd P. Silverstein 
> Journal of Chemical Education 1998 _75_ (1), 116 
> 
> DOI: 10.1021/ed075p116 
> 
> https://pubs.acs.org/doi/abs/10.1021/ed075p116 [2] 
> 
> Stefano 
> 
> On 19/09/2018 10:40, Stefano Trapani wrote: 
> 
> Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : 
> 
> (where hydrophobic interactions result from van der Waals forces in an 
> aqueous environment). 
> 
> Hi 
> 
> I am not sure that, if one is to give a concise definition of hydrophobic 
> "interactions", this would be a convenient one, because it may lead someone 
> to identify vdW forces as the main factor that maintains apolar aggregated 
> molecules together in aqueous environment. I have seen many students (and 
> PhD's) believing to the equality: hydrophobic 'forces'=vdW forces (and not 
> understanding, for example, that the side chains of a Ser and an Ile can also 
> establish vdW interactions). 
> 
> It is true that apolar groups that aggregate establish van der Waals 
> interactions (like any molecule in contact with another one) but these 
> microscopic (real) forces are not (as far as I know) the main reason of 
> aggregation in aqueous environment. 
> 
> The hydrophobic effect seem to be of a mainly entropic nature (and it has 
> much more to do with hydrogen bonds than van der Waals forces): 
> 
> https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [3] 
> 
> https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [4] 
> 
> Being mainly of an entropic nature, hydrophobic "contacts" are not the direct 
> result of real microscopic "forces" that act between apolar groups. The terms 
> "forces" and "interactions" in widely used expressions like "hydrophobic 
> forces" and "hydrophobic interactions" are somehow misleading. 
> 
> Best 
> 
> ---
> Stefano Trapani
> 
> Maître de Conférences
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1]
> -
> Centre de Biochimie Structurale (CBS)
> 29 rue de Navacelles
> 34090 MONTPELLIER Cedex, France
> 
> Tel : +33 (0)4 67 41 77 29
> Fax : +33 (0)4 67 41 79 13
> -
> Université de Montpellier
> CNRS UMR 5048
> INSERM UMR 1054
> -
> 
> -- 
> This message has been scanned for viruses and 
> dangerous content by MAILSCANNER [5], and is 
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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Frank von Delft]

Hi Stefano - could you elaborate?

Certainly the medicinal chemists go on a great deal about how deltaH 
balances deltaS and how it's bloody hard to know what is what even when 
you try to measure it.  Which is what that abstract also goes on about.



On 19/09/2018 10:54, Stefano Trapani wrote:


Le 2018-09-19 11:59, Frank von Delft a écrit :

I believe medicinal chemists do indeed talk about "enthalpic 
interactions".  Frank



Not a good choice either (à mon avis ...)


The Real Reason Why Oil and Water Don't Mix

Todd P. Silverstein
Journal of Chemical Education *1998* /75/ (1), 116

DOI: 10.1021/ed075p116

https://pubs.acs.org/doi/abs/10.1021/ed075p116

Stefano

On 19/09/2018 10:40, Stefano Trapani wrote:


Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit :

(where hydrophobic interactions result from van der Waals forces
in an aqueous environment).

Hi

I am not sure that, if one is to give a concise definition of 
hydrophobic "interactions", this would be a convenient one, because 
it may lead someone to identify vdW forces as the main factor that 
maintains apolar aggregated molecules together in aqueous 
environment. I have seen many students (and PhD's) believing to the 
equality: hydrophobic 'forces'=vdW forces (and not understanding, 
for example, that the side chains of a Ser and an Ile can also 
establish vdW interactions).


It is true that apolar groups that aggregate establish van der Waals 
interactions (like any molecule in contact with another one) but 
these microscopic (real) forces are not (as far as I know) the main 
reason of aggregation in aqueous environment.


The hydrophobic effect seem to be of a mainly entropic nature (and 
it has much more to do with hydrogen bonds than van der Waals forces):


https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause

https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force

Being mainly of an entropic nature, hydrophobic "contacts" are not 
the direct result of real microscopic "forces" that act between 
apolar groups. The terms "forces" and "interactions" in widely used 
expressions like "hydrophobic forces" and "hydrophobic interactions" 
are somehow misleading.


Best

---
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-

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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Stefano Trapani]

 

Le 2018-09-19 11:59, Frank von Delft a écrit : 

> I believe medicinal chemists do indeed talk about "enthalpic interactions". 
> Frank

Not a good choice either (à mon avis ...) 

 

THE REAL REASON WHY OIL AND WATER DON'T MIX

Todd P. Silverstein 
Journal of Chemical Education 1998 _75_ (1), 116 

DOI: 10.1021/ed075p116 

https://pubs.acs.org/doi/abs/10.1021/ed075p116 [6] 

Stefano 

> On 19/09/2018 10:40, Stefano Trapani wrote: 
> 
> Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : 
> 
> (where hydrophobic interactions result from van der Waals forces in an 
> aqueous environment). 
> 
> Hi 
> 
> I am not sure that, if one is to give a concise definition of hydrophobic 
> "interactions", this would be a convenient one, because it may lead someone 
> to identify vdW forces as the main factor that maintains apolar aggregated 
> molecules together in aqueous environment. I have seen many students (and 
> PhD's) believing to the equality: hydrophobic 'forces'=vdW forces (and not 
> understanding, for example, that the side chains of a Ser and an Ile can also 
> establish vdW interactions). 
> 
> It is true that apolar groups that aggregate establish van der Waals 
> interactions (like any molecule in contact with another one) but these 
> microscopic (real) forces are not (as far as I know) the main reason of 
> aggregation in aqueous environment. 
> 
> The hydrophobic effect seem to be of a mainly entropic nature (and it has 
> much more to do with hydrogen bonds than van der Waals forces): 
> 
> https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [2] 
> 
> https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [3] 
> 
> Being mainly of an entropic nature, hydrophobic "contacts" are not the direct 
> result of real microscopic "forces" that act between apolar groups. The terms 
> "forces" and "interactions" in widely used expressions like "hydrophobic 
> forces" and "hydrophobic interactions" are somehow misleading. 
> 
> Best 
> 
> ---
> Stefano Trapani
> 
> Maître de Conférences
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1]
> -
> Centre de Biochimie Structurale (CBS)
> 29 rue de Navacelles
> 34090 MONTPELLIER Cedex, France
> 
> Tel : +33 (0)4 67 41 77 29
> Fax : +33 (0)4 67 41 79 13
> -
> Université de Montpellier
> CNRS UMR 5048
> INSERM UMR 1054
> -
> 
> -- 
> This message has been scanned for viruses and 
> dangerous content by MAILSCANNER [4], and is 
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[2] https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause
[3] https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force
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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Frank von Delft]

I believe medicinal chemists do indeed talk about "enthalpic 
interactions".  Frank


On 19/09/2018 10:40, Stefano Trapani wrote:


Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit :

(where hydrophobic interactions result from van der Waals forces in 
an aqueous environment).



Hi

I am not sure that, if one is to give a concise definition of 
hydrophobic "interactions", this would be a convenient one, because it 
may lead someone to identify vdW forces as the main factor that 
maintains apolar aggregated molecules together in aqueous environment. 
I have seen many students (and PhD's) believing to the equality: 
hydrophobic 'forces'=vdW forces (and not understanding, for example, 
that the side chains of a Ser and an Ile can also establish vdW 
interactions).


It is true that apolar groups that aggregate establish van der Waals 
interactions (like any molecule in contact with another one) but these 
microscopic (real) forces are not (as far as I know) the main reason 
of aggregation in aqueous environment.


The hydrophobic effect seem to be of a mainly entropic nature (and it 
has much more to do with hydrogen bonds than van der Waals forces):


https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause

https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force

Being mainly of an entropic nature, hydrophobic "contacts" are not the 
direct result of real microscopic "forces" that act between apolar 
groups. The terms "forces" and "interactions" in widely used 
expressions like "hydrophobic forces" and "hydrophobic interactions" 
are somehow misleading.


Best

---
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-

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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Stefano Trapani]

 

Le 2018-09-18 19:31, Daniel M. Himmel, Ph. D. a écrit : 

> (where hydrophobic interactions result from van der Waals forces in an 
> aqueous environment).

Hi 

I am not sure that, if one is to give a concise definition of
hydrophobic "interactions", this would be a convenient one, because it
may lead someone to identify vdW forces as the main factor that
maintains apolar aggregated molecules together in aqueous environment. I
have seen many students (and PhD's) believing to the equality:
hydrophobic 'forces'=vdW forces (and not understanding, for example,
that the side chains of a Ser and an Ile can also establish vdW
interactions). 

It is true that apolar groups that aggregate establish van der Waals
interactions (like any molecule in contact with another one) but these
microscopic (real) forces are not (as far as I know) the main reason of
aggregation in aqueous environment. 

The hydrophobic effect seem to be of a mainly entropic nature (and it
has much more to do with hydrogen bonds than van der Waals forces): 

https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause [1] 

https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force [2] 

Being mainly of an entropic nature, hydrophobic "contacts" are not the
direct result of real microscopic "forces" that act between apolar
groups. The terms "forces" and "interactions" in widely used expressions
like "hydrophobic forces" and "hydrophobic interactions" are somehow
misleading. 

Best 

---
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-
Centre de Biochimie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-

 

Links:
--
[1] https://en.wikipedia.org/wiki/Hydrophobic_effect#Cause
[2] https://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force

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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Daniel M. Himmel, Ph. D.]

Sorry.  I may have been unclear.  H-bonds are actually a subset of dipole
interactions.

On Tue, Sep 18, 2018 at 1:57 PM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

> By the way, distinguishing between dipole and ionic (salt bridge)
> interactions could
> be a slippery slope, because which one you have sometimes depends on the
> protonation
> state of the protein(s), which is pH dependent.
>
> -Daniel
>
>
> On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. <
> danielmhim...@gmail.com> wrote:
>
>>
>>
>> Sheila,
>>
>> Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions
>> are often collectively called
>> electrostatic interactions.  Note that dipole interactions involve
>> partial charges.  If you want to exclude
>> dipole interactions, you have say so specifically in your manuscript.
>> Non-bonded interactions include
>> both electrostatic and van der Waals contacts (where hydrophobic
>> interactions result from van der Waals
>> forces in an aqueous environment).  Water can also interact with dipoles
>> (partial charges), so it would
>> NOT be correct to use the term "hydrophilic" if you were excluding
>> dipolar interactions.
>>
>> -Daniel
>>
>>
>> On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko <
>> sheila_bore...@hotmail.com> wrote:
>>
>>> Dear all,
>>>
>>>  I had some literature search, but could not find clearly. Would
>>> there be an appropriate term to call the sum of hydrogen bonds (HB) and
>>> salt bridges (SB)? What about "hydrophilic interactions" or "polar
>>> interactions"? I am analyzing the different number of theses interactions
>>> in different monomers of my protein, as a totality I wanted to cite
>>> (compare) the number of HB + SB, yet I think to specify them separately
>>> could take out some focus of the discussion.
>>>
>>>  Thank you,
>>>
>>>
>>> Sheila
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>



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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Daniel M. Himmel, Ph. D.]

By the way, distinguishing between dipole and ionic (salt bridge)
interactions could
be a slippery slope, because which one you have sometimes depends on the
protonation
state of the protein(s), which is pH dependent.

-Daniel


On Tue, Sep 18, 2018 at 1:31 PM Daniel M. Himmel, Ph. D. <
danielmhim...@gmail.com> wrote:

>
>
> Sheila,
>
> Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions
> are often collectively called
> electrostatic interactions.  Note that dipole interactions involve partial
> charges.  If you want to exclude
> dipole interactions, you have say so specifically in your manuscript.
> Non-bonded interactions include
> both electrostatic and van der Waals contacts (where hydrophobic
> interactions result from van der Waals
> forces in an aqueous environment).  Water can also interact with dipoles
> (partial charges), so it would
> NOT be correct to use the term "hydrophilic" if you were excluding dipolar
> interactions.
>
> -Daniel
>
>
> On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko 
> wrote:
>
>> Dear all,
>>
>>  I had some literature search, but could not find clearly. Would
>> there be an appropriate term to call the sum of hydrogen bonds (HB) and
>> salt bridges (SB)? What about "hydrophilic interactions" or "polar
>> interactions"? I am analyzing the different number of theses interactions
>> in different monomers of my protein, as a totality I wanted to cite
>> (compare) the number of HB + SB, yet I think to specify them separately
>> could take out some focus of the discussion.
>>
>>  Thank you,
>>
>>
>> Sheila
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Daniel M. Himmel, Ph. D.]

Sheila,

Hydrogen bonds, ionic (i.e. salt bridge), and polar (dipole) interactions
are often collectively called
electrostatic interactions.  Note that dipole interactions involve partial
charges.  If you want to exclude
dipole interactions, you have say so specifically in your manuscript.
Non-bonded interactions include
both electrostatic and van der Waals contacts (where hydrophobic
interactions result from van der Waals
forces in an aqueous environment).  Water can also interact with dipoles
(partial charges), so it would
NOT be correct to use the term "hydrophilic" if you were excluding dipolar
interactions.

-Daniel


On Mon, Sep 17, 2018 at 4:17 PM Sheila Boreiko 
wrote:

> Dear all,
>
>  I had some literature search, but could not find clearly. Would there
> be an appropriate term to call the sum of hydrogen bonds (HB) and salt
> bridges (SB)? What about "hydrophilic interactions" or "polar
> interactions"? I am analyzing the different number of theses interactions
> in different monomers of my protein, as a totality I wanted to cite
> (compare) the number of HB + SB, yet I think to specify them separately
> could take out some focus of the discussion.
>
>  Thank you,
>
>
> Sheila
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Pavel Afonine]

Nonbonded interactions? (if you approach this from classic geometry
restraints used in refinement programs)

Pavel

On Mon, Sep 17, 2018 at 2:09 PM Joel Tyndall 
wrote:

> Hi,
>
>
>
> Polar interactions seems to make the most sense. This is what Pymol uses
> as I don’t  think it differentiates
>
>
>
> J
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Sheila
> Boreiko
> *Sent:* Tuesday, 18 September 2018 8:06 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] collective term for hydrogen bonds and salt bridges
>
>
>
> Dear all,
>
>  I had some literature search, but could not find clearly. Would there
> be an appropriate term to call the sum of hydrogen bonds (HB) and salt
> bridges (SB)? What about "hydrophilic interactions" or "polar
> interactions"? I am analyzing the different number of theses interactions
> in different monomers of my protein, as a totality I wanted to cite
> (compare) the number of HB + SB, yet I think to specify them separately
> could take out some focus of the discussion.
>
>  Thank you,
>
>
> Sheila
>
>
> --
>
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Re: [ccp4bb] collective term for hydrogen bonds and salt bridges

[Joel Tyndall]

Hi,

Polar interactions seems to make the most sense. This is what Pymol uses as I 
don't  think it differentiates

J

From: CCP4 bulletin board  On Behalf Of Sheila Boreiko
Sent: Tuesday, 18 September 2018 8:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] collective term for hydrogen bonds and salt bridges


Dear all,

 I had some literature search, but could not find clearly. Would there be 
an appropriate term to call the sum of hydrogen bonds (HB) and salt bridges 
(SB)? What about "hydrophilic interactions" or "polar interactions"? I am 
analyzing the different number of theses interactions in different monomers of 
my protein, as a totality I wanted to cite (compare) the number of HB + SB, yet 
I think to specify them separately could take out some focus of the discussion.

 Thank you,

Sheila



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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[ccp4bb] collective term for hydrogen bonds and salt bridges

[Sheila Boreiko]

Dear all,


 I had some literature search, but could not find clearly. Would there be 
an appropriate term to call the sum of hydrogen bonds (HB) and salt bridges 
(SB)? What about "hydrophilic interactions" or "polar interactions"? I am 
analyzing the different number of theses interactions in different monomers of 
my protein, as a totality I wanted to cite (compare) the number of HB + SB, yet 
I think to specify them separately could take out some focus of the discussion.

 Thank you,

Sheila



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1