ams 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 estimat
ds 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: s
>> ----------
>> *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
rgy
> 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
> *Assunt
cp4bb] 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
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 wa
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 m
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 n
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), 1
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
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
m
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, becaus
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.
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-bond
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
>
>
>
> D
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 bond
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
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