From owner-chemistry@ccl.net Thu Dec  1 01:01:01 2011
From: "Christopher Cramer cramer[A]umn.edu" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Delta G of solution calculation?
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X-Original-From: Christopher Cramer <cramer * umn.edu>
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Date: Wed, 30 Nov 2011 23:38:49 -0600
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Sent to CCL by: Christopher Cramer [cramer**umn.edu]

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This question, in various forms, does just keep coming up...

While I'm going to take the opportunity to refer to a detailed, formal, =
and I hope dispositive paper just published by the Minnesota group (doi =
10.1021/jp205508z), I'll also make some effort here to be more cookbooky =
in an explanation here. Pedagogy in front! Not just for Gaussian, but =
more general.

The free energy of solvation is, clearly, defined as the DIFFERENCE in =
the free energy of a species in the gas phase and in solution. Free =
energy is an ensemble property, not a molecular property, so we are =
immediately faced with the need to make some approximations in order to =
render the modeling tractable.

In the gas phase, those approximations are by now fairly standard and =
nearly universal. We make the ideal-gas approximation (so that the =
partition function of a mole of molecules is simply the product of =
Avogadro's number of molecular partition functions), and we make the =
rigid rotator and harmonic oscillator approximations to simplify the =
rovibrational partition functions, and, voila, we have a means to =
compute a standard state free energy (Gibbs free energy -- free enthalpy =
for my colleagues in (far more logical) German-speaking countries). =
Pretty much every electronic structure program on earth will do this for =
you when you run a vibrational frequency calculation in the gas phase. =
Poof -- you get E, H, S (third law), and G (and Cv too, if you care).

Note that you should be careful to recognize that (i) unless you =
overrode it, the program chose some default standard state concentration =
(1 bar? 1 atm? you should know...) and temperature (nearly always 298 K) =
and scale factor for vibrational frequencies (typically 1, but that =
might not be the best value for a given level of theory) and (ii) the =
harmonic oscillator approximation is catastrophically bad for super-low =
frequency vibrations (below, say, 50 wavenumbers, to pick an arbitrary =
value). There are fixes for the latter problem, but I'll let someone =
else post about that.

Now, what about G of a solute in solution? Well, to begin, since we're =
not dealing with a pure component anymore (at least, not if the solvent =
is different than the solute), we need to assume that we have an ideal =
solution, and we should recognize that we're talking about a partial =
molar quantity (more often referred to in the rigorous literature as a =
chemical potential than a free energy, but that's a matter of =
tradition). In any case, we need to assemble a free energy as a sum of

electronic energy (i.e., potential and kinetic energy of electrons for a =
fixed set of nuclear positions)

coupling to medium (which includes electrostatic and non-electrostatic =
components, although, it being chemistry, EVERYTHING is electrostatic... =
-- in practice, however, with continuum models, electrostatic means what =
you get by assuming the molecule is a charge distribution in a cavity =
embedded in a classical dielectric medium in which case one can apply =
the Poisson equation -- non-electrostatic is everything else -- =
dispersion, cavitation, covalent components of hydrogen bonding, =
hydrophobic effects, you name it)

temperature dependent translational (?), rotational (?), vibrational, =
and conformational contributions -- the question marks indicate =
conceptual issues

So, a few points to bear in mind. The optimal geometry in solution is =
unlikely to be the same as that in the gas phase -- but it might be =
close. You just have to decide for yourself if you want to reoptimize or =
not.

Same for the vibrational and conformational contributions to free energy =
in solution -- they might be very, very close to those in the gas phase =
-- or they might not. If you assume that they ARE the same, you avoid =
having to do a frequency calculation in solution (and you avoid =
wondering what it means to do vibrational frequencies in a continuum, =
which in principle means a surrounding that is in equilibrium with the =
solute -- but how can a medium composed of molecules be fully in =
equilibrium with a molecular solute on the timescale of the solute's =
vibrations, since the solvent vibrations are on the same timescale?)

Note that if I assume no change in the various parts of the free energy =
EXCEPT for the electronic energy and solute-solvent coupling (more on =
that momentarily), life is pretty easy. The free energy of solvation is =
the difference in the self-consistent reaction-field (SCRF) energy =
INCLUDING non-electrostatic effects, and the electronic energy in the =
gas phase. That is, I look at the expectation value of <H+(1/2)V> for =
the solvated wave function, where V is the reaction field operator, add =
non-electrostatic effects (typically NOT dependent on the quantum wave =
function, so added post facto, although there are a few exceptions in =
the literature), subtract the expectation value of <H> for the gas-phase =
wave function (note that you might have done the two expectation values =
at different geometries, or you might have used the gas-phase geometry =
for both -- your choice -- the former is more "physical", certainly, but =
the latter is a useful approximation in many instances), and you are =
done. You've got the free energy of solvation FOR IDENTICAL =
STANDARD-STATE CONCENTRATIONS. That is, the number you have in hand =
assumes no change in standard-state concentration. However, many =
experimental solvation free energies are tabulated for, say, 1 atm =
gaseous standard states and 1 M solution standard states. To compare the =
computed value to the tabulated value, one needs to correct for the =
standard-state concentration difference.

In the interest of the cookbook, let me be more practical. Thus, let's =
say that I compute a gas-phase G value, including all contributions, =
electronic and otherwise of

-3.000 00 a.u.

and, let's say that the electronic energy alone in the gas phase is

-3.020 00 a.u.  (so ZPVE and thermal contributions to G are +0.020 00 =
a.u.)

and, finally, let's say that my SCRF calculation provides an electronic =
energy INCLUDING non-electrostatic effects of

-3.030 00 a.u.

In that case, my free energy of solvation is -0.010 00 a.u. (difference =
of -3.030 00 and -3.020 00 a.u.) And, if I want to think about my free =
energy in solution, I can make the assumption that there is no change in =
the ZPVE and thermal contributions, in which case I would have G in =
solution equals -3.010 00 a.u. (which is gas-phase G of -3.000 00 a.u. =
plus free energy of solvation -0.010 00 a.u.)

But, just to be clear, if my gas phase G referred to a 1 atm standard =
state concentration, for an ideal gas at 298 K and 1 atm, that implies a =
molarity of 1/24.5 M. If I want my G in solution to be for a 1 M =
standard state, I need to pay the entropy penalty to compress my =
concentration from 1/24.5 M to 1 M, which is about 1.9 kcal/mol (the =
proof is left to the reader...) So, my 1 M free energy in solution is =
not -3.010 00 but rather about -3.006 99 a.u.

The above is an example of how almost all free energies of solvation and =
free energies in solution are computed in the literature using continuum =
solvation models (at least if they're done properly!)

Lots of important details glossed over a bit above (in the interests of =
clarity, I demur). But, to be more thorough, let's note:

1)  Why was it (1/2)V in the SCRF calculation? -- the 1/2 comes from =
linear response theory and assumes that you spend precisely half of the =
favorable coupling energy organizing the medium so that it provides a =
favorable reaction field.

2)  How can there be a translational partition function for a solute in =
solution? There isn't one -- but there is something called a =
liberational free energy associated with accessible volume, and Ben-Naim =
showed some time ago that the value is identical to that for the a =
particle-in-a-box having the same standard-state concentration -- i.e., =
there is no change on going from gas-phase translational partition =
function to liberational partition function for the same standard-state =
concentration for an ideal solution. When there are issues with =
non-accessible volume, however, account must be taked (cf. Flory-Huggins =
theory).

3)  How can there be a rotational partition function for a solute in =
solution? There isn't one -- solute rotations become librations that are =
almost certainly intimately coupled with first-solvation-shell motions. =
In essence, assuming no change in "rotational partition function" =
implies assuming no free energetic consequence associated with moving =
> from rotations to librations. This remains a poorly resolved question, =
but, in practice, since most continuum solvation models are =
semiempirical in nature (having been parameterized against experimental =
data) any actual changes in free energy have been absorbed in the =
parameterization as best as possible. If you find that unsatisfying, =
hey, feel free not to use continuum solvent models -- it's certainly ok =
by me...

4)  Where did those non-electrostatic effects come from? Every model is =
different in that regard, and I won't attempt to summarize a =
review's-worth of material in an email. Lots of nice Chem. Rev. articles =
over the years on continuum models if you want to catch up.

Finally, what is described above is a popular approach for computing =
solvation free energies and free energies in solution, but by no means =
the only approach out there. A non-exhaustive list to compute either or =
both solvation free energies or free energies in solution includes =
free-energy perturbation from explicit simulations, RISM-based models, =
fragment-based models derived from a statistical mechanical approach =
(including COSMO-RS and variations on that theme), fragment-based models =
> from expert learning, and models relying on alternative physicochemical =
approaches to computing interaction energies (e.g., SPARC). These =
alternative models can be quantal, classical, or SMILESal (which is to =
say, more in the realm of chemoinformatics than physical chemistry). Let =
a thousand flowers bloom.

I hope that this post serves as a useful archival reference for CCL =
users present and future. Best wishes to all for a peaceful winter =
solstice (or summer, for my antipodeal colleagues).

Chris



On Nov 30, 2011, at 1:46 PM, Close, David M. CLOSED#,#mail.etsu.edu =
wrote:

>   Does anyone know how Gaussian calculates deltaG of solvation?  This =
was in G98 and was automatic.  In G03 one had to add SCFVAC in the =
scrf(CPCM,read) read list to get the delta G result.  I have several =
questions about the methods used.  I presume that during the SCRF =
calculation the program has to have a separate SCF calculation on the =
input molecule  in the gas phase, along with a frequency calculation to =
know the free energy of the gas phase structure.  Is this correct?  If =
so, are the ZPE and free energy correction terms multiplied by a scale =
factor (0.92 for example?).  Also to do solvation energy calculations =
one need to convert the gas phase reference state from 1 atmos. to 1 M.  =
Does the program report this corrected delta G value?=20
>   My reason for asking is that I have done these actual calculations =
separately with energy/frequency calculations on the neutral and anion, =
and I get slightly difference answers from those answers using SCFVAC, =
and I need to know why this is?
>   Regards, Dave Close.

--

Christopher J. Cramer
Elmore H. Northey Professor
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-7541
Mobile: (952) 297-2575
email:  cramer|a|umn.edu
jabber:  cramer|a|jabber.umn.edu
http://pollux.chem.umn.edu
(website includes information about the textbook "Essentials
    of Computational Chemistry:  Theories and Models, 2nd Edition")








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	charset=us-ascii

<html><head><base href=3D"x-msg://31/"></head><body style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; ">This question, in various forms, does just keep =
coming up...<div><br></div><div>While I'm going to take the opportunity =
to refer to a detailed, formal, and I hope dispositive paper just =
published by the Minnesota group (doi&nbsp;10.1021/jp205508z), I'll also =
make some effort here to be more cookbooky in an explanation here. =
Pedagogy in front! Not just for Gaussian, but more =
general.</div><div><br></div><div>The free energy of solvation is, =
clearly, defined as the DIFFERENCE in the free energy of a species in =
the gas phase and in solution. Free energy is an ensemble property, not =
a molecular property, so we are immediately faced with the need to make =
some approximations in order to render the modeling =
tractable.</div><div><br></div><div>In the gas phase, those =
approximations are by now fairly standard and nearly universal. We make =
the ideal-gas approximation (so that the partition function of a mole of =
molecules is simply the product of Avogadro's number of molecular =
partition functions), and we make the rigid rotator and harmonic =
oscillator approximations to simplify the rovibrational partition =
functions, and, voila, we have a means to compute a standard state free =
energy (Gibbs free energy -- free enthalpy for my colleagues in (far =
more logical) German-speaking countries). Pretty much every electronic =
structure program on earth will do this for you when you run a =
vibrational frequency calculation in the gas phase. Poof -- you get E, =
H, S (third law), and G (and Cv too, if you =
care).</div><div><br></div><div>Note that you should be careful to =
recognize that (i) unless you overrode it, the program chose some =
default standard state concentration (1 bar? 1 atm? you should know...) =
and temperature (nearly always 298 K) and scale factor for vibrational =
frequencies (typically 1, but that might not be the best value for a =
given level of theory) and (ii) the harmonic oscillator approximation is =
catastrophically bad for super-low frequency vibrations (below, say, 50 =
wavenumbers, to pick an arbitrary value). There are fixes for the latter =
problem, but I'll let someone else post about =
that.</div><div><br></div><div>Now, what about G of a solute in =
solution? Well, to begin, since we're not dealing with a pure component =
anymore (at least, not if the solvent is different than the solute), we =
need to assume that we have an ideal solution, and we should recognize =
that we're talking about a partial molar quantity (more often referred =
to in the rigorous literature as a chemical potential than a free =
energy, but that's a matter of tradition). In any case, we need to =
assemble a free energy as a sum of</div><div><br></div><div>electronic =
energy (i.e., potential and kinetic energy of electrons for a fixed set =
of nuclear positions)</div><div><br></div><div>coupling to medium (which =
includes electrostatic and non-electrostatic components, although, it =
being chemistry, EVERYTHING is electrostatic... -- in practice, however, =
with continuum models, electrostatic means what you get by assuming the =
molecule is a charge distribution in a cavity embedded in a classical =
dielectric medium in which case one can apply the Poisson equation -- =
non-electrostatic is everything else -- dispersion, cavitation, covalent =
components of hydrogen bonding, hydrophobic effects, you name =
it)</div><div><br></div><div>temperature dependent translational (?), =
rotational (?), vibrational, and conformational contributions -- the =
question marks indicate conceptual issues</div><div><br></div><div>So, a =
few points to bear in mind. The optimal geometry in solution is unlikely =
to be the same as that in the gas phase -- but it might be close. You =
just have to decide for yourself if you want to reoptimize or =
not.</div><div><br></div><div>Same for the vibrational and =
conformational contributions to free energy in solution -- they might be =
very, very close to those in the gas phase -- or they might not. If you =
assume that they ARE the same, you avoid having to do a frequency =
calculation in solution (and you avoid wondering what it means to do =
vibrational frequencies in a continuum, which in principle means a =
surrounding that is in equilibrium with the solute -- but how can a =
medium composed of molecules be fully in equilibrium with a molecular =
solute on the timescale of the solute's vibrations, since the solvent =
vibrations are on the same timescale?)</div><div><br></div><div>Note =
that if I assume no change in the various parts of the free energy =
EXCEPT for the electronic energy and solute-solvent coupling (more on =
that momentarily), life is pretty easy. The free energy of solvation is =
the difference in the self-consistent reaction-field (SCRF) energy =
INCLUDING non-electrostatic effects, and the electronic energy in the =
gas phase. That is, I look at the expectation value of &lt;H+(1/2)V&gt; =
for the solvated wave function, where V is the reaction field operator, =
add non-electrostatic effects (typically NOT dependent on the quantum =
wave function, so added post facto, although there are a few exceptions =
in the literature), subtract the expectation value of &lt;H&gt; for the =
gas-phase wave function (note that you might have done the two =
expectation values at different geometries, or you might have used the =
gas-phase geometry for both -- your choice -- the former is more =
"physical", certainly, but the latter is a useful approximation in many =
instances), and you are done. You've got the free energy of solvation =
FOR IDENTICAL STANDARD-STATE CONCENTRATIONS. That is, the number you =
have in hand assumes no change in standard-state concentration. However, =
many experimental solvation free energies are tabulated for, say, 1 atm =
gaseous standard states and 1 M solution standard states. To compare the =
computed value to the tabulated value, one needs to correct for the =
standard-state concentration difference.</div><div><br></div><div>In the =
interest of the cookbook, let me be more practical. Thus, let's say that =
I compute a gas-phase G value, including all contributions, electronic =
and otherwise of</div><div><br></div><div>-3.000 00 =
a.u.</div><div><br></div><div>and, let's say that the electronic energy =
alone in the gas phase is</div><div><br></div><div>-3.020 00 a.u. =
&nbsp;(so ZPVE and thermal contributions to G are +0.020 00 =
a.u.)</div><div><br></div><div>and, finally, let's say that my SCRF =
calculation provides an electronic energy INCLUDING non-electrostatic =
effects of</div><div><br></div><div>-3.030 00 =
a.u.</div><div><br></div><div>In that case, my free energy of solvation =
is -0.010 00 a.u. (difference of -3.030 00 and -3.020 00 a.u.) And, if I =
want to think about my free energy in solution, I can make the =
assumption that there is no change in the ZPVE and thermal =
contributions, in which case I would have G in solution equals -3.010 00 =
a.u. (which is gas-phase G of -3.000 00 a.u. plus free energy of =
solvation -0.010 00 a.u.)</div><div><br></div><div>But, just to be =
clear, if my gas phase G referred to a 1 atm standard state =
concentration, for an ideal gas at 298 K and 1 atm, that implies a =
molarity of 1/24.5 M. If I want my G in solution to be for a 1 M =
standard state, I need to pay the entropy penalty to compress my =
concentration from 1/24.5 M to 1 M, which is about 1.9 kcal/mol (the =
proof is left to the reader...) So, my 1 M free energy in solution is =
not -3.010 00 but rather about -3.006 99 =
a.u.</div><div><br></div><div>The above is an example of how almost all =
free energies of solvation and free energies in solution are computed in =
the literature using continuum solvation models (at least if they're =
done properly!)</div><div><br></div><div>Lots of important details =
glossed over a bit above (in the interests of clarity, I demur). But, to =
be more thorough, let's note:</div><div><br></div><div>1) &nbsp;Why was =
it (1/2)V in the SCRF calculation? -- the 1/2 comes from linear response =
theory and assumes that you spend precisely half of the favorable =
coupling energy organizing the medium so that it provides a favorable =
reaction field.</div><div><br></div><div>2) &nbsp;How can there be a =
translational partition function for a solute in solution? There isn't =
one -- but there is something called a liberational free energy =
associated with accessible volume, and Ben-Naim showed some time ago =
that the value is identical to that for the a particle-in-a-box having =
the same standard-state concentration -- i.e., there is no change on =
going from gas-phase translational partition function to liberational =
partition function for the same standard-state concentration for an =
ideal solution. When there are issues with non-accessible volume, =
however, account must be taked (cf. Flory-Huggins =
theory).</div><div><br></div><div>3) &nbsp;How can there be a rotational =
partition function for a solute in solution? There isn't one -- solute =
rotations become librations that are almost certainly intimately coupled =
with first-solvation-shell motions. In essence, assuming no change in =
"rotational partition function" implies assuming no free energetic =
consequence associated with moving from rotations to librations. This =
remains a poorly resolved question, but, in practice, since most =
continuum solvation models are semiempirical in nature (having been =
parameterized against experimental data) any actual changes in free =
energy have been absorbed in the parameterization as best as possible. =
If you find that unsatisfying, hey, feel free not to use continuum =
solvent models -- it's certainly ok by me...</div><div><br></div><div>4) =
&nbsp;Where did those non-electrostatic effects come from? Every model =
is different in that regard, and I won't attempt to summarize a =
review's-worth of material in an email. Lots of nice Chem. Rev. articles =
over the years on continuum models if you want to catch =
up.</div><div><br></div><div>Finally, what is described above is a =
popular approach for computing solvation free energies and free energies =
in solution, but by no means the only approach out there. A =
non-exhaustive list to compute either or both solvation free energies or =
free energies in solution includes free-energy perturbation from =
explicit simulations, RISM-based models, fragment-based models derived =
> from a statistical mechanical approach (including COSMO-RS and =
variations on that theme), fragment-based models from expert learning, =
and models relying on alternative physicochemical approaches to =
computing interaction energies (e.g., SPARC). These alternative models =
can be quantal, classical, or SMILESal (which is to say, more in the =
realm of chemoinformatics than physical chemistry). Let a thousand =
flowers bloom.</div><div><br></div><div>I hope that this post serves as =
a useful archival reference for CCL users present and future. Best =
wishes to all for a peaceful winter solstice (or summer, for my =
antipodeal =
colleagues).</div><div><br></div><div>Chris</div><div><br></div><div><br><=
/div><div><br><div><div>On Nov 30, 2011, at 1:46 PM, Close, David M. =
CLOSED#,#mail.etsu.edu wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; =
font-family: Helvetica; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: =
none; white-space: normal; widows: 2; word-spacing: 0px; =
-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: =
0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div =
lang=3D"EN-US" link=3D"blue" vlink=3D"purple"><div class=3D"WordSection1" =
style=3D"page: WordSection1; "><div style=3D"margin-top: 0in; =
margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: =
11pt; font-family: Calibri, sans-serif; ">&nbsp; Does anyone know how =
Gaussian calculates deltaG of solvation?&nbsp; This was in G98 and was =
automatic.&nbsp; In G03 one had to add SCFVAC in the scrf(CPCM,read) =
read list to get the delta G result.&nbsp; I have several questions =
about the methods used.&nbsp; I presume that during the SCRF calculation =
the program has to have a separate SCF calculation on the input molecule =
&nbsp;in the gas phase, along with a frequency calculation to know the =
free energy of the gas phase structure.&nbsp; Is this correct?&nbsp; If =
so, are the ZPE and free energy correction terms multiplied by a scale =
factor (0.92 for example?).&nbsp; Also to do solvation energy =
calculations one need to convert the gas phase reference state from 1 =
atmos. to 1 M.&nbsp; Does the program report this corrected delta G =
value?&nbsp;<o:p></o:p></div><div style=3D"margin-top: 0in; =
margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: =
11pt; font-family: Calibri, sans-serif; ">&nbsp;&nbsp;My reason for =
asking is that I have done these actual calculations separately with =
energy/frequency calculations on the neutral and anion, and I get =
slightly difference answers from those answers using SCFVAC, and I need =
to know why this is?<o:p></o:p></div><div style=3D"margin-top: 0in; =
margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: =
11pt; font-family: Calibri, sans-serif; ">&nbsp; Regards, Dave =
Close.<o:p></o:p></div></div></div></span></blockquote></div><br><div>
<span class=3D"Apple-style-span" style=3D"border-collapse: separate; =
color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; =
font-variant: normal; font-weight: normal; letter-spacing: normal; =
line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: =
0px; text-transform: none; white-space: normal; widows: 2; word-spacing: =
0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span =
class=3D"Apple-style-span" style=3D"border-collapse: separate; color: =
rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: =
normal; font-variant: normal; font-weight: normal; letter-spacing: =
normal; line-height: normal; orphans: 2; text-indent: 0px; =
text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; =
-webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: =
0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><div style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: medium; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><div style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; "><span class=3D"Apple-style-span" =
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0px; margin-bottom: 0px; margin-left: 0px; "><font face=3D"Helvetica" =
size=3D"3" style=3D"font: normal normal normal 12px/normal Helvetica; =
">--</font></p><p style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; font: normal normal normal =
12px/normal Helvetica; min-height: 14px; "><br></p><p style=3D"margin-top:=
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face=3D"Helvetica" size=3D"3" style=3D"font: normal normal normal =
12px/normal Helvetica; ">Christopher J. Cramer</font></p><p =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Elmore H. Northey Professor</p><p style=3D"margin-top:=
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face=3D"Helvetica" size=3D"3" style=3D"font: normal normal normal =
12px/normal Helvetica; ">University of Minnesota</font></p><p =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font face=3D"Helvetica" size=3D"3" style=3D"font: =
normal normal normal 12px/normal Helvetica; ">Department of =
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margin-bottom: 0px; margin-left: 0px; "><font face=3D"Helvetica" =
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626-7541</font></p><p style=3D"margin-top: 0px; margin-right: 0px; =
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">Mobile: (952) 297-2575</font></p><p style=3D"margin-top: 0px; =
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href=3D"mailto:cramer|a|umn.edu">cramer|a|umn.edu</a></font></p><p =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">jabber: &nbsp;<a =
href=3D"mailto:cramer|a|jabber.umn.edu">cramer|a|jabber.umn.edu</a></p><p =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font face=3D"Helvetica" size=3D"3" style=3D"font: =
normal normal normal 12px/normal Helvetica; "><a =
href=3D"http://pollux.chem.umn.edu">http://pollux.chem.umn.edu</a></font><=
/p><p style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font face=3D"Helvetica" size=3D"3" style=3D"font: =
normal normal normal 12px/normal Helvetica; ">(website includes =
information about the textbook "Essentials</font></p><p =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><font face=3D"Helvetica" size=3D"3" style=3D"font: =
normal normal normal 12px/normal Helvetica; "><span =
class=3D"Apple-converted-space">&nbsp; &nbsp;<span =
class=3D"Apple-converted-space">&nbsp;</span></span>of Computational =
Chemistry:<span class=3D"Apple-converted-space">&nbsp;<span =
class=3D"Apple-converted-space">&nbsp;</span></span>Theories and Models, =
2nd Edition")</font></p><br =
class=3D"Apple-interchange-newline"></div></div></span><br =
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From owner-chemistry@ccl.net Thu Dec  1 06:30:01 2011
From: "quartarolo|a|unical.it" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL:G: wb97XD in g09
Message-Id: <-45955-111201054105-16600-rH6Mvcxb9vDNqqjUZsLyGg#server.ccl.net>
X-Original-From: quartarolo]_[unical.it
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Date: Thu, 01 Dec 2011 11:40:54 +0100
MIME-Version: 1.0


Sent to CCL by: quartarolo _ unical.it
Dear all,
I'm running a calculation with Gaussian09 for a Lutetium complex using  
the wB97XD functional.
The program stops with the following message:
"R6DR0: No vdW radius available for IA= 71".
Is there a way to define this parameter manually in the input file and  
eventually where to search for vdW radius of lutetium.

best regards

Quartarolo Domenico

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From owner-chemistry@ccl.net Thu Dec  1 07:14:01 2011
From: "psavita savita.pundlik-*-crl-global.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Delta G of solution calculation?
Message-Id: <-45956-111201033052-29106-CvYc2+ae9se+8v+wRzQjBQ]=[server.ccl.net>
X-Original-From: psavita <savita.pundlik#crl-global.com>
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Date: Thu, 1 Dec 2011 14:00:42 +0530
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Sent to CCL by: psavita [savita.pundlik^crl-global.com]
<font face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=
=3D"2"> <div>Hello,<br><br>I would like to thank Dr. Christopher for such a=
 detail view of the concept of solvation free energy<br>and also Dr. David =
for raising the query.<br><br>Best Regards,<br><br></div> <div><font face=
=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=3D"2"> <div=
><font style=3D"font-family: Georgia,Default Serif,serif; font-weight: bold=
;" color=3D"#0000ff"><font color=3D"#999900">Savita Pundlik</font></font><b=
r style=3D"font-family: Georgia,Default Serif,serif;"><span style=3D"font-f=
amily: Georgia,Default Serif,serif;"><font><font color=3D"#999900">Computat=
ional Materials </font></font></span><font color=3D"#999900">Research &amp;=
 Innovation Group</font><br style=3D"font-family: Georgia,Default Serif,ser=
if;"><span style=3D"font-family: Georgia,Default Serif,serif; font-weight: =
bold;"><font><font color=3D"#999900">Computational Research Laboratories Lt=
d.,</font></font></span><br style=3D"font-family: Georgia,Default Serif,ser=
if;"><span style=3D"font-style: italic; font-family: Georgia,Default Serif,=
serif;"><font><font color=3D"#999900">Taco House, Damle Path, Off Law Colle=
ge Road</font></font></span><br style=3D"font-style: italic; font-family: G=
eorgia,Default Serif,serif;"><span style=3D"font-style: italic; font-family=
: Georgia,Default Serif,serif;"><font><font color=3D"#999900">Pune - 411004=
, India.</font></font></span><br><br><br></div></font><br> <div><br></div><=
font color=3D"#990099">-----owner-chemistry+psavita=3D=3Dcrlindia.com(0)ccl.n=
et wrote: -----<br><br></font><blockquote style=3D"padding-right: 0px; padd=
ing-left: 5px; margin-left: 5px; border-left: 2px solid #000000; margin-rig=
ht: 0px;">To: "Pundlik, Savita Sunil " <a class=3D"moz-txt-link-rfc=
2396E" href=3D"mailto:psavita(0)crlindia.com">&lt;psavita(0)crlindia.com&gt;</a=
><br>From: "Christopher Cramer cramer[A]umn.edu" <a class=3D"moz-txt-link-r=
fc2396E" href=3D"mailto:owner-chemistry(0)ccl.net">&lt;owner-chemistry(0)ccl.ne=
t&gt;</a><br>Sent by: <a class=3D"moz-txt-link-abbreviated" href=3D"mailto:=
owner-chemistry+psavita=3D=3Dcrlindia.com(0)ccl.net">owner-chemistry+psavita=
=3D=3Dcrlindia.com(0)ccl.net</a><br>Date: 12/01/2011 11:08AM<br>Subject: CCL:=
G: Gaussian Delta G of solution calculation?<br><br>This question, in vario=
us forms, does just keep coming up... <div><br></div> <div>While I'm going =
to take the opportunity to refer to a detailed, formal, and I hope disposit=
ive paper just published by the Minnesota group (doi&nbsp;10.1021/jp205508z=
), I'll also make some effort here to be more cookbooky in an explanation h=
ere. Pedagogy in front! Not just for Gaussian, but more general.</div> <div=
><br></div> <div>The free energy of solvation is, clearly, defined as the D=
IFFERENCE in the free energy of a species in the gas phase and in solution.=
 Free energy is an ensemble property, not a molecular property, so we are i=
mmediately faced with the need to make some approximations in order to rend=
er the modeling tractable.</div> <div><br></div> <div>In the gas phase, tho=
se approximations are by now fairly standard and nearly universal. We make =
the ideal-gas approximation (so that the partition function of a mole of mo=
lecules is simply the product of Avogadro's number of molecular partition f=
unctions), and we make the rigid rotator and harmonic oscillator approximat=
ions to simplify the rovibrational partition functions, and, voila, we have=
 a means to compute a standard state free energy (Gibbs free energy -- free=
 enthalpy for my colleagues in (far more logical) German-speaking countries=
). Pretty much every electronic structure program on earth will do this for=
 you when you run a vibrational frequency calculation in the gas phase. Poo=
f -- you get E, H, S (third law), and G (and Cv too, if you care).</div> <d=
iv><br></div> <div>Note that you should be careful to recognize that (i) un=
less you overrode it, the program chose some default standard state concent=
ration (1 bar? 1 atm? you should know...) and temperature (nearly always 29=
8 K) and scale factor for vibrational frequencies (typically 1, but that mi=
ght not be the best value for a given level of theory) and (ii) the harmoni=
c oscillator approximation is catastrophically bad for super-low frequency =
vibrations (below, say, 50 wavenumbers, to pick an arbitrary value). There =
are fixes for the latter problem, but I'll let someone else post about that=
.</div> <div><br></div> <div>Now, what about G of a solute in solution? Wel=
l, to begin, since we're not dealing with a pure component anymore (at leas=
t, not if the solvent is different than the solute), we need to assume that=
 we have an ideal solution, and we should recognize that we're talking abou=
t a partial molar quantity (more often referred to in the rigorous literatu=
re as a chemical potential than a free energy, but that's a matter of tradi=
tion). In any case, we need to assemble a free energy as a sum of</div> <di=
v><br></div> <div>electronic energy (i.e., potential and kinetic energy of =
electrons for a fixed set of nuclear positions)</div> <div><br></div> <div>=
coupling to medium (which includes electrostatic and non-electrostatic comp=
onents, although, it being chemistry, EVERYTHING is electrostatic... -- in =
practice, however, with continuum models, electrostatic means what you get =
by assuming the molecule is a charge distribution in a cavity embedded in a=
 classical dielectric medium in which case one can apply the Poisson equati=
on -- non-electrostatic is everything else -- dispersion, cavitation, coval=
ent components of hydrogen bonding, hydrophobic effects, you name it)</div>=
 <div><br></div> <div>temperature dependent translational (?), rotational (=
?), vibrational, and conformational contributions -- the question marks ind=
icate conceptual issues</div> <div><br></div> <div>So, a few points to bear=
 in mind. The optimal geometry in solution is unlikely to be the same as th=
at in the gas phase -- but it might be close. You just have to decide for y=
ourself if you want to reoptimize or not.</div> <div><br></div> <div>Same f=
or the vibrational and conformational contributions to free energy in solut=
ion -- they might be very, very close to those in the gas phase -- or they =
might not. If you assume that they ARE the same, you avoid having to do a f=
requency calculation in solution (and you avoid wondering what it means to =
do vibrational frequencies in a continuum, which in principle means a surro=
unding that is in equilibrium with the solute -- but how can a medium compo=
sed of molecules be fully in equilibrium with a molecular solute on the tim=
escale of the solute's vibrations, since the solvent vibrations are on the =
same timescale?)</div> <div><br></div> <div>Note that if I assume no change=
 in the various parts of the free energy EXCEPT for the electronic energy a=
nd solute-solvent coupling (more on that momentarily), life is pretty easy.=
 The free energy of solvation is the difference in the self-consistent reac=
tion-field (SCRF) energy INCLUDING non-electrostatic effects, and the elect=
ronic energy in the gas phase. That is, I look at the expectation value of =
&lt;H+(1/2)V&gt; for the solvated wave function, where V is the reaction fi=
eld operator, add non-electrostatic effects (typically NOT dependent on the=
 quantum wave function, so added post facto, although there are a few excep=
tions in the literature), subtract the expectation value of &lt;H&gt; for t=
he gas-phase wave function (note that you might have done the two expectati=
on values at different geometries, or you might have used the gas-phase geo=
metry for both -- your choice -- the former is more "physical", certainly, =
but the latter is a useful approximation in many instances), and you are do=
ne. You've got the free energy of solvation FOR IDENTICAL STANDARD-STATE CO=
NCENTRATIONS. That is, the number you have in hand assumes no change in sta=
ndard-state concentration. However, many experimental solvation free energi=
es are tabulated for, say, 1 atm gaseous standard states and 1 M solution s=
tandard states. To compare the computed value to the tabulated value, one n=
eeds to correct for the standard-state concentration difference.</div> <div=
><br></div> <div>In the interest of the cookbook, let me be more practical.=
 Thus, let's say that I compute a gas-phase G value, including all contribu=
tions, electronic and otherwise of</div> <div><br></div> <div>-3.000 00 a.u=
.</div> <div><br></div> <div>and, let's say that the electronic energy alon=
e in the gas phase is</div> <div><br></div> <div>-3.020 00 a.u. &nbsp;(so Z=
PVE and thermal contributions to G are +0.020 00 a.u.)</div> <div><br></div=
> <div>and, finally, let's say that my SCRF calculation provides an electro=
nic energy INCLUDING non-electrostatic effects of</div> <div><br></div> <di=
v>-3.030 00 a.u.</div> <div><br></div> <div>In that case, my free energy of=
 solvation is -0.010 00 a.u. (difference of -3.030 00 and -3.020 00 a.u.) A=
nd, if I want to think about my free energy in solution, I can make the ass=
umption that there is no change in the ZPVE and thermal contributions, in w=
hich case I would have G in solution equals -3.010 00 a.u. (which is gas-ph=
ase G of -3.000 00 a.u. plus free energy of solvation -0.010 00 a.u.)</div>=
 <div><br></div> <div>But, just to be clear, if my gas phase G referred to =
a 1 atm standard state concentration, for an ideal gas at 298 K and 1 atm, =
that implies a molarity of 1/24.5 M. If I want my G in solution to be for a=
 1 M standard state, I need to pay the entropy penalty to compress my conce=
ntration from 1/24.5 M to 1 M, which is about 1.9 kcal/mol (the proof is le=
ft to the reader...) So, my 1 M free energy in solution is not -3.010 00 bu=
t rather about -3.006 99 a.u.</div> <div><br></div> <div>The above is an ex=
ample of how almost all free energies of solvation and free energies in sol=
ution are computed in the literature using continuum solvation models (at l=
east if they're done properly!)</div> <div><br></div> <div>Lots of importan=
t details glossed over a bit above (in the interests of clarity, I demur). =
But, to be more thorough, let's note:</div> <div><br></div> <div>1) &nbsp;W=
hy was it (1/2)V in the SCRF calculation? -- the 1/2 comes from linear resp=
onse theory and assumes that you spend precisely half of the favorable coup=
ling energy organizing the medium so that it provides a favorable reaction =
field.</div> <div><br></div> <div>2) &nbsp;How can there be a translational=
 partition function for a solute in solution? There isn't one -- but there =
is something called a liberational free energy associated with accessible v=
olume, and Ben-Naim showed some time ago that the value is identical to tha=
t for the a particle-in-a-box having the same standard-state concentration =
-- i.e., there is no change on going from gas-phase translational partition=
 function to liberational partition function for the same standard-state co=
ncentration for an ideal solution. When there are issues with non-accessibl=
e volume, however, account must be taked (cf. Flory-Huggins theory).</div> =
<div><br></div> <div>3) &nbsp;How can there be a rotational partition funct=
ion for a solute in solution? There isn't one -- solute rotations become li=
brations that are almost certainly intimately coupled with first-solvation-=
shell motions. In essence, assuming no change in "rotational partition func=
tion" implies assuming no free energetic consequence associated with moving=
 from rotations to librations. This remains a poorly resolved question, but=
, in practice, since most continuum solvation models are semiempirical in n=
ature (having been parameterized against experimental data) any actual chan=
ges in free energy have been absorbed in the parameterization as best as po=
ssible. If you find that unsatisfying, hey, feel free not to use continuum =
solvent models -- it's certainly ok by me...</div> <div><br></div> <div>4) =
&nbsp;Where did those non-electrostatic effects come from? Every model is d=
ifferent in that regard, and I won't attempt to summarize a review's-worth =
of material in an email. Lots of nice Chem. Rev. articles over the years on=
 continuum models if you want to catch up.</div> <div><br></div> <div>Final=
ly, what is described above is a popular approach for computing solvation f=
ree energies and free energies in solution, but by no means the only approa=
ch out there. A non-exhaustive list to compute either or both solvation fre=
e energies or free energies in solution includes free-energy perturbation f=
rom explicit simulations, RISM-based models, fragment-based models derived =
&gt; from a statistical mechanical approach (including COSMO-RS and variati=
ons on that theme), fragment-based models from expert learning, and models =
relying on alternative physicochemical approaches to computing interaction =
energies (e.g., SPARC). These alternative models can be quantal, classical,=
 or SMILESal (which is to say, more in the realm of chemoinformatics than p=
hysical chemistry). Let a thousand flowers bloom.</div> <div><br></div> <di=
v>I hope that this post serves as a useful archival reference for CCL users=
 present and future. Best wishes to all for a peaceful winter solstice (or =
summer, for my antipodeal colleagues).</div> <div><br></div> <div>Chris</di=
v> <div><br></div> <div><br></div> <div><br> <div> <div>On Nov 30, 2011, at=
 1:46 PM, Close, David M. CLOSED#,#mail.etsu.edu wrote:</div><br class=3D"A=
pple-interchange-newline"><blockquote type=3D"cite"><span class=3D"Apple-st=
yle-span" style=3D"border-collapse: separate; font-family: Helvetica; font-=
style: normal; font-variant: normal; font-weight: normal; letter-spacing: n=
ormal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: n=
one; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;"=
> <div link=3D"blue" vlink=3D"purple" lang=3D"EN-US"> <div class=3D"WordSec=
tion1" style=3D"page: WordSection1;"> <div style=3D"margin: 0in 0in 0.0001p=
t; font-size: 11pt; font-family: Calibri,sans-serif;">&nbsp; Does anyone kn=
ow how Gaussian calculates deltaG of solvation?&nbsp; This was in G98 and w=
as automatic.&nbsp; In G03 one had to add SCFVAC in the scrf(CPCM,read) rea=
d list to get the delta G result.&nbsp; I have several questions about the =
methods used.&nbsp; I presume that during the SCRF calculation the program =
has to have a separate SCF calculation on the input molecule &nbsp;in the g=
as phase, along with a frequency calculation to know the free energy of the=
 gas phase structure.&nbsp; Is this correct?&nbsp; If so, are the ZPE and f=
ree energy correction terms multiplied by a scale factor (0.92 for example?=
).&nbsp; Also to do solvation energy calculations one need to convert the g=
as phase reference state from 1 atmos. to 1 M.&nbsp; Does the program repor=
t this corrected delta G value?&nbsp;<o:p></o:p></div> <div style=3D"margin=
: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri,sans-serif;">&nbs=
p;&nbsp;My reason for asking is that I have done these actual calculations =
separately with energy/frequency calculations on the neutral and anion, and=
 I get slightly difference answers from those answers using SCFVAC, and I n=
eed to know why this is?<o:p></o:p></div> <div style=3D"margin: 0in 0in 0.0=
001pt; font-size: 11pt; font-family: Calibri,sans-serif;">&nbsp; Regards, D=
ave Close.<o:p></o:p></div></div></div></span></blockquote></div><br> <div>=
=0D<span class=3D"Apple-style-span" style=3D"border-collapse: separate; fon=
t-family: Helvetica; font-style: normal; font-variant: normal; font-weight:=
 normal; letter-spacing: normal; line-height: normal; orphans: 2; text-inde=
nt: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing=
: 0px; font-size: medium;"><font color=3D"#000000"><span class=3D"Apple-sty=
le-span" style=3D"border-collapse: separate; font-family: Helvetica; font-s=
ize: medium; font-style: normal; font-variant: normal; font-weight: normal;=
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family: Helvetica; font-size: medium; font-style: normal; font-variant: nor=
mal; font-weight: normal; letter-spacing: normal; line-height: normal; orph=
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: 2; word-spacing: 0px;"><font color=3D"#000000"> <div style=3D"word-wrap: =
break-word;"><span class=3D"Apple-style-span" style=3D"border-collapse: sep=
arate; font-family: Helvetica; font-size: 12px; font-style: normal; font-va=
riant: normal; font-weight: normal; letter-spacing: normal; line-height: no=
rmal; orphans: 2; text-indent: 0px; text-transform: none; white-space: norm=
al; widows: 2; word-spacing: 0px;"><font color=3D"#000000"> <div style=3D"w=
ord-wrap: break-word;"> <div><p style=3D"margin: 0px;"><font style=3D"font:=
 12px Helvetica;" face=3D"Helvetica" size=3D"3">--</font> </p><p style=3D"m=
argin: 0px; font: 12px Helvetica; min-height: 14px;"><br> </p><p style=3D"m=
argin: 0px;"><font style=3D"font: 12px Helvetica;" face=3D"Helvetica" size=
=3D"3">Christopher J. Cramer</font> </p><p style=3D"margin: 0px;">Elmore H.=
 Northey Professor </p><p style=3D"margin: 0px;"><font style=3D"font: 12px =
Helvetica;" face=3D"Helvetica" size=3D"3">University of Minnesota</font> </=
p><p style=3D"margin: 0px;"><font style=3D"font: 12px Helvetica;" face=3D"H=
elvetica" size=3D"3">Department of Chemistry</font> </p><p style=3D"margin:=
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207 Pleasant St. SE</font> </p><p style=3D"margin: 0px;"><font style=3D"fon=
t: 12px Helvetica;" face=3D"Helvetica" size=3D"3">Minneapolis, MN 55455-043=
1</font> </p><p style=3D"margin: 0px;"><font style=3D"font: 12px Helvetica;=
" face=3D"Helvetica" size=3D"3">--------------------------</font> </p><p st=
yle=3D"margin: 0px;"><font style=3D"font: 12px Helvetica;" face=3D"Helvetic=
a" size=3D"3">Phone:<span class=3D"Apple-converted-space">&nbsp;<span class=
=3D"Apple-converted-space">&nbsp;</span></span>(612) 624-0859 || FAX:<span =
class=3D"Apple-converted-space">&nbsp;<span class=3D"Apple-converted-space"=
>&nbsp;</span></span>(612) 626-7541</font> </p><p style=3D"margin: 0px;"><f=
ont style=3D"font: 12px Helvetica;" face=3D"Helvetica" size=3D"3">Mobile: (=
952) 297-2575</font> </p><p style=3D"margin: 0px;"><font style=3D"font: 12p=
x Helvetica;" face=3D"Helvetica" size=3D"3">email: &nbsp;<a href=3D"mailto:=
cramer:=5F:umn.edu">cramer:=5F:umn.edu</a></font> </p><p style=3D"margin: 0=
px;">jabber: &nbsp;<a href=3D"mailto:cramer:=5F:jabber.umn.edu">cramer:=5F:=
jabber.umn.edu</a> </p><p style=3D"margin: 0px;"><font style=3D"font: 12px =
Helvetica;" face=3D"Helvetica" size=3D"3"><a href=3D"http://pollux.chem.umn=
.edu">http://pollux.chem.umn.edu</a></font> </p><p style=3D"margin: 0px;"><=
font style=3D"font: 12px Helvetica;" face=3D"Helvetica" size=3D"3">(website=
 includes information about the textbook "Essentials</font> </p><p style=3D=
"margin: 0px;"><font style=3D"font: 12px Helvetica;" face=3D"Helvetica" siz=
e=3D"3"><span class=3D"Apple-converted-space">&nbsp; &nbsp;<span class=3D"A=
pple-converted-space">&nbsp;</span></span>of Computational Chemistry:<span =
class=3D"Apple-converted-space">&nbsp;<span class=3D"Apple-converted-space"=
>&nbsp;</span></span>Theories and Models, 2nd Edition")</font> </p><br clas=
s=3D"Apple-interchange-newline"></div></div></font></span><br class=3D"Appl=
e-interchange-newline"></div></font></span><br class=3D"Apple-interchange-n=
ewline"></div></font></span><br class=3D"Apple-interchange-newline"></div><=
/font></span><br class=3D"Apple-interchange-newline"></font></span><br clas=
s=3D"Apple-interchange-newline">=0D</div><br></div></blockquote><br></div><=
/font>=0D<br/>=


From owner-chemistry@ccl.net Thu Dec  1 11:25:01 2011
From: "Carlos T Nieto eneas]|[usal.es" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Additional imaginary frecuencies: tested almost everything
Message-Id: <-45957-111201112411-2977-QtKyvBRBcANIkg63+rkrjA+*+server.ccl.net>
X-Original-From: "Carlos T Nieto" <eneas,usal.es>
Date: Thu, 1 Dec 2011 11:24:09 -0500


Sent to CCL by: "Carlos T Nieto" [eneas,+,usal.es]

Hi, everybody

One of the typical problems in a optimization is the appearrance of additional imaginary frecuencies in optimization or transition state minimizations.

Im an user of Jaguar. In many frequency calculations i obtain small negative frequencies, e.g. <
-30 cm-1.It's very frequently i obtained it in:

     - Solvent calculations
     - Transition states when freezing atoms involved in it. It's to
optimize the different substituents.

When this frequencies are associated with certain type of easy
identifiable displacement, i modify the geometry along the suspected
vibration and reoptimize. This works well. Nevertheless, the most
difficult cases is when the displacement is difficult (some type of small
apparent rotation where almost all atoms participate) i don't know how to disturb it. It often appears when i freeze atoms, let's say to block the atoms involved in a TS to add substituents and reoptimize or in solvent calculations.

With this type of frequencies i've tried several ways, but inefficiently:

 - Disturbing bulky groups and reoptimizing.
 - Some authors suggest it's a problem of the grid build up of the dft
process. I tried to change to fine or ultrafine type grids without success.
 - Other opinion is that is a mathematical artefact and such frequencies
could be ignored. I've cheked a few publications and it's indicated.
 - In Transition state searchs, the small negative frequency is the
eigenvector n 2. Trying to force to search along eigenvector 1 or lowest
eigenvector doesn't works again.

So, What else can i do? I'm not sure if i'm doing something wrong... Is
there a way to getting rid of it? If not, May i accept the result and
ignore the small imaginary frequency? Other authors said that, accepting
this, it's not accurate taking the thermodinamic data from the frequency
calculations...

Will be reportable my results ignoring this additional frecuencies? Shall I indicate them?

Ill appreciate all the ideas from you.


From owner-chemistry@ccl.net Thu Dec  1 15:22:01 2011
From: "Bradley Welch bwelch5^_^slu.edu" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Additional imaginary frecuencies: tested almost everything
Message-Id: <-45958-111201132220-7816-KJOdXVkl4zqCQ5ozch2dxg::server.ccl.net>
X-Original-From: Bradley Welch <bwelch5*slu.edu>
Content-Type: multipart/alternative; boundary=14dae93409556b72bf04b30beebc
Date: Thu, 1 Dec 2011 12:22:12 -0600
MIME-Version: 1.0


Sent to CCL by: Bradley Welch [bwelch5..slu.edu]
--14dae93409556b72bf04b30beebc
Content-Type: text/plain; charset=ISO-8859-1

What method are you using? Some of the functionals are known for causing
small imaginary frequencies and can be ignored.


Bradley Welch

On Thu, Dec 1, 2011 at 10:24 AM, Carlos T Nieto eneas]|[usal.es <
owner-chemistry*ccl.net> wrote:

>
> Sent to CCL by: "Carlos T Nieto" [eneas,+,usal.es]
>
> Hi, everybody
>
> One of the typical problems in a optimization is the appearrance of
> additional imaginary frecuencies in optimization or transition state
> minimizations.
>
> Im an user of Jaguar. In many frequency calculations i obtain small
> negative frequencies, e.g. <
> -30 cm-1.It's very frequently i obtained it in:
>
>     - Solvent calculations
>     - Transition states when freezing atoms involved in it. It's to
> optimize the different substituents.
>
> When this frequencies are associated with certain type of easy
> identifiable displacement, i modify the geometry along the suspected
> vibration and reoptimize. This works well. Nevertheless, the most
> difficult cases is when the displacement is difficult (some type of small
> apparent rotation where almost all atoms participate) i don't know how to
> disturb it. It often appears when i freeze atoms, let's say to block the
> atoms involved in a TS to add substituents and reoptimize or in solvent
> calculations.
>
> With this type of frequencies i've tried several ways, but inefficiently:
>
>  - Disturbing bulky groups and reoptimizing.
>  - Some authors suggest it's a problem of the grid build up of the dft
> process. I tried to change to fine or ultrafine type grids without success.
>  - Other opinion is that is a mathematical artefact and such frequencies
> could be ignored. I've cheked a few publications and it's indicated.
>  - In Transition state searchs, the small negative frequency is the
> eigenvector n 2. Trying to force to search along eigenvector 1 or lowest
> eigenvector doesn't works again.
>
> So, What else can i do? I'm not sure if i'm doing something wrong... Is
> there a way to getting rid of it? If not, May i accept the result and
> ignore the small imaginary frequency? Other authors said that, accepting
> this, it's not accurate taking the thermodinamic data from the frequency
> calculations...
>
> Will be reportable my results ignoring this additional frecuencies? Shall
> I indicate them?
>
> Ill appreciate all the ideas from you.>
>
>

--14dae93409556b72bf04b30beebc
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

What method are you using? Some of the functionals are known for causing sm=
all imaginary frequencies and can be ignored.=A0<div><br></div><div><br></d=
iv><div>Bradley Welch=A0<br><br><div class=3D"gmail_quote">On Thu, Dec 1, 2=
011 at 10:24 AM, Carlos T Nieto eneas]|[<a href=3D"http://usal.es">usal.es<=
/a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry*ccl.net">owner-=
chemistry*ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: &quot;Carlos T Nieto&quot; [eneas,+,<a href=3D"http://usal.=
es" target=3D"_blank">usal.es</a>]<br>
<br>
Hi, everybody<br>
<br>
One of the typical problems in a optimization is the appearrance of additio=
nal imaginary frecuencies in optimization or transition state minimizations=
.<br>
<br>
Im an user of Jaguar. In many frequency calculations i obtain small negativ=
e frequencies, e.g. &lt;<br>
-30 cm-1.It&#39;s very frequently i obtained it in:<br>
<br>
 =A0 =A0 - Solvent calculations<br>
 =A0 =A0 - Transition states when freezing atoms involved in it. It&#39;s t=
o<br>
optimize the different substituents.<br>
<br>
When this frequencies are associated with certain type of easy<br>
identifiable displacement, i modify the geometry along the suspected<br>
vibration and reoptimize. This works well. Nevertheless, the most<br>
difficult cases is when the displacement is difficult (some type of small<b=
r>
apparent rotation where almost all atoms participate) i don&#39;t know how =
to disturb it. It often appears when i freeze atoms, let&#39;s say to block=
 the atoms involved in a TS to add substituents and reoptimize or in solven=
t calculations.<br>

<br>
With this type of frequencies i&#39;ve tried several ways, but inefficientl=
y:<br>
<br>
=A0- Disturbing bulky groups and reoptimizing.<br>
=A0- Some authors suggest it&#39;s a problem of the grid build up of the df=
t<br>
process. I tried to change to fine or ultrafine type grids without success.=
<br>
=A0- Other opinion is that is a mathematical artefact and such frequencies<=
br>
could be ignored. I&#39;ve cheked a few publications and it&#39;s indicated=
.<br>
=A0- In Transition state searchs, the small negative frequency is the<br>
eigenvector n 2. Trying to force to search along eigenvector 1 or lowest<br=
>
eigenvector doesn&#39;t works again.<br>
<br>
So, What else can i do? I&#39;m not sure if i&#39;m doing something wrong..=
. Is<br>
there a way to getting rid of it? If not, May i accept the result and<br>
ignore the small imaginary frequency? Other authors said that, accepting<br=
>
this, it&#39;s not accurate taking the thermodinamic data from the frequenc=
y<br>
calculations...<br>
<br>
Will be reportable my results ignoring this additional frecuencies? Shall I=
 indicate them?<br>
<br>
Ill appreciate all the ideas from you.<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
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<br>
<br>
</blockquote></div><br></div>

--14dae93409556b72bf04b30beebc--


From owner-chemistry@ccl.net Thu Dec  1 15:57:00 2011
From: "Carlos T Nieto eneas:-:usal.es" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Additional imaginary frecuencies: tested almost everything
Message-Id: <-45959-111201154843-4582-M1PxjFsrfP+cd2wt04BJcw---server.ccl.net>
X-Original-From: "Carlos T  Nieto" <eneas{=}usal.es>
Date: Thu, 1 Dec 2011 15:48:41 -0500


Sent to CCL by: "Carlos T  Nieto" [eneas]_[usal.es]
Hi, everybody
>
> One of the typical problems in a optimization is the appearrance of
> additional imaginary frecuencies in optimization or transition state
> minimizations.
>
> Im an user of Jaguar. In many frequency calculations (DFT-B3LYP) i obtain small negative frequencies, e.g. <
> -30 cm-1.It's very frequently i obtained it in:
>
>     - Solvent calculations
>     - Transition states when freezing atoms involved in it. It's to
> optimize the different substituents.
>
> When this frequencies are associated with certain type of easy
> identifiable displacement, i modify the geometry along the suspected
> vibration and reoptimize. This works well. Nevertheless, the most
> difficult cases is when the displacement is difficult (some type of small
> apparent rotation where almost all atoms participate) i don't know how to
> disturb it. It often appears when i freeze atoms, let's say to block the
> atoms involved in a TS to add substituents and reoptimize or in solvent
> calculations.
>
> With this type of frequencies i've tried several ways, but inefficiently:
>
>  - Disturbing bulky groups and reoptimizing.
>  - Some authors suggest it's a problem of the grid build up of the dft
> process. I tried to change to fine or ultrafine type grids without success.
>  - Other opinion is that is a mathematical artefact and such frequencies
> could be ignored. I've cheked a few publications and it's indicated.
>  - In Transition state searchs, the small negative frequency is the
> eigenvector n 2. Trying to force to search along eigenvector 1 or lowest
> eigenvector doesn't works again.
>
> So, What else can i do? I'm not sure if i'm doing something wrong... Is
> there a way to getting rid of it? If not, May i accept the result and
> ignore the small imaginary frequency? Other authors said that, accepting
> this, it's not accurate taking the thermodinamic data from the frequency
> calculations...
>
> Will be reportable my results ignoring this additional frecuencies? Shall
> I indicate them?
>
> Ill appreciate all the ideas from you.>


From owner-chemistry@ccl.net Thu Dec  1 16:32:00 2011
From: "Guilherme Cordeiro guilhermecord^_^gmail.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Problem in converting output file
Message-Id: <-45960-111201161910-12329-QOVQhdPDDUtAYXk1KfXKuA]|[server.ccl.net>
X-Original-From: "Guilherme  Cordeiro" <guilhermecord%gmail.com>
Date: Thu, 1 Dec 2011 16:19:08 -0500


Sent to CCL by: "Guilherme  Cordeiro" [guilhermecord~~gmail.com]
Dear CCL members,

I have converted a *.chk file to a *.pdb file by using NewZmat. The thing is that everytime I try to open up the *.pdb at Autodock 4.2 I get an error message like "unknown ligand file type PDB". Can anyone help me solving this?

Thanks in advance.


From owner-chemistry@ccl.net Thu Dec  1 17:47:00 2011
From: "Alec Young alecyoung76(0)yahoo.com" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL:G: Basis sets for Xe
Message-Id: <-45961-111201165536-23916-9vYtzCEF0CDgFjgyTXpMHg a server.ccl.net>
X-Original-From: "Alec  Young" <alecyoung76*_*yahoo.com>
Date: Thu, 1 Dec 2011 16:55:27 -0500


Sent to CCL by: "Alec  Young" [alecyoung76[#]yahoo.com]
Deal All,

I used M052X/6-31+G* in gaussian trying to optimize the distance between Xe and a ethylene. And I got this error:

"Atomic number out of range for 6-31G basis set."

What basis set can I use?

Thanks,

-Alec


From owner-chemistry@ccl.net Thu Dec  1 19:21:00 2011
From: "Bradley Welch bwelch5,slu.edu" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL:G: Basis sets for Xe
Message-Id: <-45962-111201191828-18419-VWstJOGad5QzTdZFo7RUmQ.@.server.ccl.net>
X-Original-From: Bradley Welch <bwelch5^slu.edu>
Content-Type: multipart/alternative; boundary=90e6ba6e836c1ee81104b310e82f
Date: Thu, 1 Dec 2011 18:18:21 -0600
MIME-Version: 1.0


Sent to CCL by: Bradley Welch [bwelch5,slu.edu]
--90e6ba6e836c1ee81104b310e82f
Content-Type: text/plain; charset=ISO-8859-1

For the Xe atom you could use a ECP like the lanl2dz.


Assuming you have the computational resources......K.A Peterson
et.alproduced a DZ basis set for Xe.

The reference for the article covering the batch of atoms Xenon is in is

K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and
M. Dolg, J. Chem. Phys. 119, 11113 (2003)



Bradley Welch

On Thu, Dec 1, 2011 at 3:55 PM, Alec Young alecyoung76(0)yahoo.com <
owner-chemistry * ccl.net> wrote:

>
> Sent to CCL by: "Alec  Young" [alecyoung76[#]yahoo.com]
> Deal All,
>
> I used M052X/6-31+G* in gaussian trying to optimize the distance between
> Xe and a ethylene. And I got this error:
>
> "Atomic number out of range for 6-31G basis set."
>
> What basis set can I use?
>
> Thanks,
>
> -Alec>
>
>

--90e6ba6e836c1ee81104b310e82f
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

For the Xe atom you could use a ECP like the lanl2dz.=A0<div><br></div><div=
><br></div><div>Assuming you have the computational resources......K.A Pete=
rson <a href=3D"http://et.al">et.al</a> produced a DZ basis set for Xe.=A0<=
/div>
<div><br></div><div>The reference for the article covering the batch of ato=
ms Xenon is in is=A0</div><div><br></div><div><pre style=3D"font-family: Co=
urier, fixed; font-size: 9pt; background-color: rgb(255, 255, 255); margin-=
left: 10px; ">
K.A. Peterson, D. Figgen, E. Goll, H. Stoll, and
M. Dolg, J. Chem. Phys. 119, 11113 (2003)</pre></div><div><br></div><div><b=
r></div><div>Bradley Welch=A0<br><br><div class=3D"gmail_quote">On Thu, Dec=
 1, 2011 at 3:55 PM, Alec Young alecyoung76(0)<a href=3D"http://yahoo.com">=
yahoo.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry * ccl.n=
et">owner-chemistry * ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: &quot;Alec =A0Young&quot; [alecyoung76[#]<a href=3D"http://=
yahoo.com" target=3D"_blank">yahoo.com</a>]<br>
Deal All,<br>
<br>
I used M052X/6-31+G* in gaussian trying to optimize the distance between Xe=
 and a ethylene. And I got this error:<br>
<br>
&quot;Atomic number out of range for 6-31G basis set.&quot;<br>
<br>
What basis set can I use?<br>
<br>
Thanks,<br>
<br>
-Alec<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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--90e6ba6e836c1ee81104b310e82f--


From owner-chemistry@ccl.net Thu Dec  1 19:56:01 2011
From: "Chenghua Zhang zchua126.com]=[126.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Basis sets for Xe
Message-Id: <-45963-111201192809-29693-awHiMKLvLoVDXS5HZNHwzA===server.ccl.net>
X-Original-From: "Chenghua Zhang" <zchua126.com~!~126.com>
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	boundary="----=_Part_224553_516749418.1322785675590"
Date: Fri, 2 Dec 2011 08:27:55 +0800 (CST)
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Sent to CCL by: "Chenghua Zhang" [zchua126.com^-^126.com]
------=_Part_224553_516749418.1322785675590
Content-Type: text/plain; charset=GBK
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Hi, you can read some references or check the "basis set exchange" (https://bse.pnl.gov/bse/portal)


--

Sincerely
Chenghua Zhang
College of Chemistry
Sichuan University, China.




------=_Part_224553_516749418.1322785675590
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<div style="line-height:1.7;color:#000000;font-size:14px;font-family:arial"><DIV>Hi, you can read some references or check the "basis set exchange" (<A href="https://bse.pnl.gov/bse/portal">https://bse.pnl.gov/bse/portal</A>)<BR><BR></DIV>
<DIV>--<BR>
<DIV>Sincerely</DIV>
<DIV>Chenghua Zhang</DIV>
<DIV>College of Chemistry</DIV>
<DIV>Sichuan University, China.</DIV></DIV>
<DIV id="divNeteaseMailCard"></DIV>
<DIV><BR></DIV><PRE><BR></PRE></div><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>
------=_Part_224553_516749418.1322785675590--


From owner-chemistry@ccl.net Thu Dec  1 20:31:01 2011
From: "dipankar roy theodip(a)gmail.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL:G: Basis sets for Xe
Message-Id: <-45964-111201193517-31964-yz+OX65ybN35A1C75sGAIg\a/server.ccl.net>
X-Original-From: dipankar roy <theodip-x-gmail.com>
Content-Type: multipart/alternative; boundary=00151747be6a23806a04b31124ea
Date: Thu, 1 Dec 2011 19:35:08 -0500
MIME-Version: 1.0


Sent to CCL by: dipankar roy [theodip%a%gmail.com]
--00151747be6a23806a04b31124ea
Content-Type: text/plain; charset=ISO-8859-1

Hi,
You can try basis sets like def2-TZVP or modified correlation consistent
basis sets of Dunning with ECPs. You can get them from EMSL basis set
exchange.

best,
Dipankar Roy

-----------------------------------
Dr. Dipankar Roy
Research Associate
Hunter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------


On Thu, Dec 1, 2011 at 4:55 PM, Alec Young alecyoung76(0)yahoo.com <
owner-chemistry,+,ccl.net> wrote:

>
> Sent to CCL by: "Alec  Young" [alecyoung76[#]yahoo.com]
> Deal All,
>
> I used M052X/6-31+G* in gaussian trying to optimize the distance between
> Xe and a ethylene. And I got this error:
>
> "Atomic number out of range for 6-31G basis set."
>
> What basis set can I use?
>
> Thanks,
>
> -Alec>
>
>


--

--00151747be6a23806a04b31124ea
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi,<div>You can try basis sets like=A0<span class=3D"Apple-style-span" styl=
e=3D"font-family: &#39;Trebuchet MS&#39;, Arial, Helvetica, sans-serif; fon=
t-size: 14px; line-height: 22px; background-color: rgb(255, 255, 255); ">de=
f2-TZVP or modified correlation consistent basis sets of Dunning with ECPs.=
 You can get them from EMSL basis set exchange.=A0</span></div>
<div><br></div><div>best,</div><div>Dipankar Roy<br><br>-------------------=
----------------<div>Dr. Dipankar Roy</div><div>Research Associate</div><di=
v>Hunter College (CUNY)</div><div>695 Park Avenue</div><div>New York, USA</=
div>
<div>NY-10065</div><div>-----------------------------------</div><div><br><=
/div><br><div class=3D"gmail_quote">On Thu, Dec 1, 2011 at 4:55 PM, Alec Yo=
ung alecyoung76(0)<a href=3D"http://yahoo.com">yahoo.com</a> <span dir=3D"l=
tr">&lt;<a href=3D"mailto:owner-chemistry,+,ccl.net">owner-chemistry,+,ccl.net<=
/a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: &quot;Alec =A0Young&quot; [alecyoung76[#]<a href=3D"http://=
yahoo.com" target=3D"_blank">yahoo.com</a>]<br>
Deal All,<br>
<br>
I used M052X/6-31+G* in gaussian trying to optimize the distance between Xe=
 and a ethylene. And I got this error:<br>
<br>
&quot;Atomic number out of range for 6-31G basis set.&quot;<br>
<br>
What basis set can I use?<br>
<br>
Thanks,<br>
<br>
-Alec<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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</blockquote></div><br><br clear=3D"all"><div><br></div>-- <br><br>
</div>

--00151747be6a23806a04b31124ea--


From owner-chemistry@ccl.net Thu Dec  1 23:22:00 2011
From: "psavita savita.pundlik=-=crl-global.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Query for Rosetta software
Message-Id: <-45965-111201231738-32616-bqy2sFboJ+w4Fl7bN8aj1Q]*[server.ccl.net>
X-Original-From: psavita <savita.pundlik*crl-global.com>
Content-Transfer-Encoding: quoted-printable
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	charset=ISO-8859-1
Date: Fri, 2 Dec 2011 09:47:29 +0530
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MIME-Version: 1.0


Sent to CCL by: psavita [savita.pundlik:_:crl-global.com]
<font face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=
=3D"2"> <div><font><font><font face=3D"Default Sans Serif,Verdana,Arial,Hel=
vetica,sans-serif" size=3D"2"><font face=3D"Default Sans Serif,Verdana,Aria=
l,Helvetica,sans-serif" size=3D"2">Dear All,<br><br>We are trying to run De=
novo structure prediction using Rosetta standalone =0Dprogram.We could not =
find the module 'picker.linuxgccrelease =0D(0)best-fragments-protocol.flags' =
in the rosetta bundle. So we are unable to=0D generate the fragments.Can an=
yone<font><font face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-ser=
if" size=3D"2"> let us know from where to download it.</font></font><br><br=
>Is there any tool available which can perform the same task of fragment ge=
neration and will be compatible with rosetta?<br><br>regards,</font></font>=
</font></font></div> <div><font face=3D"Default Sans Serif,Verdana,Arial,He=
lvetica,sans-serif" size=3D"2"> <div><font style=3D"font-family: Georgia,De=
fault Serif,serif; font-weight: bold;" color=3D"#0000ff"><font color=3D"#99=
9900">Savita Pundlik</font></font><br style=3D"font-family: Georgia,Default=
 Serif,serif;"><span style=3D"font-family: Georgia,Default Serif,serif;"><f=
ont><font color=3D"#999900">Computational Materials </font></font></span><f=
ont color=3D"#999900">Research &amp; Innovation Group</font><br style=3D"fo=
nt-family: Georgia,Default Serif,serif;"><span style=3D"font-family: Georgi=
a,Default Serif,serif; font-weight: bold;"><font><font color=3D"#999900">Co=
mputational Research Laboratories Ltd.,</font></font></span><br style=3D"fo=
nt-family: Georgia,Default Serif,serif;"><span style=3D"font-style: italic;=
 font-family: Georgia,Default Serif,serif;"><font><font color=3D"#999900">T=
aco House, Damle Path, Off Law College Road</font></font></span><br style=
=3D"font-style: italic; font-family: Georgia,Default Serif,serif;"><span st=
yle=3D"font-style: italic; font-family: Georgia,Default Serif,serif;"><font=
><font color=3D"#999900">Pune - 411004, India.</font></font></span><br></di=
v></font><br></div></font>=0D<br/>=


From owner-chemistry@ccl.net Thu Dec  1 23:56:00 2011
From: "Abrash, Sam sabrash#,#richmond.edu" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL:G: Basis sets for Xe
Message-Id: <-45966-111201233119-21484-NOMRagMlHv97xt5EuExcvQ\a/server.ccl.net>
X-Original-From: "Abrash, Sam" <sabrash##richmond.edu>
Content-Language: en-US
Content-Type: multipart/alternative;
	boundary="_000_DB1DF332AFC21544BA642BA6B7D4654D368B6570E6UREXCHANGESCC_"
Date: Thu, 1 Dec 2011 23:31:06 -0500
MIME-Version: 1.0


Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu]
--_000_DB1DF332AFC21544BA642BA6B7D4654D368B6570E6UREXCHANGESCC_
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: quoted-printable

In addition to finding a basis set for Xe, it's important to understand why=
 6-31G is not extended as far as Xe.  For very heavy atoms such as Xe, the =
very large nuclear charge means that core electrons are moving at speeds at=
 which special relativity has an important effect on the results.  One such=
 results is that the bond lengths calculated for very heavy atoms using the=
 Dirac equation, which includes the effect of special relativity are shorte=
r than those from the Schrodinger equation, which ignores relativistic effe=
cts.  This shortening of bond lengths is called relativistic contraction.

The way that this is handled for most of us is to use basis sets in which t=
he functions for the core electrons are replaced by potential energy functi=
ons which have been calculated using the dirac equation.  These are called =
relativistic effective core potentials, although they are usually simply re=
ferred to as ECPs.  The valence electrons are treated with normal basis fun=
ctions since electron shielding means that their average velocities are far=
 from the relativistic limit.  Using these ECP basis sets has two attractiv=
e outcomes.  First, it means that the relativistic effects are accounted fo=
r.  Second, since the large number of core electrons is replaced by a relat=
ively small number of potential functions, the computational expense is sub=
stantially reduced compared to all electron bases.

I hope this is helpful.

Best regards,
Sam

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone:  804-289-8248
Fax:  804-287-1897
E-mail:  sabrash : richmond.edu<mailto:sabrash : richmond.edu>
Web-page:  http://www.richmond.edu/~sabrash<http://oncampus.richmond.edu/~s=
abrash>
"In 1893 Charles Hinton left Japan to become a mathematics instructor at Pr=
inceton University, where he invented a baseball-pitching machine that used=
 gunpowder to propel the balls, like a cannon.  After several accidents, th=
e device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian St=
eward and Jack Cohen, The Science of Diskworld III

> From: owner-chemistry+sabrash=3D=3Drichmond.edu : ccl.net [mailto:owner-chemi=
stry+sabrash=3D=3Drichmond.edu : ccl.net] On Behalf Of dipankar roy theodip(a=
)gmail.com
Sent: Thursday, December 01, 2011 7:35 PM
To: Abrash, Sam
Subject: CCL:G: Basis sets for Xe

Hi,
You can try basis sets like def2-TZVP or modified correlation consistent ba=
sis sets of Dunning with ECPs. You can get them from EMSL basis set exchang=
e.

best,
Dipankar Roy

-----------------------------------
Dr. Dipankar Roy
Research Associate
Hunter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------


On Thu, Dec 1, 2011 at 4:55 PM, Alec Young alecyoung76(0)yahoo.com<http://y=
ahoo.com> <owner-chemistry*_*ccl.net<mailto:owner-chemistry*_*ccl.net>> wro=
te:

Sent to CCL by: "Alec  Young" [alecyoung76[#]yahoo.com<http://yahoo.com>]
Deal All,

I used M052X/6-31+G* in gaussian trying to optimize the distance between Xe=
 and a ethylene. And I got this error:

"Atomic number out of range for 6-31G basis set."

What basis set can I use?

Thanks,

-Alec



-=3D This is automatically added to each message by the mailing script =3D-=
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<html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D"urn:schemas-micr=
osoft-com:office:office" xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns:m=3D"http://schemas.microsoft.com/office/2004/12/omml" xmlns=3D"http:=
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<o:shapedefaults v:ext=3D"edit" spidmax=3D"1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext=3D"edit">
<o:idmap v:ext=3D"edit" data=3D"1" />
</o:shapelayout></xml><![endif]--></head><body lang=3DEN-US link=3Dblue vli=
nk=3Dpurple><div class=3DWordSection1><p class=3DMsoNormal><span style=3D'c=
olor:blue'>In addition to finding a basis set for Xe, it&#8217;s important =
to understand why 6-31G is not extended as far as Xe.&nbsp; For very heavy =
atoms such as Xe, the very large nuclear charge means that core electrons a=
re moving at speeds at which special relativity has an important effect on =
the results.&nbsp; One such results is that the bond lengths calculated for=
 very heavy atoms using the Dirac equation, which includes the effect of sp=
ecial relativity are shorter than those from the Schrodinger equation, whic=
h ignores relativistic effects.&nbsp; This shortening of bond lengths is ca=
lled relativistic contraction.<o:p></o:p></span></p><p class=3DMsoNormal><s=
pan style=3D'color:blue'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal><=
span style=3D'color:blue'>The way that this is handled for most of us is to=
 use basis sets in which the functions for the core electrons are replaced =
by potential energy functions which have been calculated using the dirac eq=
uation.&nbsp; These are called relativistic effective core potentials, alth=
ough they are usually simply referred to as ECPs.&nbsp; The valence electro=
ns are treated with normal basis functions since electron shielding means t=
hat their average velocities are far from the relativistic limit.&nbsp; Usi=
ng these ECP basis sets has two attractive outcomes.&nbsp; First, it means =
that the relativistic effects are accounted for.&nbsp; Second, since the la=
rge number of core electrons is replaced by a relatively small number of po=
tential functions, the computational expense is substantially reduced compa=
red to all electron bases.<o:p></o:p></span></p><p class=3DMsoNormal><span =
style=3D'color:blue'><o:p>&nbsp;</o:p></span></p><p class=3DMsoNormal><span=
 style=3D'color:blue'>I hope this is helpful.<o:p></o:p></span></p><p class=
=3DMsoNormal><span style=3D'color:blue'><o:p>&nbsp;</o:p></span></p><p clas=
s=3DMsoNormal><span style=3D'color:blue'>Best regards,<o:p></o:p></span></p=
><p class=3DMsoNormal><span style=3D'color:blue'>Sam<o:p></o:p></span></p><=
p class=3DMsoNormal><span style=3D'color:blue'><o:p>&nbsp;</o:p></span></p>=
<p class=3DMsoNormal><span style=3D'color:blue'>Samuel A. Abrash<br>Departm=
ent of Chemistry<br>University of Richmond<br>Richmond, VA 23173<br>Phone:&=
nbsp; 804-289-8248<br>Fax:&nbsp; 804-287-1897<br>E-mail:&nbsp; <a href=3D"m=
ailto:sabrash : richmond.edu">sabrash : richmond.edu</a><br>Web-page:&nbsp; <a =
href=3D"http://oncampus.richmond.edu/~sabrash">http://www.richmond.edu/~sab=
rash</a><o:p></o:p></span></p><p class=3DMsoNormal><span style=3D'font-size=
:11.0pt;font-family:"Calibri","sans-serif";color:blue'>&quot;In 1893&nbsp;C=
harles Hinton&nbsp;left Japan to become a mathematics instructor at Princet=
on University, where he invented a&nbsp;baseball-pitching machine that used=
 gunpowder to propel the balls, like a cannon.&nbsp; After several accident=
s, the device was abandoned and Hinton lost his job ...&quot; Terry Pratche=
tt, Ian Steward and&nbsp;Jack Cohen, The Science of Diskworld III<o:p></o:p=
></span></p><p class=3DMsoNormal><span style=3D'color:blue'><o:p>&nbsp;</o:=
p></span></p><p class=3DMsoNormal><b><span style=3D'font-size:10.0pt;font-f=
amily:"Tahoma","sans-serif"'>From:</span></b><span style=3D'font-size:10.0p=
t;font-family:"Tahoma","sans-serif"'> owner-chemistry+sabrash=3D=3Drichmond=
.edu : ccl.net [mailto:owner-chemistry+sabrash=3D=3Drichmond.edu : ccl.net] <b>=
On Behalf Of </b>dipankar roy theodip(a)gmail.com<br><b>Sent:</b> Thursday,=
 December 01, 2011 7:35 PM<br><b>To:</b> Abrash, Sam<br><b>Subject:</b> CCL=
:G: Basis sets for Xe<o:p></o:p></span></p><p class=3DMsoNormal><o:p>&nbsp;=
</o:p></p><p class=3DMsoNormal>Hi,<o:p></o:p></p><div><p class=3DMsoNormal>=
You can try basis sets like&nbsp;<span class=3Dapple-style-span><span style=
=3D'font-size:10.5pt;font-family:"Trebuchet MS","sans-serif";background:whi=
te'>def2-TZVP or modified correlation consistent basis sets of Dunning with=
 ECPs. You can get them from EMSL basis set exchange.&nbsp;</span></span><o=
:p></o:p></p></div><div><p class=3DMsoNormal><o:p>&nbsp;</o:p></p></div><di=
v><p class=3DMsoNormal>best,<o:p></o:p></p></div><div><p class=3DMsoNormal>=
Dipankar Roy<br><br>-----------------------------------<o:p></o:p></p><div>=
<p class=3DMsoNormal>Dr. Dipankar Roy<o:p></o:p></p></div><div><p class=3DM=
soNormal>Research Associate<o:p></o:p></p></div><div><p class=3DMsoNormal>H=
unter College (CUNY)<o:p></o:p></p></div><div><p class=3DMsoNormal>695 Park=
 Avenue<o:p></o:p></p></div><div><p class=3DMsoNormal>New York, USA<o:p></o=
:p></p></div><div><p class=3DMsoNormal>NY-10065<o:p></o:p></p></div><div><p=
 class=3DMsoNormal>-----------------------------------<o:p></o:p></p></div>=
<div><p class=3DMsoNormal><o:p>&nbsp;</o:p></p></div><p class=3DMsoNormal><=
o:p>&nbsp;</o:p></p><div><p class=3DMsoNormal>On Thu, Dec 1, 2011 at 4:55 P=
M, Alec Young alecyoung76(0)<a href=3D"http://yahoo.com">yahoo.com</a> &lt;=
<a href=3D"mailto:owner-chemistry*_*ccl.net">owner-chemistry*_*ccl.net</a>&=
gt; wrote:<o:p></o:p></p><p class=3DMsoNormal style=3D'margin-bottom:12.0pt=
'><br>Sent to CCL by: &quot;Alec &nbsp;Young&quot; [alecyoung76[#]<a href=
=3D"http://yahoo.com" target=3D"_blank">yahoo.com</a>]<br>Deal All,<br><br>=
I used M052X/6-31+G* in gaussian trying to optimize the distance between Xe=
 and a ethylene. And I got this error:<br><br>&quot;Atomic number out of ra=
nge for 6-31G basis set.&quot;<br><br>What basis set can I use?<br><br>Than=
ks,<br><br>-Alec<br><br><br><br>-=3D This is automatically added to each me=
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