From owner-chemistry@ccl.net Sun Jun 22 13:57:00 2014 From: "Thomas Manz thomasamanz+/-gmail.com" To: CCL Subject: CCL:G: Chargemol 3.0 released Message-Id: <-50270-140622135423-5032-dd/qhvoo6wlJ+yQz5t5gKw]-[server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=001a11c252c64c8a2504fc706a6a Date: Sun, 22 Jun 2014 11:54:16 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz()gmail.com] --001a11c252c64c8a2504fc706a6a Content-Type: text/plain; charset=UTF-8 Brian Salter-Duke and Alex Granovsky, Thanks for your comments. You are correct that for purposes of running the Chargemol program, the EDFs don't need to be in the .wfx file. The currently released version of the Chargemol program automatically generates EDFs from core electron reference densities if the EDFs are not in the .wfx file. When the EDFs are provided in the .wfx file, the EDFs are directly read and used from the .wfx file. Below is a list of the information that needs to be present in the .wfx file for running the Chargemol program. Please see http://aim.tkgristmill.com/wfxformat.html for additional formatting details. There is no required order for the data sections. Sincerely, Tom Manz GTO <-- Indicates the basis set primitives are Cartesian Gaussian type orbitals (Note: The net charge of the system or unit cell.) 0.00000000000000E+000 (Note: This number includes Ghost atoms (if present).) 3 (Note: Ghost atoms have atomic number of zero.) 8 1 1 (Note: Ghost atoms have nuclear charge of 0.0.) 8.00000000000000E+000 1.00000000000000E+000 1.00000000000000E+000 (Note: When an ECP is used, the nuclear charge is less than the atomic number by the number of core electrons modeled by the ECP. For example, Zr (atomic number 40) with 28 electrons replaced by ECP has a nuclear charge of 12.0 = 40 - 28.) (Note: These are in bohrs.) 0.00000000000000E+000 0.00000000000000E+000 2.40242907000000E-001 <--- XYZ coords for first atom 0.00000000000000E+000 1.43244242000000E+000 -9.60971627000000E-001 -1.75417809000000E-016 -1.43244242000000E+000 -9.60971627000000E-001 (Number of Cartesian Gaussian primitives.) 21 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 3 3 3 (Note: The numbers correspond to the above Nuclear Cartesian Coordinates. For example, Primitive Center = 2 means center the primitive at the position (X,Y,Z) = (0.00000000000000E+000, 1.43244242000000E+000, -9.60971627000000E-001), because this is the second entry in the Nuclear Cartesian Coordinates above.) 1.30709321000000E+002 2.38088661000000E+001 6.44360831000000E+000 5.03315132000000E+000 1.16959612000000E+000 3.80388960000000E-001 5.03315132000000E+000 5.03315132000000E+000 5.03315132000000E+000 1.16959612000000E+000 1.16959612000000E+000 1.16959612000000E+000 3.80388960000000E-001 3.80388960000000E-001 3.80388960000000E-001 3.42525091000000E+000 6.23913730000000E-001 1.68855404000000E-001 3.42525091000000E+000 6.23913730000000E-001 1.68855404000000E-001 (Specifies the type of Cartesian primitive: S, PX, PY, PZ, DXX, DYY, etc.) 1 1 1 1 1 1 2 3 4 2 3 4 2 3 4 1 1 1 1 1 1 5 (Note: Eigenvalues of the first-order density matrix.) 2.00000000000000E+000 2.00000000000000E+000 2.00000000000000E+000 2.00000000000000E+000 2.00000000000000E+000 (Note: One MO per line. The three possible choices are: Alpha and Beta, Alpha, and Beta) Alpha and Beta Alpha and Beta Alpha and Beta Alpha and Beta Alpha and Beta (Note: Eigenvectors of the first-order density matrix.) 1 4.22735025664585E+000 4.08850914632625E+000 1.27420971692421E+000 -6.18883321546465E-003 8.27806436882009E-003 6.24757868903820E-003 0.00000000000000E+000 0.00000000000000E+000 -6.97905144921135E-003 0.00000000000000E+000 0.00000000000000E+000 -4.38861481239680E-003 0.00000000000000E+000 0.00000000000000E+000 -6.95230322147800E-004 -1.54680714141406E-003 -1.49600452906993E-003 -4.66239267760156E-004 -1.54680714141406E-003 -1.49600452906993E-003 -4.66239267760156E-004 2 -9.93934027465106E-001 -9.61289724159333E-001 -2.99592018377613E-001 -2.02159553670646E-001 2.70404733783394E-001 2.04078487063151E-001 0.00000000000000E+000 0.00000000000000E+000 -2.05880464366463E-001 0.00000000000000E+000 0.00000000000000E+000 -1.29463160155366E-001 0.00000000000000E+000 0.00000000000000E+000 -2.05091397601904E-002 4.30931212730961E-002 4.16777908960109E-002 1.29891469789185E-002 4.30931212730961E-002 4.16777908960109E-002 1.29891469789185E-002 3 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 -0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 1.02652120092148E+000 0.00000000000000E+000 0.00000000000000E+000 6.45504074642182E-001 0.00000000000000E+000 0.00000000000000E+000 1.02258690941279E-001 0.00000000000000E+000 1.24402010368969E-001 1.20316208759709E-001 3.74973069812026E-002 -1.24402010368969E-001 -1.20316208759709E-001 -3.74973069812026E-002 4 -4.42374945058045E-001 -4.27845789719456E-001 -1.33340844570570E-001 -1.28852672024973E-001 1.72350857743564E-001 1.30075763838210E-001 0.00000000000000E+000 0.00000000000000E+000 1.26652576885278E+000 0.00000000000000E+000 0.00000000000000E+000 7.96425386733271E-001 0.00000000000000E+000 0.00000000000000E+000 1.26167162499928E-001 -8.17067717603127E-002 -7.90232326554732E-002 -2.46280899645633E-002 -8.17067717603127E-002 -7.90232326554732E-002 -2.46280899645633E-002 5 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 -0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 1.67545019558903E+000 0.00000000000000E+000 0.00000000000000E+000 1.05356803847979E+000 0.00000000000000E+000 0.00000000000000E+000 1.66902878951205E-001 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 ===Optional Information Follows=== A) For periodic systems specify the following (Note: The Number of Translation Vectors can be 0 (nonperiodic system), 1, 2, or 3.) 2 (Note: For periodic systems, the lattice vectors (in bohrs) should be provided in the same XYZ coordinate system as the nuclear positions listed above.) 5.000000000000E+000 -2.38088661000000E+000 0.000000000000E+000 <--- first lattice vector 0.000000000000E+000 0.000000000000E+000 4.357000000000E+000 <--- second lattice vector B) EDFs for core electrons replaced by effective core potentials (See http://aim.tkgristmill.com/wfxformat.html for info on how to specify EDFs.) --001a11c252c64c8a2504fc706a6a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Brian Salter-Duke and Alex Granovsky,

Thanks for your comments.=C2=A0
You are correct= that for purposes of running the Chargemol program, the EDFs don't nee= d to be in the .wfx file.=C2=A0The currently released version of the Chargemol prog= ram automatically generates EDFs from core electron reference densities if = the EDFs are not in the .wfx file.=C2=A0When the EDFs are provided in the .wfx file= , the EDFs are directly read and used from the .wfx file.

Below is a list of the informati= on that needs to be present in the .wfx file for running the Chargemol prog= ram.=C2=A0Please see=C2=A0http://aim.tkgristmill.com/wfxformat.html=C2=A0for additional formatting details.=C2= =A0There= is no required order for the data sections.

Sincer= ely,

Tom Manz
=
<Keywords>
GTO =C2=A0 =C2=A0 <-- Indicates the basis set p= rimitives are Cartesian Gaussian type orbitals
</Keywords>

= <Net Charge> =C2=A0 =C2=A0 (Note: The net charge of the system or uni= t cell.)
0.00000000000000E+000
</Net Charge>

<Number of Nuclei> =C2=A0(Note: This numbe= r includes Ghost atoms (if present).)
3
</Number of Nuclei>
=
<Atomic Numbers> =C2=A0 =C2=A0 (Note: Ghost atoms have atomic num= ber of zero.)
8
1
1
</Atomic Numbers>

<Nuclear Charges> =C2= =A0 (Note: Ghost atoms have nuclear charge of 0.0.)
8.00000000000000E+00= 0
1.00000000000000E+000
1.00000000000000E+000
</Nuclear Charges= >

(Note: When an ECP is used, the nuclear charge is less than the atomic = number by the number of core electrons modeled by the ECP. For example, Zr = (atomic number 40) with 28 electrons replaced by ECP has a nuclear charge o= f 12.0 =3D 40 - 28.)

<Nuclear Cartesian Coordinates> =C2=A0 =C2=A0 =C2=A0 (Note: These= are in bohrs.)
0.00000000000000E+000 0.00000000000000E+000 2.4024290700= 0000E-001 =C2=A0 =C2=A0 <--- XYZ coords for first atom
0.000000000000= 00E+000 1.43244242000000E+000 -9.60971627000000E-001
-1.75417809000000E-016 -1.43244242000000E+000 -9.60971627000000E-001
<= ;/Nuclear Cartesian Coordinates>

<Number of Primitives> =C2= =A0 =C2=A0 =C2=A0(Number of Cartesian Gaussian primitives.)
21
</N= umber of Primitives>

<Primitive Centers>
1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 2 2 2 3 3=
3
</Primitive Centers>

(Note: The numbers correspond to= the above Nuclear Cartesian Coordinates. For example, Primitive Center =3D= 2 means center the primitive at the position (X,Y,Z) =3D (0.00000000000000= E+000, 1.43244242000000E+000, -9.60971627000000E-001), because this is the = second entry in the Nuclear Cartesian Coordinates above.)

<Primitive Exponents>
1.30709321000000E+002 2.38088661000000E+= 001 6.44360831000000E+000 5.03315132000000E+000
1.16959612000000E+000 3.= 80388960000000E-001 5.03315132000000E+000 5.03315132000000E+000
5.033151= 32000000E+000 1.16959612000000E+000 1.16959612000000E+000 1.16959612000000E= +000
3.80388960000000E-001 3.80388960000000E-001 3.80388960000000E-001 3.4252509= 1000000E+000
6.23913730000000E-001 1.68855404000000E-001 3.4252509100000= 0E+000 6.23913730000000E-001
1.68855404000000E-001
</Primitive Exp= onents>

<Primitive Types> =C2=A0 =C2=A0(Specifies the type of Cartesian p= rimitive: S, PX, PY, PZ, DXX, DYY, etc.)
1 1 1 1 1 1 2 3 4 2
3 4 2 3 = 4 1 1 1 1 1
1
</Primitive Types>

<Number of Occupied = Molecular Orbitals>
5
</Number of Occupied Molecular Orbitals>

<Molecular Or= bital Occupation Numbers> =C2=A0(Note: Eigenvalues of the first-order de= nsity matrix.)
2.00000000000000E+000 =C2=A0=C2=A0
2.00000000000000E+0= 00
2.00000000000000E+000
2.00000000000000E+000
2.00000000000000E+000
</Molecular Orbital Oc= cupation Numbers>

<Molecular Orbital Spin Types> =C2=A0(Not= e: One MO per line. The three possible choices are: Alpha and Beta, Alpha, = and Beta)
Alpha and Beta
Alpha and Beta
Alpha and Beta
Alpha and Beta
Alp= ha and Beta
</Molecular Orbital Spin Types>

<Molecular O= rbital Primitive Coefficients> =C2=A0(Note: Eigenvectors of the first-or= der density matrix.)
<MO Number>
1
</MO Number>
4.22735025664585E+000 4.088= 50914632625E+000 1.27420971692421E+000 -6.18883321546465E-003
8.27806436= 882009E-003 6.24757868903820E-003 0.00000000000000E+000 0.00000000000000E+0= 00
-6.97905144921135E-003 0.00000000000000E+000 0.00000000000000E+000 -4.38861= 481239680E-003
0.00000000000000E+000 0.00000000000000E+000 -6.9523032214= 7800E-004 -1.54680714141406E-003
-1.49600452906993E-003 -4.6623926776015= 6E-004 -1.54680714141406E-003 -1.49600452906993E-003
-4.66239267760156E-004
<MO Number>
2
</MO Number>
-= 9.93934027465106E-001 -9.61289724159333E-001 -2.99592018377613E-001 -2.0215= 9553670646E-001
2.70404733783394E-001 2.04078487063151E-001 0.0000000000= 0000E+000 0.00000000000000E+000
-2.05880464366463E-001 0.00000000000000E+000 0.00000000000000E+000 -1.29463= 160155366E-001
0.00000000000000E+000 0.00000000000000E+000 -2.0509139760= 1904E-002 4.30931212730961E-002
4.16777908960109E-002 1.29891469789185E-= 002 4.30931212730961E-002 4.16777908960109E-002
1.29891469789185E-002
<MO Number>
3
</MO Number>
0.= 00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 -0.00000000= 000000E+000
0.00000000000000E+000 0.00000000000000E+000 0.00000000000000= E+000 1.02652120092148E+000
0.00000000000000E+000 0.00000000000000E+000 6.45504074642182E-001 0.0000000= 0000000E+000
0.00000000000000E+000 1.02258690941279E-001 0.0000000000000= 0E+000 1.24402010368969E-001
1.20316208759709E-001 3.74973069812026E-002= -1.24402010368969E-001 -1.20316208759709E-001
-3.74973069812026E-002
<MO Number>
4
</MO Number>
-= 4.42374945058045E-001 -4.27845789719456E-001 -1.33340844570570E-001 -1.2885= 2672024973E-001
1.72350857743564E-001 1.30075763838210E-001 0.0000000000= 0000E+000 0.00000000000000E+000
1.26652576885278E+000 0.00000000000000E+000 0.00000000000000E+000 7.9642538= 6733271E-001
0.00000000000000E+000 0.00000000000000E+000 1.2616716249992= 8E-001 -8.17067717603127E-002
-7.90232326554732E-002 -2.46280899645633E-= 002 -8.17067717603127E-002 -7.90232326554732E-002
-2.46280899645633E-002
<MO Number>
5
</MO Number>
0= .00000000000000E+000 0.00000000000000E+000 0.00000000000000E+000 -0.0000000= 0000000E+000
0.00000000000000E+000 0.00000000000000E+000 1.6754501955890= 3E+000 0.00000000000000E+000
0.00000000000000E+000 1.05356803847979E+000 0.00000000000000E+000 0.0000000= 0000000E+000
1.66902878951205E-001 0.00000000000000E+000 0.0000000000000= 0E+000 0.00000000000000E+000
0.00000000000000E+000 0.00000000000000E+000= 0.00000000000000E+000 0.00000000000000E+000
0.00000000000000E+000
</Molecular Orbital Primitive Coefficients><= div>

=3D=3D=3DOptional Information Follows=3D= =3D=3D

A) For periodic systems specify the followin= g

<Number of Translation Vectors> =C2=A0(Note: The Number of Translatio= n Vectors can be 0 (nonperiodic system), 1, 2, or 3.)
2
</Number o= f Translation Vectors>

<Translation Vectors> =C2=A0 =C2=A0 = =C2=A0 (Note: For periodic systems, the lattice vectors (in bohrs) should b= e provided in the same XYZ coordinate system as the nuclear positions liste= d above.)
5.000000000000E+000 -2.38088661000000E+000 0.000000000000E+000 =C2=A0 =C2= =A0<--- first lattice vector
0.000000000000E+000 0.000000000000E+000 = 4.357000000000E+000 =C2=A0 =C2=A0<--- second lattice vector
</Tran= slation Vectors>

B) EDFs for core electrons replaced by effective core potentials
(Se= e=C2=A0http://aim.tkgristmill.com/wfxformat.html=C2=A0for info on how to s= pecify EDFs.)

--001a11c252c64c8a2504fc706a6a-- From owner-chemistry@ccl.net Sun Jun 22 21:01:00 2014 From: "Radoslaw Kaminski rkaminski.rk%a%gmail.com" To: CCL Subject: CCL:G: LANL2DZ basis set and atomic orbitals for transitiom metals Message-Id: <-50271-140622205958-10112-C7FUfj+ZWgxVGhoEKEGePg(-)server.ccl.net> X-Original-From: "Radoslaw Kaminski" Date: Sun, 22 Jun 2014 20:59:57 -0400 Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk_+_gmail.com] Dear All, I have an another question. Not being a computational chemist brings from time to time more surprises. We performed computations in GAUSSIAN09 some single-point calculations at the PBE1PBE/LANL2DZ level of theory. The compound has several Ag and Cu centres. After that we did a population analysis to see what are the percentage contributions of atomic orbitals to computed molecular orbitals. We obtained comparable results with some programs such as AOMIX or GAUSSUM. What we observe that there is a significant 5pz(Ag) orbital contribution for the molecular orbital of interest (in our case LUMO). Very surprisingly a 1s(Ag) also contributes significantly. This is very strange since we would not expect such a contribution from a core orbital to LUMO. I looked into the GAUSSIAN output file and see the following (just for one silver atom): Molecular Orbital Coefficients: 1 2 3 4 5 O O O O O Eigenvalues -- -14.39364 -14.38781 -14.38525 -14.38095 -10.26451 1 1 Ag 1S -0.00001 0.00036 0.00034 0.00007 -0.00007 2 2S 0.00007 0.00004 0.00004 0.00001 -0.00001 3 3S -0.00049 0.00209 0.00202 -0.00020 -0.00010 4 4PX -0.00001 0.00005 -0.00006 0.00000 -0.00001 5 4PY 0.00000 -0.00006 0.00003 -0.00001 -0.00001 6 4PZ -0.00001 0.00000 -0.00001 0.00001 0.00000 7 5PX -0.00062 0.00091 -0.00106 0.00020 -0.00023 8 5PY -0.00041 -0.00138 0.00087 -0.00018 0.00006 9 5PZ -0.00009 0.00007 -0.00023 0.00019 -0.00034 10 6PX -0.00064 -0.00020 0.00016 0.00023 -0.00051 11 6PY 0.00106 -0.00011 0.00036 -0.00052 -0.00105 12 6PZ -0.00034 0.00021 -0.00010 -0.00001 -0.00019 13 7D 0 0.00000 0.00001 0.00000 -0.00001 0.00001 14 7D+1 0.00000 0.00000 -0.00002 0.00000 0.00001 15 7D-1 -0.00001 -0.00001 0.00001 0.00000 0.00000 16 7D+2 0.00001 0.00002 0.00000 0.00001 0.00000 17 7D-2 0.00001 0.00002 0.00000 -0.00001 -0.00001 18 8D 0 0.00006 -0.00008 -0.00001 0.00004 -0.00006 19 8D+1 -0.00001 -0.00003 0.00014 -0.00002 -0.00003 20 8D-1 -0.00002 0.00004 -0.00006 -0.00002 0.00000 21 8D+2 0.00003 -0.00014 0.00005 -0.00004 0.00001 22 8D-2 -0.00016 -0.00023 -0.00007 0.00006 0.00003 What about the higher s orbitals? Are they somehow missing from the ECP formulation of this basis set, or are they somehow renumbered? Or simply it is the case I don't see them anywhere because I should change some settings in GAUSSIAN? Best wishes, Radek PS. Thanks to many of you who responded to my previous post. We actually used a ChemCraft software (it was the fastest), but tested other ones (e.g. Chimera), and they worked well:) From owner-chemistry@ccl.net Sun Jun 22 21:49:00 2014 From: "Nico G nicogreen6(-)gmail.com" To: CCL Subject: CCL: Reaction Coordinate Message-Id: <-50272-140622214400-27829-oaST1ZfkIX5ERrKFo8gb9g^-^server.ccl.net> X-Original-From: Nico G Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 22 Jun 2014 22:43:51 -0300 MIME-Version: 1.0 Sent to CCL by: Nico G [nicogreen6##gmail.com] Dear All, I'm analyzing a reaction coordinate performing IRC calculations from the TSs. I found a complex when going to reactants. Is there a way to follow the path from the complex to the reactants? Kind Regards, Nico