About me


Personal Info

Name: Joaquin Barroso-Flores

Born: March 15th, 1978 Mexico City

Education:

  • Chemistry Faculty, National Autonomous University of Mexico (UNAM). Chemist (graduated with honors, 2001)
  • Chemistry Faculty, National Autonomous University of Mexico (UNAM). PhD in chemistry (2001 – 2005)

Downloadable CVBarroso CV 2012 English

Current work: Associate researcher at the Joint Center for Research in Sustainable Chemistry (CCIQS), which is part of the Institute of Chemistry from the National Autonomous University of Mexico (UNAM). This center is located at the city of Toluca, 100 km west from Mexico City. (Link to official site on Instituto de Química)

Current projects: DFT and Molecular Dynamics calculations on calixarene systems as drug delivery agents.

ResearchGate profile: Dr. Joaquín Barroso-Flores

Academia.edu profile: Dr. Joaquín Barroso-Flores

Open Researcher & Contributor ID (ORCID): 0000-0003-0554-7569

ResearcherID: D-1790-2011

Professional Experience:

  • Associate Researcher at Instituto de Química, UNAM. Mexico. (May 2010 – present)
  • Postdoc researcher at Facultatea de Chemie si Ingenieria Chimica, Universitatea Babes-Bolyai; Cluj-Napoca, Romania. Click on the following link to find out more about the MOLSEN project, currently under development by our team at Babes-Bolyai. (Dec. 2008 – Jan 2010)
  • Associate Research Fellow at Centro de Investigacion en Polimeros (COMEXgroup) (2006 – 2008)
  • TA electromagnetism with Prof. Dr. Germund Hojer at the Chemistry Faculty, UNAM (2003 – 2005)
  • High School Chemistry teacher at Escuela Preparatoria Logos (Chemistry I & II) (2002 – 2003)

Research interests: Theoretical chemistry; Computational chemistry; Description of molecular properties in weakly interacting systems through assessment of electron density distribution.

Published papers:

  • Rodrigo Galindo-Murillo, María Eugenia Sandoval-Salinas, and Joaquín Barroso-Flores “In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study” J. Chem. Theory Comp.  (2014) DOI: 10.1021/ct4004178
  • Pezhman Zarabadi-Poor; Alireza Badiei; Ali Akbar Yousefi; Joaquín Barroso-Flores “SELECTIVE OPTICAL SENSING OF HG(II) IN AQUEOUS MEDIA BY H-ACID/SBA-15: A COMBINED EXPERIMENTAL AND THEORETICAL STUDY” Journal of Chemical Physics C 2013, 117 (18), 9281-9289
  • Sandra Hidalgo-Bonilla; Ricardo Peyrot; Vojtech Jancik; Joaquín Barroso-Flores; Marisol Reyes-Lezama; Mónica Moya-Cabrera “MOLECULAR HETEROBIMETALLIC ALUMINOXANES AND ALUMINOXANE SULFIDES CONTAINING GROUP 4 METALS” European Journal of Inorganic Chemistry 2013, 16, 2849-2857
  • Azucena Garduño-Alva, M. Carmen Ortega-Alfaro, José G. López-Cortés, Isabel Chávez, Joaquin Barroso-Flores, Rubén A. Toscano, Henri Rudler, and Cecilio Álvarez-Toledano “Synthesis of new γ-lactones from preactivated monosubstituted pyrazines and TMS–ketene acetals” Can. J. Chem. 2012, 90 (5): 469-482
  • Joaquín Barroso-Flores, Petronela Maria Petrar; Ioan Silaghi-Dumitrescu, Sandor Kunsagi-Mate “Ab initio calculations of electronic interactions in inclusion comoplexes of calix- and thiacalix[n]arenes and block s cations” J. Incl. Phenom. Macrocycl. Chem. 2012 online first DOI: 10.1007/s10847-012-0144-6
  • Jocelyn Alcántara-García, Vojtech Jancik, Joaquín Barroso, Raymundo Cea-Olivares, Mónica Moya-Cabrera, “Coordination Diversity of Aluminum centers Molded by Triazole Based Chalcogen Ligands” Inorganic Chemistry (2009) 48, 13 5545-5558.
  • Joaquín Barroso-Flores, J. A. Cogordan “Influence of Intramolecular Sn-Chalcogen interactions on the conformational preferences for three Diorganotin (IV) Xanthates.” Journal of Organometallic Chemistry 691 (2006) 4937-4944.
  • Óscar Baldovino-Pantaleón, Joaquí­n Barroso-Flores, J.A. Cogordan, Simón Hernández-Ortega, Rubén A. Toscano, David Morales-Morales, “Phosphane-free C-C Heck couplings catalyzed by Pd(II) fluorinated aniline complexes of the type trans-[PdCl2(NH2ArF)2]” Journal of Molecular Catalysis A. Chemical 247 (2005) 65-72.
  • Joaquí­n Barroso-Flores, Raymundo Cea-Olivares, Rubén A. Toscano, J. A. Cogordan, “Synthesis of the anisobidentate compound bis(2-amino-cyclopent-1-ene-carbodithioate)diethyltin (IV). Experimental and theoretical study” Journal of Organometallic Chemistry 689 (2004) 2096-2102.
  • Joaquín Barroso-Flores, J. A. Cogordan “A theoretical approach on the secondary interactions formed in common organotellurium (IV) compounds. Uncommon geometries explained.” In writing.
  • Joaquín Barroso-Flroes, J. A. Cogordan “The Local Bond Order revisited”. In writing.

Languages: English, Romanian, German, Spanish

  1. Claudio Téllez

    Apreciado Joaquin: Conozco algunos de los próceres que mencionas en el Bolg. Cea Olivares, e algunosde los vampiritos. Haiduc tal vez. Estuve varias veces en México, una de ellas convidaddo por Jacobo Gomez Lara, ya fallecido, otras por Victor Castaño. bueno..
    mi pregunta esla siguiente como buen novato. Estudiando el complexo bis-dietilditiocarbamato de Cu(II) enconbtré transferencia de carga entre:

    Donador ACEEPTOR ENERGIA
    85 LP(2) S8 LP* Cu1 31.14

    esto está muy padre y pudeo visualizar el orbital 85
    en Gaussian View y en el Chemcraft. Como visualizao el orbital 83? Si es antiligante deve estar arriba de l LUMO y no abajo del HOMO.

    Puede usted ayudarme co la ayuda? Apreciaria enormemente.

    Un abrazo extensivo a L. Haiduc.

    Calduio Téllez

  2. Claudio Téllez

    Apreciado Joaquin: Conozco algunos de los próceres que mencionas en el Blog. Cea Olivares, e algunos de los vampiritos. Haiduc tal vez. Estuve varias veces en México, una de ellas convidado por Jacobo Gomez Lara, ya fallecido, otras por Victor Castaño. bueno..
    mi pregunta es la siguiente como buen novato. Estudiando el complexo bis-dietilditiocarbamato de Cu(II) encontré transferencia de carga entre:

    Donador ACEPTOR ENERGIA
    85 LP(2) S8 LP* Cu1 31.14

    esto está muy padre y puedo visualizar el orbital 85
    en Gaussian View y en el Chemcraft. Como visualizo el orbital 83? Si es antiligante deve estar arriba de l LUMO y no abajo del HOMO.

    Puede usted ayudarme con mi duda? Apreciaria enormemente.

    Un abrazo extensivo a L. Haiduc.
    (texto corrigido!)

    Claudio Téllez

    • Apreciado Claudio

      Me da gusto saber que a través del blog has viajado mentalmente a México nuevamente, por supuesto que pasaré tus saludos al Dr. Haiduc en breve.
      En cuanto a tu pregunta: Creo que hay un error de interpretación; según entiendo las lineas que me pones corresponden al análisis de perturbaciones a segundo orden (el cual se obtiene por default o con la opción E2PERT según el programa que uses). En esta sección el número 85 NO hace referencia al orbital, sino a la interacción (la interacción perturbativa número 85 que pasó el umbral -threshold- de 0.5 kCal/mol para ser impreso). Si estás graficando el ORBITAL NATURAL 85 quien sabe que sea lo que estás viendo, pero no corresponde a la interacción que describes. Lo que podrías hacer (asumiendo que etiendo tu intención) es buscar a que NBO corresponde el LP(2) del S8, es decir buscar su número en donde se encuentra la descripción de todos los NBO’s (ve mi post sobre el análisis de resultados NBO), graficarlo y hacer lo mismo para el LP* de Cu1. Molekel y Gaussview pueden presentar superficies simultaneamente (OJO! no es lo mismo que sumar las superficies, esto es completamente distinto). Así graficadas puedes analizar como se están traslapando ambos NBOs. Desconozco el resto de tu archivo pero me imagino que esta interacción es importante en la formación de tu complejo (¿tiolato?),revisa que no tengas interacciones perturbativas con mayores energías que pudieran ser más importantes que esta.

      Espero que te sea de ayuda. No dudes en contactarme por este medio o por mail para cualquier otra duda.

      Saludos hasta allá

  3. I’m post graduated chemsitry student and I’m trying to learn gaussian, I use gaussian 03 for win. I am studying on TD DFT study a dinitrile compound. After 6 days processing, because of electricity
    cutting, my gaussian job is terminated and computer is closed. I want to resumption my job but I dont know how to do it. is it possible? or should I open
    latest out file and restart process.
    I tried “Geom=check guess=read” functions but I thought I didnt manage

    My input file;
    %chk=C:/Users/TURKR/Desktop/tddft50trs.chk
    %mem=100MW
    %nproc=1
    #p td=(singlets,nstates=50) b3lyp/6-311+g(d) guess=save geom=connectivity
    pop=full gfinput

    final part of my out file;

    Cannot handle 2e integral symmetry, ISym2E=1.
    CISAX: IP= 1 NPass= 3 NMax= 34.
    CISAX will form 34 AO SS matrices at one time.
    NMat= 34 NSing= 34.
    NMat= 34 NSing= 34.
    NMat= 32 NSing= 32.
    Cannot handle 2e integral symmetry, ISym2E=1.
    CISAX: IP= 1 NPass= 3 NMax= 34.
    CISAX will form 34 AO SS matrices at one time.
    NMat= 34 NSing= 34.
    NMat= 34 NSing= 34.
    NMat= 32 NSing= 32.
    Root 1 has converged.
    Root 2 has converged.
    Root 3 has converged.
    Root 4 has converged.
    Root 5 has converged.
    Root 6 has converged.
    Root 7 has converged.
    Root 8 has converged.
    Root 9 has converged.
    Root 10 has converged.
    Root 11 has converged.
    Root 12 has converged.
    Root 13 not converged, maximum delta is 0.001146383849072
    Root 14 not converged, maximum delta is 0.001076901825947
    Root 15 has converged.
    Root 16 has converged.
    Root 17 has converged.
    Root 18 has converged.
    Root 19 has converged.
    Root 20 has converged.
    Root 21 has converged.
    Root 22 has converged.
    Root 23 has converged.
    Root 24 has converged.
    Root 25 has converged.
    Root 26 has converged.
    Root 27 has converged.
    Root 28 not converged, maximum delta is 0.001298203075257
    Root 29 has converged.
    Root 30 has converged.
    Root 31 has converged.
    Root 32 not converged, maximum delta is 0.001487599984012
    Root 33 not converged, maximum delta is 0.002130187054738
    Root 34 not converged, maximum delta is 0.009687228977448
    Root 35 not converged, maximum delta is 0.014708674044360
    Root 36 has converged.
    Root 37 not converged, maximum delta is 0.001056178564194
    Root 38 not converged, maximum delta is 0.001307476560090
    Root 39 not converged, maximum delta is 0.001281081401660
    Root 40 has converged.
    Root 41 not converged, maximum delta is 0.001061548241041
    Root 42 not converged, maximum delta is 0.001573623655971
    Root 43 has converged.
    Root 44 has converged.
    Root 45 has converged.
    Root 46 has converged.
    Root 47 not converged, maximum delta is 0.001567486009780
    Root 48 not converged, maximum delta is 0.005544365303514
    Root 49 not converged, maximum delta is 0.015140942251070
    Root 50 not converged, maximum delta is 0.016487405708613
    Excitation Energies [eV] at current iteration:
    Root 1 : 3.097975009587616 Change is -0.000001105943253
    Root 2 : 3.583514852565895 Change is -0.000007448515000
    Root 3 : 3.617241820182027 Change is -0.000021813870515
    Root 4 : 3.991502586858061 Change is -0.000023174927667
    Root 5 : 4.138876536189863 Change is -0.000007145969739
    Root 6 : 4.211283026540273 Change is -0.000007302963600
    Root 7 : 4.270327709174773 Change is -0.000012531626331
    Root 8 : 4.368328284874000 Change is -0.000005937553695
    Root 9 : 4.445535867701103 Change is -0.000032779976579
    Root 10 : 4.540640063389401 Change is -0.000002225280201
    Root 11 : 4.656404960218242 Change is -0.000023209382109
    Root 12 : 4.714797549284374 Change is -0.000019602079988
    Root 13 : 4.754991510970658 Change is -0.00001

    • Hi Turker

      I’m catching up with my email and my blog comments today and I saw you already asked the CCL community. To restart a job you have to use the keywords geom=check guess=check but also you have to allocate the checkpoint file in the default location. NOW! you have to also type %NoSave below the %chk=filename.chk line, that way it will read it and wont write it! Be careful because if you don’t write that line then you will loose your checkpoint. I think the idea of copying and renaming it is a good one, try it but also use the %NoSave option I write about here.

      Have a nice day!

    • Hello I’m surfing the net and I found you are know everything about gaussian03.

      I have some problems and don’t know how can solve my problems.

      In my thesis I being involved to find HOMO and LOMO wave function but I found HOMO only in wfn file

      Please help to find LOMO wave function

      Please

  4. We are carrying out our calculations using G03W and GVW3.09.I have recently purchased G09W. But it is not possible now to submit the job from G03W to G09W.
    Can you kindly guide me in this direction?

    • If I understand correctly you have GaussView installed along G03 and now you changed to G09 and as a consequence you cant link GaussView with G09. It has to do with the way Gaussview is installed so:
      1) uninstall everything!!
      2) install G09W
      3) Install GaussView

      I hope this helps

  5. We are carrying out our calculations using G03W and GV3.09. I have recently purchased G09W. But it is not possible now to submit the job from GV3.09 to G09W.
    Can you kindly guide me in this direction?

  6. Hi Dr. Joaquin

    I am trying to optimize metal complexes of phthalocyanine derivatives by using ONIOM method. I completed optimization of Zn-Phthalocyanine and calculated IR and UV. But I couldn’t optimize Cu-Pht and Co-Pht and I haven’t tried Ni-Pht yet. I met an error message in optimization of Cu-Pht. I think that For metal complex, ONIOM method is more complicated than general single layer methods.
    Could you help me, please

    Best Regards

    Command line my out file:

    #p opt=(tight,maxcycle=512,gdiis) freq=noraman oniom(b3lyp/6-31g:pm3mm) geom=connectivity int=ultrafine scf=maxcycle=512

    Error message:

    Warning! Cu atom 209 has 11 valence electrons but only 4 basis functions.This is less than a minimal basis set!

    IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000ScaDFX= 1.000000 1.000000 1.000000 1.000000IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0NAtoms= 209 NActive= 209 NUniq= 209 SFac= 1.00D+00 NAtFMM= 60 Big=TLeave Link 301 at Thu Nov 25 11:42:58 2010, MaxMem= 104857600 cpu: 0.0

    (Enter C:\G03W\l401.exe)Simple Huckel Guess.NBasis= 620 NMin= 625 so simple Huckel guess is impossible.Error termination via Lnk1e in C:\G03W\l401.exe at Thu Nov 25 11:43:02 2010.Job cpu time: 0 days 0 hours 0 minutes 12.0 seconds.File lengths (MBytes): RWF= 52 Int= 0 D2E= 0 Chk= 1 Scr= 1

    • Hi Turker

      Your basis set is just too small, try changing it for 6-311G(d,p) perhaps, or get one with a pseudopotential such as SDD or LANL2DZ. Check Gaussian’s manual for a wider variety of basis sets available for Cu and the other metallic ions you are studying.

      • Hi Dr. Joaquin
        I am appriciated for your advices. You are right, I think semiemprical method isn’t suitable for Cu, Co and Ni atoms. LANL2DZ is good but too slow for the compound, so I have tried ONIOM method (DFT631G:PM3MM). I also tried LANL2DZ:PM3MM and only PM3MM. Results were same. One more interesting point; when I used molecular mechanics instead of PM3MM (for example ONIOM631G:UFF), I didn’t meet an error.
        I am an amateur, I am studying and studying :)
        thanks, happy new years

  7. Dear Dr. Barroso:

    I am trying to optimize a structure in which Zn is octahedrally coordinated with two citrate molecules. When I optimize this structure the bonding between Zn and the two citrate molecules dissapears. I know this complex is possible since I got the structure from the authors of a published crystallography paper. This is my input:

    %chk=octacomplex.chk
    %mem=70MW
    %nprocshared=2
    # opt rb3lyp/6-311+g(d,p) guess=(local,save) geom=connectivity

    Title Card Required

    -4 1
    C 0.00000000 0.00000000 0.00000000
    O 0.00000000 0.00000000 1.44957233
    H 0.84063190 0.00000000 1.70043798
    C -1.45846423 -0.22289327 -0.45896769
    O -2.29631461 -0.61293155 0.41986215
    O -1.72466070 -0.03349046 -1.65301136
    C 0.88489416 -1.13110147 -0.54914157
    H 0.78695471 -1.14345589 -1.51425010
    H 1.80867833 -0.90423719 -0.35833379
    O -0.35546025 -2.74486386 0.71897856
    C 0.55671496 1.33042743 -0.51066400
    H 1.47945129 1.40232696 -0.21933614
    H 0.56235260 1.30216071 -1.48011487
    C -0.17273032 2.58702456 -0.08041309
    O -1.40015281 2.55436371 0.08757794
    O 0.51874797 3.64592327 0.04721742
    C -2.70592252 -3.08341975 4.08248350
    O -2.70592252 -3.08341975 2.63291117
    H -3.54664302 -3.08346576 2.38205127
    C -1.24759139 -2.86049159 4.54141854
    O -0.40960791 -2.47048821 3.66262135
    O -0.98130632 -3.04984838 5.73545646
    C -3.59086117 -1.95223738 4.63158667
    H -3.49287722 -1.93996386 5.59673360
    H -4.51473395 -2.17914766 4.44078464
    C -3.34303653 -0.55032925 4.12272545
    O -2.35059538 -0.33852100 3.36347229
    O -4.12000079 0.34887973 4.48811035
    C -3.26277058 -4.41381229 4.59311486
    H -4.18537380 -4.48574672 4.30181964
    H -3.26836372 -4.38562647 5.56260412
    C -2.53332530 -5.67040942 4.16286395
    O -1.30581420 -5.63770256 3.99486717
    O -3.22475909 -6.72938904 4.03527183
    Zn -1.35300556 -1.54173288 2.04124462
    C 0.63698091 -2.53305560 -0.04027460
    O 1.42338885 -3.44322386 -0.41004057

    1 2 1.0 4 1.0 7 1.0 11 1.0
    2 3 1.0 35 1.0
    3
    4 5 1.0 6 2.0
    5 35 1.0
    6
    7 8 1.0 9 1.0 36 1.0
    8
    9
    10 36 1.0 35 1.0
    11 12 1.0 13 1.0 14 1.0
    12
    13
    14 15 2.0 16 2.0
    15
    16
    17 18 1.0 20 1.0 23 1.0 29 1.0
    18 19 1.0 35 1.0
    19
    20 21 2.0 22 2.0
    21 35 1.0
    22
    23 24 1.0 25 1.0 26 1.0
    24
    25
    26 27 1.0 28 2.0
    27 35 1.0
    28
    29 30 1.0 31 1.0 32 1.0
    30
    31
    32 33 2.0 34 2.0
    33
    34
    35
    36 37 2.0
    37

    1 2 1.0 4 1.0 7 1.0 11 1.0
    2 3 1.0 35 1.0
    3
    4 5 1.5 6 2.0
    5 35 1.0
    6
    7 8 1.0 9 1.0 36 1.0
    8
    9
    10 36 1.5 35 1.0
    11 12 1.0 13 1.0 14 1.0
    12
    13
    14 15 2.0 16 2.0
    15
    16
    17 18 1.0 20 1.0 23 1.0 29 1.0
    18 19 1.0 35 1.0
    19
    20 21 1.5 22 2.0
    21 35 1.0
    22
    23 24 1.0 25 1.0 26 1.0
    24
    25
    26 27 1.5 28 2.0
    27 35 1.0
    28
    29 30 1.0 31 1.0 32 1.0
    30
    31
    32 33 2.0 34 2.0
    33
    34
    35
    36 37 2.0
    37

    Any help would be greatly appreciated.

    Best regards,

    Gabriela Arias

    • Hola Gabriela!

      What do you mean it disappears? If you mean you can no longer see it in a visualizer such as GaussView then you have nothing to worry about, sometimes visualizers have different thresholds for painting a bond or not.
      Your initial bond lengths (Zn-O) where taken from the crystallographic data, right? How much longer are those bonds after optimization?
      Take a look on the bond indexes to assert that the bond is lost or if it is just an artifact from the visualizer.

      I need more information to help you out but I hope this sets you on the right path.

      Happy holidays!

      • Dear Dr. Barroso:

        Thanks for your quick response. In the optimized structure, Zn is no longer coordinated with the citrate molecules, so it is not a visualization problem. The distance between Zn and the binding sites in the optimized structure is about 0.10 longer than in the crystallographic data.

        Happy Christmas,

        Gabriela Arias

      • Hola de nuevo Gabriela!

        Wouldn’t this mean your bonding is mainly ionic in nature? I mean, if the distances are so similar after the opt procedure and the bond order is so low then there is probably no covalent bond there to begin with! Try running a bond order calculation (I suggest NBO with BNDIDX keyword for a Wiberg analysis)on the initial and final structures just to make sure. Also employing Generalize Valence Bond theory could throw some light on to why are your bonds disappearing in the gas phase. Thanks for stopping by.

        Have a great year!

  8. Hi Dr. Barboso

    I’m facing some troubles trying to visualize NBOs. I’ve optimized some molecules using g09 and then I made a single point calculation for each one and added some keywords for a NBO analysis. The problem is: when I try to visualize the NBO orbitals using GV 5.0, only the the usual MOs show up.

    The CMO, NRT and other default analysis performed by NBO were in the .log file as they should be. The only problem is visualizing the orbitals.

    I used the following keywords:

    ——-

    #T M062X/cc-pvtz sp Pop=(NBORead,savenbos)

    $NBO NRT CMO plot file=job $END

    ——-

    I appreciate any help you can provide me.

    With regards,

    Italo

    • Hi Italo
      I assume you already read my post (in this same blog) about how to visualize NBO’s with GaussView. Maybe there is something about the 5.0 version. I don’t know if I have it available but if I do I will run some tests and will let you know.

      In the mean time I hope you have a nice day

    • Dear Italo,

      Did you get solution for your error?
      Kindly share with me, I am having the same kind of error.

      Many thanks,
      Bijan

  9. Tijesunimi Odebode

    I am trying to visualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian calculations on. I read an article online that says that for MOLDEN to find all required information in the output file, I need to run a single point calculation at the desired level of theory including the pop=full and gfinput keywords. I entered the above in my input file and the following is my input:

    %chk=Chlorin-1_b3lyp_go
    %mem=23000mb
    %nprocshared=8
    # b3lyp/6-31G(d) sp scf=tight pop=full gfinput maxdisk=50gb

    b3lyp geometry optimization using Gaussian
    Chlorin-sp-1

    The mem value in the run script is 23500mb and maxdisk=50gb. However, when I run this job, an error message comes up which says: ‘galloc: cannot allocate memory.’ I tried increasing the memory on the run script to 24000mb but I keep getting the message ‘Requested node configuration unavailable.’ I do not know what the problem is. Is there a problem with my input file or what else do you think I should do. I am sorry if I did not do a good job expalaining the problem; I am new to this. Thanks a lot for your anticipated response.

    • Hi Tijesunimi!
      Sorry for the delay in my response. The error is very simple, you are trying to allocate A LOT of memory in the %mem part of your link0!
      I don’t know what kind of processor are you using but if you already have the optimized structure and you only want to plot the orbitals then run this job (at the SAME level of theory than your opt) but get rid of those options (I mean %mem and maxdisk) let the program use the defaults. Also you can drop the %nprocshared=8 Gaussian will never use them all efficiently anyway. I hope this helps, please try it and PLEASE LET ME KNOW how it went ok?
      I see you are working in photosynthesis, interesting because I’ve been thinking on doing that myself :) If your chlorin molecule is too big then perhaps you can run it with %mem=300MB or something. Asking for 23GB just wont work :)

      Take care and thanks for reading!

  10. Joaquin, primero que todo, mis mas sinceras y grandes felicitaciones por tu blog, y tu esmero por ayudar a lagente a tra ves de el.
    Segundo quisiera saber si existe alguna manera usando Gaussian 03 de hacer el calculo de un “ground state” pero “quitando” el lone pair de el nitrogeno, o los dos lone pairs del oxigeno y asi obtener un nuevo “ground state” donde estos lone pairs no son tenidos en cuenta y ver la diferencia entre estructuras….mil gracias por cualquier ayuda que me puedas dar

    • Hola Henry

      Mil perdones por la tardanza de mi respuesta. Muchas gracias por tus palabras acerca del blog, espero que pueda seguir a la altura por mucho tiempo (contestar prontamente podría ser una buena manera de empezar).
      Vi que pusiste esta misma pregunta en CCL pero ya no vi que respuestas obtuviste.
      Sugiero que le entres al esquema NBODel, este método elimina interacciones particulares (elementos de la Matriz de Fock) y calcula la nueva función de onda con las condiciones dadas.
      la forma de usarlo sería poner en el route section pop=NBODel y al final de la molécula

      $NBO $END
      $DEL
      delete n orbitals
      i
      j
      k
      $END

      donde n es el numero de orbitales a eliminar e ijk son las etiquetas NBO de cada uno. Corre un calculo NBO inicial (pop=NBO) luego localiza los pares libre etiquetados como LP, copia los números y ahora sí corres el cálculo con NBODel. Busca en este mismo blog el post sobre como interpretar NBO para más ayuda.

      Espero que te haya servido Henry! Gracias por tus comentarios y por leer este blog!

      Cheers!

  11. Send me the details of calculating first order hyperpolarizability from G03output usning freq=raman keyword.
    Thanking you

  12. Dear Dr. Barroso,
    thank you for your illuminative blog!
    Perhaps you have a quick answer to my question:
    I managed to display the HOMO of a molecule in GaussView 5.04 – but I can’t do two things:
    – change the orbital colors to anything other than red and green;
    – export the surface as an image file (preferably a vector image, of course)
    Do you know how to do this?
    Thanks a million!
    David

    • Hi David!

      Thank you very much for your kind words. About your questions: 1) I don’t think you can change the colors, I haven’t tried. Probably you need to do it externally with photoshop or something.
      2) you can save it as a picture file (gif, tiff, jpg, etc.) but not as a vector file.
      GaussView is not the best solution for this sort of high performance rendering you are trying to achieve. Let me suggest VMD, I believe that could be more up your alley ;-)

      Thanks for reading!

      • Hi,
        I was actually looking for some hints on the internet about changing the orbital colours in Gaussview and ended up with this blog. Though, I was not able to get the answer here, I had a play around Gaussview and finally found the way to change orbital colours. Go to File—Preferences—Colors—Surface Colors. You should be able to change the colors there. I hope this is useful.

        Thanks
        Shanthi

  13. Hi Dr. Barroso,

    Sorry, I would like to ask a simple question. I ran a basic job as follow from a Gaussian textbook.

    #T RHF/6-31G(d) Pop=Full Test

    Formaldehyde Single Point

    0 1
    C 0.0 0.0 0.0
    O 0.0 1.22 0.0
    H 0.94 -0.54 0.0
    H -0.94 -0.54 0.0

    But, an error message showed up saying,

    galloc: could not allocate memory.: Cannot allocate memory
    galloc: could not allocate memory.

    I saw one of your previous reply, but I don’t have %mem in the input.
    Could you please tell me where has gone wrong?

    Thanks a lot,
    jovis

  14. Dear Dr. Barroso, I have a problems with my input file for G03W
    here is my input

    %mem=100MB
    %chk=dai.chk
    #n pop=(NBO,savenbo)density=current rmp2/aug-cc-pvdz scf=tight

    NBO-HF at MP2 wfn

    0 1
    S,0.,0.,0.5909815593
    C,0.,0.,-1.0398818668
    H,0.,0.9356771308,-1.6155519262
    H,0.,-0.9356771308,-1.6155519262

    but when I was running programme I got the error with

    Sorting of NBOs: 48 30 47 45 46 64 56 29 28 44
    Sorting of NBOs: 43 42 27 26 25 41 63 55 40 62
    Sorting of NBOs: 54 24 23 22 53 61 60 52 59 51
    Sorting of NBOs: 21 39 38 37 36 58 50 20 57 49
    Sorting of NBOs: 35 34 33 19 18 17 32 16 31 15
    Sorting of NBOs: 14 13 65 67 68 66 12 2 1 11
    Sorting of NBOs: 3 4 6 10 9 7 8 5
    NBStor is confused about NOcc.
    Error termination via Lnk1e in C:\G03W\l607.exe at Mon Jul 18 07:45:50 2011

    Please tell me why? And could you help me to fix it?
    Many thanks to you!
    Regards!
    Dai.

    • Hello Dai

      I get this question a lot and I still haven’t found a right solution, I need to work on it a little bit more. This has to do with a warning that NBO sends you if the occupation of each orbital doesn’t follow the aufbau principle, i.e., the energy and the population don’t follow the same order. Try the following:
      1) Make sure you are working with a minimum of the PES by performing a vibrational frequency analysis (you probably already did but its better to be sure)
      2) Change your basis set. Although NBO is not so sensitive to change in basis set there could be a reorthonormalization problem with the particular one you are using.

      Hope this works. Thanks for reading

      • Hi Dr.!
        I guess I’ve just found that my problem depends on my program,, that is G03 doesn’t include NBO5.G so I can’t perform NBO analysis with MP2 wavefunction (keyword: density=current). DO you agree with me?
        Regards!
        Dai

      • I think its a good idea, Dai! Calculate the mp2 wavefunction and then perform the nbo on it, it might work. Try it and please let me know how it goes ok?

        Have a nice day and keep coming back!

  15. It’s ok but I used G09, not G03. You can’t perform NBO on G03, you only perform NBO analysis from HF-wfn. I’ve just know that.
    Thank for you kind, Dr.!
    Regards!
    p.s: you dont mind if I will have questions for you in the future?

  16. Dear Dr. Barroso,

    I have performed two calculations using Nosymm keyword with G09. I know that in this way all calculation are performed in the Input Orientation. However in one calculations I obteined a Z-Matrix orientation, while for the other I have an Input Orientation.
    I ckecked the output, in both cases the symmetry was turned off. The only difference between the calculations is the size of the system, for the system with 61 atoms I have Z-Matrix Orientation , for smaller system I have Input Orientation (In both cases the command used where the same).

    Do you where these differences come from. Is there some way to control it?
    Thanks in advance.

    • Hello Fernanda

      First I appologize for the lateness of my response. As far as I know there is no way to control this since the program will re-orientate the molecule to where its best suited even if the symmetry is turned off. the symmetry option is more related to the symmetry of the wavefunction, which is a consequence of the symetry of the molecule; a molecule could be symetric and the wavefunction can be made non-symetric with this option. However orientations are a bit harder to control.

      Hope this helps!

  17. dear Dr Barroso.
    please help me to know how i can calculate bond order in NBO (G03).
    I know how can i calculate wiberg bond index, are these two parameters equal?

    • Hello Mohamad!
      They are definitely not the same thing since their definitions are diferent. If you run a full population analysis with nbo pop=(full,nboread) and then you use bndidx in the line:
      $NBO BNDIDX NAO $END
      you will find both bond orders (Wiberg bond index and Bond Order in the NAO basis)

      I hope this helps

      Have a nice day

  18. what should be the input file for the optimization of metal complex of phthalocyanine in g03w rather than using oniom calculations?

  19. Hi, Dr. I research in computational chemistry with use Gaussian 03/gaussview 05 software . so , I need a more tutorial or learning in field .please guide me for useful link, literature, book and journal particular commends in Gaussian program. thanks

  20. Greetings! Thanks for following my blog “Word Play – A Place For Pleasurable Procrastination”! I’ll try my best to keep you entertained. :-)

  21. Sir, I try to optimised a cluster of TiO2 which is designed by PBC. But after 6 minute of running in Gaussian 09 windows version, an error via Lnk1e in C:\G09W\l401.exe is appeared. I m very much new in this field. So, I aspect your kind help…

  22. Hi Dr. Barroso,

    I just stumpled upon your great blog! My question is closely realted to Debajyotis. I am trying to set up a PBC calculation on a measured crystal structure, but I always end up with the same error in the MO guess:

    Dimensions of /B2/ exceeded in AtP2B2.
    Error termination via Lnk1e in c:\program files\G09W\l401.exe

    I am using #p pbepbe/3-21g/auto and I really dont have a clue whats the problem. He has almost 200 atoms in the unit cell, maybe its to large? But he doesnt complain about the memory….

    Thanks a lot for your kind assistance!

  23. Hello,

    This is my first time posting. I am new to computational chemistry and Gaussian. I’m using Gaussian09.
    My general concern is that when something goes wrong – as it seems to every single day – I don’t know where to look for resolution of the various error messages. I usually Google the error and look to CCL.net. But, some errors are so obscure that I don’t get any relevant search results. Even though I am in grad school, I’m the only person in my lab-group who does computational chemistry. One other person does some work with ADF.

    My specific concerns are with organometallic complexes – finding reaction paths for now. I have been having a lot of trouble optimizing a lanthanide complex Ce(IV) Ce(III). I finally got an successful SCF calculation using SCF=QC. But, using guess=read, I keep getting an error that says Gaussian doesn’t see the basis set info in my checkpoint file. But, I’m supplying it in my input file.

    • Hello! Welcome to my blog and definitely welcome to the obscure world of Gaussian error messages. You will be surprised when you begin to solve them on your own in no time but it will take patience and many trials.
      Your address suggests you attend the UCLA so you must have a valid Gaussian license, don’t be shy and directly ask their help desk they are very helpful and prompt.
      If you use the option guess=read then the program gets the coefficients from the check file but tries to get the corresppnding basis set from it too. Try using the GEN option to override the search for the BS in the chk file along with the previous keyword. Not sure if itll work but is worth the try!

      Hope this helps. Have a nice day

      • Thanks for the suggestion and the welcome! Since I am using pseudo potentials, I used gen and specified my basis sets in the input file. So, it was odd that Gaussian didn’t read them.
        I submitted my query to Gaussian tech support.
        Are there any other resources you can recommend?

        I frequently come across old CCL.net postings about error messages. The Aeleen Frisch book was good for starters, but there are a lot of topics not covered.

        Thanks again.

      • I would suggest to subscribe to the CCL, if you have an email with an unlimited amount of space like yahoo or gmail (practically) you can store all the threads. This way you can create your own database; sometimes when you search their archives you find the same post various times but answers come harder to find. This is what I do, anyway.

        Why do you need the guess to be read from the chk file? is your system too big?

        Have a nice day and please share the answer you get from Gaussian Inc if you can.

  24. Hi. I am with same problem of the Anja. If the pabukha user found the answer, could post here? I am working with glycine crystal. Thanks.

  25. Hi, I got a response from Gaussian. BTW – I checked the box to alert me when there’s a response but I didn’t get one.
    Here’s the response.

    (The first response was that there may be a problem with the location or corruption of the chk file I was referring the input to. But I saw that that wasn’t it. Here is the follow up e-mail from Gaussian.)

    There are a few things to try that would save a good amount of computational time over simply switching to the QC SCF procedure. If you are running into SCF convergence difficulties, here are a few general guidelines to follow that can be helpful to you:

    1) “SCF=NoVarAcc”. This one requests the use of full integral accuracy from the first SCF cycle. The default is to use lower accuracy in the first few cycles in interest of speed and then switch to full accuracy as the SCF approaches convergence. In some difficult cases, the initial lower integral accuracy is not good enough and the SCF procedure might do a lot of useless iterations. This option never hurts, it would make the first few cycles a little slower but the overall time may be lower if it takes fewer cycles to get close to convergence.

    2) Increase integral accuracy. The default thresholds are set for an integral accuracy of 10^-10. In some cases when using very diffuse functions, one might need to use tighter thresholds since there will be very small quantities being computed. The integral accuracy is controlled with “Integral=(Acc2E=N)” in G09 or by “IOp(5/87=N)” in G03. The default is N=10. One may try increasing the accuracy by one or two orders of magnitude (i.e. N=11 or N=12).

    3) Tighten the grid for numerical integration in DFT (This does not apply to non-DFT jobs such as HF, MP2, etc.). The default (“Fine”) grid for numerical integration is adequate for most purposes but in some cases the small numerical noise might make difficult SCF convergence and the SCF procedure takes too many iterations when it is close to convergence. If the problem is with large oscillations in early SCF cycles, this is likely not going to help. One can tighten the grid with “Integral=(Grid=XXXXX)”, where XXXXX is the value of the integration grid (see the documentation of the “Integral” keyword for more details). In most cases, tightening the grid to the “Ultrafine” grid is sufficient.

    4) “SCF=NoIncFock”. Turning off the incremental Fock formation can help in cases with very diffuse functions. This increases the computational cost of the SCF calculation as it requests the recomputation of the full Fock matrix at each SCF cycle, instead of only doing an incremental Fock formation (default). The increase in cost with respect to the default SCF procedure is lower than doing QC SCF (QC SCF is not available for SCRF calculations).

    5) “SCF=Fermi”. This one does a combination of things including Fermi broadening, damping and level shifting, deciding dynamically the most suitable strategy. It can be helpful in cases with oscillations in early cycles of the SCF procedure.

    6) “SCF=XQC” (Note that QC SCF is not available for SCRF calculations). Turns on the QC SCF procedure after the maximum number of regular SCF cycles have been done without convergence (if the SCF is converged in fewer cycles with the regular SCF procedure, then the QC step is skipped). The maximum number of regular SCF cycles by default is 128, and this can be controlled by “SCF=(MaxConventionalCyc=N)”. The QC procedure is much slower than the regular SCF procedure but it is very robust and almost guaranteed to converge to an SCF solution. It also has higher chance to converge to the nearest SCF solution (which could be an unstable solution) than the regular SCF procedure, so it is strongly recommended to check for instabilities. The “SCF=XQC” option thus provides a fall-back solution when the regular SCF procedure fails to converge.

  26. Hola Dr. Barroso me encantaría realizar mi verano de investigación con usted

  27. Fernando Cisneros

    Buenas Tardes!!! Dr. Joaquin

    A mi también me gustaría trabajar con usted en el verano próximo.
    Y estuve revisando los programas de veranos de investigación y el que más me llamo la atención fue el de Delfín y vi que usted estuvo registrado el del año pasado, y quisiera saber si para este año también estará?

    Bueno saludos desde León, Gto! y de antemano muchas gracias.

  28. Cordial saludo.
    Dr Barroso le escribo porque tengo una duda, tratando de hacer calculos con “counterpoise correction” no se a que distancia debo colocar los reactantes, ya que el valor obtenido de “Counterpoise: corrected energy” disminuye a medida que la distancia entre los reactivos aumenta; si tiene alguna sugerencia le agradezco su puntual colaboracion.

    • Emiliano,
      me parece que lo más pertinente en este momento es que busques la literatura correspondiente al método Counterpoise para calcular el BSSE (Basis Set Superposition Error).
      Cuando quieres calcular la energía de una ‘supermolécula’ (más de un fragmento unidos no covalentemente) se produce un artificio matemático por el cual la densidad electrónica de una molécula es transferida a la base de la otra (de ahí el nombre de superposición de funciones de base), con lo que la energía queda sobreestimada. El método Counterpoise corrige este efecto. Ese traslapamiento será mayor a medida que estén más cerca los fragmentos, como ya lo viste. La pregunta no es a que distancia los colocas, sino que es lo que quieres calcular y porque la corrección por counterpoise es importante. Otra manera de decirlo es que el BSSE (calculado por counterpoise) no es una cantidad/propiedad física sino un artificio ocasionado por la manera en que son construidas las funciones de onda.

      Espero que te sirva. Gracias por leer el blog!

  29. #Teaching Hello, could you please explain what is the difference between MRMP2 method introduced by Hirao and CASPT2. Thanks in advance!

  30. HI Dr, thank you for this useful blog. I have a question please: I want to evaluate the solvent effect on fluorine molecule, I tried variable solvent but the energy is the same energy of F2 in a gase phase. Can you help me please to find the right key words to run the job on gaussian09.
    Can I modify the dielectric constant for a solvent? when I use the word dielectric i obtain a message error saying that there is a syntax error.

    thank you very much for your help.

    • Hello Wiem,

      Thank you very much for your kind words about my blog!
      What keywords are you using now? Perhaps you are using the Onsager method (which for a non polar molecule as F2 is equal to a gas phase calculation). Try using the PCM or CPCM models with available solvents in gaussian. You can change the dielectric constant but I don’t recommend it; if you want to define your own solvent you need data as the molar volume of it among other things so try to stick to what is already well defined.

      I hope this helps!

      • Hello Dr Barrosso, thank you for your quick response, the problem is that i tried every key word existing in the manual of G09, but i can’t find a notable difference with the gas phase or between solvents! (notice: i did try just few of them) Here are some energies: E(phase gase)= -195.9816245 u.a , using CPCM E(water)=-195.9816792 u.a E(CCl4)= -195.981655u.a E( Ethanol)=-195.9816777 u.a ,, using PCM E(water) = -195.9816786 u.a , using SMD E(water)=-195.9781132 u.a , E(ethanol) = -195.9806675 u.a

        Do you think that it is useless to modulate the solvent effect on this molecule?

        Thank you very much.

      • Hello sir,
        I’m running gaussian calculations for isomers in different solvents using different methods and different basis sets..for example with B3LYP and MP2 with 2 basis sets each..
        when I’m performing Optimization getting error as error in internal coordinate system with some methods..I can not change the geometry bcoz i need to use same geometry for all methods..i tried by giving different keywords likeGuess=AM1, SCF=QC,
        OPT=mod redundant .OPT Guess=Mix etc…. but for some it didn’t work with any of these…pls help me regarding this..

        One more problem is during freq calculations some times its giving so many errors like could not allocate memory , use 2340000 instead of 11196670 …. i tried by changing mem% and MaxDisk…

      • Regarding your first question, there is little that can be done if you can’t change the geometry. Have you considered making partial optimizations? That might work.
        About your second question, try using rwf partition files. Google “efficiency considerations site:gaussian.com” for a link to a useful tutorial on the matter

        Have a nice day!

  31. I like Doctor Joaquin investigate computational chemistry issues with you that would be possible … and good conduct publications

  32. Hello Doctor
    I am working on my thesis and I need to obtain uv-vis spectra of some quinoline carboxaldehyde molecules in gaussian 03. please if you can help me necessary procedure for performing uv-vis because I am totally clueless.
    Thank alot

  33. Hello Dr. Joaquin Barroso-Flores
    I am new to Gaussian and have access to Gaussian 9.0 and Gaussview. I want to generate potential energy surface for a molecule (using scan option around one torison angle). Could you please let me know if there is any link available providing step wise directions to submit and analyse job ?
    Thanks & Regards
    Rajni

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Follow

Get every new post delivered to your Inbox.

Join 1,221 other followers

%d bloggers like this: