From owner-chemistry@ccl.net Mon Jun 16 03:33:01 2014 From: "Ramon Crehuet rcsqtc-#-iqac.csic.es" To: CCL Subject: CCL: Prasenjit - Quering about Transition States Message-Id: <-50222-140616032803-3741-pGDiVp1ighV498Yf1rQN7w(a)server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 16 Jun 2014 09:27:11 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc-x-iqac.csic.es] Dear Prasenjit, Chain-of-State methods, such as the String method or the NEB can locate Transition States with only the structures of reactants and products. But these methods perform local minimisations, and are thus subject to a reasonable initial guess. In other words, you have to try different initial guesses to have some confidence you have found the lowest MEPs. Black-box methods do not exist to fully describe a complex reaction mechanism. You'll have to think of different reaction mechanisms, explore the energy surface, try to locate intermediates, etc. Chain-of-state methods are implemented in, for example, pDynamo https://sites.google.com/site/pdynamomodeling/ Although this code was designed to do QM/MM calculations, it can do pure QM calculations as well. Hope this helps, Ramon Crehuet On 13/06/14 23:56, Prasenjit Seal seal.prasenjit*_*gmail.com wrote: > Hi, > > I am having a problem dealing with transition states. For some of my systems, > I have no idea what the reaction path will look like, no idea of the > transition states, no idea of the reaction mechanism. > > What I have in hand is only the structures of the reactants and products. Is > there any software available which can solve my problem? > > I would really appreciate if someone has some idea regarding this matter. > > Some of these type of reactions are > > 1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2 > > 2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2 > > Please note that Si2H4(-) is silylene anions and not silene. Same goes for > Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions. > > Thanks and best regards, > Prasenjit -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of Catalonia IQAC - CSIC http://www.iqac.csic.es/qteor https://twitter.com/rcrehuet http://ramoncrehuet.wordpress.com/ Tel. +34 934006116 Jordi Girona 18-26 08034 Barcelona (Spain) From owner-chemistry@ccl.net Mon Jun 16 16:18:01 2014 From: "Patrizia Calaminici pcalamin],[cinvestav.mx" To: CCL Subject: CCL: Prasenjit - Quering about Transition States Message-Id: <-50223-140616105347-2674-OPYBOhNxxiooABKVUCTQww[*]server.ccl.net> X-Original-From: Patrizia Calaminici Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_ADB6DC46AB9A5F4EA8A097875C2190A227B5A71ECINVESTAVMB01ci_" Date: Mon, 16 Jun 2014 14:57:48 +0000 MIME-Version: 1.0 Sent to CCL by: Patrizia Calaminici [pcalamin*cinvestav.mx] --_000_ADB6DC46AB9A5F4EA8A097875C2190A227B5A71ECINVESTAVMB01ci_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, You could use the hierarchical transition state search algorithm implemented in the density functional theory program deMon2k which allows to find transition states knowing only the structures of the reactants and products. In case of interest, details about the deMon2k code can be found at: http://www.demon-software.com/public_html/index.html . Regards, Patrizia Calaminici |-|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D|-| Prof. Dr. Patrizia Calaminici Departamento de Quimica, CINVESTAV, Centro De Investigacion Y De Estudios Avanzados, Av. Instituto Politecnico Nacional, 2508 A.P. 14-740 Mexico D.F. 07000 MEXICO Tel: 5255-5-747-3911 (Office) 5255-5-747-3800 Ext. 4411, 4465 (Labs) Fax: 5255-5-747-3389 E-mails: pcalamin|-|cinvestav.mx, calaminicipatrizia|-|gmail.com http://www.quimica.cinvestav.mx/Directorio/Investigadores/DraCalaminici= Patrizia.aspx Secretary: Miss. Lorena Sanchez Mendoza Tel: 5255-5-747-3800 Ext. 4408 E-mail: lsmendoza|-|cinvestav.mx |-|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D|-| ________________________________ > From: owner-chemistry+pcalamin=3D=3Dcinvestav.mx|-|ccl.net [owner-chemistry+p= calamin=3D=3Dcinvestav.mx|-|ccl.net] on behalf of Prasenjit Seal seal.prasenj= it*_*gmail.com [owner-chemistry|-|ccl.net] Sent: Friday, June 13, 2014 4:56 PM To: Patrizia Calaminici Subject: CCL: Prasenjit - Quering about Transition States Hi, I am having a problem dealing with transition states. For some of my system= s, I have no idea what the reaction path will look like, no idea of the tra= nsition states, no idea of the reaction mechanism. What I have in hand is only the structures of the reactants and products. I= s there any software available which can solve my problem? I would really appreciate if someone has some idea regarding this matter. Some of these type of reactions are 1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2 2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2 Please note that Si2H4(-) is silylene anions and not silene. Same goes for = Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions. Thanks and best regards, Prasenjit --_000_ADB6DC46AB9A5F4EA8A097875C2190A227B5A71ECINVESTAVMB01ci_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable


Hi,

You could use the hierarchical transition state search algorithm
implemented in the density functional theory program deMon2k
which allows to find transition states knowing only the
structures of the reactants and products.

In case of interest, details about the deMon2k code can be found at:

http://www.demon-software.com/public_html/index.html .


Regards,

Patrizia Calaminici


   
|-|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D|-|
    Prof. Dr. Patrizia= Calaminici
    Departamento de Quimica,
    CINVESTAV, Centro De Investigacion &n= bsp;       
    Y De Estudios Avanzados,     &n= bsp;            = ;  
    Av. Instituto Politecnico Nacional, 2508 &= nbsp; 
    A.P. 14-740 Mexico D.F. 07000     &n= bsp;       
    MEXICO 
   
    Tel: 5255-5-747-3911 (Office)    &nb= sp;         
         5255-5-747-3800 Ext. = 4411, 4465 (Labs) 
    Fax: 5255-5-747-3389       = ;            &n= bsp;   
    E-mails: pcalamin|-|cinve= stav.mx,
&n= bsp;            calaminicipatrizia|-|gmail.com 
    http://www.quimica.cinvestav.mx/Directorio/Investigadores/DraCalaminiciPatr= izia.aspx

    Secretary: Miss. Lorena Sanchez Mendoza
    Tel: 5255-5-747-3800 Ext. 4408
    E-mail: lsmendoza|-|cin= vestav.mx
|-|=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D|-|
From: owner-chemistry+pcalamin=3D=3Dcin= vestav.mx|-|ccl.net [owner-chemistry+pcalamin=3D=3Dcinvestav.mx|-|ccl.net] = on behalf of Prasenjit Seal seal.prasenjit*_*gmail.com [owner-chemistry|-|ccl= .net]
Sent: Friday, June 13, 2014 4:56 PM
To: Patrizia Calaminici
Subject: CCL: Prasenjit - Quering about Transition States

Hi,

I am having a problem dealing with transition states. For some of my s= ystems, I have no idea what the reaction path will look like, no idea of th= e transition states, no idea of the reaction mechanism.

What I have in hand is only the structures of the reactants and produc= ts. Is there any software available which can solve my problem? 

I would really appreciate if someone has some idea regarding this matt= er.

Some of these type of reactions are

1. Si2H5(-) + SiH4 ------> Si3H7(-) + H2

2. Si2H4(-) + SiH4 ------> Si3H6(-) + H2

Please note that Si2H4(-) is silylene anions and not silene. Same goes= for Si3H6(-). Si2H5(-) and Si3H7(-) are radical anions.  

Thanks and best regards,
Prasenjit
To: CCL Subject: CCL: Virtual Conference on Computational Chemistry-(1st-31st August 2014)-Call for abstracts-Final Call Message-Id: <-50224-140616215807-29042-WHMdOwdiAMMuaDJQp+4Mzg]|[server.ccl.net> X-Original-From: "Prof Ponnadurai Ramasami" Content-Language: en-gb Content-Type: multipart/alternative; boundary="----=_NextPart_000_0015_01CF89F1.05787DE0" Date: Tue, 17 Jun 2014 05:57:27 +0400 MIME-Version: 1.0 Sent to CCL by: "Prof Ponnadurai Ramasami" [ramchemi[]intnet.mu] This is a multipart message in MIME format. ------=_NextPart_000_0015_01CF89F1.05787DE0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Sir/Madam, =20 Greetings from Mauritius. =20 A Virtual Conference (online conference) on Computational Chemistry will = be organised by the Computational Chemistry Group = of the University of = Mauritius. =20 The Virtual Conference will be held from 1st to 31st August 2014. =20 You are invited to submit an abstract to be considered for the Virtual = Conference. The deadline for submission is 30th June 2014. =20 All topics related to Computational Chemistry may be considered. =20 Please visit the website of the Conference and let me know if you need = more details. =20 http://sites.uom.ac.mu/vccc2014/ =20 Looking forward for your participation. =20 Prof Ponnadurai Ramasami Chairman of the Organising Committee =20 How the virual conference will take place? * There will be a call for abstracts. * Scientific committee will evaluate suitability of each submitted = abstract. * For each accepted abstract, author/s will be invited to submit the = e-presentation in MS Word, MS Powerpoint, PDF or any other relevant = format. Some examples are: (1) PDF format = (15-20 pages) (2) Powerpoint format = (15-20 slides) (3) Video (10-15 = minutes) * E-presentations will be displayed on the website (secured). * Registered participants will be able to download all the = e-presentations. * Participants can ask questions by sending email/s (using the online = platform) to the corresponding author for each e-presentation. * When a participant sends an email, the same email is received by all = the registered participants. However, it is the responsibility of the = corresponding author to reply to the question/s being asked within 24 = hours. When the corresponding author responds by replying the email, the = same is received by all the participants. =20 =C2=B7 Full paper (optional) will be reviewed and accepted = papers will be collected in the conference proceedings. =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 =20 ------=_NextPart_000_0015_01CF89F1.05787DE0 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear Sir/Madam,

 

Greetings > from Mauritius.

 

A Virtual Conference (online conference) on Computational Chemistry will = be organised by the Computational Chemistry Group of the University of Mauritius.

  

The Virtual Conference will be held from 1st to = 31st August 2014.

 

You are invited to submit an abstract to be considered for the Virtual Conference. The deadline for submission is 30th June = 2014.

 

All topics related to Computational Chemistry may be considered.

 

Please visit the website of the Conference and let me know if you need more = details.

 

http://sites.uom.ac.mu/vccc2014/

 

Looking forward for your participation.

 

Prof Ponnadurai Ramasami

Chairman of the Organising Committee

 

 How the virual conference will take place?

  • There = will be a call for abstracts.
  • Scientific committee will evaluate suitability of each submitted abstract.
  • For each = accepted abstract, author/s will be invited to submit the e-presentation in = MS Word, MS Powerpoint, PDF or any other relevant format. Some = examples are:
    (1) PDF format (15-20 pages)
    (2) Powerpoint format (15-20 slides)
    (3) Video (10-15 minutes)
  • E-presentations will be displayed on the website (secured).
  • Registered participants will be able to download all the = e-presentations.
  • Participants can ask questions by sending email/s (using the online platform) to the corresponding author for each e-presentation.
  • When a = participant sends an email, the same email is received by all the registered participants. However, it is the responsibility of the = corresponding author to reply to the question/s being asked within 24 hours. When = the corresponding author responds by replying the email, the same is received by all = the participants.
     

=C2=B7=      &nb= sp;   Full paper (optional) will be reviewed and accepted papers will be collected = in the conference proceedings.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

------=_NextPart_000_0015_01CF89F1.05787DE0-- From owner-chemistry@ccl.net Mon Jun 16 22:52:00 2014 From: "Thomas Manz tmanz%x%nmsu.edu" To: CCL Subject: CCL:G: Chargemol 3.0 released Message-Id: <-50225-140616224841-9772-E89d1liw94YrZPwA/AECLQ[-]server.ccl.net> X-Original-From: Thomas Manz Content-Type: multipart/alternative; boundary=047d7bdc878402ec0604fbff2e57 Date: Mon, 16 Jun 2014 20:48:33 -0600 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [tmanz|*|nmsu.edu] --047d7bdc878402ec0604fbff2e57 Content-Type: text/plain; charset=UTF-8 Hi, I just wanted to let everyone know about the release of Chargemol version 3.0, which performs Density Derived Electrostatic and Chemical (DDEC) atomic population analysis. The latest version has the following features: 1) Computes net atomic charges, atomic spin moments, and now effective bond orders (EBOs) for nonperiodic and periodic materials. For each atom, the sum of effective bond orders (SEBO) is also computed and printed. The program analyzes output from GAUSSIAN 09 (.wfx files), VASP, and a variety of other quantum chemistry programs. 2) Atomic dipole and quadrupole moments are computed for all systems. For nonperiodic materials, the total system dipole and quadrupole moments are also computed. The latest version adds the computation and printing of the traceless quadrupole tensor eigenvalues. 3) A new constraint has been added to improvement the treatment in ionic systems containing small cations. For example, it was noticed that in crystals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too contracted and too positively charged. This has been fixed by constraining the rate of decay of atomic weights to be no faster than exp(-3*r) in regions where atoms overlap. 4) To improve the speed, the program has been translated from Matlab into Fortran code. The Fortran code is parallelized with OpenMP allowing it to run on multiple processors with a shared memory (i.e., single node, multiple processors). A serial version of the Fortran code is also available. 5) Precompiled Windows and Linux binaries and the uncompiled sourcecode are available. Many users can utilize the precompiled executables without recompiling the program. 6) The program is free to download from ddec.sourceforge.net. The download includes a manual explaining how to install and run the program. Sincerely, Tom Manz --047d7bdc878402ec0604fbff2e57 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,

I just wanted to let everyone know about the re= lease of Chargemol version=C2=A03.0, which performs Density Derived Electro= static and Chemical (DDEC)=C2=A0atomic population analysis.

The late= st version has the following features:

1) Computes net atomic charges, atomic spin moments, and now effective = bond=C2=A0orders (EBOs) for nonperiodic and periodic materials. For each at= om, the sum of=C2=A0effective bond orders (SEBO) is also computed and print= ed. The program=C2=A0analyzes output from GAUSSIAN 09 (.wfx files), VASP, a= nd a variety of other=C2=A0quantum chemistry programs.

2) Atomic dipole and quadrupole moments are computed for all systems. F= or=C2=A0nonperiodic materials, the total system dipole and quadrupole momen= ts are=C2=A0also computed. The latest version adds the computation and prin= ting of the=C2=A0traceless quadrupole tensor eigenvalues.

3) A new constraint has been added to improvement the treatment in ioni= c systems containing small cations. For example, it was noticed that in cry= stals such as Na2Cl and Li-Ru-O, the Na and Li atoms become too contracted = and too positively charged. This has been fixed by constraining the rate of= decay of atomic weights to be no faster than exp(-3*r) in regions where at= oms overlap.

4) To improve the speed, the program has been translated from Matlab in= to=C2=A0Fortran code. The Fortran code is parallelized with OpenMP allowing= it to=C2=A0run on multiple processors with a shared memory (i.e., single n= ode,=C2=A0multiple processors). A serial version of the Fortran code is als= o
available.

5) Precompiled Windows and Linux binaries and the uncompi= led sourcecode are=C2=A0available. Many users can utilize the precompiled e= xecutables without=C2=A0recompiling the program.

6) The program is f= ree to download from ddec.sourcefor= ge.net. The download=C2=A0includes a manual explaining how to install a= nd run the program.

Sincerely,

Tom Manz
--047d7bdc878402ec0604fbff2e57--