Marco Antonio Chaer Nascimento: A Festschrift from Theoretical Chemistry Accounts

132 Pages·2014·3.41 MB·English

by  Fernando R. Ornellas

Highlights in Theoretical Chemistry 4
Series Editors: Christopher J. Cramer · Donald G. Truhlar
Fernando R. Ornellas
Maria João Ramos Editors
Marco Antonio
Chaer Nascimento
A Festschrift from Theoretical Chemistry Accounts
Highlights in Theoretical Chemistry
Vol. 4
Series Editors: Ch.J. Cramer • D.G. Truhlar

Forfurthervolumes:
http://www.springer.com/series/11166

Fernando R. Ornellas • Maria João Ramos
Volume Editors
Marco Antonio Chaer
Nascimento
A Festschrift from Theoretical Chemistry Accounts
With contributions from

Adelia J. A. Aquino • Xavier Assfeld • Mario Barbatti
Patricia Barragán • María M. Branda • Benedito J. Costa Cabral
Sylvio Canuto • Nuno M. F. S. A. Cerqueira • Kaline Coutinho
Rachel Crespo-Otero • Marcus V. A. Damasceno
Gerardo Delgado-Barrio • Mostafa A. El-Sayed
Pedro A. Fernandes • Tertius L. Fonseca • Silvia Fuente
Herbert C. Georg • Rodrigo M. Gester • Francesc Illas
Kenneth Irving • P. Lazzeretti • Hans Lischka • Antonio Monari
Irina S. Moreira • Vudhichai Parasuk • Rita Prosmiti
Patricio F. Provasi • Maria João Ramos • João V. Ribeiro
Jean-Louis Rivail • Cristina Sanz-Sanz • Marc E. Segovia
Kanjarat Sukrat • Paul Szymanski • Daniel Tunega
Alvaro Valdés • Oscar N. Ventura • Thibaut Very
Pablo Villarreal
Volume Editors
Fernando R. Ornellas Maria João Ramos
Departamento de Química Fundamental REQUIMTE - Depart. de Química e Bioquímica
Instituto de Química Faculty of Science
University of São Paulo University of Porto
São Paulo, Brazil Porto, Portugal

Originally Published in Theor Chem Acc, Volume 131 (2012)
© Springer-Verlag Berlin Heidelberg 2012
ISSN 2194-8666 ISSN 2194-8674 (electronic)
ISBN 978-3-642-41162-5 ISBN 978-3-642-41163-2 (eBook)
DOI 10.1007/978-3-642-41163-2
SpringerHeidelberg New York DordrechtLondon

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Contents
Preface ................................................................................................................................. 1
Fernando R. Ornellas, Maria João Ramos

Some recent developments in photoelectrochemical water splitting using
nanostructured TiO : a short review ............................................................................... 7
2
Paul Szymanski, Mostafa A. El-Sayed

Role of step sites on water dissociation on stoichiometric ceria surfaces ..................... 19
Silvia Fuente, María M. Branda, Francesc Illas

Proton exchange reactions of C2–C4 alkanes sorbed in ZSM-5 zeolite ....................... 27
Kanjarat Sukrat, Daniel Tunega, Adelia J. A. Aquino, Hans Lischka,
Vudhichai Parasuk

Effects of mutations on the absorption spectra of copper proteins:
a QM/MM study. ................................................................................................................ 39
Antonio Monari, Thibaut Very, Jean-Louis Rivail, Xavier Assfeld

Structure and electronic properties of hydrated mesityl oxide:
a sequential quantum mechanics/molecular mechanics approach ............................... 4 9
Marcus V. A. Damasceno, Benedito J. Costa Cabral, Kaline Coutinho

Density functional and chemical model study of the competition between
methyl and hydrogen scission of propane and (cid:533)-scission of the propyl radical .......... 6 3
Marc E. Segovia, Kenneth Irving, Oscar N. Ventura

CompASM: an Amber-VMD alanine scanning mutagenesis plug-in ........................... 81
João V. Ribeiro, Nuno M. F. S. A. Cerqueira, Irina S. Moreira, Pedro A. Fernandes,
Maria João Ramos

Spectrum simulation and decomposition with nuclear ensemble: formal
derivation and application to benzene, furan and 2-phenylfuran ................................ 89
Rachel Crespo-Otero, Mario Barbatti

Methods of continuous translation of the origin of the current density revisited ....... 1 03
P. Lazzeretti

A simple analysis of the influence of the solvent-induced electronic polarization
on the 15N magnetic shielding of pyridine in water ........................................................ 117
Rodrigo M. Gester, Herbert C. Georg, Tertius L. Fonseca, Patricio F. Provasi,
Sylvio Canuto

Theoretical simulations of the vibrational predissociation spectra
of H+ and D+c lusters.. ....................................................................................................... 125
5 5
Alvaro Valdés, Patricia Barragán, Cristina Sanz-Sanz, Rita Prosmiti,
Pablo Villarreal, Gerardo Delgado-Barrio
v
TheorChemAcc(2013)132:1319
DOI10.1007/s00214-012-1319-3
PREFACE
Preface
Fernando R. Ornellas • Maria Joa˜o Ramos
Publishedonline:12January2013
(cid:2)Springer-VerlagBerlinHeidelberg2013
ThisissueofTheoreticalChemistryAccountsisdedicated
to Professor Marco Antonio Chaer Nascimento on the
occasion of his 65th birthday. Professor Chaer played a
pioneering and active role in the early stages and latter
developmentsofresearchactivitiesintheoreticalchemistry
in Brazil. As part of this commemoration, an international
scientificmeetingalsotookplaceinRiodeJaneiro,Brazil,
in the week of June 11–13, 2012. This special volume
containsaselectedsampleofcontributionsfromhisformer
students, colleagues, and collaborators.
After successfully completing his doctorate at Caltech
under the supervision of Professor William A. Goddard in
1977, Professor Chaer was faced with the decision of
pursuing an academic career in United States or to return chemistry graduate research program in Brazil, it had
homeandworkontheestablishmentofagraduateresearch definitelyacharacterofitsown,beingstronglyfocusedon
program in the Physical Chemistry Department of the theoretical chemistry and spectroscopy. This initiative sets
Federal University of Rio de Janeiro (UFRJ, in Portu- a high level standard in human resources formation that
guese). Fortunately, for us, he chose the latter one. This served as model for similar research programs established
decision had a profound impact on the academic activities later in the country. It is a motive of pride for us to see
of the department which, although excelling in under- former students of his group working all over Brazil and
graduate teaching, had no research activity whatsoever. even abroad.
Notwithstanding the fact that it was not the first physical One of his first initiative immediatelyafter his return to
Brazil, together with Professor D. Guenzburger, was to
organize a national meeting putting together Brazilian
Publishedaspartofthespecialcollectionofarticlescelebratingthe
theoretical chemists along with some distinguished inter-
65thbirthdayofProfessorMarcoAntonioChaerNascimento.
nationalspeakerstoknoweachotherresearchinterestsand
F.R.Ornellas(&) to discuss and implement actions to farther the quality of
DepartamentodeQu´ımicaFundamental,InstitutodeQu´ımica, theworkinthefield.ThisfirstmeetinginRiodeJaneiroin
UniversidadedeSa˜oPaulo,Av.Prof.LineuPrestes,
1981wasthenucleusofthebiannualBrazilianSymposium
748,Sa˜oPaulo05508-000,Brazil
ofTheoreticalChemistry(SBQT,inPortuguese),nowinits
e-mail:[email protected]
17th edition and organized by national and local commit-
M.J.Ramos tees. Professor Chaer was also the Coordinator of the 10th
Requimte,DepartamentodeQu´ımicaeBioqu´ımica,Faculdade
edition of SBQT in 1999, and also of two other interna-
deCieˆncias,UniversidadedoPorto,RuadoCampoAlegres/n,
tional Molecular Modeling Conferences (1992 and 1994),
4169-007Porto,Portugal
e-mail:[email protected] held in Rio de Janeiro, that were instrumental in showing
123
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TheorChemAcc(2013)132:1319
the growing impact that theoretical chemistry techniques sign of upcoming retirement, some of his former students
may have in helping solving large-scale chemical and and collaborators decided to pay this tribute to him on the
chemical engineering problems. occasionofhis65thbirthday.Certainly,thebesthonorsare
All these actions, together with his intense participation those received in life, during the peak of activity. Within
in the advisory board of funding agencies in Brazil, cer- that spirit, in the name of all people that worked with him
tainly helped to recognize theoretical chemistry as an and were positively influenced by him, we take this
independent sub-area of research in physical chemistry by opportunitytomake thisjust homage.
the Brazilian most important federal funding agencies
Andre´ G. H. Barbosa, Clarissa O. da Silva,
(CNPq and CAPES) in the last decades.
Ma´rcio Soares Pereira
In summary, Professor Nascimento helped to shape
TheoChem in Rio Committee
Brazilian theoretical chemistry research by participating
directlyorindirectlyintheformationofnumerousstudents, Maria Joa˜o Ramos
someofwhicharenowindependentprofessionalswiththeir Fernando R. Ornellas
own groups. While he is still working with absolutely no Guest Editors
123
2 Reprinted from the journal
TheorChemAcc(2013)132:1319
List of Publications of Professor 22. Oliveira HCB, Nascimento MAC (2008) Int J Quan-
tum Chem 108:2540–2549.
Marco Antonio Chaer Nascimento
23. Fernandez-LimaFA,BeckerC,GilliK,RussellWK,
Nascimento MAC, Russell DH (2008) J Phys Chem
A 112:11061–11066.
1. Fernandez-Lima FA, Nascimento MAC, da Silveira
24. FlorianoWB,DomontG,NascimentoMAC(2007)J
EF (2012) Nuclear Instr & Meth Phys Res B 273:
Phys Chem B 111:1893–1899.
102–104.
25. CardozoTM,NascimentoMAC(2007)JMolStruct-
2. Barbatti M, Nascimento MAC (2012) Int J Quantum
Theochem 811:337–343.
Chem 112:3169–3173.
26. Lavor CC, Liberti L, Maculan N, Nascimento MAC
3. Freitas GN, Garrido JD, Ballester MY, Nascimento
(2007) Europhys Lett 77:50006-1-50006-5.
MAC (2012) J Phys Chem A 112:7677–7685.
27. Fernandez-Lima FA, Ponciano CR, Nascimento
4. Fernandez-Lima FA, Henkes AV, da Silveira EF,
MAC (2007) Chem Phys Lett 445:147–151.
Nascimento MAC (2012) J Phys Chem C 116:
28. Fernandez-Lima FA, Cardozo TM, Ponciano CR,
4965–4969.
Nascimento MAC (2007) J Phys Chem A
5. Fantuzzi F, Messias Cardozo T, Nascimento MAC
111:8302–8307.
(2012) Phys Chem Chem Phys 14:5479–5488.
29. Fernandez-Lima FA, Ponciano CR, Silveira EF,
6. Fernandez-Lima FA, Henkes AV, da Silveira EF, Nascimento MAC (2007) Chem Phys 340:127–133.
Nascimento MAC (2012) J Phys Chem C 116: 30. Bitzer R, Pereira R, Rocco AM, Santos OS, Nasci-
4965–4969. mento MAC, Filgueiras CA J Organomet Chem
7. PereiraMS,daSilvaAM,NascimentoMAC(2011)J (2006) 691:2005–2013.
Phys Chem 115:10104–10113. 31. PereiraMS,NascimentoMAC(2006)JPhysChemB
8. ArrateJDG,NascimentoMAC,BallesterMY(2010)
110:3231–3238.
Int J Quantum Chem 110:549–557.
32. Henriques E, Nascimento MAC, Ramos MJ (2006)
9. Cardozo TM, Nascimento-Freitas G, Nascimento Int J Quantum Chem 106:2107.
MAC (2010) J Phys Chem A 114:8798–8805. 33. Fernandez-Lima FA, Ponciano CR, Silveira EF,
10. CardozoTM,NascimentoMAC(2009)JChemPhys Nascimento MAC (2006) J Phys Chem B 110:
130:104102-1-104102-8. 10018–10024.
11. Fernandez-LimaFA,PoncianoCR,NascimentoMAC, 34. Fernandez-Lima FA, Ponciano CR, Silveira EF,
SilveiraEF(2009)JPhysChemA113:1813–1821. Nascimento MAC (2006) Chem Phys Lett
12. Liberti L, Lavor CC, Maculan N, Nascimento MAC 426:351–356.
(2009) Discrete Appl Math 157:1309–1318. 35. Andrade MD, Mundin K, Nascimento MAC, Malb-
13. Fernandez-Lima FA, Cardozo TM, Silveira EF, Na- ouissonL(2006)IntJQuantumChem106:2700–2705.
scimentoMAC(2009)ChemPhysLett474:185–189. 36. Pereira MS, Nascimento MAC (2005) Chem Phys
14. Barros PR, Stassen H, Freitas MS, Carlini CR, Lett 406:446–451.
Nascimento MAC, Follmer C (2009) Biochim Bio- 37. Collado V, Fernandez-Lima FA, Ponciano CR,
physActa:ProteinsandProteomics1794:1848–1854. Nascimento MAC, Velazquez L, Silveira EF (2005)
15. CardozoTM,NascimentoMAC(2009)JPhysChem Phys Chem Chem Phys 7:1971–1976.
A 113:12541. 38. LavorCC,CardozoTM,NascimentoMAC(2005)Int
16. Fernandez-Lima FA, Vilela-Neto OP, Pimentel AS, J Quantum Chem 103:500–504.
Pacheco MAC, Ponciano CR, Nascimento, MAC, 39. Cardozo TM, Nascimento MAC (2005) J Mat Sci
SilveiraEF(2009)JPhysChemA113:15031–15040. Lett 40:3549–3551.
17. Milas I, Silva AM, Nascimento MAC (2008) Appl 40. BitzerR,BarbosaAGH,SilvaCO,NascimentoMAC
Catalysis A 333:17–22, 2008. (2005) Carbohydrate Res 340:2171–2184.
18. Nascimento MAC (2008) J Brazilian Chem Soc 41. Milas I, Nascimento MAC (2005) Chem Phys Lett
19:245–256. 418:364–368.
19. Sobrinho AMC, Nascimento MAC (2008) Int J 42. Silva CO, Barbosa AGH, Silva EL, Nascimento
Quantum Chem 108:2595–2602. MAC (2004) Theor Chem Acc 111:231–236.
20. Andrade MD, Nascimento MAC (2008) Int J Quan- 43. Barbosa AGH, Nascimento MAC (2004) Int J
tum Chem 108:2486–2498. Quantum Chem 99:317–324.
21. Silva AM, Nascimento MAC (2008) J Phys Chem A 44. Silva CO, Nascimento MAC (2004) Carbohydrate
112:8916–8919. Res 339:113–122.
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TheorChemAcc(2013)132:1319
45. Floriano WB, Nascimento MAC (2004) Brazilian J 72. Nascimento MAC, Silva EC, Silva CO (1999) Int J
Phys 34:38–41. Quantum Chem 74:417–422.
46. SilvaCO,NascimentoMAC(2004)TheorChemAcc 73. Melo A, Ramos MJ, Floriano WB, Gomes JANF,
112:342–348. Lea˜o JFR, Magalha˜es AL, Maigret B, Nascimento
47. SilvaAM,NascimentoMAC(2004)ChemPhysLett MAC, Reuter N. (1998) J Mol Struct 463:81–90.
393: 173–178. 74. Nascimento MAC, Floriano WB, Domont G, God-
48. Lins JOMA, Nascimento MAC (2004) Chem Phys dard WA (1998) Protein Sci 7:2301–2313.
Lett 391: 9–15. 75. Nascimento MAC, Lins JOMA (1997) Mol Eng
49. Barbatti M, Nascimento MAC (2003) J Chem Phys 7:309–316.
119:5444–544803. 76. Nascimento MAC (1997) Mol Eng 7:87–108.
50. Milas I, Nascimento MAC (2003) Chem Phys Lett 77. Nascimento MAC, Barbosa AGH (1997) Chem Phys
373:379–384. Lett 279:119–121.
51. Silva CO, Silva EC, Nascimento MAC (2003) Chem 78. Nascimento MAC, Silva CO, Silva EC, Azevedo JA
Phys Lett 381:244–246. (1996) Int J Quantum Chem 60:433–438.
52. Nascimento MAC, Barbosa AGH Progr Theor Chem 79. Nascimento MAC, Blaszkowsli SR, Santen RV
& Phys (2003) 12:247–267. (1996) J Phys Chem 100:3463–3472.
53. Barbatti M, Nascimento MAC (2003) Brazilian J 80. Nascimento MAC, Lins JOMA (1996) J Mol Struct
Phys 33:792–797. 371:237–243.
54. Pereira MS, Nascimento MAC (2003) Theor Chem 81. Nascimento MAC, Mota-Neto JD (1996) J Phys
Acc 110:441–445. Chem 100:15105–15110.
55. Barbatti M, Jalbert G, Nascimento MAC (2002) J 82. Nascimento MAC, Silva EC, Silva CO (1995)
Phys Chem A 106:551–555. Astrophys J 439:1044–1045.
56. Silva CO, Nascimento MAC (2002) Adv Chem Phys 83. Nascimento MAC, Miranda MP, Bielschowsky CE
123:423–468. (1995) J Phys B 28:L15–18.
57. Barbosa AGH, Nascimento MAC (2002) Mol Phys 84. Nascimento MAC, Blazskowski SR, Floriano WB
100:1677–1680. (1995) J Mol Struct 335:51–57.
58. Barbosa AGH, Nascimento MAC (2002) Theor 85. Nascimento MAC, Silva EC, Silva CO (1995) Int J
Comput Chem 10:117–142. Quantum Chem S29:639–646.
59. Nascimento MAC (2001) Chem Phys Lett 86. Nascimento MAC, Blaskowski SR, Santen RV
343:15–20. (1994) J Phys Chem 98:12938–12944.
60. NascimentoMAC(2001)ChemPhysLett.338:67–73. 87. Nascimento MAC, Hollauer E (1993) J Chem Phys
61. Nascimento MAC (2001) J Chem Phys 99:1207–1214.
114:7066–7072. 88. Nascimento MAC, Craw, JS, Pava˜o AC (1993) Int J
62. NascimentoMAC(2001)JChemPhys114:2213–2218. Quantum Chem 48:219–224.
63. Nascimento MAC (2001) J Computer-Aided Mol 89. Nascimento MAC, Hollauer E (1993) Chem Phys
Design 15:309–322. 174:79–83
64. Nascimento MAC (2001) Phys Status Solidi A 90. Nascimento MAC, Blaskowski SR (1993) J Mol
187:1–14. Struct 287:67–75.
65. Nascimento MAC (2001) Progr Theor Chem & Phys 91. Nascimento MAC, Silva SC (1992) J Mol Struct
7:39–76. 282:51–57.
66. NascimentoMAC,SilvaEC,SilvaCO(2000)JPhys 92. Nascimento MAC, Hollauer E, Bielchowsky CE
Chem B 104:2402–2409. (1992) Phys Rev A 45:7942–7947.
67. Nascimento MAC (2000) J Chem Phys 93. Nascimento MAC, Hollauer E (1991) Chem Phys
113:4230–4237. Lett 184:470–478.
68. Nascimento MAC (1999) J Mol Struct - Theochem 94. Nascimento MAC, Hollauer E (1991) Chem Phys
464:239–247. Lett 181:463–466.
69. NascimentoMAC,SilvaEC,SilvaCO(1999)JPhys 95. Craw JS, Nascimento MAC, Ramos MN (1991) J
Chem A 103:11194–11199. Chem Soc Faraday Trans 87:1293–1296.
70. Nascimento MAC, Esteves PM, Mota CJA (1999) J 96. Craw JS, Nascimento MAC, Neves MR (1991)
Phys Chem B 103:10417–10420. Spectrochim Acta A 47:69–73.
71. Nascimento MAC, Ramos MJ, Floriano WB (1999) 97. Nascimento MAC, Craw JS (1990) Chem Phys Lett
Int J Quantum Chem 74:299–314. 172:265–269.
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