9th Congress on Electronic Structure: Principles and Applications (ESPA 2014): A Conference Selection from Theoretical Chemistry Accounts

229 Pages·2016·11.165 MB·English

by  Manuel F. Ruiz-Lopez, Francisco J. Olivares del Valle (eds.)

Highlights in Theoretical Chemistry 11
Series Editors:
Christopher J. Cramer · Donald G. Truhlar
Manuel F. Ruiz-Lopez
Editors
Francisco J. Olivares del Valle
9th Congress on Electronic
Structure: Principles and
Applications (ESPA 2014)
A Conference Selection from Theoretical Chemistry
Accounts
Highlights in Theoretical Chemistry
Vol. 11
Series Editors: Christopher J. Cramer • Donald G. Truhlar
More information about this series at http://www.springer.com/series/11166

Manuel F. Ruiz-Lopez • Francisco J. Olivares del Valle
Volume Editors
9th Congress on Electronic
Structure: Principles and
Applications (ESPA 2014)
A Conference Selection from Theoretical
Chemistry Accounts
With contributions from

Diego R. Alcoba • Ibon Alkorta • Xavier Assfeld • Luis Miguel Azofra
V. G. Baonza • Zoila Barandiarán • Gian Luigi Bendazzoli • Oriana Brea
Luigi Cavallo • M. Natália D. S. Cordeiro • Christopher J. Cramer
Hugo Gattuso • Élise Dumont • Stefano Evangelisti • A. V. Evstafev
José L. C. Fajín • Edoardo Fertitta • R. Franco • Juan Frau • Laura Gagliardi
José R. B. Gomes • Leticia González • Ana M. Graña • Raymond Grüber
Francesc Illas • F. Izquierdo-Ruiz • Georgia M. A. Junqueira
Yukio Kawashima • Tsutomu Kawatsu • Muammar El Khatib • Daniel Kinzel
T. Latychevskaia • Paolo Lazzeretti • Luis Lain • Thierry Leininger
Diego López-Carballeira • Marcos Mandado • M. Marqués
Ana África Márquez García • Marilia T. C. Martins-Costa • J. M. Menéndez
Josef Michl • Antonio Monari • A. Morales-García • Ibério de P. R. Moreira
Francisco Muñoz • Rana Obaid • Yudai Ogata • Josep M. Oliva
Francisco J. Olivares del Valle • Ofelia B. Oña • Markus Oppel
E. V. Orlenko • F. E. Orlenko • Joaquín Ortega-Castro • Francisco Partal Ureña
Beate Paulus • Quan Manh Phung • Ignacio Pérez-Juste • Albert Poater
María del Carmen Ramírez Avi • Nicolás Ramos-Berdullas • J. M. Recio
Daniel Reta Mañeru • Manuel F. Ruiz-López • Fernando Sato
Steve Scheiner • Luis Seijo • David Semrouni • Christian Solís-Calero
Masanori Tachikawa • Kaito Takahashi • Filipe Teixeira • Alicia Torre
Sai Vikrama Chaitanya Vummaleti • Sara Watanabe
Volume Editors
Manuel F. Ruiz-Lopez Francisco J. Olivares del Valle
Campus Vandoeuvre-lès-Nancy Campus Badajoz
Université de Lorraine Universidad de Extremadura
Nancy, France Badajoz, Spain

Originally published in Theor Chem Acc, Volume 133 (2014), volume 134 (2015),
© Springer-Verlag Berlin Heidelberg 2014, 2015
ISSN 2194-8666 I SSN2194-8674 (electronic)
Highlights in Theor etical Chemistry
ISBN 978-3-662-48793-8 ISBN 978-3-662-49221-5 (eBook)
DOI 10.1007/978-3-662-49221-5

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Contents
Preface to the ESPA-2014 special issue ............................................................................ 1
Manuel F. Ruiz-López, Francisco J. Olivares del Valle

AMOEBA force field parameterization of the azabenzenes ........................................... 3
David Semrouni, Christopher J. Cramer, Laura Gagliardi

Triplet–singlet gap in structurally flexible organic diradicals ....................................... 15
Daniel Reta Mañeru, Ibério de P. R. Moreira, Francesc Illas

Separating nuclear spin isomers using a pump–dump laser scheme ............................. 25
Rana Obaid, Daniel Kinzel, Markus Oppel, Leticia González

Spin delocalization in hydrogen chains described with the spin-partitioned
total position-spread tensor................................................................................................ 33
Muammar El Khatib, Oriana Brea, Edoardo Fertitta, Gian Luigi Bendazzoli,
Stefano Evangelisti, Thierry Leininger, Beate Paulus

Invariant time-dependent exchange perturbation theory and its application
to the particles collision problem ....................................................................................... 41
E. V. Orlenko, T. Latychevskaia, A. V. Evstafev, F. E. Orlenko

On the definition of molecular dynamic magnetizability ................................................ 57
Paolo Lazzeretti

Toward (car)borane-based molecular magnets ............................................................... 69
Josep M. Oliva, Diego R. Alcoba, Ofelia B. Oña, Alicia Torre, Luis Lain,
Josef Michl

Theoretical analysis of vibrational modes in uranyl aquo chloro complexes ............... 77
F. Izquierdo-Ruiz, J. M. Menéndez, J. M. Recio

Theoretical study of nonlinear optical properties of cobalt bis (dicarbollide)
derivatives: the effect of substituents ................................................................................ 85
Georgia M. A. Junqueira, Fernando Sato

The driving force role of ruthenacyclobutanes ................................................................ 93
Sai Vikrama Chaitanya Vummaleti, Luigi Cavallo, Albert Poater

Study of electron transport in polybenzenoid chains covalently attached
to gold atoms through unsaturated methylene linkers .................................................... 99
Nicolás Ramos-Berdullas, Ana M. Graña, Marcos Mandado

Revisiting the mechanism and the influence of the excitation wavelength
on the surface-enhanced Raman scattering of the pyridine–Ag system ..................... 113
20
Nicolás Ramos-Berdullas, Diego López-Carballeira,
Marcos Mandado, Ignacio Pérez-Juste

Effect of van der Waals interactions in the DFT description
of self-assembled monolayers of thiols on gold ................................................................ 127
José L. C. Fajín, Filipe Teixeira, José R. B. Gomes,
M. Natália D. S. Cordeiro
v
vi Contents
Structural relaxation effects on the lowest 4f(cid:237)5d transition
of Ce3+ in garnets ................................................................................................................. 141
Quan Manh Phung, Zoila Barandiarán, Luis Seijo

A local topological view of pressure-induced polymorphs in SiO ................................ 151
2
A. Morales-García, M. Marqués, J. M. Menéndez, R. Franco,
V. G. Baonza, J. M. Recio

Noncovalent interactions in dimers and trimers of SO and CO ................................... 159
3
Luis Miguel Azofra, Ibon Alkorta, Steve Scheiner

Is the structure of hydroxide dihydrate OH(cid:237)(H O) ? An ab initio
2 2
path integral molecular dynamics study ........................................................................... 167
Yudai Ogata, Yukio Kawashima, Kaito Takahashi, Masanori Tachikawa

Solvation effects on electronic polarization and reactivity indices
at the air–water interface: insights from a theoretical study
of cyanophenols ................................................................................................................... 173
Marilia T. C. Martins-Costa, Manuel F. Ruiz-Lopez

Electronic structure of kaempferol–Cu2+ coordination compounds:
a DFT, QTAIM and NBO study in the gas phase ............................................................ 181
María del Carmen Ramírez Avi, Ana África Márquez García,
Francisco Partal Ureña

Scavenger mechanism of methylglyoxal by metformin. A DFT study .......................... 191
Christian Solís-Calero, Joaquín Ortega-Castro, Juan Frau, Francisco Muñoz

Effects of monohydration on an adenine–thymine base pair ......................................... 205
Sara Watanabe, Yudai Ogata, Tsutomu Kawatsu, Yukio Kawashima,
Masanori Tachikawa

DFT investigation of the formation of linear aminols as the first step
toward the induction of oxidatively generated interstrand
cross-link DNA lesions ........................................................................................................ 217
Raymond Grüber, Élise Dumont

Modeling DNA electronic circular dichroism by QM/MM methods
and Frenkel Hamiltonian ................................................................................................... 225
Hugo Gattuso, Xavier Assfeld, Antonio Monari
Theor Chem Acc (2015) 134:92
DOI 10.1007/s00214-015-1687-6
P REFACE
Preface to the ESPA-2014 special issue
Manuel F. Ruiz-López1 · Francisco J. Olivares del Valle2
Published online: 11 July 2015
© Springer-Verlag Berlin Heidelberg 2015
This issue of Theoretical Chemistry Accounts collects a Poster Presentations. The meeting was attended by a total
compilation of research works presented at the 9th edition number of 178 participants coming from different universi-
of the E lectronic Structure: Principles and Applications ties around the world. The offi cial picture of the meeting is
conference (ESPA-2014) held in Badajoz, Spain, on the shown in Fig. 2 . Most of the participants came from Spain,
July 2–4, 2014. but delegates from 14 other countries were present, which
The ESPA conferences were initiated in 1998, and since include (in alphabetic order) Austria, Brazil, Czech Repub-
then, they have been organized every 2 years. The previous lic, Denmark, France, Germany, Italy, Japan, the Nether-
editions were organized in Madrid (1998), San Sebastián lands, Portugal, Russia, Sweden, UK and the USA.
(2000), Sevilla (2002), Valladolid (2004), Santiago de Together with a high-quality scientifi c program, the
Compostela (2006), Palma de Mallorca (2008), Oviedo organizers tried to provide delegates with the opportunity
(2010) and Barcelona (2012). The ESPA conferences were to experience the Extremadura region as part of the con-
initially intended to bring together the Spanish community gress. To this aim, an engaging social program was designed
in the fi eld of Theoretical and Computational Chemistry. starting on the evening of July 2 with a welcome reception
However, ESPA has grown over time in terms of national at the Archeological Museum of Badajoz. Besides, the del-
and international participation, and in the last years, it has egates enjoyed a mid-conference excursion to the old town
become a key scientifi c event of international reputation. of Cáceres, a UNESCO World Heritage Site since 1986.
ESPA-2014 was organized by the Quantum Chemistry Finally, the congress was closed with a banquet at the Ethno-
and Molecular Modelling (QCAMM) group of the Univer- graphic Museum gardens of the magnifi cent city of Olivenza.
sity of Badajoz (see Fig. 1 ) . Four main topics were covered As an important satellite event of the ESPA-2014 con-
in the conference: “Theory, Methods and Foundations,” ference, the Third Annual Workshop of the Joint Doctor-
“Materials Science,” “Structure and Chemical Reactivity” ate Program on Theoretical Chemistry and Computational
and “Environmental Effects and Modelling.” They were Modelling (TCCM) took place on July 1 at the Faculty of
properly represented by means of nine invited Plenary Sciences of the University of Extremadura. Such a work-
Talks, twenty-four Oral Communications and about 120 shop event is regularly organized for Ph.D. students, as a
complementary training of the TCCM doctorate program,
and offers them the opportunity to present their research
Published as part of the special collection of articles derived
from the 9th Congress on Electronic Structure: Principles and work via oral communications at the end of the fi rst year of
Applications (ESPA 2014). the doctorate studies.
D uring the conference, the members of the organizing
* Manuel F. Ruiz-López
committee brought to the attention of the delegates the
[email protected]
extremely diffi cult situation that is presently facing the
* Francisco J. Olivares del Valle
Spanish research system as a consequence of the drastic
[email protected]
R + D funding reduction decided by the Spanish govern-
1 University of Lorraine , Nancy , France ment. A document describing this situation, known as the
2 University of Badajoz , Badajoz , Spain “Badajoz Manifesto,” was sent to the media. It stated, in
1 3
Reprinted from the journal 1
Theor Chem Acc (2015) 134:92
Fig. 1 T he ESPA 2014 Organizing Committee, from l eft to r ight: Rute Barata Morgado (Ph.D. student), Prof. Francisco J. Olivares del
Dr. José Carlos Corchado Martín-Romo, Glauco Garrido Almeida Valle (Chairman) and Dr. Manuel Angel Aguilar Espinosa. Dr. Igna-
(guest Ph.D. student), Dr. María de la Luz Sánchez Mendoza, Dr. cio Fernández Galván (not in the picture) was also a member of the
Aurora Muñoz Losa, Dr. María Elena Martín Navarro (Secretary), Organizing Committee
Fig. 2 T he ESPA 2014 offi cial picture with the 178 delegates coming from 15 different countries
particular, that such an unprecedented budget reduction has The next ESPA conference will be organized in 2016
marked a turning point for the Spanish scientifi c growth, in the city of Castellón, Spain, close to the Mediterranean
while it is creating a great discouragement of the Spanish Sea. All our best wishes to the organizers for a successful
young talents, who do not see any perspectives to develop a conference, and we hope to see you there!
scientifi c carrier in their country.
1 3
2 Reprinted from the journal
Theor Chem Acc (2015) 134:1590
DOI 10.1007/s00214-014-1590-6
R EGULAR ARTICLE
AMOEBA force fi eld parameterization of the azabenzenes
David Semrouni · Christopher J. Cramer ·
Laura Gagliardi
Received: 30 August 2014 / Accepted: 21 October 2014 / Published online: 11 November 2014
© Springer- Verlag Berlin Heidelberg 2014
Abstract W e present an extension of the AMOEBA force Keywords Polarizable force fi eld · Intermolecular
fi eld to several common organic heterocycles, namely pyri- interactions · Molecular mechanics · Pi stacking
dine, pyrazine, pyrimidine, pyridazine, the three unique
triazines, and the two unique tetrazines . Atomic multipoles
for newly defi ned atom types were obtained from quantum 1 Introduction
chemical calculations on the isolated molecules. Atomic
polarizability parameters are maintained at their standard Assessment of chemical properties can often require a
AMOEBA values for corresponding atomic classes while computationally costly sampling of a high-dimensional
standard van der Waals parameters are rescaled to repro- phase space in order accurately to predict ensemble-aver-
duce C CSD( T) intermolecular interaction energies of aged values. Molecular mechanics simulations offer an
selected dimer structures. In order to improve vibrational effi cient way to sample such ensembles, with the quality
frequencies that are important both spectroscopically and of the results depending on the ability of the force fi eld
for fl exible dynamics, parameters for covalent terms, i.e., adequately to describe the energetics of the system under
bond-stretching, angle-bending, and stretch-bend terms, the conditions of the simulation. The range of applicability
were optimized and added to the existing AMOEBA force of a particular force fi eld depends both upon its functional
fi eld. We validate our force fi eld through comparison of form (e.g., the degree to which it employs harmonic terms
molecular structural, vibrational, electrostatic, and ener- vs anharmonic, and the degree to which it includes cross-
getic properties— i ncluding intermolecular interaction terms (which couple different internal coordinates), high-
energies— t o reliable quantum chemical data for the vari- order electric multipoles , or polarization) and its various
ous systems of interest. parameters. Force fi elds are usually made more accurate
through the proliferation of atom types, i.e., atoms of the
same element that, as a consequence of belonging to differ-
ent chemical functional groups, have interaction energies
Published as part of the special collection of articles derived
from the 9 th Congress on Electronic Structure: Principles and that are computed using different parameters.
Applications (E SPA 2014). O ne such force fi eld, AMOEBA, was originally devoted
to water and biomolecules, but it now also fi nds use for
Electronic supplementary material The online version of this
more general applications involving organic molecules.
article (doi: 10.1007/s00214-014-1590-6 ) contains supplementary
We here present an extension of AMOEBA through a com-
material, which is available to authorized users.
plete parameterization of the stable a zabenzene series, i.e.,
D. Semrouni · C. J. Cramer ( * ) · L. Gagliardi (* ) six-membered N-heterocyclic rings incorporating varying
Department of Chemistry, Chemical Theory Center,
numbers of N atoms from 1 to 4. Such heterocycles are
and Supercomputing Institute , University of Minnesota ,
found widely in various pi-conjugated systems [ 1 ] and their
207 Pleasant St. SE , Minneapolis , MN 55455 , USA
e-mail: [email protected] derivatives are ubiquitous in biological [ 2 ] and pharmaceu-
tical [3 ] compounds, as well as a number of metal– o rganic
L. Gagliardi
e-mail: [email protected] cages [ 4 – 6 ] and frameworks [ 7 – 9 ]. Thus, we focus here on
1 3
Reprinted from the journal 3