molecular dynamics simulation scandium singlet liquid ammonia ab initio qmmm md methods
The Third Basic Science International Conference - 2013
i
Preface
All praises are due to Allah, God Almighty, Who made this annual event of successful. The “3rd
Annual Basic Science International Conference (BaSIC-2013)” is an annual scientific event organized
by the Faculty of Mathematics and Natural Sciences, Brawijaya University. As a basic science conference,
it covered a wide range of topics on basic science: physics, biology, chemistry, mathematics and statistics.
In 2013, the conference took a theme of “Basic Science Advances in Energy, Health and Environment”
as those three aspects of life are hot issues.
The conference in 2013 was the continuation of the preceding conferences initiated in 2011 as the
International Conference on Basic Science (ICBS), where it was a transformation from the similar
national events the faculty had organized since 2004. What also changed in year 2013 was the use of the
ISSN for the conference proceedings book, instead of an ISBN used in previous proceedings books. The
change was based on the fact that BaSIC is an annual event, and, therefore, the use of ISSN is more
appropriate. The proceedings book was also divided into four books: Physics, Biology, Chemistry and
Mathematics, each with a different ISSN. The proceedings were also published in electronic forms that can
be accessed from BaSIC website. I am glad that for the first time both types of publication can be realized.
This event is aimed to promote scientific research activities by Indonesian scientists, especially
those of Brawijaya University, in a hope that they may interact and build up networks and collaborations
with fellow overseas counterparts who participated in the conference. This is in line with university vision
as a World Class Entrepreneurial University.
I am grateful to all the members of the program committee who contributed for the success in
framing the program. I also thank all the delegates who contributed to the success of this conference by
accepting our invitation and submitting articles for presentation in the scientific program. I am also
indebted to PT Semen Gresik and PT PLN (Persero) for their support in sponsoring this event.
I wish for all of us a grand success in our scientific life. And I do hope that the coming conferences
will pick up similar success, and even better.
Malang, April 2013
Johan Noor, Ph.D.
Conference Chairperson
The Third Basic Science International Conference - 2013
ii
Foreword by the Rector of Brawijaya University
First of all I would like to congratulate the Organizing Committee for the success in organizing this
amazing event. I believe all dedicated time and efforts will contribute to the advancement of our beloved
university.
I would like to welcome all participants, domestic and overseas, especially the distinguished invited
speakers, to Malang, to the conference. An international conference is a good means to establish and build
relationships and collaborations among participants. So, I hope this conference will facilitate all of you, the
academicians and scientists, to setup a network of mutual and beneficial collaboration. As a university with
a vision to be “A World Class Entrepreneurial University”, Brawijaya University will support all efforts to
realize that dream.
Finally, I do hope that the conference will run smoothly and nicely and is not the last one. I would
like to thank all parties who have lent their hands in making this conference happened.
Malang, April 2013
Prof. Dr. Yogi Sugito
Rector, Brawijaya University
The Third Basic Science International Conference - 2013
iii
Table of Contents
Preface .............................................................................................................................................................. i
Foreword by the Rector of Brawijaya University ........................................................................................... ii
Table of Contents ........................................................................................................................................... iii
Program Committee ....................................................................................................................................... iv
Scientific Program......................................................................................................................................... vii
Scientific Papers
Invited Papers
Cluster Dynamics by Ultra-Fast Shape Recognition Technique.................................................... I01
Nanotechnology Development Strategy for Supporting National Industry in Indonesia .............. I02
Role of Atomic Scale Computational Research in the Nanoscale Materials ................................. I03
Paeonilorin(PF) Strongly Effects Immuno System........................................................................ I04
Investigating Chlamydia trachomatis using mathematical and computational.............................. I05
Recent Trends in Liquid Chromatography for Bioanalysis ........................................................... I06
Submitted Papers
Analysis of Inorganic Compounds Cr, Cd, CN, Mn, and Pb in RAW Water and Water Filtration
Results in Jakarta-Indonesia.......................................................................................................... C02
Pervaporation through NaA Zeolite Membranes - A Review....................................................... C03
Optimization of NaOH as the cleaning of Polyethersulfone (PES) membrane fouled by Palm oil
mill effluent................................................................................................................................... C08
Room-Temperature Synthesis of TiO2 - Chitosan Nanocomposites Photocatalyst ..................... C10
Structure of Hf(IV) in aqueous solution - An ab initio QM/MM MD approach .......................... C15
Molecular Dynamics Simulation of Scandium (I) Singlet In Liquid Ammonia By AB Initio
QM/MM MD Methods.................................................................................................................. C16
The Third Basic Science International Conference - 2013
Author List
Acknowledgement
iv
The Third Basic Science International Conference - 2013
Program Committee
Patrons
Rector, Universitas Brawijaya
Dean, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya
Advisory Boards
Associate Deans 1, 2 and 3, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya
Chairperson
Johan A.E. Noor, Ph.D.
Deputy-Chair
Dr. Suharjono
Secretary
Agus Naba, Ph.D.
Treasurers
Mrs. Sri Purworini
Mrs. Rustika Adiningrum
Mr. Surakhman
Secretariat & Registration
Dr. Masruroh
dr. Kusharto
Mr. Sugeng Rianto
Mr. Gancang Saroja
Conference Web
Agus Naba, Ph.D.
Publication & Proceedings
Arinto Y.P. Wardoyo, Ph.D.
Mr. Wasis
Public Relations & Sponsorship
Chomsin S. Widodo, Ph.D.
Mr. Moch. Djamil
Mrs. Firdy Yuana
Venue
Mr. Ahmad Hidayat
Dr. Ahmad Nadhir
Mr. Sunariyadi
Mr. Purnomo
Mr. Karyadi Eka Putra
Accommodation & Hospitality
Ms. Siti J. Iswarin
Mrs. Lailatin Nuriyah
v
The Third Basic Science International Conference - 2013
Mrs. Nur Azizah
Mr. Robi A. Indrajit
Mrs. Trivira Meirany
Master of Ceremony
Himafis
Transportation, Excursion & Social Events
Djoko Santjojo, Ph.D.
Dr. Sukir Maryanto
Mr. Wahyudi
Mrs. Arnawati
Workshop, Poster & Scientific Exhibitions
Hari Arief Dharmawan, Ph.D.
Mr. Pudji Santoso
Mr. Sahri
Mr. Murti Adi Widodo
Documentation
Mauludi A. Pamungkas, Ph.D.
Mr. Susilo Purwanto
General Supports
Himafis
Scientific Program
Dr. rer.nat. M. Nurhuda
Dr. Sunaryo
Mr. Agus Prasmono
Local Scientific Committees (Reviewers & Editors)
Physics
Dr. rer.nat. Abdurrouf
Adi Susilo, Ph.D.
Mr. Unggul P. Juswono
Dr.-Ing. Setyawan P. Sakti
Biology
Dr. Moch. Sasmito Djati
Dr. Muhaimin Rifai
Dr. Catur Retnaningdyah
Chemistry
Dr. Masruri
Dr. Ahmad Sabarudin
Dr. Lukman Hakim
Mathematics
Dr. Agus Suryanto
Dr. Wuryansari M.K.
Dr. Rahma Fitriani
Dr. Solimun
vi
The Third Basic Science International Conference - 2013
International Scientific Committee and Editors
A/Prof. Lilibeth dlC. Coo, University of the Philippines, the Philippines
Prof. Dr. Gereon Elbers, FH Aachen, Germany
Prof. S.K. Lai, National Central University, Taiwan
Prof. Kwang-Ryeol Lee, Korean Institute of Science and Technology, Korea
A/Prof. Dann Mallet, Queensland University of Technology, Australia
Prof. Lidia Morawska, Queensland University of Technology, Australia
Prof.Dr. Petr Solich, Charles University, Czech Republic
Dr. Michitaka Suzuki, Nagoya University, Japan
Prof. Hideo Tsuboi, Nagoya University, Japan
Prof. Jia-Lin Wang, National Central University, Taiwan
vii
The Third Basic Science International Conference - 2013
viii
Scientific Program
Time
07.30 – 08.00
08.00 – 08.30
08.30 – 09.00
09.00 – 09.45
09.45 – 10.30
10.30 – 11.15
11.15 – 12.00
12.00 – 13.00
13.00 – 15.00
15.00 – 16.30
16.30 – 17.00
17.00 – 19.00
19.00 – 22.00
Day One – 16 April 2013
Registration
Inaugural Session, Welcome Remarks
and Opening Ceremony
Coffee Break
Day Two – 17 April 2013
Poster Preparation
Poster Session (08.30-09.30)
Invited Speaker 1
(Majapahit Hall)
Prof. Lidia Morawska, Queensland
University of Technology, Australia
Title: “Emissions to the Air: from
Multidisciplinary Science to
Applications”
Coffee Break (09.30 – 10.00)
Invited Speaker 2
Dr. rer. nat. M. Nurhuda, Universitas
Brawijaya
Title: “Towards Energy Security for the
Poor”
Invited Speaker 3
Prof. S.K. Lai, National Central Univ.,
Taiwan
Title: “Cluster Dynamics by Ultra-Fast
Parallel Session (start at 10.00)
Shape Recognition Technique”
Invited Speaker 4
Dr. Nurul Taufiqurrochman*, Indonesian
Nanotech Society
Title:”Nanotechnology Development
Strategy for Supporting National Industry
in Indonesia”
Lunch Break
Parallel Session
Parallel Session
Closing Ceremony
Free Time
Conference Gala Dinner
The Third Basic Science International Conference - 2013
ix
Parallel Session Day One - 16 April 2013
Majapahit 1 Room: Chemistry
Time
Paper ID
13.00-13.30
Invited
C01
C02
13.30-14.30
C03
C04
C05
C06
C07
14.30-15.30
C08
Author(s)
Prof. Petr Solich
Title
Recent Trends in Liquid Chromatography for
Bioanalysis
2+
Liquid-Liquid Extraction of UO2 cation by 18Membered Crown Ethers: A DFT Study using
A Continuum Solvation Model
Analysis of Inorganic Compounds Cr, Cd, CN,
Mn, and Pb in RAW Water and Water
Filtration Results in Jakarta-Indonesia
Pervaporation through NaA Zeolite
Membranes – A Review
Inhibition of citric acid on the precipitation of
calcium sulphate dihydrate (CaSO4.2H2O)
Saprizal Hadisaputra,
Harno Dwi Pranowo, and
Ria Armunanto
Heruna Tanty,
Margaretha Ohyver, Tati
Herlina, and Nurlelasari
Subriyer Nasir, Anthony
B. Hamzah
S.Muryanto and E.
Supriyo
Hermin Sulistyarti,
A New Spectrophotometric Method for Iodide
Atikah, Sita Febriyanti,
Determination
Asdauna
Discussion/Question/Answer
Chandrawati Cahyani,
Optimum Condition for Separation of Two
Edi Priyo Utomo, and Wa Immiscible Liquids,Patchouli Oil and Water,
Ode Cakra Nirwana
and the Design of Separator
Free Radical Scavenging Ability of Xanthone
Rurini Retnowati, Unggul
Isolated from the Mangostene Pericarp
Pundjung Juswono,
(Garcinia Mangostana L.) by Electron Spin
Oktawirandy Rajaki
Resonance (ESR)
Muhammad Said, Abdul
Optimization of NaOH as the cleaning agent of
Wahab Mohammad, Akil
Polyethersulfone (PES) membrane fouled by
Ahmad
Palm oil mill effluent
Discussion/Question/Answer
Moderator
Akhmad
Sabarudin,
D.Sc.
Masruri, PhD
The Third Basic Science International Conference - 2013
x
Parallel Session Day Two 17 April 2013
Majapahit 1 Room: Chemistry
Time
Paper ID
C10
C14
10.00-11.00
C15
C16
C11
C12
11.00-12.00
C13
C17
12.00-13.00
Author(s)
Imelda Fajriati, Mudasir,
Endang Tri Wahyuni
Masruri and Malcolm D.
McLeod
Suwardi,Harno Dwi
Pranowo dan Ria
Armunanto
Crys Fajar Partana, Ria
Armunanto, Harno Dwi
Pranowo, M Utoro
Yahya
Title
Room-Temperature Synthesis of TiO2 –
Chitosan Nanocomposite Photocatalyst
Amino acid-based ligand for the osmium
catalyzed asymmetric aminohydroxylation
reaction in styrene
Structure of Hf(IV) in aqueous solution – An
ab initio QM/MM MD approach
Moderator
Akhmad
Sabarudin,
D.Sc.
Molecular Dynamics Simulation of
Scandium(I) Singlet in Liquied Ammonia by
ab initio QM/MM MD
Discussion/Question/Answers
Silver(I) and mercury(II) complexes derived
Rosenani A. Haque,
from nitrile-functionalized N-heterocyclic
Choo Sze Yii and
carbene: Synthesis, crystal structure, DNA
Srinivasa Budagumpi
binding and nuclease studies
Nurul Filzah Ghazali
Synthesis and Spectroscopy of Dibutyltin (lV)
and Ibrahim Baba
Dithiocarbamates Compounds
Nur Fariza Abdul
Studies of Parameter Effects on LipaseRahman, Mahiran Basri catalyzed Synthesis of Engkabang Fat Esters
Assessment of Hydrochemical Interactions
Abdolhamid Ansari,
Zahra Sajadi and Jaber between Galendar's Aquifer and Geological
Formations
Mozafarizadeh
Discussion/Question/Answers
LUNCH TIME
Lukman
Hakim,
D.Sc.
Scientific Papers
Invited Papers
The Third Basic Science International Conference - 2013
C16-1
Molecular Dynamics Simulation of Scandium (I) Singlet
In Liquid Ammonia By AB Initio QM/MM MD Methods
Crys F Partana1,*, Ria Armunanto2, Harno D Pranowo2, M Utoro Yahya2
Abstract— Study of structural properties of Sc+ singlet in liquid
ammonia has been carried out by means of the ab initio QM/MM
molecular dynamics simulation approach. Structural properties of
Sc+ in liquid ammonia have been evaluated on the basis of a
molecular dynamics (MD) simulation by the ab initio quantum
mechanical/molecular mechanical (QM/MM MD) method at
Restricted Hartree–Fock (RHF) level using LANL2DZ ECP basis
sets for Scndium and Dunning double-ζ plus polarization (DZP) for
liquid ammonia, respectively. Solvation structure of Sc+ in liquid
ammonia was characterized using RDF, CND, and ADF data
obtained from trajectory files. The first solvation shells consist of 6
liquid ammonia molecules, with Sc+_N distance of 2.197 Å.
Keywords: ab initio, liquid ammonia, Sc+ singlet, Solvation
QM/MM MD simulation
I. INTRODUCTION
S
candium (Sc) is one of the transition metal plays an
important role in the metabolism of living things. The
research on scandium metal function as in suppressing the
formation of harmful bacteriostatic in Klebsiella pneumoniae
is present in serum have been carried out [1]. Scandium
complex of enterochelin promote bacteriostasis P.aeruginosa
in serum and also provide a therapeutic effect against infection
with P. aeruginosa in living organisms. Scandium can also
function as antibodies [2].
Structure and dynamics of ions dissolved by the solvent can
be determined in two ways: by experiment and computer
simulation. Determination of structure and dynamics of ion
solvation through experiments require some equipment, such
as: X-ray diffraction, neutron diffraction, electron diffraction,
spectroscopic methods, NMR and some of the equipment
based on the method of scattering the others. Determination of
structure and solvation dynamics through computer
simulations performed by Monte Carlo simulation (MC) and
Molecular Dynamics (MD) [3].
Ray diffraction techniques (X rays, neutrons, electrons) give
information about the structure of complex compounds such
as ion-ligand bond distance and coordination number of ionligand complex, while the NMR provides information on the
nature of dynamics known as residence time of the average
ligand in the solvation layer. NMR technique provide the
solvation number (if ion strongly bound to the ligand), but
NMR technique can not follow the process of fast ligand
exchange [4]. It also can not detect the dynamics of
condensation occurring in unit time under a 10-9 second.
Similar situation for a femtosecond (10-15 second) laser pulse
spectroscopy which can not describe accurately the nature of
the dynamics of the solution. This information indicates that
the way the experiment has the weakness in the detection limit
the movement of molecules in solution. This experimental
weaknesses can be solved by computer simulation [5].
This research is using quantum mechanical/molecular
mechanical mechanics dynamics (QM/MM MD) method. This
method was chosen because it takes relatively quick and fairly
accurate results, provides the proper basis set is used and
involves many body potential.
Electron configuration of scandium (Sc) in the ground state
is 1s2 2s2 2p6 3s2 3p6 3d1 4s2. Sc+ initial electron configuration
(low spin/triplet) is 1s2 2s2 2p6 3s2 3p6 3d1 4s1 whereas highspin configuration of Sc+ (singlet) is 1s2 2s2 2p6 3s2 3p6 3d2
4s0.
II. EXPERIMENTAL SECTION
A.
Materials
This research is a theoretical study of metal ion interaction
Sc+ singlet in liquid ammonia as a ligand by using ab initio
calculation method. Sc+ as central metal ion is surrounded by
as many as 215 molecules of NH3.
B. Instrumentation
Hardware
A set of complete computer with specs Processor Intel ®
Pentium Core 2 Quad 2.4 GHz, Random Access Memory
(RAM) 3.34 GB effective, Graphic Array Video Card
NVIDIA ® 512 MB, Hard disk with a partition of 120 GB.
Software
• Gaussian 2003 is used to obtain the best basis set for the
system under study.
• Turbomole version 5.10 is used for collecting energy points
on a variety of different points of energy of pair potentials, as
well as many body effect of energy correction (three body).
• MD simulation programQM/MM MD, which is a special
program that is used to simulate the QM/MM MD to obtain
energy data systems and time-dependent coordinates data.
1)
Departement of Chemistry, Faculty of mathematics and natural sciences,
States University of Yogyakarta
2)
Departement of Chemistry, Faculty of mathematics and natural sciences
Gadjah Mada University, Yogyakarta
Procedure
The Third Basic Science International Conference - 2013
Determination of coordinates of Sc- NH3 in Cartesian
coordinates
Initial geometry of Sc in NH3 is modeled in threedimensional Cartesian coordinates to adjust the angle and
distance between atoms in the system. Based on experiments
that the H-N-H angle of 106,68° and N-H bond lengths of
1,0124Å [7]
Table 1
Initial Geometry of Sc in NH3 in Cartesian coordinates
Atoms
X (Å)
Y(Å)
Z (Å)
Sc
0,000000
0,000000
1,400000
N
0,000000
0,000000
0,000000
H
0,000000
0,937002
-0,383001
H
0,812002
-0,468001
-0,383001
H
-0,812002
-0,468001
-0,383001
C16-2
E
qM qi Ai Bi Ci Di
a b c d
rMi rMi rMi rMi
i 1 rMi
3
2bd
fit
(2)
Where a, b, c, d, Ai, Bi, Ci and Di are the optimized
parameters summarized in Table 1, RMi distance of the i-th of
atom of Sc and NH3, qi and qM is the charge of atoms of Sc
and NH3.
Simulation protocol
The simulations were performed for one Sc+ and 215
ammonia molecules in a cubic box, at 235.16 K, which
corresponds to the experimental density of 0.690 g/cm3.
Periodic boundary conditions were applied to the simulation
box and the temperature was kept constant by the Berendsen
algorithm [8]. A flexible ammonia model which includes an
intramolecular term was used [7]. Accordingly, the time step
of the simulation was set to 0.2 fs, which allows for explicit
movement of hydrogens. A cut-off of 12.0 Å was set except
for N–H and H–H non-Coulombic interactions for which it
was set to 6.0 and 5.0 Å .
Selection of the best basis set
From several basis pairs that have tested the set of the
basis set that does not cause a significant change in the charge
of ion scandium (Sc) and has a profile curve of binding energy
of Sc-N distance in accordance with the profile curve of
Lennard-Jones potential. From the results obtained by the set
of the basis set selection Lanl2dz ecp for scandium atoms and
DZP for the atoms of hydrogen and nitrogen.
Preparation of Sc-NH3 pair potential
In preparation of the pair potential equation, it takes
Sc-NH3 energy points at various distances Sc against NH3 and
at various angles theta (θ) and phi (Φ.). The points of this
energy is used to construct pair potential functions.
Pair potential function for Sc-NH3 interaction has been
formulated through the calculation of ab initio methods at the
Restricted Hartree-Fock (RHF) for scandium singlet ion (sc+).
The minimum energy system ( E 2b ) between Sc and
NH3 is calculated by reduction of Sc-NH3 complex energy
with the energy of the respective monomers
E Sc and E NH 3
E 2b E Sc NH E Sc E NH 3
in mathematical form is:
3
(1)
Data points of energy at various angles theta and phi are
obtained, then further processed by fitting two bodies. Fitting
the energy conducted to obtain some form of mathematical
equations that represent functions that energy with the
algorithm. The algorithm used in the preparation of analytical
potential functions with the least square method of LavenbergMarguart. Potential equation form two bodies Sc+-NH3 is as
follows:
Figure 1. Curve of pair potential function for Sc-NH3 with
the basis set LANL2DZ –DZP
Simulation QM/MM MD
A classical molecular dynamics simulation was carried out
for 100 ps using the pair potential function. The subsequent
QM/MM simulation was performed for 10 ps after 20 ps of reequilibration. The ab initio HF formalism with the same basis
sets used for the potential construction was applied to the ion
and the full first solvation shell, and for the remaining MM
region the same 2-body potential as in the classical simulation
was used. According to the Sc–N RDF of the classical
simulation, the QM radius had to be set to 3.2 Å in order to
include the full first solvation shell. A smoothing function was
applied to the transition region between QM and MM regions
[8]. The force of the system, Fsystem, is defined as
Fsystem = FMM + S(FQM - FQM/MM)
(4)
where FMM is the MM force of the full system, FQM the QM
force in the QM region and FQM/MM the MM force in the QM
region. S denotes the smoothing function. Free migration of
ligands between QM and MM region is enabled in this
approach
The Third Basic Science International Conference - 2013
III. RESULTS AND DISCUSSION
A.
Radial Distribution Functions
Radial distribution function (RDF) is distance
distribution function of Sc-NH3. RDF of the Sc-N, Sc-H and
the number of its integration obtained from QM/MM MD
simulations are shown in Figures 2 and some characteristic
value are listed in table 2 and table 3. Figure 1 shows the first
shell solvation Sc+ by liquid ammonia is represented by the
first peak of RDF Sc-N 2.197Å centered.
C16-3
of Sc+-N occurred at distances shorter than the first peak of
Sc+-H RDF. This phenomenon indicates that the solvation in
the first shell has a fixed structure with nitrogen atoms leads to
the ions Sc+, while the hydrogen atoms away from Sc+.
Table 3
Characteristic values of the radial distribution functions
for Sc+ in liquid ammonia
rM 1
rm1
Sc
Sc
N
H
1.88
2.54.
2.74
3,37
N m1 rM 2
6
18
4,03
4.23
rm 2 N m2
6.81
6.95
~16
B. Coordination Number Distribution
Based on the analysis of the coordination number or the
number of ligands that surround the central atom in both
solvation first shell and second solvation on the shell as well
as the percentage likelihood that there could be analyzed based
on information obtained from the CND. Distribution of
coordination number for Sc+-NH3 system is shown in Figure 3.
In the first shell solvation solvation numbers indicate the
number 6 with an abundance of 90,66% while in the second
shell solvation show number ~16 with the accuration of
21,30%
Figure 2. Sc-N and Sc-H radial distribution function
In figure 2 shows that at a distance of 2.95 peak of
RDF Sc+-H reaches a maximum value of the first and was
down to a minimum value at a distance of 3.45 Å. This peak
shows the first shell solvation of the H atoms of the molecule
NH3. RDF integration numbers Sc+-H in the first solvation
shell amounted to 6. The second peak occurs in Sc+-H distance
of 5.32 Å and reaches a minimum at a distance of 6.44 Å.
RDF integration Numbers Sc+-H in the second solvation shell
amounted to ~16.
RDF integration Numbers Sc+-H well in the first solvation
shell or the shell the second solvation according to the RDF
Sc-N. RDF peak of Sc+-H both in the form of ramps (not
sharply) suggests that the second shell solvation structure can
not be determined precisely.
C. Angular Distribution Functions
Analysis of solvation structure of Sc+-NH3 is done by
evaluating the angle distribution function (ADF) as result of
MM/MD simulation. ADF gives information about the
distribution of bond angle formed between the N-Sc+-N. From
the angle distribution of N-Sc-N (figure 4) shows a dominant
peak at an angle of 85o distance of 2.197 Å. This indicates
that the simulation of Sc+ in liquid ammonia show the
existence of complexes with a non rigid shape.
Table 2
Optimized parameter of the analytical Sc+-H2O
pair potential function
A
A
(kcal mol-1 A5) (kcal mol-1 A7)
A
A
(kcal mol-1 A9) (kcal
mol-1
12
A )
Sc+- N
-7624.28775
41844.02312
-59090.0078
30000.42401
Sc+- H
-486.58718
7596.26736
-20518.3923
20472.10809
Distance N and H of Sc+ based RDF simulation results in
the first solvation shell is 2.197Å and 2.95 Å. This distance
difference indicates that the first peak of RDF Sc+-N do not
overlap with the first peak of Sc+-H RDF and RDF first peak
Figure 3. Coordination number distribution of Sc+
in liquid ammonia obtained from QM/MM MD
The Third Basic Science International Conference - 2013
Figure 4 Angular Distribution Function of O-Sc+-O
angles obtained by QM/MM MD simulation
IV. CONCLUSION
QM/MM MD simulation methods is used to study the
solvation structure of Sc+ ions in liquid ammonia, in order to
produce information about the solvation structure of Sc+ ions
in liquid ammonia binds six (6) liquid ammonia molecule. The
distance between Sc+ with the N of NH3 molecules in first
solvation shell is 2.197 Å. Greatest probability for finding N
in the second solvation shell is at a distance of 5.5 Å, with a
number of integration in the second solvation shell amounted
to ~ 16.
REFERENCES
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
Roger, H.J., Synge, C., Woods, V.E., 1980, Antibacterial Effect of Scandium
and Indium Complexes of Enterochelin on Klebsiella pneumoniae,
Antimicrob Agents Chemother, 18, 63-68.
Silva, J. J. R., Williams, R. J. P., 1991, The Biological Chemistry of The
Elements, Claredon Press, Oxford.
Pranowo, H.D. dan Hetadi AKR., 2011, Pengantar Kimia Komputasi,
Austrian-Indonesian Centre for Computational Chemistry (AIC),
Jurusan Kimia Fakultas MIPA Universitas Gajah Mada, Yogyakarta
Armunanto, R., Schwenk, C.F., Rode, B.M., 2004, Gold(I) in Liquid
Ammonia: Ab inito QM/MM Molecular Dynamics Simulations. J. Am.
Chem. Soc., 126, 9934.
Rode, B.M., and Hofer, T.S., 2006, How to Access Structure and
Dynamics of Solutions: the Capabilities of Computational Methods,
Pure Applied Chemistry, 78, 525–539.
Armunanto, R., Schwenk, C. F., Randolf, B. R., & Rode, B. M. (2004).
Ag (I) ion in liquid ammonia. Chemical physics letters, 388(4), 395–
399.
Kheawsrikul, S., Hannongbua, S. V., Kokpol, S. U., & Rode, B. M.
(1989). A Monte Carlo study on preferential solvation of lithium (I) in
aqueous ammonia. J. Chem. Soc., Faraday Trans. 2, 85(6), 643–649.
M.P. Allen, D.J. Tildesley, 1987., Computer Simulation of Liquids,
Oxford University Press.
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i
Preface
All praises are due to Allah, God Almighty, Who made this annual event of successful. The “3rd
Annual Basic Science International Conference (BaSIC-2013)” is an annual scientific event organized
by the Faculty of Mathematics and Natural Sciences, Brawijaya University. As a basic science conference,
it covered a wide range of topics on basic science: physics, biology, chemistry, mathematics and statistics.
In 2013, the conference took a theme of “Basic Science Advances in Energy, Health and Environment”
as those three aspects of life are hot issues.
The conference in 2013 was the continuation of the preceding conferences initiated in 2011 as the
International Conference on Basic Science (ICBS), where it was a transformation from the similar
national events the faculty had organized since 2004. What also changed in year 2013 was the use of the
ISSN for the conference proceedings book, instead of an ISBN used in previous proceedings books. The
change was based on the fact that BaSIC is an annual event, and, therefore, the use of ISSN is more
appropriate. The proceedings book was also divided into four books: Physics, Biology, Chemistry and
Mathematics, each with a different ISSN. The proceedings were also published in electronic forms that can
be accessed from BaSIC website. I am glad that for the first time both types of publication can be realized.
This event is aimed to promote scientific research activities by Indonesian scientists, especially
those of Brawijaya University, in a hope that they may interact and build up networks and collaborations
with fellow overseas counterparts who participated in the conference. This is in line with university vision
as a World Class Entrepreneurial University.
I am grateful to all the members of the program committee who contributed for the success in
framing the program. I also thank all the delegates who contributed to the success of this conference by
accepting our invitation and submitting articles for presentation in the scientific program. I am also
indebted to PT Semen Gresik and PT PLN (Persero) for their support in sponsoring this event.
I wish for all of us a grand success in our scientific life. And I do hope that the coming conferences
will pick up similar success, and even better.
Malang, April 2013
Johan Noor, Ph.D.
Conference Chairperson
The Third Basic Science International Conference - 2013
ii
Foreword by the Rector of Brawijaya University
First of all I would like to congratulate the Organizing Committee for the success in organizing this
amazing event. I believe all dedicated time and efforts will contribute to the advancement of our beloved
university.
I would like to welcome all participants, domestic and overseas, especially the distinguished invited
speakers, to Malang, to the conference. An international conference is a good means to establish and build
relationships and collaborations among participants. So, I hope this conference will facilitate all of you, the
academicians and scientists, to setup a network of mutual and beneficial collaboration. As a university with
a vision to be “A World Class Entrepreneurial University”, Brawijaya University will support all efforts to
realize that dream.
Finally, I do hope that the conference will run smoothly and nicely and is not the last one. I would
like to thank all parties who have lent their hands in making this conference happened.
Malang, April 2013
Prof. Dr. Yogi Sugito
Rector, Brawijaya University
The Third Basic Science International Conference - 2013
iii
Table of Contents
Preface .............................................................................................................................................................. i
Foreword by the Rector of Brawijaya University ........................................................................................... ii
Table of Contents ........................................................................................................................................... iii
Program Committee ....................................................................................................................................... iv
Scientific Program......................................................................................................................................... vii
Scientific Papers
Invited Papers
Cluster Dynamics by Ultra-Fast Shape Recognition Technique.................................................... I01
Nanotechnology Development Strategy for Supporting National Industry in Indonesia .............. I02
Role of Atomic Scale Computational Research in the Nanoscale Materials ................................. I03
Paeonilorin(PF) Strongly Effects Immuno System........................................................................ I04
Investigating Chlamydia trachomatis using mathematical and computational.............................. I05
Recent Trends in Liquid Chromatography for Bioanalysis ........................................................... I06
Submitted Papers
Analysis of Inorganic Compounds Cr, Cd, CN, Mn, and Pb in RAW Water and Water Filtration
Results in Jakarta-Indonesia.......................................................................................................... C02
Pervaporation through NaA Zeolite Membranes - A Review....................................................... C03
Optimization of NaOH as the cleaning of Polyethersulfone (PES) membrane fouled by Palm oil
mill effluent................................................................................................................................... C08
Room-Temperature Synthesis of TiO2 - Chitosan Nanocomposites Photocatalyst ..................... C10
Structure of Hf(IV) in aqueous solution - An ab initio QM/MM MD approach .......................... C15
Molecular Dynamics Simulation of Scandium (I) Singlet In Liquid Ammonia By AB Initio
QM/MM MD Methods.................................................................................................................. C16
The Third Basic Science International Conference - 2013
Author List
Acknowledgement
iv
The Third Basic Science International Conference - 2013
Program Committee
Patrons
Rector, Universitas Brawijaya
Dean, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya
Advisory Boards
Associate Deans 1, 2 and 3, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya
Chairperson
Johan A.E. Noor, Ph.D.
Deputy-Chair
Dr. Suharjono
Secretary
Agus Naba, Ph.D.
Treasurers
Mrs. Sri Purworini
Mrs. Rustika Adiningrum
Mr. Surakhman
Secretariat & Registration
Dr. Masruroh
dr. Kusharto
Mr. Sugeng Rianto
Mr. Gancang Saroja
Conference Web
Agus Naba, Ph.D.
Publication & Proceedings
Arinto Y.P. Wardoyo, Ph.D.
Mr. Wasis
Public Relations & Sponsorship
Chomsin S. Widodo, Ph.D.
Mr. Moch. Djamil
Mrs. Firdy Yuana
Venue
Mr. Ahmad Hidayat
Dr. Ahmad Nadhir
Mr. Sunariyadi
Mr. Purnomo
Mr. Karyadi Eka Putra
Accommodation & Hospitality
Ms. Siti J. Iswarin
Mrs. Lailatin Nuriyah
v
The Third Basic Science International Conference - 2013
Mrs. Nur Azizah
Mr. Robi A. Indrajit
Mrs. Trivira Meirany
Master of Ceremony
Himafis
Transportation, Excursion & Social Events
Djoko Santjojo, Ph.D.
Dr. Sukir Maryanto
Mr. Wahyudi
Mrs. Arnawati
Workshop, Poster & Scientific Exhibitions
Hari Arief Dharmawan, Ph.D.
Mr. Pudji Santoso
Mr. Sahri
Mr. Murti Adi Widodo
Documentation
Mauludi A. Pamungkas, Ph.D.
Mr. Susilo Purwanto
General Supports
Himafis
Scientific Program
Dr. rer.nat. M. Nurhuda
Dr. Sunaryo
Mr. Agus Prasmono
Local Scientific Committees (Reviewers & Editors)
Physics
Dr. rer.nat. Abdurrouf
Adi Susilo, Ph.D.
Mr. Unggul P. Juswono
Dr.-Ing. Setyawan P. Sakti
Biology
Dr. Moch. Sasmito Djati
Dr. Muhaimin Rifai
Dr. Catur Retnaningdyah
Chemistry
Dr. Masruri
Dr. Ahmad Sabarudin
Dr. Lukman Hakim
Mathematics
Dr. Agus Suryanto
Dr. Wuryansari M.K.
Dr. Rahma Fitriani
Dr. Solimun
vi
The Third Basic Science International Conference - 2013
International Scientific Committee and Editors
A/Prof. Lilibeth dlC. Coo, University of the Philippines, the Philippines
Prof. Dr. Gereon Elbers, FH Aachen, Germany
Prof. S.K. Lai, National Central University, Taiwan
Prof. Kwang-Ryeol Lee, Korean Institute of Science and Technology, Korea
A/Prof. Dann Mallet, Queensland University of Technology, Australia
Prof. Lidia Morawska, Queensland University of Technology, Australia
Prof.Dr. Petr Solich, Charles University, Czech Republic
Dr. Michitaka Suzuki, Nagoya University, Japan
Prof. Hideo Tsuboi, Nagoya University, Japan
Prof. Jia-Lin Wang, National Central University, Taiwan
vii
The Third Basic Science International Conference - 2013
viii
Scientific Program
Time
07.30 – 08.00
08.00 – 08.30
08.30 – 09.00
09.00 – 09.45
09.45 – 10.30
10.30 – 11.15
11.15 – 12.00
12.00 – 13.00
13.00 – 15.00
15.00 – 16.30
16.30 – 17.00
17.00 – 19.00
19.00 – 22.00
Day One – 16 April 2013
Registration
Inaugural Session, Welcome Remarks
and Opening Ceremony
Coffee Break
Day Two – 17 April 2013
Poster Preparation
Poster Session (08.30-09.30)
Invited Speaker 1
(Majapahit Hall)
Prof. Lidia Morawska, Queensland
University of Technology, Australia
Title: “Emissions to the Air: from
Multidisciplinary Science to
Applications”
Coffee Break (09.30 – 10.00)
Invited Speaker 2
Dr. rer. nat. M. Nurhuda, Universitas
Brawijaya
Title: “Towards Energy Security for the
Poor”
Invited Speaker 3
Prof. S.K. Lai, National Central Univ.,
Taiwan
Title: “Cluster Dynamics by Ultra-Fast
Parallel Session (start at 10.00)
Shape Recognition Technique”
Invited Speaker 4
Dr. Nurul Taufiqurrochman*, Indonesian
Nanotech Society
Title:”Nanotechnology Development
Strategy for Supporting National Industry
in Indonesia”
Lunch Break
Parallel Session
Parallel Session
Closing Ceremony
Free Time
Conference Gala Dinner
The Third Basic Science International Conference - 2013
ix
Parallel Session Day One - 16 April 2013
Majapahit 1 Room: Chemistry
Time
Paper ID
13.00-13.30
Invited
C01
C02
13.30-14.30
C03
C04
C05
C06
C07
14.30-15.30
C08
Author(s)
Prof. Petr Solich
Title
Recent Trends in Liquid Chromatography for
Bioanalysis
2+
Liquid-Liquid Extraction of UO2 cation by 18Membered Crown Ethers: A DFT Study using
A Continuum Solvation Model
Analysis of Inorganic Compounds Cr, Cd, CN,
Mn, and Pb in RAW Water and Water
Filtration Results in Jakarta-Indonesia
Pervaporation through NaA Zeolite
Membranes – A Review
Inhibition of citric acid on the precipitation of
calcium sulphate dihydrate (CaSO4.2H2O)
Saprizal Hadisaputra,
Harno Dwi Pranowo, and
Ria Armunanto
Heruna Tanty,
Margaretha Ohyver, Tati
Herlina, and Nurlelasari
Subriyer Nasir, Anthony
B. Hamzah
S.Muryanto and E.
Supriyo
Hermin Sulistyarti,
A New Spectrophotometric Method for Iodide
Atikah, Sita Febriyanti,
Determination
Asdauna
Discussion/Question/Answer
Chandrawati Cahyani,
Optimum Condition for Separation of Two
Edi Priyo Utomo, and Wa Immiscible Liquids,Patchouli Oil and Water,
Ode Cakra Nirwana
and the Design of Separator
Free Radical Scavenging Ability of Xanthone
Rurini Retnowati, Unggul
Isolated from the Mangostene Pericarp
Pundjung Juswono,
(Garcinia Mangostana L.) by Electron Spin
Oktawirandy Rajaki
Resonance (ESR)
Muhammad Said, Abdul
Optimization of NaOH as the cleaning agent of
Wahab Mohammad, Akil
Polyethersulfone (PES) membrane fouled by
Ahmad
Palm oil mill effluent
Discussion/Question/Answer
Moderator
Akhmad
Sabarudin,
D.Sc.
Masruri, PhD
The Third Basic Science International Conference - 2013
x
Parallel Session Day Two 17 April 2013
Majapahit 1 Room: Chemistry
Time
Paper ID
C10
C14
10.00-11.00
C15
C16
C11
C12
11.00-12.00
C13
C17
12.00-13.00
Author(s)
Imelda Fajriati, Mudasir,
Endang Tri Wahyuni
Masruri and Malcolm D.
McLeod
Suwardi,Harno Dwi
Pranowo dan Ria
Armunanto
Crys Fajar Partana, Ria
Armunanto, Harno Dwi
Pranowo, M Utoro
Yahya
Title
Room-Temperature Synthesis of TiO2 –
Chitosan Nanocomposite Photocatalyst
Amino acid-based ligand for the osmium
catalyzed asymmetric aminohydroxylation
reaction in styrene
Structure of Hf(IV) in aqueous solution – An
ab initio QM/MM MD approach
Moderator
Akhmad
Sabarudin,
D.Sc.
Molecular Dynamics Simulation of
Scandium(I) Singlet in Liquied Ammonia by
ab initio QM/MM MD
Discussion/Question/Answers
Silver(I) and mercury(II) complexes derived
Rosenani A. Haque,
from nitrile-functionalized N-heterocyclic
Choo Sze Yii and
carbene: Synthesis, crystal structure, DNA
Srinivasa Budagumpi
binding and nuclease studies
Nurul Filzah Ghazali
Synthesis and Spectroscopy of Dibutyltin (lV)
and Ibrahim Baba
Dithiocarbamates Compounds
Nur Fariza Abdul
Studies of Parameter Effects on LipaseRahman, Mahiran Basri catalyzed Synthesis of Engkabang Fat Esters
Assessment of Hydrochemical Interactions
Abdolhamid Ansari,
Zahra Sajadi and Jaber between Galendar's Aquifer and Geological
Formations
Mozafarizadeh
Discussion/Question/Answers
LUNCH TIME
Lukman
Hakim,
D.Sc.
Scientific Papers
Invited Papers
The Third Basic Science International Conference - 2013
C16-1
Molecular Dynamics Simulation of Scandium (I) Singlet
In Liquid Ammonia By AB Initio QM/MM MD Methods
Crys F Partana1,*, Ria Armunanto2, Harno D Pranowo2, M Utoro Yahya2
Abstract— Study of structural properties of Sc+ singlet in liquid
ammonia has been carried out by means of the ab initio QM/MM
molecular dynamics simulation approach. Structural properties of
Sc+ in liquid ammonia have been evaluated on the basis of a
molecular dynamics (MD) simulation by the ab initio quantum
mechanical/molecular mechanical (QM/MM MD) method at
Restricted Hartree–Fock (RHF) level using LANL2DZ ECP basis
sets for Scndium and Dunning double-ζ plus polarization (DZP) for
liquid ammonia, respectively. Solvation structure of Sc+ in liquid
ammonia was characterized using RDF, CND, and ADF data
obtained from trajectory files. The first solvation shells consist of 6
liquid ammonia molecules, with Sc+_N distance of 2.197 Å.
Keywords: ab initio, liquid ammonia, Sc+ singlet, Solvation
QM/MM MD simulation
I. INTRODUCTION
S
candium (Sc) is one of the transition metal plays an
important role in the metabolism of living things. The
research on scandium metal function as in suppressing the
formation of harmful bacteriostatic in Klebsiella pneumoniae
is present in serum have been carried out [1]. Scandium
complex of enterochelin promote bacteriostasis P.aeruginosa
in serum and also provide a therapeutic effect against infection
with P. aeruginosa in living organisms. Scandium can also
function as antibodies [2].
Structure and dynamics of ions dissolved by the solvent can
be determined in two ways: by experiment and computer
simulation. Determination of structure and dynamics of ion
solvation through experiments require some equipment, such
as: X-ray diffraction, neutron diffraction, electron diffraction,
spectroscopic methods, NMR and some of the equipment
based on the method of scattering the others. Determination of
structure and solvation dynamics through computer
simulations performed by Monte Carlo simulation (MC) and
Molecular Dynamics (MD) [3].
Ray diffraction techniques (X rays, neutrons, electrons) give
information about the structure of complex compounds such
as ion-ligand bond distance and coordination number of ionligand complex, while the NMR provides information on the
nature of dynamics known as residence time of the average
ligand in the solvation layer. NMR technique provide the
solvation number (if ion strongly bound to the ligand), but
NMR technique can not follow the process of fast ligand
exchange [4]. It also can not detect the dynamics of
condensation occurring in unit time under a 10-9 second.
Similar situation for a femtosecond (10-15 second) laser pulse
spectroscopy which can not describe accurately the nature of
the dynamics of the solution. This information indicates that
the way the experiment has the weakness in the detection limit
the movement of molecules in solution. This experimental
weaknesses can be solved by computer simulation [5].
This research is using quantum mechanical/molecular
mechanical mechanics dynamics (QM/MM MD) method. This
method was chosen because it takes relatively quick and fairly
accurate results, provides the proper basis set is used and
involves many body potential.
Electron configuration of scandium (Sc) in the ground state
is 1s2 2s2 2p6 3s2 3p6 3d1 4s2. Sc+ initial electron configuration
(low spin/triplet) is 1s2 2s2 2p6 3s2 3p6 3d1 4s1 whereas highspin configuration of Sc+ (singlet) is 1s2 2s2 2p6 3s2 3p6 3d2
4s0.
II. EXPERIMENTAL SECTION
A.
Materials
This research is a theoretical study of metal ion interaction
Sc+ singlet in liquid ammonia as a ligand by using ab initio
calculation method. Sc+ as central metal ion is surrounded by
as many as 215 molecules of NH3.
B. Instrumentation
Hardware
A set of complete computer with specs Processor Intel ®
Pentium Core 2 Quad 2.4 GHz, Random Access Memory
(RAM) 3.34 GB effective, Graphic Array Video Card
NVIDIA ® 512 MB, Hard disk with a partition of 120 GB.
Software
• Gaussian 2003 is used to obtain the best basis set for the
system under study.
• Turbomole version 5.10 is used for collecting energy points
on a variety of different points of energy of pair potentials, as
well as many body effect of energy correction (three body).
• MD simulation programQM/MM MD, which is a special
program that is used to simulate the QM/MM MD to obtain
energy data systems and time-dependent coordinates data.
1)
Departement of Chemistry, Faculty of mathematics and natural sciences,
States University of Yogyakarta
2)
Departement of Chemistry, Faculty of mathematics and natural sciences
Gadjah Mada University, Yogyakarta
Procedure
The Third Basic Science International Conference - 2013
Determination of coordinates of Sc- NH3 in Cartesian
coordinates
Initial geometry of Sc in NH3 is modeled in threedimensional Cartesian coordinates to adjust the angle and
distance between atoms in the system. Based on experiments
that the H-N-H angle of 106,68° and N-H bond lengths of
1,0124Å [7]
Table 1
Initial Geometry of Sc in NH3 in Cartesian coordinates
Atoms
X (Å)
Y(Å)
Z (Å)
Sc
0,000000
0,000000
1,400000
N
0,000000
0,000000
0,000000
H
0,000000
0,937002
-0,383001
H
0,812002
-0,468001
-0,383001
H
-0,812002
-0,468001
-0,383001
C16-2
E
qM qi Ai Bi Ci Di
a b c d
rMi rMi rMi rMi
i 1 rMi
3
2bd
fit
(2)
Where a, b, c, d, Ai, Bi, Ci and Di are the optimized
parameters summarized in Table 1, RMi distance of the i-th of
atom of Sc and NH3, qi and qM is the charge of atoms of Sc
and NH3.
Simulation protocol
The simulations were performed for one Sc+ and 215
ammonia molecules in a cubic box, at 235.16 K, which
corresponds to the experimental density of 0.690 g/cm3.
Periodic boundary conditions were applied to the simulation
box and the temperature was kept constant by the Berendsen
algorithm [8]. A flexible ammonia model which includes an
intramolecular term was used [7]. Accordingly, the time step
of the simulation was set to 0.2 fs, which allows for explicit
movement of hydrogens. A cut-off of 12.0 Å was set except
for N–H and H–H non-Coulombic interactions for which it
was set to 6.0 and 5.0 Å .
Selection of the best basis set
From several basis pairs that have tested the set of the
basis set that does not cause a significant change in the charge
of ion scandium (Sc) and has a profile curve of binding energy
of Sc-N distance in accordance with the profile curve of
Lennard-Jones potential. From the results obtained by the set
of the basis set selection Lanl2dz ecp for scandium atoms and
DZP for the atoms of hydrogen and nitrogen.
Preparation of Sc-NH3 pair potential
In preparation of the pair potential equation, it takes
Sc-NH3 energy points at various distances Sc against NH3 and
at various angles theta (θ) and phi (Φ.). The points of this
energy is used to construct pair potential functions.
Pair potential function for Sc-NH3 interaction has been
formulated through the calculation of ab initio methods at the
Restricted Hartree-Fock (RHF) for scandium singlet ion (sc+).
The minimum energy system ( E 2b ) between Sc and
NH3 is calculated by reduction of Sc-NH3 complex energy
with the energy of the respective monomers
E Sc and E NH 3
E 2b E Sc NH E Sc E NH 3
in mathematical form is:
3
(1)
Data points of energy at various angles theta and phi are
obtained, then further processed by fitting two bodies. Fitting
the energy conducted to obtain some form of mathematical
equations that represent functions that energy with the
algorithm. The algorithm used in the preparation of analytical
potential functions with the least square method of LavenbergMarguart. Potential equation form two bodies Sc+-NH3 is as
follows:
Figure 1. Curve of pair potential function for Sc-NH3 with
the basis set LANL2DZ –DZP
Simulation QM/MM MD
A classical molecular dynamics simulation was carried out
for 100 ps using the pair potential function. The subsequent
QM/MM simulation was performed for 10 ps after 20 ps of reequilibration. The ab initio HF formalism with the same basis
sets used for the potential construction was applied to the ion
and the full first solvation shell, and for the remaining MM
region the same 2-body potential as in the classical simulation
was used. According to the Sc–N RDF of the classical
simulation, the QM radius had to be set to 3.2 Å in order to
include the full first solvation shell. A smoothing function was
applied to the transition region between QM and MM regions
[8]. The force of the system, Fsystem, is defined as
Fsystem = FMM + S(FQM - FQM/MM)
(4)
where FMM is the MM force of the full system, FQM the QM
force in the QM region and FQM/MM the MM force in the QM
region. S denotes the smoothing function. Free migration of
ligands between QM and MM region is enabled in this
approach
The Third Basic Science International Conference - 2013
III. RESULTS AND DISCUSSION
A.
Radial Distribution Functions
Radial distribution function (RDF) is distance
distribution function of Sc-NH3. RDF of the Sc-N, Sc-H and
the number of its integration obtained from QM/MM MD
simulations are shown in Figures 2 and some characteristic
value are listed in table 2 and table 3. Figure 1 shows the first
shell solvation Sc+ by liquid ammonia is represented by the
first peak of RDF Sc-N 2.197Å centered.
C16-3
of Sc+-N occurred at distances shorter than the first peak of
Sc+-H RDF. This phenomenon indicates that the solvation in
the first shell has a fixed structure with nitrogen atoms leads to
the ions Sc+, while the hydrogen atoms away from Sc+.
Table 3
Characteristic values of the radial distribution functions
for Sc+ in liquid ammonia
rM 1
rm1
Sc
Sc
N
H
1.88
2.54.
2.74
3,37
N m1 rM 2
6
18
4,03
4.23
rm 2 N m2
6.81
6.95
~16
B. Coordination Number Distribution
Based on the analysis of the coordination number or the
number of ligands that surround the central atom in both
solvation first shell and second solvation on the shell as well
as the percentage likelihood that there could be analyzed based
on information obtained from the CND. Distribution of
coordination number for Sc+-NH3 system is shown in Figure 3.
In the first shell solvation solvation numbers indicate the
number 6 with an abundance of 90,66% while in the second
shell solvation show number ~16 with the accuration of
21,30%
Figure 2. Sc-N and Sc-H radial distribution function
In figure 2 shows that at a distance of 2.95 peak of
RDF Sc+-H reaches a maximum value of the first and was
down to a minimum value at a distance of 3.45 Å. This peak
shows the first shell solvation of the H atoms of the molecule
NH3. RDF integration numbers Sc+-H in the first solvation
shell amounted to 6. The second peak occurs in Sc+-H distance
of 5.32 Å and reaches a minimum at a distance of 6.44 Å.
RDF integration Numbers Sc+-H in the second solvation shell
amounted to ~16.
RDF integration Numbers Sc+-H well in the first solvation
shell or the shell the second solvation according to the RDF
Sc-N. RDF peak of Sc+-H both in the form of ramps (not
sharply) suggests that the second shell solvation structure can
not be determined precisely.
C. Angular Distribution Functions
Analysis of solvation structure of Sc+-NH3 is done by
evaluating the angle distribution function (ADF) as result of
MM/MD simulation. ADF gives information about the
distribution of bond angle formed between the N-Sc+-N. From
the angle distribution of N-Sc-N (figure 4) shows a dominant
peak at an angle of 85o distance of 2.197 Å. This indicates
that the simulation of Sc+ in liquid ammonia show the
existence of complexes with a non rigid shape.
Table 2
Optimized parameter of the analytical Sc+-H2O
pair potential function
A
A
(kcal mol-1 A5) (kcal mol-1 A7)
A
A
(kcal mol-1 A9) (kcal
mol-1
12
A )
Sc+- N
-7624.28775
41844.02312
-59090.0078
30000.42401
Sc+- H
-486.58718
7596.26736
-20518.3923
20472.10809
Distance N and H of Sc+ based RDF simulation results in
the first solvation shell is 2.197Å and 2.95 Å. This distance
difference indicates that the first peak of RDF Sc+-N do not
overlap with the first peak of Sc+-H RDF and RDF first peak
Figure 3. Coordination number distribution of Sc+
in liquid ammonia obtained from QM/MM MD
The Third Basic Science International Conference - 2013
Figure 4 Angular Distribution Function of O-Sc+-O
angles obtained by QM/MM MD simulation
IV. CONCLUSION
QM/MM MD simulation methods is used to study the
solvation structure of Sc+ ions in liquid ammonia, in order to
produce information about the solvation structure of Sc+ ions
in liquid ammonia binds six (6) liquid ammonia molecule. The
distance between Sc+ with the N of NH3 molecules in first
solvation shell is 2.197 Å. Greatest probability for finding N
in the second solvation shell is at a distance of 5.5 Å, with a
number of integration in the second solvation shell amounted
to ~ 16.
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[2]
[3]
[4]
[5]
[6]
[7]
[8]
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Silva, J. J. R., Williams, R. J. P., 1991, The Biological Chemistry of The
Elements, Claredon Press, Oxford.
Pranowo, H.D. dan Hetadi AKR., 2011, Pengantar Kimia Komputasi,
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Jurusan Kimia Fakultas MIPA Universitas Gajah Mada, Yogyakarta
Armunanto, R., Schwenk, C.F., Rode, B.M., 2004, Gold(I) in Liquid
Ammonia: Ab inito QM/MM Molecular Dynamics Simulations. J. Am.
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Rode, B.M., and Hofer, T.S., 2006, How to Access Structure and
Dynamics of Solutions: the Capabilities of Computational Methods,
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Armunanto, R., Schwenk, C. F., Randolf, B. R., & Rode, B. M. (2004).
Ag (I) ion in liquid ammonia. Chemical physics letters, 388(4), 395–
399.
Kheawsrikul, S., Hannongbua, S. V., Kokpol, S. U., & Rode, B. M.
(1989). A Monte Carlo study on preferential solvation of lithium (I) in
aqueous ammonia. J. Chem. Soc., Faraday Trans. 2, 85(6), 643–649.
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