virtual conference on computational...

Virtual Conference on

Computational Chemistry

VCCC-2015

1-31August 2015

Table of Contents Page

Members of the Organising Committee 1

Members of the International Advisory Committee 2

Message from the Chairman of the Organising Committee 4

Presentations

P-1 Theoretical Prediction of the Stepwise Protonation Constants of

1,4,7,12-Tetraazadodecane

A. S. Adeyinka and I. Cukrowski

5

P-2 Excitation Energy Transference in the FMO Complex: Looking for the Best Model

for Photosynthesis

M. E. Sandoval-Salinas and J. Barroso-Flores

6

P-3 Application of Quantum Chemistry to Evaluate Radiative Forcing for an Emerging

Class of Atmospheric Pollutants

P. Blowers, S. Golawski, B. Diallo, M. Flammia, B. Safavinia, M. Gonzalez and

R. Petronella

7

P-4 Maximum Likelihood Estimation in Determination of Power of the Error in

Bivariate Linear Models involving Generalized Gauss-Laplace Distributed

Variables

L. Jäntschi and S. D. Bolboacă

8

P-5 The Reactivity of Unsymmetrical Pincer Ligands and the Nature of the Bonding in

Unsymmetrical Pincer Palladacycles

S. Boonseng, G. W. Roffe, J. Spencer and H. Cox

9

P-6 A Computational Survey on Optoelectronic Properties of Indazolone Derivatives

P. Ranjan, S. Venigalla, S. Dhail, S. Roy, A. Kumar, L. Ledwani and T. Chakraborty

10

P-7 Ensemble-Based Virtual Screening: Hit Compounds against Mycobacterium

tuberculosis Isocitrate Lyase

Y. S. Choong, Y.-V. Lee and H. A. Wahab

11

P-8 DFT Studies of the MTSL Nitroxide Side Chain in the Aurora Kinase Activation

Loop

M. G. Concilio, A. J. Fielding, R. Bayliss and S. Burgess

12

P-9 External and Intramolecular Influences on Spiropyran - Merocyanine

Interconversion

C. D. Simpson, N. L. Haworth, S. Ciampi and M. L. Coote

13

P-10 GIAO Calculations of Chemical Shifts in 1,4-Diaryl-2-mercaptoimidazoles

Derivatives

G. K. Gupta, P. Saini and V. Kumar

14

P-11 Full Factorial Analysis on One-Cage Pentagonal Faced Nanostructures

S. D. Bolboacă and L. Jäntschi

15

P-12 Coinage Metals Binding as Main Group Elements: Structure and Bonding of the

Carbene Complexes [TM(cAAC)2] and [TM(cAAC)2]+ (TM = Cu, Ag, Au)

P. Jerabek and G. Frenking

16

P-13 Self-Interaction Corrected Density Functional Calculations of Molecules and Solids

H. Jónsson

17

P-14 Constitutional Isomers in Drug Discovery: A Case Study Featuring G-Protein

Coupled Receptor Ligands

P. S. Kharkar, N. U. Sahu and S. Warrier

18

P-15 Catalytic Strategy of Adenosine Triphosphate Hydrolysis in Myosin Motor

F. A. Kiani

19

P-16 Polarizable Embedding - From Solvents to Heterogeneous Environments

J. Kongsted

20

P-17 Comparative DFT Study of the M-L Binding Energies (M = Sc, Ti, V, Cr, Mn, Fe,

Co, Ni, Cu and Zn; L = Porphine, P, and P4-Substituted Porphine, P(P)4)

A. E. Kuznetsov

21

P-18 Is it Worth Making? Assessing the Information Content of New Structures

M. D. Mackey, T. Cheeseright, R. Lawrence, G. Tedesco, S. Tomasio and P. Tosco 22

P-19 Application of Variational - Perturbation Method for Calculating the Electric Dipole

Moment of Molecule HD

E. Maksimova

23

P-20 Intuitive and Counterintuitive Noncovalent Interactions of Aromatic π Regions and

π-Hole Regions with the Hydrogen and the Nitrogen of HCN

J. S. Murray and P. Politzer

24

P-21 Electronic, Optical and Magnetic Properties of Si-Doped Au Nanoalloy Clusters

P. Ranjan, A. Kumar and T. Chakraborty

25

P-22 An ELF Quantum Topological Analysis of the Mechanism of the Ketene-Imine

Staudinger Reaction

M. Ríos-Gutiérrez and L. R. Domingo

26

P-23 Maximum Power Point Tracking of Photovoltaic Systems using Extremum Seeking

Control

S. Z. Sayed Hassen

27

P-24 Computational Investigation of Spectroscopic Properties of Fluorescent 3-Vinyl

Indoles by DFT and TD-DFT

S. Chemate, S. Lanke and N. Sekar

28

P-25 Gene Expression Profiles and Protein-Protein Interaction Network Analysis in AIDS

patients with HIV-Associated Encephalitis and Dementia

S. Shityakov, T. Dandekar and C. Förster

29

P-26 Conformational Free Energy in a Chromatographic Stationary Phase by

Nonequilibrium Pulling within Gibbs-Ensemble Monte Carlo Simulation

P. Siders

30

P-27 In silico Protein Structure Prediction and Molecular Docking Study of

Sarco/Endoplasmic Reticulum Calcium-ATPase in Toxoplasma gondii

M. Y. Chong, I. K. S. Yap and W. K. Yam

31

Author Index 32

1

Sponsors of VCCC-2015

University of Mauritius

Mauritius Tourism Promotion Authority

2

Members of the Organising Committee of VCCC-2015

Patrons (University of Mauritius)

Prof Roomeela Mohee, Vice-Chancellor

Prof Anwar Hussein Subratty, Pro-Vice-Chancellor (Academia)

Assoc Prof Thanika Devi Juwaheer, Pro-Vice-Chancellor (Planning and Resources)

Mrs Sharda Rekhadevi Issur-Goorah, Registrar

Prof Muddun Bhuruth, Dean of the Faculty of Science

Assoc Prof Archana Bhaw-Luximon, Head of the Department of Chemistry

Members (Computational Chemistry Group)

Prof Ponnadurai Ramasami (Chairman)

Dr Lydia Rhyman

Miss Hanusha Bhakhoa

Mr Jalal Zumar Ahmud Laloo

3

Members of the International Advisory Committee of VCCC-2015

Dr H. H. Abdallah Iraq

Prof E. F. Archibong Namibia

Dr P. Blowers USA

Prof T. Brinck Sweden

Prof I. Cernusak Slovakia

Prof M. Coote Australia

Dr H. Cox UK

Prof J. M. Dyke UK

Prof T. Ford South Africa

Prof G. Frenking Germany

Prof R. Hoffmann USA

Prof R. Kakkar India

Dr J. S. Murray USA

Prof H. F. Schaefer III USA

Prof A. Simas Brazil

Prof Z. Shuai China

Prof A. J. Thakkar Canada

Prof J. Z. H. Zhang USA

Prof M. A. Zottola USA

4

Message from the Chairman of the Organising Committee

On behalf of the Organising Committee, I have the pleasure to welcome you all

for the Virtual Conference on Computational Chemistry (VCCC-2015).

This is the third virtual conference which the computational chemistry group of

the University of Mauritius will be organising. As we celebrate the

International Year of light, IYL 2015, the dessimination of findings to peers is

an important component of research. In the past, researchers had to travel to

be on the same platform for a meeting. However, it is now possible to have a

virtual meeting, e-presentations and live interations.

VCCC-2015 will involve selected 27 presentations and for one month, 1st-31

st August 2015,

participants will be on the same virtual platform to discuss and brainstorm about their research work.

It is interesting to note the participation of young scientists in this virtual conference and the use of

video presentation. On 12th

August 2015, we will celebrate “Schrödinger Day” to mark the birthday of

Erwin Rudolf Josef Alexander Schrödinger, the father of quatum mechanics.

I hope that all participants of the VCCC-2015 will gather innovative ideas to promote their research.

Invited full papers of VCCC-2015 will be peer reviewed and the accepted papers will be published in a

special issue of the Journal of Computational Science.

To conclude, I would like to thank the University of Mauritius for providing all the facilities for the

holding of VCCC-2015. In particular, a special thanks goes to MrsRageenee Venethethan for setting

up the website and virtual platform of the conference.

I would like to thank all the participants who will be involved in the virtual platform of VCCC-2015.

I would like also to thank all the sponsors, the International Advisory Members, the Organising

Committee members (Dr Lydia Rhyman, Miss Hanusha Bhakhoa and Mr Jalal Zumar Ahmud Laloo)

for their invaluable help in organising this virtual conference.

I wish you all a successful and informative e-meeting.

Ponnadurai Ramasami

Chairman of VCCC-2015

Presentations

5

P-1

Theoretical Prediction of the Stepwise Protonation Constants of

1,4,7,12-Tetraazadodecane

A. S. Adeyinka* and I. Cukrowski

Department of Chemistry, University of Pretoria, South Africa

*Author for correspondence e-mail: [email protected]

Proton transfer is one of the most important processes in chemical and biochemical systems [1-2].

Consequently, the ability of a molecule to accept or donate a proton is crucial and fundamental to our

understanding of the pathways/mechanisms for several important reactions in living systems e.g. those

involving polyamines [2]. In spite of the availability of reliable experimental data (such as protonation

constants, enthalpies of reactions, etc., compiled by Martell and Smith [3]), the evaluation of

theoretical/computational data is of fundamental importance to chemists due to several reasons [4].

Therefore, in this work, we embarked on theoretical prediction of protonation constants for 1,4,7,12-

tetraazadodecane (2-2-4-tet). A new protocol recently developed by us, which also incorporates an

isodesmic reaction methodology, was used. This protocol successfully predicted protonation constants

of the well-known Trien (2-2-2-tet) within a fraction of a log unit; thus giving us confidence to apply it

as a predictive tool. To this effect, (i) protonation constants, as well as (ii) NMR shifts one should

record from a real NMR pH-titration experiment conducted to determine protonation constants will be

reported. Although synthetic aliphatic polyamines have been identified as new drug templates in

medicinal chemistry [5], 2-2-4-tet has not been synthesized (it is not available from any recognized

catalog). This might be due to the challenges of synthesizing unsymmetrical aliphatic polyamines [6].

Hence, this work is significant in that it provides information which can be used to assess the viability

of computational modelling techniques in predicting species distribution and assessing the potential use

or (bio)activity of a compound prior to embarking on a challenging synthetic procedure.

References

1. R. Casasnovas, J. Ortega-Castro, J. Frau, J. Donoso and F. Munoz, International Journal of

Quantum Chemistry, 114, 2014, 1350-1363.

2. J. Ho, Australian Journal of Chemistry, 67, 2014, 1441-1460.

3. R. M. Smith and A. E. Martell, NIST Standard Reference Database 46, NIST Critically Selected

Stability Constants of Metal Complexes Database, Version 8.0

4. K. K. Govender and I. Cukrowski, Journal of Physical Chemistry A, 114, 2010, 1868-1878.

5. C. Melchiorre, M. L. Bolognesi, A. Minarini, M. Rosini and V. Tumiatti, Journal of Medicinal

Chemistry, 53, 2010, 5906-5914.

6. T. Pirali, G. Callipari, E. Ercolano, A. A. Genazzani, G. B. Giovenzana and G. C. Tron, Organic

Letters, 10, 2008, 4199-4202.

6

P-2

Excitation Energy Transference in the FMO Complex: Looking for the Best Model

for Photosynthesis

M. E. Sandoval-Salinas and J. Barroso-Flores*

Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Universidad Nacional

Autónoma de México, México


The Fenna-Mathews-Olson (FMO) complex is part of the Photosystem II of green sulfur bacteria,

responsible for the energy transference from the light-harvesting complex to the reaction center. FMO

is a trimeric protein, holding seven bacteriochlorophyll-a molecules (BChl-a) in each monomer, which

act like a grid for the energy transfer process [1].

Herein, we present a comparison of three quantum mechanical, TD-DFT (SVWN/6-311++G**) based

models in order to describe the possible mechanisms of energy transfer in the FMO throughout the

available excited states:

a) Förster theory for singlet exciton migration [2].

𝑘𝐸𝑇 =2𝜋

ℎ|𝑉𝑚𝑛|

2𝑂𝐼

b) Modified Marcus’ theory for singlet exciton migration [3].

𝑘𝐸𝑇 =𝑉𝑚𝑛2

ℎ√

𝜋

𝜆𝑘𝐵𝑇𝑒𝑥𝑝 (−

𝜆

4𝑘𝐵𝑇)

c) Singlet fission for triplet exciton migration [4].

References

1. J. M. Olson, Photosynthesis Research, 80, 2004, 181-187.

2. T. Forster, Journal of Biomedical Optics, 17, 2012, 011002.

3. V. Stehr, R. F. Fink, B. Engels, P. Jens and C. Deibel, Journal of Chemical Theory and

Computation, 10, 2014, 1242-1255.

4. M. B. Smith and J. Michl, Chemical Reviews, 110, 2010, 6891-6936.

Figure 2: Scheme for the singlet fission.

Figure 1: Scheme for singlet migration.

7

P-3

Application of Quantum Chemistry to Evaluate Radiative Forcing for an Emerging

Class of Atmospheric Pollutants

P. Blowers*, S. Golawski, B. Diallo, M. Flammia, B. Safavinia, M. Gonzalez and

R. Petronella

Department of Chemical and Environmental Engineering, The University of Arizona, USA


Accurate values of global warming potentials (GWPs) can be predicted with the combination of

computational chemistry and thermodynamic or kinetic information about degradation pathways. There

is a useful tool for being able to theoretically predict radiative forcing values for computing GWPs of

new and emerging molecules that could represent an environmental threat. Data recently published

about the molecule perfluorotributylamine concluded that the GWP is lower than what we would

expect. This study predicts the radiative forcing, and then GWP, using computational chemistry

techniques. Based on trends of increased fluorination and carbon chain length, we predict that the GWP

will be significantly higher than that currently reported in the literature.

8

P-4

Maximum Likelihood Estimation in Determination of Power of the Error in

Bivariate Linear Models involving Generalized Gauss-Laplace Distributed

Variables

L. Jäntschi1 and S. D. Bolboacă

2*

1Department of Physics and Chemistry, Technical University of Cluj-Napoca, Romania

2Department of Medical Informatics and Biostatistics, Iuliu Haţieganu University of Medicine and

Pharmacy, Romania


Normal distribution of errors is one assumption for linear regression analysis [1]. Due to its relative

easy interpretation [2], linear regression analysis is used in structure-activity/property analyses to

quantitatively relate chemical features to biological activity or property [3]. A new approach that

maximizes the probability of observing the event according with the random error has been recently

introduced to solve simple linear regression [4]. The reported results obtained on ten classes of

compounds proved that in 93% of cases the power of the error was significantly different by the

expected value of two [4]. An implementation for linear regression analysis with two independent

variables is proposed in this research. The input values are the results obtained by classical regression

analysis, named coefficients of the independent variables, population mean and population standard

deviation obtained for the power of the error equal with two. The outputs are the optimal solution for

above-coefficients identified by the implemented algorithm to maximize the likelihood of observation

according to the random error. The proposed algorithm was tested on two sets of compounds, one with

estrogen binding affinity (logRBA, n = 132) [5], and the other one with toxicity on Tetrahymena

pyriformis (log1/IGC50, n = 250) [6]. The optimization results are presented in the Table 1.

Table 1

Set MLR MLE

q σ μ a1 a2 q σ μ a1 a2

1 2 1.3938 -4.2841 -2.6302·10-2

3.6793·10-2

1.6604 1.3799 -4.5305 -2.3326·10-2

3.7609·10-2

2 2 0.5490 -0.4790 0.4950 -2.4180·10-1

0.9684 0.5554 -0.7980 0.5797 -0.3251 q = power of the error; σ = population standard deviation; μ = population mean (intercept); a1,2 = coefficients of independent variables

On both sets of compounds, the power of the error proved significantly different by the expected value

of two (p < 0.001). The proposed approach proved feasible for estimating the parameters of the

bivariate linear regression under the assumption that the errors are Gauss-Laplace general distributed.

References

1. S. D. Bolboacă and L. Jäntschi, Biomath, 2, 2013, Article ID 1309089.

2. P. Liu and W. Long, International Journal of Molecular Sciences, 10, 2009, 1978-1998.

3. M. Goodarzi, B. Dejaegher, and Y. V. Heyden, Journal of AOAC International, 95, 2012, 636-651.

4. L. Jäntschi, L. L. Pruteanu, A. C. Cozma and S. D. Bolboacă, Computational and Mathematical

Methods in Medicine, 2015, 2015, Article ID 360752.

5. J. Li and P. Gramatica, Molecular Diversity, 14, 2010, 687-696.

6. M. T. D. Cronin, A. O. Aptula, J. C. Duffy, T. I. Netzeva, P. H. Rowe, I. V. Valkova and T. W.

Schultz, Chemosphere, 49, 2002, 1201-1221.

9

P-5

The Reactivity of Unsymmetrical Pincer Ligands and the Nature of the Bonding in

Unsymmetrical Pincer Palladacycles

S. Boonseng, G. W. Roffe, J. Spencer and H. Cox*

Department of Chemistry, School of Life Sciences, University of Sussex, Brighton, BN1 9QJ, UK


Pincer palladacycles have a great number of applications, particularly as catalysts (or precatalysts) in

organic synthesis such as the Heck reaction or the Suzuki coupling reaction. These complexes consist

of a Pd centre with a tridentate ligand. In general, the complex is stabilised by the metal-carbon bond,

avoiding decomposition of the complex, while the donor atoms can influence the reactivity, stability

and performance as a catalyst. The role of the donor atoms in three unsymmetrical pincer ligands,

referred to as YCY'-pincer ligands, where Y or Y' = N, S, or P, i.e., 2-(Me2NCH2)-6-(MeSCH2)C6H4

(NCS), 2-(MeSCH2)-6-(Me2PCH2)C6H4 (SCP) and 2-(Me2NCH2)-6-(Me2PCH2)C6H4 (NCP), is

determined. The thermodynamic and kinetic stabilities are investigated in terms of a simple formation

reaction of the unsymmetrical pincer palladacycle (PdYCY'), and compared with the symmetrical

pincer palladacycle analog (PdYCY) [1]. The atoms in molecules (AIM) theory [1] is used to determine

the nature of the bond interactions between the donor atoms of the ligand and Pd. All calculations were

performed using DFT at the B97XD/6-311++G(2df,2p)[SDD]//PBE/6-31+G(d,p)[SDD] level of

theory, where [SDD] is the ECP used for the metal. For the AIM analysis, it is necessary to use the

DGDZVP all-electron basis set for Pd in order that the bond paths can be accurately traced. It is found

that the Gibbs free energy of the reaction: Pincer ligand + PdCl2 pincer palladacycle + HCl, is

negative indicating that the formation is spontaneous. Along the reaction pathway, the barrier for C-H

activation is the rate-determining step in all cases. This energetic data is supported by the charge

density analysis at the bond critical points. The Laplacian of the charge density (∇2ρ(r)) and the total

electron density (H(r)) indicate that in all cases the bonding has partial covalent character, i.e., ∇2ρ(r) >

0 and H(r) < 0. It is found that the Pd-Y bond strengths in the unsymmetrical pincer palladacycles are

effected by a trans influence which results in a strengthening of the strongest bond (Pd-P) and a

weakening of the weakest bond (Pd-N) when compared with PdNCN, PdSCS and PdPCP, the

symmetric pincer palladacycle analogs [2].

References

1. R. F. W. Bader, Atoms in Molecules: A Quantum Theory, Oxford University Press, 1st Edition,

1990.

2. S. Boonseng, G. Roffe, J. Spencer and H. Cox, Dalton Transactions, 44, 2015, 7570-7577.

10

P-6

A Computational Survey on Optoelectronic Properties of Indazolone Derivatives

P. Ranjan1

, S. Venigalla2

, S. Dhail

2, S. Roy

3, A. Kumar

1, L. Ledwani

2 and

T. Chakraborty2*

1Department of Mechatronics Engineering, Manipal University Jaipur, Dehmi-Kalan, Jaipur-303007,

India 2Department of Chemistry, Manipal University Jaipur, Dehmi-Kalan, Jaipur-303007, India

3Department of Chemistry, Raja Ranjit Kishore Government Polytechnic College (under DTET-WB),

West Midnapore, West Bengal, India

*Author for correspondence e-mails: [email protected],

[email protected]

Due to many fold applications in the field of lighting and display, study about optoelectronic property

of organic light-emitting device (OLED) is an active field of research. Though several reports are

available on synthetic processes of OLEDs, theoretical analysis of optoelectronic property of OLEDs is

very limited. Recently, Roy et al. has synthesized some indazolone derivatives which have

optoelectronic property and can be useful as OLEDs. In this study, we have made a theoretical analysis

of those indazolones using density functional theory (DFT). The qualitative correlation made in this

report, between experimental quantum yields of indazolones and computed conceptual DFT based

global descriptors, is very much distinct. Our computed data also predicts that some of the instant

compounds will be potential candidates for electroluminescence devices as they have better charge

transfer abilities and more balanced charge transfer rates. Finally, a modelling has been performed to

make a quantitative correlation in terms of multi-linear regression analysis. The high regression

coefficient explores the possibility of synthesis of new materials of congeneric series.

11

P-7

Ensemble-Based Virtual Screening: Hit Compounds against Mycobacterium

tuberculosis Isocitrate Lyase

Y. S. Choong1*, Y.-V. Lee

1 and H. A. Wahab

2

1Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Malaysia

2School of Pharmaceutical Sciences, Universiti Sains Malaysia, Malaysia


The continuing rise in the tuberculosis incidence and drug resistance strains has driven the urgent need

for new therapy [1]. Isocitrate lyase (ICL) is one of the enzymes involved in the dormant phase of

Mycobacterium tuberculosis [2]. ICL could be the possible new drug target, as studies showed that the

inhibition of ICL can eliminate M. tuberculosis in murine model [3]. In this work, the search of the

possible lead compounds for ICL was performed via virtual screening on NADI database, which

consists of more than 4000 natural compounds from Malaysia plants. Virtual screening approach offers

a time and cost effective alternative for lead discovery. Prior to virtual screening, molecular dynamics

simulation was performed to obtain the ensemble conformations of ICL. A total of 5 conformations

were obtained from 20 ns of molecular dynamics simulation. Results showed that 50% from the top

ranking compounds possess structural similarity consisting of linear aromatic backbone. These

hydrophobic compounds are favourable within the hydrophobic binding pocket of ICL. The linear

aromatic back bone could be one of the key entities for ICL inhibitor for the future formulation of new

tuberculosis therapy.

References

1. http://www.who.int/mediacentre/factsheets/fs104/en/ (Accessed May 2015)

2. J. C. Betts, P. T. Lukey, L. C. Robb, R. A. McAdam and K. Duncan, Molecular Microbiology, 43,

2002, 717-731.

3. E. J. Munoz-Elias and J. D. McKinney, Nature Medicine, 11, 2005, 638-644.

12

P-8

DFT Studies of the MTSL Nitroxide Side Chain in the Aurora Kinase Activation

Loop

M. G. Concilio1*, A. J. Fielding

1, R. Bayliss

2 and S. Burgess

2

1Photon Science Institute, University of Manchester, Oxford Road, Manchester, M13 9PY, UK 2Department of Biochemistry, Henry Wellcome Building, University of Leicester, Leicester,

LE1 9HN, UK


A quantum-mechanical (QM) method rooted on density functional theory (DFT) linked to the

stochastic Liouville equation (SLE) in the Fokker Planck (FP) form has been employed to sample the

conformational space and to calculate the electron paramagnetic resonance (EPR) spectrum of the

methane-thiosulfonate spin label (MTSL) attached to the Aurora-A kinase activation loop [1-2]. The

features of the calculated energy surface allowed us to describe the system in a limited number of

rotamers stabilised by interactions of the MTSL side chain and neighbouring residues. The relevant

magnetic parameters and the EPR spectrum were subsequently calculated from the trajectories of the

spin probe in the protein environment. The comparison between theoretical and experimental

continuous wave (CW) EPR spectra revealed some small differences in the EPR line shape which

arises from the combinations of g- and A-values obtained from the conformations selected (Figure 1).

This theoretical approach can be used to recognise the contribution of MTSL rotamers to the EPR

spectrum in order to help extract structural/dynamics properties of protein from the experimental data.

Figure 1: Two examples of DFT structures and respective simulated EPR spectra (red lines). The

experimental EPR spectrum is represented by the black lines.

References

1. D. T. Warshaviak, L. Serbulea, K. N. Houk and W. L. Hubbell, The Journal of Physical Chemistry

B, 115, 2011, 397-405.

2. A. Polimeno and H. J. Freed, The Journal of Physical Chemistry, 99, 1995, 10995-11006.

http://www.ncbi.nlm.nih.gov/pubmed?term=Warshaviak%20DT%5BAuthor%5D&cauthor=true&cauthor_uid=21162593

http://www.ncbi.nlm.nih.gov/pubmed?term=Serbulea%20L%5BAuthor%5D&cauthor=true&cauthor_uid=21162593

http://www.ncbi.nlm.nih.gov/pubmed?term=Houk%20KN%5BAuthor%5D&cauthor=true&cauthor_uid=21162593

http://www.ncbi.nlm.nih.gov/pubmed?term=Houk%20KN%5BAuthor%5D&cauthor=true&cauthor_uid=21162593

http://www.ncbi.nlm.nih.gov/pubmed/21162593

http://www.ncbi.nlm.nih.gov/pubmed/21162593

13

P-9

External and Intramolecular Influences on Spiropyran – Merocyanine

Interconversion

C. D. Simpson1, N. L. Haworth

1, S. Ciampi

2 and M. L. Coote

1*

1ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian

National University, ACT 2601, Australia 2ARC Centre of Excellence for Electromaterials Science, Intelligent Polymer Research Institute,

University of Wollongong, Wollongong, NSW 2500, Australia


Spiropyrans (SP) are a class of photochromic dye that can undergo reversible ring opening to the

merocyanine (MC) form in response to a broad range of physical and chemical stimuli (Figure 1). Here,

we use theory to investigate the effects that both external and intramolecular factors have on the

kinetics and thermodynamics of this process, so as to aid the design of sensors for properties such as

the hydrogen bonding ability of the solvent [1]. Intramolecular factors have been investigated by

studying various derivatives of spiropyran with electron withdrawing or electron donating substituents

added to the indoline and/or the benzopyran groups. Additionally, we have investigated the impact on

the reaction profile when the R2 group is able to hydrogen bond to the ketone oxygen of the MC forms.

External influences studied include solvent effects and the presence of an external electric field.

Solvent effects have been investigated using continuum solvent models to explore the dielectric effects

of various solvents on the MC ↔ SP interconversion. In addition, just as the R2 group can hydrogen

bond to the MC ketone group, so too can solvents that act as hydrogen bond donors. This effect has

been studied using explicit solvent molecules. Electric field effects on the surface have been probed as

it has been observed experimentally that the SP form is not found at the surface of an electrode. Here,

we investigate the proposal that the electric field effects experienced by the molecule as it passes

through the electrical double layer shift the equilibrium towards an MC form.

Figure 1: SP/MC interconversion. There are three different isomers of the ring-opened merocyanine

(MC1, MC2 and MC3) that can interconvert via two different transition states (TSA and TSB). MC1

and MC3 can also undergo ring closure to form SP via TSD and TSC, respectively [1].

Reference

1. S. Ciampi, P. K. Eggers, N. L. Haworth, N. Darwish, P. Wagner, M. L. Coote, G. G. Wallace and

C. L. Raston, Chemical Communications, 51, 2015, 4815-4818.

14

P-10

GIAO Calculations of Chemical Shifts in 1,4-Diaryl-2-mercaptoimidazoles

Derivatives

G. K. Gupta1*, P. Saini

2 and V. Kumar

3

1Department of Pharmaceutical Chemistry, M. M. College of Pharmacy, M. M. University, Mullana,

Ambala, Haryana, India 2Department of Chemistry, BITS Pilani, KK Birla Goa Campus, Goa, India

3Department of Chemistry, M. M. University, Mullana, Ambala, Haryana, India


After the geometry optimization at B3LYP/6-31+G(d,p) and B3LYP/6-311G levels, the calculations of

the NMR chemical shifts of a series of 1,4-diaryl-2-mercaptoimidazole derivatives were carried out by

means of Gauge Including Atomic Orbitals (GIAO) method at B3LYP/6-31+G(d,p) and B3LYP/6-

311G levels, respectively. The 13

C NMR chemical shifts calculated at both levels are in agreement with

the observed values. By virtue of a series of linear correction equations (δpred. = a + b δcalcd) of the 13

C

chemical shifts, accurate prediction of 13

C chemical shifts was achieved for the new 1,4-diaryl-2-

mercaptoimidazole compounds. For the 13

C NMR chemical shifts calculated at B3LYP/6-31+G(d,p)

level, the linear correlation of δpred. with δexptl. is excellent, and the square of the correlation coefficient,

r2, is more than 0.8.

15

P-11

Full Factorial Analysis on One-Cage Pentagonal Faced Nanostructures

S. D. Bolboacă1 and L. Jäntschi

2*

1Department of Medical Informatics and Biostatistics, Iuliu Haţieganu University of Medicine and

Pharmacy, Romania

2Department of Physics and Chemistry, Technical University of Cluj-Napoca, Romania


Dodecahedrane is a chemical compound with high symmetry, which has in each vertex a carbon atom

that bonds three neighboring carbon atoms and one hydrogen atom [1]. In fact, dodecahedrane is only

one representative of a series of congeners, which allow conducting a stability study in the series.

The elementary unit of one-cage pentagonal face structure was used to construct the whole class of

compounds using three atoms from the same period which allow formation of at

least three bonds: boron, carbon, and nitrogen. The elementary structure was split

in four layers and on each layer one atom could take places (either C = carbon, N

= nitrogen, B = boron).

A total number of 81 structures (34) could be constructed based on four layers

(L1-L4) and three levels (C, N, B) but due to symmetry, just 45 of them are

distinct.

The distinct structures of this family of cages were taken into study. Full factorial

analysis (including all 45 congeners) was applied on distinct one-cage structures

to characterize the family. In the first step of the analysis, the geometry of structures was optimized

with Spartan software (v.10) using Møller Plesset method (MP2 level of theory) with 6-31G*

(polarized valence split) basis set. In the second step of the analysis, the values of the following

properties were calculated with Spartan software: volume, surface area, ovality, HOMO energy,

LUMO energy, polarizability, dipole moment, entropy, enthalpy, and energy (at zero point). In the third

step, full factorial analysis was conducted for three distinct cases, with C, N, or B as reference and

other two atoms as factors [2]. A program was implemented for full factorial analysis and its

applicability is presented. The first model in the full factorial analysis takes all factors and all possible

interactions between factors that lead to a model with a determination coefficient of one (always true in

the full factorial analysis). A stepwise backward method is implemented to withdraw from the model

the less influential factors or interactions and to calculate the models characteristics. Good models with

goodness-of-fit higher than 0.95 were obtained on the investigated structures with factors that ranged

from two (enthalpy with C and N, respectively as reference) to twenty-seven (HOMO energy with C as

reference). The highest correlation coefficient was obtained for energy as property of interest in models

with four factors and any of the investigated atoms as reference (r = 0.9999). The highest correlation

coefficient was obtained when carbon atom was the reference in 67% of cases.

References

1. R. J. Ternansky, D. W. Balogh and L. A. Paquette, Journal of the American Chemical Society, 104,

1982, 4503-4504;

2. L. Jäntschi, General Chemistry Course, AcademicDirect, 2013.

Available at: http://ph.academicdirect.org/General_Chemistry_Course_v5.pdf

16

P-12

Coinage Metals Binding as Main Group Elements: Structure and Bonding of the

Carbene Complexes [TM(cAAC)2] and [TM(cAAC)2]+ (TM = Cu, Ag, Au)

P. Jerabek* and G. Frenking

Philipps-Universität Marburg, FB Chemie, Marburg, Germany


Quantum chemical calculations using density functional theory have been carried out for the cyclic

(alkyl)(amino)carbene (cAAC) complexes of the Group 11 atoms [TM(cAAC)2] (TM = Cu, Ag, Au)

and their cations [TM(cAAC)2]+. The nature of the metal−ligand bonding was investigated with the

charge and energy decomposition analysis EDA-NOCV.

The calculations show that the TM−C bonds in the charged adducts

[TM(cAAC)2]+ are significantly longer than in the neutral complexes

[TM(cAAC)2], but the cations have much higher bond dissociation

energies than the neutral molecules. The intrinsic interaction energies

Eint in [TM(cAAC)2]+ take place between TM

+ in the

1S electronic

ground state and (cAAC)2.

In contrast, the metal−ligand interactions in [TM(cAAC)2] involve the

TM atoms in the excited 1P state yielding strong TM p() → (cAAC)2

-backdonation, which is absent in the cations. The calculations suggest that the cAAC ligands in

[TM(cAAC)2] are stronger -acceptors than -donors. The trends of the intrinsic interaction energies

and the bond dissociation energies of the metal−ligand bonds in [TM(cAAC)2] and [TM(cAAC)2]+ give

the order Au > Cu > Ag.

Calculations at the nonrelativistic level give weaker TM−C bonds, particularly for the gold complexes.

The trend for the bond strength in the neutral and charged adducts without relativistic effects becomes

Cu > Ag > Au. The EDA-NOCV calculations suggest that the weaker bonds at the nonrelativistic level

are mainly due to stronger Pauli repulsion and weaker orbital interactions. The NBO picture of the

C−TM−C bonding situation does not correctly represent the nature of the metal−ligand interactions in

[TM(cAAC)2].

References

1. P. Jerabek, H. W. Roesky, G. Bertrand and G. Frenking, Journal of the American Chemical Society,

136, 2014, 17123-17135.

2. D. S. Weinberger, N. A. SK, K. C. Mondal, M. Melaimi, G. Bertrand, A. C. Stückl, H. W. Roesky,

B. Dittrich, S. Demeshko, B. Schwederski, W. Kaim, P. Jerabek and G. Frenking, Journal of the

American Chemical Society, 136, 2014, 6235-6238.

3. D. S. Weinberger, M. Melaimi, C. E. Moore, A. L. Rheingold, G. Frenking, P. Jerabek and

G. Bertrand, Angewandte Chemie International Edition, 52, 2013, 8964-8967.

17

P-13

Self-Interaction Corrected Density Functional Calculations of Molecules and Solids

H. Jónsson1,2,3

*

1Faculty of Physical Sciences, University of Iceland, Reykjavík, Iceland

2Department of Applied Physics, Aalto University, Espoo, Finland

3Department of Chemistry, Brown University, Providence, RI, USA


The Perdew-Zunger self-interaction correction (PZ-SIC) [1] to Kohn-Sham density functionals can

improve the accuracy of the calculated results in many respects. The long range effective potential for

the electrons then gains the correct -1/r dependence so that Rydberg excited states of molecules and

clusters of molecules can be calculated [2,3]. Also, localized electronic states are shifted down in

energy to a larger extent than delocalized states so that the balance between localization and

delocalization becomes more accurate. As a result, localized defect states in semi-conductors and

insulators located within the band gap can be characterized [4,5]. The calculations are, however, more

challenging since the energy functional is no longer unitary invariant and each step in the self-

consistency procedure needs to include an inner loop where unitary optimization is carried out [6,7]. In

addition to improved accuracy, the PZ-SIC calculations also produce a unique set of optimal orbitals

which are generally localized and correspond well to chemical intuition (such as sp2

and sp3 orbitals). It

has become evident that the optimal orbitals need to be complex valued functions [8]. If they are

restricted to real valued functions, the energy of atoms and molecules is less accurate and the calculated

structure of molecules can even be incorrect [9]. The energy functionals obtained by applying PZ-SIC

to gradient dependent Kohn-Sham functionals are examples of an extended functional form where the

orbital densities play a key role, not just the total electron density. We argue that such orbital density

functional theory (ODFT) is the next logical step beyond Kohn-Sham DFT and the results of our recent

variational, self-consistent PZ-SIC calculations with complex optimal orbitals indicate that meaningful

orbital energies and orbital densities can be obtained, as well as much improved total energy of ground

and excited states. The development of an optimal ODFT functional remains to be carried out,

however, but a small, initial step has been taken in that direction [10].

References 1. J. P. Perdew and A. Zunger, Physical Review B, 23, 1981, 5048-5079.

2. H. Gudmundsdóttir, Y. Zhang, P. M. Weber and H. Jónsson, The Journal of Chemical Physics, 141, 2014,

234308.

3. H. Gudmundsdóttir, Y. Zhang, P. M. Weber and H. Jónsson, The Journal of Chemical Physics, 139, 2013,

194102.

4. H. Jónsson, Proceedings of the National Academy of Sciences, 108, 2011, 944-949.

5. Á. Valdés, J. Brillet, M. Grätzel, H. Gudmundsdóttir, H. A. Hansen, H. Jónsson, P. Klüpfel, G.-J. Kroes,

F. Le Formal, I. C. Man, R. S. Martins, J. K. Nørskov, J. Rossmeisl, K. Sivula, A. Vojvodic and M. Zäch,

Physical Chemistry Chemical Physics, 14, 2012, 49-70.

6. S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation, 10, 2014, 5324-5337. 7. S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation, 9, 2013, 5365-5372.

8. S. Klupfel, P. J. Klupfel and H. Jónsson, Physical Review A, 84, 2011, 050501.

9. S. Klupfel, P. J. Klupfel and H. Jónsson, The Journal of Chemical Physics, 137, 2012, 124102.

10. E. Ö. Jónsson, S. Lehtola and H. Jónsson, Procedia Computer Science (In Press).

18

P-14

Constitutional Isomers in Drug Discovery: A Case Study Featuring G-Protein

Coupled Receptor Ligands

P. S. Kharkar*, N. U. Sahu and S. Warrier

Department of Pharmaceutical Chemistry, SPP School of Pharmacy and Technology Management,

SVKM’s NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai 400 056. India


Constitutional isomers are molecules with same molecular formula (MF) but different molecular

connectivity. Unlike stereoisomers, constitutional isomers are relatively unexplored with reference to

novel chemical space. We accidently stumbled upon this concept – ‘replace a substructure in a lead

molecule with its constitutional isomer to generate structural and/or chemical novelty. Several

brainstorming sessions finally convinced us to really dig it deep.

In the present study, we have worked on a case study involving GPCR ligands for the very reason that

GPCRs are the molecular targets for > 30% of the currently marketed drugs. In the systematic

exploration, a thorough understanding of the structural features of the GPCR ligands and the molecular

interactions with their receptors was developed, followed by the application of the constitutional isomer

concept. Various aspects such as observed molecular interactions, novelty, synthetic feasibility and

related issues are discussed at length. In our opinion, the presented study is likely to spark young and

bright minds in the computational arena to take this concept to the next level where it is accepted and

used by the scientific community in a broader perspective.

.

19

P-15

Catalytic Strategy of Adenosine Triphosphate Hydrolysis in Myosin Motor

F. A. Kiani1,2

*

1Research Center for Modeling and Simulation (RCMS), National University of Sciences and

Technology (NUST), Sector H-12, Islamabad, Pakistan

2Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld-368, D-69120,

Universität Heidelberg, Germany

*Authors for correspondence e-mail: [email protected]

Myosin is a molecular motor responsible for muscle contraction. During the Lymn-Taylor muscle

contraction cycle [1], myosin utilizes the chemical energy obtained from the hydrolysis of adenosine

triphosphate (ATP) to perform mechanical work. Using combined quantum mechanical/molecular

mechanical (QM/MM) calculations, we have determined the mechanism of ATP hydrolysis in myosin

[2]. Hydrolysis occurs via a sequential mechanism [3] in which Pγ-O bond scission of ATP results in a

stable intermediate, consisting of adenosine diphosphate (ADP3-

) and metaphosphate (PγO3-) [4]. This

Pγ-O bond scission transfers one negative charge from the γ-phosphate to ADP (ADP2-

–PγO32-

→

ADP3-

+ PγO3-). To deal with this additional charge of ADP

3-, point charges of the classical atoms

surrounding the ATP moiety in myosin need to be upscaled [4]. After the nucleophilic attack of the

lytic water molecule on PγO3-, proton is transferred from the lytic water molecule to γ-phosphate via

one of many possible proton wires. Similar catalytic mechanism has been proposed in other enzymes

such as kinesin [5], F1-ATPase [6] and EcorV [7].

Figure 1: A snapshot of the binding site of myosin.

References

1. R. W. Lymn and E. W. Taylor, Biochemistry, 10, 1971, 4617-4624.

2. F. A. Kiani and S. Fischer, Proceedings of the National Academy of Sciences, 111, 2014, E2947-

E2956.

3. F. A. Kiani and S. Fischer, Current Opinion in Structural Biology, 31, 2015, 115-123.

4. F. A. Kiani and S. Fischer, Journal of Biological Chemistry, 288, 2013, 35569-35580.

5. M. J. McGrath, I.-F. Kuo, S. Hayashi and S. Takada, Journal of the American Chemical Society, 135,

2013, 8908-8919.

6. S. Hayashi, H. Ueno, A. R. Shaikh, M. Umemura, M. Kamiya, Y. Ito, M. Ikeguchi, Y. Komoriya, R.

Iino and H. Noji, Journal of the American Chemical Society, 134, 2012, 8447-8457.

7. F. A. Kiani and S. Fischer, Molecular Catalysts: Structure and Functional Design. With a Foreword by

Nobel Laureate Roald Hofmann, Wiley-VCH Verlag GmbH & Co. KGaA, 359-376.

20

P-16

Polarizable Embedding - From Solvents to Heterogeneous Environments

J. Kongsted*

Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark


In this talk, I will introduce and review the polarizable embedding (PE) method [1,2]. This

computational model has recently been developed with the aim of enabling calculations of general

molecular response properties for large and complex systems. The PE model is a focused

computational approach building on the concepts from mixed quantum mechanics/molecular

mechanics (QM/MM) schemes. It thus represents a focused model in which different parts of a large

molecular system are described using different levels of approximations, i.e. the central part of the

system is described using a given quantum chemical model whereas the environment is described using

classical physics, i.e. in terms of a molecular mechanical force field. A key concept associated with the

PE model is the introduction of quantum mechanical response theory in combination with polarizable

force fields. This allows for calculation and simulation of general molecular properties, i.e. properties

relevant for optical and magnetic spectroscopies. I will discuss some recent applications of the PE

model aimed at elucidating optical and magnetic properties of both solute-solvent and heterogeneous

molecular systems highlighting the general flexibility and accuracy of this computational model.

Figure 1: The photoactive yellow protein. The chromophore has been highlighted.

References

1. J. M. Olsen, K. Aidas and J. Kongsted, Journal of Chemical Theory and Computation, 6, 2010,

3721-3734.

2. T. Schwabe, M. T. P. Beerepoot, J. M. H. Olsen and J. Kongsted, Physical Chemistry Chemical

Physics, 17, 2015, 2582-2588.

21

P-17

Comparative DFT Study of the M-L Binding Energies

(M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn; L = Porphine, P,

and P4-Substituted Porphine, P(P)4)

A. E. Kuznetsov*

Departamento de Química, Universidade Federal de São Carlos, São Carlos - SP - Brasil


We performed comparative DFT study of the binding energies between the first-row transition metals

M (M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu and Zn) and two ligands of the similar type: porphine, P, and

its completely P-substituted counterpart, P(P)42-

, using several density functionals and the split-valence

polarized 6-31G* basis set. We studied both neutral, M2+

-L, and cationic, M3+/4+

-L, species. The main

findings of our research summarize as follows: (i) complete substitution of all the pyrrole nitrogens

with P-atoms generally does not affect the ground spin state of metalloporphyrins; (ii) generally, for the

MP(P)4 compounds, calculated HOMO/LUMO gaps and optical gaps are smaller than for their MP

counterparts; (iii) the trends in the changes of the binding energies between Mn+

and P(P)42-

/N42-

are

very similar for both ligands (see Figure 1 for the M2+

-L binding energies). The complete substitution

of the pyrrole nitrogens by the P-atoms generally decreases the Mn+

-ligand binding energies. All the

MP(P)4 compounds studied are stable according to the calculated binding energy values and therefore

can be potentially synthesized.

Figure 1: Binding energy changes for the M

2+P(P)4

2- (red triangles) and corresponding M

2+P

2- (green

crosses) compounds.

22

P-18

Is it Worth Making? Assessing the Information Content of New Structures

M. D. Mackey*, T. Cheeseright, R. Lawrence, G. Tedesco,

S. Tomasio and

P. Tosco

Cresset, Cambridge, UK


We have recently presented a method of summarizing the information obtained from 3D activity cliff

analysis: Examination of all pairs of molecules can distinguish between apparent cliffs that are outliers,

or due to measurement error, and those which consistently point to particular electrostatic and steric

features having a large impact on activity.

To do this, it has proved essential to allow for alignment noise: No 3D alignment technique is perfect,

so we apply a Bayesian analysis to correct for potential misalignments and for the case where a

molecule is aligned correctly, except for a flexible substituent whose conformation is under-

constrained. We used the recent AZ/CCDC alignment validation data set to determine valid estimates

for the Bayesian priors.

As an extension of this technique, it is possible to mine the data for a simple picture of explored

pharmacophoric space, corrected for the conformational and alignment flexibility of each molecule.

This provides an invaluable picture to the chemist of which parts of property space around a molecule

have been adequately explored. When considering a new molecule for synthesis, it is possible to

compute the amount that this would increase the explored pharmacophoric space and hence present an

‘information content’ score for the new molecule: if we made and tested this new molecule, how much

would it actually increase the SAR information content of the data set?

The combination of this with the activity cliff summary data, allows a simple qualitative evaluation of

the SAR of a data set in 3D, alongside guidance on which parts of pharmacophoric space have been

mined out and which remain underexplored. We present the application of these techniques to several

literature data sets.

23

P-19

Application of Variational - Perturbation Method for Calculating the Electric

Dipole Moment of Molecule HD

E. Maksimova*

Department of Physics, Saint Petersburg State University, Russian Federation


In the present work, the effect of isotopic asymmetry of the homopolar molecules on their electrical

properties is studied. It is known that in homopolar molecules with isotopic species infrared (IR)

transitions are not allowed, but electric dipole moment is observed due to the breakdown of the Born-

Oppenheimer approximation.

The variational-perturbation method allowing to calculate with increased precision the wave function

for hydrogen-deuteride molecule was proposed. The function of the dipole moment of molecules such

as HD, HT, or DT, depending on the isotopic mass difference parameter, is computed. At large

internuclear distances, this function behaves asymptotically as the 4R , where R is the distance between

the nuclei.

24

P-20

Intuitive and Counterintuitive Noncovalent Interactions of Aromatic π Regions and

π-Hole Regions with the Hydrogen and the Nitrogen of HCN

J. S. Murray and P. Politzer

CleveTheoComp, 1951 W. 26th

Street, Suite 409, Cleveland, OH 44113 USA

Department of Chemistry, University of New Orleans, New Orleans, LA 70148 USA


We have investigated intuitive and counterintuitive complex formation between eight aromatic

molecules and HCN. In four of the former, the π regions had negative electrostatic potentials; in the

other four, the π regions had positive potentials (π-hole regions [1]). Each aromatic molecule was

allowed to interact through its π region, whether negative or positive (π-hole), with both the hydrogen

(positive potential) of HCN and the nitrogen (negative potential). In eight cases, therefore, interaction

was intuitively favorable (positive/negative) while in the other eight, the ground state electrostatic

potentials would make an attractive interaction counterintuitive (positive/positive or negative/negative).

The intuitive interactions all led to bound complexes, and five of the counterintuitive did as well [2].

The formation of the five counterintuitive complexes is explained in terms of polarization/dispersion,

which the electrostatic potentials of the molecules prior to interaction cannot show. Very good

correlations were obtained, for the intuitive and also the counterintuitive complexes, between the

computed interaction energies and values predicted solely on the basis of the most positive and the

most negative electrostatic potentials in the π regions and on the HCN [2].

References

1. J. S. Murray, P. Lane, T. Clark, K. E. Riley, P. Politzer, J. Mol. Model. 18, 541-548 (2012).

2. J. S. Murray, Z. P.-I. Shields, P. G. Seybold, P. Politzer, J. Comput. Sci., 2015, DOI:

10.1006/j.jocs.2015.02.001.

25

P-21

Electronic, Optical and Magnetic Properties of Si-Doped Au Nanoalloy Clusters

P. Ranjan1, A. Kumar

1 and T. Chakraborty

2*

1Department of Mechatronics Engineering, Manipal University Jaipur, Rajasthan, India

2Department of Chemistry, Manipal University Jaipur, India

*Author for correspondence e-mails: [email protected],

[email protected]

Due to significant applications in the field of science and engineering, nowadays Si-doped Au

nanoalloy clusters are extensively popular. A deep insight is required to explore the properties of such

compounds. The clusters formed between Au and Si have gained a considerable interest because they

possess unique optical, electronic and magnetic properties, which have applications in the field of

radiotherapy, imaging of cancer cells, biophysics and nanoscience. They have remarkable catalytic

properties. Density Functional Theory (DFT) is one of most successful approaches to study the

electronic properties of matter. Recently, conceptual DFT based descriptors have been invoked to

correlate the experimental properties of nano compounds and composites. In this venture, the

electronic, optical and magnetic properties of AunSi (n = 1-8) nanoalloy clusters are systematically

investigated by DFT in the theoretical frame of the generalized gradient approximation (GGA)

exchange-correlation function. The Au4Si nanoalloy cluster exhibits strongest electronic stability with a

band gap of 3.337 eV. The calculated HOMO-LUMO gap possesses interesting odd-even oscillation

behaviour, indicating that even numbered clusters show higher stability in comparison with odd

numbered clusters. All Raman and vibrational spectra exhibit many significant modes. Ferroelectric

and ferromagnetic behaviours are observed in the Au-Si nanoalloy clusters, indicating their potential

applications in optical devices.

26

P-22

An ELF Quantum Topological Analysis of the Mechanism of the Ketene-Imine

Staudinger Reaction

M. Ríos-Gutiérrez* and L. R. Domingo

Department of Organic Chemistry, University of Valencia, Spain


The analysis of the electron density reorganisation to evidence the bonding changes along a reaction

path is the most attractive method to characterise a reaction mechanism. An appealing procedure that

provides a straightforward connection between the electron density distribution and the chemical

structure is the study of the quantum chemical topology of the electron density based on the electron

localisation function (ELF). In this sense, this methodology has become a powerful tool in the study of

the mechanism of organic reactions.

Herein, an ELF quantum topological analysis of the bonding changes along the ketene-imine

Staudinger reaction between methyl-cyano ketene 1 and N-methyl phenylimine 2 yielding -lactam

trans-3 is performed (Scheme 1), allowing a complete characterisation of the molecular mechanism [1].

This reaction takes place through a two-step mechanism, in which the first step is associated with the

formation of the NC single bond along the nucleophilic attack of the imine nitrogen lone pair on the

central carbon of the ketene, yielding the zwitterionic intermediate ZWn, while the second step is

associated with a ring-closure process achieved by the C-to-C coupling of two pseudoradical centers

generated in the previous phases [2].

C

C

O

CNMe

+N

Me

Ph

C N

Me

Ph

O

C

CN

Me

N

O Me

PhMeNC

TS1n

ZWn trans-3

TS2n

1 2

Scheme 1: Two-step mechanism of the ketene-imine Staudinger reaction.

The present ELF quantum topological analysis makes it possible to reject those studies based on the

frontier molecular orbital (FMO) theory, in which HOMO/LUMO interactions along the nucleophilic

attack of the imines on the ketenes and a feasible torquoelectronic effect along the conrotatory ring-

closure step control the cis/trans stereoselectivity in the formation of lactams.

References

1. L. R. Domingo, M. Ríos-Gutiérrez and J. A. Sáez, RSC Advances, 5, 2015, 37119-37129.

2. L. R. Domingo, RSC Advances, 4, 2014, 32415-32428.

27

P-23

Maximum Power Point Tracking of Photovoltaic Systems using

Extremum Seeking Control

S. Z. Sayed Hassen*

Electrical and Electronic Engineering Department, Faculty of Engineering, University of Mauritius,

Réduit 80837, Mauritius


Growing concerns about rising energy demand and the environmental impacts of fossil fuel have been

driving research and development in alternative sources of energy during the last few decades. We are

at a point in time now where it is clear to energy experts that solar energy, in particular that coming

from photovoltaic (PV) cells, is going to be the most important source of renewable energy up to the

year 2040. Engineering challenges however are very much present in that the energy conversion

efficiency of PV cells is still quite low and the initial cost of investment remains high. While research

using state of the art computational tools are constantly twisting and manipulating the chemical

properties of the PV cells in an effort to improve their ability to absorb sunlight, electrical engineers are

side by side designing sophisticated controllers that can squeeze every little bit of juice from the PV

panels. This presents its own set of challenges as the power obtained from a PV cell/panel is a

nonlinear function of its temperature as well as the level of solar irradiation, see Figure 1.

It is clear from above that for a given set of environmental conditions, PV panels exhibit a desirable

unique operating point, also known as the Maximum Power Point (MPP), where the obtained PV

power is maximum. In addition, the drift phenomena arising over the lifetime of a PV system means

that the MPP varies over a large area. In this work, we initially describe the intermediate conversion

stage between a PV source and an electrical load. We then investigate the capability of a relatively new

control technique applied to the conversion stage, known as extremum seeking control, to maximize the

power obtained from PV cells. The main advantage of the approach proposed is that it seeks an

extremum (in this case maximum) of the plant without requiring a mathematical model of the PV

panel. In other words, it can tolerate uncertainties arising due to variation in solar irradiation level as

well as temperature, and only requires that an extremum exists. The performance of the control

approach is evaluated based on the speed at which it seeks and reaches the extremum as well as its

ability to derive maximum power from the PV panel once it has reached the maxima. Simulation

results are presented to validate the approach on a realistic model built in MATLAB and experimental

results on a practical system is in progress.

Figure 1

28

P-24

Computational Investigation of Spectroscopic Properties of Fluorescent 3-Vinyl

Indoles by DFT and TD-DFT

S. Chemate, S. Lanke and N. Sekar*

Department of Dyestuff Technology, Institute of Chemical Technology, Mumbai- 400 019, India


The geometry and electronic absorption spectral properties of donor-π-acceptor (D-π-A) dyes based on

indole core were evaluated by density functional theory (DFT) and time-dependent density functional

theory (TD-DFT). In this, the donor group (D) is an electron rich unit, linked through a π bridge spacer

to the electron-acceptor group (A). In polar solvent, large red shift in fluorescence emission is observed

which can be attributed to the intramolecular charge transfer (ICT) polar excited state. Experimental

absorption and emission wavelengths are in good agreement with those predicted using the TD-

B3LYP/6-311+G(d) method. These data highlight the effectiveness of DFT and TD-DFT for

simulation D-π-A chromophore and provide insight into the challenges involved in designing novel D-

π-A chromophore. The largest wavelength difference between the experimental and computed

electronic absorption maxima was 50 nm and the smallest wavelength difference between the

experimental and computed electronic absorption maxima was 13 nm. For emission, a large difference

of 65 nm was observed and the smallest wavelength difference was 1 nm. The ground state and excited

state dipole moments in different solvents were determined using experimental solvatochromic data.

The dipole of the dyes with electron withdrawing group (–CN and –NO2) at para position of the

acceptor phenyl ring are higher than other dyes.

29

P-25

Gene Expression Profiles and Protein-Protein Interaction Network Analysis in

AIDS patients with HIV-Associated Encephalitis and Dementia

S. Shityakov1*, T. Dandekar

2 and C. Förster

1

1Department of Anesthesia and Critical Care, University of Würzburg, Würzburg, Germany

2Department of Bioinformatics, University of Würzburg, Würzburg, Germany


Central nervous system dysfunction is an important cause of morbidity and mortality in patients with

human immunodeficiency virus type 1 (HIV-1) infection and acquired immunodeficiency virus

syndrome (AIDS). Patients with AIDS are usually affected by HIV-associated encephalitis (HIVE)

with viral replication limited to cells of monocyte origin. To examine the molecular mechanisms

underlying HIVE-induced dementia, the GSE4755 Affymetrix data were obtained from the Gene

Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) between the

samples from AIDS patients with and without apparent features of HIVE-induced dementia were

identified. In addition, protein-protein interaction (PPI) networks were constructed by mapping DEGs

into PPI data to identify the pathways that these DEGs are involved in. The results revealed that the

expression of 1528 DEGs, is mainly involved in the immune response, regulation of cell proliferation,

cellular response to inflammation, signal transduction and viral replication cycle. Heat shock protein

alpha, class A member 1 (HSP90AA1) and fibronectin 1 (FN1) were detected as hub nodes with degree

values > 130. In conclusion, the results indicate that HSP90A and FN1 play important roles in HIVE

pathogenesis.

30

P-26

Conformational Free Energy in a Chromatographic Stationary Phase by

Nonequilibrium Pulling within Gibbs-Ensemble Monte Carlo Simulation

P. Siders*

Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota, USA


In supercritical fluid chromatography, a mobile phase consisting mainly or wholly of carbon dioxide

interacts with a stationary phase that contains alkylsilanes bonded to silica [1]. Temperature and

pressure slightly above critical make the fluid carbon dioxide dense and highly compressible. Gibbs-

ensemble Monte Carlo simulation [2] is suitable for studying mobile-stationary interaction. The present

work describes such simulation in detail, including force fields and their validation.

An important factor in mobile-stationary

interaction is conformation of the alkylsilanes,

whether extended into the mobile phase or

collapsed against the silica. Conformational

free energy has been calculated from

nonequilibrium work. Figure 1 shows the work

and free energy for pulling a cluster of four C8-

silanes from a bent to a fully-extended

configuration. The end-to-end distance zee of

each silane was gradually changed from 4.4 Å

to 10.7 Å. The exponential of –βW was

averaged over 32 pulling experiments. The

quantities graphed, in units of Kelvin, are the

minimum work, the average cumulative work,

and the free energy calculated from the

Jarzynski equation [3].

Collapsed

conformations have the lowest free energy; there is a small barrier to a free-energy plateau of partial

extensions; fully-extended conformations are improbable.

Results of pulling experiments are compared to conformational averages from equilibrium hybrid

Monte Carlo simulations in which both collapsed and extended conformations persist over many

cycles. Conformational relaxation during equilibrium simulations is small in extent and is slow.

References

1. G. Guiochon and A. Tarafder, Journal of Chromatography A, 1218, 2011, 1037-1114.

2. S. C. McGrother and K. E. Gubbins, Molecular Physics, 97, 1999, 955-965.

3. C. Dellago and G. Hummer, Entropy, 16, 2014, 41-61.

Figure 1

31

P-27

In silico Protein Structure Prediction and Molecular Docking Study of

Sarco/Endoplasmic Reticulum Calcium-ATPase in Toxoplasma gondii

M. Y. Chong, I. K. S. Yap and W. K. Yam*

School of Pharmacy, International Medical University, No. 126, Jalan 19/155B, Bukit Jalil 57000

Kuala Lumpur, Malaysia


Toxoplasmosis is a life-threatening foodborne disease caused by foodborne apicomplexan parasite,

Toxoplasma gondii. Currently, major efforts are being made in search of better anti-toxoplasma drug as

current treatment for toxoplasmosis has many adverse effects and do not attack the encysted

bradyzoites. Earlier published work indicated that the inhibition of sarco/endoplasmic reticulum

calcium-ATPase (TgSERCA) could perturb calcium homeostasis in T. gondii. TgSERCA is essential

for secretion and motility of parasite. The absence of three-dimensional experimental information on

TgSERCA has motivated the prediction of its structure using homology modelling method. This model

can be used to aid the rational drug designing process by predicting its active sites, and identifying

potential substrates and possible interactions through molecular docking studies. Comparative

modelling suite MODELER9v12 was used in conjunction with validation servers such as PROCHECK,

PROSA and ERRAT to predict a model for TgSERCA. Autodockv4.2 was used to perform molecular

docking studies. The present findings showed that the binding sites of TgSERCA were mainly in the

cleft between transmembrane 3, 5 and 7, and was proved to be valid via docking simulation. The

putative binding modes of the five ligands (thapsigargin, artemisinin, artemisone, artesuante and

primaquine) on TgSERCA were mainly due to hydrophobic and hydrogen bond interactions. In

conclusion, the molecular studies of the 3D model of TgSERCA presented here indicated TgSERCA

can be used as potential drug target and downstream enzymatic studies in the future.

Author Index

32

Authors Abstract number(s) Page(s)

Adeyinka, A. S. P-1 5

Barroso-Flores, J. P-2 6

Bayliss, R. P-8 12

Blowers, P. P-3 7

Bolboacă, S. D. P-4, P-11 8, 15

Boonseng, S. P-5 9

Burgess, S. P-8 12

Chakraborty, T. P-6, P-21 10, 25

Cheeseright, T. P-18 22

Chemate, S. P-24 28

Chong, M. Y. P-27 31

Choong, Y. S. P-7 11

Ciampi, S. P-9 13

Concilio, M. G. P-8 12

Coote, M. L. P-9 13

Cox, H. P-5 9

Cukrowski, I. P-1 5

Dandekar, T. P-25 29

Dhail, S. P-6 10

Diallo, B. P-3 7

Domingo, L. R. P-22 26

Fielding, A. J. P-8 12

Flammia, M. P-3 7

Förster, C. P-25 29

Frenking, G. P-12 16

Golawski, S. P-3 7

Gonzalez, M. P-3 7

Gupta, G. K. P-10 14

Haworth, N. L. P-9 13

Jäntschi, L. P-4, P-11 8, 15

Jerabek, P. P-12 16

Jónsson, H. P-13 17

Kharkar, P. S. P-14 18

Kiani, F. A. P-15 19

Kongsted, J. P-16 20

Kumar, A. P-6, P-21 10, 25

Kumar, V. P-10 14

Kuznetsov, A. E. P-17 21

33

Lanke, S. P-24 28

Lawrence, R. P-18 22

Ledwani, L. P-6 10

Lee, Y. - V. P-7 11

Mackey, M. D. P-18 22

Maksimova, E. P-19 23

Murray, J. S. P-20 24

Petronella, R. P-3 7

Politzer, P. P-20 24

Ranjan, P. P-6, P-21 10, 25

Ríos-Gutiérrez, M. P-22 26

Roffe, G. W. P-5 9

Roy, S. P-6 10

Safavinia, B. P-3 7

Sahu, N. U. P-14 18

Saini, P. P-10 14

Sandoval-Salinas, M. E. P-2 6

Sayed Hassen, S. Z. P-23 27

Sekar, N. P-24 28

Shityakov, S. P-25 29

Siders, P. P-26 30

Simpson, C. D. P-9 13

Spencer, J. P-5 9

Tedesco, G. P-18 22

Tomasio, S. P-18 22

Tosco, P. P-18 22

Venigalla, S. P-6 10

Wahab, H. A. P-7 11

Warrier, S. P-14 18

Yam, W. K. P-27 31

Yap, I. K. S. P-27 31

virtual conference on computational...

Documents