- Email: [email protected]
Proceedings of the Virtual Conference on Computational Science (VCCC-2015): Special Issue of the Journal of Computational Science
Journal of Computational Science 17 (2016) 271–272
Contents lists available at ScienceDirect
Journal of Computational Science journal homepage: www.elsevier.com/locate/jocs
Preface
Proceedings of the Virtual Conference on Computational Science (VCCC-2015): Special Issue of the Journal of Computational Science a b s t r a c t This is a preface of a special issue of the Journal of Computational Science consisting of selected papers from the Virtual Conference on Computational Chemistry held from 1st to 31st August 2015. A perspective of the accepted papers is provided. The citations of papers from precedent special issues of the virtual conference are also presented. © 2016 Published by Elsevier B.V.
This special issue is dedicated to the Virtual Conference on Computational Chemistry, VCCC-2015. The issue highlights papers selected from online presentations of VCCC-2015. VCCC-2015 was organized from 1st to 31st August 2015. This is the third virtual conference which was started in 2013. The month of August was chosen to commemorate the birth anniversary of Erwin Rudolf Josef Alexander Schrödinger, the father of quantum mechanics, on 12th August. There were 30 presentations for the virtual conference with 100 participants from 30 countries. A secured platform was used for virtual interactions of the participants. After the virtual conference, there was a call for full papers to be considered for publication in the conference proceedings. Nine manuscripts were received and they were processed and reviewed as per the policy of this journal. This special issue is a collection of the three accepted manuscripts. Politzer et al. [1] carried out a comparative analysis of electrostatic potential maxima and minima on molecular surfaces. They computed the most positive and most negative values of the electrostatic potentials on the surfaces of a series of molecules, some of which contain atoms from the second and third rows of Groups IV, VI and VII. They used the Hartree-Fock and density functional theory methods and different basis sets. The functionals used are B3LYP and M06-2X. They concluded that (a) For a given basis set, the three methods give essentially comparable results. (b) Hydrogens do not require either polarization or diffuse functions, not even when the potential of interest is on the hydrogen. (c) Polarization functions are essential, for first-row as well as higher-row atoms; diffuse functions are less important. (d) The recommended basis set for electrostatic potential calculations, of those investigated, is the 6-31G(d). Larger basis sets are not needed for this purpose. (e) If the 6-31G(d) is precluded (e.g. by the size of the system or by the presence of fourth-row atoms), then the 3-21G(d) is likely to be an acceptable alternative.
http://dx.doi.org/10.1016/j.jocs.2016.11.005 1877-7503/© 2016 Published by Elsevier B.V.
Choong and Yung-Hung [2] gives overview on outer membrane protein simulations. Membrane proteins (MPs) play an important role in cellular processes such as protein folding, catalysis and molecular recognition. The study of MPs in lipids environment is difficult by experiment alone but has progressed with computer simulation. It is now possible to consider a larger range of MPs to be simulated in order to elucidate the structure-function relationship. They discussed the general flow on MD simulations for the investigation of MP dynamics. Choi et al. [3] used computer modeling to identify common therapeutic targets for selected neurodegenerative disorders. Neurodegenerative disorders (NDs) are a heterogeneous group of disorders generally characterized by a profound decrease in the size and volume of the human brain due to death of neurons. They selected six common neurodegenerative diseases, Alzheimer’s disease (AD), Parkinson’s disease (PD), Amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), Prion disease and Dentatorubral-pallidoluysian atrophy (DRPLA) for identification of common regulatory target proteins. They identified a total of sixteen common proteins as target proteins by disease pathway analysis and previous studies based on their association with more than two NDs, including AD. They constructed an interaction network of each of the sixteen target proteins against causative proteins selected from all six NDs by using the STRING 9.1 program. They suggested that CASP-3 and CASP-8 were associated with the maximum number of selected NDs based on Pathway analysis and the protein–protein interaction network and therefore may be the most potent target proteins for treatment of multineurodegenerative diseases. At this point, it is interesting to point out that from the previous proceedings, papers have been cited as summarized in Table 1. On a concluding remark, VCCC-2015 was a successful event and the accepted papers in this special issue range from fundamental
272
Preface / Journal of Computational Science 17 (2016) 271–272
Table 1 Title of papers and number of citations from special issue of VCCC-2013 and VCCC-2014. Title of papers
Number of citations (November 2016)
Proceedings of the Virtual Conference on Computational Chemistry, VCCC-2013, Journal of Computational Science High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine [4] E-science infrastructures for molecular modeling and parametrization [5] Factors affecting the strengths of -hole electrostatic potentials [6] First order derivatives of thermodynamic functions under assumption of no chemical changes revisited [7] Proceedings of the Virtual Conference on Computational Chemistry, VCCC-2014, Journal of Computational Science Structure based designing and ADME-T studies of butenolide derivatives as potential agents against receptor ICAM-1: A drug target for cerebral malaria [8] Intuitive and counterintuitive noncovalent interactions of aromatic regions with the hydrogen and the nitrogen of HCN [9] In search of novel anti-inflammatory agents: Computational repositioning of approved drugs [10] Adsorption of sarin on MgO nanotubes: Role of doped and defect sites [11] Synthesis, spectroscopic characterization, electronic and optical studies of (2Z)-5,6-dimethyl-2-[(4-nitrophenyl)methylidene]-2,3-dihydro-1-benzofuran-3-one [12]
to applied interdisciplinary chemistry and they should be useful to those working in the fields. Acknowledgements The author would also like to thank the Organising and International Advisory Committee members and the participants of VCCC-2015, Prof. Peter Sloot (the Editor-in-Chief of this journal) and the anonymous reviewers for their useful comments to improve the manuscripts. References [1] K.E. Riley, K.-A. Tran, P. Lane, J.S. Murray, P. Politzer, Comparative analysis of electrostatic potential maxima and minima on molecular surfaces, as determined by three methods and a variety of basis sets, J. Comput. Sci. 17 (2016) 270–281. [2] Y.S. Choong, R.L. Yung-Hung, A general overview on outer membrane protein (Omp) simulations, J. Comput. Sci. 17 (2016) 282–288. [3] K. Ahmad, M.H. Baig, G.K. Gupta, M.A. Kamal, N. Pathak, I. Choi, Identification of common therapeutic targets for selected neurodegenerative disorders: an in silico approach, J. Comput. Sci. 17 (2016) 289–303. [4] M.H. Almatarneh, M. Altarawneh, R.A. Poirier, I.A. Saraireh, High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine, J. Comput. Sci. 5 (2014) 568–575. [5] N. Shen, Y. Fan, S. Pamidighantam, E-science infrastructures for molecular modeling and parametrization, J. Comput. Sci. 5 (2014) 576–589. [6] J.S. Murray, L. Macaveiu, P. Politzer, Factors affecting the strengths of -hole electrostatic potentials, J. Comput. Sci. 5 (2014) 590–596.
3 23 28 1 1 10 2 1 1
[7] L. Jäntschi, S.D. Bolboac˘a, First order derivatives of thermodynamic functions under assumption of no chemical changes revisited, J. Comput. Sci. 5 (2014) 597–602. [8] D. Choudhary, G.K. Gupta, S.L. Khokra, Nisha, Structure based designing and ADME-T studies of butenolide derivatives as potential agents against receptor ICAM-1: a drug target for cerebral malaria, J. Comput. Sci. 10 (2015) 156–165. [9] J.S. Murray, Z. Peralta-Inga Shields, P.G. Seybold, P. Politzer, Intuitive and counterintuitive noncovalent interactions of aromatic regions with the hydrogen and the nitrogen of HCN, J. Comput. Sci. 10 (2015) 209–216. [10] P.S. Kharkar, S. Borhade, A. Dangi, S. Warrier, In search of novel anti-inflammatory agents: computational repositioning of approved drugs, J. Comput. Sci. 10 (2015) 217–224. [11] N. Sharma, R. Kakkar, Adsorption of sarin on MgO nanotubes: role of doped and defect sites, J. Comput. Sci. 10 (2015) 225–236. [12] Diwaker, C.S.C. Kumar, A. Kumar, S. Chandraju, C.K. Quah, H.-K. Fun, Synthesis, spectroscopic characterization, electronic and optical studies of (2Z)-5,6dimethyl-2-[(4-nitrophenyl)methylidene]-2,3-dihydro-1-benzofuran-3-one, J. Comput. Sci. 10 (2015) 237–246.
Ponnadurai Ramasami a,b Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius b Department of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg, South Africa E-mail address: [email protected] a
Contents lists available at ScienceDirect
Journal of Computational Science journal homepage: www.elsevier.com/locate/jocs
Preface
Proceedings of the Virtual Conference on Computational Science (VCCC-2015): Special Issue of the Journal of Computational Science a b s t r a c t This is a preface of a special issue of the Journal of Computational Science consisting of selected papers from the Virtual Conference on Computational Chemistry held from 1st to 31st August 2015. A perspective of the accepted papers is provided. The citations of papers from precedent special issues of the virtual conference are also presented. © 2016 Published by Elsevier B.V.
This special issue is dedicated to the Virtual Conference on Computational Chemistry, VCCC-2015. The issue highlights papers selected from online presentations of VCCC-2015. VCCC-2015 was organized from 1st to 31st August 2015. This is the third virtual conference which was started in 2013. The month of August was chosen to commemorate the birth anniversary of Erwin Rudolf Josef Alexander Schrödinger, the father of quantum mechanics, on 12th August. There were 30 presentations for the virtual conference with 100 participants from 30 countries. A secured platform was used for virtual interactions of the participants. After the virtual conference, there was a call for full papers to be considered for publication in the conference proceedings. Nine manuscripts were received and they were processed and reviewed as per the policy of this journal. This special issue is a collection of the three accepted manuscripts. Politzer et al. [1] carried out a comparative analysis of electrostatic potential maxima and minima on molecular surfaces. They computed the most positive and most negative values of the electrostatic potentials on the surfaces of a series of molecules, some of which contain atoms from the second and third rows of Groups IV, VI and VII. They used the Hartree-Fock and density functional theory methods and different basis sets. The functionals used are B3LYP and M06-2X. They concluded that (a) For a given basis set, the three methods give essentially comparable results. (b) Hydrogens do not require either polarization or diffuse functions, not even when the potential of interest is on the hydrogen. (c) Polarization functions are essential, for first-row as well as higher-row atoms; diffuse functions are less important. (d) The recommended basis set for electrostatic potential calculations, of those investigated, is the 6-31G(d). Larger basis sets are not needed for this purpose. (e) If the 6-31G(d) is precluded (e.g. by the size of the system or by the presence of fourth-row atoms), then the 3-21G(d) is likely to be an acceptable alternative.
http://dx.doi.org/10.1016/j.jocs.2016.11.005 1877-7503/© 2016 Published by Elsevier B.V.
Choong and Yung-Hung [2] gives overview on outer membrane protein simulations. Membrane proteins (MPs) play an important role in cellular processes such as protein folding, catalysis and molecular recognition. The study of MPs in lipids environment is difficult by experiment alone but has progressed with computer simulation. It is now possible to consider a larger range of MPs to be simulated in order to elucidate the structure-function relationship. They discussed the general flow on MD simulations for the investigation of MP dynamics. Choi et al. [3] used computer modeling to identify common therapeutic targets for selected neurodegenerative disorders. Neurodegenerative disorders (NDs) are a heterogeneous group of disorders generally characterized by a profound decrease in the size and volume of the human brain due to death of neurons. They selected six common neurodegenerative diseases, Alzheimer’s disease (AD), Parkinson’s disease (PD), Amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), Prion disease and Dentatorubral-pallidoluysian atrophy (DRPLA) for identification of common regulatory target proteins. They identified a total of sixteen common proteins as target proteins by disease pathway analysis and previous studies based on their association with more than two NDs, including AD. They constructed an interaction network of each of the sixteen target proteins against causative proteins selected from all six NDs by using the STRING 9.1 program. They suggested that CASP-3 and CASP-8 were associated with the maximum number of selected NDs based on Pathway analysis and the protein–protein interaction network and therefore may be the most potent target proteins for treatment of multineurodegenerative diseases. At this point, it is interesting to point out that from the previous proceedings, papers have been cited as summarized in Table 1. On a concluding remark, VCCC-2015 was a successful event and the accepted papers in this special issue range from fundamental
272
Preface / Journal of Computational Science 17 (2016) 271–272
Table 1 Title of papers and number of citations from special issue of VCCC-2013 and VCCC-2014. Title of papers
Number of citations (November 2016)
Proceedings of the Virtual Conference on Computational Chemistry, VCCC-2013, Journal of Computational Science High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine [4] E-science infrastructures for molecular modeling and parametrization [5] Factors affecting the strengths of -hole electrostatic potentials [6] First order derivatives of thermodynamic functions under assumption of no chemical changes revisited [7] Proceedings of the Virtual Conference on Computational Chemistry, VCCC-2014, Journal of Computational Science Structure based designing and ADME-T studies of butenolide derivatives as potential agents against receptor ICAM-1: A drug target for cerebral malaria [8] Intuitive and counterintuitive noncovalent interactions of aromatic regions with the hydrogen and the nitrogen of HCN [9] In search of novel anti-inflammatory agents: Computational repositioning of approved drugs [10] Adsorption of sarin on MgO nanotubes: Role of doped and defect sites [11] Synthesis, spectroscopic characterization, electronic and optical studies of (2Z)-5,6-dimethyl-2-[(4-nitrophenyl)methylidene]-2,3-dihydro-1-benzofuran-3-one [12]
to applied interdisciplinary chemistry and they should be useful to those working in the fields. Acknowledgements The author would also like to thank the Organising and International Advisory Committee members and the participants of VCCC-2015, Prof. Peter Sloot (the Editor-in-Chief of this journal) and the anonymous reviewers for their useful comments to improve the manuscripts. References [1] K.E. Riley, K.-A. Tran, P. Lane, J.S. Murray, P. Politzer, Comparative analysis of electrostatic potential maxima and minima on molecular surfaces, as determined by three methods and a variety of basis sets, J. Comput. Sci. 17 (2016) 270–281. [2] Y.S. Choong, R.L. Yung-Hung, A general overview on outer membrane protein (Omp) simulations, J. Comput. Sci. 17 (2016) 282–288. [3] K. Ahmad, M.H. Baig, G.K. Gupta, M.A. Kamal, N. Pathak, I. Choi, Identification of common therapeutic targets for selected neurodegenerative disorders: an in silico approach, J. Comput. Sci. 17 (2016) 289–303. [4] M.H. Almatarneh, M. Altarawneh, R.A. Poirier, I.A. Saraireh, High level ab initio, DFT, and RRKM calculations for the unimolecular decomposition reaction of ethylamine, J. Comput. Sci. 5 (2014) 568–575. [5] N. Shen, Y. Fan, S. Pamidighantam, E-science infrastructures for molecular modeling and parametrization, J. Comput. Sci. 5 (2014) 576–589. [6] J.S. Murray, L. Macaveiu, P. Politzer, Factors affecting the strengths of -hole electrostatic potentials, J. Comput. Sci. 5 (2014) 590–596.
3 23 28 1 1 10 2 1 1
[7] L. Jäntschi, S.D. Bolboac˘a, First order derivatives of thermodynamic functions under assumption of no chemical changes revisited, J. Comput. Sci. 5 (2014) 597–602. [8] D. Choudhary, G.K. Gupta, S.L. Khokra, Nisha, Structure based designing and ADME-T studies of butenolide derivatives as potential agents against receptor ICAM-1: a drug target for cerebral malaria, J. Comput. Sci. 10 (2015) 156–165. [9] J.S. Murray, Z. Peralta-Inga Shields, P.G. Seybold, P. Politzer, Intuitive and counterintuitive noncovalent interactions of aromatic regions with the hydrogen and the nitrogen of HCN, J. Comput. Sci. 10 (2015) 209–216. [10] P.S. Kharkar, S. Borhade, A. Dangi, S. Warrier, In search of novel anti-inflammatory agents: computational repositioning of approved drugs, J. Comput. Sci. 10 (2015) 217–224. [11] N. Sharma, R. Kakkar, Adsorption of sarin on MgO nanotubes: role of doped and defect sites, J. Comput. Sci. 10 (2015) 225–236. [12] Diwaker, C.S.C. Kumar, A. Kumar, S. Chandraju, C.K. Quah, H.-K. Fun, Synthesis, spectroscopic characterization, electronic and optical studies of (2Z)-5,6dimethyl-2-[(4-nitrophenyl)methylidene]-2,3-dihydro-1-benzofuran-3-one, J. Comput. Sci. 10 (2015) 237–246.
Ponnadurai Ramasami a,b Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius b Department of Applied Chemistry, University of Johannesburg, Doornfontein, Johannesburg, South Africa E-mail address: [email protected] a