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  Current Research Projects

Interaction of DNA Nucelobases with Noble Metals Two possible structures of the Ag-adenine-thymine complex
The underlying mechanisms behind the double helix structure of the DNA are the formation of hydrogen bonds between complementary base pairs and the relative orientations of successive base pairs along two polynucleotide strands. These nucleotides carry the cellular information for replication and synthesis, thus playing a critical role in metabolism, cellular signaling and enzymatic activity. Drug therapies, particularly those that seek to enhance or inhibit the cellular activities facilitated by these nucleotides, work by the binding of site-targeted drugs to specific nucleotides to achieve this end. For example, atoms of heavy metals such as platinum and ruthenium play a key role in anti-cancer drugs that act as intercalating agents and preferentially bind the drug molecule to a nucleotide in DNA, thereby interfering with the process of normal synthesis and transcription of DNA. It is now well established that the platinum-based anti-cancer drug cisplatin (Cl2H6N2Pt), works by the binding of platinum to two 7N guanine sites, thereby causing intrastrand and interstrand cross-links, the basis of the drugs efficacy in fighting cancer by inhibiting further uncontrolled growth of the tumorous cells. In this project we are interested in investigating, using ab ibitio computations, alternatives to cisplatin. Systems of interest are small neutral and charged clusters of silver and gold.



Current collaborators

Sudha Srinivas - Faculty

Recent Publications in this Project

Paulo H. Acioli and Sudha Srinivas, "Silver- and gold-mediated nucleobase bonding", J. Mol. Model. 20(8), 2391 (2014).

Acknowledgments

We acknowledge the financial support provided by an Extramural Associate Research Development Award (EARDA) Type G11 grant (5G11HD049644-03) from the National Institutes of Health and administered by Northeastern Illinois University, Chicago, IL.



Two possible structures of the Ag-guanine-cytosine complex

Stable structures of gas phase a) guanine-Ag-guanine; b) guanine-Au-guanine; and c) guanine-Pt-guanine complexes


Small Clusters and Ligand Interactions Lowest Energy Structures of AgN, N=1,4
Metals and noble metals have an important role in catalytic processes such as those in the pharmaceutical, automobile and petroleum indistries. Catalysts have been used in the chemical industry for a long time, however an atomic level understanding of catalysis is still lacking and therefore catalysts have traditionally been developed on a trial and error basis. This picture has been changing recently, thanks to development of faster and more powerfull computers and quantum chemistry computational methods. These developments are allowing the computational modeling of metal and metal-ligand interactions and their role in heterogenous catalysis at reasonable costs.

We are currently interested in understanding the nature of bonding of ligands such as oxygen (O2), carbon monoxide (CO) and carbon dioxide (CO2) to small clusters of noble metals and its implications on catalys. We use density functional theory calculations to model the interactions between the clusters and the molecules, the structural and electronic properties of the cluster-molecule system. The long-term goal of this project is to understand how clusters of noble metals like silver interact with small ligand molecules to gain an insight into the catalytic properties of similar metals at a microscopic level.



Current collaborators

Sudha Srinivas - Faculty

Students Involved in the Project

Current
Cesar Bustos
David Capotaq
John Gonzales
Biguun S. Woods

Former
Greg Freimark
Steve Burkland
Indira Bambur
Michael Cline
Narin Ratanavade


Recent Publications in this Project

Paulo H. Acioli, Steve Burkland, and Sudha Srinivas, "An exploration of the potential energy surface of the seven atom silver cluster and a carbon monoxide ligand", Eur. Phys. J. D, 66 215 (2012).

This articles was featured on the cover of the August 2012 Issue of the European Physics Journal D.

Paulo H. Acioli, N. Ratanavade, M. R. Cline, and Sudha Srinivas, "Density functional Theory study of Ag-Cluster/CO Interactions", in ICCS 2009, Part II, Lecture Notes in Computer Science 5545, G. Allen et al., Eds., Springer-Verlag, Berlin-Heildelberg, 2009, pp. 203-210.

Acknowledgments

This work was partially supported by a NEIU - COR grant (2007-2008) and a NEIU-SCSE grant (Summer 2009).



Lowest Energy Structures of Ag(CO)X, X=1,3

Lowest Energy Structures of Ag2(CO)X, X=1,6


Lowest Energy Structures of Ag3(CO)X, X=1,6


Lowest Energy Structures of Ag4(CO)X, X=1,8

Computational Vibrational Spectroscopy C2v global minimum of the PES of H5+.
Vibrational spectroscopy can provide insight about the structure and reactivity of gas phase molecules. In particular, I am interested in studying the effects of impurities in the excited state spectra of helium clusters and in the general properties of the ground and excited states of H5+. In the case of He clusters, these systems have being studied in the past, but most of the studies were restricted to the ground state. I am interested in studying their excited states. The main goal is to understand the difference between the spectra of the pure He clusters and the spectra as an impurity is added. This study will focus in the energies of the excited states and in their pair density functions. The understanding of these differences at the molecular level is of great importance to shed light in such a fascinating systems, which display exotic properties such as superfluidity in bulk quantities. The main challenge to carry out such study is to solve the multidimensional integrals that appear in the eigenvalue problems defined by the time-independent Shrödinger equation. One can overcome such challenge with the use of correlation function quantum Monte Carlo (CFQMC), a technique that we have shown to be effective in treating the vibrational spectrum, beyond the harmonic approximation, of systems with more than four atoms. Quantum Monte Carlo techniques can be also utilized to study H5+. This molecule is of particular interest in the physics and chemistry of interstellar medium. It is a weakly bound complex important in reactions involving H3+ and H2. One of the questions is to decide if the complex, in its ground state is symmetric or if it resembles H2 bound to H3+. Another important aspect is to study the isotope effects when H atoms are replaced by deuterium.



Current collaborators

Prof. Joel M. Bowman
Emory University

Prof. Geraldo Magela e Silva
Universidade de Brasilia - Brazil

Prof. Ricardo Gargano
Universidade de Brasilia - Brazil

Dr. Angelo Marconi Maniero
Universidade Federal da Bahia - Brazil


Recent Publications in this Project

Angelo M. Maniero, Paulo H. Acioli, Geraldo Magela e Silva, Ricardo Gargano, "Theoretical calculations of a new potential energy surface for the H + Li2 reaction", Chem. Phys. Lett. 490(4-6), 123 (2010).

G. M. e Silva, R. Gargano, W. B. da Silva, L. F. Roncaratti, and Paulo H. Acioli, "Quantum Monte Carlo and Genetic Algorithm Study of the Potential Energy Surface of the H5+ Molecule", Int. J. Quant. Chem. 108 (13), 2318 (2008).

Paulo H. Acioli, Z. Xie, B. J. Braams, and J. M. Bowman, "Vibrational Ground State properties of H5+ and its Isotopomers from Diffusion Monte Carlo Calculations", J. Chem. Phys. 128, 104318 (2008).

A. M. Maniero and P. H. Acioli , "Potential energy curves of Li2 and LiH from a full configuration interaction pseudopotential procedure". Int. J. Quant. Chem. 103 , 711 (2005).

Acknowledgments

This work was partially supported by the National Science Foundation through Research Opportunity Award as Supplemental Funding to CHE-0446527 (JM Bowman - PI).


D2d saddle point of the PES of H5+.


HH pair distribution function of the H5+. The vertical sticks represent the bond lengths at the C2v global minimum (solid) and at the lowest D2d (dashed) saddle point of the PES.

Energy landscape of the reactants, intermediate complexes, and products for scattering reactions of H3+ and H2 and isotopomers.

Wind Power Generation A Wind Turbine Made of Recycled Materials
The ever growing development of new technologies demands a continuous growth in energy production. Traditional energy production relies heavily on fossil fuels. At the current production rate the known deposits of coal, oil, and natural gas are expected to last for 148, 43, and 61 years, respectively. In addition, fossil fuels have a harmful impact in our environment. For instance, it is estimated that 90% of the greenhouse effect emissions in the US come from the burning of fossil fuels. Hidroelectric power plants are cleaner but they have a huge impact in the environment. The impact can be physical or biological. These effects start during the construction of the dam and they can change river itself as well as the surrounding ecosystem. The blocking of the flow of water have also a huge impact as the land that gets flooded could be home of many endangered species, could have been used for residence or even agriculture. Nuclear power plants are somewhat clean during the production stage. However, there is a big risk of nuclear accidents such as the Chernobyl disaster in 1987 and the Fukushima I nuclear accident in 2011. To address the ever growing energy demand and to reduce the negative environmental impacts there is a push for cleaner and renewable sources of energy. Ethanol is a cleaner alternative to oil. However, large scale alcohol production for energy production does create other issues such as the use of land for non food producing agriculture. Solar and wind producing generators are a greener alternative. Although wind and solar farming also have negative environmental impact and the cost and efficiency are still far from ideal many governments are still promoting the construction of vast wind "farms," and encouraging private companies with subsidies and regulatory support. The goals of this project are: 1) to study the viability of the use of wind and solar generators around NEIU neighborhood; 2) To research the basic physics of electric power generation in general, and wind power generation in particular; 3) Design and build a wind power generator that would be adequate for low power applications in a urban environment; 4) Write a wind generation booklet to be distribute in local mid and high schools to aid students that are interested in developing renewable energy science projects.



Students Involved in the Project
Sergio Guerrero
Max Hansen
Thomas McLaughlin
Esosa Ogbomo
Steve Roothaan
Caroline Williams

Recent Presentations in this Project
Esosa Ogbomo, Thomas McLaughlin, Max Hansen, and Paulo Acioli, "Building a Wind Turbine from Recycled Components", Poster presented at the Annual SACNAS meeting, Seattle, Oct. 2012.

Steven Roothaan, Caroline Williams, Sergio Guerrero, and Paulo Acioli, "Optimization of H-Darrieus Vertical Axis Wind Turbine Design for Application in Urban Areas", Poster presented at the Annual SACNAS meeting, Seattle, Oct. 2012.

Acknowledgments
This work supported by a USDA-CREEAR grant.


Response of a Vertical Axis Wind Turbine in Turbulent Air


Last Updated: 4/01/2009 .
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