We are interested in monitoring and controlling dynamics of molecular processes. There are several problems of current interest – use of control theory to design shaped laser pulses to achieve prescribed dynamical targets, understanding the photophysics of nanobio systems like nucleic acid systems tagged with nanoparticles like gold clusters. Structural studies to investigate reaction pathways and to explain and predict products obtained in experiments with organic compounds of biological relevance using quantum chemical methods is another area of our activity. We have also worked on classical complex systems where noise can be used to enhance the response of a system to external drives.

Graduates with research training in dynamics and structure of molecular systems studies will be equipped to carry on further research in frontiers of molecular physics and in applied areas like nanoelectronics, quantum computing, etc.

SUB AREAS

The aim of the project is to use optimal control theory (OCT) to design of laser pulses for controlling molecular motion and photodissociation processes. We have worked extensively on a diatomic molecule and have recently started to investigate the control of the quantum state populations and the energy distribution in a biologically important molecule, carbonmonoxymyoglobin Using density functional theory we have computed potential energy and dipole moment surfaces for the C-O and Fe-C stretching coordinates of a 48 atom model system representing the heme active site of the system. We solve the quantum mechanical time-dependent Schroedinger equation and model the effect of an infrared laser pulse on the biological molecule. By performing this calculation many times, and by using the powerful apparatus of OCT, we are able to design laser pulses which will control the flow of energy into the different bonds of carbonmonoxymyoglobin and we plan to control the details of the photodissociation process which will result from the absorption of infrared radiation.

1. S Sharma, H Singh*, J. Harvey and G G Balint-Kurti, Design of infrared laser pulse to control the multiphoton dissociation of the Fe-CO bond in CO-heme compounds, J. Chem. Phys. 133, (2010) 174103.
2. S Sharma, H Singh* and G G Balint-Kurti, Genetic algorithm optimization of laser pulses for molecular quantum state excitation J. Chem. Phys. 132, (2010) 064108-1-10.
3. P. Kumar, S. Sharma and H. Singh*, Optimally controlled vibrational population transfer in a diatomic quantum system, J. Theo. Comp. Chem. 8, (2009) 157 -180.

Single molecule Deoxyribonucleic acid (DNA) is a key building block in nanotechnology. A range of different nanoparticles and nanoclusters have been assembled on single DNA molecules for a variety of purposes. We have been working on formulating theoretically the fluorescent resonant transfer of energy (FRET) between an emitter like a dye and an acceptor like a nanocluster of gold particles tagged to the two ends of a biopolymer (H Singh and B Bagchi 2005, Current Science, 89 (10) 1710-19; S Saini, H Singh and B Bagchi, 2006, J. Chem. Sci., 118 23-35.). Analyses of FRET data are useful to monitor single molecule dynamics of DNA and they form a popular area of research. We are considering investigation of several aspects of photophysical properties of DNA prototypes using nanoparticles. This involves theoretical formulation of FRET and related phenomena to examine the dynamics and energetics in DNA, and electronic structure and relevant properties calculations using ab initio quantum mechanical methods for the core of the problem and semi-empirical or other methods for the periphery of the system. Diverse combinations for the nanoparticle clusters are conceived. Electrodynamic methods will be used to study plasmonic excitations in nano-clusters coupled with DNA and linear optical properties.

1. P. Sharma, S. Sharma, A. Mitra and H. Singh, A Theoretical Study on Interaction of Small Gold Clusters Aun (n = 4, 6, 8) with xDNA Base Pairs, J. Biomol. Str. Dyn. 27 (2009) 65-82.
2. P Sharma, H Singh, S Sharma and H Singh, Binding of gold nanoclusters with size-expanded DNA bases: A computational study of structural and electronic properties, J. Chem . Theo. Comp.(ACS) 3 (2007) 2301-2311.
3. S Saini, H Singh and B Bagchi, Fluorescence energy resonance transfer in chemistry and biology: Non-Förster distance dependence of the FRET rate, J. Chem. Sci. 118 (2006) 23-35.
4. H Singh and B Bagchi, Non-Forster distance and orientation dependence of energy transfer and applications of fluorescence resonance energy transfer to polymers and nanoparticles: How accurate is the spectroscopic ruler with 1/R6 rule? Current Sci., 89 (2005) 1710.-1717

1. H Singh, A Simple Experiment to Study the Statistical Properties of Two or Three State Dynamics, in Probability and Statistics, eds., M Delampady, T Krishnan and S Ramasubramanian, Universities Press, Hyderabad, India, 2001.
2. R Rai and H Singh, Stochastic Resonance without an external drive in a simple prey-predator model, Phys. Rev. E 62 (2000) 8804-7.
3. R Rai and H Singh, Hysteresis Studies in a Noisy Auto-associative Neural Network, Phys. Rev. E 61 (2000) 968-71.
4. R Rai and H Singh, Investigations on Stochastic Resonance in Isomerization Processes Using Discrete Time Maps, Indian J. Chem. Special issue on Theoretical Chemistry 39A (2000) 330-336.

We have been working on quantum chemical calculations to investigate reactivity of organic compounds and we have explained counter-intuitive structural behaviour of complex reactive systems, e. g., preferential trimerization of 5-amino-methyl furan carboxylic acid. The electronic structure calculations are helpful not only to explain the reactivity observed in the laboratory, it empowers the synthetic chemist with a predictive power and ability to design pathways with selective and judicious choices. We are now considering furanoid sugar amino acids that are similar in complexity to the systems we have worked on before and also present rich architectural terrain to explore. Carbopeptoids based on these units act as robust peptidomimetic building blocks and exhibit turn structures making them ideal targets for extensive investigations

The amino Furan carboxylic acid derivative compounds have been studied by us at relatively lower levels of theory. We now wish to explore much higher levels of calculations, using MP2, CI for correlation energies and DFT based methods to explore these. Among other features, electrostatic orbital interactions, diverse population analyses and atoms in molecules parameters like bond critical points and eccentricities etc. will be calculated.This work is in collaboration with Dr T K Chakraborty of IICT, Hyderabad

1. T K Chakraborty , N. V. Suresh Kumar, S Roy, S Dutta, A Kunwar, B Sridhar, H Singh*,Stereochemical control in the structures of linear δ,α-hybrid tripeptides containing tetrahydrofuran amino acids, J. Phys. Org. Chem.(2011), in press.
2. N V S Kumar, P Sharma, H Singh*, D Koley, S Roy, T K Chakraborty , Preferential mode of cyclization of tetrahydrofuran amino acids: Some theoretical insights, J. Phys. Org. Chem 23(2009) 238-245.