University of Southern California (USC)

After the workshop we visited Anna Krylov's group at USC where we meet many interesting people who work on the exciting projects. Vadim Mozhayskiy investigates topology of the Jahn–Teller intersections and is the author of the ezSpectrum program which computes photoelectron/photodetachment spectra taking into account Franck-Condon factors. He also creates beautiful artworks for the journal covers. Evgeny Epifanovsky created a new library for the tensor operations which will be used for all currently available and new coupled-cluster methods and other methods which use tensor formalism within Q-Chem program package. Dr. Debashree Ghosh works on implementation of the gradients for the EFP method. We would like also thank Dr. Kadir Diri for useful advice about our computational cluster and Dr. Arik Landau for his help with basis sets employed in RI-MP2 calculations. (Photos from USC Campus)



More photos from Pasadena and San Francisco

Los Angeles, California, Dec-14-2009

Q-Chem Workshop at Berkeley

In the begging of December we attended Q-Chem Workshop at University of California Berkeley. Q-Chem developers presented and discussed recent features which will be included in the forecoming major release of Q-Chem. Peter Gill's group presented developments grounded on the dual basis method for DFT (dual grids and functionals). The group of Martin Head-Gordon presented developments in ab-initio methods for the systems with strong correlation. Anna Krylov's group reported advances in the spin-flip and EOM coupled-cluster methods. Lyudmila Slipchenko and me presented implementation of QM/MM based on effective fragment potential (EFP) force field and its applications. (Photos from Berkeley)

Berkeley, California, Dec-10-2009

Wind Turbines Farm

Wind power along with solar energy and biofuels is a source of renewable energy. This weekend I visited one of the wind farms near Brookston, Indiana. Indeed, the wind turbines are pretty large with the tower height 230–260 ft (70–80 m) and rotor diameter approximately 260 ft (80 m). The turbines operate at wind speed range 8–56 mph (3.5–25 m/s) producing 1,500 kW of electrical energy each. (Photos)

Brookston, Indiana, Nov-8-2009

Purdue Campus Tour

Finally, I have settled down in West Lafayette. There are some photos with my first impressions from the university campus. (Photos)


West Lafayette, Oct-1-2009

Prof. Slipchenko's Group Home Page

Welcome to http://www.chem.purdue.edu/slipchenko/ our group's home page! We just created a new site where you can find information about us, our research activities, useful computational chemistry resources and many other things related to our group.
West Lafayette, Oct-1-2009

Moving to Indiana

Photo by Unknown Truck Driver
On the 700 miles long way I have crossed five states: Mississippi, Tennessee, Arkansas, Illinois, and Indiana.
Mississippi–Indiana, Aug-2-2009

Graduation, 2009

Photo by Bakhtiyor Rasulev
It tooks four years to get my Ph.D and now I am very glad to go further!
Jackson, Aug-1-2009

Gordon Research Conference on Biological Molecules in the Gas Phase and in Solution

Few days ago I participated in the Gordon Research Conference on Biological Molecules in the Gas Phase and in Solution. It was held in Tilton School in New Hampshire (see photos from this trip). The conference gathered many renowned as well as young scientists. Not surprisingly that the most wanted molecules for many researches are proteins from the small peptide chains to the large enzyme complexes. I would like to mention several groups which work on experimental study of biological molecule in the gas phase. At the end of the note I decided to put a glossary of some experimental techniques widely used in these studies.

Prof. David Clemmer's group at University of Indiana use Ion Mobility Mass Spectrometry (IMMS) of proteins. They investigate conformational changes of the proteins in the gas phase.

Prof. Steven Boxer's group at Stanford University use modifications of Förster Resonance Energy Transfer (FRET) technique which allows them to determine distance between labels attached to the molecules and thus determines conformation of the molecule [1, 2]. They also use Stark spectroscopy to investigate local electrostatic field in the protein molecules and investigate how this field affects the chemical reactivity of the proteins [3, 4].

Prof. Timothy Zwier at Purdue University use very sensitive spectroscopic techniques including double resonance spectroscopy to sample conformational space including high energy local minima of the small molecules [5].

Prof. David Pratt at University of Pittsburgh work on fundamental physical chemistry problems using high resolution UV/Vis and Stark spectroscopy to study electronic dipole moments [6] and charge transfer in the small biological molecules and their hydrogen bonded complexes.

I would also especially emphasize theoretical work by Dr. Alexandre Tkatchenko at Fritz-Haber-Institut who developed theoretical method for accurate and efficient computation of Van der Vaals interactions. The method is based on evaluation of electronic density and it is independent on the DFT functional used [7].

I have presented on the conference my recently published work on kinetic simualtion of the gas phase experiments [8].

Glossary
IMMS (Ion Mobility Mass Spectrometry)—is a combined technique where ions under an applied electrical potential gradient are first separated by drift time through some neutral gas similarly to the gas chromatography technique before being introduced into a mass spectrometer. Ion mobility is determined by the drift time which in turn is a measure of the radius relative to the charge of the ion [9]. Then separated by the drift time the ions are analyzed by mass spectrometry measuring the mass-to-charge ratio of the ions. Currently this technique is used for infestation of the protein conformations in the gas phase.



FRET (Förster Resonance Energy Transfer) spectroscopy—is a technique based on the energy transfer from electronically excited donor chromophore molecule to an acceptor situated in proximity (ca 10 nm) through non radiative dipole–dipole coupling. Thus knowing fluorescence spectra of the chromophores and fluorescence quenching due to non radiative relaxation it is possible to estimate relative positions of the donor and acceptor in the molecule. Information about relative positions of the chromophore is used to determione conformation of the large molecule. This methods is used both for investigation of proteins and nucleic acid. Sometimes several labels with different fluorescence spectra can be attached to the one large molecule and thus provide more detailed information about the conformation [10].

Stark Spectroscopy—is a high resolution UV/Vis spectroscopic technique based on the Stark effect [11]. The Stark effect is manifested in the shifting of spectral lines of a moleucle in preence of external electric field. The amount of shifting is called the Stark shift. In the spectroscopy based on Stark effect the small label molecule which has spectral lines with a large Stark shift attached to a protein or other molecules of interest. The Stark shift of spectral lines of the label molecule due to an electric field of the protein (where the label is attached) can be used as a measure of electric field of the protein. Informartion about electric field of the protein is valuable for undestanding of the protein chemical reactivity.

References
1) X. Shi et al. Biochemistry, 46, 14403 (2007); 2) K. P. Kent et al. J. Am. Chem. Soc. 130, 9664 (2008); 3) L. N. Silverman et al. J. Phys. Chem. A, 112, 10244 (2008); 4) S. G. Boxer et al. J. Phys. Chem. B, 113, 2972 (2009); 5) N. R. Pillsbury et al. J. Phys. Chem. A, 113, 126 (2009); 6) D. M. Miller et al. J. Phys. Chem. A, 113, 6964 (2009); 7) A. Tkatchenko et al. Phys. Rev. Lett. 102, 073005 (2009); 8) D. Kosenkov et al. J. Phys. Chem.  B 113, 6140 (2009); 9) Wikipedia article on Mass Spectrometry; 10) Wikipadia article on Förster Resonance Energy Transfer; 11) Wikipadia article on Stark effect.
Tilton School, New Hampshire Jul-10-2009

New England's Trip

I just got back from Tilton, New Hampshire. There are three photo galleries with New England's impressions: Tilton Village, Tilton School, and our traditional photos of chipmunks and squirrels.

Photo by Dmytro Kosenkov

Photo by Dmytro Kosenkov

Photo by Dmytro Kosenkov

Tilton, New Hampshire, Jul-10-2009

What’s Next?

After the graduation in August, 2009 I will join Prof. Slipchenko’s Theoretical Chemistry Group at Purdue University as a postdoc. I am very happy to have the opportunity to work on development of new methods of quantum chemistry for simulation of biological molecules in solvents and accounts for electronic excitations.
Jackson, Jun-8-2009

Ph.D. Defense

On Friday May 29, 2009 I defended my Ph.D. thesis!
Dmytro Kosenkov Title: „Thermodynamic and Kinetic Simulations on Biological Molecules in Gas Phase and in Solution: Evaporation, Isomerization, and Hydrogen Bonding“

I am glad to complete this important step in my education! Thank for all of you who helped me during my graduate studies and supported during the defense. Special thanks to my dissertation committee who made this event possible: Dr. Jerzy Leszczynski, Dr. Paresh C. Ray, Dr. Glake Hill, Dr. Tigran V. Shahbazyan, Dr. Ming-Ju Huang, and Dr. Lеоnid Gоrb. Members of our dissertation committee
Jackson, May-29-2009

One Day Two Prizes

On April 27, we celebrated Annual Chemistry Day at Jackson State University. I was recognized with two awards: „Best Graduate Poster“ and „Best Oral Presentation at Annual Meeting of Mississippi Academy of Sciences“. I appreciate my supervisors, colleagues and friends whose support made this possible.
Jackson, Apr-27-2009

Scenic Views of Utah

Last week we attended 237^th National Meeting of American Chemical Society in Salt Lake City, Utah. After the conference we visited several interesting places in this state. It is interesting that in Utah the weather changes significantly from North to South. While in Salt Lake City it is windy and snowing, warm weather under clear sky welcomes you on South. This is due to mountain ranges which cross the state. Photo by Dmytro Kosenkov
We have visited only three of more then dozen state and national parks of Utah: Great Salt Lake, Antelope Island, and Arches National Park.
Salt Lake City, Mar-30-2009

Interdisciplinary Center for Nanotoxicity (ICN): New Center—New Web Site

A new web site (http://icnanotox.org/) for our Interdisciplinary Center for Nanotoxicity (ICN) has been launched. The web site was created by Olexandr Isayev. The site is based on the up-to-date content management system and has many other useful features. We are glad to have a brand new web site!
Jackson, Feb-05-2009