Research Projects

Hydra­tion of Nucleic Acid Bases

Com­pre­hen­sive study on inter­ac­tions between Nucleic Acid Bases (NABs) Cover arti­cle! A. Fur­manchuk, O. Isayev, O. Shishkin, L. Gorb, J. Leszczyn­ski. Phys. Chem. Chem. Phys., 2010, In press. link and bulk water envi­ron­ment has been per­formed with use of Car-Parrinello Mol­e­c­u­lar Dynam­ics. Detailed analy­sis of aver­age num­ber, life times and mobil­ity of water mol­e­cules, ori­en­ta­tion and 3D orga­ni­za­tion of hydro­gen bond net­work in the first hydra­tion shell of ade­nine, gua­nine, cyto­sine and thymine has been car­ried out. Effect of hydra­tion by bulk water envi­ron­ment has been com­pared with the data from poly­hy­drated com­plexes of NABs.

Dur­ing bulk water hydra­tion the pres­ence of mixed Hw…N/Hw…pi type of bond­ing is detected for imino nitro­gen atoms. For­ma­tion of three hydro­gen bonds to car­bonyl groups reflects sig­nif­i­cance of polar­iz­ing effects of aque­ous envi­ron­ment. Hydra­tion of hydropho­bic sites revealed pres­ence of extremely weak bond­ing. Hydra­tion of C₆–H₆ site of thymine is stand­ing sig­nif­i­cantly apart from the hydra­tion of other hydropho­bic sites. An aver­age coör­di­na­tion num­bers of ade­nine, gua­nine, cyto­sine and thymine in bulk water envi­ron­ment are 6.87, 8.52, 6.12 and 6.42 water mol­e­cules, cor­re­spond­ingly. Life time of water mol­e­cules in the first hydra­tion shell varies from 1 to 3 ps.

An ab ini­tio Mol­e­c­u­lar Dynam­ics Study of the Ini­tial Chem­i­cal Events in CL-20^†

CL-20 or (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane) † O. Isayev, L. Gorb, M. Qasim, J. Leszczyn­ski. J. Phys. Chem. B, 2008, 112, 11005. link.
Please also come to hear me at upcom­ing Spring 2008 ACS National Meet­ing, New Orleans, LA (April 6 – 10, 2008).belongs to the class of high-energy nitramine explo­sives. To improve atom­istic under­stand­ing of the ther­mal decom­po­si­tion in gas phase and bulk CL-20 we per­formed series of ab ini­tio mol­e­c­u­lar dynam­ics simulations.

Unlike other nitramines like RDX/HMX we found only one dis­tinct ini­tial reac­tion chan­nel (homol­y­sis of N-NO₂ bond) dur­ing uni­mol­e­c­u­lar decom­po­si­tion. We did not observe any HONO elim­i­na­tion reac­tion under these cir­cum­stances. Whereas, ring break­ing reac­tion fol­lowed by NO₂ fis­sion. There­fore, in spite lim­ited sam­pling that pro­vide mostly qual­i­ta­tive pic­ture, we pro­posed scheme of uni­mol­e­c­u­lar decom­po­si­tion of CL-20. The aver­aged prod­ucts pop­u­la­tion over all tra­jec­to­ries is esti­mated at 4 HCN, 2 — 4 NO₂, 2 — 4 NO, ~1 CO, and ~1 OH mol­e­cule per one CL-20.

Our sim­u­la­tions pro­videSev­eral ani­ma­tion movies are avail­able:
Uni­mol­e­c­u­lar decom­po­si­tion.
(about 3 min­utes, 37 Mb)
Decom­po­si­tion in crys­tal CL-20.
(about 1 minute, 13 Mb)
First movie has been fea­tured on AHPCRC booth at SC06 expo­si­tion. a detailed descrip­tion of the chem­i­cal processes in the ini­tial stages of ther­mal decom­po­si­tion con­densed CL-20. They allow us to elu­ci­date key fea­tures of such process: com­po­si­tion of pri­mary reac­tion prod­ucts, reac­tion tim­ing, Arrhe­nius behav­ior of the sys­tem, etc. They clearly indi­cate that the pri­mary reac­tions lead­ing to NO₂, NO, N₂O and N₂ occur at very early stages. We also esti­mate acti­va­tion bar­rier for the for­ma­tion of NO₂ which is essen­tially deter­mines over­all decom­po­si­tion kinet­ics and effec­tive rate con­stants for NO₂ and N₂. Cal­cu­lated bulk decom­po­si­tion path­ways cor­re­lates with avail­able con­densed phase exper­i­men­tal data. Unfor­tu­nately, com­par­i­son of the pre­dicted gas phase mech­a­nism is not possible.

Struc­ture of Liq­uid Water from ab ini­tio Mol­e­c­u­lar Dynam­ics at the Com­plete Plane Wave Basis Set Limit

Water the most impor­tant liq­uid on Earth. Due to its crit­i­cal role in many chem­i­cal and bio­log­i­cal processes, a detailed under­stand­ing of the struc­tural and dynam­i­cal prop­er­ties of water is essen­tial. As a result of many exper­i­men­tal and the­o­ret­i­cal stud­ies, a qual­i­ta­tive pic­ture of the local sol­va­tion shell struc­ture and dynam­ics of liq­uid water has emerged.

Unfor­tu­nately, the results obtained from dif­fer­ent ab ini­tio mol­e­c­u­lar dynam­ics (AIMD) stud­ies of liq­uid water do not always agree with each other and often show dis­agree­ment with exper­i­ment. It has been even argued that the lack of agree­ment results from an irre­pro­ducibil­ity of AIMD sim­u­la­tions of liq­uid water at ambi­ent con­di­tion lead­ing to a wide range of struc­tural and dynam­i­cal prop­er­ties.¹1.J. G. Gross­man, E. Schwe­gler, E. W. Draeger, F. Gygi, and G. Galli, J. Chem. Phys. 120 (2004), 300.;
E. Schwe­gler, J. C. Gross­man, F. Gygi, and G. Galli, J. Chem. Phys. 121 (2004), 5400.
2.H.-S. Lee and M. E. Tuck­er­man J. Chem. Phys. 125 (2006), 154507;
H.-S. Lee and M. E. Tuck­er­man J. Chem. Phys. 126 (2007), 164501.

Recently, this issue has been addressed by the another com­pu­ta­tional approach employ­ing a dis­crete vari­able rep­re­sen­ta­tion (DVR) basis set rather than plane wave basis set.² This study showed more accu­rate RDF val­ues com­pared to ear­lier works.

In an effort to access this prob­lem we per­formed series of AIMD very near the com­plete basis set limit. Com­par­i­son with the results obtained with the com­mon setup demon­strates the effects basis set com­plete­ness on the struc­tural and dynamic prop­er­ties of liq­uid water.