Ab initio quantum mechanical calculations of the physical properties of metallized DNA fragments

16.06.2012
 
Fresh issue

 

Ab initio quantum mechanical calculations of the physical properties of metallized DNA fragments


Organization of the Executive:
Department of Molecular Biophysics, ILTPE - B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine

Leader:
Rubin, Yu., D.Sc., senior research fellow ILTPE
e-mail: rubin@ilt.kharkov.ua


Performed by:
Rubin, Yu. - D.Sc., Senior Research Fellow ILTPE
Belous L. -  Ph.D., head of grid-technology departament of  ILTPE

Virtual organization of the projectCompuChemGridUA


Duration of the project: 2010 – 2012

The aim of the project
Elucidation of the features of the physical properties of metallized DNA by nickel ions in comparison with DNA containing zinc ions.

State of the problem
In recent years, the attention was attracted of many metallized DNA (M-DNA)researchers. In the metallized DNA in a slightly alkaline environment of transition metal ions are  built-in between the bases of nucleic acids instead of iminoproton, forming one-dimensional chain. X-ray data on this structure are absent. Such DNA conducts electric current and is  interesting to nanotechnology as nanowires and biosensors.


Scientific novelty of the premise and execution
Earlier experiments have shown that a number of physico-chemical properties of Ni-DNA (stability, the conditions of formation, etc.) differ from the physico-chemical properties of Zn-DNA. Theoretically predicted that the mechanisms of conduction of electrical current for the Ni-DNA and the Zn-DNA are different. It is of interest to determine the causes of these differences, in particular, with the help of molecular modeling, electronic structure, energy characteristics of the fragments of the M-DNAs with these metal ions. Under the fragments we understand base pair stacking dimers and trimers of nucleic acid base pairs with built-in nickel and zinc ions between the bases. To model the physical properties of M-DNA fragments using quantum mechanical density functional methods (such as M05 and M06 functionals), the methods of Muller-Pleset (MP2, MP3) and methods of coupling clusters (CCSD). Calculations performed with the help of software packages NWChem, Gaussian via using of the VO  CompuChemGridUA resources and BITP NASU, ICYB NASU clusters.


Expected Results
With the help of DFT methods and MP2 calculations are carried out of the spatial structure, of the electronic structure (shape and energy of HOMO and LUMO, the energy of electronically excited states), the energies of interactions in base pairs, stacking dimer and trimer of base pairs of nucleic acids with nickel ions. These characteristics will be compared with our previous calculations of similar physical characteristics of the M-DNA with zinc ions.


Illustrations of the calculations


 

A
B
C

 

Fig. A. Optimized molecular structures of M-DNA fragments with zinc ions: A-stacking dimer, B- stacking trimer, C- stacking tetramer.




Draw_2_a.png
A B

 

Fig. 2. HOMO’s of stacking dimer with two zinc ions (A) and stacking trimer with three zinc ions (B).

 

Publications

  1. Yury V. Rubin, Leonid F. Belous and Аnatolij А. Yakuba, Electronic and molecular structure of M-DNA fragments // J Mol Mod., (2011) 17:997–1006 read here
  2. Рубин Ю.В.,  Белоус Л.Ф. Aв  initio  расчеты молекулярной структуры фрагментов нуклеиновых кислот .// Материалы 7 Международной  конференции “Актуальные вопросы биологической физики и химии”  Севастополь, апрель 2011, Изд Сев НТУ с 175-177
  3. Yury.V. Rubin,  Leonid F. Belous Ab initio Modeling of Molecular Structure and Inside Interactions in Nucleic Acid Fragments Abstracts of International Symposium МACC-4 Lviv ,28-June-2 July,  2011
  4. Рубин Ю.В., Белоус Л.Ф., Якуба А.А.Головинский А.Л. Савин Ю.В.  Компьютерное моделирование электронной и молекулярнаой структуры фрагментов металлизированной ДНК : стекинг димеров и тримеров//Труды междунар конф «Параллельные вычислительные технологии» изд.ЮУГУ Челябинск, 2009, с 667-672, электронная версия  http://agora.guru.ru/pavt 

C целью изучения молекулярной структуры металлизированной ДНК (М-ДНК) и механизмов проводимости в ней, нами проведен квантово-механический ab initio расчет электронной и пространственной структуры, термодинамических характеристик стекинг димера и тримера пар оснований нуклеиновых кислот c ионами цинка (AT)(CG) 2Zn2+ и (CG)(AT)(CG)3Zn2+, а также димера и тримера этих пар оснований (АТ)(CG) и (CG)(АТ)(CG) без иона цинка. Такая М-ДНК, с расположенными между основаниями ионами переходных металлов, способна проводить электрический ток и представляет большой интерес для нанотехнологий. Расчет выполнялся с помощью метода МР2 и пакета Gamess на кластере СКИТ-3 Института Кибернетики им. В.М. Глушкова НАН Украины (Rpeak=7.4 Tflops).


      5.      Rubin Yu.V., Belous L.F., Yakuba A.A. Modeling  of electronic and molecular structures of M-DNA fragments: from monomer to  stacking oligomers //Abstracts of 3 International Simposium MACC-3,  Odessa, 29 of June-3 July, 2009read here

 

Metallized DNA (M-DNA) with transition metal ions placed between nucleic bases has the conductance ability and this is the fact of great interest for nanotechnology To study the molecular structure of M-DNA and conductance mechanisms in it the quantum-chemistry calculations were performed to obtain electronic and spatial structures, thermodynamic characteristics of stacking dimers, trimers and tetramers of nucleic acids base pairs, both with n zinc ions (n=2,3,4) together with hydroxyls and without such ions. The calculations of these properties of GC pairs with Mg2+, Ni2+ ,Cd2+ and hydroxyl were carried out too. Geometry optimisations of oligomers studied were performed at MP2 level of theory and by using M06 functional, being employed     6-31G* basis sets. The interaction energies were calculated at the usual scheme with including BSSE by using 6-31+G* basis sets.
Calculations performed at MP2 level of theory demonstrated that stacking oligomers of nucleic acid bases with zinc ions have bridges between base pairs. The inter-plane distance in the dimers, in trimers and in tetramers is equal to 3.2Å. The highest occupied molecular orbitals (НОМО) in dimer and trimer of base pairs with zinc ions include MOs of bases being adjacent in the stack .
The interaction energies between base pairs in stacking dimer without zinc ions (AT)(CG) and in stacking dimer with zinc ions (AT)(CG)·2Zn2+ are of 11.0 kcal/mol and 37.4 kcal/mol respectively. H-bond interaction energies in oligomers studied were calculated too.
Middle base pairs in stacking trimers and tetramer studied are more planar in comparison with outer pairs.


     6.Рубин Ю.В., Белоус Л.Ф., Якуба А.А. Молекулярная и электронная  структуры фрагмента металлизированной  ДНК - пары аденин-тимин с ионом  цинка. //'Доповiдi НАН Украiни' 2008, 5, с.186-191 читать

 

To study physical properties of fragments of metallic DNA (M-DNA), molecular and electronic structures and thermodynamic characteristics of the adenine-thymine pair with a Zn structures and thermodynamic characteristics of the adenine-thymine pair with a Zn2+ 2 + ion (the ion (the ion was placed between nucleic acid bases) and of components forming this pair are calculated ion was placed between nucleic acid bases) and of components forming this pair are calculated at the МР2/6–31 +G* level of theory. at the МР2/6-31 + G * level of theory. As well, the calculations were performed for adeni- As well, the calculations were performed for adenine-thymine-Zn ne-thymine-Zn 2+ 2 + -hydroxyl. -Hydroxyl. It was revealed that the following bond lengths changed in investi- It was revealed that the following bond lengths changed in investigated complexes: on the N3-C2-N1-C6-N10 fragment in the adenine, on С2-N3-C4-C5-C6-N1 gated complexes: on the N3-C2-N1-C6-N10 fragment in the adenine, on С2-N3-C4-C5-C6-N1 fragment on the pyrimidine ring, and on C4-O8 in thymine, in comparison with neutral mo- fragment on the pyrimidine ring, and on C4-O8 in thymine, in comparison with neutral molecules. lecules. Charges on atoms changed at the same fragments. Charges on atoms changed at the same fragments. In the complexes calculated, the In the complexes calculated, the interaction energies of base pairs with Zn interaction energies of base pairs with Zn 2+ 2 + are significantly higher than that of imino-proton are significantly higher than that of imino-proton with the AT pair or that of Zn with the AT pair or that of Zn2+2+ with its hydrate shell (6 water molecules). with its hydrate shell (6 water molecules). The HOMO and The HOMO and LUMO analyses of the ATZn LUMO analyses of the ATZn++ triple complex and the AT pair showed the increase of sizes of triple complex and the AT pair showed the increase of sizes of the triple complex LUMO, which points to a possibility of the electron delocalization over the the triple complex LUMO, which points to a possibility of the electron delocalization over the whole complex.


      7. Rubin Yu.V., Belous L.F., Yakuba A.A. Molecular and Electronic Structure of  M-DNA Fragments.  In book abstracts “NATO Advanced Research Workshop ‘Molecular Self-Organisation…” Kyiv, June, 2008 

     8.  Rubin Yu.V., Belous L.F., Yakuba A.A. Physico-Chemical Properties of M-DNA Fragments  In Boook of Abstracts on International Symposium SNCTA-08 Kharkov, August 2008  read here

 

To study M-DNA physico-chemical prpoperties (such DNA with transition metal ions placed between the nucleic bases is capable to conduct an electric current) and its conductivity mechanisms we carried out ab initio quantum-mechanical calculations of electronic and spatial structure, thermodynamic characteristics, electronic transition energies of Adenine-Thymine (АТ) and Guanine-Cytosine (GC) base pair complexes with Zn2+and Ni2+, ATZnOH(2H2O) and GCZnOH(2H2O)clusters, (GC)(AT) and (CG)(AT) stacking dimers with 2Zn2+ , two hydroxyls and two water molecules.. The calculations were performed at MP2 level of theory using 6-31+G* and 6-31G* basis sets.
The interaction energy of Zn2+ in a triple complex with adenine and thymine is considerably higher, than one of imino-proton in АТ pair. Orbitals of Ni ion take part in forming HOMO and LUMO of AT and GC pairs with Ni2+ complexes.LUMO of triple ATZn+ complex includes adenine, thymine and Zn ion orbitals, that specifies electron delocalization within the complex in the excited state. The calculations of electronic transition energies has shown the decrease of the first singlet transition energies in complexes of АТ and GC pairs with Ni ion from 4.5 ev to 0.5 - 0.6 ev, that is the precondition of significant narrowing the band gap in M-DNA.
Calculations of (AT)(GC) and (AT)(CG) stacking dimers with 2Zn ions, two hydroxyls and two water molecules shown that Zn ions repulsion doesn’t occur as a results of a significant decrease of positive charges on Zn ions and existence of hydroxyl bridging. between Zn ions. in these dimers. Molecular structure of nucleic bases in stacking dimers are similar to ones of nucleic bases in ATZnOH (2H2O) and GCZnOH(2H2O) clusters. Zn ions creates 4 bonds (with N1 of purines , with N3 of pyrimidines and with hydroxyls and water molecules) in stacking dimers..Interaction energy between ATZnOH (H2O) and CGZnOH(H2O) is equal to 37.0 kcal/mol in (AT)(CG) stacking dimer. The first excited state energy is equal to 3.28ev (0.0026). in this dimer.


      9.  Rubin Yu. V.*, Belous L.F.*, Yakuba A.A**Ab initio Post-Hartree-Fock Study of M-DNA Fragments: molecular and Electronic Structure of AT and GC pairs with Zn 2+  //Book of Abstacts  2 Int Symposium ‘ Methods and Applications of Computational Chemistry’ Kyiv, July 2007, p.61 read here

 

To study physical properties of fragments of metallic DNA (M-DNA),  olecular and electronic structures and thermodynamic characteristics of adenine-thymine and guanine cytosine pairs with Zn2+ ion (the ion was placed between nucleic acid bases) and of components forming these pairs were calculated at МР2/6-31+G* level of theory. As well, calculations were performed for adenine-thymine-Zn2+-hydroxyl and guanine-cytosine-Zn2+ hydroxyl complexes. It was revealed that bond lengths changed in three- and four-member complexes: on the fragment close by the site of interaction with Zn2+ (N3-C2-N1-C6-N10 fragment) in adenine, on С2-N3-C4-C5-C6-N1 fragment on the pyrimidine ring and on C6 O10 in guanine, in comparison with neutral molecules. Charges on atoms changed at the same fragments. In the complexes calculated the interaction energies of base pairs of with Zn2+ are significantly higher than that of iminoproton with AT and GC pairs or that of Zn2+ with its hydrate shell (6 water molecules). HOMO and LUMO analysis of the ATZn+ triple complex and AT pair showed the increase of sizes of triple complex LUMO, which points to a possibility of electron delocalization over the whole complex. A mechanism of electric current in M-DNA is discussed.


    10. Белоус Л.Ф., Гречнев Г.Е., Рубин Ю.В., Степанян С.Г. Нанотехнологии и компьютерное моделирование //  Труды Всерос. Научн. Конф. “Научный сервис в сети Интернет: технологии параллельного программирования” – Москва: Изд МГУ -2006 - с.5-8