theoretical ab initio study of the electric field effects on ...

UDC 53(05)

ISSN 1330-0008 CODEN FIZAE4

FIZIKA A A JOURNAL OF EXPERIMENTAL AND THEORETICAL PHYSICS CLASSICAL PHYSICS ATOMIC AND MOLECULAR PHYSICS CONDENSED MATTER PHYSICS PLASMA PHYSICS TEACHING AND HISTORY OF PHYSICS

Recognized by the European Physical Society

Volume 17

2008

Numbers 1 – 4

Zagreb Complete volume 17

online: http://fizika.hfd.hr

Published by the Croatian Physical Society

Fizika A

Vol. 17 Nos. 1 – 4

January – December 2008

pp. 1 – 178

FIZIKA A (Zagreb)

Printed issue: ISSN 1330-0008

A JOURNAL OF EXPERIMENTAL AND THEORETICAL PHYSICS Published by the Croatian Physical Society Editor: Associate Editors:

K. Ilakovac, Faculty of Science, University of Zagreb ´, Institute of Physics, Zagreb K. Biljakovic ˇ c ˇevic ´, “R. Boˇsković” Institute, Zagreb D. Sok Editorial Board

´ E. Babic University of Zagreb, Zagreb, Croatia

´ S. Bariˇ sic University of Zagreb, Zagreb, Croatia

L. Colombo R. Boˇsković Institute, Zagreb, Croatia

J. R. Cooper IRC in Superconductivity University of Cambridge, Cambridge, United Kingdom

J. Friedel Université Paris Sud, Orsay, France

P. Fulde Max-Planck-Institut f¨ ur Festkörperforschung, Stuttgart, Germany ˇ ´ M. Sunji c University of Zagreb, Zagreb, Croatia

R. Blinc J. Stefan Institute & University of Ljubljana, Ljubljana, Slovenia ˇic ´ A. Dulc R. Boˇsković Institute & University of Zagreb, Zagreb, Croatia C. Rizzuto Interuniv. Consortium for the Physics of Matter, Genova, Italy

Subscription rate per volume of Fizika A (one printed issue per year incl. CDROM): For Croatia: Members of the Croatian Physical Society 50 HRK, institutions 200 HRK; foreign orders $ 60 plus postal charges. Fizika A & B one volume, CD-ROM only, $ 15 plus postal charges. Correspondence and/or calls regarding submission of manuscripts, enquiries, proofs, subscriptions, renewals, address changes and missing or damaged copies address to: Editorial Office, Fizika, Bijeniˇcka 32, HR-10000 Zagreb, Croatia Tel. +385-1-4680055, Fax. +385-1-4480336, E-mail: [email protected] Payments should be made by bank transfer, check or bank money order. Payments in HRK should be made to bank account no. 30102–678–4202 Payments in foreign currency should be made – bank transfer to ZBZ dd SWIFT ZABA HRXX, account no. 25731-32 39 853 (HFD) – checks should be sent to the Editorial Office, the payment to: The Croatian Physical Society, account no. 25731-32 39 853. The journal Fizika A (Zagreb) is financially supported by the Ministry of Science Education and Sports of the Republic of Croatia Fizika A (Zagreb) is available online (URL: http://fizika.hfd.hr) and on CD-ROM. CD-ROM editions of Fizika A (Zagreb) Vol. 6 (1997) and further issues are available. c Croatian Physical Society Copyright

CONTENTS, FIZIKA A, VOLUME 17 (2008) (by subfields) Note: The page numbering of articles is done when articles are ready for publication and placed online on Fizika web pages. In these Contents, the articles are rearranged according to the subfields of physics represented in the journal. Therefore, page numbering is not consecutive.

CLASSICAL PHYSICS T. Ivezić: Lorentz and “apparent” transformations of the electric and magnetic fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1

Chengshi Liu: Action principle for a kind of mechanical system with friction force . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 R. A. El-Nabulsi: Subdiffusion over fractional quantum paths without fractional derivative (LETTER) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 A. Biswas and E. Zerrad: Soliton perturbation theory for the Kawahara equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

ATOMIC AND MOLECULAR PHYSICS Z. Zhang: New exact solutions to the generalized nonlinear Schrödinger equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 S. N. Tiwary, R. Kumar and R. P. K. Ray: Electron impact excitation of autoionizing level in Na (LETTER) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

CONDENSED MATTER PHYSICS A. M. Abou El Soud, B. S. Farag, I. S. Ahmed Farag, S. A. Gad and H. A. Zayed: Crystal structure and optical properties of quaternary systems of Bi-Sb-Te-Se . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 S. Harir, M. Bennai and Y. Boughaleb: Ground state energy of 2D extended Hubbard model for finite size system with an exact diagonalization . . 59 R. Ghazy: Suitable solvent of a new copolymer as a pre-investigation of its static laser scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 A. M. Vora: Lattice dynamics of equiatomic binary alloys . . . . . . . . . . . . . . . . 87 Z. Shaqiri, D. Angelov, E. Vidolova-Angelova: Measurement of the intersystem crossing yield of s4 U within tRNA by time-resolved absorption bleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 S. K. Srivastava and A. Badahur: Surface plasmon satellites in core-level X-ray photoemission spectra of late transition-metal compounds . . . . . 117 Mohanned J. Al-Anber, Zainab S. Abdalla and Afrodet A. Salih: Theoretical ab initio study of the electric field effects on the structure and stability of G:C base pair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

PLASMA PHYSICS L. Settaouti and A. Settaouti: Monte Carlo simulation of radio frequency plasmas in O2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Kh. H. El-Shorbagy: Impurity of dust-acoustic plasma instability due to trapped ions (LETTER) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

TEACHING AND HISTORY OF PHYSICS C. Hunte: The Jones-Mueller transformation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 C. Hunte: A theoretical investigation of light scattering in chiral nematic liquid crystals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 R. Artuković: Motion of two discs joined by strings in S-type connection . . 165

Authors are advised to consult “Instructions for Authors” on Fizika web pages at http://fizika.phy.hr before starting preparations of the manuscript for submission for publication in Fizika A.

CONTENTS, FIZIKA A, VOLUME 17 (2008) (by page numbers) Note: The page numbering of articles is done when articles are ready for publication and placed online on Fizika web pages. In these Contents, the articles are arranged according to the page number. N o 1. T. Ivezić: Lorentz and “apparent” transformations of the electric and magnetic fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 A. M. Abou El Soud, B. S. Farag, I. S. Ahmed Farag, S. A. Gad and H. A. Zayed: Crystal structure and optical properties of quaternary systems of Bi-Sb-Te-Se . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Chengshi Liu: Action principle for a kind of mechanical system with friction force . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 L. Settaouti and A. Settaouti: Monte Carlo simulation of radio frequency plasmas in O2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 C. Hunte: The Jones-Mueller transformation . . . . . . . . . . . . . . . . . . . . . . . . 51 N o 2. S. Harir, M. Bennai and Y. Boughaleb: Ground state energy of 2D extended Hubbard model for finite size system with an exact diagonalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Kh. H. El-Shorbagy: Impurity of dust-acoustic plasma instability due to trapped ions (LETTER) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 R. A. El-Nabulsi: Subdiffusion over fractional quantum paths without fractional derivative (LETTER) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 R. Ghazy: Suitable solvent of a new copolymer as a pre-investigation of its static laser scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 N o 3. A. M. Vora: Lattice dynamics of equiatomic binary alloys . . . . . . . . . . . 87 A. Biswas and E. Zerrad: Soliton perturbation theory for the Kawahara equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103 Z. Shaqiri, D. Angelov, E. Vidolova-Angelova: Measurement of the intersystem crossing yield of s4 U within tRNA by time-resolved absorption bleaching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .109 S. K. Srivastava and A. Badahur: Surface plasmon satellites in corelevel X-ray photoemission spectra of late transition-metal compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 N o 4.

Z. Zhang: New exact solutions to the generalized nonlinear Schrödinger equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125 C. Hunte: A theoretical investigation of light scattering in chiral nematic liquid crystals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 Mohanned J. Al-Anber, Zainab S. Abdalla and Afrodet A. Salih: Theoretical ab initio study of the electric field effects on the structure and stability of G:C base pair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151 S. N. Tiwary, R. Kumar and R. P. K. Ray: Electron impact excitation of autoionizing level in Na (LETTER) . . . . . . . . . . . . . . . . . . . . . . . . . . 159 R. Artuković: Motion of two discs joined by strings in S-type connection 165

INSTRUCTIONS Fizika A is a journal publishing the results of original experimental and theoretical research work in classical physics, atomic and molecular physics, condensed matter physics, plasma physics and teaching and history of physics. Contributions written in English, French, German or Russian are accepted. They should be submitted in duplicate, typed on good quality paper on one side only, with double spacing and wide margins, with original drawings of figures and one further copy of the title and abstract in English if the original is in a different language. The abstract should not exceed 600 letters including all symbols. The front page of each manuscript should include the title of the paper, author’s full name(s), affiliation(s) with full adress(es) and preferably the UDC and PACS classification numbers. To speed up communication, authors are encouraged to provide e-mail adress, FAX and telephone numbers. Unless requested othervise, the e-mail address and/or FAX number will be published with the author’s address. International system of units (SI) should be used whenever possible, particularly in quoting final results and in table and figure inscriptions. The figures should preferably be produced by a laser printer on good-quality white paper or drawn in Indian ink on tracing paper. Figures should be fully lettered. Black and white photographs on glossy paper with high contrast are accepted. Reduction to about 1/3 of the original size is usually used. The lettering in the figures must be large enough to make the final size at least 1.5 mm high. All figures should be numbered consecutively with Arabic numerals in order of appearance in the text, and each should have a descriptive caption. Each table should be numbered sequentially and should have a descriptive caption. References should be numbered consecutively with Arabic numbers in square brackets. In the text the abbreviation et al. should not be used for papers written by two authors. All references should be listed on a separate sheet and should include the names of all authors. (Except for very large collaborations of more than about 10 authors.) The references should be written using the following style: [5] S. Smith and J. K. Jones, Phys. Rev. 295 (1972) 422. Equations should be written carefully and clearly and numbered sequentially on the right-hand side. Special care should be paid to all symbols that can be misread, confused or are ambiguous (e.g. to distinguish between subscripts and superscripts). Please add a note in the margin to avoid such ambiguities or to explain special symbols. The footnotes should be numbered in Arabic superscripts and placed at the bottom of the page in which they appear in the manuscript. When typing the manuscript, authors are strongly advised to consult recent issues of Fizika. A shorter paper, not subdivided into sections, of less than 600 words in length, with a modest number of illustrations and a short abstract, should be submitted as “Letter to the Editor”. For refereeing purposes only, papers including figures may also be sent by FAX. After the paper has been accepted for publication, the author(s) will be advised to send two original copies, including figures, to the Editor for further processing. To speed up the publication, the authors of accepted papers are encouraged to send a source file of their papers in standard LATEX(style “article”) or in plain TEXwithout any author-defined styles and/or macros, and figures in PostScript format. This can be done by electronic mail or on a floppy disc (MS-DOS). Please read “Instructions for Authors” on our home pages. When submitting a paper, the authors should include a covering letter, signed by one of the authors, clearly requesting publication of the paper in the journal Fizika. The submission of the paper will be taken to imply that no copyright will thereby be infringed. There is no page charge for publication of papers and authors are entitled to 30 free reprints. The manuscripts of papers accepted for publication are not returned. Manuscripts for publication and all correspondence should be sent to: The Editor, Fizika, Bijeniˇcka c. 32, HR-10000 Zagreb, CROATIA. FAX +385-1-4680 336 or +385-14680 055, e-mail: [email protected].

SERVICE FOR THE READERS OF THE JOURNALS FIZIKA A & B The contents and abstracts of Fizika A and Fizika B since 1992 (in hypertext) and full articles since 1997 (in ps and pdf formats) are available on the computer network Internet. They can be accessed by using the following URL of our home pages: http://fizika.phy.hr/ or

http://fizika.hfd.hr/

Printed ISSN 1330–0008 Online ISSN 1333–9125 CD ISSN 1333–8390 CODEN FIZAE4

THEORETICAL AB INITIO STUDY OF THE ELECTRIC FIELD EFFECTS ON THE STRUCTURE AND STABILITY OF G:C BASE PAIR MOHANNED J. AL-ANBERa , ZAINAB S. ABDALLAb and AFRODET A. SALIHb a

Physical Department, College of Science, Basrah University, Basrah, Iraq

b

Chemical Department, College of Science, Basrah University, Basrah, Iraq Received 27 May 2008; Accepted 17 December 2008 Online 12 February 2009

The effect of applied external electric field on DNA occurs mostly at high field intensity. The results of a theoretical ab initio study of effects of applied electric field on G:C base pair components are reported. The geometries of the local minima were optimized without the symmetry restrictions by the gradient procedure at density-functional level of the theory and were verified by calculations of the second derivative of energy. The standard CEP-31G basis set was used. The geometrical parameters, relative stability and interaction energies are reported. The electric field mutation could be classified as a multi-point mutation. PACS numbers: 87.15.-v, 87.15.Aa

UDC 539.199, 539.194

Keywords: DFT, DNA, ab initio calculation, electric field effect, mutating

1. Introduction After accurately describing the structure of DNA, Watson and Crick suggested the effects of spontaneous mutations on DNA [1]. DNA can be damaged by many different sorts of mutagens. These include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. The type of DNA damage produced depends on the type of mutagen. For example, UV light mostly damages DNA by producing thymine dimers, which are cross-links between adjacent pyrimidine bases in a DNA strand [2]. On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, as well as double-strand breaks [3]. It has been estimated that in each human cell, about 500 bases suffer oxidation damage per day [4,5]. The most serious damage of these oxidative lesions are the double-strand breaks, as these lesions are difficult to repair and can FIZIKA A (Zagreb) 17 (2008) 4, 151–158

151

al-anber et al.: Theoretical ab initio study of the electric field . . .

produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations [6]. Chemically induced or exogenous methylation occurs as a result of exposure to chemical agents such as nitrosamines, di-methyl sulfate, and 1,3-bis(2-chloroethyl)-1-nitrosourea. Recently, attention has been given to the nitrosamines, which are a principle alkaloids found in tobacco smoke (they make methylation base pairs) [7]. However, partly due to its influence on hydrogen bonding, methylation is the most pro-mutagenic methyl adduct formed and can both silence gene expression and cause point mutations [8]. Epigenetic methylation occurs at the guanine and cytosine of CpG islands in DNA and is regulated by an organism’s methyltransferases and other enzymes. These enzymes interact with DNA by flipping the target base out of the double helix and into its active site [9]. The term base flipping is commonly used to describe the rotation of single base out of the double helix as a result of attractive and repulsive forces imparted by enzyme’s active site constituents. The aim of this theoretical investigation is to use ab initio approaches [10] to characterize the nature of changes in the interaction energy and molecular structure in G:C base pairs under the applied external electric field. To accomplish this, we analyzed the changes in the molecular geometry and the interaction energy components [11].

2. Theoretical approach and computational details Theoretical calculations are used to bridge gaps in the understanding of experimental results. In many cases the results of the experimental methods are unable to accurately describe small components of a complex biochemical. The methods of molecular quantum mechanics can be used to investigate properties beyond the scope of current crystallographic methods. The molecular quantum techniques allow us to study optical, magnetic and electronic properties which are not easily measured experimentally. The molecular quantum mechanics provides the interaction energies that are not provided by the X-ray and NMR experiments. The theoretical methods can be used to further investigate and predict the physical and chemical nature of hydrogen bonding interactions. The predictive power of computational biology for DNA has been confirmed in the recent experimental investigation which concluded that amino groups in cytosine and adenine are non-planar [12]. This was postulated and predicted by the molecular quantum calculations over 10 years ago [13]. Ab initio calculations were performed to study the G:C base pair using the Gaussian 98 program [14]. The geometries for normal (field-off) and electric fieldon G:C base pairs were fully optimized at density-functional-theory (DFT) level with the CEP-31G basis set using the gradient optimization method. The applied DFT method used the B3LYP hybrid functional (a parameterized combination of Becke’s exchange functional, the Lee, Yang and Parr correlation functional and the exact exchange) [15]. 152

FIZIKA A (Zagreb) 17 (2008) 4, 151–158


3. Stability of cytosine, guanine and G:C base pairs The change in optimized total energies (∆Et = Enormal − Efield ), as a function of applied electric field, of guanine, cytosine and G:C base pairs considered in this study are collected in Tables 1, 2 and 3, respectively. Calculations for the guanine and cytosine alone (in gas phase) gave changes in stability of these molecules. The applied electric field in the x direction decreases the guanine stability, while its stability increases for other directions. The applied electric field in the z direction, which is perpendicular to the plane of guanine molecule, shows low effect compared with the y direction. In the case of cytosine base the applied electric field in the x and y directions decrease the stability, while the z direction field show low increases in the cytosine stability. For a weak applied electric field in the x direction, the stability of the G:C base pair decreases, but as the field increases, the stability increases. The applied electric fields in the y and z directions produces a decrease of G:C base pair stability. These two directions showed approximately the same effect. The enzyme of helicase, which is unwinding DNA, is corresponding hard in the operation of separating the double helix of DNA. TABLE 1. The total energies (in Kcal/mol) of guanine at different levels of the electric field in the x, y and z direction, estimated at the B3LYP/CEP-31G level. Electric field (a.u.)

x-direction

y-direction

z-direction

0.0001

–0.10089

0.156969

0.000205

0.0010

–1.05025

1.600899

0.008105

0.0100

–5.24153

19.22036

0.060635

TABLE 2. The total energies (in Kcal/mol) of cytosine at different levels of the electric field in the x, y and z direction, estimated at the B3LYP/CEP-31G level. Electric field (a.u.)

x-direction

y-direction

z-direction

0.0001

–0.12064

–0.14021

8.58E-05

0.0010

–1.18499

–1.43871

0.00879

0.0100

–13.762

–2.73721

0.919663

TABLE 3. The total energies (in Kcal/mol) of G:C base pairs at different levels of the electric field in the x, y and z direction, estimated at the B3LYP/CEP-31G level. Electric field (a.u.)

x-direction

y-direction

z-direction

0.0001

–0.16795

–0.0269

–0.00334

0.0010

1.788492

–0.20783

–0.28902

0.0100

27.27538

–0.38876

–20.1515

FIZIKA A (Zagreb) 17 (2008) 4, 151–158

153


4. Hydrogen bonding energy of G:C base pairs The less computationally expensive B3LYP/CEP-31G method describes hydrogen bonding interactions in G:C base pairing in good agreement with higherlevel MP2 calculations [16]. Normal of G:C base pairs considered in this study are shown in Fig. 1. The hydrogen bonding (HB) energy of normal G:C base pair, E HB = EG:C −[ECytosine +EGuanine ], without electric field, is equal to –34.05268053 Kcal/mol. The hydrogen bonding energies between the G:C base pair as a function of the electric field, are shown in Table 4. It should be noted that, for the applied electric field in the x direction of G:C base pair coincident with axes of hydrogen bonding complexes, they differ significantly from the other two directions

Fig. 1. The optimized normal G:C base pair at the B3LYP/CEP-31G level. TABLE 4. The hydrogen bonding energies (in Kcal/mol) of G:C base pairs at different levels of the electric field in the x, y and z direction, estimated at the B3LYP/CEP-31G level. Electric field (a.u.)

x-direction

y-direction

z-direction

0.0001

–34.1063

–34.009

–34.0491

0.0010

–38.0764

–33.6827

–33.7468

0.0100

–80.3316

–30.6528

–12.9209

with respect to intermolecular bond distances. In the former case, the hydrogen bonding energy increases, while in other two directions, the hydrogen bonding energy decreases. The applied electric field in the z direction, coincident with the normal direction to the plane of the G:C base pair, does not show large effect in 154

FIZIKA A (Zagreb) 17 (2008) 4, 151–158


this direction. The applied electric field in the direction of the hydrogen bond may interfere in the enzyme role in the separation of the DNA sheets, which may lead to errors in the processes of DNA copying. In general, we hypothesize that the genes in the electric field may be silenced, because of the inability of bases to flip out of the double helix into the active site of enzymes due to the stronger hydrogen binding interactions. In an aberrant G:C base pair in an electric field at an O17 atom, the electric field acts on the hydrogen bond causing it to lose its ability to participate in one of its three hydrogen bonds, leaving it susceptible to mis-pairing with bases, which is typical for two hydrogen bonds in thymine. This case may be similar to the methylation effect [16].

5. Geometry analysis of G:C base pairs The changes in the optimized hydrogen bond distances as a function of applied electric field, ∆rHB , are collected in Table 5. The calculations were made for a normal G:C base pair in order to note the electric field effect on the hydrogen bond distances. The calculations of the effect of the electric field (equal to 0.0001 au) in x, y and z directions produce hydrogen bond distances that closely resemble those of normal G: C base pair. For the electric field equal to 0.001 au in x and y directions, the most pro-mutagenic of all fields, differences from normal G:C pairing are found in two ways. First, the change of the hydrogen bond distance between guanine (H25) and cytosine (N6) atoms is 0.164 ˚ A. Second, there is a 0.321 ˚ A extension of the hydrogen bond distance between guanine (O8) and cytosine (H29) atoms, more than in the above case. This indicates an opening of the hydrogen bond at the down site of the pair and TABLE 5. The change in the hydrogen bond distances (˚ A) of G:C base pair under electric field at the B3LYP/CEP-31G level. Electric field (a.u.)

∆r(O17 − H13 )

∆r(H25 − N6 )

∆r(H29 − O8 )

Ex (0.0001)

0.001

0.001

0

Ex (0.001)

0.03

0.164

0.321

Ex (0.01)

–0.227

–0.041

0.24

Ey (0.0001)

0.001

0

0

Ey (0.001)

0.03

0.164

0.321

Ey (0.01)

0.016

–0.0058

–0.0079

Ez (0.0001)

–0.003

0.001

0

Ez (0.001)

–0.0117

–0.0156

–0.0176

Ez (0.01)

–0.227

–0.041

0.24

FIZIKA A (Zagreb) 17 (2008) 4, 151–158

155


the middle site. The electric field effects on the G:C base pair differs from the effect of tobacco smoke, which is doing methylation in the G:C base pair, according to results of G. Forde et al. [16]. Due to the changes in the properties of regions of DAN by methylation, the third hydrogen bonding between the G:C base pair decreases, while with the electric field it does not change. From the geometrical data, it should be noted that the geometrical factors due to all electric field effects differ significantly with respect to the intermolecular bond distances. The effect of the electric field on the hydrogen bond distances is large when the external electric field is applied in the directions coincident with the plane of G:C base pair. Moreover, the applied strong electric field, in the direction that is coincident with the plane of G:C base pair, is significant enough to disrupt two of the three hydrogen bonds in the G:C base pair.

6. Conclusion In summary, the results of our calculations show that the applied electric field on G:C base pairs causes significant changes in the interaction between guanine and cytosine compared to the Watson-Crick hydrogen-bonding pattern. This probably is a result of inductive and steric effects. As a result, the changes in G:C hydrogen bonding energies may increase the energy required for base flipping and it may exceed that what is provided by the enzyme responsible for this process. Our results are summed up by the following: • Based on our data, the effects of high electric field may introduce significant changes in the geometrical parameters of base pairs. In the case ∆rH29−O8 = 0.321 ˚ A, which is known to cause base transitions, it is shown that one of the hydrogen bonds is lost. As a result, DNA polymerase under the high electric field could incorporate a thymine into the daughter strand produced from a guanine. • We have found that changes in the interaction energies in G:C base pairs (with applied electric field) do directly correlate to adduct pro-mutagenicity. • Our data reveal that electrostatic contributions predominate in interactions of all investigated complexes. • The order of stability of guanine, cytosine and G:C base pair is a function of electric field intensity and direction. • The applied high electric field on G:C base pair increases intermolecular bonding energies. • Finally, the electric field may be able to produce the multi-point mutations. References [1] J. Watson and F. Crick, Nature 171 (1953) 737. [2] T. Douki, A. Reynaud-Angelin, J. Cadet and E. Sage, Biochemistry 42 (2003) 9221. [3] J. Cadet, T. Delatour, T. Douki, D. Gasparutto, J. Pouget, J. Ravanat and S. Sauvaigo, Mutat. Res. 424 (1999) 9. 156

FIZIKA A (Zagreb) 17 (2008) 4, 151–158

al-anber et al.: Theoretical ab initio study of the electric field . . . [4] M. Shigenaga, C. Gimeno and B. Ames, Proc. Natl. Acad. Sci. USA 86 (1989) 9697. [5] R. Cathcart, E. Schwiers, R. Saul and B. Ames, Proc Natl. Acad. Sci. USA 81 (1984) 5633. [6] K. Valerie and L. Povirk, Oncogene 22 (2003) 5792. [7] S. Hecht, Chem. Res. Toxicol. 11 (1998) 560. [8] B. Singer and D. Grunberger, Molecular Biology of Mutagens and Carcinogens, Plenum Press, New York (1983). [9] R. Roberts, Cell 82 (1995) 9. [10] J. Sponer, J. Leszczynski and P. Hobza, J. Phys. Chem. 100 (1996) 1965. [11] W. Sokalski, S. Roszak and K. Pecul, Chem. Phys. Lett. 153 (1988) 153. [12] F. Dong and R. Miller Science 298 (2002) 1227. [13] J. Leszczynski, Int. J. Quantum Chem., Quantum Biol. Symp. 19 (1992) 43. [14] M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, N. Rega, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. AlLaham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian 98, Gaussian Inc., Pittsburgh PA, 1998. [15] A. Becke, J. Chem. Phys. 98 (1993) 5648. [16] G. Forde, A. Flood, L. Salter, G. Hill, L. Gorb and J. Leszczynski, J. Bio. Struc. Dynam. 20 (2003) 811.

FIZIKA A (Zagreb) 17 (2008) 4, 151–158

157


ˇ ˇ ˇ TEORIJSKO AB INITIO PROUCAVANJE UCINAKA ELEKTRICNOG – U I STABILNOST BAZNOG PARA G:C POLJA NA GRAD Uˇcinak vanjskog elektriˇcnog polja na DNA javlja se najˇceˇsće za jaka polja. Izvjeˇsćujemo o ishodima prouˇcavanja uˇcinaka vanjskog elektriˇcnog polja na sastavnice baznog para G:C polazeći od osnova teorije. Razmjeˇstaj lokalnih minimuma smo optimizirali bez ograniˇcenja na uvjete simetrije rabeći gradijentan postupak na razini teorije funkcionala gustoće i provjerili raˇcunima drugih derivacija energije. Primijenili smo uobiˇcajen osnovni skup CEP-31G. Izvjeˇsćujemo o promjenama razmaka, stabilnosti i energijama med–udjelovanja. Mutacije elektriˇcnim poljem mogle bi se razvrstati u viˇsemjesne mutacije.

158

FIZIKA A (Zagreb) 17 (2008) 4, 151–158