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*[Thesis Title Pages*]
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039 Computer Studies of Molecular Structure
013 and Function.
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055 Thesis presented for the degree of Doctor of Philosophy
012 :A. Dearing,
017 :Linacre College,
008 :Oxford.
016 :September 1978.
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051 This thesis is dedicated to George, without whom we
042 would have had very little to write about.
006 .tg NI
048 :"Tis pleasant sure, to see one's name in print;
049 :A book's a book, although there's nothing in't."
006 .sp 1c
007 :Byron.
037 :"English Bards and Scotch Reviewers."
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018 C_o_n_t_e_n_t_s_._
006 .ll -7
008 Abstract
007 Preface
006 .in 14
007 .ti -14
060 ChapterZ1ZZ:ZZIntroduction to biological systems of interest
044 and to techniques adopte . . .
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*[Chapter 2.1*]
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057 Chapter 2 : Methods for Calculating Interaction Energies.
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041 :"We use the classical theory on Mondays,
040 :Wednesdays and Fridays, and the quantum
034 :theory on Tuesdays, Thursdays and
012 :Saturdays."
018 :Sir William Bragg
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064 Some of the calculations we shall perform require decisions
071 to be made as to the stability of given structures and conformations of
053 molecular systems. Largely, these involve measuring
064 the energy of the systems, but, because of the assumptions which
061 have to be made in the calculations, great care must be taken
028 in interpreting the results.
071 A complete theoretical determination of the equilibrium properties
053 of a system would require evaluation of free energies
060 associated with the system, taking into account such factors
067 as solvation, other species presen . . .
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*[Chapter 3.1.1*]
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045 Chapter 3 : Studies of DNA Helix Flexibility.
005 .tc :
040 :"So it does?" said Pooh. "It goes in?"
027 :"So it does?" said Piglet.
020 :"And it comes out?"
027 :"Doesn't it?" said Eeyore.
036 :"It goes in and out like anything."
032 :"Winnie-the-Pooh", A.A. Milne.
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057 We have seen that models suggested for intercalation
048 and for processes leading to frameshift mutation
063 involve changes in the structure of the nucleic acid molecules.
074 In this chapter, we study how physical and chemical constraints limit what
052 structural changes can occur in the DNA double helix
036 in order to determine how reasonable
038 these models for the interactions are.
072 Let us look first of all at structural changes occurring in nucleic
074 acids during intercalation. We have seen in chapter 1 that intercalation . . .
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*[Chapter 4.1.1*]
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106 C_h_a_p_t_e_r_ _4_ _:_ _U_s_e_ _o_f_ _I_n_t_e_r_a_c_t_i_v_e_ _G_r_a_p_h_i_c_s_ _f_o_r_ _E_x_p_l_o_r_i_n_g_
006 .sp 1c
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038 C_o_m_p_l_e_x_ _S_t_r_u_c_t_u_r_e_s_._
005 .tc :
027 :"One picture is worth more
024 :than a thousand words."
005 :Anon
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069 Theoretical studies in chemistry are of little value, unless the
073 problems requiring solution can be formulated in a reasonable manner, and
066 unless the results obtained can be presented in some way which can
063 easily be understood. When the problem is to study properties
074 associated with the structure of a macromolecule, as it is in this thesis,
067 it is generally helpful to use some form of visual model to present
047 results, and in fact such a model can be useful
021 throughout the study.
061 Mechanical models have been used in this wa . . .
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*[Chapter 5.1*]
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059 Chapter 5 : Refinement of Approximate Molecular Structures.
005 .tc :
030 :"You've never had it so good"
010 :Macmillan
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050 Basic thermodynamics shows that the degree to
063 which a given reaction will progress depends on the free energy
059 change in that reaction; the more negative the free energy
060 change, the more that reaction will tend to completion. In
060 terms of the structure of a molecular complex, the lower the
060 free energy of a given configuration, the more probable that
061 configuration is. For reasons discussed in chapter 2, it is
072 assumed that the internal energy of the complex *Iin vacuo *Nis the most
059 important term in producing this free energy and that other
050 terms, whilst perhaps not paralleling the internal
047 energy, do not outweigh it. Likely structures
064 for a complex therefore correspond to low energy configurati . . .
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*[Chapter 6.1*]
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059 Chapter 6 : Other Factors Affecting Molecular Interactions.
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027 :"Non omnia possumus omnes"
018 :Virgil, Eclogues.
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065 In this chapter, we shall discuss certain limitations of the
060 methods used to study intercalation. The chapter is brief,
060 even though the points not considered far outnumber the ones
060 we did consider, because it is merely intended to illustrate
019 these shortcomings.
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016 6.1 : Solvation.
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066 The major criticism of the methods of conformational analysis
059 used must be that they ignore completely the effects of the
070 environment. This environment includes not only the solvent (water),
070 but also salt ions, and the influence that these have on intercalation
069 is demonstrated clearly by the variation in the degree of interaction
067 with ionic strength*S1*N. Also, the va . . .
