Helix-coil transition of Poly(L-glutamic acid) in N-methylacetamide

The folding of randomly coiled poly(L -glutamic acid) to the helical state has been studied in N-methylacetamide by titration methods. Since this solvent would be expected to form amide-peptide group hydrogen bonds with the unfolded form of the polymer, to a first approximation no helix stabilization could come from intrapolymer hydrogen bonds. The titration data, collected from 30 to 70°C yield the following values per residue for the thermodynamic parameters governing the coil-helix reaction for the uncharged polymer: ΔG_30°C°, ?1. 9 ± 0.1 kcal; Δ H°, 0 ± 0.1 kcal; ΔS_30°C°, 6.3 ± 0.6 eu. In N-methyl acetamide, the helix is an order of magnitude more stable than in water, and this stabilization appears to be entirely the result of the entropy gained by solvent molecules which are released from the polymer upon folding.     

Nucleic acid-solvent interactions: temperature dependence of the heat of solution of thymine in water and ethanol

The heats of solution of thymine in water and ethanol have been determined calorimetrically as a function of temperature. These data, along with solubility data, have been used to calculate the thermodynamic quantities (ΔG_t, ΔH_t, ΔS_t and ΔC_p,t) associated with the transfer of thymine from ethanol to water. Since ΔS_t = ?2 cal/mole deg and ΔC_p,t = 0, it has been concluded that hydrophobic bonding does not play an important role in the thermocynamic stability of nucleic acids. However, large heat capacities of solution of thymine are observed in both solvents (ΔC°_p2 = 45 ± 4 cal/mole deg). This is explained in terms of temperature variation in the degree of solvent–solute hydrogen bonding. It is our proposal that the components of macromolecules (i.e., nucleic acid bases and amino acids) do not make all possible hydrogen bonds with the solvent in the vicinity of room temperature. Thus the thermodynamic contribution of hydrogen bonding to the stability of macromolecules in aqueous solution must be reassessed.     

Correlation of Tm and sequence of DNA duplexes with delta H computed by an improved empirical potential method

T_m values for 20 DNA duplexes with different repeating base sequences provided the data base for developing a rational and relatively simple methodology for computing apparent enthalpies for the helix → coil transitions of DNA helices, ΔH _calc. The computational variables and their range of acceptable values were selected on the basis of physically plausible arguments. Over 350,000 different combinations of the variables were tested for degree of fit. It was therby possible to find a combination giving a high degree of linear fit between T_m and ΔH _calc (correlation coefficient, 0.99), with T_m values deviating (on average) from the regression line by only ±2.17°C. Most of this uncertainty is attributed to experimental limitations, although computational approximations also contribute. With ΔH _calc for the melting of each of the unique complementary dinucleotide fragments computed by the method developed, it is possible to estimate T_m and (relative) ΔH _calc reliable for the melting of any particular DNA [with base pairs G(I)·C and A·T] given only its base sequence. The ΔH_calc values for the complementary dinucleotide fragments, together with statistical considerations, make it apparent that T_m of DNAs with repeating base sequence show only an approximate linear dependence on G·C content because A·T and G·G pairs do not contribute to helix stability independently of the base-pair sequence in which they occur. In fact, the nearestneighbor stacking interactions are so significant that certain complementary dinucleotide fragment sequences with 0,50, and 100% G·C content have the same stability.     

Three-stranded helix-coil equilibrium in polyuridylic acid-adenosine complex

Interaction of poly U (polyuridylic acid) and adenosine is studied by following the changes in ultraviolet absorbance in the wavelength region near the isochromic wave-length for the complex formation. The interaction is studied as a function of temperature, concentration of adenosine, and ionic strength, while the concentration of poly U was held constant. It is confirmed that only the three-stranded complex with the stoichiometry 1A to 2U is formed and that it dissociates directly into free poly U and adenosine. No discontinuity of any kind was apparent in the melting curves, and poly U was found to possess no ordered structure above 10°C under the conditions used. The results were, therefore, analyzed in terms of an exact helix–coil equilibrium theory using the mismatching model, i.e., assuming that either completely formed base triplet or completely free unbonded bases only exist, and that the two sections of the polymer chains forming closed loops need not contain the same number of unbonded bases. Self-association of free adenosine was taken into consideration. (Base triplet is analog of base pair for a three-stranded helical complex. It refers to a unit of three coplanar bases, in this case two uracils and one adenine, hydrogen bonded to one another to form a triplet. Such triplets may stack over one another along the helical axis, and when they are so stacked the bases of two triplets next to each other may have stacking interactions between them.) The values for enthalpy and entropy changes, both per mole of base triplets, were obtained for the following processes at neutral pH and moderate to high salt concentrations. (1) Growfh: Binding of one adenosine molecule to two uracil residues (one from each poly U strand) to form a base triplet next to an already formed base triplet with which it has stacking interactions, a process that involves both hydrogen bonding and base stacking interactions, ΔH_s, = ?19 ± 2 kcal, ΔS_s = ?55 ± 6 clausius; (2) Initiation: Binding of one adenosine molecule to two uracil residues (one from each poly U strand) to form an isolated base triplet, a process that involves only hydrogen bonding interactions, ΔH_b* = 4.5 ± 2 kcal, ΔS_b* = 6.6 ± 3 clausius; and (3)Interruption: Unstacking of two stacked base triplets initially next to each other by formation of an interruption (viz. a closed loop) between them, a process that involves only base stacking interactions, ΔH_b = 23.5 ± 3 kcal, ΔS_b = 61.6 ± 7 clausius, where the entropy changes include contributions other than the configurational entropy of closed loops. The discrepancy between our results and the calorimetric ΔH_s of ?13 kcal is attributed to (i) the possible effects of salt arid polymer on the self-association of free adenosine, (ii) the uncertainty in the value of the parameter for the probability of ring closure, and (iii) the contributions due to the partial molal enthalpy of the solvent and the unstacking of any poly U structure to the calorimetric enthalpy.     

Conformational studies of poly-L-alanine in water

The conformational properties of poly-L -alanine have been examined in aqueous solutions in order to investigate the influence of hydrophobic interactions on the helix–random coil transition. Since water is a poor solvent for poly-L -alanine, water-soluble copolymers of the type (D , L -lysine)_m–(L alanine)_n-(D , L -lysine)_m, having 10, 160, 450, and 1000 alanyl residues, respectively, in the central block, were synthezised. The optical rotatory dispersion of the samples was investigated in the range 190–500 mμ, and the rotation at 231 mμ was related to the α-helix content, θ_H, of the alanine section. In salt-free solutions, at neutral pH, the three large polymers show high θ_H values, which are greatly reduced when the temperature is increased from 5 to 80°C. No helicity was observed for the small (n = 10) polymer. By applying the Lifson-Roig theory, the following parameters were obtained for the transition of a residue from a coil to a helical state: ν = 0.012; ΔH = ?190 ± 40 cal./mole; ΔS = ?0.55 ± 0.12 e.u. Since ΔH and ΔS differ from the values expected for a process involving only the formation of a hydrogen bond, and in a manner predicted by theories for the influence of hydrophobic bonding on helix stability, it is concluded that a hydrophobic interaction is also involved. In the presence of salt (0.2M NaCl), or when the ε-amino groups of the lysyl residues are not protonated (pH = 12), the helical form of the two large polymers (n = 450 and n = 1000) is more stable than in water. Since the electrostatic repulsion between the lysine end blocks is greatly reduced under these conditions, the alanine helical sections fold back on themselves, and this conformation is stabilized by interchain hydrophobia bonds. This structure was predicted by the theory for the equilibrium between such interacting helices, non-interacting helices, and the random coil.     

X-Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl-(Aib-Pro)4methyl ester. Evidence for a novel helical structure

The synthesis of the octapeptide, benzyloxycarbonyl-(α-aminoisobutyryl-L-prolyl)₄-methyl ester [Z-(Aib-Pro)₄-OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen–deuterium exchange. ¹³C studies are consistent with a structure involving only trans Aib-Pro bonds, while ir experiments support a hydrogen-bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 3₁₀ helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III β-turns with Aib and Pro at the corners and stabilized by 4 → 1 intramolecular hydrogen bonds.     

Solution properties of synthetic polypeptides. XII. Enthalpy changes accompanying helix-coil transition of polypeptide

For helix-coil transitions of polypeptide in binary mixtures consisting of helix-forming solvent and coil solvent, the transition enthalpy ΔH(T,x) has been found to depend significantly on temperature (T) and solvent composition (x). For such systems, calorimetric measurements may yield some averages of ΔH(T,x) which are no longer amenable to direct comparison with ΔH itself. Theoretical equations relating calorimetric data to ΔH(T,x) are derived and tested favorably with experimental data. It is demonstrated that the transition enthaply from heat capacity measurements is approximately equal to ΔH_cfm, while those from heat of dilution and heat of solution measurements are equal to ΔH_c. Here ΔH_c denotes the value of ΔH at the transition point and f_m represents the maximum helical content attained in a thermally induced transition. The discrepancies among calorimetric data are also discussed.     

Solvent isotope effect on the differences in structure and stability between normal and deuterated proteins

Differential scanning microcalorimetry was used to investigate the enthalpy (ΔH_d) and the temperature (t_d) of thermal denaturation of normal (nondeuterated) (H-PC) and deuterated (D-PC) phycocyanins in D₂O solvent. Values of t_d in D-PC are about 5–7°C lower than those in H-PC. The magnitudes of ΔH_d in D-PC are only 21–32% of those in H-PC. During the protein unfolding, the heat-capacity changes (ΔC_p) in D-PC are also lower than those in H-PC. CD was employed to evaluate the secondary structure and the urea denaturation of these proteins in D₂O solvent. These proteins have about the same α-helix content. D-PC is less resistant to the denaturant urea than is H-PC. In general, the apparent free-energy change in the process of protein unfolding at zero denaturant concentration is higher in H-PC than in D-PC. Comparisons of the present results for D₂O solvent with those previously reported for H₂O reveal that solvent isotope effect essentially does not change the α-helix content in H-PC and D-PC. However, D-PC or H-PC has a higher random-coil content in its secondary structure in D₂O than in H₂O. Substitution of H₂O with D₂O as the solvent increases t_d in both D-PC and H-PC, lowers ΔH_d in H-PC, and greatly lowers ΔH_d in D-PC. The deuterium solvent isotope effect does not change ΔC_p in H-PC but lowers ΔC_p in D-PC. In the urea denaturation, the magnitudes of (C_u)_1/2 in H-PC and D-PC are not affected by such a solvent effect, whereas those of ΔG are greatly increased. These results are correlated with the structure and stability of the proteins.     

Synthesis and conformational study of peptides possessing helically arranged ΔZPhe side chains

Z-Dehydrophenylalanine (Δ^zPhe) possessing four oligopeptides, Boc-(L -Ala-Δ^zPhe-Aib)_n-OCH₃ (n = 1–4: Boc, t-butoxycarbonyl; Aib, α-aminoisobutyric acid), were synthesized, and their solution conformations were investigated by ¹H-nmr, ir, uv, and CD spectroscopy and theoretical CD calculation. ¹H-nmr (the solvent accessibility of NH groups) and ir studies indicated that all the NH groups except for those belonging to the N-terminal L -Ala-Δ^zPhe moiety participate in intramolecular hydrogen bonding in chloroform. This suggests that the peptides n = 2–4 have a 4 → 1 hydrogen-bonding pattern characteristic of 3₁₀-helical structures. The uv spectra of all these peptides recorded in chloroform and in trimethyl phosphate showed an intense maximum around 276 nm assigned to the Δ^zPhe chromophores. The corresponding CD spectra of the peptides n = 2–4 showed exciton couplets with a negative peak at longer wavelengths, whereas that of the peptide n = 1 showed only weak signals. Theoretical CD spectra were calculated for the peptides n = 2–4 of several helical conformations, on the basis of exciton chirality method. This calculation indicated that the three peptides form a helical conformation deviating from the perfect 3₁₀-helix that contains three residues per turn, and that their side chains of Δ^z Phe residues are arranged regularly along the helix. The center-to-center distance between the nearest phenyl pair(s) was estimated to be ～ 5.5 Å. The chemical shifts of the Δ^zPhe side-chain protons (H^β and aromatic H) for the peptides n = 2–4 indicated anisotropic shielding effect of neighboring phenyl group(s); the effect also supports a regular arrangement of the Δ^z Phe side chains along the helical axis. © 1993 John Wiley & Sons, Inc.     

Thermodynamics of the helix-coil transition in polypeptides in mixed organic solvents: the influence of inert solvent and side chain

The thermally induced coil–helix transition of poly(γ-benzyl-L -glutamate) (PBLG) and poly(γ-methyl-L -glutamate) (PMLG) in binary solvent mixtures was investigated by calorimetric and optical rotatory dispersion (ORD) measurements. Dichloroacetic acid was the common active solvent, and the inert solvent was one of the chlorinated hydrocarbons, such as chloroform, 1,3-dichloropropane, 1-chlorobutane, or 1-chlorooctane. The thermodynamic parameters characterizing the intramolecular polypeptide and polypeptide–solvent interactions were calculated using the Karasz and Gajnos theoretical model [(1973) J. Phys. Chem. 77 , 1139–1145]. It was found that the enthalpy (ΔH₁) and entropy (ΔS₁) of helix stabilization in the absence of the active solvent depend on the inert solvent, but only in the case of PBLG. This is explained by the additional helix stabilization achieved by the stacking of the benzyl groups. The stacking is more pronounced in less polar chlorinated hydrocarbons with longer aliphatic chains. The results obtained indicate that the maximum helix stability is reached in chlorinated hydrocarbons with 12 C atoms. In the case PMLG, with an aliphatic ester side group, ΔH₁ and ΔS₁ are independent of the inert solvent. The ORD measurements were used to determine the maximum fraction of helicity attained at constant solvent composition and the transition temperature, T_c, at the point where f_H = 0.5. It was found that, for the same solvent composition, T_c was higher than the temperature of the midpoint of the calorimetric peak. This is explained by the fact that the maximum fraction of helicity is less than unity. The finite transition width was taken into account by calculating the phase boundaries for different fractions of helicity using the value of σ estimated from the calorimetric and van't Hoff enthalpies in the usual manner.     

f-Element/crown ether complexes. 16. Synthesis,crystallization and crystal structure of [Dy(OH2)8]Cl3·18-crown-6·4H2O

When crystals of [Dy(OH₂)₇(OHMe)] [DyCl(OH₂)₂(18- crown-6)]₂Cl₇·2H₂O [1] are allowed to warm from 5 °C to ambient temperature (22 °C) under the original solvent mixture (1:3 CH₃OH: CH₃CN), they redissolve and the title complex can be isolated by slow evaporation of the resulting solution. The crystal structure of this complex, [Dy(OH₂)₈]Cl₃·18-crown-₆·4H₂O, has been determined. It crystallizes in the monoclinic space group, P2₁/c, with a = 10.395(1), b = 18.684(1), c = 16.259- (3) Å, β= 102.56(1)°, and D_calc = 1.61 g cm⁻³ for Z = 4. A final conventional R value of 0.041 was obtained by least-squares refinement using 3453 independent observed [F_o⩾5σ(F_o)] reflections. The [Dy(OH₂)₈]³⁺ cations and crown ether molecules are hydrogen bonded in a polymeric chain with the crown molecules separating the cations and a total of seven DyOH₂···O(crown ether) hydrogen bonds. The chains are connected by a hydrogen bonding network consisting of the cations, chloride ions, and uncoordinated water molecules. The geometry of the cation is best described as a bicapped trigonal prism with distortions on the reaction pathway toward dodecahedral symmetry. The two capping atoms average 2.41(1) Å from Dy, the remaining DyO distances average 2.38(2) Å. The 18-crown-6 molecule has the D_3d conformation normally observed except for a distortion of one OCCO unit containing the oxygen atom accepting two hydrogen bonds.     

Theoretical study of the triangular bonding complex formed by carbon tetrabromide, a halide, and a solvent molecule in the gas phase

MP2(full)/aug-cc-pVDZ(-PP) computations predict that new triangular bonding complexes (where X^? is a halide and H–C refers to a protic solvent molecule) consist of one halogen bond and two hydrogen bonds in the gas phase. Carbon tetrabromide acts as the donor in the halogen bond, while it acts as an acceptor in the hydrogen bond. The halide (which commonly acts as an acceptor) can interact with both carbon tetrabromide and solvent molecule (CH₃CN, CH₂Cl₂, CHCl₃) to form a halogen bond and a hydrogen bond, respectively. The strength of the halogen bond obeys the order CBr₄???Cl^? > CBr₄???Br^? > CBr₄???I^?. For the hydrogen bonds formed between various halides and the same solvent molecule, the strength of the hydrogen bond obeys the order C-H???Cl^? > C-H???Br^? > C-H???I^?. For the hydrogen bonds formed between the same halide and various solvent molecules, the interaction strength is proportional to the acidity of the hydrogen in the solvent molecule. The diminutive effect is present between the hydrogen bonds and the halogen bond in chlorine and bromine triangular bonding complexes. Complexes containing iodide ion show weak cooperative effects.

Metal complexes of cyclic diamines,dissociation kinetics of bis(1,5-diazacyclo-octane)nickel(II) in acidic and basic solution,and electrochemical studies

The preparation of the planar yellow [Ni([8]aneN₂)₂](ClO₄)₂ is described. The complex dissociates in basic solution, with rate = k_OH[NiL][OH^?] (L = 1,5-diazacyclo-octane). At 25 °C, k_OH = 4.5 x 10^?2 M^?1 s^?1 and the corresponding activation parameters are ΔH^≠ = 69.2 kJ mol^?1 and ΔS₂₉₈^≠ = ?38.6 J K^?1 mol^?1. Acid catalysed dissociation in quite slow even in strongly acidic solutions. The kinetic data in this case can be fitted to the expression K_obs = k_o + K_H[H⁺], where k_o relates to a solvolytic pathway and k_H to the acid catalysed pathway. At 60 °C, K_o = 2 x 10^?5 s^?1 and k_H is 2 x 10^?5 M^?1 s^?1. Possible mechanisms for these reactions are considered.The Ni(II)/Ni(III) redox couple for NiLⁿ⁺ is irreversible on Pt using MeCN as solvent.     

Experimental theromodynamics of the helix-random coil transition. I. Influence of polymer concentration and solvent composition in the PBG-DCA-EDC system

The course of the reversible helix formation of poly(γ-benzyl L -glutamate) (PBG) dissolved in a mixture of dichloroacetic acid (DCA) and 1,2-dichloroethane (EDC) was followed by measuring the heat capacity and the optical rotation of the system through the transition region. The results of these measurements indicate that the transition enthalpy ΔH the transition temperature T_c, and the Zimm-Bragg parameter σ depend considerably on the PBG concentration as well as on the composition of the solvent. For the standard state of infinite dilution, however, a linear extrapolation of the measured ΔH if values results in a standard value ΔH° = 950 cal./mole, independent of the solvent composition. The results of the calorimetric measurements are discussed in relationship to changes in optical rotation. Some peculiarities in the measured thermodynamic and optical properties in solutions with relatively high content of dichloroacetic acid are reported.     

Étude thermodynamique de la transition hélice–pelote statistique en solvants mixtes de différents esters de l'acide poly(L-glutamique)

Helix–coil transition of poly(γ-methyl-L -glutamate), poly(γ-ethyl-L -glutamate), and poly(γ-benzyl-L -glutamate) has been studied in mixed solvents by calorimetry, polarimetry, and viscometry. The experimental data have allowed the evaluation of solvation enthalpy Δh_b, equilibrium constant K for hydrogen bond formation between the active solvent component and CO and NH groups, and the cooperativity parameter σ. The conformational transition of polypeptides in solution in a mixed solvent containing enough active solvent to maintain the coiled conformation has been produced by dilution with the helix-supporting solvent for the measurements of enthalpy of transition Δh_s. The average value for Δh_s is 3550 ± 300 J/mol and is practically independent of the nature of the side chain for the dichloroacetic acid-ethylene dichloride solvent pair at 25°C. A noticeable concentration effect exists in the case of poly(γ-benzyl-L -glutamate). The helical conformation is less stable for poly(γ-ethyl-L -glutamate), and this is explained by a steric effect hindering the access of dichloroacetic acid to side chains. Constant K has been calculated using polarimetric data and also from values of Δh_s obtained at different temperatures using the Bixon and Lifson theory on the one hand and that of Sayama and coworkers on the other hand. Values of σ for poly(γ-ethyl-L -glutamate) have been calculated according to both theories mentioned, and the results show that the two sets of values are quite similar. The constant σ depends on the nature of the active solvent, on temperature, and on the binary-solvent composition. These conclusions are confirmed by viscometric results. Values of Δh_b calculated from constant K are 5230 J/mol when Bixon and Lifson theory is used and 5569 J/mol when the theory at Sayama and coworkers is used. In both cases the value for Δh_b is much lower than that of an intramolecular hydrogen bond. Experimental results suggest that the solvation mechanism would proceed in a manner so that mechanisms described in both theories are involved.     

Solvent‐tunable morphology and emission of pyrene‐dipeptide organogels

Two pyrene based organogelators in which the pyrene moiety has been linked to the diphenylalanine dipeptide have been synthesized. We show how the solvent can tune both the morphology and the optical properties of the organogels: spherical aggregates with quenched emission were obtained in acetonitrile, whereas an entangled fibrillar network with enhanced emission was formed in o‐dichlorobenzene. Fourier transform infrared spectroscopy, circular dichroism and nuclear magnetic resonance spectroscopy experiments suggest that both π–π stacking and hydrogen bonding contribute to the formation of the supramolecular networks. Ultraviolet–visible and steady state emission studies demonstrated the formation of I‐aggregates in acetonitrile. In contrast, in o‐dichlorobenzene, the formation of J‐type aggregates leads to assemblies with enhanced emission. These results give some insight into the important role of the gelling solvent in the morphology of the supramolecular gels and may help in the design of new soft‐materials. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

A nuclear magnetic resonance study of the kinetics of ligand exchange reactions in uranyl complexes. VII. Acetylacetonate exchange in bis(acetylacetonato)(N,N-dimethylformamide)dioxouranium(VI)

The exchange reaction of acac(acetylacetonate) in UO₂(acac)₂dmf (dmf=N,N-dimethylformamide) in o-dichlorobenzene has been studied by the NMR line-broadening method. The exchange rate depends on the concentration of the enol isomer of acetylacetone in its low region, and approaches the limiting value in its high region. It is proposed that the exchange reaction proceeds through the mechanism in which the dissociation of one end of the chelated acac is the rate-determining step. The kinetic parameters for this step are as follows: k (25 °C)=5.03 × 10⁻³ s⁻¹, ΔH3=91.6 ± 3.8 kJ mol⁻¹, and ΔS3 =17.2 ± 10.5 JK⁻¹ mol⁻¹. The exchange rate becomes slower by the addition of free DMF. This may be due to the competition of DMF with the enol isomer of acetylacetone in attacking a four-coordinated intermediate in the equatorial plane.     

Structure of the planar complex of N4-methoxycytosine with adenine,and its relevance to the mechanism of hydroxylamine mutagenesis

Infrared, and ¹H- and ¹³C-NMR spectroscopy has been applied to a study of the planar interaction in apolar media between 1-substituted N⁴-methoxycytosine (and the corresponding 5-melhyl analogue) and 9-substituted adenines. In both chloroform and carbon tetrachloride solutions, the exocyclic N⁴-methoxy group of N⁴-methoxycytosine, and of 5-methyl N⁴-methoxy-cytosine (which is in the oxime form under these conditions), is so oriented that it is predominantly syn to the ring N(3), and neither compound forms planar auto-associates. In chloroform solution, both the N(3)-H and the C(2)O interact weakly with the solvent, the interaction being of the nature of non-typical hydrogen bonding The ¹³C-NMR chemical shift of the C(2) of N⁴-methoxycylosine is modified during formation of hetero-associates with 9-substituted adenine, in accordance with the C(2)O of the former being the acceptor of an adenine ammo proton. The resulting planar hetero-associate is a non-Watson-Crick type of base-pair. This was further substantiated by infrared absorption studies of the carbonyl frequency during complex formation. The results are examined in the light of the mechanism of hydroxylamine (and methoxyamine) mutagenesis.     

Interactions of molecules with nucleic acids. IV. Binding energies and conformations of acridine and phenanthridine compounds in the two principal and in several unconstrained dimer-duplex intercalation sites

The binding positions and relative minimum binding energies are calculated for complexes of 9-aminoacridine, proflavine, N-methylphenanthridinium, and ethidium in theoretically determined intercalation sites in B-DNA (sites I and II) and in unconstrained dimer-duplex sites. The selection of site I in B-DNA by these compounds agrees with the theoretical interpretation of studies of unwinding angles in closed circular DNA in all cases but ethidium, which is predicted to select site II. The most stable binding positions of the acridines and ethidium in unconstrained dimer-duplex units agree with experimental results of intercalation complexes of dinucleoside monophosphate units. Base-pair specificity for Watson-Crick pairing is examined. The energy of an intercalation complex is partitioned into ΔE₂₃, the energy required to open base pairs BP₂ and BP₃ in B-DNA to a site, and ΔE_In, the energy change when a free molecular intercalates. ΔE₂₃ depends strongly on the base-pair sequence, whereas ΔE_In for the four molecules studied does not. The three most stable sequences contain (pyrimidine)p(purine) units, and this provides a rationale for the exclusive formation of crystals of intercalation complexes with these units. In spite of this selectivity, the distribution of G?C and A?T base pairs is equal for these three units and persists as the more unstable sequences are included. Therefore, specificity arises from the interaction between the base pairs and the 2′-deoxyribose 5′-monophosphate backbone for the opening of B-DNA to an intercalation site and not from the interaction between the chromophore and the DNA.