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PubMed2006

Thermodynamics of pyridine coordination in 1,4-phenylene bridged bimetallic (Pd, Pt) complexes containing two N,C,N' motifs, 1,4-M2-[C6(CH2NR2)4-2,3,5,6].

The thermodynamics of pyridine coordination in 1,4-phenylene-bridged binuclear palladium and platinum organometallic complexes [1,4-(MOTf)2-&{C6(CH2NR2)4-2,3,5,6}] (11, M =Pd, Pt; R =CH3, C2H5, R2 = -(CH2)5-) are measured by 1H NMR in DMSO-d6. The coordination of substituted pyridines by bimetallic complexes 11 or 12 in DMSO is found to proceed via two effectively independent metalligand binding events, and the association constants for pyridine coordination and rate constants for pyridine exchange are nearly identical to those measured previously on monometallic analogs. A linear free energy relationship between the association constant for pyridine coordination and the inductive Hammett constant of the pyridine substituent is observed, and the sensitivity (rho = -1.7 to -2.1) in DMSO depends only slightly on metal (Pd vs Pt) and spectator ligand (pincer dialkylamine vs triarylphosphine). The association constant for a particular pyridine ligand, however, varies by roughly 3 orders of magnitude across the series of metal complexes. The effective independence of the two coordination sites and the range of available thermodynamic and kinetic behaviors of the coordination guide the use of these versatile building blocks in metallosupramolecular applications.

Organometallic Compounds↗

PubMed2001

Thermodynamic versus kinetic products of DNA alkylation as modeled by reaction of deoxyadenosine.

Alkylating agents that react through highly electrophilic quinone methide intermediates often express a specificity for the weakly nucleophilic exocyclic amines of deoxyguanosine (dG N(2)) and deoxyadenosine (dA N(6)) in DNA. Investigations now indicate that the most nucleophilic site of dA (N1) preferentially, but reversibly, conjugates to a model ortho-quinone methide. Ultimately, the thermodynamically stable dA N(6) isomer accumulates by trapping the quinone methide that is transiently regenerated from collapse of the dA N1 adduct. Alternative conversions of the dA N1 to the dA N(6) derivative by a Dimroth rearrangement or other intramolecular processes are not competitive under neutral conditions, as demonstrated by studies with [6-(15)N]-dA. Both a model quinone methide precursor and its dA N1 adduct yield a similar profile of deoxynucleoside products when treated with an equimolar mixture of dC, dA, dG, and T. Consequently, the most readily observed products of DNA modification resulting from reversible reactions may reflect thermodynamic rather than kinetic selectivity.

Alkylation↗

PubMed2002

Synthesis of a negatively charged dibenzofuran-based beta-turn mimetic and its incorporation into the WW miniprotein-enhanced solubility without a loss of thermodynamic stability.

A versatile synthesis has been developed to functionalize the 4-(2-aminoethyl)-6-dibenzofuran propionic acid residue (1a) at the 2 and 8 positions with a variety of different substructures. The unfunctionalized version of this peptidomimetic (1a) is known to facilitate beta-hairpin formation in a variety of small peptides and proteins in aqueous solution when incorporated in place of the i + 1 and i + 2 residues of a beta-turn. In this study, we append propionate substituents on 1a at the 2 and 8 positions to successfully overcome solubility problems encountered with the incorporation of 1a in place of the i + 1 and i + 2 residues of the beta-turn in loop 1 of the WW domain. The thermodynamic stability of several WW domain analogues incorporating residues 1a and 1b was compared to that of the wild-type sequence revealing comparable DeltaG(H(2)O) unfolding values at 4 degrees C ranging from 3 to 3.6 kcal/mol. WW domains incorporating residue 1b exhibit improved solubility (exceeding 100 microM) and resistance to aggregation without compromising thermodynamic stability.

Amino Acid Sequence↗

PubMed2002

Enantiomeric resolution of 2-aryl propionic esters with hyperthermophilic and mesophilic esterases: contrasting thermodynamic mechanisms.

The enantiomeric resolution of 2-aryl propionic esters by hyperthermophilic and mesophilic esterases was found to be governed by contrasting thermodynamic mechanisms. Entropic contributions predominated for mesophilic esterases from Candida rugosa and Rhizomucor miehei, while enthalpic forces controlled this resolution by the esterase from the extremely thermoacidophilic archaeon, Sulfolobus solfataricus P1. This disparity in thermodynamic mechanism can be attributed to the differences in conformational flexibility of mesophilic and thermophilic enzymes as they relate to the temperature range (4-70 degrees C) examined.

Candida↗

PubMed2003

Theoretical elucidation of kinetic and thermodynamic control of radical addition regioselectivity.

The cyclizations of two structurally similar 2-oxo-5-hexenyl-type radicals have been investigated by ab initio and density functional (UB3LYP/6-31+G**//UHF/6-31G* and UB3LYP/6-31G*//UB3LYP/6-31G*) calculations. The origin of apparently contradictory reports of 6-endo and 5-exo cyclizations is determined. Kinetic control favors 6-endo cyclization, while thermodynamic control gives 5-exo cyclization, and the observation of different products from different research groups arises from the difference in experimental conditions used by the two groups. The outcome of a new cyclization reaction was predicted by using these theoretical techniques. Kinetic control is predicted to yield exclusively the products of 6-endo cyclization, while thermodynamic control would lead to an approximately equal mixture of one 6-endo and one 5-exo cyclized product. Experimental studies revealed that the reaction yields only the products of 6-endo cyclization through kinetic control.

Alkenes↗

PubMed2003

Thermodynamic contributions of the ordered water molecule in HIV-1 protease.

Binding between biomolecules is usually accompanied by the formation of direct interactions with displacement of water from the binding sites. In some cases, however, the interactions are mediated by ordered water molecules, whose effect on binding affinity and the other thermodynamic functions is unclear. In this work, we compute the contribution of one such water molecule, the strongly bound water molecule at the binding site of HIV-1 protease, to the thermodynamic properties using statistical mechanical formulas for the energy and entropy. The requisite correlation functions are obtained by molecular dynamics simulations. We find that the entropic penalty of ordering is large but is outweighed by the favorable water-protein interactions. We also find a large negative contribution from this water molecule to the heat capacity. This approach could be useful in rational drug design by estimating which bound water molecules would be most favorable to displace.

Entropy↗

PubMed2003

Dynamic equilibrium of a supramolecular dimeric rhomboid and trimeric hexagon and determination of its thermodynamic constants.

A supramolecular dimeric rhomboid and its trimeric counterpart, a hexagon, are generated by design via the directional bonding methodology of self-assembly. The different-sized supramolecular macrocycles formed by Pt-coordination undergo a concentration- and temperature-dependent dynamic equilibrium. The two structures are characterized by multinuclear NMR and ESI-MS. Extensive study of the dynamic equilibrium of the two species in solution is performed to obtain its thermodynamic properties. By varying the ionic strength, mu, of the solutions, the true thermodynamic equilibrium constant, K, is determined at each experimental temperature (K(253) = 36 +/- 7, K(273) = 18 +/- 6, K(293) = 10 +/- 3, K(313) = 9 +/- 2, K(333) = 5 +/- 2, and K(353) = 3.0 +/- 0.2). By applying these values of true K at the respective temperatures to the van't Hoff equation extended with the entropy term, the standard enthalpy and entropy changes are determined for the equilibrium: with Delta H degrees = -18 +/- 1 kJ mol(-1) and Delta S degrees = -43 +/- 4 J mol(-1) K(-1), respectively, for the forward reaction (rhomboid to hexagon) of the equilibrium. The rhomboid is selectively crystallized, and its crystal structure is determined by X-ray diffraction. The structure reveals a significant amount of porosity as well as distortion of the rhomboid from planarity, leading to channels that can be observed from two viewing positions of the packing.

Crystallization↗

PubMed2003

Thermodynamic hydride donor abilities of [HW(CO)4L]- complexes (L = PPh3, P(OMe)3, CO) and their reactions with [C5Me5Re(PMe3)(NO)(CO)]+.

The thermodynamic hydride donor abilities of [HW(CO)(5)](-) (40 kcal/mol), [HW(CO)(4)P(OMe(3))](-) (37 kcal/mol), and [HW(CO)(4)(PPh(3))](-) (36 kcal/mol) have been measured in acetonitrile by either equilibrium or calorimetric methods. The hydride donor abilities of these complexes are compared with other complexes for which similar thermodynamic measurements have been made. [HW(CO)(5)](-), [HW(CO)(4)P(OMe(3))](-), and [HW(CO)(4)(PPh(3))](-) all react rapidly with [CpRe(PMe(3))(NO)(CO)](+) to form dinuclear intermediates with bridging formyl ligands. These intermediates slowly form [CpRe(PMe(3))(NO)(CHO)] and [W(CO)(4)(L)(CH(3)CN)]. The structure of cis-[HW(CO)(4)(PPh(3))](-) has been determined and has the expected octahedral structure. The hydride ligand bends away from the CO ligand trans to PPh(3) and toward PPh(3).

Carbon Monoxide↗

PubMed2003

Ion solvation thermodynamics from simulation with a polarizable force field.

Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable force field and perturbation techniques to directly compute absolute solvation free energies for potassium, sodium, and chloride ions in liquid water and formamide. Corresponding calculations are also performed with two widely used nonpolarizable force fields. The simulations with the polarizable force field accurately reproduce in vacuo quantum mechanical results, experimental ion-cluster solvation enthalpies, and experimental solvation free energies for whole salts, while the other force fields do not. The results indicate that calculations with a polarizable force field can capture the thermodynamics of ion solvation and that the solvation free energies of the individual ions differ by several kilocalories from commonly cited values.

Anions↗

PubMed2004

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein.

In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.

Amino Acid Sequence↗

PubMed2004

Kinetic and thermodynamic preferences in aryl vs benzylic C-H bond activation with cationic Pt(II) complexes.

Anhydrous cationic Pt(II) complexes [(NN)Pt(CH3)(CF3CD2OD)]+ (1, NN = ArN=C(Me)-C(Me)=NAr), which are obtained by reaction of (NN)Pt(CH3)2 with B(C6F5)3 in CF3CD2OD, activate C-H bonds of benzene and methylbenzenes, with enhanced reactivity compared to the previously prepared equilibrium mixtures with the (thermodynamically favored) aquo complexes. For methylbenzenes (toluene, p-xylene, mesitylene), activation at the aromatic and benzylic positions are kinetically competitive, but the product of the latter is strongly favored thermodynamically. This unusual trend is attributed to formation of eta3-benzyl structures, which can be observed spectroscopically for 1,4-diethylbenzene activation.

Benzyl Compounds↗

PubMed2004

Metal clips induce folding of a short unstructured peptide into an alpha-helix via turn conformations in water. Kinetic versus thermodynamic products.

Short peptides corresponding to two to four alpha-helical turns of proteins are not thermodynamically stable helices in water. Unstructured octapeptide Ac-His1-Ala2-Ala3-His4-His5-Glu6-Leu7-His8-NH(2) (1) reacts with two [Pd((15)NH(2)(CH(2))(2)(15)NH(2))(NO(3))(2)] in water to form a kinetically stable intermediate, [[Pden](2)[(1,4)(5,8)-peptide]](2), in which two 19-membered metallocyclic rings stabilize two peptide turns. Slow subsequent folding to a thermodynamically more stable two-turn alpha-helix drives the equilibrium to [[Pden](2)[(1,5)(4,8)-peptide]] (3), featuring two 22-membered rings. This transformation from unstructured peptide via turns to an alpha-helix suggests that metal clips might be useful probes for investigating peptide folding.

Circular Dichroism↗

PubMed2004

Thermodynamic characterization of the binding of tetrahydropterins to phenylalanine hydroxylase.

Phenylalanine hydroxylase (PAH) is the key enzyme in the catabolism of L-Phe. The natural cofactor of PAH, 6R-tetrahydrobiopterin (BH4), negatively regulates the enzyme activity in addition to being an essential cosubstrate for catalysis. The analogue 6-methyltetrahydropterin (6M-PH4) is effective in catalysis but does not regulate PAH. Here, the thermodynamics of binding of BH4 and 6M-PH4 to human PAH have been studied by isothermal titration calorimetry. At neutral pH and 25 degrees C, BH4 binds to PAH with higher affinity (Kd = 0.75 +/- 0.18 microM) than 6M-PH4 (Kd = 16.5 +/- 2.7 microM). While BH4 binding is a strongly exothermic process (DeltaH = -11.8 +/- 0.4 kcal/mol) accompanied by an entropic penalty (-TDeltaS = 3.4 +/- 0.4 kcal/mol), 6M-PH4 binding is both enthalpically (DeltaH = -3.3 +/- 0.3 kcal/mol) and entropically (-TDeltaS = -3.2 kcal/mol) driven. No significant changes in binding affinity were observed in the 5-35 degrees C temperature range for both pterins at neutral pH, but the enthalpic contribution increased with temperature rendering a heat capacity change (DeltaCp) of -357 +/- 26 cal/mol/K for BH4 and -63 +/- 12 cal/mol/K for 6M-PH4. Protons do not seem to be taken up or released upon pterin binding. Structure-based energetics calculations applied on the molecular dynamics simulated structures of the complexes suggest that in the case of BH4 binding, the conformational rearrangement of the N-terminal tail of PAH contribute with favorable enthalpic and unfavorable entropic contributions to the intrinsic thermodynamic parameters of binding. The entropic penalty is most probably associated to the reduction of conformational flexibility at the protein level and disappears for the L-Phe activated enzyme. The calculated energetic parameters aid to elucidate the molecular mechanism for cofactor recognition and the regulation of PAH by the dihydroxypropyl side chain of BH4.

Biopterins↗

PubMed2005

Thermodynamics of DNA hybridization on gold nanoparticles.

Dynamic light scattering is used as a sensitive probe of hybridization on DNA-functionalized colloidal gold nanoparticles. When a target DNA strand possesses an 8 base "dangling end", duplex formation on the surface of the nanoparticles leads to an increase in hydrodynamic radius. Duplex melting is manifested in a drop in hydrodynamic radius with increasing temperature, and the concentration dependence of the melting temperature provides a measure of the thermodynamics of binding. The hybridization thermodynamics are found to be significantly lower at higher hybridization densities than those previously reported for initial hybridization events. The pronounced deviation from Langmuir adsorption behavior is greater for longer duplexes, and it is, therefore, consistent with electrostatic repulsion between densely packed oligonucleotides. The results have implications for sensing and DNA-directed nanoparticle assembly.

DNA↗

PubMed2005

Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras.

PNA-DNA chimeras present the interesting properties of PNA, such as the high binding affinity to complementary single-strand (DNA or RNA), and the resistance to nuclease and protease degradation. At the same time, the limitations of an oligomer containing all PNA residues, such as low water solubility, self-aggregation, and low cellular uptake, are effectively overcome. Further, PNA-DNA chimeras possess interesting biological properties as antisense agents. We have explored the ability of PNA-DNA chimeric strands to assemble in quadruplex structures. The rate constant for association of the quadruplexes and their thermodynamic properties have been determined by CD spectroscopy and differential scanning calorimetry (DSC). Thermal denaturation experiments indicated higher thermal and thermodynamic stabilities for chimeric quadruplexes in comparison with the corresponding unmodified DNA quadruplex. Singular value decomposition analysis (SVD) suggests the presence of kinetically stable intermediate species in the quadruplex formation process. The experimental results have been discussed on the basis of molecular dynamic simulations. The ability of PNA-DNA chimeras to form stable quadruplex structures expands their potential utility as therapeutic agents.

Calorimetry↗

PubMed2006

Thermodynamic analysis of autonomous parallel beta-sheet formation in water.

We report the first thermodynamic analysis of parallel beta-sheet formation in a model system that folds in aqueous solution. NMR chemical shifts were used to determine beta-sheet population, and van't Hoff anaysis provided thermodynamic parameters. Our approach relies upon the d-prolyl-1,1-dimethyl-1,2-diaminoethane unit to promote parallel beta-sheet formation between attached peptide strands. The development of a macrocyclic reference molecule to provide chemical shift data for the fully folded state was crucial to the quantitative anaylsis.

Models, Chemical↗

PubMed2006

Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions.

The effect of molecular crowding on the structure and stability of biomolecules has become a subject of increasing interest because it can clarify how biomolecules behave under cell-mimicking conditions. Here, we quantitatively analyzed the effects of molecular crowding on the thermodynamics of antiparallel G-quadruplex formation via Hoogsteen base pairs and of antiparallel hairpin-looped duplex (HP duplex) formation via Watson-Crick base pairs. The free energy change at 25 degrees C for G-quadruplex formation decreased from -3.5 to -5.5 kcal mol(-1) when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt %, whereas that of duplex formation increased from -9.8 to -6.9 kcal mol(-1). These results showed that the antiparallel G-quadruplex is stabilized under molecular crowding conditions, but that the HP duplex is destabilized. Moreover, plots of stability (ln K(obs)) of the DNA structures versus water activity (ln a(w)) demonstrated that the ln K(obs) for G-quadruplex formation decreased linearly as the ln a(w) increased, whereas that for duplex formation increased linearly with the increase in ln a(w), suggesting that the slope approximately equals the number of water molecules released or taken up during the formation of these structures. Thus, molecular crowding affects the thermodynamics of DNA structure formation by altering the hydration of the DNA. The stabilization of the DNA structures with Hoogsteen base pairs and destabilization of DNA structures with Watson-Crick base pairs under molecular crowding conditions lead to structural polymorphism of DNA sequences regulated by the state of hydration.

Base Pairing↗

PubMed1990

Thermodynamics of the interaction of inhibitors with the binding site of recombinant human renin.

The independent subsite model is widely used for the design of peptide inhibitors of enzymes with extended active sites. This model assumes that the subsites are independent of each other and that the free energies of binding contributed by the several subsites are additive. We questioned the strict application of this model for structure-activity studies, since one can, a priori, conceive of likely deviations from this model. Accordingly, we tested the independent subsite model by measuring the thermodynamic binding parameters of a series of peptide inhibitors of human renin. This enzyme-inhibitor system was chosen as a model by virtue of the high degree of specificity of renin for its natural substrate, angiotensinogen, and the availability of a large number of structurally similar peptide inhibitors. Although we found the general mode of binding of these renin inhibitors to be primarily hydrophobic, serious deviations from additivity and independent subsite model constraints were observed. We conclude that an important determinant of binding is most probably the conformation assumed by the peptide inhibitor in solution. Thus, we suggest that caution be exercised in using affinity constants to assess the interactions of peptide inhibitors with human renin and possibly with other enzymes having extended binding sites. Furthermore, the thermodynamic parameters of a class of compounds provide more information as to the mode of binding of ligands to their respective receptors than do dissociation constants.

Amino Acid Sequence↗