Theoretical prediction of solubility, reactivity and degradation pathways of selected azo disperse dyes

Abstract :Ph.D. (Chemistry

Superacid Chemistry on Mildly Acidic Water

The mechanism of proton transfer across water−hydrophobic media boundaries is investigated in experiments in which the protonation of gaseous n-hexanoic acid (PCOOH) upon collision with liquid water microjets is monitored by online electrospray mass spectrometry as a function of pH. Although PCOOH(aq) is a very weak base (pK_(BH+) < −3), PCOOH(g) is converted to PC(OH)_2^+ on pH < 4 water via a process that ostensibly retains some of the exoergicity of its gas-phase counterpart, PCOOH + H_3O^+ = PC(OH)_2^+ + H_2O, ΔG < −22 kcal mol^(−1). The large kinetic isotope effects observed on H_2O/D_2O microjets, PC(OH)_2^+/PC(OH)OD^+ = 88 and PC(OH)OD^+/PC(OD)_2^+ = 156 at pD = 2, and their inverse dependences on pH indicate that PCOOH(g) hydronation on water (1) involves tunneling, (2) is faster than H-isotope exchange, and (3) is progressively confined to the outermost layers as water becomes more acidic. Proton transfers across steep water density gradients appear to be promoted by both dynamic and thermodynamic factors

Ligand Substitution Processes

From the preface: The subject of the mechanistic study of ligand substitution reactions is currently undergoing an exciting growth. New fast-reaction techniques have removed the upper limit on rates that can be measured, and extension to less familiar central metal atoms has begun in earnest. This might seem the wrong moment for review of the field. As yet, definitive treatment is possible only for those complexes involving monodentate ligands with cobalt(III) and platinurn(II). But, because information is so extensive for these systems, it is clear that they are functioning as models from which concepts and experiments are generated for application over the fast-growing range of the subject. We believe that this is an important moment to reopen debate on fundamentals so that concepts will be most felicitously formulated to aid growth of understanding. This monograph is centrally concerned with three aspects of those fundamentals. We have attempted to develop an approach to classification of ligand substitution reactions that is adapted to what seem to have emerged as the characteristic features of these reactions and is susceptible to operational tests. (We do recognize that any such scheme of ideas is necessarily obsolescent once it is formulated since new experiments will certainly follow immediately.) We have tried to evaluate the basis for making generalizations about ligand substitution processes and to formulate tests to show whether new reactions fall within familiar patterns. Finally, we have sought to base the models of ligand substitution processes in the language of molecular-orbital theory. We believe that MO theory is most useful, because it may be used to correlate rate data on complexes with the extensive information available from spectral and magnetic studies, yet differs from crystal-field theory in providing a natural place for consideration of the bonding electrons, which must be a principal determinant of reaction processes. To keep this essay within bounds, we assume familiarity with the elements of experimental kinetics, transition-state theory, and the simple molecular-orbital theory of complexes. Introductory physical chemistry, some familiarity with the study of reaction mechanisms, and mastery of one of the qualitative treatments of MO theory as applied to transition-metal complexes should provide sufficient background. Thus, we hope that this book will be useful to students, relatively early in their careers, who wish to explore this field. Our debts to very many workers will be obvious throughout. We want to record here our special personal debt to Professors Ralph G. Pearson and Fred Basolo and to Dr. Martin Tobe. We particularly thank Professor George S. Hammond for his interest and enthusiasm in this project. Professor Hammond carefully read and criticized the entire manuscript in the final drafts. We received many other valuable criticisms at various stages of this project from Professors R. D. Archer, F. Basolo, J. O. Edwards, J. Finholt, P. Haake, J. Halpern, A. Kropf, R. G. Pearson, S. I. Shupack, M. S. Silver, and C. Walling, and Dr. U. Belluco and Dr. L. Cattalini. We very much appreciate their help and probably should have followed their suggestions more closely. We warmly acknowledge expert assistance from Mrs. Madeline deFriesse, Miss Jan Denby, and Mrs. Diane Celeste in preparation of the manuscript. COOPER H. LANGFORD HARRY B. GRAY Amherst, Massachusetts New York, New York October 196

Inhibitor Synthesis and Biophysical Characterization of Protein–Ligand–Solvent Interactions An Analysis of the Thermodynamics and Kinetics of Ligand Binding to Thermolysin

In the pre-clinical development stages of most drug design campaigns, the equilibrium binding affinity of a prospective lead candidate, in the form of an IC50, Kd or ΔG° value, is the most commonly employed benchmark parameter for its effectiveness as a putative drug. Hydrogen bonding, van der Waals and electrostatic interactions, as well as hydrophobic effects are among the most prominent factors that contribute to binding. In structure based design approaches, these interactions can routinely be linked to a structural motif of a drug molecule, which can greatly assist in the construction of compounds with a desired set of properties. Equilibrium binding affinity can also be expressed in terms of kinetics, were the steady-state constant Kd is defined as the ratio of the rate constants of dissociation (kd) and association (ka). The thermodynamic expression ΔG° can be subdivided into an enthalpic (ΔH°) and an entropic (–TΔS°) term. In either case, the molecular mechanisms that define the kinetics of binding or the compensation of enthalpic and entropic contributions are not fully understood. The goal of this dissertation is the in-depth investigation of the molecular processes that drive protein–ligand interactions. A special focus is set on the partitioning of thermodynamic and kinetic parameters into their respective microscopic elements. For this, the metalloprotease thermolysin (TLN) is used as a model system. This protein is well characterized and represents a robust system with excellent crystallographic properties and a thoroughly documented inhibitor class. The first publication (Chapter 2) presents an improved strategy for the synthesis and purification of phosphonamidate peptides that are known as potent inhibitors of TLN. Due to the inherent instability of the phosphorous–nitrogen bond, the introduction of polar functional groups into the inhibitor scaffold is quite challenging. Here, a synthetic strategy is presented that minimizes the amount of hydrolysis during peptide coupling, deprotection and purification through the use of an allyl-based protection system and a solid-phase extraction (SPE) protocol for the final purification step. This allows the synthesis of highly pure TLN inhibitors incorporating a variety of functional groups for use in biophysical experiments. In the second publication (Chapter 3), a strategy for the design of inhibitors is highlighted, which relies on the targeted design of water networks that are formed around a protein–ligand complex. Based on information from a previous study, the shape of a hydrophobic portion of a TLN ligand is altered in a way that allows a beneficial stabilization of water molecules in the first solvation layer of the complex. Supported by molecular dynamics simulations, a series of diastereomeric inhibitors is synthesized and the binding process is characterized by X-ray crystallography, isothermal titration calorimetry (ITC) and surface plasmon resonance spectroscopy (SPR). The optimization of the hydrophobic P2’ moiety results in a 50-fold affinity enhancement compared to the original methyl substituted ligand. This improvement is mainly driven by a favorable enthalpic term that originates from the stabilization of water polygons in the solvation shell. In the follow-up study in Chapter 4, the binding signature of a series of inhibitors that place a charged and polar moiety in the solvent exposed S2’ pocket of TLN is investigated. Here, a partially hydrated ammonium group is gradually retracted deeper into the hydrophobic protein environment. From the crystal structures it is evident that the polar ligands do not recruit an increased amount of water molecules into their solvation layer when compared to related analogues that feature a purely aliphatic residue at the solvent interface. The penalty for the partial desolvation of the charged functional group, in combination with the lack of a strongly ordered water network, results in a severe affinity decrease that is driven by an unfavorable enthalpic term. The deep, hydrophobic S1’ pocket of TLN determines the substrate specificity of the protease and is commonly addressed by high affinity inhibitors. Experimental evidence from previous studies suggests, however, that this apolar crevice is only poorly solvated in the absence of an interaction partner. With the study in Chapter 5, an attempt for the experimental analysis of the hydration state of the S1’ pocket is presented. For this, a special inhibitor is designed that transforms the protein pocket into a cavity, while simultaneously providing enough empty space for the accommodation of several water molecules. A detailed analysis of an experimentally phased electron density map reveals that the cavity remains completely unsolvated and thus, vacuous. As an intriguing prospect for the exploitation of such poorly hydrated protein pockets in drug design, the placement of an iso-pentyl moiety in the ligand’s P1’ position results in a dramatic, enthalpically driven gain in affinity by a factor of 41 000. With a detailed structural analysis of a series of chemically diverse TLN inhibitors, the kinetics of the protein–ligand binding process are investigated in Chapter 6. From the SPR derived kinetic information, it becomes apparent that the nature of the functional group in the P2’ position of a thermolysin inhibitor has a significant impact on its dissociation kinetics. This property can be linked to the interaction between the respective functionality of a ligand and Asn112, a residue that lines the active site of the protease and is commonly believed to align a substrate for proteolytic cleavage. This residue undergoes a significant conformational change when the protein transitions from its closed state to its open form, from which a ligand is released. Interference with this retrograde induced-fit mechanism through strong hydrogen-bonding interactions to an inhibitor results in a pronounced deceleration of the dissociation process. The case of the known inhibitor ZFPLA demonstrates that a further restriction of the rotation of Asn112 by a steric barrier in the P1 position of a ligand, can reduce the rate constant of dissociation by a factor of 74 000. Fragment-based lead discovery has become a popular method for the generation of prospective drug molecules. The weak affinity of fragments and the necessity for high concentrations, however, can result in false-positive signals from the initial binding assays that routinely plague fragment-based screening. The pursuit of such a “red herring” can lead to a significant loss of time and resources. In Chapter 7, a molecule that emerged as one of the most potent binders from an elaborate fragment screen against the aspartic protease endothiapepsin is identified as a false-positive. Detailed crystallographic, HPLC and MS experiments reveal that the affinity detected in multiple assays can in fact be attributed to another compound. This entity is formed from the initially employed molecule in a reaction cascade that results in a major rearrangement of its heterocyclic core structure. Supported by quantum chemical calculations and NMR experiments, a mechanism for the formation of the elusive compound is proposed and its binding mode analyzed by X-ray crystallography

The effect of 4-substitution on some properties of the O–H bond in 1-naphthols

The effects of 4-substitution on some of those properties of the O–H bond in 1-naphthols which reflect its hydrogen bonding tendency have been studied. The properties investigated were the near infrared O–H stretching frequencies in cyclohexane and dioxan solutions, the association constant of complex formation with dioxan and the affinity of adsorption at an activated alumina/solution interface. A series of 4-substituted-1-naphthols has been prepared and comparisons in behaviour with 4-substituted phenols have been made throughout. [Continues.

Electronic Control of Spin-Crossover Properties in Four-Coordinate Bis(formazanate) Iron(II) Complexes

The transition between spin states in d-block metal complexes has important ramifications for their structure and reactivity, with applications ranging from information storage materials to understanding catalytic activity of metalloenzymes. Tuning the ligand field (Delta(O)) by steric and/or electronic effects has provided spin-crossover compounds for several transition metals in the periodic table, but this has mostly been limited to coordinatively saturated metal centers in octahedral ligand environments. Spin-crossover complexes with low coordination numbers are much rarer. Here we report a series of four-coordinate, (pseudo)tetrahedral Fe(II) complexes with formazanate ligands and demonstrate how electronic substituent effects can be used to modulate the thermally induced transition between S = 0 and S = 2 spin states in solution. All six compounds undergo spin-crossover in solution with T-1/2 above room temperature (300-368 K). While structural analysis by X-ray crystallography shows that the majority of these compounds are low-spin in the solid state (and remain unchanged upon heating), we find that packing effects can override this preference and give rise to either rigorously high-spin (6) or gradual spin-crossover behavior (5) also in the solid state. Density functional theory calculations are used to delineate the empirical trends in solution spin-crossover thermodynamics. In all cases, the stabilization of the low-spin state is due to the pi-acceptor properties of the formazanate ligand, resulting in an "inverted" ligand field, with an approximate "two-over-three" splitting of the d-orbitals and a high degree of metal-ligand covalency due to metal -> ligand pi-backdonation. The computational data indicate that the electronic nature of the para-substituent has a different influence depending on whether it is present at the C-Ar or N-Ar rings, which is ascribed to the opposing effect on metal-ligand sigma- and pi-bonding

Examining the PM6 semiempirical method for pKa prediction across a wide range of oxyacids

The pK~a~ estimation ability of the semiempirical PM6 method was evaluated across a broad range of oxyacids and compared to results obtained using the SPARC software program. Compound classes under consideration included acetic acids, alicyclic and aromatic heterocyclic acids, benzoic acids, boronic acids, hydroxamic acids, oximes, peroxides, peroxyacids, phenols, &#x3b1;-saturated acids, &#x3b1;-saturated alcohols, sulfinic acids, &#x3b1;-unsaturated acids, and &#x3b1;-unsaturated alcohols. PM6 accurately predicts the acidity of acetic and benzoic acids and their derivatives, but is less reliable for alicyclic and aromatic heterocyclic acids and phenols. &#x3b1;-Saturated acids are reliably modeled by PM6 except for polyacid derivatives with &#x3b1;-alcohol moieties. &#x3b1;-Saturated alcohols only appear to yield reliable PM6 results where an &#x3b1;-hydroxy or &#x3b1;-alkoxy moiety is absent. Carboxylic acids with simple &#x3b1;-alkene unsaturation are well approximated by PM6 except where alkyne &#x3b1;-unsaturation or &#x3b1;-carboxylation are also present. The PM6 and SPARC methods exhibit approximately equal pKa prediction performance for the acetic, alicyclic, and benzoic acids. SPARC outperforms PM6 on the peroxides, peroxyacids, phenols, and &#x3b1;-saturated acids and &#x3b1;-saturated alcohols. pKa values for boron, nitrogen, and sulfur oxyacids do not appear to be reliably estimated by either the PM6 or SPARC methods. The findings will help guide the potential appropriateness of results from the PM6 pK~a~ estimation method for waste treatment and environmental fate investigations