Patrick Kearney

Bio: Patrick Kearney is an academic researcher from Exelixis. The author has contributed to research in topics: Kinase & Unfolded protein response. The author has an hindex of 16, co-authored 25 publications receiving 2160 citations.

Rothemund and Adler-Longo reactions revisited: synthesis of tetraphenylporphyrins under equilibrium conditions

Abstract: We present a new synthetic strategy for preparing tetraphenylporphyrins that should greatly expand synthetic entries into porphyrin containing model systems. Pyrrole and the desired benzaldehyde react reversibly at room temperature with trace acid catalysis to form the cyclic tetraphenylporphyrinogen at thermodynamic equilibrium. An oxidant is then added to irreversibly convert the porphyrinogen to the porphyrin. The greater stability of the cyclic porphyrinogen over the open-chain polypyrrylmethanes occurs when the reaction is performed at moderate dilution (10-2 M). The reaction at high dilution or high concentration affords a negligible yield of the cyclic porphyrinogen. Porphyrinogen exchange reactions provide proof of equilibrium. This methodology is complementary to the Adler-Longo procedure, allowing small quantities of porphyrins to be prepared from sensitive aldehydes in 30-40% yield without difficult purification problems. This methodology is also extended to the preparation of meso-tetraalkylporphyrins and one hybrid porphyrin containing both aryl and alkyl substituents. The mild reaction conditions and convenience of this method permit consideration of new design strategies in preparing complex porphyrins.

Molecular recognition in aqueous media. New binding studies provide further insights into the cation-π interaction and related phenomena

Abstract: We describe a large number of binding studies in aqueous media designed to provide new insights into noncovalent binding interactions, especially the cation-π interaction. The studies include 7 different hosts, over 70 guests, and over 150 new binding constants. In addition to the now standard NMR methods, circular dichroism has proven to be an especially useful tool for determining aqueous binding constants. We have found that, in addition to the alkyliminium and tetraalkylammonium guests we have studied previously, sulfonium and guanidinium guests also show substantial cation-π effects. Bromination of the host greatly enhances its binding ability in a general fashion, primarily as a result of hydrophobic interactions. Addition of methoxy groups did not enhance binding, apparently as a result of a collapse of the host into a conformation that is not suitable for binding. Replacement of two benzene rings of the host by furans or thiophenes also did not enhance binding. Ab initio calculations provide a rationalization for this effect and suggest a clearer model for the cation-π interaction.

Phosphatidylinositol 3-kinase inhibitors and methods of their use

Abstract: The present invention comprises small molecule inhibitors of phosphatidylinositol 3-kinase (PI3K), which is associated with a number of malignancies such as ovarian cancer, cervical cancer, breast cancer, colon cancer, rectal cancer, and glioblastomas, among others. Accordingly, the compounds of the present invention are useful for treating, preventing, and/or inhibiting these diseases.

Cation-π Interactions in Chemistry and Biology: A New View of Benzene, Phe, Tyr, and Trp

Abstract: Cations bind to the π face of an aromatic structure through a surprisingly strong, noncovalent force termed the cation-π interaction. The magnitude and generality of the effect have been established by gas-phase measurements and by studies of model receptors in aqueous media. To first order, the interaction can be considered an electrostatic attraction between a positive charge and the quadrupole moment of the aromatic. A great deal of direct and circumstantial evidence indicates that cation-π interactions are important in a variety of proteins that bind cationic ligands or substrates. In this context, the amino acids phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp) can be viewed as polar, yet hydrophobic, residues.

Dynamic covalent chemistry.

Abstract: Dynamic covalent chemistry relates to chemical reactions carried out reversibly under conditions of equilibrium control. The reversible nature of the reactions introduces the prospects of "error checking" and "proof-reading" into synthetic processes where dynamic covalent chemistry operates. Since the formation of products occurs under thermodynamic control, product distributions depend only on the relative stabilities of the final products. In kinetically controlled reactions, however, it is the free energy differences between the transition states leading to the products that determines their relative proportions. Supramolecular chemistry has had a huge impact on synthesis at two levels: one is noncovalent synthesis, or strict self-assembly, and the other is supramolecular assistance to molecular synthesis, also referred to as self-assembly followed by covalent modification. Noncovalent synthesis has given us access to finite supermolecules and infinite supramolecular arrays. Supramolecular assistance to covalent synthesis has been exploited in the construction of more-complex systems, such as interlocked molecular compounds (for example, catenanes and rotaxanes) as well as container molecules (molecular capsules). The appealing prospect of also synthesizing these types of compounds with complex molecular architectures using reversible covalent bond forming chemistry has led to the development of dynamic covalent chemistry. Historically, dynamic covalent chemistry has played a central role in the development of conformational analysis by opening up the possibility to be able to equilibrate configurational isomers, sometimes with base (for example, esters) and sometimes with acid (for example, acetals). These stereochemical "balancing acts" revealed another major advantage that dynamic covalent chemistry offers the chemist, which is not so easily accessible in the kinetically controlled regime: the ability to re-adjust the product distribution of a reaction, even once the initial products have been formed, by changing the reaction's environment (for example, concentration, temperature, presence or absence of a template). This highly transparent, yet tremendously subtle, characteristic of dynamic covalent chemistry has led to key discoveries in polymer chemistry. In this review, some recent examples where dynamic covalent chemistry has been demonstrated are shown to emphasise the basic concepts of this area of science.

Functional oligothiophenes: molecular design for multidimensional nanoarchitectures and their applications.

Abstract: 3.2. Thienothiophenes 1216 3.2.1. Thieno[3,4-b]thiophene Analogues 1216 3.2.2. Thieno[3,2-b]thiophene Analogues 1217 3.2.3. Thieno[2,3-b]thiophene Analogues 1218 3.3. , ′-Bridged Bithiophenes 1219 3.3.1. Dithienothiophene (DTT) Analogues 1220 3.3.2. Dithieno[3,2-b:2′3′-d]thiophene-4,4-dioxides 1221 3.3.3. Dithienosilole (DTS) Analogues 1221 3.3.4. Cyclopentadithiophene (CPDT) Analogues 1221 3.3.5. Nitrogen and Phosphor Atom Bridged Bithiophenes 1222