Electronic Spectroscopy of 2-Phenyl-1,3,2-benzodioxaborole and Its Derivatives: Important Building Blocks of Covalent Organic Frameworks.

Aryl boronate esters, such as 2-phenyl-1,3,2-benzodioxaborole (1), are important components in the formation of a variety of covalent organic frameworks. The addition of substituents on the aromatic rings of aryl boronate esters has the potential to modify the structure, reactivity, and electronic properties of the resulting materials, and so, it is useful to understand at a more fundamental level the properties of these important compounds. Experimental measurements and computational investigations are presented herein that provide insight regarding the structural and electronic properties of parent aryl boronate ester 1 as well as three substituted derivatives: 2-(o-tolyl)-1,3,2-benzodioxaborole (2), 2-(2,6-dimethylphenyl)-1,3,2-benzodioxaborole (3), and 2-(4-(tert-butyl)phenyl)-1,3,2-benzodioxaborole (4). Electronic spectroscopy combined with excited-state calculations reveal two closely spaced electronic states, S1 and S2, which appear to have excitation primarily localized on the aromatic system of the phenyl substituent or the catecholborane moiety, respectively. Interestingly, the ortho-dimethyl derivative (3) shows a significantly red-shifted electronic origin with an extensive vibronic progression of a low-frequency torsional motion about the C-B bond. Franck-Condon calculations on the ab initio determined ground- and excited-state potentials very accurately reproduce this spectrum, confirming the nonplanar ground state of this compound.

Quantitative probing of subtle interactions among H-bonds in alpha hydroxy carboxylic acid complexes.

Hydrogen (H) bonds are of fundamental importance in a wide range of molecular sciences. While the study of two-center H-bonding AH is well advanced, much remains to be learned in a quantitative and definitive manner for complexes with multiple H-bonds. Exemplary cases are in the category of alpha hydroxy carboxylic acids, i.e., the complexes of glycolic acid with water and formic acid. In glycolic acid, an intramolecular H-bond forms between the carboxyl group and the alpha OH group. The alpha OH stretching frequency may be affected upon complexing with water or formic acid. Direct study of glycolic acid complexes is unfortunately very difficult. However, an aromatic analogue, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), permits detailed and accurate gas phase spectroscopic studies. Since computational analysis establishes that H-bonding is very similar from glycolic acid complexes to 9HFCA complexes, direct studies on 9HFCA complexes by laser spectroscopy also deduce new and subtle information for glycolic acid complexes in terms of molecular structures, binding strength, and collective effects of multiple H-bonds associated with anti-cooperativity and cooperativity.

Communication: Physical origins of ionization potential shifts in mixed carboxylic acids and water complexes.

The ionization potential (IP) of the aromatic alpha hydroxy carboxylic acid, 9-hydroxy-9-fluorene carboxylic acid (9HFCA), is shifted by complexation with hydrogen bonding ligands such as water and formic acid. Generalized Kohn-Sham energy decomposition analysis decomposes the intermolecular binding energies into a frozen energy term, polarization, correlation, and/or dispersion energy terms, as well as terms of geometric relaxation and zero point energy. We observe that in each dimer the attractive polarization always increases upon ionization, enhancing binding in the cation and shifting the IP toward the red. For 9HFCA-H2O, a substantial decrease of the repulsive frozen energy in cation further shifts the IP toward red. For 9HFCA-HCOOH, the increase of the frozen energy actually occurs in the cation and shifts the IP toward blue. Consistent with the experimental measurements, our analysis provides new, non-intuitive perspectives on multiple hydrogen bonds interactions in carboxylic acids and water complexes.

Characterization of two adenosine analogs as fluorescence probes in RNA.

The fluorescence properties of two adenosine analogs, 2-(3-phenylpropyl)adenosine [A-3CPh] and 2-(4-phenylbutyl)adenosine [A-4CPh], are reported. As monomers, the quantum yields and the mean lifetimes are 0.011 and 6.22 ns for A-3CPh and 0.007 and 7.13 ns for A-4CPh, respectively. Surprisingly, the quantum yields of the two probes are enhanced 11- to 82-fold upon incorporation into RNA, while the mean lifetimes decrease 23-40%. The data suggest that a subpopulation of molecules is responsible for the fluorescence characteristics and that the distribution of emitting and non-emitting structures is altered upon incorporation of the probes into RNA. Thus, although both adenosine analogs have low quantum yields as monomers, their fluorescence signals are significantly enhanced in RNA. Thermodenaturation experiments and CD spectroscopy indicate that incorporation of the adenosine analogs into three different RNAs does not alter their global structure or stability. Therefore, these probes should be useful for probing events occurring close to the site of modification.

Characterization of the dynamics of an essential helix in the U1A protein by time-resolved fluorescence measurements.

The RNA recognition motif (RRM), one of the most common RNA-binding domains, recognizes single-stranded RNA. A C-terminal helix that undergoes conformational changes upon binding is often an important contributor to RNA recognition. The N-terminal RRM of the U1A protein contains a C-terminal helix (helix C) that interacts with the RNA-binding surface of a beta-sheet in the free protein (closed conformation), but is directed away from this beta-sheet in the complex with RNA (open conformation). The dynamics of helix C in the free protein have been proposed to contribute to binding affinity and specificity. We report here a direct investigation of the dynamics of helix C in the free U1A protein on the nanosecond time scale using time-resolved fluorescence anisotropy. The results indicate that helix C is dynamic on a 2-3 ns time scale within a 20 degrees range of motion. Steady-state fluorescence experiments and molecular dynamics simulations suggest that the dynamical motion of helix C occurs within the closed conformation. Mutation of a residue on the beta-sheet that contacts helix C in the closed conformation dramatically destabilizes the complex (Phe56Ala) and alters the steady-state fluorescence, but not the time-resolved fluorescence anisotropy, of a Trp in helix C. Mutation of Asp90 in the hinge region between helix C and the remainder of the protein to Ala or Gly subtly alters the dynamics of the U1A protein and destabilizes the complex. Together these results show that helix C maintains a dynamic closed conformation that is stable to these targeted protein modifications and does not equilibrate with the open conformation on the nanosecond time scale.