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One of the more difficult concepts introduced in the first-year undergraduate course, general chemistry, is that of chirality. Typically, left and right hands are the common, macroscopic objects of reference used to demonstrate the quality of being nonsuperimposable, followed by the use of a mirror and molecular models, to illustrate molecular enantiomers. While this approach works well as an introduction, and the handedness model becomes more useful in organic chemistry where absolute R- and S-configuration assignment becomes necessary, it does not help the general chemistry student to determine molecular chirality or "handedness" at this basic level. Much of the difficulty stems from the representation of 3-dimensional (3-D) structures on the 2-dimensional (2-D) paper plane. While detailed flowcharts exist for molecules of varying orbital hybridization and geometry, these are more suited to advanced students in inorganic chemistry and are not designed to be mentally retained or learned. Additionally, the process of determining R- and S-configurations for carbon tetrahedral centers in organic chemistry is more complex as ligands must be ranked according to Cahn-Ingold-Prelog (CIP) rules. Previous publications have addressed this topic thoroughly. A simple method is presented here (called clocking) which introduces the concept of chirality for general chemistry and primes the way for more complex chirality assignments in higher level courses.

Research has been conducted on the Cys beta93 sulfhydryl group. The conformational consequences of the chemically modifying the Cys beta93 sulfhydryl group of the deoxy and CO-saturated derivatives of the human adult hemoglobin have been investigated via the use of the maleimide and mixed disulfide reagents and the results are reported.

Time-resolved fluorescence anisotropy and steady-state UV resonance Raman (UVRR) spectroscopies were performed to characterize the dynamics involved in the enzymatic activity of Yersinia protein tyrosine phosphatases (PTPase). The results indicated that the catalytic WpD loop motion in wild-type Yersinia proceeds continuously and rapidly in the absence of substrate with the rates of opening and closing of the loop almost the same such that the distribution of open and closed W354 conformers is nearly equal. Upon ligand binding, the rate of opening was observed to be quite slow while the rapid rate of closing is maintained, resulting to a predominance of the WpD closed loop conformation.

Hydrogen bonding at the indole amine, weaker, electrostatic cation-[pi] and anion-quadrapole interactions, and environmental hydrophobicity are examined to gain insight into factors which contribute to sterically hindered ranges of dihedral angle that reduce the possible [X.sup.2,1] to one or two. The full width half-maximum bandwidth (fwhm) of the W3 band measurement is suggested as a primary screen for evaluating the applicability of the ?W3-[X.sup.2,1] relationship.

Modulation of reactivity and conformation within the T-quaternary state of hemoglobin are evaluated and examined using a combination of mutagenesis and sol-gel encapsulation. A qualitative model presented suggests that different T-quaternary structures modulate the stability of different alphabeta dimer conformations within the tetramer.

The Raman UV resonance spectroscopies are used to study the conformational properties of both the deoxy and deoxy-turned-carbonmonoxy (CO) derivatives of Hb-A derived from encapsulation protocols. The results show that the initial deoxy-HbA populations are conformationally indistinguishable with respect to the encapsulation protocol.

Severalnonradiative processes compete with tryptophan fluorescenceemission. The difficulty in spectral interpretation lies in associatingspecific molecular environmental features with these processes andthereby utilizing the fluorescence spectral data to identify the localenvironment of tryptophan. Here, spectroscopic and molecular modelingstudy of Lys-Trp dipeptide charged species shows that backbone-ringinteractions are undistinguished. Instead, quantum mechanical groundstate isosurfaces reveal variations in indole π electron distributionand density that parallel charge (as a function of pK1, pK2, and pKR) on the backbone and residues. A pattern of aromaticity-associatedquantum yield and fluorescence lifetime changes emerges. Where quantumyield is high, isosurfaces have a charge distribution similar to thehighest occupied molecular orbital (HOMO) of indole, which is thedominant fluorescent ground state of the 1Latransition dipole moment. Where quantum yield is low, isosurfacecharge distribution over the ring is uneven, diminished, and evenfound off ring. At pH 13, the indole amine is deprotonated, and Lys-Trpquantum yield is extremely low due to tautomer structure that concentratescharge on the indole amine; the isosurface charge distribution bearsscant resemblance to the indole HOMO. Such greatly diminished fluorescencehas been observed for proteins where the indole nitrogen is hydrogenbonded, lending credence to the association of aromaticity changeswith diminished quantum yield in proteins as well. Thus tryptophanground state isosurfaces are an indicator of indole aromaticity, signalingthe partition of excitation energy between radiative and nonradiativeprocesses. [ABSTRACT FROM AUTHOR]

Although tryptophan is a natural probe of protein structure, interpretation of its fluorescence emission spectrum is complicated by the presence of two electronic transitions, 1 La and 1 Lb. Theoretical calculations show that a point charge adjacent to either ring of the indole can shift the emission maximum. This study explores the effect of pyrrole and benzyl ring substitutions on the transitions' energy via absorption and fluorescence spectroscopy, and anisotropy and lifetime measurements. The survey of indole derivatives shows that methyl substitutions on the pyrrole ring effect 1 La and 1 Lb energies in tandem, whereas benzyl ring substitutions with electrophilic groups lift the 1 La/1 Lb degeneracy. For 5- and 6-hydroxyindole in cyclohexane, 1 La and 1 Lb transitions are resolved. This finding provides for 1 La origin assignment in the absorption and excitation spectra for indole vapor. The 5- and 6-hydroxyindole excitation spectra show that despite a blue-shifted emission spectrum, both the 1 La and 1 Lb transitions contribute to emission. Fluorescence lifetimes of 10 ns for 5-hydroxyindole are consistent with a charge acceptor-induced increase in the nonradiative rate (1). [ABSTRACT FROM AUTHOR]

The correlation of the UVRR vW3 mode with the tryptophan χ2,1 dihedral angle [Maruyama and Takeuchi (1995) J. Raman Spectrosc. 26, 319; Miura et al. (1989) J. Raman Spectrosc. 20, 667; Takeuchi (2003) Biopolymers 72, 305] has been extended to a full, 3600 rotation. The 3-fold periodicity of the relationship (cos 3χ2,1) over 360° results in up to six dihedral angles for a given vW3. Consideration of a Newman plot of dihedral angles for proteinaceous tryptophans taken from the Protein Data Bank shows that sterically hindered ranges of dihedral angle reduce the possible χ2,1 to one or two. However, not all proteinaceous tryptophans follow the vW3-χ2,1 relationship. Hydrogen bonding at the indole amine, weaker, electrostatic cation-π and anion-quadrapole interactions, and environmental hydrophobicity are examined as possible contributing factors to noncompliance with the relationship. This evaluation suggests that cumulative weak electrostatic and nonpolar interactions, contributing to steric hindrance, characterize the environment of tryptophans that obey the vW3-χ2,1 relationship, matching that of the crystalline tryptophan derivatives used to formulate the relationship. In the absence of methods to quantify these weak interactions, measurement of the full width half-maximum bandwidth (fwhm) of the W3 band is suggested as a primary screen for evaluating the applicability of the vW3-χ2,1 relationship. [ABSTRACT FROM AUTHOR]

Evaluates the conformational consequences of chemically modifying the Cys beta93 sulfhydryl group of both the deoxy and carbon monoxide-saturated derivatives of human adult hemoglobin. Effect of the conformation of both linker chemistry and poly(ethylene glycol) size; Generation of several derivatives through a maleimide reaction with sulfhydryl.

Although tryptophan is a natural probe of protein structure, interpretation of its fluorescence emission spectrum is complicated by the presence of two electronic transitions, (1)L(a) and (1)L(b). Theoretical calculations show that a point charge adjacent to either ring of the indole can shift the emission maximum. This study explores the effect of pyrrole and benzyl ring substitutions on the transitions' energy via absorption and fluorescence spectroscopy, and anisotropy and lifetime measurements. The survey of indole derivatives shows that methyl substitutions on the pyrrole ring effect (1)L(a) and (1)L(b) energies in tandem, whereas benzyl ring substitutions with electrophilic groups lift the (1)L(a)/(1)L(b) degeneracy. For 5- and 6-hydroxyindole in cyclohexane, (1)L(a) and (1)L(b) transitions are resolved. This finding provides for (1)L(a) origin assignment in the absorption and excitation spectra for indole vapor. The 5- and 6-hydroxyindole excitation spectra show that despite a blue-shifted emission spectrum, both the (1)L(a) and (1)L(b) transitions contribute to emission. Fluorescence lifetimes of 1(0) ns for 5-hydroxyindole are consistent with a charge acceptor-induced increase in the nonradiative rate (1)., (© 2012 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2012 The American Society of Photobiology.)

The correlation of the UVRR nuW3 mode with the tryptophan chi(2,1) dihedral angle [Maruyama and Takeuchi (1995) J. Raman Spectrosc. 26, 319; Miura et al. (1989) J. Raman Spectrosc. 20, 667; Takeuchi (2003) Biopolymers 72, 305] has been extended to a full, 360 degrees rotation. The 3-fold periodicity of the relationship (cos 3chi(2,1)) over 360 degrees results in up to six dihedral angles for a given nuW3. Consideration of a Newman plot of dihedral angles for proteinaceous tryptophans taken from the Protein Data Bank shows that sterically hindered ranges of dihedral angle reduce the possible chi(2,1) to one or two. However, not all proteinaceous tryptophans follow the nuW3-chi(2,1) relationship. Hydrogen bonding at the indole amine, weaker, electrostatic cation-pi and anion-quadrapole interactions, and environmental hydrophobicity are examined as possible contributing factors to noncompliance with the relationship. This evaluation suggests that cumulative weak electrostatic and nonpolar interactions, contributing to steric hindrance, characterize the environment of tryptophans that obey the nuW3-chi(2,1) relationship, matching that of the crystalline tryptophan derivatives used to formulate the relationship. In the absence of methods to quantify these weak interactions, measurement of the full width half-maximum bandwidth (fwhm) of the W3 band is suggested as a primary screen for evaluating the applicability of the nuW3-chi(2,1) relationship.

Previous mutational studies on Tyr42alpha variants as well as the current studies on the mutant hemoglobin alphaY42A show that the intersubunit interactions associated with Tyr42alpha significantly stabilize the alpha1beta2 interface of the quaternary-T deoxyhemoglobin tetramer. However, crystallographic studies, UV and visible resonance Raman spectroscopy, CO combination kinetic measurements, and oxygen binding measurements on alphaY42A show that the intersubunit interactions formed by Tyr42alpha have only a modest influence on the structural properties and ligand affinity of the deoxyhemoglobin tetramer. Therefore, the alpha1beta2 interface interactions associated with Tyr42alpha do not contribute significantly to the quaternary constraints that are responsible for the low oxygen affinity of deoxyhemoglobin. The slight increase in the ligand affinity of deoxy alphaY42A correlates with small, mutation-induced structural changes that perturb the environment of Trp37beta, a critical region of the quaternary-T alpha1beta2 interface that has been shown to be the major source of quaternary constraint in deoxyhemoglobin.