Color vision: "OH-site" rule for seeing red and green

Eyes gather information, and color forms an extremely important component of the information, more so in the case of animals to forage and navigate within their immediate environment. By using the ONIOM (QM/MM) (ONIOM = our own N-layer integrated molecular orbital plus molecular mechanics) method, we report a comprehensive theoretical analysis of the structure and molecular mechanism of spectral tuning of monkey red- and green-sensitive visual pigments. We show that interaction of retinal with three hydroxyl-bearing amino acids near the β-ionone ring part of the retinal in opsin, A164S, F261Y, and A269T, increases the electron delocalization, decreases the bond length alternation, and leads to variation in the wavelength of maximal absorbance of the retinal in the red- and green-sensitive visual pigments. On the basis of the analysis, we propose the "OH-site" rule for seeing red and green. This rule is also shown to account for the spectral shifts obtained from hydroxyl-bearing amino acids near the Schiff base in different visual pigments: at site 292 (A292S, A292Y, and A292T) in bovine and at site 111 (Y111) in squid opsins. Therefore, the OH-site rule is shown to be site-specific and not pigment-specific and thus can be used for tracking spectral shifts in any visual pigment.     

The Effects of Ring Strain on Cyclic Tetraaryl[5]cumulenes

Cyclic tetraaryl[5]cumulenes ( 1 a–f ) have been synthesized and studied as a function of increasing ring strain. The magnitude of ring strain is approximated by the extent of bending of the cumulenic core as assessed by a combination of X-ray crystallographic analysis and DFT calculations. Trends are observed in ¹³C NMR, UV-vis, and Raman spectra associated with ring strain, but the effects are small. In particular, the experimental HOMO-LUMO gap is not appreciably affected by bending of the [5]cumulene framework from ca. 174° (λ_max=504 nm) in 1 a to ca. 178° (λ_max=494 nm) in 1 f .     

Synthesis of chlorophyll-a derivatives possessing the 3-(2-acylethenyl) group by cross-aldol condensation and their optical properties

Chlorophyll-a derivatives possessing a trans-2-acylethenyl group at the C3-position were prepared by cross-aldol (Claisen-Schmidt) condensation of methyl pyropheophorbide-d having the C3-formyl group with ketones bearing α-hydrogen atoms including (un)substituted acetophenones, acetylarenes, and alkanones under basic conditions. The Qy absorption and fluorescence emission bands of the synthetic chalcone analogs in dichloromethane were largely dependent on the C3³-substituents. Especially, the introduction of electron-donating and withdrawing groups to the C3³-phenyl ring resulted in bathochromic and hypsochromic shifts of the maxima, respectively. Furthermore, fluorescence quantum yields and lifetimes were largely suppressed by the substitution with a nitro group on the C3³-phenyl ring.     

Bivariate distributions in statistical spectroscopy studies: IV. Interacting particle Gamow-Teller strength densities and β-decay rates offp-shell nuclei for presupernova stars

A method to calculate temperature dependent-decay rates is developed by writing the expression for the rates explicitly in terms of bivariateGT strength densities (I _O ^H _(GT)) for a given hamiltonianH=h+V and state densities of the parent nucleus besides having the usual phase space factors. The theory developed in the preceding paper (III) for constructing NIP strength densities is applied for generatingI _O ^h _(GT) and thenI _O ^H _(GT) is constructed using the bivariate convolution formI _O ^H _(GT)= _S I _O(GT) ^h,S _O(GT) ^V,S ; _BIV-G . The spreading bivariate Gaussian _O(GT) ^V ;BIV-G, forfp-shell nuclei, is constructed by assuming that the marginal centroids are zero, the marginal variances are same as the corresponding state density variances and fixing the bivariate correlation coefficient using experimental-decay half lifes. With the deduced values of 0.67,-S-decay rates for^61,62Fe and^62–64Co isotopes are calculated at presupernova matter densities=10⁷–10⁹ gm/cc, temperaturesT=(3–5)×10⁹ K and electron fractions Y_e=0.43–0.5. The convolution form forI _O(GT) ^H led to a simple expression for calculatingGT non-energy weighted sum rule strength and it describes (within 10%) the shell model results offp-shell nuclei.The work presented in this paper has grown out of many discussions and correspondence one of the authors (VKBK) has with J.B. French in the last five years and also out of an ongoing project one of the authors (VKBK) is carrying out with J.B. French and R.U. Haq. Thanks are due to K. Kar and S. Sarkar for supplying some of their results before publishing. The authors thank V. Potbhare for his interest in the work presented in this paper.     

Facile iodination of the vinyl groups in protoporphyrin IX dimethyl ester and subsequent transformation of the iodinated moieties

Iodination of protoporphyrin IX dimethyl ester using phenyliodine bis(trifluoroacetate) (PIFA) and I₂ was studied. Iodine added to both the C3- and C8-vinyl groups equally to afford the iodohydrin or iodoether in the presence of water or alcohol, respectively. Any meso-hydrogen atom was not substituted by an iodine atom under these conditions, although both the vinyl group and one of the meso positions of methyl pyropheophorbide-a bearing a chlorin π-system, a chlorophyll-a derivative, was modified with PIFA and I₂. The reaction intermediates derived from the porphyrin were more reactive than those from the chlorin and liable to form intermolecular linkages. The obtained 2-iodo-1-hydroxyethyl group was transformed into a formyl group by a mild treatment. The corresponding iodoether moiety was readily converted into the acetyl group under basic conditions. These transformations were also applicable to smaller olefins such as styrene.     

Local physical quantities for spin based on the relativistic quantum field theory in molecular systems

Local physical quantities for spin are investigated on the basis of the four‐ and two‐component relativistic quantum theory. In the quantum field theory, local physical quantities for spin such as the spin angular momentum density, spin torque density, zeta force density, and zeta potential play important roles in spin dynamics. We discuss how to calculate these local physical quantities based on the two‐component relativistic quantum theory. Some different types of relativistic numerical calculations of local physical quantities in Li atom and C₆H₆ are demonstrated and compared. Local physical quantities for each orbital are also discussed, and it is seen that a total local zeta potential is given as a result of some cancellation of large contributions from each orbital. © 2016 Wiley Periodicals, Inc.