Amendra Fernando

New insights in the photochromic spiro-dihydroindolizine/betaine-system†‡

We have revisited the photochromic spiro-dihydroindolizine/betaine system by comparing state-of-the-art density functional theory calculations with experimental data. Time-dependent density functional theory calculations are employed to examine the transformations occurring after photoexcitation. This study confirms that photoexcitation of the spiro-dihydroindolizine leads to the formation of the cis-betaine. However, isomerization to the trans-betaine follows through a complicated and formerly unknown potential energy landscape, which consists of a network of transition states and intermediates. The available pathways across this potential energy landscape will determine the kinetics of the forward reaction from the cis-betaine to the trans-betaine and then, even more importantly, the back-reaction. Virtually all practical applications of this optical switch rely on these reactions and, therefore, occur within this landscape. Predicting the network of transition states and intermediates for substituted spiro-dihydroindolizine/betaine systems will enable the in-silico design of optical switches with enhanced performance.

Insights from Theory and Experiment on the Photochromic spiro-Dihydropyrrolo–Pyridazine/Betaine System

We elucidated the photochromic spiro-4a,5-dihydropyrrolo[1,2-b]pyridazine/betaine (DPP/betaine) system by comparing state-of-the-art density functional theory calculations with nanosecond/millisecond UV-vis absorption spectroscopy, as well as steady-state absorption and cyclization kinetics. Time-dependent density functional theory calculations are employed to examine the transformations occurring after photoexcitation. This study shows that the photochromic spiro-4a,5-dihydropyrrolo[1,2-b]pyridazine and spiro-1,8a-dihydroindolizine (DHI) systems react according to similar pathways. However, notable differences exist. Although photoexcitation of the spiro-DPP system also leads to cis-betaines, which then isomerize to trans-betaines, we found two distinct classes of cis isomers (cis-betaine rotamer-1 and cis-betaine rotamer-2), which do not exist in spiro-1,8a-dihydroindolizine. Similar to our previous study on the spiro-DHI/betaine system, a complicated potential-energy landscape between cis and trans isomers exists in the spiro-DPP system, consisting of a network of transition states and intermediates. Because the spiro-DPP/betaine is even more complicated than the spiro-DHI/betaine system, (substituted) photochromic systems featuring a 4a,5-dihydropyrrolo[1,2-b]pyridazine functional unit will require thorough in silico design to function properly as logical gates or in devices for information storage.

Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9

CRISPR-Cas9 is a genome editing technology with major impact in life sciences. In this system, the endonuclease Cas9 generates double strand breaks in DNA upon RNA-guided recognition of a complementary DNA sequence, which strictly requires the presence of a protospacer adjacent motif (PAM) next to the target site. Although PAM recognition is essential for cleavage, it is unknown whether and how PAM binding activates Cas9 for DNA cleavage at spatially distant sites. Here, we find evidence of a PAM-induced allosteric mechanism revealed by microsecond molecular dynamics simulations. PAM acts as an allosteric effector and triggers the interdependent conformational dynamics of the Cas9 catalytic domains (HNH and RuvC), responsible for concerted cleavage of the two DNA strands. Targeting such an allosteric mechanism should enable control of CRISPR-Cas9 functionality.

Theoretical Investigation of Water Oxidation on Fully Saturated Mn2O3 and Mn2O4 Complexes

Understanding the factors that affect efficiency of manganese oxides as water oxidation catalysts is an essential step toward developing commercially viable electrocatalysts. It is important to understand the performance of the smallest versions of these catalysts, which will in return be advantageous with bottom up catalytic design. Density functional theory calculations have been employed to investigate water oxidation processes on Mn2(μ-OH)(μ-O)(H2O)3(OH)5 (Mn2O4·6H2O), Mn2(μ-OH)2(H2O)3(OH)4 (Mn2O3·6H2O), and Mn2(μ-OH)2(H2O)4(OH)4 (Mn2O3·7H2O) complexes. The effect of different oxidation states of manganese is considered in this study. Thermodynamically, the lowest energy pathway for the fully saturated Mn2O4·6H2O complex occurs through a nucleophilic attack of a solvent water molecule to a Mn(IV1/2)O oxo moiety. The lowest energy pathway on the Mn2O3·6H2O complex proceeds with an attack of Mn(VI)O group to the surface hydroxo group on the same manganese atom; this pathway is related to the third lowest energy pathway on the Mn2O4·6H2O complex. The water oxidation process on the fully saturated Mn2O3·7H2O complex also involves a nucleophilic attack from a solvent water molecule to a Mn(V)O moiety. The formation of these manganese oxo groups can be used as a descriptor for selecting a manganese-based water splitting catalyst due to the high electrochemical potentials required for the generation of these groups.