Ultrafast Spectroscopy of Hydroxy-Substituted Azobenzenes in Water.

Ultrafast UV/Vis pump/probe experiments on ortho-, meta- and para-hydroxy-substituted azobenzenes (HO-ABs), as well as for sulfasalazine, an AB-based drug, were performed in aqueous solution. For meta-HO-AB, AB-like isomerisation behaviour can be observed, whereas, for ortho-HO-AB, fast proton transfer occurs, resulting in an excited keto species. For para-HO-AB, considerable keto/enol tautomerism proceeds in the ground state, so after excitation the trans-keto species isomerises into the cis form.

Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation.

Transcription factor IIS (TFIIS) is a protein known for catalyzing the cleavage reaction of the 3'-end of backtracked RNA transcript, allowing RNA polymerase II (Pol II) to reactivate the transcription process from the arrested state. Recent structural studies have provided a molecular basis of protein-protein interaction between TFIIS and Pol II. However, the detailed dynamic conformational changes of TFIIS upon binding to Pol II and the related thermodynamic information are largely unknown.

A theoretical study of the photochemistry of indigo in its neutral and dianionic (leucoindigo) forms.

A thorough analysis of the single and double proton transfer and the internal rotations of neutral indigo and its dianionic leucoindigo form has been performed for the ground and first singlet excited electronic states using, respectively, DFT and TDDFT state-of-the-art methods. Our theoretical analysis discloses that the diketo isomer is the most stable one in the ground state of indigo but not in leucoindigo where the dienol minimum is more stable. Single and double proton transfer processes are not energetically favored in the ground electronic state but a single proton transfer gives a more stable tautomer in the excited electronic state of indigo whereas a double proton transfer is energetically favorable in the excited state of leucoindigo.

On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations.

We use thermodynamic integration (TI) and explicit solvent molecular dynamics (MD) simulation to estimate the absolute free energy of host-guest binding. In the unbound state, water molecules visit all of the internally accessible volume of the host, which is fully hydrated on all sides. Upon binding of an apolar guest, the toroidal host cavity is fully dehydrated; thus, during the intermediate λ stages along the integration, the hydration of the host fluctuates between hydrated and dehydrated states.

Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics.

In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry.

Identification of potential small molecule binding pockets on Rho family GTPases.

Rho GTPases are conformational switches that control a wide variety of signaling pathways critical for eukaryotic cell development and proliferation. They represent attractive targets for drug design as their aberrant function and deregulated activity is associated with many human diseases including cancer. Extensive high-resolution structures (>100) and recent mutagenesis studies have laid the foundation for the design of new structure-based chemotherapeutic strategies.

Thermodynamic integration to predict host-guest binding affinities.

An alchemical free energy method with explicit solvent molecular dynamics simulations was applied as part of the blind prediction contest SAMPL3 to calculate binding free energies for seven guests to an acyclic cucurbit-[n]uril host. The predictions included determination of protonation states for both host and guests, docking pose generation, and binding free energy calculations using thermodynamic integration. We found a root mean square error (RMSE) of 3.

Bipyridyl derivatives as photomemory devices: a comparative electronic-structure study.

The two isoelectronic bipyridyl derivatives [2,2'-bipyridyl]-3,3'-diamine (BP(NH(2))(2)) and [2,2'-bipyridyl]-3,3'-diol (BP(OH)(2)) are experimentally known to undergo very different excited-state double proton transfer processes that result in fluorescence quantum yields that differ by four orders of magnitude. Such differences have been theoretically explained in terms of topographical features in the potential energy surface and the likely presence of conical intersections. The hypothetical hybrid compound [2,2'-bipyridyl]-3-amin-3'-ol (BP(OH)(NH(2))) presents intermediate photochemical features of its "ancestors".

Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline.

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a (pi,pi( *)) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet (pi,pi( *)) excited electronic states.

Study of the photochemical properties and conical intersections of [2,2'-bipyridyl]-3-amine-3'-ol.

The two isoelectronic bipyridyl derivatives [2,2'-bipyridyl]-3,3'-diamine and [2,2'-bipyridyl]-3,3'-diol are experimentally known to undergo very different excited-state double-proton-transfer processes, which result in fluorescence quantum yields that differ by four orders of magnitude. In a previous study, these differences were explained from a theoretical point of view, because of topographical features in the potential energy surface and the presence of conical intersections (CIs). Here, we analyze the photochemical properties of a new molecule, [2,2'-bipyridyl]-3-amine-3'-ol [BP(OH)(NH(2))], which is, in fact, a hybrid of the former two.

Electronic and quantum dynamical insight into the ultrafast proton transfer of 1-hydroxy-2-acetonaphthone.

The ultrafast proton-transfer dynamics of 1-hydroxy-2-acetonaphthone has been theoretically analyzed in the ground and first singlet excited electronic states by density functional theory calculations and quantum dynamics. The potential energies obtained in the ground electronic state reveal that the proton-transfer process does not lead to a stable keto tautomer unless the transfer of the hydrogen from the enol form is accompanied by an internal rotation of the newly formed O-H bond. Calculations in the first singlet excited electronic state point to a very low barrier for the formation of the keto tautomer.

A comparative study on the photochemistry of two bipyridyl derivatives: [2,2'-bipyridyl]-3,3'-diamine and [2,2'-bipyridyl]-3,3'-diol.

The two isoelectronic bipyridyl derivatives, [2,2'-bipyridyl]-3,3'-diamine and [2,2'-bipyridyl]-3,3'-diol, are experimentally known to undergo very different excited-state double-proton-transfer processes, which result in fluorescence quantum yields that differ by four orders of magnitude. Herein, density functional theory (DFT), time-dependent DFT (TDDFT), and complete active space self-consistent field (CASSCF) calculations are used to study the double-proton-transfer processes in the ground and first singlet pi-->pi* excited state. The quantum-chemistry calculations indicate 1) the existence of only one energy minimum in the ground electronic state corresponding to reactants (thus avoiding the possibility of a fast fluorescent relaxation process from the photoproducts region), 2) an endoergic process of the complete double proton transfer, and 3) the presence of a conical intersection in the excited intermediate region of [2,2'-bipyridyl]-3,3'-diamine.

Theoretical study on the excited-state intramolecular proton transfer in the aromatic schiff base salicylidene methylamine: an electronic structure and quantum dynamical approach.

The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theoretically analyzed in the ground and first singlet (pi,pi) excited electronic states by density functional theory calculations and quantum wave-packet dynamics. The potential energies obtained through electronic calculations that use the time-dependent density functional theory formalism, which predict a barrierless excited-state intramolecular proton transfer, are fitted to a reduced three-dimensional potential energy surface. The time evolution in this surface is solved by means of the multiconfiguration time-dependent Hartree algorithm applied to solve the time-dependent Schrödinger equation.