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. Aided by TD-DFT calculations, insight is provided into different deactivation pathways for HO-AB, and reveals the role of hydroxy groups in the photochemistry of ABs, as well as their acetylation regarding sulfasalazine. Hydroxy groups are position-specific substituents for AB, which allow tuning of the timescale of thermal relaxation, as well as the amount and contribution of the keto species to photochemical processes.

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. Here we use computational approaches to investigate the conformational space of TFIIS in the Pol II-bound and Pol II-free (unbound) states. Our results reveal two distinct conformations of TFIIS: the closed and the open forms. The closed form is dominant in the Pol II-free (unbound) state of TFIIS, whereas the open form is favorable in the Pol II-bound state. Furthermore, we discuss the free energy difference involved in the conformational changes between the two forms in the presence or absence of Pol II. Additionally, our analysis indicates that hydrophobic interactions and the protein-protein interactions between TFIIS and Pol II are crucial for inducing the conformational changes of TFIIS. Our results provide novel insights into the functional interplay between Pol II and TFIIS as well as mechanism of reactivation of Pol II transcription by TFIIS.

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. The internal rotations are not thermodynamically allowed except for the keto-enol tautomer where a full rotation of the inter-ring C-C bond leads to another stable keto-enol structure. A preliminary analysis of the plausible conical intersections for both indigo and leucoindigo allows the discussion of the likely deactivation paths that will follow light irradiation. Our results point to a very different photochemistry of the two molecules. For indigo the proton transfer can only take place through tunneling so the main deactivation path would involve a conical intersection accessed directly upon internal rotation of the keto-keto tautomer. For leucoindigo a richer photochemistry is expected as the single and double proton transfer processes are energetically open. The more favorable path involves single proton transfer followed by a trans to cis isomerization and a second proton transfer. This process competes on equal grounds with several non-radiative decays through conical intersections. All these results are in agreement with the experimental facts known to date.

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. Estimating free energies by TI can be especially challenging when there is a considerable difference in hydration between the two states of interest. We investigate these aspects using the popular TIP3P and TIP4P water models. TI free energy estimates through MD largely depend on water-related interactions, and water dynamics significantly affect the convergence of binding free energy calculations. Our results indicate that wetting/dewetting transitions play a major role in slowing the convergence of free energy estimation. We employ two alternative approaches-one analytical and the other empirically based on actual MD sampling-to correct for the standard state free energy. This correction is sizable (up to 4 kcal/mol), and the two approaches provide corrections that differ by about 1 kcal/mol. For the system considered here, the TIP4P water model combined with an analytical correction for the standard state free energy provides higher overall accuracy. This observation might be transferable to other systems in which water-related contributions dominate the binding process.

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. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra.

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. Although the inhibition of Rho signaling with drug-like compounds is an active area of current research, very little attention has been devoted to directly inhibiting Rho by targeting potential allosteric non-nucleotide binding sites. By avoiding the nucleotide binding site, compounds may minimize the potential for undesirable off-target interactions with other ubiquitous GTP and ATP binding proteins. Here we describe the application of molecular dynamics simulations, principal component analysis, sequence conservation analysis, and ensemble small-molecule fragment mapping to provide an extensive mapping of potential small-molecule binding pockets on Rho family members. Characterized sites include novel pockets in the vicinity of the conformationaly responsive switch regions as well as distal sites that appear to be related to the conformations of the nucleotide binding region. Furthermore the use of accelerated molecular dynamics simulation, an advanced sampling method that extends the accessible time-scale of conventional simulations, is found to enhance the characterization of novel binding sites when conformational changes are important for the protein mechanism.

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 3.6 kcal mol(-1) from the reference experimental results, with an R(2) correlation of 0.51. The agreement with experiment for the largest contributor to this error, guest 6, is improved by 1.7 kcal mol(-1) when a periodicity-induced free energy correction is applied. The corrections for the other ligands were significantly smaller, and altogether the RMSE was reduced by 0.4 kcal mol(-1). We link properties of the host-guest systems during simulation to errors in the computed free energies. Overall, we show that charged host-guest systems studied here, initialized in unconfirmed docking poses, present a challenge to accurate alchemical simulation methods.

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". In this report we analyze the photochemical properties of a whole family of "dark" (not fluorescent) states that can be accessed from each bipyridyl derivative upon irradiation of light of a given wavelength and their potential application as photomemory devices. In the light of our density functional theory (DFT), time-dependent DFT (TDDFT), and complete active space self-consistent field (CASSCF) calculations, BP(NH(2))(2) is the more likely candidate to become a photomemory device.

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. The electronic energies obtained by the time-dependent density functional theory formalism have been fitted to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.

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. Our density functional theory (DFT), time-dependent DFT (TDDFT), and complete active space self-consistent field (CASSCF) calculations indicate that the double-proton-transfer process in the ground and first singlet pi-->pi* excited state in BP(OH)(NH(2)) presents features that are between those of their "parents". The presence of two CIs and the role they may play in the actual photochemistry of BP(OH)(NH(2)) and other bipyridyl derivatives are also discussed.

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. The analysis of the calculated frequencies of the two tautomers in the excited state unveils a coupling of the skeletal motions (low frequency modes) with the proton-transfer process, as it has been stated from time-resolved experiments. The electronic energies obtained by the time-dependent density functional theory formalism have been fitted to a monodimensional potential energy surface in order to perform an exact quantum dynamics study of the process. Our results show that the proton-transfer process is completed within 25.5 fs, in remarkable good agreement with experiments.

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. These facts explain the very low fluorescence quantum yield in [2,2'-bipyridyl]-3,3'-diamine compared to [2,2'-bipyridyl]-3,3'-diol.

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. It is shown that the excited-state proton transfer occurs within 11 fs for hydrogen and 25 fs for deuterium, so that a large kinetic isotope effect is predicted. These results are compared to those of the only previous theoretical work published on this system [Zgierski, M. Z.; Grabowska, A. J. Chem. Phys. 2000, 113, 7845], reporting a configuration interaction singles barrier of 1.6 kcal mol(-1) and time reactions of 30 and 115 fs for the hydrogen and deuterium transfers, respectively, evaluated with the semiclassical instanton approach.