A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction

Computational studies for the development of extracellular vesicle-based biosensors

Cancer affects millions of people, and early detection and efficient treatment are two strong levers to hurdle this disease. Recent studies on exosomes, a subset of extracellular vesicles, have deliberately shown the potential to function as a biomarker or treatment tool, thereby attracting the attention of researchers who work on developing biosensors. Due to the ability of computational methods to predict of the behavior of biomolecules, the combination of experimental and computational methods would enhance the analytical performance of the biosensor, including sensitivity, accuracy, and specificity, even detecting such vesicles from bodily fluids. In this regard, the role of computational methods such as molecular docking, molecular dynamics simulation, and density functional theory is overviewed in the development of biosensors. This review highlights the investigations and studies that have been reported using these methods to design exosome-based biosensors. This review concludes with the role of the quantum mechanics/molecular mechanics method in the investigation of chemical processes of biomolecular systems and the deficiencies in using this approach to develop exosome-based biosensors. In addition, the artificial intelligence theory is explained briefly to show its importance in the study of these biosensors.

PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics

PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.

MiMiC: A high-performance framework for multiscale molecular dynamics simulations

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.g., CPU/GPU), and keep their setup and execution as close as possible to the original. At the moment, MiMiC offers an efficient implementation of electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) that has demonstrated unprecedented parallel scaling in simulations of large biomolecules using CPMD and GROMACS as QM and MM engines, respectively. However, as it is designed for high flexibility with general multiscale models in mind, it can be straightforwardly extended beyond QM/MM. In this article, we illustrate the software design and the features of the framework, which make it a compelling choice for multiscale simulations in the upcoming era of exascale high-performance computing.

Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM

Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.

Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM

We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible.

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics

The impact of different initial conditions in non-adiabatic trajectory surface hopping dynamics within a hybrid quantum mechanical/molecular mechanics scheme is investigated. The influence of a quantum sampling, based on a Wigner distribution, a fully thermal sampling, based on classical molecular dynamics, and a quantum sampled system, but thermally equilibrated with the environment, is investigated on the relaxation dynamics of solvated fulvene after light irradiation. We find that the decay from the first singlet excited state to the ground state shows high dependency on the initial condition and simulation parameters. The three sampling methods lead to different distributions of initial geometries and momenta, which then affect the fate of the excited state dynamics. We evaluated both the effect of sampling geometries and momenta, analysing how the ultrafast decay of fulvene changes accordingly. The results are expected to be of interest to decide how to initialize non-adiabatic dynamics in the presence of the environment. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.

Review on the QM/MM Methodologies and Their Application to Metalloproteins

The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.

Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores

Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.

QM/MM Nonadiabatic Dynamics: the SHARC/COBRAMM Approach

We present the SHARC/COBRAMM approach to enable easy and efficient excited-state dynamics simulations at different levels of electronic structure theory in the presence of complex environments using a quantum mechanics/molecular mechanics (QM/MM) setup. SHARC is a trajectory surface-hoping method that can incorporate the simultaneous effects of nonadiabatic and spin-orbit couplings in the excited-state dynamics of molecular systems. COBRAMM allows ground- and excited-state QM/MM calculations using a subtractive scheme, with electrostatic embedding and a hydrogen link-atom approach. The combination of both free and open-source program packages provides a modular and extensive framework to model nonadiabatic processes after light irradiation from the atomistic scale to the nano-scale. As an example, the relaxation of acrolein from S₁ to T₁ in solution is provided.

Concerted hydrolysis mechanism of HIV-1 natural substrate against subtypes B and C-SA PR: insight through molecular dynamics and hybrid QM/MM studies

It is well known that understanding the catalytic mechanism of HIV-1 PR is the rationale on which its inhibitors were developed; therefore, a better understanding of the mechanism of natural substrate hydrolysis is important. Herein, the reaction mechanism of HIV-1 natural substrates with subtypes B and common mutant in South Africa (subtype C-SA) protease were studied through transition state modelling, using a general acid-general base (GA-GB) one-step concerted process. The activation free energies of enzyme-substrate complexes were compared based on their rate of hydrolysis using a two-layered ONIOM (B3LYP/6-31++G(d,p):AMBER) method. We expanded our computational model to obtain a better understanding of the mechanism of hydrolysis as well as how the enzyme recognises or chooses the cleavage site of the scissile bonds. Using this model, a potential substrate-based inhibitor could be developed with better potency. The calculated activation energies of natural substrates in our previous study correlated well with experimental data. A similar trend was observed for the Gag and Gag-Pol natural substrates in the present work for both enzyme complexes except for the PR-RT substrate. Natural bond orbital (NBO) analysis was also applied to determine the extent of charge transfer within the QM part of both enzymes considered and the PR-RT natural substrate. The result of this study shows that the method can be utilized as a dependable computational technique to rationalize lead compounds against specific targets.

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

We provide a perspective of the induced dipole formulation of polarizable QM/MM, showing how efficient implementations will enable their application to the modeling of dynamics, spectroscopy, and reactivity in complex biosystems.

Subatomic resolution X-ray structures of green fluorescent protein

Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.

UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level

The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright ¹ππ* and the lowest energy dark ¹nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the ¹n_Oπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional ¹n_Nπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the ¹n_Oπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.

Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols

The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm^-1 red shift of the C₁₃₍₁₎ carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q _x electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.

Relationship between Excited State Lifetime and Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau-Zener Model

We show that the speed of the chromophore photoisomerization of animal rhodopsins is not a relevant control knob for their light sensitivity. This result is at odds with the momentum-driven tunnelling rationale (i.e., assuming a one-dimensional Landau-Zener model for the decay: Zener, C. Non-Adiabatic Crossing of Energy Levels. Proc. R. Soc. London, Ser. A 1932, 137 (833), 696-702) holding that a faster nuclear motion through the conical intersection translates into a higher quantum yield and, thus, light sensitivity. Instead, a model based on the phase-matching of specific excited state vibrational modes should be considered. Using extensive semiclassical hybrid quantum mechanics/molecular mechanics trajectory computations to simulate the photoisomerization of three animal rhodopsin models (visual rhodopsin, squid rhodopsin and human melanopsin), we also demonstrate that phase-matching between three different modes (the reactive carbon and hydrogen twisting coordinates and the bond length alternation mode) is required to achieve high quantum yields. In fact, such "phase-matching" mechanism explains the computational results and provides a tool for the prediction of the photoisomerization outcome in retinal proteins.

Evolution of the Excitonic State of DNA Stacked Thymines: Intrabase ππ* → S0 Decay Paths Account for Ultrafast (Subpicosecond) and Longer (>100 ps) Deactivations

Monomer-like ring puckering decay paths for two stacked quantum mechanical thymines inside a solvated DNA duplex described at the molecular mechanics level are mapped using a hybrid CASPT2//CASSCF/MM protocol that accounts for steric, electronic and electrostatic interactions within the nucleobases native environment. Asymmetric stacking between nucleobases open ups different intrabase ππ* decay paths accounting for distinctive excited state lifetimes, spanning the subps to subns time window.

Photoinduced formation mechanism of the thymine–thymine (6–4) adduct in DNA; a QM(CASPT2//CASSCF):MM(AMBER) study

Out-of-plane puckering of the C_4′ atom forming a new CC bond seems essential for oxetane formation.

Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6-4 Thymine-Thymine Photodimerization in a DNA Duplex

The T-T photodimerization paths leading to the formation of cyclobutane pyrimidine dimer (CPD) and 6-4 pyrimidine pyrimidone (64-PP), the two main DNA photolesions, have been resolved for a T-T step in a DNA duplex by two complementary state-of-the-art quantum mechanical approaches: QM(CASPT2//CASSCF)/MM and TD-DFT/PCM. Based on the analysis of several different representative structures, we define a new-ensemble of cooperating geometrical and electronic factors (besides the distance between the reacting bonds) ruling T-T photodimerization in DNA. CPD is formed by a barrierless path on an exciton state delocalized over the two bases. Large interbase stacking and shift values, together with a small pseudorotation phase angle for T at the 3'-end, favor this reaction. The oxetane intermediate, leading to a 64-PP adduct, is formed on a singlet T→T charge-transfer state and is favored by a large interbase angle and slide values. A small energy barrier (<0.3 eV) is associated to this path, likely contributing to the smaller quantum yield observed for this process. Eventually, a clear directionality is always shown by the electronic excitation characterizing the singlet photoactive state driving the photodimerization process: an exciton that is more localized on T³ and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints.

On the Simulation of Two-dimensional Electronic Spectroscopy of Indole-containing Peptides

A benchmark study of low-cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near-ultraviolet (UV) pump visible (VIS) probe (i.e. two-color) two-dimensional electronic spectra (2DES) of homo- and hetero-aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited-state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm^-1 . The 18-24 k cm^-1 spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge-transfer signatures in stacked aggregates. The small peptide Trp-cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge-transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near-UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra-short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited-state absorption signals can be correlated to the polarity of the relevant states.

Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted ¹(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.

Spectral lineshapes in nonlinear electronic spectroscopy

We outline a computational approach for nonlinear electronic spectra, which accounts for the electronic energy fluctuations due to nuclear degrees of freedom and explicitly incorporates the fluctuations of higher excited states, induced by the dynamics in the photoactive state(s). This approach is based on mixed quantum-classical dynamics simulations. Tedious averaging over multiple trajectories is avoided by employing the linearly displaced Brownian harmonic oscillator to model the correlation functions. The present strategy couples accurate computations of the high-lying excited state manifold with dynamics simulations. The application is made to the two-dimensional electronic spectra of pyrene, a polycyclic aromatic hydrocarbon characterized by an ultrafast (few tens of femtoseconds) decay from the bright S2 state to the dark S1 state. The spectra for waiting times t2 = 0 and t2 = 1 ps demonstrate the ability of this approach to model electronic state fluctuations and realistic lineshapes. Comparison with experimental spectra [Krebs et al., New Journal of Physics, 2013, 15, 085016] shows excellent agreement and allows us to unambiguously assign the excited state absorption features.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate

The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.

Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level

Benzophenone, the parent of the diarylketone family, is a versatile compound commonly used as a UV blocker. It may also trigger triplet-based DNA photosensitization. Therefore, benzophenone is involved in DNA photodamage induction. In the absence of experimentally resolved structure, the mechanism of DNA damage production remains elusive. Employing a hybrid quantum mechanics/molecular mechanics approach, here we address the spin transfer mechanism between this drug and proximal thymine, that is, the DNA nucleobase most prone to suffer triplet damages.

Spectral properties and isomerisation path of retinal in C1C2 channelrhodopsin

Computed torsion profiles along the reactive coordinate in S₁reveal a two-path deactivation mechanism for retinal in C1C2 channelrhodopsin.

Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back

L_a and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.

Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy

We review the most recent experimental and computational efforts aimed at exposing the very early phases of the ultrafast isomerization in visual Rhodopsins and we discuss future advanced experiments and calculations.

Tracking conformational dynamics of polypeptides by nonlinear electronic spectroscopy of aromatic residues: a first-principles simulation study

The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principles simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant noninteracting aromatic residues. The π-stacking and excitonic coupling effects are included through ab initio simulations based on multiconfigurational methods within a hybrid quantum mechanics/molecular mechanics scheme. It is shown that linear absorption spectroscopy in the ultraviolet (UV) region is unable to resolve the unstacking dynamics characterized by the three-step process: T-shaped→twisted offset stacking→unstacking. Conversely, pump-probe spectroscopy can be used to resolve aromatic interactions by probing in the visible region, the excited-state absorptions (ESAs) that involve charge-transfer states. 2D UV spectroscopy offers the highest sensitivity to the unfolding process, by providing the disentanglement of ESA signals belonging to different aromatic chromophores and high correlation between the conformational dynamics and the quartic splitting.

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-allantoin, because the enzymes converting allantoin into allantoate are specific for the (S) isomer. The enzyme allantoin racemase catalyzes the reversible conversion between the two allantoin enantiomers, thus ensuring the overall efficiency of the catabolic pathway and preventing allantoin accumulation. On the basis of recent crystallographic and biochemical evidence, allantoin racemase has been assigned to the family of cofactor-independent racemases, together with other amino acid racemases. A detailed computational investigation of allantoin racemase has been carried out to complement the available experimental data and to provide atomistic insight into the enzymatic action. Allantoin, the natural substrate of the enzyme, has been investigated at the quantum mechanical level, in order to rationalize its conformational and tautomeric equilibria, playing a key role in protein-ligand recognition and in the following catalytic steps. The reaction mechanism of the enzyme has been elucidated through quantum mechanics/molecular mechanics (QM/MM) calculations. The potential energy surface investigation, carried out at the QM/MM level, revealed a stepwise reaction mechanism. A pair of cysteine residues promotes the stereoinversion of a carbon atom of the ligand without the assistance of cofactors. Electrostatic fingerprint calculations are used to discuss the role of the active site residues in lowering the pK_a of the substrate. The planar unprotonated intermediate is compared with the enolic allantoin tautomer observed in the active site of the crystallized enzyme. Finally, the enzymatic catalysis featured by allantoin racemase (AllR) is compared with that of other enzymes belonging to the same family.

Modelling time-resolved two-dimensional electronic spectroscopy of the primary photoisomerization event in rhodopsin

Time-resolved two-dimensional (2D) electronic spectra (ES) tracking the evolution of the excited state manifolds of the retinal chromophore have been simulated along the photoisomerization pathway in bovine rhodopsin, using a state-of-the-art hybrid QM/MM approach based on multiconfigurational methods. Simulations of broadband 2D spectra provide a useful picture of the overall detectable 2D signals from the near-infrared (NIR) to the near-ultraviolet (UV). Evolution of the stimulated emission (SE) and excited state absorption (ESA) 2D signals indicates that the S1 → SN (with N ≥ 2) ESAs feature a substantial blue-shift only after bond inversion and partial rotation along the cis → trans isomerization angle, while the SE rapidly red-shifts during the photoinduced skeletal relaxation of the polyene chain. Different combinations of pulse frequencies are proposed in order to follow the evolution of specific ESA signals. These include a two-color 2DVis/NIR setup especially suited for tracking the evolution of the S1 → S2 transitions that can be used to discriminate between different photochemical mechanisms of retinal photoisomerization as a function of the environment. The reported results are consistent with the available time-resolved pump-probe experimental data, and may be used for the design of more elaborate transient 2D electronic spectroscopy techniques.

Disentangling Peptide Configurations via Two-Dimensional Electronic Spectroscopy: Ab Initio Simulations Beyond the Frenkel Exciton Hamiltonian

Two-dimensional (2D) optical spectroscopy techniques based on ultrashort laser pulses have been recently extended to the optical domain in the ultraviolet (UV) spectral region. UV-active aromatic side chains can thus be used as local highly specific markers for tracking dynamics and structural rearrangements of proteins. Here we demonstrate that 2D electronic spectra of a model proteic system, a tetrapeptide with two aromatic side chains, contain enough structural information to distinguish between two different configurations with distant and vicinal side chains. For accurate simulations of the 2DUV spectra in solution, we combine a quantum mechanics/molecular mechanics approach based on wave function methods, accounting for interchromophores coupling and environmental effects, with nonlinear response theory. The proposed methodology reveals effects, such as charge transfer between vicinal aromatic residues that remain concealed in conventional exciton Hamiltonian approaches. Possible experimental setups are discussed, including multicolor experiments and signal manipulation techniques for limiting undesired background contributions and enhancing 2DUV signatures of specific electronic couplings.

Mapping atomic motions with ultrabright electrons: the chemists' gedanken experiment enters the lab frame

This review documents the development of high-bunch charge electron pulses with sufficient combined spatiotemporal resolution and intensity to literally light up atomic motions. This development holds promise in coming to a first-principles understanding of diverse problems, ranging from molecular reaction dynamics and structure-function correlations in biology to cooperativity in strongly correlated electron-lattice systems. It is now possible to directly observe the key modes involved in propagating structural changes and the enormous reduction in dimensionality that occurs in barrier crossing regions, which is central to chemistry and makes reaction mechanisms transferrable concepts. This information will help direct theoretical advances that will undoubtedly lead to generalized principles with respect to scaling relations in structural dynamics that will bridge chemistry to biology. In this quest, the limitations and future directions for further development are discussed to give an overview of the present status of the field.

Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins

Modelling of retinal photoisomerization in different environments is reviewed and ultimate ultrafast electronic spectroscopy is proposed for obtaining new insights.