Unrevealing the Nitrogen Elusive Chirality of 3-Sulfanyl and 3-Sulfinyl N-Tosyl Isoindolinones by ECD Spectra: An Experimental and Theoretical Investigation

The nitrogen-hybridization/pyramidalization of two solvated N-tosylisoindolinone derivatives having chiral residues in adjacent (I) or adjacent and distal (II) position has been investigated by a theoretical-computational procedure based on Molecular Dynamics simulations and Quantum-Chemical calculations. After validation of our methodology in providing a reliable repertory of conformations by modeling the electronic circular dichroism (EDC) spectra, the electronic features associated with N-pyramidalization were further characterized through Natural Bond Order (NBO) analysis. Comparing against the N-geometry observed in crystal structures as a reference, our findings reveal that the presence of neighbouring chiral centers induces a more pronounced N-pyramidalization in solution than in the solid state, both in I and II. Furthermore, NBO analysis confirms that the N-lactam mostly retains the sp2 character but exhibits slight configurational distortion (ξI=13°; ξII=21°), which significantly influences the chiroptical activities observed in ECD spectra of I and II. This substantiates the N-lactams as configurationally stable chiral centers.

On the Statistical Regime, Coherence versus Incoherence and Ergodicity of Quantum Vibrational Trajectories in Soft Condensed Molecular Systems

A theoretical-computational procedure, recently proposed for modelling Vibrational Energy Relaxation (VER) processes of a molecule (Quantum Center, QC) embedded in a complex atomic-molecular system, is extended and applied for analyzing in detail the features of the QC density matrix (DM) temporal evolution. The results, obtained using aqueous azide ion as a case study, show the total lack of coherence in the DM, when the system is prepared to be initially in a pure vibrational eigenstate. This finding is fully in line with the statistical interpretation of the process typically adopted also in the experimental studies where the relaxation processes are all described within the typical schemes of chemical kinetics. Consistently, when the initial vibrational state corresponds to an eigenstate mixture, although initially coherent, the DM relaxes to a fully incoherent condition with a mean lifetime related to the one of the diagonal elements relaxation. These specific DM features turn out to be essentially governed by the thermal equilibrium condition of the atomic-molecular classical coordinates which drive the ensemble of the quantum-trajectories toward the observed statistical regime. Finally, from the analysis of a single long timescale quantum vibrational trajectory it also clearly emerges its ergodic behaviour.

Evidence of a Distinctive Enantioselective Binding Mode for the Photoinduced Radical Cyclization of α-Chloroamides in Ene-Reductases

We demonstrate here through molecular simulations and mutational studies the origin of the enantioselectivity in the photoinduced radical cyclization of α-chloroacetamides catalyzed by ene-reductases, in particular the Gluconobacter oxidans ene-reductase and the Old Yellow Enzyme 1, which show opposite enantioselectivity. Our results reveal that neither the π-facial selectivity model nor a protein-induced selective stabilization of the transition states is able to explain the enantioselectivity of the radical cyclization in the studied flavoenzymes. We propose a new enantioinduction scenario according to which enantioselectivity is indeed controlled by transition-state stability; however, the relative stability of the prochiral transition states is not determined by direct interaction with the protein but is rather dependent on an inherent degree of freedom within the substrate itself. This intrinsic degree of freedom, distinct from the traditional π-facial exposure mode, can be controlled by the substrate conformational selection upon binding to the enzyme.

Plasmon-enhanced circular dichroism spectroscopy of chiral drug solutions

We investigate the potential of surface plasmon polaritons at noble metal interfaces for surface-enhanced chiroptical sensing of dilute chiral drug solutions with nl volume. The high quality factor of surface plasmon resonances in both Otto and Kretschmann configurations enables the enhancement of circular dichroism differenatial absorption thanks to the large near-field intensity of such plasmonic excitations. Furthermore, the subwavelength confinement of surface plasmon polaritons is key to attain chiroptical sensitivity to small amounts of drug volumes placed around ≃100 nm by the metal surface. Our calculations focus on reparixin, a pharmaceutical molecule currently used in clinical studies for patients with community-acquired pneumonia, including COVID-19 and acute respiratory distress syndrome. Considering realistic dilute solutions of reparixin dissolved in water with concentration ≤5 mg/ml and nl volume, we find a circular-dichroism differential absorption enhancement factor of the order ≃20 and chirality-induced polarization distortion upon surface plasmon polariton excitation. Our results are relevant for the development of innovative chiroptical sensors capable of measuring the enantiomeric imbalance of chiral drug solutions with nl volume.

What Contributes to the Measured Chiral Optical Response of the Glutathione-Protected Au25 Nanocluster?

The water-soluble glutathione-protected [Au₂₅(GSH)₁₈]^-1 nanocluster was investigated by integrating several methodologies such as molecular dynamics simulations, essential dynamics analysis, and state-of-the-art time-dependent density functional theory calculations. Fundamental aspects such as conformational, weak interactions and solvent effects, especially hydrogen-bonds, were included and found to play a fundamental role in assessing the optical response of this system. Our analysis demonstrated not only that the electronic circular dichroism is extremely sensitive to the solvent presence but also that the solvent itself plays an active role in the optical activity of such system, forming a chiral solvation shell around the cluster. Our work demonstrates a successful strategy to investigate in detail chiral interfaces between metal nanoclusters and their environments, applicable, e.g., to chiral electronic interactions between clusters and biomolecules.

Direct Regioselective Hydro(hetero)arylation/Cyclocondensation Reactions of β-(2-Aminophenyl)-α,β-ynones by Means of Transition-Metal Catalysis/Brønsted Acid Synergism: Experimental Results and Computational Insights

Experimental results and computational insights explain the key role of transition-metal catalysis/Brønsted acid synergism in the achievement of the sequential regioselective direct heteroarylation/cyclocondensation reactions of β-(2-aminophenyl)-α,β-ynones with a variety of electron-rich aromatic heterocyclic/arenes to afford quinoline-(hetero)aromatic hybrids. The first approach to the synthesis of 4-(1H-pyrrol-2-yl)quinolines is described. The effectiveness of various transition metals is compared.

Theoretical-Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method

The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical-computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming the good performances of MD-PMM in modeling different spectral features in complex atomic-molecular systems, as already reported in previous studies. The underlying strategy of the method was to perform a preliminary long timescale MD simulation of the chromophore followed by the extraction of the relevant conformations through essential dynamics analysis. On this (limited) number of relevant conformations, the ECD spectrum was calculated via the PMM approach. This study showed that MD-PMM was able to reproduce the essential features of the ECD spectrum (i.e., the position, the intensity, and the shape of the bands) of d-glucose and d-galactose while avoiding the rather computationally expensive aspects, which were demonstrated to be important for the final outcome, such as (i) the use of a large number of chromophore conformations; (ii) the inclusion of quantum vibronic coupling; and (iii) the inclusion of explicit solvent molecules interacting with the chromophore atoms within the chromophore itself (e.g., via hydrogen bonds).

The Conformational Dynamics of the Ligands Determines the Electronic Circular Dichroism of the Chiral Au38(SC2H4Ph)24 Cluster

Effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of the chiral Au₃₈(SC₂H₄Ph)₂₄ cluster are investigated. We adopt a computational protocol in which ECD spectra are calculated via the first principle polTDDFT approach on a series of conformations extracted from MD simulations by using Essential Dynamics (ED) analysis, and then properly weighted to predict the final spectrum. We find that the experimental spectral features are well reproduced, whereas significant discrepancies arise when the spectrum is calculated using the experimental X-ray structure. This result unambiguously demonstrates the need to account for the conformational effects in the ECD modeling of chiral nanoclusters. The present procedure proved to be able of capturing the essential conformational features of the dynamic Au₃₈(SC₂H₄Ph)₂₄ system, opening the possibility to model the ECD of soluble chiral nanoclusters in a realistic way.

Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II

Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.

Electrochemical-Induced Cascade Reaction of 2-Formyl Benzonitrile with Anilines: Synthesis of N-Aryl Isoindolinones

An electrochemical initiated tandem reaction of anilines with 2-formyl benzonitrile has been developed. Thus, unprecedented 3-N-aryl substituted isoindolinones have been conveniently achieved by constant current electrolysis in a divided cell using catalytic amount of electricity and supporting electrolyte and a Pt-cathode as working electrode. The origin of the electrochemical activation as well as the mechanism of the subsequent chemical cascade reactions have been investigated by DFT calculations.

A computational approach for modeling electronic circular dichroism of solvated chromophores

The present study consists in a novel computational protocol to model the UV-circular dichroism spectra of solvated species. It makes use of quantum-chemical calculations on a series of conformations of a flexible chromophore or on a series of chromophore/solvent clusters extracted from molecular dynamic simulations. The protocol is described and applied to the aqueous cationic tripeptide GAG⁺ and to the aqueous neutral decapeptide (GVGVP)₂ . The protocol has proven able to: (i) properly consider the conformational motion of solute in the given environment; (ii) give the actual statistical weight of each conformational state; (iii) provide a reliable quantum mechanical method able to reproduce the spectral features. Temperature effects on conformations and spectral properties are properly taken into account. The role of explicit solvent on the conformational analysis and the spectra calculation is discussed. The comparison of the calculated circular dichroism spectra with experimental ones recorded at different temperatures represents a strict validation test of the method.

Theoretical-Computational Modeling of Gas-State Thermodynamics in Flexible Molecular Systems: Ionic Liquids in the Gas Phase as a Case Study

A theoretical-computational procedure based on the quasi-Gaussian entropy (QGE) theory and molecular dynamics (MD) simulations is proposed for the calculation of thermodynamic properties for molecular and supra-molecular species in the gas phase. The peculiarity of the methodology reported in this study is its ability to construct an analytical model of all the most relevant thermodynamic properties, even within a wide temperature range, based on a practically automatic sampling of the entire conformational repertoire of highly flexible systems, thereby bypassing the need for an explicit search for all possible conformers/rotamers deemed relevant. In this respect, the reliability of the presented method mainly depends on the quality of the force field used in the MD simulations and on the ability to discriminate in a physically coherent way between semi-classical and quantum degrees of freedom. The method was tested on six model systems (n-butane, n-butane, n-octanol, octadecane, 1-butyl-3-methylimidazolium hexafluorophosphate and 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic pairs), which, being experimentally characterized and already addressed by other theoretical-computational methods, were considered as particularly suitable to allow us to evaluate the method's accuracy and efficiency, bringing out advantages and possible drawbacks. The results demonstrate that such a physically coherent yet relatively simple method can represent a further valid computational tool that is alternative and complementary to other extremely efficient computational methods, as it is particularly suited for addressing the thermodynamics of gaseous systems with a high conformational complexity over a large range of temperature.

Correction: Theoretical and experimental study on the O(3P) + 2,5-dimethylfuran reaction in the gas phase

Correction for 'Theoretical and experimental study on the O(³P) + 2,5-dimethylfuran reaction in the gas phase' by Andrea Giustini et al., Phys. Chem. Chem. Phys., 2021, 23, 19424-19434, DOI: 10.1039/D1CP01724A.

Stationary and Time-Dependent Carbon Monoxide Stretching Mode Features in Carboxy Myoglobin: A Theoretical-Computational Reappraisal

The stationary and time-dependent infrared spectrum (IR) of the CO stretching mode (ν_CO) in carboxymyoglobin (MbCO), a longstanding problem of biophysical chemistry, has been modeled through a theoretical-computational method specifically designed for simulating quantum observables in complex atomic-molecular systems and based on a combined application of long time scale molecular dynamics simulations and quantum-chemical calculations. This study is basically focused on two aspects: (i) the origin of the stationary IR substates (termed as A₀, A₁, and A₃) and (ii) the modeling and the interpretation of the ν_CO energy relaxation. The results, strengthened by a more than satisfactory agreement with the experimental data, concisely indicate that (i) the conformational His64-FeCO relevant substates, i.e., characterized by the formation-disruption of the H-bond between the above moieties, are the main responsible of the presence of two distinct and well separated (A₀ and A₁/A₃) spectroscopic regions; (ii) the characteristic bimodal shape of the A₁/A₃ spectral region, according to our model, is the result of the fluctuation of the electric field pattern as provided by the protein-solvent framework perturbing the bound His64-CO-Heme complex; and (iii) the electric field pattern, in conjunction with the relatively high density of MbCO vibrational states, is also the main determinant of the ν_CO energy relaxation, characterizing its kinetic efficiency.

Theoretical and experimental study on the O(3P) + 2,5-dimethylfuran reaction in the gas phase

In this work we report a joint experimental and computational study on the 2,5-dimethylfuran oxidation reaction in the gas phase initiated by atomic oxygen O(3P). The experiments have been performed by using vacuum-ultraviolet synchrotron radiation at the Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory (LBNL), at a temperature of 550 K and a pressure of 8 Torr. The experimental data were supported by quantum-chemical calculations along with a kinetic model, also taking into account the possible involvement of different magnetic states, performed in the framework of the RRKM theory. Propyne, acetaldehyde, methylglyoxal, dimethylglyoxal, 3-penten-2-one, 2,5-dimethylfuran-3(2H)-one, and 1,2-diacetyl ethylene have been identified as the main primary products arising under the conditions of the experiment. Our computational model suggests that these species can be formed at the concentration and branching ratio experimentally observed only in the presence of a non-negligible fraction of non-thermalized intermediates.

A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the N_imino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C-Br^…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).

Cooperative protein-solvent tuning of proton transfer energetics: carbonic anhydrase as a case study

We investigate the coupling between the proton transfer (PT) energetics and the protein-solvent dynamics using the intra-molecular PT in wild type (wt) human carbonic anhydrase II and its ten-fold faster mutant Y7F/N67Q as a test case. We calculate the energy variation upon PT, and from that we also calculate the PT reaction free energy, making use of a hybrid quantum mechanics/molecular dynamics approach. In agreement with the experimental data, we obtain that the reaction free energy is basically the same in the two systems. Yet, we show that the instantaneous PT energy is on average lower in the mutant possibly contributing to the faster PT rate. Analysis of the contribution to the PT energetics of the solvent and of each protein residue, also not in the vicinity of the active site, provides evidence for electrostatic tuning of the PT energy arising from the combined effect of the solvent and the protein environment. These findings open up a way to the more general task of the rational design of mutants with either enhanced or reduced PT rate.

Experimental and computational evidence on gold-catalyzed regioselective hydration of phthalimido-protected propargylamines: an entry to β-amino ketones

The results of our investigations on the Au-catalyzed regioselective hydration reaction of both alkyl- and aryl-substituted N-propargyl phthalimides directed to the selective formation of the corresponding β-phthalimido ketones are described. Experimental data, in particular the observed regioselectivity, have been qualitatively supported by quantum-chemical calculations carried out on model systems in the framework of Density Functional Theory (DFT) followed by quantum theory of atoms in molecules (QTAIMS). Our results suggest that the electronic features of the initial adduct between the propargyl triple bond and the Au(i) catalyst, in particular the character of the gold-triple bond interaction, are essential for the observed regioselectivity. Other effects, such as the presence of the solvent and the formation of a H-bond between the water molecule and the phthalimido moiety, although apparently irrelevant for the regioselectivity, have proven to be kinetically and catalytically rather important.

A general model for Covid-19 epidemic kinetics: application to italian and german data

In this paper we report the description, implementation and application of a kinetic model designed for describing the Covid-19 epidemic spread in Italy and Germany in the period between February and June 2020 coinciding with the beginning of the statistical regime of the epidemic spread and the application of restrictive government measures aimed at its containment. The model, which makes use of a limited number of parameters, in spite of its simplicity is able of capturing the essential physical features of the epidemic spread highlighting the essential role of the restrictive measures and in particular the timeliness of their application for the containment of the most dramatic consequences. This work also confirms how the epidemic spread, if considered during its statistical-regime evolution, can be properly described - and hence probably better understood - using languages and methodologies typically adopted for chemical processes, such as the Mass Action Law and Chemical Kinetics.

Experimental results and computational insight into sequential reactions of β-(2-aminophenyl)-α,β-ynones with aryl isocyanates/benzoyl isothiocyanate

The selective formation of quinazoline vs. benzoxazine  and benzothiazine derivatives from β-(2-aminophenyl)-α,β-ynones and aryl isocyanates/benzoyl isothiocyanate was explored. DFT calculations provide a plausible rationale.

Modelling vibrational relaxation in complex molecular systems

In this paper we show how it is possible to treat the quantum vibrational relaxation of a chromophore, embedded in a complex atomic-molecular environment, via the explicit solution of the time-dependent Schroedinger equation once using a proper separation between quantum and semiclassical degrees of freedom. The rigorous theoretical framework derived, based on first principles and making use of well defined approximations/assumptions, is utilized to construct a general model for the kinetics of the vibrational relaxation as obtained by the direct evaluation of the density matrix for all the relevant quantum state transitions. Application to (deuterated) N-methylacetamide (the typical benchmark used as a model for the amino acids) shows that the obtained theoretical-computational approach captures the essential features of the experimental process, unveiling the basic relaxation mechanism involving several vibrational state transitions.

Embedding calix[4]resorcinarenes in liposomes: Experimental and computational investigation of the effect of resorcinarene inclusion on liposome properties and stability

Two calix[4]resorcinarenes, which differ in the length of the alkyl chain on the methylene bridge between the aromatic rings, have been embedded in unilamellar liposomes prepared from 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine in three host/guest ratios, following two different procedures. The effect of the insertion of the guests has been evaluated through the measurements of the viscosity and the kinetic stability of the liposomal systems by means of the fluorescent probes pyrene and 5(6)-carboxyfluorescein. The presence of the guests reduces the viscosity of the liposomes, suggesting a modification of the bilayer structure. However, this does not affect liposome stability. A calix[4]resorcinarene cavitand with a more rigid conformation compared to the parent resorcinarene, has been also synthetized and embedded in liposomes. The free energy of the insertion of the substrates in the lipid bilayer has been evaluated through Molecular Dynamics simulations.

Effect of the Incorporation of Functionalized Cyclodextrins in the Liposomal Bilayer

Liposomes loaded with drug–cyclodextrin complexes are widely used as drug delivery systems, especially for species with low aqueous solubility and stability. Investigation of the intimate interactions of macrocycles with liposomes are essential for formulation of efficient and stable drug-in-cyclodextrin-in-liposome carriers. In this work, we reported the preparation of unilamellar vesicles of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) embedded with native β-cyclodextrin and two synthetic derivatives: heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMCD) and heptakis(2,3-di-O-acetyl)-β-cyclodextrin (DACD). We then studied the effect of these macrocycles on the liposomal size, membrane viscosity, and liposomal stability at different temperatures and concentrations. We observed that TMCD and DACD affected vesicle size and the change of size was related to CD concentration. Irrespective of its nature, the macrocycle established interactions with the phospholipidic head groups, preventing cyclodextrins to diffuse into the lipid bilayer, as confirmed by molecular dynamics simulations. Such supramolecular structuring improves liposome stability making these colloid systems promising carriers for biologically active compounds.

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory

Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.

On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study

We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.

Exploring the role of L209 residue in the active site of NDM-1 a metallo-β-lactamase

Background

New Delhi Metallo-β-Lactamase (NDM-1) is one of the most recent additions to the β-lactamases family. Since its discovery in 2009, NDM-1 producing Enterobacteriaceae have disseminated globally. With few effective antibiotics against NDM-1 producers, there is an urgent need to design new drug inhibitors through the help of structural and mechanistic information available from mutagenic studies.

Results/Conclusions

In our study we focus the attention on the non-catalytic residue Leucine 209 by changing it into a Phenylalanine. The L209F laboratory variant of NDM-1 displays a drastic reduction of catalytic efficiency (due to low k_cat values) towards penicillins, cephalosporins and carbapenems. Thermofluor-based assay demonstrated that NDM-1 and L209F are stable to the temperature and the zinc content is the same in both enzymes as demonstrated by experiments with PAR in the presence of GdnHCL. Molecular Dynamics (MDs) simulations, carried out on NDM-1 and L209F both complexed and uncomplexed with Benzylpenicillin indicate that the point mutation produces a significant mechanical destabilization of the enzyme and also an increase of water content. These observations clearly show that the single mutation induces drastic changes in the enzyme properties which can be related to the observed different catalytic behavior.

Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems

In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems.

A theoretical-computational procedure, based on Molecular Dynamics simulations, is proposed for modelling the kinetics of non-adiabatic processes in very complex systems.

Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein

Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical-molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.

Crabrolin, a natural antimicrobial peptide: structural properties

A joint application of experimental and computational approaches has revealed the exceptionally high attitude of crabrolin, a 13-residue peptide with sequence FLPLILRKIVTAL-NH₂ , to adopt alpha-helix conformation not only in membrane-mimicking solvents but also in the presence of a not negligible amount of water. Our study shows that this propensity essentially resides in the intrinsic thermodynamic stability of alpha-helix conformation whose kinetic stability is drastically reduced in water solvent. Our analysis suggests that this is due to two effects enhanced by water: a more local effect consisting of the demolition of intra-peptide H-bonds, essential for the alpha-helix formation, and a bulk - electrostatic - effect favoring conformational states more polar than alpha-helix. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Visualizing Excited-State Dynamics of a Diaryl Thiophene: Femtosecond Stimulated Raman Scattering as a Probe of Conjugated Molecules

Conjugated organic polymers based on substituted thiophene units are versatile building blocks of many photoactive materials, such as photochromic molecular switches or solar energy conversion devices. Unraveling the different processes underlying their photochemistry, such as the evolution on different electronic states and multidimensional structural relaxation, is a challenge critical to defining their function. Using femtosecond stimulated Raman scattering (FSRS) supported by quantum chemical calculations, we visualize the reaction pathway upon photoexcitation of the model compound 2-methyl-5-phenylthiophene. Specifically, we find that the initial wavepacket dynamics of the reaction coordinates occurs within the first ≈1.5 ps, followed by a ≈10 ps thermalization. Subsequent slow opening of the thiophene ring through a cleavage of the carbon-sulfur bond triggers an intersystem crossing to the triplet excited state. Our work demonstrates how a detailed mapping of the excited-state dynamics can be obtained, combining simultaneous structural sensitivity and ultrafast temporal resolution of FSRS with the chemical information provided by time-dependent density functional theory calculations.

Folding propensity of anoplin: A molecular dynamics study of the native peptide and four mutated isoforms

Anoplin, a cationic decapeptide amide GLLKRIKTLL-NH2 derived from venom sac of the solitary wasp Anoplius samariensis has been investigated through Molecular Dynamics. The wild-type (WT) and four isoforms were simulated both in water and in the membrane-mimicking solvent trifluoroethanol (TFE). In water all the investigated species, found to be in rapid equilibrium between different conformational states, can be considered as unfolded. On the other hand, in TFE all the systems enhance their rigidity and, in general, show α-helix as the main folded conformation. Interestingly, a semi-quantitative thermodynamic analysis has suggested that the folding driving force is not always the same being in some cases (e.g., the WT Anoplin) of entropic nature and in other cases of energetic nature.

Photoexcitation and relaxation kinetics of molecular systems in solution: towards a complete in silico model

A theoretical–computational method is proposed for modelling the complete kinetics – from photo-excitation to relaxation – of a chromophore in solution.

The Perfect Enzyme : Revisiting the Modelling of Initial Proton Transfer in Triosephosphate Isomerase

DESCRIPTION

The understanding of the factors governing the enzyme catalysis is one of the most important goals of biochemistry and biophysics. In this context the contribution of theoretical research might be of high relevance. However, despite the huge amount of proposed approaches, the modelling of enzyme reactions still represents a very difficult task and a definitive and conclusive theoretical-computational strategy is still far from being available. In this study, after a presentation of the main difficulties associated to a coherent and possibly rigorous modelling of these processes, we present a computational theoretical method specifically designed for addressing complex molecular systems eventually applied to a benchmark reaction: the initial proton transfer in Triosephosphate Isomerase. This latter species, termed as the 'perfect enzyme' because of its exceptional ability as catalyst, provides an excellent test for evaluating the different environmental and intrinsic determinants at the basis of enzyme activity.

A few key residues determine the high redox potential shift in azurin mutants

The wide range of variability of the reduction potential (E(0)) of blue-copper proteins has been the subject of a large number of studies in the past several years. In particular, a series of azurin mutants have been recently rationally designed tuning E(0) over a very broad range (700 mV) without significantly altering the redox-active site [Marshall et al., Nature, 2009, 462, 113]. This clearly suggests that interactions outside the primary coordination sphere are relevant to determine E(0) in cupredoxins. However, the molecular determinants of the redox potential variability are still undisclosed. Here, by means of atomistic molecular dynamics simulations and hybrid quantum/classical calculations, the mechanisms that determine the E(0) shift of two azurin mutants with high potential shifts are unravelled. The reduction potentials of native azurin and of the mutants are calculated obtaining results in good agreement with the experiments. The analysis of the simulations reveals that only a small number of residues (including non-mutated ones) are relevant in determining the experimentally observed E(0) variation via site-specific, but diverse, mechanisms. These findings open the path to the rational design of new azurin mutants with different E(0).

Essential dynamics for the study of microstructures in liquids

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic-molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen-bonded clusters.

Structural basis of the transactivation deficiency of the human PPARγ F360L mutant associated with familial partial lipodystrophy

The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for this reason, they are the targets of antidiabetic and hypolipidaemic drugs. In the last decade, some rare mutations in human PPARγ that might be associated with partial lipodystrophy, dyslipidaemia, insulin resistance and colon cancer have emerged. In particular, the F360L mutant of PPARγ (PPARγ2 residue 388), which is associated with familial partial lipodystrophy, significantly decreases basal transcriptional activity and impairs stimulation by synthetic ligands. To date, the structural reason for this defective behaviour is unclear. Therefore, the crystal structure of PPARγ F360L together with the partial agonist LT175 has been solved and the mutant has been characterized by circular-dichroism spectroscopy (CD) in order to compare its thermal stability with that of the wild-type receptor. The X-ray analysis showed that the mutation induces dramatic conformational changes in the C-terminal part of the receptor ligand-binding domain (LBD) owing to the loss of van der Waals interactions made by the Phe360 residue in the wild type and an important salt bridge made by Arg357, with consequent rearrangement of loop 11/12 and the activation function helix 12 (H12). The increased mobility of H12 makes the binding of co-activators in the hydrophobic cleft less efficient, thereby markedly lowering the transactivation activity. The spectroscopic analysis in solution and molecular-dynamics (MD) simulations provided results which were in agreement and consistent with the mutant conformational changes observed by X-ray analysis. Moreover, to evaluate the importance of the salt bridge made by Arg357, the crystal structure of the PPARγ R357A mutant in complex with the agonist rosiglitazone has been solved.

Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution

A computational approach, based on molecular dynamics simulations and quantum-chemical calculations, is proposed for modelling the photo-induced charge separation and the kinetics of the subsequent charge recombination (CR) processes in solution.