Theoretical modeling of UV-Vis absorption and emission spectra in liquid state systems including vibrational and conformational effects: the vertical transition approximation

In this paper we describe in detail a general and efficient methodology, based on the perturbed matrix method and molecular dynamics simulations, to model UV-Vis absorption and emission spectra including vibrational and conformational effects. The basic approximation used is to consider all the chromophore atomic coordinates as semiclassical degrees of freedom, hence allowing the calculation of the complete spectral signal by using the electronic vertical transitions as obtained at each possible chromophore configuration, thus including the contributions of vibrations and conformational transitions into the spectrum. As shown for the model system utilized in this paper, solvated 1-phenyl-naphthalene, such an approximation can be rather accurate to reproduce the absorption and emission spectral line shape and properties when, as it often occurs, the vertical vibronic transition largely overlaps the other non-negligible vibronic transitions

Renormalization group approach to vibrational energy transfer in protein

Renormalization group method is applied to the study of vibrational energy transfer in protein molecule. An effective Lagrangian and associated equations of motion to describe the resonant energy transfer are analyzed in terms of the first-order perturbative renormalization group theory that has been developed as a unified tool for global asymptotic analysis. After the elimination of singular terms associated with the Fermi resonance, amplitude equations to describe the slow dynamics of vibrational energy transfer are derived, which recover the result obtained by a technique developed in nonlinear optics [S.J. Lade, Y.S. Kivshar, Phys. Lett. A 372 (2008) 1077].Comment: 11 page

Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human $\beta$-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced beta-Gaussian model to identify, with negligible computational expenditure, the most significant distortion occurring in thermal equilibrium and the associated time scales. The application of this strategy allows to gain considerable insight into the putative functional movements and, furthermore, helps to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

Recurrence quantification analysis as a tool for the characterization of molecular dynamics simulations

A molecular dynamics simulation of a Lennard-Jones fluid, and a trajectory of the B1 immunoglobulin G-binding domain of streptococcal protein G (B1-IgG) simulated in water are analyzed by recurrence quantification, which is noteworthy for its independence from stationarity constraints, as well as its ability to detect transients, and both linear and nonlinear state changes. The results demonstrate the sensitivity of the technique for the discrimination of phase sensitive dynamics. Physical interpretation of the recurrence measures is also discussed.Comment: 7 pages, 8 figures, revtex; revised for review for Phys. Rev. E (clarifications and expansion of discussion)-- addition of the 8 postscript figures previously omitted, but unchanged from version

Effect of Some Macrocyclic Ligands on the Rate of Reduction of Perchlorate Ion by Titanium(III)

Complexation with cyclam increases the rate of reduction of perchlorate ion by TiIII (in acidic, aqueous, 4 mol dm-3 LiCl Solutions at 25 °C) relative to the rate of the corresponding reduction of Ti3+. A modified cyclam with pendant amine and p-aminobenzyl functional groups is more effective in this regard than is cyclam itself. Both redox reactions are acid catalyzed. The data is consistent with involvement of an intermediate containing two TiIII centers

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

Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis

Background: the theoretical modelling of reactions occurring in liquid phase is a research line of primary importance both in theoretical–computational chemistry and in the context of organic and biological chemistry. Here we present the modelling of the kinetics of the hydroxide-promoted hydrolysis of phosphoric diesters. (2) Method: the theoretical–computational procedure involves a hybrid quantum/classical approach based on the perturbed matrix method (PMM) in conjunction with molecular mechanics. (3) Results: the presented study reproduces the experimental data both in the rate constants and in the mechanistic aspects (C–O bond vs. O–P bond reactivity). The study suggests that the basic hydrolysis of phosphodiesters occurs through a concerted (Formula presented.) mechanism, with no formation of penta-coordinated species as reaction intermediates. (4) Conclusions: the presented approach, despite the approximations, is potentially applicable to a large number of bimolecular transformations in solution and therefore leads the way to a fast and general method to predict the rate constants and reactivities/selectivities in complex environments

A statistical mechanical model of supercooled water based on minimal clusters of correlated molecules

In this paper, we apply a theoretical model for fluid state thermodynamics to investigate simulated water in supercooled conditions. This model, which we recently proposed and applied to sub- and super-critical fluid water [Zanetti-Polzi et al., J. Chem. Phys. 156(4), 44506 (2022)], is based on a combination of the moment-generating functions of the enthalpy and volume fluctuations as provided by two gamma distributions and provides the free energy of the system as well as other relevant thermodynamic quantities. The application we make here provides a thermodynamic description of supercooled water fully consistent with that expected by crossing the liquid-liquid Widom line, indicating the presence of two distinct liquid states. In particular, the present model accurately reproduces the Widom line temperatures estimated with other two-state models and well describes the heat capacity anomalies. Differently from previous models, according to our description, a cluster of molecules that extends beyond the first hydration shell is necessary to discriminate between the statistical fluctuation regimes typical of the two liquid states

Fit between humanitarian professionals and project requirements: hybrid group decision procedure to reduce uncertainty in decision-making

Choosing the right professional that has to meet indeterminate requirements is a critical aspect in humanitarian development and implementation projects. This paper proposes a hybrid evaluation methodology for some non-governmental organizations enabling them to select the most competent expert who can properly and adequately develop and implement humanitarian projects. This methodology accommodates various stakeholders’ perspectives in satisfying the unique requirements of humanitarian projects that are capable of handling a range of uncertain issues from both stakeholders and project requirements. The criteria weights are calculated using a two-step multi-criteria decision-making method: (1) Fuzzy Analytical Hierarchy Process for the evaluation of the decision maker weights coupled with (2) Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) to rank the alternatives which provide the ability to take into account both quantitative and qualitative evaluations. Sensitivity analysis have been developed and discussed by means of a real case of expert selection problem for a non-profit organisation. The results show that the approach allows a decrease in the uncertainty associated with decision-making, which proves that the approach provides robust solutions in terms of sensitivity analysis

Salification Controls the In-Vitro Release of Theophylline

Sustained released formulation is the most used strategy to control the efficacy and the adverse reactions of an API (active pharmaceutical ingredient) with a narrow therapeutic index. In this work, we used a different way to tailor the solubility and diffusion of a drug. Salification of Theophylline with Squaric Acid was carried out to better control the absorption of Theophylline after administration. Salification proved to be a winning strategy decreasing the dissolution of the APIs up to 54% with respect to Theophylline. Most importantly, this was accomplished in the first 10 min of the dissolution process, which are the most important for the API administration. Two polymorphs were identified and fully characterized. Theophylline squarate was discovered as trihydrate (SC-XRD) and as a metastable anhydrous form. Indeed, during the Variable Temperature-XRPD experiment, the trihydrate form turned back into the two starting components after losing the three molecules of water. On the other hand, the synthesis of the trihydrate form was observed when a simple mixing of the two starting components were exposed to a high humidity relative percentage (90% RH)