DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method

Excited state relaxation mechanisms and tautomerism effects in 2,6-Diamino-8-Azapurine

The photochemistry of 9H-2,6-diamino-8-azapurine (9H-8AZADAP), a promising fluorescent probe, was investigated using the Multi-State Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2) quantum chemical method, along with the Average Solvent Electrostatic Configuration and Free Energy Gradient (ASEC-FEG) and Polarizable Continuum Model (PCM) to take into account water solvation effects. For both isolated and solvated species, the main photochemical event is initiated by the absorption of light from ground-state to the bright 1(ππ* La) state, which undergoes barrierless evolution to its minimum energy region (1(ππ* La)min) without crossing any other potential energy surface (PES). Subsequently, the excess of energy is released through fluorescence. From the 1(ππ* La)min region, two radiationless decay pathways back to the initial ground state, mediated by two distinct conical intersections between the ground and 1(ππ* La) states, are found to be unlikely due to the presence of high energy barriers in both environments. Our results also indicate that the solvation effects are more pronounced when using the ASEC-FEG method, which predicts larger structural and energy changes, especially concerning energetic barriers. Based on the free energy perturbation theory (FEP), a hypothetical thermodynamic cycle was devised, from which we infer that in an aqueous environment the N3 site is the most favorable for protonation. We also conclude that the 8H-8AZADAP tautomer is responsible for the fluorescent band observed experimentally at 410 nm and elucidates the mechanism of phototautomerism.

Exploring Mechanism and Kinetics of 1,4-Dioxane Oxidative Degradation by OH Radical: A Computational Quantum Chemistry Investigation

This study aims to shed light on the mechanism and kinetics of 1,4-dioxane degradation by hydroxyl radical (OH) across various solvation conditions to evaluate electronic and structural properties at the MP2/aug-cc-pVTZ level. Transition states (TS) structures determined in the gas phase and SMD solvation model reveal similar hydrogen abstraction patterns. In contrast, the explicit solvation model (ES) introduces significant changes, suggesting a kinetic preference for axial pathways. The reaction rate constants, employing Deformed Transition State Theory (d-TST), are consistently higher for axial abstraction. The preference for axial hydrogen abstraction, solvation effects on transition states, and temperature-dependent rate constants are highlighted. Furthermore, the identification of carbon-carbon orbital distortion suggests potential bond breakage. This research provides valuable insights into the reaction between 1,4-dioxane and OH radical across different solvation models and enhances the understanding of the advanced oxidative process.

Ab initio electronic absorption spectra of para-nitroaniline in different solvents: Intramolecular charge transfer effects

Intramolecular charge transfer (ICT) effects of para-nitroaniline (pNA) in eight solvents (cyclohexane, toluene, acetic acid, dichloroethane, acetone, acetonitrile, dimethylsulfoxide, and water) are investigated extensively. The second-order algebraic diagrammatic construction, ADC(2), ab initio wave function is employed with the COSMO implicit and discrete multiscale solvation methods. We found a decreasing amine group torsion angle with increased solvent polarity and a linear correlation between the polarity and ADC(2) transition energies. The first absorption band involves π → π* transitions with ICT from the amine and the benzene ring to the nitro group, increased by 4%-11% for different solvation models of water compared to the vacuum. A second band of pNA is characterized for the first time. This band is primarily a local excitation on the nitro group, including some ICT from the amine group to the benzene ring that decreases with the solvent polarity. For cyclohexane, the COSMO implicit solvent model shows the best agreement with the experiment, while the explicit model has the best agreement for water.

Structural Properties of [N1888][TFSI] Ionic Liquid: A Small Angle Neutron Scattering and Polarizable Molecular Dynamics Study

In this study, we investigate the quaternary ammonium-based ionic liquid (QAIL), methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, [N1888][TFSI], utilizing small angle neutron scattering (SANS) measurements and polarizable molecular dynamics (MD) simulations to characterize the short- and long-range liquid structure. Scattering structure factors show signatures of three length scales in reciprocal space indicative of alternating polarity (k ∼ 0.44 Å-1), charge (k ∼ 0.75 Å-1), and neighboring or adjacent (k ∼ 1.46 Å-1) domains. Excellent agreement between simulation and experimental scattering structure factors validates various simulation analyses that provide detailed atomistic characterization of the different length scale correlations. The first solvation shell structure is illustrated by obtaining radial, angular, dihedral, and combined distribution functions, where two dominant spatial motifs, N+···N- and N+···O-, compete for optimal packing around the polar head of the [N1888]+ cation. Intermediate and long-range structures are governed by the balance between local electroneutrality and octyl chain networking, respectively. By computing the charge-correlation structure factor, SZZ, and the spatial extent of the octyl chain network using graph theory, the bulk-phase structure of [N1888][TFSI] is characterized in terms of electrostatic screening and apolar domain formation length scales.

Does Positron Attachment Take Place in Water Solution?

We performed a computational study of positron attachment to hydrated amino acids, namely glycine, alanine, and proline in the zwitterionic form. We combined the sequential quantum mechanics/molecular mechanics (s-QM/MM) method with various levels of any particle molecular orbital (APMO) calculations. Consistent with previous studies, our calculations indicate the formation of energetically stable states for the isolated and microsolvated amino acids, in which the positron localizes around the carboxylate group. However, for the larger clusters, composed of 7 to 40 water molecules, hydrogen bonding between the solute and solvent molecules disfavors positron attachment to the amino acids, giving rise to surface states in which the positron is located around the water-vacuum interface. The analysis of positron binding energies, positronic orbitals, radial probability distributions, and annihilation rates consistently pointed out the change from positron-solute to positron-solvent states. Even with the inclusion of an electrostatic embedding around the aggregates, the positrons did not localize around the solute. Positron attachment to molecules in the gas phase is a well-established fact. The existence of hydrated positronic molecules could also be expected from the analogy with transient anion states, which are believed to participate in radiation damage. Our results indicate that positron attachment to hydrated biomolecules, even to zwitterions with negatively charged carboxylated groups, would not take place. For the larger clusters, in which positron-water interactions are favored, the calculations indicate an unexpectedly large contribution of the core orbitals to the annihilation rates, between 15 and 20%. Finally, we explored correlations between positron binding energies (PBEs) and dipole moments, as well as annihilation rates and PBEs, consistent with previous studies for smaller clusters.

Calculation of the geometry, absorption spectrum, and first hyperpolarizability of 4,5-dicyanoimidazole derivatives in solution. A multiscale ASEC-FEG study

We investigate the effects of solvents on the geometry, absorption spectrum, and first hyperpolarizability of six push-pull molecules, each containing a 4,5-dicyanoimidazole group as an electron acceptor and a N,N-dimethylamino group as an electron donor, with systematically extended π-conjugated systems. Geometry optimizations in dichloromethane, methanol, water, and formamide under normal thermodynamic conditions were performed using the average solvent electrostatic configuration-free energy gradient method, which employs a discrete solvent model. The conformational structure of molecules is moderately affected by the environment, with the π-conjugated system becoming more planar in protic solvents. Solvent effects on the first hyperpolarizability result in marked increases that are in line with the red shifts of the absorption spectrum. The hyperpolarizability of smaller molecules within the set may be significantly influenced by the effects of geometry relaxation in highly polar protic solvents. The results illustrate the role of hydrogen bonds in the structure and electronic properties of push-pull molecules in protic environments. For smaller molecules, hydrogen bonds significantly contribute to enhancing the hyperpolarizability, but the effect of these specific interactions becomes less significant with the length of the π-conjugated system.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Unraveling the Impact of Flexibility and Solvent Effects on the UV-Vis Absorption Spectrum of Subphthalocyanine in Liquid Chloroform within the Born-Oppenheimer Molecular Dynamics Approach

A study based on Born-Oppenheimer molecular dynamics (BOMD) of the subphthalocyanine (SubPc) with a chloride attached to the central boron atom was carried out. The BOMD simulation is used to access the dynamic evolution of the SubPc in liquid chloroform, and the electronic absorption spectrum is calculated using the Time-Dependent Density Functional Theory (TDDFT) considering explicit solvent models. We show that the conformational changes and solvent effects produce a red shift of the Q-band, where the largest contribution is due to the geometry changes of the symmetric structure of SubPc. A large splitting (0.2 eV) of the first electronic transition is also described, and it originates as a shoulder in the Q-band, which according to previous experimental studies is attributed to a vibronic origin. The red shift is obtained in agreement with experiment within less than 0.1 eV. The splitting is a consequence of the symmetry breaking in the SubPc central ring structure occurring during the molecular dynamics, with a significant contribution to the large red shift and the broadening of the spectrum.

Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution

Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2'-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method.

Biotransformation of 1-nitro-2-phenylethane ⟶ 2-phenylethanol from fungi species of the Amazon biome: an experimental and theoretical analysis

CONTEXT

Natural products and their biotransformation procedures are a powerful source of new chromophores with potential applications in fields like biology, pharmacology and materials science. Thus, this work discusses about the extraction procedure of 1-nitro-2-phenylethane (1N2PE) from Aniba canelilla, its biotransformation setup into 2-phenylethanol (2PE) using four fungi, Lasiodiplodia caatinguensis (phytopathogenic fungus from Citrus sinensis), Colletotrichum sp. (phytopathogenic fungus from Euterpe oleracea), Aspergillus flavus and Rigidoporus lineatus isolated from copper mining waste located in the interior of the Brazilian Amazon. A detailed experimental and theoretical vibrational analysis (IR and Raman) have allowed us to perform some charge transfer effects on the title compounds (push-pull effect) by monitoring specific vibrational modes of their electrophilic and nucleophilic molecular sites. The solvent interactions promote molecular conformations that affect the vibrational spectra of the donor and acceptor groups, as can be seen comparatively in the gas and aqueous solution spectra, an effect possibly related to the bathochromic shift in the calculated optical spectrum of the compounds. The nonlinear optical behavior shows that while the solvent reduces the response of 1N2PE, the response of 2PE increases the optical parameters, which presents low refractive index (n) and first hyperpolarizability. (β ) is almost eight times that reported for urea (42.79 a.u.), a common nonlinear optical material. Furthermore, the bioconversion goes from an electrophilic to a nucleophilic compound, affecting its molecular reactivity.

METHODS

1N2PE was obtained from Aniba canelilla, whose essential oil is constituted of∼ 80 % of 2PE. The A. canelilla essential oil was extracted under hydrodistillation. The biotransformation reactions were performed in autoclaved liquid media (100 mL) composed of malt extract (2%) in 250 mL Erlenmeyer flask. Each culture was incubated in an orbital shaker (130 rpm) at32 ∘ C during 7 days and after that, 50 mg of 1N2PE (80%) were diluted in 100μ L of dimethylsulfoxide (DMSO) and added to the reactions flasks. Aliquots (2 mL) were removed using ethyl acetate (2 mL) and analyzed by GC-MS (fused silica capillary col1umn, Rtx -5MS 30 m× 0.25 mm× 0.25μ m) in order to determine the amount of 1N2PE biotransformation. FTIR 1N2PE and 2PE spectra were obtained by attenuated total reflectance (ATR), using a Agilent CARY 630 spectrometer, in the spectral region 4000-650 cm− 1 . The quantum chemical calculations were carried out in the Gaussian 09 program while the DICE code was used to perform the classical Monte Carlo simulations and generate the liquid environment using the classical All-Atom Optimized parameters for Liquid Simulations (AA-OPLS). All nonlinear optical properties, reactive parameters, and electronic excitations were calculated using the Density Functional Theory framework coupled to the standard 6-311++G(d,p) basis set.

Temperature Dependence of Hydrogen Bond Networks of Liquid Water: Thermodynamic Properties and Structural Heterogeneity from Topological Descriptors

Topological analyses of hydrogen bond networks were performed based on the complex network and island statistics of liquid water at different temperatures. The influence of temperature on the liquid water structures and the topological properties of the hydrogen bond networks was investigated by Metropolis Monte Carlo simulations with the TIP4P/2005 potential model. The bilinear behavior of the second peak in the radial distribution function with the temperature was properly reproduced by these simulations. The average connectivity also displayed a bilinear behavior consistent with being a local descriptor. The semiglobal average path length (or geodesic distance) descriptor showed an unprecedented trimodal distribution, whose areas were dependent on the temperature. Considering equilibrium between these three sets of networks, standard enthalpy and entropy of equilibrium were determined for the first time, providing new insights into the structural heterogeneities of liquid water with interesting perspectives for modeling these quantitative properties of hydrogen bond networks.

Solvation effects on glyphosate protonation and deprotonation states evaluated by mass spectrometry and explicit solvation simulations

Glyphosate is a widely used herbicide, and its protonation and deprotonation sites are fundamental to understanding its properties. In this work, the sodiated, protonated, and deprotonated glyphosate were evaluated in the gas phase by infrared multiple photon dissociation spectroscopy to determine the exact nature of these coordination, protonation, and deprotonation states in the gas phase. In this context, Natural Bond Orbital analyses were carried out to unravel interactions that govern glyphosate (de)protonation states in the gas phase. The solvent effect on the protonation/deprotonation equilibria was also investigated by implicit (Solvation Model Based on Density and polarizable continuum models) and explicit solvation models (Monte Carlo and Molecular Dynamics simulations). These results show that glyphosate is protonated in the phosphonate group in the gas phase because of the strong hydrogen bond between the carboxylic oxygen (O7) and the protonated phosphonate group (O8-H19), while the most stable species in water is protonated at the amino group because of the preferential interaction of the NH₂ ⁺ group and the solvent water molecules. Similarly, deprotonated glyphosate [Glyp-H]^- was shown to be deprotonated at the phosphonate group in the gas phase but not in solution, also because of the preferential solvation of the NH₂ ⁺ group present in the other deprotomers. Therefore, these results show that the stabilization of the protonated amino group by the solvent molecules is the governing factor of the (de)protonation equilibrium of glyphosate in water.

The Importance of the Density Functional Theory Exchange-Correlation Hartree-Fock Term in Magnetic Resonance: Application to an Aqueous Environment

Within the framework of Density Functional Theory (DFT), the relevance of the term Hartree-Fock exchange (HFE) for a variety of molecular properties is a critical point. For this reason, we spend efforts to understand these relationships in nuclear magnetic resonance (NMR) parameters in a water solvent. This work takes advantage of the appropriate aug-cc-pVTZ-J basis set and the Minnesota family of DFT methods, which consider different portions of HFE contributions. With regard to solvent participation, the results are based on a sequential Monte Carlo/Quantum Mechanics procedure, which builds the structures of the liquid under realistic thermodynamic conditions. Compared to the accurate results of second-order polarization propagator approximation (SOPPA) and experimental data, all NMR parameters show a huge dependence on the size of the HFE contribution. For instance, the inclusion of this term in ¹J_OH and ²J_HH indirect spin-spin couplings does vary with 49.661 and 25.459 Hz, respectively. The M06-HF method accounts for 100% of HFE and better matches the σ_O and σ_H shielding constants. On the other hand, ¹J_OH and ²J_HH demand a medium contribution (54% of HFE), the best description being associated with the M06-2X method. Thus, the dependence varies regarding the phenomenology of the property in focus and the order for independent treatments. For elements that participate in hydrogen bonds simultaneously as donor and acceptor actors, the results indicate that explicit solvent molecules must be considered in the quantum mechanical calculations for better modeling of paramagnetic shielding constants.

The Effect of Surface Composition on the Selective Capture of Atmospheric CO2 by ZIF Nanoparticles: The Case of ZIF-8

We performed theoretical studies of CO₂ capture in atmospheric conditions by the zeolitic imidazolate framework-8 (ZIF-8) via classical Monte Carlo (MC) simulations with Metropolis sampling and classical molecular dynamics (MD) simulations in the NVT and NPT ensembles and different thermodynamic conditions. The ZIF-8 framework was described by varying unit cell dimensions in the presence of pure gases of CO₂, N₂, O₂, Ar, and H₂O steam as well as binary mixtures of CO₂:N₂ and CO₂:H₂O in s 1:1 concentration. Different chemical compositions of the framework surface was considered to provide an accurate treatment of charge and charge distribution in the nanoparticle. Hence, surface groups were represented as unsaturated zinc atom (Zn⁺²), 2-methylimidazole (mImH), and deprotonated 2-methylimidazole (mIm^-). Force field reparameterization of the surface sites was required to reproduce the interactions of the gas molecules with the ZIF-8 surface consistent with quantum mechanics (QM) calculations and Born-Oppenheimer molecular dynamics (BOMD). It was observed that ZIF-8 selectively captures CO₂ due to the negligible concentrations of N₂, O₂, Ar, and H₂O. These molecules spontaneously migrate to the inner pores of the framework. At the surface, there is a competitive interaction between H₂O, CO₂, and N₂, for the positively charged ZIF-8 nanoparticle with a large binding energy advantage for water molecules (on average -62, -15, and -8 kcal/mol respectively). For the neutral ZIF-8 nanoparticle, the water molecules dominate the interactions due to the occurrence of hydrogen bond with the imidazolate groups at the surface. Simulations of binary mixtures of CO₂/water steam and CO₂/N₂ were performed to investigate binding competition between these molecules for the framework positively charged and neutral surfaces. It was found that water molecules drastically block the interaction between CO₂ molecules and the framework surface, decreasing CO₂ capture in the central pore, and CO₂ molecules fully block the interaction between N₂ molecules and the framework. These findings show that CO₂ capture by ZIF-8 is possible in atmospheric environments only upon dehydration of the atmospheric gas. It further shows that ZIF-8 capture of CO₂ from the atmospheric environment is dependent on thermodynamic conditions and can be increased by decreasing temperature and/or increasing pressure.

Free-Energy Landscape of the SN2 Reaction CH3Br + Cl- → CH3Cl + Br- in Different Liquid Environments

This work describes in detail the reaction path of the well-known S_N2 reaction CH₃Br + Cl^- → CH₃Cl + Br^-, whose reaction rate has a huge variation with the solvent in the gas phase and in protic and aprotic liquid environments. We employed the ASEC-FEG method to optimize for minima (reactants and products) and saddle points (transition states) in the in-solution free-energy hypersurface. The method takes atomistic details of the solvent into account. A polarizable continuum model (PCM) has also been employed for comparison. The most perceptive structural changes are noted in aqueous solution by using the ASEC-FEG approach. The activation energies in all solvents, estimated by means of free-energy perturbation calculations, are in good agreement with the experimental data. The total solute-solvent hydrogen bonds play an important role in the increased barrier height observed in water and are therefore crucial to explain the huge decrease in the kinetic constant. It is also found that the hydration shell around the ions breaks itself spontaneously to accommodate the molecule, thus forming minimum energy complexes.

Unraveling the acid-base characterization and solvent effects on the structural and electronic properties of a bis-bidentate bridging ligand

Understanding the interactions and the solvent effects on the distribution of several species in equilibrium and how it can influence the ¹H-NMR properties, spectroscopy (UV-vis absorption), and the acid-base equilibria can be especially challenging. This is the case of a bis-bidentate bridging ligand bis(2-pyridyl)-benzo-bis(imidazole), where the two pyridyl and four imidazolyl nitrogen atoms can be protonated in different ways, depending on the solvent, generating many isomeric/tautomeric species. Herein, we report a combined theoretical-experimental approach based on a sequential quantum mechanics/molecular mechanics procedure that was successfully applied to describe in detail the acid-base characterization and its effects on the electronic properties of such a molecule in solution. The calculated free-energies allowed the identification of the main species present in solution as a function of the solvent polarity, and its effects on the magnetic shielding of protons (¹H-NMR chemical shifts), the UV-vis absorption spectra, and the acid-base equilibrium constants (pK_as) in aqueous solution. Three acid-base equilibrium constants were experimentally/theoretically determined (pK_a1 = 1.3/1.2, pK_a2 = 2.1/2.2 and pK_a5 = 10.1/11.3) involving mono-deprotonated and mono-protonated cis and trans species. Interestingly, other processes with pK_a3 = 3.7 and pK_a4 = 6.0 were also experimentally determined and assigned to the protonation and deprotonation of dimeric species. The dimerization of the most stable neutral species was investigated by Monte Carlo simulations and its electronic effects were considered for the elucidation of the UV-vis absorption bands, revealing transitions mainly with the charge-transfer characteristic and involving both the monomeric species and the dimeric species. The good matching of the theoretical and experimental results provides an atomistic insight into the solvent effects on the electronic properties of this bis-bidentate bridging ligand.

Multicomponent Quantum Mechanics/Molecular Mechanics Study of Hydrated Positronium

We propose a model for solvated positronium (Ps) atoms in water, based on the sequential quantum mechanics/molecular mechanics (s-QM/MM) protocol. We developed a Lennard-Jones force field to account for Ps-water interactions in the MM step. The repulsive term was obtained from a previously reported model for the solvated electron, while the dispersion constant was derived from the Slater-Kirkwood formula. The force field was employed in classical Monte Carlo (MC) simulations to generate Ps-solvent configurations in the NpT ensemble, while the quantum properties were computed with the any-particle molecular orbital method in the subsequent QM step. Our approach is general, as it can be applied to other liquids and materials. One basically needs to describe the solvated electron in the environment of interest to obtain the Ps solvation model. The thermodynamical properties computed from the MC simulations point out similarities between the solvation of Ps and noble gas atoms, hydrophobic solutes that form clathrate structures. We performed convergence tests for the QM step, with particular attention to the choice of basis set and expansion centers for the positronic and electronic subsystems. Our largest model was composed of the Ps atom and 22 water molecules in the QM region, corresponding to the first solvation shell, surrounded by 128 molecules described as point charges. The mean electronic and positronic vertical detachment energies were (4.73 ± 0.04) eV and (5.33 ± 0.04) eV, respectively. The latter estimates were computed with Koopmans' theorem corrected by second-order self-energies, for a set of statistically uncorrelated MC configurations. While the Hartree-Fock wave functions do not properly account for the annihilation rates, they were useful for numerical tests, pointing out that annihilation is more sensitive to the choice of basis sets and expansion centers than the detachment energies. We further explored a model with reduced solute cavity size by changing the Ps-solvent force field. Although the pick-off annihilation lifetimes were affected by the cavity size, essentially the same conclusions were drawn from both models.

Theoretical investigation of the cooperative effect of solvent: a case study

The effect of solvent was investigated at the DFT level, M06-2X/6-31++G(d,p), for the implicit, namely the universal solvent model based on solute electron density (SMD), and hybrid solvation models, and...

Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions

We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.

Preferential solvation and optical properties of eumelanin building blocks in binary mixture of methanol and water

Employing a sequential quantum mechanical/molecular mechanical approach for polar protic solvents, we study the absorption spectrum of eumelanin building blocks including monomers, dimers, and tetramers in pure water and methanol and three water-methanol binary mixtures having water molar fractions (Xw = 0.25, 0.50, and 0.75). The binary mixture of solvents is a common situation in experiments, but theoretical studies are limited to the use of continuum models. Here, we use explicit solvent molecules, and specific solute-solvent interaction is analyzed and seen to play an important role. Effects of the electronic polarization of solute by the environment were included using a reliable iterative scheme. The results illustrate that the monomers, dimers, and tetramers are preferably solvated by methanol, but the composition of the mixture in the vicinity of the solute molecules is different from the bulk composition with a preferential microsolvation (hydrogen bonds) in water for most species considered. It is observed that the short-range electrostatic polarization effects of the hydrogen bonds lead to a slight blue shift of the excitation energies when the concentration of water in the mixture is enhanced. For the same species, there is an enhancement of the higher-energy absorption intensity caused by long-range electrostatic interactions with the environment and that the behavior of the experimental spectrum, which is characterized by a nearly monotonic decay from the ultraviolet to the infrared, is qualitatively reproduced by the superposition of the absorption spectra of monomers, dimers, and tetramers in the liquid phase.

Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems

We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.

A QM/MM study of the conformation stability and electronic structure of the photochromic switches derivatives of DHA/VHF in acetonitrile solution

We present a detailed theoretical study of the electronic absorption spectra and thermochemistry of molecular photoswitches composed of one and two photochromic units of dihydroazulene (DHA)/vinylheptafulvene (VHF) molecules. Six different isomers are considered depending on the ring opening/closure forms of the DHA units. The solvent effect of acetonitrile is investigated using a sequential Molecular Mechanics/Quantum Mechanics approach. The thermochemical investigations of these photochromic molecules were performed using the Free Energy Perturbation method, and the simulations were performed using Configurational Bias Monte Carlo. We show that to open the 5-member ring of the DHA, there is no significant gain in thermal release of energy for the back reaction when a unit or two DHA units are considered. Overall, we found agreement between the solvation free energy based on Monte Carlo simulations and the continuum solvent model. However, the cavitation term in the continuum model is shown to be a source of disagreement when the non-electrostatic terms are compared. The electronic absorption spectra are calculated using TDDFT CAM-B3LYP/cc-pVDZ. Agreement with experiment is obtained within 0.1 eV, considering statistically uncorrelated configurations from the simulations. Inhomogeneous broadening is also considered and found to be well described in all cases.

Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT-GIAO-NMR calculations

In this work, we observe the behavior of the dipole moment, atomic charges, solute-solvent interactions and NMR spectroscopy of aliphatic amino acids in a water solution via the computational simulations of classical molecular dynamics and DFT quantum calculations. Our results indicate that the convergence of the atomic charge of the solute, from an iterative process, together with the dipole moment of the amino acid, alters the lifetime of hydrogen bonds present in the first solvation shell, resulting in the modification of its structure and dynamics. Using GIAO-DFT-NMR calculations, we assessed the impact of these structural solute-solvent modifications on the magnetic shielding constants of the solute carbon atoms. In this sense, we evaluate the importance of an update in parameters that describe atomic charges present in the CHARMM36 force field.

3,4-Methylenedioxypyrovalerone (MDPV) Sensing Based on Electropolymerized Molecularly Imprinted Polymers on Silver Nanoparticles and Carboxylated Multi-Walled Carbon Nanotubes

3,4-methylenedioxypyrovalerone (MDPV) is a harmful and controlled synthetic cathinone used as a psychostimulant drug and as sport-enhancing substance. A sensor was developed for the direct analysis of MDPV by transducing its oxidation signal by means of an electropolymerized molecularly imprinted polymer (e-MIP) built in-situ on the screen-printed carbon electrode's (SPCE) surface previously covered with multi-walled carbon nanotubes (MWCNTs) and silver nanoparticles (AgNPs). Benzene-1,2-diamine was used as the functional monomer while the analyte was used as the template monomer. Each step of the sensor's development was studied by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) in a solution containing ferricyanide, however no redox probe was required for the actual MDPV measurements. The interaction between the poly(o-phenylenediamine) imprinted polymer and MDPV was studied by density-functional theory (DFT) methods. The SPCE-MWCNT-AgNP-MIP sensor responded adequately to the variation of MDPV concentration. It was shown that AgNPs enhanced the electrochemical signal by around a 3-fold factor. Making use of square-wave voltammetry (SWV) the developed sensor provided a limit of detection (LOD) of 1.8 μmol L-1. The analytical performance of the proposed sensor paves the way to the development of a portable device for MDPV on-site sensing to be applied in forensic and doping analysis.

Electroanalytical profiling of cocaine samples by means of an electropolymerized molecularly imprinted polymer using benzocaine as the template molecule

Cocaine samples were ‘finger-printed’ using e-MIPs, constructed on the surface of portable SPCEs. The SWV data with suitable chemometric analysis provides valuable information about the drugs’ provenience which is crucial to tackle drug traffic.

A new interpretation of the absorption and the dual fluorescence of Prodan in solution

Remarkable interest is associated with the interpretation of the Prodan fluorescent spectrum. A sequential hybrid Quantum Mechanics/Molecular Mechanics method was used to establish that the fluorescent emission occurs from two different excited states, resulting in a broad asymmetric emission spectrum. The absorption spectra in several solvents were measured and calculated using different theoretical models presenting excellent agreement. All theoretical models [semiempirical, time dependent density functional theory and and second-order multiconfigurational perturbation theory] agree that the first observed band at the absorption spectrum in solution is composed of three electronic excitations very close in energy. Then, the electronic excitation around 340 nm-360 nm may populate the first three excited states (π-π^*L_b, n-π^*, and π-π^*L_a). The ground state S₀ and the first three excited states were analyzed using multi-configurational calculations. The corresponding equilibrium geometries are all planar in vacuum. Considering the solvent effects in the electronic structure of the solute and in the solvent relaxation around the solute, it was identified that these three excited states can change the relative order depending on the solvent polarity, and following the minimum path energy, internal conversions may occur. A consistent explanation of the experimental data is obtained with the conclusive interpretation that the two bands observed in the fluorescent spectrum of Prodan, in several solvents, are due to the emission from two independent states. Our results indicate that these are the n-π^* S₂ state with a small dipole moment at a lower emission energy and the π-π^*L_b S₁ state with large dipole moment at a higher emission energy.

Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tz, tz, and tz

The photophysical relaxation pathways of ^tzA, ^tzG, and ^tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying ¹(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the ¹(ππ*)_min region, the conical intersection with the ground state ((ππ*/GS)_CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.

15N NMR Shifts of Eumelanin Building Blocks in Water: A Combined Quantum Mechanics/Statistical Mechanics Approach

Theoretical results for the magnetic shielding of protonated and unprotonated nitrogens of eumelanin building blocks including monomers, dimers, and tetramers in gas phase and water are presented. The magnetic property in water was determined by carrying out Monte Carlo statistical mechanics sampling combined with quantum mechanics calculations based on the gauge-including atomic orbitals approach. The results show that the environment polarization can have a marked effect on nitrogen magnetic shieldings, especially for the unprotonated nitrogens. Large contrasts of the oligomerization effect on magnetic shielding show a clear distinction between eumelanin building blocks in solution, which could be detected in nuclear magnetic resonance experiments. Calculations for a π-stacked structure defined by the dimer of a tetrameric building block indicate that unprotonated N atoms are significantly deshielded upon π stacking, whereas protonated N atoms are slightly shielded. The results stress the interest of NMR experiments for a better understanding of the eumelanin complex structure.