Novel Approach for Predicting Vertical Electron Attachment Energies in Bulk-Solvated Molecules.

When low-energy electrons interact with molecules, they can give rise to transient anion states commonly known as resonances. These states are formed through vertical electron attachment processes and have the potential to induce various forms of DNA lesions, including base damage, single- and double-strand breaks, cross-links, and clustered lesions that are challenging to repair. So far, most experimental and theoretical studies have investigated the formation of resonances of (bio)molecules in the gas phase or in microsolvated environments. Since cellular environments are mainly composed of water molecules, it is crucial to understand how bulk water affects the resonances of (bio)molecules. Given the existing gap in studies on resonances of bulk-solvated molecules, we propose a novel theoretical-computational approach to address this void. Our approach combines the multibasis-set (time-dependent-)density functional theory and self-consistent sequential quantum mechanics/molecular mechanics polarizable electrostatic embedding methods. We apply this combined methodology to predict the vertical electron attachment energies of 1-methyl-5-nitroimidazole (1M5NI), a well-known radiosensitizer model, in bulk water. In addition, we analyze the rapid mutual polarization between the resonances (both shape- and core-excited) of 1M5NI and the surrounding bulk water environment. For comparison, we also studied the isolated and microsolvated 1M5NI. Overall, while the polarization of the environment is clearly sensitive to the solute charge, causing a significant impact on the vertical electron affinity and consequently on the attachment electron energies, it does not have a significant impact on the excitation energies of the anion.

New insights into the interaction of emodin with lipid membranes.

Emodin is a natural anthraquinone derivative found in nature, widely known as an herbal medicine. Here, the partition, location, and interaction of emodin with lipid membranes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) are experimentally investigated with different techniques. Our studies have considered the neutral form of emodin (EMH) and its anionic/deprotonated form (EM-), and their interaction with a more and less packed lipid membrane, DMPC at the gel and fluid phases, respectively. Though DSC results indicate that the two species, EMH and EM-, similarly disrupt the packing of DMPC bilayers, spin labels clearly show that EMH causes a stronger bilayer disruption, both in gel and fluid DMPC. Fluorescence spectroscopy shows that both EMH and EM- have a high affinity for DMPC: the binding of EM- to both gel and fluid DMPC bilayers was found to be quite similar, and similar to that of EMH to gel DMPC, Kp = (1.4 ± 0.3)x103. However, EMH was found to bind twice more strongly to fluid DMPC bilayers, Kp = (3.2 ± 0.3)x103. Spin labels and optical absorption spectroscopy indicate that emodin is located close to the lipid bilayer surface, and suggest that EM- is closer to the lipid/water interface than EMH, as expected. The present studies present a relevant contribution to the current understanding of the effect the two species of emodin, EMH and EM-, present on different microregions of an organism, as local pH values can vary significantly, can cause in a neutral lipid membrane, either more or less packed, liked gel and fluid DMPC, respectively, and could be extended to lipid domains of biological membranes.

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.

Elucidating the conformational change and electronic absorption spectrum of p-dimethylamino-cinnamaldehyde merocyanine across different solvent polarities.

We present a theoretical study on the structural and electronic properties of the p-dimethylamino-cinnamaldehyde (DMACA) merocyanine molecule in solvents of different polarities by combining the free energy gradient and the average solvent electrostatic configuration methods via an iterative procedure based on the sequential quantum mechanics/molecular mechanics hybrid methodology. Studying such a system in solution is a crucial step for understanding the solvent effects on its properties, which can have implications in fields such as optoelectronics and biophysics. We found that the DMACA molecule presents different geometries in nonpolar and polar solvents, changing from a polyene-like structure with a pyramidal dimethylamino group (in gas phase or nonpolar solvents) to a cyanine-like structure with a planar dimethylamino group in water due to the stabilizing effect of hydrogen bonds between DMACA and water. The molecular absorption spectrum showed a significant change, increasing solvent polarity with a large shift of the lower energy band, while the other two low lying bands did not shift significantly. The study accurately described the solvatochromic shift of the lowest-energy band and analyzed the structure of the excited states in terms of the one-electron transition density matrix, which showed that the dominant excited state (associated with the first lower energy band) is characterized by a local excitation on the benzene ring with charge transfer character to the carbon conjugated segment.

Spectroscopic characterization of different protonation/deprotonation states of Barbaloin in aqueous solution.

Barbaloin (10-glucopyranosyl-1,8-dihydroxy-3-(hydroxymethyl)-9(10H)-anthraquinone: aloin A), present in Aloe species, is widely used in food, cosmetic and pharmaceutical industries. Here we characterize its optical absorption and emission spectra in aqueous solution at different pH values. Through pH titration, using both absorption and fluorescence spectroscopy, two pKa values for Barbaloin were determined: pKa1=9.6±0.6 and pKa2=12.6±0.8. These acidity constants were found to be higher than those found for Emodin, a similar molecule which lacks the sugar moiety present in Barbaloin. Performing quantum mechanical calculations for non-ionized, singly, doubly, and triply deprotonated forms of Barbaloin in vacuum and in water, we assigned the positions of the site for the first and third deprotonation in the anthraquinone group, and the second deprotonation in the glucose group. The instability of Barbaloin in high pH solutions is discussed here, and the optical absorption and fluorescence spectra due to products resulted from Barbaloin degradation at high pH is well separated from the Barbaloin original spectra. Biological fluids have specific pH values to maintain homeostasis, hence determining the pKa of Barbaloin is important to evaluate the mechanism of action of this drug in different parts of an organism as well as to predict pharmacological relevant parameters, such as absorption, distribution, metabolism, and excretion.

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.

Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape.

The surface assessment via grid evaluation (SuAVE) software was developed to account for the effect of curvature in the calculations of structural properties of chemical interfaces regardless of the chemical composition, asymmetry, and level of atom coarseness. It employs differential geometry techniques, enabling the representation of chemical surfaces as fully differentiable. In this article, we present novel developments of SuAVE to treat closed surfaces and complex cavity shapes. These developments expand the repertoire of curvature-dependent analyses already available in the previous version of SuAVE (e.g., area per lipid, density profiles, membrane thickness, deuterium-order parameters, volume per lipid, and surface curvature angle) to include new functionalities applicable to soft matter (e.g., sphericity, average radius, principal moment of inertia, and roundness) and crystalline porous materials (e.g., pore diameter, internal void volume, total area, and the total void volume of the unit cell structure). SuAVE can accurately handle chemical systems with high and low atom density as demonstrated for two distinct chemical systems: the lipid A vesicle and a set of selected metal-organic frameworks. The SuAVE software v2.0 is fully parallel and benefits from a compiler that supports OpenMP. SuAVE is freely available from https://github.com/SuAVE-Software/source and https://www.biomatsite.net/.

Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration.

BP100, a short antimicrobial peptide, produces membrane perturbations that depend on lipid structure and charge, salts presence, and peptide/lipid molar ratios. As membrane perturbation mechanisms are not fully understood, the atomic scale nature of peptide/membrane interactions requires a close-up view analysis. Molecular Dynamics (MD) simulations are valuable tools for describing molecular interactions at the atomic level. Here, we use MD simulations to investigate alterations in membrane properties consequent to BP100 binding to zwitterionic and anionic model membranes. We focused on membrane property changes upon peptide binding, namely membrane thickness, order parameters, surface curvature, lipid lateral diffusion and membrane hydration. In agreement with experimental results, our simulations showed that, when buried into the membrane, BP100 causes a decrease in lipid lateral diffusion and lipid acyl-chain order parameters and sharp local membrane thinning. These effects were most pronounced on the closest lipids in direct contact with the membrane-bound peptide. In DPPG and anionic-aggregate-containing DPPC/DPPG membranes, peptide flip (rotation of its non-polar facet towards the membrane interior) induced marked negative membrane curvature and enhanced the water residence half-life time in the lipid hydrophobic core and transmembrane water transport in the direction of the peptide. These results further elucidate the consequences of the initial interaction of cationic alpha-helical antimicrobial peptides with membranes.

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 (pKas) in aqueous solution. Three acid-base equilibrium constants were experimentally/theoretically determined (pKa1 = 1.3/1.2, pKa2 = 2.1/2.2 and pKa5 = 10.1/11.3) involving mono-deprotonated and mono-protonated cis and trans species. Interestingly, other processes with pKa3 = 3.7 and pKa4 = 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.

Spectrophotometric studies of charge-transfer complexes formed with ions N,N'-alkyldiyl-bis(pyridinium) derivatives and iodide.

The charge-transfer complexes (CTC) between electron donor iodide and pyridinium dimers and monomers as acceptors have been studied spectrophotometrically in acetonitrile, DMSO and water. The dimers were: N,N'-alkyldiyl-bis(4-cyanopyridinium) and N,N'-alkyldiyl-bis(2-bromopyridinium), and the monomers were: N-alkyl-4-cyanopyridinium and N-alkyl-2-bromopyridinium, bridged by n methylene spacers. The formation constant (KCTC), molar absorptivity (εCTC), fluorescence-quenching constant (KSV) were determined. The results indicate that the stoichiometry of the CTC for dimers and monomers is 1:1 (equimolar ratio), and its formation is favored for dimers more than for monomers, especially dimers with short methylene spacers forming a "sandwiched type-complex" in which the iodide is close to the two pyridinium rings. Solvents with low polarity favored the complex, which was destroyed by the presence of water. The experimental studies were complemented with theoretical studies with quantum mechanics (QM) calculations using density functional theory (DFT) and molecular mechanics (MM) simulations with Molecular Dynamics for identify the most stable conformers in acetonitrile solution. The electronic excitations were calculated with sequential QM/MM hybrid method, showing a charge-transfer wavelength in agreement with the UV-Vis absorption spectra obtained experimentally. It confirms the "sandwiched type-complex" conformers favoring the interaction of the iodide with one pyridinium rings and simultaneously forming one, or two, hydrogen bonds with the alkyl chain and additionally, for the case of dimers, with the other pyridinium ring.

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.

Molecular Dynamics Approach to Calculate the Thermodiffusion (Soret and Seebeck) Coefficients of Salts in Aqueous Solutions.

An approach to investigate the physical parameters related to ion thermodiffusion in aqueous solutions is proposed herein by calculating the equilibrium hydration free energy and the self-diffusion coefficient as a function of temperature, ranging from 293 to 353 K, using molecular dynamics simulations of infinitely diluted ions in aqueous solutions. Several ion force field parameters are used in the simulations, and new parameters are proposed for some ions to better describe their hydration free energy. Such a theoretical framework enables the calculation of some single-ion properties, such as heat of transport, Soret coefficient, and mass current density, as well as properties of salts, such as effective mass and thermal diffusion, Soret and Seebeck, coefficients. These calculated properties are compared with experimental data available from optical measurements and showed good agreement revealing an excellent theoretical predictability of salt thermodiffusion properties. Differences in single-ion Soret and self-diffusion coefficients of anions and cations give rise to a thermoelectric field, which affects the system response that is quantified by the Seebeck coefficient. The fast and slow Seebeck coefficients are calculated and discussed, resulting in values with mV/K order of magnitude, as observed in experiments involving several salts, such as K+Cl-, Na+Cl-, H+Cl-, Na+OH-, TMA+OH-, and TBA+OH-. The present approach can be adopted for any ion or charged particle dispersed in water with the aim of predicting the thermoelectric field induced through the fluid. It has potential applications in designing electrolytes for ionic thermoelectric devices in order to harvest energy and thermoelectricity in biological nanofluids.

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.

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*Lb, n-π*, and π-π*La). 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*Lb S1 state with large dipole moment at a higher emission energy.

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

Solute-solvent systems are an important topic of study, as the effects of the solvent on the solute can drastically change its properties. Theoretical studies of these systems are done with ab initio methods, molecular simulations, or a combination of both. The simulations of molecular systems are usually performed with either molecular dynamics (MD) or Monte Carlo (MC) methods. Classical MD has evolved much in the last decades, both in algorithms and implementations, having several stable and efficient codes developed and available. Similarly, MC methods have also evolved, focusing mainly in creating and improving methods and implementations in available codes. In this paper, we provide some enhancements to a configurational bias Monte Carlo (CBMC) methodology to simulate flexible molecules using the molecular fragments concept. In our implementation the acceptance criterion of the CBMC method was simplified and a generalization was proposed to allow the simulation of molecules with any kind of fragments. We also introduce the new version of DICE, an MC code for molecular simulation (available at https://portal.if.usp.br/dice). This code was mainly developed to simulate solute-solvent systems in liquid and gas phases and in interfaces (gas-liquid and solid-liquid) that has been mostly used to generate configurations for a sequential quantum mechanics/molecular mechanics method (S-QM/MM). This new version introduces several improvements over the previous ones, with the ability of simulating flexible molecules with CBMC as one of them. Simulations of well-known molecules, such as n-octane and 1,2-dichloroethane in vacuum and in solution, are presented to validate the new implementations compared with MD simulations, experimental data, and other theoretical results. The efficiency of the conformational sampling was analyzed using the acceptance rates of different alkanes: n-octane, neopentane, and 4-ethylheptane. Furthermore, a very complex molecule, boron subphtalocyanine, was simulated in vacuum and in aqueous solution showing the versatility of the new implementation. We show that the CBMC is a very good method to perform conformation sampling of complex moderately sized molecules (up to 150 atoms) in solution following the Boltzmann thermodynamic equilibrium distribution.

SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces.

Curvature is an intrinsic feature of biological membranes underlying vital cellular processes such as endocytosis, membrane fusion-fission, trafficking, and remodeling. The continuous expansion of the spatiotemporal scales accessible to computational simulations nowadays makes possible quasi-atomistic molecular dynamics simulations of these processes. In despite of that, computation of the shapes and curvatures associated with the dynamics of biological membranes remains challenging. For this reason, the effect of curvature is often neglected in the analysis of quantities essential for the accurate description of membrane properties (e.g., area and volume per lipid, density profiles, membrane thickness). We propose an algorithm for surface assessment via grid evaluation (SuAVE) that relies on the application of a radial base function to interpolate points scattered across an interface of any shape. This enables the representation of the chemical interface as fully differentiable so that related geometrical properties can be calculated through the straightforward employment of well-established differential geometry techniques. Hence, the effect of different types or degrees of curvature can be accurately taken into account in the calculations of structural properties of any interfaces regardless of chemical composition, asymmetry, and level of atom coarseness. The main functionalities implemented in SuAVE are featured for a number of tetraacylated and hexaacylated Lipid-A membranes of distinct curvatures and a surfactant micelle. We show that the properties calculated for moderately to highly curved membranes differ significantly between curvature-dependent and -independent algorithms. The SuAVE software is freely available from www.biomatsite.net/suave-software .

X-ray Photoelectron Fingerprints of High-Valence Ruthenium-Oxo Complexes along the Oxidation Reaction Pathway in an Aqueous Environment.

Recent advances in operando-synchrotron-based X-ray techniques are making it possible to address fundamental questions related to complex proton-coupled electron transfer reactions, for instance, the electrocatalytic water splitting process. However, it is still a grand challenge to assess the ability of the different techniques to characterize the relevant intermediates, with minimal interference on the reaction mechanism. To this end, we have developed a novel methodology employing X-ray photoelectron spectroscopy (XPS) in connection with the liquid-jet approach to probe the electrochemical properties of a model electrocatalyst, [RuII(bpy)2(py)(OH2)]2+, in an aqueous environment. There is a unique fingerprint of the extremely important higher-valence ruthenium-oxo species in the XPS spectra along the oxidation reaction pathway. Furthermore, a sequential method combining quantum mechanics and molecular mechanics is used to illuminate the underlying physical chemistry of such systems. This study provides the basis for the future development of in-operando XPS techniques for water oxidation reactions.

Binding and Flip as Initial Steps for BP-100 Antimicrobial Actions.

BP100 is a short antimicrobial peptide and can also act as a molecule-carrier into cells. Like with other antimicrobial peptides, the precise mechanism of membrane disruption is not fully understood. Here we use computer simulations to understand, at a molecular level, the initial interaction between BP100 and zwitterionic/negatively charged model membranes. In agreement with experimental results, our simulations showed BP100 folded into an alpha helix when in contact with negatively charged membranes. BP100 binding induced the aggregation of negatively charged lipids on mixed membranes composed of zwitterionic and anionic lipids. The peptide in alpha-helix conformation initially interacts with the membrane via electrostatic interactions between the negatively charged lipids and the positively charged residues of the peptide. At that point the peptide flips, burying the hydrophobic residues into the bilayer highlighting the importance of the hydrophobic effect contribution to the initial interaction of cationic antimicrobial peptides with membranes.