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The Sequential Monte Carlo/Quantum Mechanics approach was used for investigate the solvent effect on the solute-solvent structure and spectroscopic properties of Damascone derivatives, Carvone, Perillaldehyde and Menthadiene in water solution. Our in-water results have shown that the dipole moment increase of the compounds are between 36% and 84% when compared with the gas phase values and a solvatochromic shift between −20 and 14 nm whereas the magnetic properties studied have indicated an NMR shift close to 10 ppm for some carbon atoms and greater than 140 ppm for oxygen atoms.

In this paper, polypeptide membranes composed by surfactant-like peptides were studied by using molecular dynamics simulations. The studied membranes are composed by 15 amino acids, being a hydrophobic part consisting of 3 isoleucine (ILE - I), 3 valine (VAL - V), 3 alanine (ALA - A), 3 glycine (GLY - G), and a hydrophilic one formed by 3 lysine (LYS - K). These amino acids were linked into two different primary sequences, I3V3A3G3K3, with the charged lysine bounded at the C-terminus and K3G3A3V3I3, with the charged lysine bounded at the N-terminus. The density profiles results, the average number of hydrogen bonds, the Coulombic and van der Waals interactions between the peptide-water (PEP-Water) and between each group of peptide residues (PEP-PEP) indicate that, despite the occurrence of much water infiltration (especially in the I3V3A3G3K3 membrane, which has greater porosity than the K3G3A3V3I3 membrane), they still maintain a membrane structure. Our results allow a better understanding of the influence of the interactions between the peptides as well as the role of each group of amino acids residues, peptide terminus and solvent in membrane stability.

In this study, we observed the structural and energetic stability of a polypeptide nanosheet formed by a polypeptide skeleton of six alanines (ALA) or leucines (LEU) and a polar head composed of aspartic acid (ASP), lysine (LYS) or arginine (ARG). The six membrane structures A6D, A6K, A6R, L6D, L6K, and L6R were subjected to molecular dynamics simulations in an ionic liquid formed by the cholinium–glycine pair [CHO][GLY]. Our results show how the hydrogen bonds between the polypeptides and the ionic liquid are structured, the energetic behavior of the nanosheet, mobility of the IL, surface topology of the membrane and the stiffness of the structure when the extraction of a polypeptide from the macro structure is carried out. Different structural combinations were considered to verify the difference due to the electrostatic behavior in the systems. Our analysis aims to contribute information that can increase the use of these organic and biodegradable materials in other environments.

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 &pi, stacked structure defined by the dimer of a tetrameric building block indicate that unprotonated N atoms are significantly deshielded upon &pi, 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.

In this work, we have investigated the interactions of polypeptides composed of the sequence of six alanines and one arginine (A6R) grouped in three nanosheet structures with maximum, intermediate,...

We present a theoretical study of the solvent influence on ANR polypeptides, with N = 1, 2, 3, 4 and 5, in the gas phase and in water solution using the sequential MC/QM methodology combined with GIAO-DFT calculations. Our findings indicate a strong solvent effect on the dipole moment, exhibiting increases of up to 61% in the values of μ in the liquid phase when compared with the respective results in the gas phase. The spatial correlation between ANR polypeptides and water was also analyzed, as well as the solvent shells that are directly involved with solute–solvent interactions, like hydrogen bonds. In addition, we have reported the solvent influence on the magnetic shielding.

We have investigated the solvent effects on the nonlinear and spectroscopic optical properties of some azo-enaminone molecules in the gas phase and in methanol and water solutions. Using the sequential Monte Carlo/Quantum Mechanics (S-MC/QM) approach, we have included the polarization of the solute due to the solvent medium. We have carried out TD-CAM-B3LYP/6-311++G(2d,2p) theoretical calculations for the electronic transitions. Solvatochromic deviations up to 25 nm in solution were observed for azo-enaminones in enol forms. Our CAM-B3LYP/6-311+G(d) calculations have indicated that the βHRS values may increase up to 100% when compared with the respective gas phase results. The magnetic signature of oxygen atoms was significantly affected by the inclusion of solvation effects.

We present calculations of nuclear magnetic shieldings of the nucleic acids adenine, cytosine, guanine e thymine in liquid water environment in normal thermodynamic condition. The study is based on a sequential approach, where a classical Monte Carlo simulation of the solvated system is performed to generate the different solute–solvent configurations to be used in the following quantum mechanics calculations of magnetic properties. We find that the environment polarization effect shields the unprotonated nitrogens, with solvent shifts for the magnetic shieldings between +10.52 and +48.95 ppm. Protonated and amino nitrogens are less shielded by amounts of −17.77 and +0.22 ppm. The results obtained from supermolecule calculations show that protonated and amino nitrogen magnetic shieldings are particularly sensitive to the hydrogen bond interactions, with solvent shifts between −5.48 and −33.42 ppm, when the first microsolvation shell is explicitly considered. In addition, the supermolecular calculations also show a marked deshielding effect for the hydrogens of the protonated nitrogens, with solvent shifts between −2.43 and −5.12 ppm. There is an overall agreement between the theoretical predictions for the 1H and 15N chemical shifts and the available experimental results.

We investigate the nuclear isotropic shielding constants and spin-spin coupling for oxygen and carbons atoms of isomers of tartaric acid in gas phase and water solutions by Monte Carlo simulation and quantum mechanics calculations using the GIAO-B3LYP approach. Solute polarization effects are included iteratively and play an important role in the quantitative determination of shielding constants. Our MP2/aug-cc-pVTZ results show substantial increases of the dipole moment in solution as compared with the gas phase results (61-221%). The solvent effects on the {\sigma}(13C) [J(C-C)] values are in general small. More appreciable solvent effects can be seen on the {\sigma}(17O) and J(C-O).

Here we present calculations of electrical, energetic and magnetic properties of the amino acids arginine, aspartic acid, glutamic acid, histidine and lysine in water solution. The molecules have charged NH31+ and COO1− terminations. The objective is to verify if the atomic charges of the CHARMM36 force field accurately describe the interactions between these amino acids and water, using Molecular Dynamics simulations. For this, the molecules were polarized in solvent medium and we have obtained new atomic charges after the simulations. A comparison of the properties of interest was made using the two charge models and the results show that, in some situations, the updated charge model can better describe the interactions between the analyzed amino acids and the water molecules.

Theoretical results for the electronic properties of eumelanin building blocks in the gas phase and water are presented. The building blocks presently investigated include the monomeric species DHI (5,6-dihydroxyindole) or hydroquinone (HQ), DHICA (5,6-dihydroxyindole-2-carboxylic acid), indolequinone (IQ), quinone methide (MQ), two covalently bonded dimers [HM ≡ HQ + MQ and IM ≡ IQ + MQ], and two tetramers [HMIM ≡ HQ + IM, IMIM ≡ IM + IM]. The electronic properties in water were determined by carrying out sequential Monte Carlo/time dependent density functional theory calculations. The results illustrate the role played by hydrogen bonding and electrostatic interactions in the electronic properties of eumelanin building blocks in a polar environment. In water, the dipole moments of monomeric species are significantly increased ([54-79]%) relative to their gas phase values. Recently, it has been proposed that the observed enhancement of the higher-energy absorption intensity in eumelanin can be explained by excitonic coupling among eumelanin protomolecules [C.-T. Chen et al., Nat. Commun. 5, 3859 (2014)]. Here, we are providing evidence that for DHICA, IQ, and HMIM, the electronic absorption toward the higher-energy end of the spectrum ([180-220] nm) is enhanced by long-range Coulombic interactions with the water environment. It was verified that by superposing the absorption spectra of different eumelanin building blocks corresponding to the monomers, dimers, and tetramers in liquid water, the behaviour of the experimental spectrum, which is characterised by a nearly monotonic decay from the ultraviolet to the infrared, is qualitatively reproduced. This result is in keeping with a "chemical disorder model," where the broadband absorption of eumelanin pigments is determined by the superposition of the spectra associated with the monomeric and oligomeric building blocks.