A Monte Carlo-Quantum Mechanics Study of the Solvent-Induced Spectral Shift and the Specific Role of Hydrogen Bonds in the Conformational Equilibrium of Furfural in Water

Simulating adsorptive expansion of zeolites: application to biomass-derived solutions in contact with silicalite

We have constructed and applied an algorithm to simulate the behavior of zeolite frameworks during liquid adsorption. We applied this approach to compute the adsorption isotherms of furfural-water and hydroxymethyl furfural (HMF)-water mixtures adsorbing in silicalite zeolite at 300 K for comparison with experimental data. We modeled these adsorption processes under two different statistical mechanical ensembles: the grand canonical (V-Nz-μg-T or GC) ensemble keeping volume fixed, and the P-Nz-μg-T (osmotic) ensemble allowing volume to fluctuate. To optimize accuracy and efficiency, we compared pure Monte Carlo (MC) sampling to hybrid MC-molecular dynamics (MD) simulations. For the external furfural-water and HMF-water phases, we assumed the ideal solution approximation and employed a combination of tabulated data and extended ensemble simulations for computing solvation free energies. We found that MC sampling in the V-Nz-μg-T ensemble (i.e., standard GCMC) does a poor job of reproducing both the Henry's law regime and the saturation loadings of these systems. Hybrid MC-MD sampling of the V-Nz-μg-T ensemble, which includes framework vibrations at fixed total volume, provides better results in the Henry's law region, but this approach still does not reproduce experimental saturation loadings. Pure MC sampling of the osmotic ensemble was found to approach experimental saturation loadings more closely, whereas hybrid MC-MD sampling of the osmotic ensemble quantitatively reproduces such loadings because the MC-MD approach naturally allows for locally anisotropic volume changes wherein some pores expand whereas others contract.

Solvent dependence of structure, charge distribution, and absorption spectrum in the photochromic merocyanine-spiropyran pair

We have studied the structures and absorption spectra of merocyanine, the photoresponsive isomer of the spiropyran (SP)-merocyanine (MC) pair, in chloroform and in water solvents using a combined hybrid QM/MM Car-Parrinello molecular dynamics (CP-QM/MM) and ZINDO approach. We report remarkable differences in the molecular structure and charge distribution of MC between the two solvents; the molecular structure of MC remains in neutral form in chloroform while it becomes charge-separated, zwitterionic, in water. The dipole moment of MC in water is about 50% larger than in chloroform, while the value for SP in water is in between, suggesting that the solvent is more influential than the conformation itself in deciding the dipole moment for the merocyanine-spiropyran pair. The calculations could reproduce the experimentally reported blue shift in the absorption spectra of MC when going from the nonpolar to the polar solvent, though the actual value of the absorption maximum is overestimated in chloroform solvent. We find that the CP-QM/MM approach is appropriate for structure modeling of solvatochromic and thermochromic molecules as this approach is able to capture the solvent and thermal-induced structural changes within the solute important for an accurate assessment of the properties.

Quantum mechanical study of the syn-anti isomerisation of 2-tellurophenecarboaldehyde: vive la différence

The syn- and anti-conformers of 2-tellurophenecarboaldehyde are studied in the gas phase. A transition state is also modelled for the syn-anti isomerisation. Computations are done using different methods namely HF, DFT/B3LYP, MP2 and CCSD(T). The basis set used for all atoms is 6-311++G(d,p) except that LanL2DZ ECP is used for tellurium atom only. The optimised molecular structures and related structural parameters of these conformers are reported. The energy differences between the syn- and anti-conformers, associated rotational barriers and thermodynamic parameters are derived from the computations. The infrared frequencies of these conformers are also reported with appropriate assignments. This study is extended to include solvent effect and the conformers are fully optimised (DFT/B3LYP) using the integral equation formalism in the Polarisable Continuum model. In the gas phase, the theoretical rate constant for the unimolecular conversion, anti conformer to transition state, is reported for the first time; DFT/B3LYP (4.82×10(30) s(-1)) and MP2 (7.81×10(30) s(-1)). It is found that the structures are not much affected by the solvents but energy difference increases and rotational barrier decreases. The results indicate that there is a close agreement with the predictions from the different theoretical methods. The results obtained are critically analysed and compared with the furan, thiophene and selenophene analogues. A major factor affecting conformational preference and the mole fraction is the charge on the chalcogen heteroatom in the ring. An interesting outcome of this work is that in both the gas phase and solutions, the syn conformer is more stable and exists almost exclusively.

Structure and UV−Vis Spectrum of C60 Fullerene in Ethanol: A Sequential Molecular Dynamics/Quantum Mechanics Study

A molecular dynamics simulation combined with semiempirical quantum mechanics calculations has been performed to investigate the structure, dynamical, and electronic properties of pure C60 in liquid ethanol. The behavior of the fullerene alcoholic solution was obtained by using the NPT ensemble under ambient conditions, including one C60 fullerene immersed in 1000 ethanol molecules. Our analyzed center-of-mass pairwise radial distribution function indicated that, on average, there are 32, 72, 132, and 187 ethanol molecules around, respectively, the first, second, third, and fourth solvation shells of the C60 molecule. To investigate the UV-vis transition energies of C60 in the presence of ethanol, we have considered constituents of the time uncorrelated supramolecular structures of the first solvation shell, i.e., clusters of C60@{EtOH}32 types. The semiempirical calculations were performed at the intermediate neglect of differential overlap level with configuration interaction singles (INDO/CIS). Our results have pointed out that the characteristic C60 UV-vis absorbance peaks are slightly shifted to longer wavelengths, as compared to the isolated molecule. These findings are in connection with the weak donor-acceptor character of the interactions involving electron lone pairs of oxygen atoms on the solvent and the fullerene surface.

Band gap and density of states of the hydrated C60 fullerene system at finite temperature

We examine the electronic properties of the hydrated C60 fullerene under ambient conditions using a sequential Monte Carlo/density functional theory scheme. In this procedure, the average electronic properties of the first hydration shell of C60 equilibrate for ca. 40 uncorrelated configurations of the fullerene aqueous solution. We obtain a systematic red-shift of 0.8 eV in the band gap of the hydrated system, which is mainly attributed to the thermal fluctuations of the aqueous environment.

Solvent effects on the UV-visible absorption spectrum of benzophenone in water: a combined Monte Carlo quantum mechanics study including solute polarization

The entire ultraviolet-visible absorption spectrum of benzophenone in water is studied and compared with the same spectrum in gas phase. Five transitions are considered, and the corresponding solvatochromic shifts are obtained and compared to experiment. Using a sequential procedure of Monte Carlo simulations and quantum mechanical calculations, liquid configurations were generated and an averaged spectrum of the solution was calculated. The solute polarization was included by an iterative procedure where the atomic charges of the solute were obtained as an average with the solvent distribution. The calculated average dipole moment of benzophenone in water, with MP26-31++G(d,p), converges to the value of 5.84+/-0.05 D, 88% larger than the gas-phase value of 3.11 D. Using 100 statistically uncorrelated configurations and solvation shells with 235 explicit water molecules selected by a minimum-distance distribution of solvent shells, instead of the usual radial distribution, the excitation energies were obtained from solute-solvent all-valence-electron INDO/CIS calculations. The shift of the weak n-pi(*) transition is obtained as 2045+/-40 cm(-1) and the strong and broad pi-pi(*) shift as -1790+/-30 cm(-1). These results are in good agreement with the experimental values of 2200 and -1600 cm(-1), respectively. Standard procedure used by common force fields to generate atomic charges to describe the electrostatic moments of the solute, with HF6-31G(d), gives a dipole moment of 3.64 D. Using these standard charges in the simulation, the average shifts are calculated as 1395+/-35 and -1220+/-25 cm(-1), both about 600 cm(-1) smaller in magnitude than those obtained with the average converged fully polarized solute. The influence of the solute polarization in the solute-solvent interaction and, in particular, in solute-solvent hydrogen bonds is analyzed.

Monte Carlo Simulation of Cisplatin Molecule in Aqueous Solution

The Lennard-Jones (12-6) parameters were obtained for all atoms of cisplatin molecule using the ab initio quantum mechanical potential energy surface for the water-cisplatin interaction as reference data. The parameters found were (epsilon/kcal.mol(-1) and sigma/angstroms) 1.0550, 3.6590 (Pt); 0.0381, 4.6272 (Cl); 0.0455, 3.3783 (N); and 0.0185, 0.0936 (H) and provided very good results for the description of the aqueous solution of cisplatin through Monte Carlo simulation. From statistical analysis of solute-solvent interactions, we observed that the NH3 groups are involved in 53% of the calculated hydrogen bonds with a significant contribution from chlorides (41%) and only 6% involving the Pt center. This is in agreement with the expected behavior for such molecules. Two hydration shells with 22 and 81 water molecules, respectively, centered around 4.6 and 7.3 angstroms were found from the center of mass pair correlation function analysis. The cisplatin atomic Lennard-Jones parameters are reported for the first time, and they might be useful for studying the structure, properties, and processes of cisplatin-like molecules in aqueous solution, including explicitly the solvent effect.

SCSA Code: Applications on the Cyclopeptide Renieramide

SCSA is an algorithm designed to get information on molecular conformational properties. The most stable conformers are determined by the homemade SCSA code, performing a multistep systematic conformational search, which involves energy and structure quantum chemical optimizations at low-level and high-level. The SCSA method was employed to analyze the conformational space of the in vacuo cyclopeptide renieramide at AM1 and B3LYP/6-31G(d) levels. Calculations at B3LYP level of the GIAO (13)C NMR chemical shifts were also performed on the final conformers. In fact, to validate the conformational search results experimental and calculated (13)C NMR spectra of renieramide were compared. Slight disagreements observed between experimental and calculated spectra could be attributed to solute-solvent interactions, which were not taken into account in the algorithm proposed here.