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.

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 SN2 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.

Applicability of DFT functionals for evaluating the first hyperpolarizability of phenol blue in solution.

The first electronic hyperpolarizability (ß) of phenol blue (PB) in several solvents in a wide range of dielectric constants is investigated using the density functional theory (DFT). The reliability of various exchange-correlation functionals is assessed by a comparison to reference Møller-Plesset second-order perturbation theory (MP2) calculations. The equilibrium geometry of PB in each solvent is obtained by using the average solvent electrostatic configuration/free energy gradient method, which performs optimizations on the free energy hyper-surface by employing iteratively the sequential quantum mechanics/molecular mechanics methodology. The dependence of ß on the bond length alternation (BLA) coordinate is rationalized by means of the two-level model. Within the employed exchange-correlation functionals, the LC-BLYP functional shows the best performance for describing the static and dynamic MP2 results of ß, which increases as the BLA diminishes, reaching a maximum in an intermediate value of BLA. The results also illustrate the role played by the difference between the ground- and excited-state dipole moments (Δµ) in determining the hyperpolarizability behavior in solution. Particularly, in the aqueous solution case, Δµ goes to around zero when BLA is near zero, leading to an abrupt decline in the ß value. The DFT results of this study, therefore, indicate a clear relationship between the first hyperpolarizability and the BLA coordinate for the PB in solution, in agreement with experiment.

Assessing the structure and first hyperpolarizability of Li@B10H14 in solution: a sequential QM/MM study using the ASEC-FEG method.

The structure and electronic properties of the lithium decahydroborate (Li@B10H14) complex in chloroform and water in normal thermodynamic conditions have been investigated using sequential QM/MM calculations by means of the average solvent electrostatic configuration (ASEC) and the Free Energy Gradient (FEG) methods. To obtain the structure of the Li@B10H14 complex in each of the solvents considered, we have performed geometry optimizations in solution using the ASEC-FEG method. The results show, for the first time with a realistic model of the molecular environment, that this alkali-metal-borane cluster is stable in chloroform but unstable in water. We have also explored the role of the electronic polarization of the solute due to solvent in the static first hyperpolarizability. The results show that, despite the reduction due to the effect of electrostatic polarization in chloroform, the Li@B10H14 complex still exhibits a large electronic first hyperpolarizability, with potential for application as a second-order nonlinear optical (NLO) material. In water, in contrast, the contribution of the excess electron for NLO responses is significantly affected by the electrostatic polarization effects. Therefore our results reveal that the influence of the environment must be considered in the design of new stable NLO materials.

Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures.

At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach. A series of Monte Carlo Metropolis simulations of the glycine molecule embedded in liquid water, followed by only a quantum mechanical calculation in each of them were carried out. Both the local and global liquid environments were emphasized to obtain nuclear magnetic resonance (NMR) parameters for the glycine molecule in liquid water. The results of the equilibrium structure in solution and the systematic study of the hydrogen bonds were used to discard the direct proton transfer from the carboxyl group to the ammonium group of the glycine molecule in water solution. The calculations of the Density Functional Theory (DFT) were performed to study the polarization of the solvent in the parameters of nuclear magnetic resonance of the glycine molecule in liquid water. DFT calculations predicted isotropic chemical changes on the H, C, N, and O atoms of glycine in liquid water solution which agree with the available experimental data.

Confirming the relationship between first hyperpolarizability and the bond length alternation coordinate for merocyanine dyes.

We investigated the first electronic hyperpolarizability of a typical merocyanine dye in several solvents in a wide range of dielectric constants. The equilibrium geometry of the molecule was obtained in each solvent by employing an optimization technique allied to atomistic simulations. The results confirm, for the first time with a realistic model of the molecular environment, the relationship between the first electronic hyperpolarizability (ß) and the bond length alternation (BLA) coordinate, with a maximum value of ß for intermediate positive BLA and a vanishing ß when the BLA goes to zero.

Elucidating the structure of merocyanine dyes with the ASEC-FEG method. Phenol blue in solution.

The electronic structure of phenol blue (PB) was investigated in several protic and aprotic solvents, in a wide range of dielectric constants, using atomistic simulations. We employed the sequential QM/MM and the free energy gradient methods to optimize the geometry of PB in each solvent at the MP2/aug-cc-pVTZ level. The ASEC mean field is used to include the ensemble average of the solute-solvent interaction into the molecular hamiltonian, both for the geometry optimization and for the calculations of the electronic properties. We found that the geometry of PB changes considerably, from a polyene-like structure in nonpolar solvents to a cyanine-like in water. Moreover, and quite interestingly, in protic solvents with higher dielectric constant than water, the structure of the molecule is less affected and lies in an intermediate state. The results illustrate the important role played by hydrogen bonds in the conformation of merocyanine dyes.

Monte Carlo-quantum mechanics study of magnetic properties of hydrogen peroxide in liquid water.

A theoretical study of magnetic properties of hydrogen peroxide in water has been carried out by means of Monte Carlo simulation and quantum mechanics calculations. The solvent effects were evaluated in supermolecular structures generated by simulations in the NPT ensemble. The solute-solvent structure was analyzed in terms of radial distribution functions, and the solute-solvent hydrogen bonds were identified with geometric and energetic criteria. Approximately three water molecules are hydrogen bonded to H2O2 (0.6 and 0.8 in each hydrogen and oxygen atom, respectively, of the H2O2). Although, on average, both hydroxyls of the peroxide are equivalent, the distribution of hydrogen-bonded water molecules is highly asymmetric. Analyzing the statistics of the hydrogen bonds, we identify that only 34% of the configurations give symmetric distributions around the two hydroxyls of the H2O2 simultaneously. The magnetic shieldings and the indirect spin-spin coupling constants were calculated at the B3LYP/aug-cc-pVTZ and aug-cc-pVTZ-J computational level. We find that the solvent shields the oxygen and unshields the hydrogen atoms of the peroxide (+5.5 and -2.9 ppm, respectively), with large fluctuation from configuration to configuration in the oxygen case, an effect largely accounted for in terms of a single hydrogen bond with H2O2 as the proton donor. The most sensitive coupling in the presence of the solvent is observed to be the one-bond J(O,H).

Ab initio study of weakly bound halogen complexes: RX⋯PH3.

Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

Electronic properties of water in liquid environment. A sequential QM/MM study using the free energy gradient method.

There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

Thermodynamic stability of hydrogen-bonded systems in polar and nonpolar environments.

The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effects were investigated using both explicit and implicit solvation models. For the explicit description of the solvent, molecular dynamics and Monte Carlo simulations in the isothermal-isobaric (NpT) ensemble combined with the free energy perturbation technique were performed to determine solvation free energies. Within the implicit solvation approach, the polarizable continuum model and the conductor-like screening model were applied. Combination of gas phase results with the results obtained from the different solvation models through an appropriate thermodynamic cycle allows estimation of complexation free energies, enthalpies, and the respective entropic contributions in solution. Owing to the strong solvation effects of water the cyclic acetic acid dimer is not stable in aqueous solution. In less polar solvents the double hydrogen bond structure of the acetic acid dimer remains stable. This finding is in agreement with previous theoretical and experimental results. A similar trend as for the acetic acid dimer is also observed for the acetamide complex. The methanol complex was found to be thermodynamically unstable in gas phase as well as in any of the three solvents.

NMR chemical shielding and spin-spin coupling constants of liquid NH3: a systematic investigation using the sequential QM/MM method.

The NMR spin coupling parameters, (1)J(N,H) and (2)J(H,H), and the chemical shielding, sigma((15)N), of liquid ammonia are studied from a combined and sequential QM/MM methodology. Monte Carlo simulations are performed to generate statistically uncorrelated configurations that are submitted to density functional theory calculations. Two different Lennard-Jones potentials are used in the liquid simulations. Electronic polarization is included in these two potentials via an iterative procedure with and without geometry relaxation, and the influence on the calculated properties are analyzed. B3LYP/aug-cc-pVTZ-J calculations were used to compute the (1)J(N,H) constants in the interval of -67.8 to -63.9 Hz, depending on the theoretical model used. These can be compared with the experimental results of -61.6 Hz. For the (2)J(H,H) coupling the theoretical results vary between -10.6 to -13.01 Hz. The indirect experimental result derived from partially deuterated liquid is -11.1 Hz. Inclusion of explicit hydrogen bonded molecules gives a small but important contribution. The vapor-to-liquid shifts are also considered. This shift is calculated to be negligible for (1)J(N,H) in agreement with experiment. This is rationalized as a cancellation of the geometry relaxation and pure solvent effects. For the chemical shielding, sigma((15)N) calculations at the B3LYP/aug-pcS-3 show that the vapor-to-liquid chemical shift requires the explicit use of solvent molecules. Considering only one ammonia molecule in an electrostatic embedding gives a wrong sign for the chemical shift that is corrected only with the use of explicit additional molecules. The best result calculated for the vapor to liquid chemical shift Delta sigma((15)N) is -25.2 ppm, in good agreement with the experimental value of -22.6 ppm.

Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition.

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation, first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

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.

Asequential Monte Carlo quantum mechanics study of the hydrogen-bond interaction and the solvatochromic shift of the n-pi* transition of acrolein in water.

The sequential Monte Carlo (MC) quantum mechanics (QM) methodology, using time-dependent density-functional theory (TD-DFT), is used to study the solvatochromic shift of the n-pi* transition of trans-acrolein in water. Using structures obtained from the isothermal-isobaric Metropolis MC simulation TD-DFT calculations, within the B3LYP functional, are performed for the absorption spectrum of acrolein in water. In the average acrolein makes one hydrogen bond with water and the hydrogen-bond shell is responsible for 30% of the total solvatochromic shift, considerably less than the shift obtained for the minimum-energy configurations. MC configurations are sampled after analysis of the statistical correlation and 100 configurations are extracted for subsequent QM calculations. All-electron TD-DFT B3LYP calculations of the absorption transition including acrolein and all explicit solvent molecules within the first hydration shell, 26 water molecules, give a solvatochromic shift of 0.18 +/- 0.11 eV. Using simple point charges to represent the solvent the shifts are calculated for the first, second, and third solvation shells. The results converge for the calculated shift of 0.20 +/- 0.10 eV in very good agreement with the experimentally inferred result of 0.20 +/- 0.05 eV. All average results presented are statistically converged.