Papers by Herbert C Georg
The Journal of chemical physics, Jan 21, 2016
The electronic structure of phenol blue (PB) was investigated in several protic and aprotic solve... more 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.
The Journal of Chemical Physics
J Phys Chem a, 2009
The NMR spin coupling parameters, 1 J(N,H) and 2 J (H,H), and the chemical shielding, σ( 15 N), o... more The NMR spin coupling parameters, 1 J(N,H) and 2 J (H,H), and the chemical shielding, σ( 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, σ( 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 ∆σ( 15 N) is -25.2 ppm, in good agreement with the experimental value of -22.6 ppm. † Part of the "Vincenzo Aquilanti Festschrift".
Pccp Physical Chemistry Chemical Physics, Feb 17, 2009
A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is m... more 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.
The Journal of Chemical Physics, Oct 1, 2010
The dipole moment (μ), linear polarizability (α), and first hyperpolarizability (β(tot)) of the a... more The dipole moment (μ), linear polarizability (α), and first hyperpolarizability (β(tot)) of the asymmetric unit of L-arginine phosphate (LAP) monohydrate crystal are investigated using the supermolecule approach in combination with an iterative electrostatic polarization scheme. Environment polarization effects are attained by assuring the convergence of the dipole moment of LAP embedded in the polarization field of the surrounding molecules whose atomic sites are treated as point charges. The results obtained show that in the presence of the embedding charges, the value of μ is increased by 9% but the static values of α and β(tot) are decreased, respectively, by 3% and 13%, as compared with the isolated situation. The MP2/6-311+G(d) model predicts for the in-crystal dipole moment the converged value of 33 D, in good concordance with the available experimental result of 32 D. Our estimates for the converged results of α and β(tot) are, respectively, 22.51×10(-24) and 5.01×10(-30) esu. Dispersion effects are found to have a small impact on the nonlinear optical responses of LAP in the visible region. In addition, MP2/6-311G results obtained for β(tot) by using isolated and embedded LAP dimers show that crystal packing effects have a significant contribution of the electrostatic interactions. Our results suggest that the role of the crystal environment is to minimize the effects of the intermolecular interactions in the electric properties. That is, μ and β(tot) gain a more additive character in the presence of the field of the embedding charges. This is specially marked for β(tot).
Chemical Physics Letters, Mar 9, 2007
Using statistically uncorrelated solute-solvent configurations generated by Monte Carlo simulatio... more Using statistically uncorrelated solute-solvent configurations generated by Monte Carlo simulation a simpler and efficient implementation of the averaged solvent electrostatic potential is made. An average configuration alone is used such that one single quantum mechanical calculation reproduces the converged statistical average obtained from the entire simulation. Applications are presented for solvent effects in a variety of properties of acetone and aminopurine in water. In all cases, excellent agreement is obtained using the average configuration and the average from the full statistical distribution.
Chemical Physics Letters, Sep 29, 2006
The electronic polarization of acetone in liquid water is obtained using an iterative procedure i... more The electronic polarization of acetone in liquid water is obtained using an iterative procedure in the sequential Monte Carlo/quantum mechanics methodology. MP2/aug-cc-pVDZ calculations of the dipole moment of acetone in water are performed on statistically uncorrelated structures extracted from isothermic-isobaric MC simulations. After electrostatic equilibrium the calculated dipole moment of acetone is obtained as 4.80 ± 0.03 D, with an increase of 60% compared to the gas phase value. This solute polarization is used to obtain the shift of 1650 ± 42 cm -1 for the n-π ∗ transition of acetone in water, in agreement with the experimental result of 1500-1700 cm -1.
Computational and Theoretical Chemistry, 2014
The Free Energy Gradient method is used to obtain the p-p * excited state structure of uracil in ... more The Free Energy Gradient method is used to obtain the p-p * excited state structure of uracil in aqueous environment. The geometry calculations are made at the CASSCF level. The CASPT2 method is employed to calculate absorption and emission energies of uracil in gas and in aqueous solution. An average discrete electrostatic model is used to include the solvent effect. The results for the calculated absorption and emission transitions are found in good agreement with experiment both in gas phase and in water. The solvent effect on the Stokes shift is also calculated in good agreement with experiment. These agreements lend additional credence to the structures obtained for the lowest p-p * excited state.
The polarization of organic molecules in different liquid environments is considered. Two importa... more The polarization of organic molecules in different liquid environments is considered. Two important aspects are discussed. First, the electronic polarization of the solute by the solvent and the corresponding changes in spectroscopic properties. Second, the structural changes induced by the solvent into the solute. This includes both geometrical aspects as well as more subtle chemical changes. For the electronic polarization we use the sequential Monte Carlo/quantum mechanics methodology. The specific case of acetone in water and homogeneous liquid acetone at normal conditions are considered. MP2/augcc-pVDZ calculations of the dipole moment of the reference solute molecule in the solvent environment are performed on statistically uncorrelated structures extracted from isothermic-isobaric MC simulations. To probe the reliability of the results this solute polarization is used to obtain the solvatochromic shift in UV-Vis absorption spectra. For the structural changes, two interesting cases are presented. First we show that geometry changes of ortho-betaine in water, is responsible for the major part of the very large solvatochromic shift. Second we show that the phenol blue possibly changes the chemical structure from a normal to a zwitterion state and this change could explain the solvent dependence of the hyperpolarizability observed experimentally.
The Journal of chemical physics, Jan 22, 2005
The sequential Monte Carlo (MC) quantum mechanics (QM) methodology, using time-dependent density-... more 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 +...
Solvation Effects on Molecules and Biomolecules, 2008
... AND SYLVIO CANUTO1 1Instituto de Fısica, Universidade de Sao Paulo, CP 66318, 05315-970 Sao... more ... AND SYLVIO CANUTO1 1Instituto de Fısica, Universidade de Sao Paulo, CP 66318, 05315-970 Sao Paulo, SP, Brazil, e-mail: [email protected] ... The calculated auto-correlation function (circles) is fitted to the exponential decay (line) and the correlation time τ is obtained using Eq. ...
The journal of physical chemistry. A, Jan 14, 2014
A theoretical study of magnetic properties of hydrogen peroxide in water has been carried out by ... more 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 calculate...
Theoretical Chemistry Accounts, 2014
ABSTRACT The nuclear magnetic resonance chemical shielding of 17O is of great importance for biom... more ABSTRACT The nuclear magnetic resonance chemical shielding of 17O is of great importance for biomolecular characterization in water environment. In these systems, oxygen atoms occupy important positions and are involved in hydrogen bonds with the water environment. In this work, different solvation models are used for the theoretical determination of the 17O chemical shielding of the nucleobase uracil and the substituted 5-fluorouracil in aqueous environment. Continuum, discrete and explicit solvent models are used, and an analysis is made of the role played by the solute polarization due the solvent. The best results are obtained using the sequential quantum mechanics/molecular mechanics methodology using an iterative procedure for the solute polarization, but a good compromise is obtained by using the electronic polarization provided by the polarizable continuum model. Quantum mechanical calculations of the chemical shieldings are made using density-functional theory in two different exchange–correlation approximations. Using an iterative procedure for the solute polarization and the mPW1PW91/aug-pcS-2 model in the electrostatic approximation, we obtained magnetic shielding constants for the two O atoms of uracil within 2 ppm of the experimental results. For 5-fluorouracil, the theoretical results, with the same model, are again in good agreement with the experimental values. An analysis of the influence of the solute–solvent hydrogen bonds in the chemical shielding of uracil case is also made, and it is concluded that the most important contribution to the calculated shielding derives from the electrostatic contribution to the solute–solvent interaction.
Theoretical Chemistry Accounts, 2012
ABSTRACT Electronic polarization induced by the interaction of a reference molecule with a liquid... more ABSTRACT Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/6-311++G (d,p) are used to analyze different aspects of the solvent effects on the 15N magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as −58.7 ppm, in good agreement with the experimental value of −56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of −61.8 ppm.
The Journal of Physical Chemistry B, 2012
There is a continuous search for theoretical methods that are able to describe the effects of the... more 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.
The Journal of Physical Chemistry A, 2009
Monte Carlo simulation and quantum mechanics calculations based on the INDO/CIS and TD-DFT method... more Monte Carlo simulation and quantum mechanics calculations based on the INDO/CIS and TD-DFT methods were utilized to study the solvatochromic shift of benzophenone when changing the environment from normal water to supercritical (P = 340.2 atm and T = 673 K) condition. Solute polarization increases the dipole moment of benzophenone, compared to gas phase, by 88 and 35% in normal and supercritical conditions, giving the in-solvent dipole value of 5.8 and 4.2 D, respectively. The average number of solute-solvent hydrogen bonds was analyzed, and a large decrease of 2.3 in normal water to only 0.8 in the supercritical environment was found. By using these polarized models of benzophenone in the two different conditions of water, we performed MC simulations to generate statistically uncorrelated configurations of the solute surrounded by the solvent molecules and subsequent quantum mechanics calculations on these configurations. When changing from normal to supercritical water environment, INDO/CIS calculations explicitly considering all valence electrons of the 235 solvent water molecules resulted in a solvatochromic shift of 1425 cm(-1) for the most intense pi-pi* transition of benzophenone, that is, slightly underestimated in comparison with the experimentally inferred result of 1700 cm(-1). TD-B3LYP/6-311+G(2d,p) calculations on the same configurations but with benzophenone electrostatically embedded in the 320 water molecules resulted in a solvatochromic shift of 1715 cm(-1) for this transition, in very good agreement with the experimental result. When using the unpolarized model of the benzophenone, this calculated solvatochromic shift was only 640 cm(-1). Additional calculations were also made by using BHandHLYP/6-311+G(2d,p) to analyze the effect of the asymptotic decay of the exchange functional. This study indicates that, contrary to the general expectation, there is a sizable solute polarization even in the low-density regime of supercritical condition and that the inclusion of this polarization is important for a reliable description of the spectral shifts considered here.
Journal of the Brazilian Chemical Society, 2007
Apresentamos um estudo QM/MM seqüencial dos deslocamentos químicos gás-líquido da água. Cálculos ... more Apresentamos um estudo QM/MM seqüencial dos deslocamentos químicos gás-líquido da água. Cálculos de química quântica extensivos, usando a teoria do funcional da densidade foram realizados para estruturas do líquido de água, geradas através de simulações de Monte Carlo e Dinâmica Molecular. A dependência do deslocamento químico com os potenciais empíricos utilizados nas simulações, com o tamanho do aglomerado e com o funcional escolhido para os cálculos quânticos foi analisada. Os resultados corrigidos devido ao erro de superposição de base estão em boa concordância com os resultados experimentais, mostrando que um potencial empírico simples associado a um funcional apropriado é capaz de descrever os deslocamentos químicos. Todos os resultados apresentados são estatisticamente convergidos.
Journal of Molecular Modeling, 2013
Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenate... more 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%).
Journal of Computational Chemistry, 2010
The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid ... more 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.
The Journal of Chemical Physics, 2007
The entire ultraviolet-visible absorption spectrum of benzophenone in water is studied and compar... more 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 MP2 / 6-31+ + G͑d , p͒, 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-* transition is obtained as 2045± 40 cm −1 and the strong and broad -* 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 HF/ 6-31G͑d͒, 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.
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Papers by Herbert C Georg