Molecular dynamics study of the tautomeric equilibrium in the 4-nitro- and 2,4,6-trichloro derivatives of 2-(N,N-dialkyloaminomethyl)phenol

 Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric equilibrium of Mannich base in methanol solution. The values obtained for the free-energy difference are in good agreement with experimental data. However, the results from quantum mechanical calculations were not as good as the results of MDTI simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell of solvent molecules in the Tomasi model of the solvent reaction field. The radial distribution functions between solute atoms and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first solvation shell than is the molecular form. Received: 26 April 2002 / Accepted: 9 September 2002 / Published online: 31 March 2003     

Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.     

Exploring the molecular mechanism for color distinction in humans

We examine here the role of the red, green, and blue human opsin structures in modulating the absorption properties of 11-cis-retinal bonded to the protein via a protonated Schiff base (PSB). We built the three-dimensional structures of the human red, green, and blue opsins using homology modeling techniques with the crystal structure of bovine rhodopsin as the template. We then used quantum mechanics (QM) combined with molecular mechanics (MM) (denoted as QM/MM) techniques in conjunction with molecular dynamics to determine how the room temperature molecular structures of the three human color opsin proteins modulate the absorption frequency of the same bound 11-cis-retinal chromophore to account for the differences in the observed absorption spectra. We find that the conformational twisting of the 11-cis-retinal PSB plays an important role in the green to blue opsin shift, whereas the dipolar side chains in the binding pocket play a surprising role of red-shifting the blue opsin with respect to the green opsin, as a fine adjustment to the opsin shift. The dipolar side chains play a large role in the opsin shift from red to green.     

Theoretical study of the role of solvent Stark effect in electron transitions

The possible influence of the solvent Stark effect (SSE) on the solvatochromic shift in electron transitions has been analyzed by using the ASEP/MD (averaged solvent electrostatic potential from molecular dynamics) method. With this purpose, four molecules, two polar (acrolein and formaldehyde) and two non-polar (p-difluorobenzene and trans-difluoroethene) have been studied in solvents of diverse polarity. Independently of the nature of the system we found that the contribution of SSE on the average value of the solvent shift or on the multipole moment values is negligible. In the case of centro-symmetric molecules, our results permit to discard the SSE as cause of the solvent shift found, which must be assigned to the electrostatic interaction of the solute quadrupole and higher multipoles with the solvent. As the SSE values provide also a measure of the errors introduced by the mean field approximation (MFA), these results indicate that MFA permits a very accurate determination of the solvent shift at the same time that it reduces drastically the computational cost. Finally, a new procedure suited to the ASEP/MD method has been presented that permits to estimate the inhomogeneous broadening of spectral bands, complementing the information provided by mean field theories. This procedure does not need additional quantum calculations and its computational cost is minimal.     

The opsin shift and mechanism of spectral tuning in rhodopsin

Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.     

Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study

The solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical∕molecular mechanical (QM∕MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM∕MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorption spectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorption spectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorption spectrum. In the solvent effect, the variation in C-C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.     

Analyzing solution-phase time-resolved x-ray diffraction data by isolated-solute models

Extracting transient structural information of a solute from time-resolved x-ray diffraction (TRXD) data is not trivial because the signal from a solution contains not only the solute-only term as in the gas phase, but also solvent-related terms. To obtain structural insights, the diffraction signal in q space is often Fourier sine transformed (FT) into r space, and molecular dynamics (MD) simulation-aided signal decomposition into the solute, cage, and solvent terms has so far been indispensable for a clear-cut assignment of structural features. Here we present a convenient method of comparative structural analysis without involving MD simulations by incorporating only isolated-species models for the solute. FT is applied to both the experimental data and candidate isolated-solute models, and comparison of the correlation factors between the experimental FT and the model FTs can distinguish the best candidate among isolated-solute models for the reaction intermediates. The low q region whose influence by solvent-related terms is relatively high can be further excluded, and this mode of truncated Fourier transform (TFT) improves the correlation factors and facilitates the comparison. TFT analysis has been applied to TRXD data on the photodissociation of C(2)H(4)I(2) in two different solvents (methanol and cyclohexane), HgI(2) in methanol, and I(3) (-) in methanol excited at 267 nm. The results are consistent with previous conclusions for C(2)H(4)I(2) in methanol and HgI(2) in methanol, and the new TRXD data reveal that the C(2)H(4)I transient radical has a bridged structure in cyclohexane and I(3) (-) in methanol decomposes into I+I(2) (-) upon irradiation at 267 nm. This TFT method should greatly simplify the analysis because it bypasses MD simulations.     

Solvent effects on internal conversions and intersystem crossings: the radiationless de-excitation of acrolein in water

An extended version of the averaged solvent electrostatic potential from molecular dynamics data (ASEP/MD) method oriented to the study of the solvent effects on internal conversion and intersystem crossing processes is presented. The method allows for the location of crossing points between free energy surfaces both in equilibrium and in frozen solvent conditions. The ground and excited states of the solute molecule are described at the complete active space self-consistent field (CASSCF) level while the solvent structure is obtained from molecular dynamics simulations. As an application, we studied the nonradiative de-excitation of s-trans-acrolein 1(n --> pi*) in aqueous solution. We found that the solvent modifies the relative stability of the different crossing points but not enough as to alter the relative order of stability with respect to the in vacuo situation. The relaxation through an equilibrium path involves a strong solvent reorganization. On the contrary, the nonequilibrium path does not involve solvent motion and the de-excitation could proceed with the same speed as in vacuo.     

Combined QM/MM study of the opsin shift in bacteriorhodopsin

Combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics simulations of bacteriorhodopsin (bR) in the membrane matrix have been carried out to determine the factors that make significant contributions to the opsin shift. We found that both solvation and interactions with the protein significantly shifts the absorption maximum of the retinal protonated Schiff base, but the effects are much more pronounced in polar solvents such as methanol, acetonitrile, and water than in the protein environment. The differential solvatochromic shifts of PSB in methanol and in bR leads to a bathochromic shift of about 1800 cm(-1). Because the combined QM/MM configuration interaction calculation is essentially a point charge model, this contribution is attributed to the extended point-charge model of Honig and Nakanishi. The incorporation of retinal in bR is accompanied by a change in retinal conformation from the 6-s-cis form in solution to the 6-s-trans configuration in bR. The extension of the pi-conjugated system further increases the red-shift by 2400 cm(-1). The remaining factors are due to the change in dispersion interactions. Using an estimate of about 1000 cm(-1) in the dispersion contribution by Houjou et al., we obtained a theoretical opsin shift of 5200 cm(-1) in bR, which is in excellent agreement with the experimental value of 5100 cm(-1). Structural analysis of the PSB binding site revealed the specific interactions that make contributions to the observed opsin shift. The combined QM/MM method used in the present study provides an opportunity to accurately model the photoisomerization and proton transfer reactions in bR.     

Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect

The low-lying singlet states (i.e. S0, S1, and S2) of the chromophore of rhodopsin, the protonated Schiff base of 11-cis-retinal (PSB11), and of its all-trans photoproduct have been studied in isolated conditions by using ab initio multiconfigurational second-order perturbation theory. The computed spectroscopic features include the vertical excitation, the band origin, and the fluorescence maximum of both isomers. On the basis of the S0-->S1 vertical excitation, the gas-phase absorption maximum of PSB11 is predicted to be 545 nm (2.28 eV). Thus, the predicted absorption maximum appears to be closer to that of the rhodopsin pigment (2.48 eV) and considerably red-shifted with respect to that measured in solution (2.82 eV in methanol). In addition, the absorption maxima associated with the blue, green, and red cone visual pigments are tentatively rationalized in terms of the spectral changes computed for PSB11 structures featuring differently twisted beta-ionone rings. More specifically, a blue-shifted absorption maximum is explained in terms of a large twisting of the beta-ionone ring (with respect to the main conjugated chain) in the visual S-cone (blue) pigment chromophore. In contrast, the chromophore of the visual L-cone (red) pigment is expected to have a nearly coplanar beta-ionone ring yielding a six double bond fully conjugated framework. Finally, the M-cone (green) chromophore is expected to feature a twisting angle between 10 and 60 degrees. The spectroscopic effects of the alkyl substituents on the PSB11 spectroscopic properties have also been investigated. It is found that they have a not negligible stabilizing effect on the S1-S0 energy gap (and, thus, cause a red shift of the absorption maximum) only when the double bond of the beta-ionone ring conjugates significantly with the rest of the conjugated chain.     

Density and viscosity of tetrabutyl ammonium hydrogen sulphate and tetrabutyl ammonium chloride salts in aqueous and methanolic solution at 303 K

Density and viscosity of tetrabutyl ammonium hydrogen sulphate and tetrabutyl ammonium chloride in water as well as in methanol have been measured at 303.15 K. Different equations proposed by Einstein, Vand, Moulik and Jones–Dole for viscosity have been applied to the experimental results. An attempt has also been made to study the solute–solute and solute–solvent interactions involved in the system and the effect of anion on cationic surfactant. Molar volumes obtained from Einstein and Vand equations are very close to each other.     

Theoretical study of the stability of myrsinone in vacuo and in solution

The stability of various conformers of myrsinone (2,3-dihydroxy-5-undecyl-1,4-benzoquinone) and its tautomer [2,3-dihydroxy-5-(undec-1-ene)-cyclohex-2-ene-1,4-dione] has been studied in vacuo and in solution on model systems with the long alkyl side chains replaced with ethyl and eth-1-ene groups, respectively. Ab initio Hartree–Fock (HF) calculations in vacuo and free-energy calculations either in chloroform or in water solution, in the framework of the polarizable continuum model, have been carried out on the 6-31G* optimized geometries obtained in vacuo and in solution (water or chloroform). The nature of the stationary points found was investigated using normal mode analysis. The energy gap between the two tautomeric forms turns out to be about 1.3 kcal/mol in vacuo and becomes about 0.3 kcal/mol in chloroform solution, whereas in water the second tautomer is favored by about 1.2 kcal/mol. The effect of second-order M?ller–Plesset (MP2) correlation corrections has been considered on both the energy and the geometry of the tautomers in vacuo, whereas in solution only their effect on the energy was taken into account. The contribution to the stability in the gas phase and in solution of the intramolecular hydrogen bonds between the hydroxy hydrogen and the quinonoid oxygen is larger at the MP2 level than at the HF one. The directionality of the hydrogen bonds between the hydroxy groups affects considerably only the stability of the isomer with the exocyclic double bond. The computed chemical shifts for the two tautomers were compared to the experimental ones. In addition the solvation properties of 2,5-dihydroxy-3-ethyl-1,4-benzoquinone and of an ortho-quinonoid system were considered in order to evaluate the effect of the repulsion between vicinal hydroxy or quinonoid groups. Received: 14 September 1999 / Accepted: 3 February 2000 / Published online: 2 May 2000     

Coupled-cluster studies of the lowest excited states of the 11-cis-retinal chromophore

The first few excited states of the 11-cis-retinal (PSB11) chromophore have been studied at the coupled-cluster approximative singles and doubles (CC2) level using triple-zeta quality basis sets augmented with double sets of polarisation functions. The two lowest vertical excitation energies of 2.14 and 3.21 eV are in good agreement with recently reported experimental values of 2.03 and 3.18 eV obtained in molecular beam measurements. Calculations at the time-dependent density functional theory (TDDFT) level using the B3LYP hybrid functional yield vertical excitation energies of 2.34 and 3.10 eV for the two lowest states. Zero-point vibrational energy (ZPVE) corrections of -0.09 and -0.17 eV were deduced from the harmonic vibrational frequencies for the ground and excited states calculated at the density functional theory (DFT) and TDDFT level, respectively, using the B3LYP hybrid functional.     

密度泛函理论研究Gd（H2O）n^3＋（n=8，9）化合物的结构及相对稳定性

用密度泛函理论方法研究了气相和水溶液中Gd（H2O）n^3＋（n=8，9）化合物的结构和相对稳定性，其中水溶剂效应利用极化连续介质方法结合多种溶质空腔模型进行模拟．气相计算得到的化合物结构与实验观察结果一致．计算结果表明，在气相中9配位Gd（H2O）9^3＋比8配位Gd（H2O）8^3＋稳定，而在水溶液中稳定顺序刚好相反，这一结果不依赖于计算中采用的空腔模型种类，而且也与实验结果吻合．最后，通过采用各种空腔模型计算Gd^3＋的水合自由能，并与实验值比较，发现当化合物只包含第一层配位水分子时，UA0、UAHF及UAKS空腔模型最适合研究Gd^3＋在水溶液中的性质．     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Conformational landscape of (R,R)-pterocarpans with biological activity in vacuo and in aqueous solution (PCM and/or water clusters)

All possible combinations of stable dihedral values have been considered in vacuo at the B3LYP/6-31G level for 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C), whose hydroxy out-out conformation had been examined earlier together with the conformational preferences of 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) at the same level (Phys. Chem. Chem. Phys. 2004, 6, 2849). The structure with O5 trans with respect to H6a (O(t)) is about 2 kcal/mol less stable in vacuo than that with one of the H6 trans to it (H(t)); in aqueous solution its energy gap is nearly conserved. The in-in arrangement of the hydroxyl groups of erybraedin turns out to be preferred in vacuo (even considering zero point and thermal effects), where pseudo H-bonds are formed between hydroxy hydrogens and pi electron distributions of prenyl groups. The continuum solvent effect (water) at the IEF-PCM/B3LYP/6-31G level on the relative stability of the various rotamers is very limited both on bitucarpin and erybraedin. Considering the dihydrated derivatives, significant differences in the solvation energy are found between the distinct hydration sites, increasing in the order: methoxy O, ring O, hydroxy O, and hydroxy H. In hydroxy-water interactions, in fact, water prefers to behave as an H-bond acceptor unless nearby bulky groups prevent its approach. Interestingly enough, a bridging water molecule between the hydroxy H of erybraedin and the prenyl group can be found. The inclusion of BSSE corrections in hydroxy-water interactions decidedly favors out-out hydrated arrangements, followed by out-in and in-out ones. Bulk solvent effects with IEF-PCM about the dihydrated systems almost invert the stability order found in vacuo. When a four-water cluster is considered using QM methods, waters gather in H-bonded pairs around the solute OH groups. MD simulations, carried out on a pterocarpan solute (J. Phys. Chem. B 2005, 109, 16918), supply water adducts consistent with a liquid state that have also been embedded in the continuum solvent.