Al3+, Ca2+, Mg2+, and Li+ in aqueous solution: calculated first-shell anharmonic OH vibrations at 300 K

The anharmonic OH stretching vibrational frequencies, ν(OH), for the first-shell water molecules around the Li(+), Ca(2+), Mg(2+), and Al(3+) ions in dilute aqueous solutions have been calculated based on classical molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations. For Li(+)(aq), Ca(2+)(aq), Mg(2+)(aq), and Al(3+)(aq), our calculated IR frequency shifts, Δν(OH), with respect to the gas-phase water frequency, are about -300, -350, -450, and -750?cm(-1), compared to -290, -290, -420, and -830?cm(-1) from experimental infrared (IR) studies. The agreement is thus quite good, except for the order between Li(+) and Ca(2+). Given that the polarizing field from the Ca(2+) ion ought to be larger than that from Li(+)(aq), our calculated result seems reasonable. Also the absolute OH frequencies agree well with experiment. The method we used is a sequential four-step procedure: QM(electronic) to make a force field+MD simulation+QM(electronic) for point-charge-embedded M(n+) (H(2)O)(y) (second?shell) (H(2)O)(z) (third?shell) clusters+QM(vibrational) to yield the OH spectrum. The many-body Ca(2+)-water force-field presented in this paper is new. IR intensity-weighting of the density-of-states frequency distributions was carried out by means of the squared dipole moment derivatives.     

Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions

A quantum mechanics/molecular mechanics (QM/MM) implementation that uses the Gaussian electrostatic model (GEM) as the MM force field is presented. GEM relies on the reproduction of electronic density by using auxiliary basis sets to calculate each component of the intermolecular interaction. This hybrid method has been used, along with a conventional QM/MM (point charges) method, to determine the polarization on the QM subsystem by the MM environment in QM/MM calculations on 10 individual H(2)O dimers and a Mg(2+)-H(2)O dimer. We observe that GEM gives the correct polarization response in cases when the MM fragment has a small charge, while the point charges produce significant over-polarization of the QM subsystem and in several cases present an opposite sign for the polarization contribution. In the case when a large charge is located in the MM subsystem, for example, the Mg(2+) ion, the opposite is observed at small distances. However, this is overcome by the use of a damped Hermite charge, which provides the correct polarization response.     

Dissection of the difference between the group I metal ions in inhibiting GSK3β: a computational study

Glycogen synthase kinase 3β (GSK3β) is a serine/threonine kinase that requires two cofactor Mg(2+) ions for catalysis in regulating many important cellular signals. Experimentally, Li(+) is a competitive inhibitor of GSK3β relative to Mg(2+), while this mechanism is not experienced with other group I metal ions. Herein, we use native Mg(2)(2+)-Mg(1)(2+) GSK3β and its Mg(2)(2+)-M(1)(+) (M = Li, Na, K, and Rb) derivatives to investigate the effect of metal ion substitution on the mechanism of inhibition through two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations and molecular dynamics (MD) simulations. The results of ONIOM calculations elucidate that the interaction of Na(+), K(+), and Rb(+) with ATP is weaker compared to that of Mg(2+) and Li(+) with ATP, and the critical triphosphate moiety of ATP undergoes a large conformational change in the Na(+), K(+), and Rb(+) substituted systems. As a result, the three metal ions (Na(+), K(+), and Rb(+)) are not stable and depart from the active site, while Mg(2+) and Li(+) can stabilize in the active site, evident in MD simulations. Comparisons of Mg(2)(2+)-Mg(1)(2+) and Mg(2)(2+)-Li(1)(+) systems reveal that the inline phosphor-transfer of ATP and the two conserved hydrogen bonds between Lys85 and ATP, together with the electrostatic potential at the Li(1)(+) site, are disrupted in the Mg(2)(2+)-Li(1)(+) system. These computational results highlight the possible mechanism why Li(+) inhibits GSK3β.     

Molecular dynamics DFT:B3LYP study of guanosinetriphosphate conversion into guanosinemonophosphate upon Mg2+ chelation of alpha and beta phosphate oxygens of the triphosphate tail

A molecular dynamics DFT:B3LYP (6-31G(**) basis set) study is used to elucidate the mechanism of guanosinetriphosphate (GTP) conversion into guanosinemonophosphate (GMP) upon the action of Mg(2+) (magnesium cofactor). The computations are carried out at 310 K in a volume of 178 water molecules, which surround the Mg(2+)-GTP complex and imitate the effect of solution. Over 5 ps, Mg(2+)-GTP appears to be fully decomposed, yielding five final products: two hydrated molecules of inorganic phosphate Pi, a hydrated Mg(2+), atomic oxygen (which in the course of a couple of subsequent reactions gains two hydrogens and converts into a water molecule) and a highly active *GMP radical. The radical production is linked to presence of Mg(2+), which initiates a radical mechanism of GTP cleavage. At the initial stage, Mg(2+) undergoes reduction to Mg(+), accompanied by the formation of an ion-radical pair with GTP, (+)Mg*-*GTP(3-). Without Mg(2+), an inert form of GMP (the ionic mechanism of GTP hydrolytic cleavage) rather than GMP is produced. *GMP production, which is similar to that of *AMP (adenosinemonophosphate), *CMP (cytidinemonophosphate), TMP (thymidinemonophosphate) and *UMP (uridinemonophosphate), plays a crucial role in DNA and RNA single chain synthesis.     

Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

Various quantum mechanical/molecular mechanical (QM/MM) geometry optimizations starting from an x-ray crystal structure and from the snapshot structures of constrained molecular dynamics (MD) simulations have been performed to characterize two dynamically stable active site structures of phosphodiesterase-5 (PDE5) in solution. The only difference between the two PDE5 structures exists in the catalytic, second bridging ligand (BL2) which is HO- or H2O. It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+. It has been demonstrated that the results of the QM/MM geometry optimizations are remarkably affected by the solvent water molecules, the dynamics of the protein environment, and the electronic embedding charges of the MM region in the QM part of the QMM/MM calculation. The PDE5(BL2 = H2O) geometries optimized by using the QM/MM method in different ways show strong couplings between these important factors. It is interesting to note that the PDE5(BL2 = HO-) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors. These results suggest the overall effects of these three important factors on the optimized geometries can roughly cancel out. However, the QM/MM calculations that only account for some of these factors could lead to considerably different geometries. These results might be useful also in guiding future QM/MM geometry optimizations on other enzymes.     

Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water

A combination of the polarizable continuum model (PCM) and the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology, PCM-MM/QM, is used to include the solute electronic polarization and then study the solvent effects on the low-lying n→π(?) excitation energy and the (15)N nuclear magnetic shielding of pyrazine and pyridazine in aqueous environment. The results obtained with PCM-MM/QM are compared with two other procedures, i.e., the conventional PCM and the iterative and sequential QM/MM (I-QM/MM). The QM calculations are made using density functional theory in the three procedures. For the excitation energies, the time-dependent B3LYP/6-311+G(d) model is used. For the magnetic shielding, the B3LYP/aug-pcS2(N)/pcS2(C,O,H) is used with the gauge-including atomic orbitals. In both cases, i.e., PCM-MM/QM and I-QM/MM, that use a discrete model of the solvent, the solute is surrounded by a first shell of explicit water molecules embedded by an electrostatic field of point charges for the outer shells. The best results are obtained including 28 explicit water molecules for the spectral calculations and 9 explicit water molecules for the magnetic shielding. Using the PCM-MM/QM methodology the results for the n→π(?) excitation energies of pyridazine and pyrazine are 32,070 ± 80 cm(-1) and 32,675 ± 60 cm(-1), respectively, in good agreement with the corresponding I-MM/QM results of 32,540 ± 80 cm(-1) and 32,710 ± 60 cm(-1) and the experimental results of 33,450-33,580 cm(-1) and 32,700-33,300 cm(-1). For the (15)N magnetic shielding, the corresponding numbers for the gas-water shifts obtained with PCM-MM/QM are 47.4 ± 1.3 ppm for pyridazine and 19.7 ± 1.1 ppm for pyrazine, compared with the I-QM/MM values of 53.4?±?1.3 ppm and 19.5 ± 1.2 ppm and the experimental results of 42-54 ppm and 17-22 ppm, respectively. The agreement between the two procedures is found to be very good and both are in agreement with the experimental values. PCM-MM/QM approach gives a good solute polarization and could be considered in obtaining reliable results within the expected QM/MM accuracy. With this electronic polarization, the solvent effects on the electronic absorption spectra and the (15)N magnetic shielding of the diazines in water are well described by using only an electrostatic approximation. Finally, it is remarked that the experimental and theoretical results suggest that the (15)N nuclear magnetic shielding of any diazine has a clear dependence with the solvent polarity but not directly with the solute-solvent hydrogen bonds.     

Adsorption and isotope effects by ion exchange with 1-aza-12-crown-4 bonded Merrifield peptide resin

Magnesium isotope effects were investigated by chemical ion exchange with synthesized 1-aza-12-crown-4 bonded Merrifield peptide resin using elution chromatography. The capacity of azacrown ion exchanger was 0.89 meq/g dry resin. The heavier isotopes of magnesium were enriched in the resin phase, while the lighter isotopes were enriched in the solution phase. The hydration effect is less than the complexation and isotope mass effects. The single stage separation factor was determined according to the method of Glueckauf from the elution curve and isotopic assays. The separation factors of 24Mg(2+)-25Mg(2+), 24Mg(2+)-26Mg(2+), and 25Mg(2+)-26Mg(2+) were 1.012, 1.023, and 1.011, respectively.     

Magnesium isotope separation by ion exchange using hydrous manganese(IV) oxide

The magnesium isotope effects were investigated by chemical ion exchange with a hydrous manganese(IV) oxide. The capacity of manganese(IV) oxide was 0.5 meq g(-1). The distribution coefficient of magnesium ions on the MnO(2) was determined by a batch method. The heavier isotopes of magnesium were enriched in the solution phase, while the lighter isotopes were enriched in the hydrous MnO(2) phase. The separation factor was determined according to the method of Glueckauf from the elution curve and isotopic assays. The separation factors of (24)Mg(2+)-(25)Mg(2+), (24)Mg(2+)-(26)Mg(2+), and (25)Mg(2+)-(26)Mg(2+) isotope pair fractionations were 1.011, 1.021, and 1.011, respectively.     

Infrared spectra of the M(NO)n (M = Sn, Pb; n = 1, 2) and PbNO- molecules

Reactions of laser-ablated tin and lead atoms with nitric oxide molecules in solid argon and neon have been investigated using matrix-isolation infrared spectroscopy. In the argon experiments, absorptions at 1560.1, 1625.8, and 1486.7 cm(-1) are assigned to the N-O stretching vibrations of the SnNO and Sn(NO)2 molecules, and absorptions at 1541.9, 1630.0, 1481.8, and 1457.5 cm(-1) are assigned to the N-O stretching vibrations of the PbNO, Pb(NO)2, and PbNO- molecules on the basis of isotopic shifts and splitting patterns. The present neon experiments only produce neutral tin and lead mononitrosyls. Density functional theory calculations have been performed on these tin and lead nitrosyls. The good agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts substantiates the identification of these nitrosyls from the matrix infrared spectra.     

Inversion vibration of PH3+(X2A2") studied by zero kinetic energy photoelectron spectroscopy

We report the first rotationally resolved spectroscopic studies on PH3+(X2A2") using zero kinetic energy photoelectron spectroscopy and coherent VUV radiation. The spectra about 8000 cm(-1) above the ground vibrational state of PH3+(X2A2") have been recorded. We observed the vibrational energy level splittings of PH3+(X2A2") due to the tunneling effect in the inversion (symmetric bending) vibration (nu2+). The energy splitting for the first inversion vibrational state (0+/0-) is 5.8 cm(-1). The inversion vibrational energy levels, rotational constants, and adiabatic ionization energies (IEs) for nu2+ = 0-16 have been determined. The bond angles between the neighboring P-H bonds and the P-H bond lengths are also obtained using the experimentally determined rotational constants. With the increasing of the inversion vibrational excitations (nu2+), the bond lengths (P-H) increase a little and the bond angles (H-P-H) decrease a lot. The inversion vibrational energy levels have also been calculated by using one dimensional potential model and the results are in good agreement with the experimental data for the first several vibrational levels. In addition to inversion vibration, we also observed firstly the other two vibrational modes: the symmetric P-H stretching vibration (nu1+) and the degenerate bending vibration (nu4+). The fundamental frequencies for nu1+ and nu4+ are 2461.6 (+/-2) and 1043.9 (+/-2) cm(-1), respectively. The first IE for PH3 was determined as 79670.9 (+/-1) cm(-1).     

QM/MM-PBSA method to estimate free energies for reactions in proteins

We have developed a method to estimate free energies of reactions in proteins, called QM/MM-PBSA. It estimates the internal energy of the reactive site by quantum mechanical (QM) calculations, whereas bonded, electrostatic, and van der Waals interactions with the surrounding protein are calculated at the molecular mechanics (MM) level. The electrostatic part of the solvation energy of the reactant and the product is estimated by solving the Poisson-Boltzmann (PB) equation, and the nonpolar part of the solvation energy is estimated from the change in solvent-accessible surface area (SA). Finally, the change in entropy is estimated from the vibrational frequencies. We test this method for five proton-transfer reactions in the active sites of [Ni,Fe] hydrogenase and copper nitrite reductase. We show that QM/MM-PBSA reproduces the results of a strict QM/MM free-energy perturbation method with a mean absolute deviation (MAD) of 8-10 kJ/mol if snapshots from molecular dynamics simulations are used and 4-14 kJ/mol if a single QM/MM structure is used. This is appreciably better than the original QM/MM results or if the QM energies are supplemented with a point-charge model, a self-consistent reaction field, or a PB model of the protein and the solvent, which give MADs of 22-36 kJ/mol for the same test set.     

Spectral characterization of a newly synthesized fluorescent semicarbazone derivative and its usage as a selective fiber optic sensor for copper(II)

In this work photoluminescent properties of highly Cu(2+) selective organic fluoroionophore, semicarbazone derivative; bis(naphtho[2,1-b]furan-2-yl)methanone semicarbazone (BNF) was investigated in different solvents (dichloromethane, tetrahydrofuran, toluene and ethanol) and in polymer matrices of polyvinylchloride (PVC) and ethyl cellulose (EC) by absorption and emission spectrometry. The BNF derivative displayed enhanced fluorescence emission quantum yield, Q(f)=6.1 x 10(-2) and molar extinction coefficient, epsilon=29,000+/-65 cm(-1)M(-1) in immobilized PVC matrix, compared to 2.6 x 10(-3) and 24,573+/-115 in ethanol solution. The offered sensor exhibited remarkable fluorescence intensity quenching upon exposure to Cu(2+) ions at pH 4.0 in the concentration range of 1.0 x 10(-9) to 3.0 x 10(-4)M [Cu(2+)] while the effects of the responding ions (Ca(2+), Hg(+), Pb(2+), Al(3+), Cr(3+), Mn(2+), Mg(2+), Sn(2+), Cd(2+), Co(2+) and Ni(2+)) were less pronounced.     

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value.     

Characterization of structure and dynamics of an aqueous scandium(iii) ion by an extended ab initio QM/MM molecular dynamics simulation

Hydration structure and dynamics of an aqueous Sc(iii) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(iii) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(iii)-O bond length of 2.14 ? was identified for six prism water molecules with one capping water located at around 2.26 ?, reproducing well the X-ray diffraction data. The Sc(iii)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(iii) ion predict a mean ligand residence time of 7.3 ps.     

Theoretical and experimental vibrational study of phenylurea: structure, solvent effect and inclusion process with the beta-cyclodextrin in the solid state

FTIR and Raman vibrational spectroscopic techniques as well as DFT quantum chemical calculation were used for characterizing conformational changes of phenylurea (a herbicide parent molecule) occurring from solid state to aqueous medium. Experimental infrared frequencies were assigned on the base of urea and benzenic derivatives spectroscopic data available in the literature and vibrational normal modes analytical calculation at the fully optimized geometry. Investigation of isotopic and solvent effects has revealed that the structure of phenylurea is particularly sensitive to the electrostatic environment via hydrogen non covalent bonds. The ability of beta-cyclodextrin (beta-CD) to form host-guest inclusion complex with phenylurea in the solid state was also evidenced by significant frequency shifts observed in the 1400-1800 cm(-1) spectral range.     

HF, MP2 and DFT calculations and spectroscopic study of the vibrational and conformational properties of N-diethylendiamine

The conformational stability and vibrational modes of the N-diethylendiamine organic cation (N-DD(2+)) were studied by experimental (Raman) spectroscopy combined with theoretical calculations. Various ab initio theories were used: Hartree-Fock (HF) theory, M?ller-Plesset second-order perturbation (MP2) theory and density functional theory (DFT). Three stable conformers of N-DD(2+), trans-trans, gauche-gauche and gauche-trans were calculated. A comparison between the computed structural parameters of the conformers at both levels of theory and the X-ray data was made. It is demonstrated that the N-DD(2+) cation adopts more probably the gauche-gauche conformation at room temperature. In order to make a more detailed interpretation of the low temperature phase transition of N-DDHP, the Raman spectra of N-DDHP were recorded at room and low temperature in the 200-3400 cm(-1) region. The vibrational frequencies of the different conformers of N-DD(2+) were also calculated using the DFT/B3LYP (6-31G(d)) level of theory. By comparison between the experimental and theoretical results, the conformational dynamic of the N-DD(2+) organic cation was confirmed. It is shown that the N-DD(2+) cation configuration changes from gauche-gauche conformer to gauche-trans conformer when decreasing the temperature.     

An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Structural and dynamical properties of Zn(II) in aqueous solution were investigated, based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation at double-zeta Hartree-Fock quantum mechanical level including the first and second hydration shells into the QM region. The inclusion of the second shell in the QM region resulted in significant changes in the properties of the hydrate. The first shell coordination number was found to be 6, the second shell consists of approximately 14 water molecules. The structural properties were determined in terms of RDF, ADF, tilt and theta angle distributions, while dynamics were characterized by mean ligand residence times, ion-ligand stretching frequencies and the vibrational and librational motions of water ligands.     

Reactions of laser-ablated zinc and cadmium atoms with CO: infrared spectra of the Zn(CO)x (x = 1-3), CdCO-, and Cd(CO)2 molecules in solid neon

Reactions of laser-ablated zinc and cadmium atoms with carbon monoxide molecules in solid neon have been investigated using matrix-isolation infrared spectroscopy. Based on the isotopic substitution, absorptions at 1852.2, 1901.9, 1945.9, and 1995.2 cm(-1) are assigned to the C-O stretching vibrations of the ZnCO, Zn(CO)(2), and Zn(CO)(3) molecules. Absorptions at 1735.8, 1961.3, and 2035.7 cm(-1) are assigned to the C-O stretching vibrations of the CdCO(-) and Cd(CO)(2) molecules. In contrast with the previous argon experiments, more species and more valuable information about the reaction of zinc and cadmium atoms with CO have been obtained in solid neon. Density functional theory calculations have been performed on these zinc and cadmium carbonyls. The agreement between the experimental and calculated vibrational frequencies, relative absorption intensities, and isotopic shifts substantiates the identification of these carbonyls from the matrix infrared spectrum. The present experiments also reveal that zinc is more reactive with CO than cadmium.