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PubMed2006

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.

Hydrogen Bonding↗
PubMed2005

Modeling effects of oxyanion hole on the ester hydrolysis catalyzed by human cholinesterases.

Molecular dynamics (MD) simulations and hydrogen bonding energy (HBE) calculations have been performed on the prereactive enzyme-substrate complexes (ES), transition states (TS1), and intermediates (INT1) for acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine (ACh), butyrylcholinesterase (BChE)-catalyzed hydrolysis of ACh, and BChE-catalyzed hydrolysis of (+)/(-)-cocaine to examine the protein environmental effects on the catalytic reactions. The hydrogen bonding of cocaine with the oxyanion hole of BChE is found to be remarkably different from that of ACh with AChE/BChE. Whereas G121/G116, G122/G117, and A204/A199 of AChE/BChE all can form hydrogen bonds with ACh to stabilize the transition state during the ACh hydrolysis, BChE only uses G117 and A199 to form hydrogen bonds with cocaine. The change of the estimated total HBE from ES to TS1 is ca. -5.4/-4.4 kcal/mol for AChE/BChE-catalyzed hydrolysis of ACh and ca. -1.7/-0.8 kcal/mol for BChE-catalyzed hydrolysis of (+)/(-)-cocaine. The remarkable difference of approximately 3 to 5 kcal/mol reveals that the oxyanion hole of AChE/BChE can lower the energy barrier of the ACh hydrolysis significantly more than that of BChE for the cocaine hydrolysis. These results help to understand why the catalytic activity of AChE against ACh is considerably higher than that of BChE against cocaine and provides valuable clues on how to improve the catalytic activity of BChE against cocaine.

Acetylcholine↗
PubMed2005

Carbohydrate intramolecular hydrogen bonding cooperativity and its effect on water structure.

Molecular dynamics (MD) simulations combined with water-water H-bond angle analysis and calculation of solvent accessible surface area and approximate free energy of solvation were used to determine the influence of hydroxyl orientation on solute hydration and surrounding water structure for a group of chemically identical solutes-the aldohexopyranose sugars. Intramolecular hydrogen bond cooperativity was closely associated with changes in water structure surrounding the aldohexopyranose stereoisomers. The OH-4 group played a pivotal role in hydration as it was able to participate in a number of hydrogen bond networks utilizing the OH-6 group. Networks that terminated within the molecule (OH-4 --> OH-6 --> O-5) had relatively more nonpolar-like hydration than those that ended in a free hydroxyl group (OH-6 --> OH-4 --> OH-3). The OH-2 group modulated the strength of OH-4 networks through syndiaxial OH-2/4 intramolecular hydrogen bonding, which stabilized and induced directionality in the network. Other syndiaxial interactions, such as the one between OH-1 and OH-3, only indirectly affected water structure. Water structure surrounding hydrogen bond networks is discussed in terms of water-water hydrogen bond populations. The impact of syndiaxial versus vicinal hydrogen bonds is also reviewed. The results suggest that biological events such as protein-carbohydrate recognition and cryoprotection by carbohydrates may be driven by intramolecular hydrogen bond cooperativity.

Carbohydrates↗
PubMed2006

Spectroscopy of the cyano radical in an aqueous environment.

The effect of bulk water on the B (2)Sigma(+) <-- X (2)Sigma(+) and A (2)Pi <-- X (2)Sigma(+) electronic transitions of the cyano radical is investigated. First, the cyano radical-water dimer is characterized to understand the nature of the interactions and parametrize molecular mechanics (MM) potentials. The carbon atom, which hosts the unpaired electron, is found to have a Lennard-Jones radius smaller than typical force fields values. Classical molecular dynamics (MD) is then used to sample water configurations around the radical, employing two sets of MM parameters for the cyano radical and water. Subsequently, vertical excitation energies are calculated using time-dependent density functional theory (TD-DFT) and equation-of-motion coupled-cluster with single and double substitutions (EOM-CCSD). The effect of water is modeled by point charges used in the MD simulations. It is found that both bands blue-shift with respect to their gas phase position; the magnitude of the shift is only weakly dependent on the method and the MM parameter set used. The calculated shifts are analyzed in terms of the solute-solvent interactions in the ground and excited states. Significant contributions come from valence repulsion and electrostatics. Consequences for experiments on ICN photodissociation in water are discussed.

Algorithms↗
PubMed2006

Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: application to H2 in losod.

The anisotropic self-diffusion of molecular hydrogen in the multiple cage clathrasil losod (LOS) is modeled by means of molecular dynamics (MD) simulations of up to 1 micros for the temperature range 900-1200 K while treating the framework as fully flexible. The LOS diffusion tensor is calculated employing an analytical method based on hopping rates. The diffusion in the c-direction of the unit cell is found to be approximately two times more rapid than in the a- and the b-directions, a characteristic of importance for the application of LOS as a membrane. The overall diffusion is based on five different hop types for which the individual hopping rates and diffusion barriers are calculated separately. We show explicitly that the shape and volume of the cages have a significant effect on the hopping rates and further that even small deformations of the circular Si6O6 apertures have a large influence on the energetic barrier for hydrogen diffusion. Compared to the single cage clathrasils dodecasil 3C (MTN) and sodalite (SOD), LOS has a lower diffusion rate. However, from a technical point of view this rate (at 573 K) is still fast enough for LOS to be interesting as a size-selective membrane or as a hydrogen-adsorption medium.

Journal Article↗
PubMed2006

Development of many-body polarizable force fields for Li-battery components: 1. Ether, alkane, and carbonate-based solvents.

Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.

Alkanes↗
PubMed2006

Photoinduced isomerization kinetics of diiodomethane in supercritical fluid solution: local density effects.

The density dependence of diiodomethane photoinduced isomerization in supercritical (sc) CO2, CHF3, and C2H6 was investigated by transient absorption spectroscopy, covering a fluid density range from 0.7 to 2.5 (in reduced units). The solvent-caged photoproduct iso-diiodomethane is formed even at the lowest density, and its yield increases about 4-fold over the whole range. At the same time, isomer formation rate constants increase by roughly an order of magnitude and show little variation between CO2, C2H6, and CHF3. Furthermore, the formation rate constant decreases significantly with increasing excitation energy. We propose an isomer formation mechanism involving a rapidly established preequilibrium between a solvent-caged iodine atom-methyliodide radical pair and a loosely bound iodine-methyliodide radical complex, from which the reaction subsequently proceeds to the isomer. The latter step seems to be controlled by collisional stabilization of the initially hot radical moiety, as the formation rate constant increases linearly with sc solvent viscosity. The model predicts a quadratic dependence of relative isomer yield on fluid density. A corresponding correlation is found with the local fluid density, calculated via solute-solvent radial distribution functions obtained from molecular dynamics (MD) simulations.

Benzene↗
PubMed2006

Effective interaction potentials for alkali and alkaline earth metal ions in SPC/E water and prediction of mean ion activity coefficients.

The potential of mean force (PMF) acting between two simple ions surrounded by SPC/E water have been determined by molecular dynamics (MD) simulations using a spherical cavity approach. Such effective ion-ion potentials were obtained for Me-Me, Me-Cl-, and Cl(-)-Cl- pairs, where Me is a Li+, Na+, K+, Mg2+, Ca2+, Sr2+, and Ba2+ cation. The ionic sizes estimated from the effective potentials are not pairwise additive, a feature in the frequently used primitive model for electrolytes. The effective potentials were used in Monte Carlo (MC) simulations with implicit water to calculate mean ion activity coefficients of LiCl, NaCl, KCl, MgCl2, CaCl2, SrCl2, and BaCl2. Predicted activities were compared with experimental ones in the electrolyte concentration range 0.1-1 M. A qualitative agreement for LiCl and a satisfactory agreement for NaCl were found, whereas the predictions for KCl by two K+ models were less coherent. In the case of alkaline earth metal ions, all experimental activities were successfully reproduced at c = 0.1 M. However, at higher concentrations, similar deviations occurred for all divalent cations, suggesting that the dependence of the permittivity on the salt concentration and the polarization deficiency arising from the ordering of water molecules in the ion hydration shells are important in such systems.

Cations, Divalent↗
PubMed2006

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

Computer Simulation↗
PubMed2006

Adsorption at the liquid-liquid interface in the biphasic rhodium catalyzed hydroformylation of olefins promoted by cyclodextrins: a molecular dynamics study.

Using molecular dynamics (MD) simulations, we investigate the interfacial distribution of partners involved in the phase transfer rhodium catalyzed hydroformylation of olefins promoted by beta-cyclodextrins (beta-CDs). The beta-CDs, the reactant (alkene), product (aldehyde), several rhodium complexes (the catalyst, its precursor, and its alkene adduct) are simulated at the water-"oil" interface, where oil is represented by chloroform or hexane. It is shown that unsubstituted beta-CD and its 6-methylated and 2,6-dimethylated analogues adsorb at the interface, whereas the liposoluble permethylated CD does not. The precursor of the catalyst [RhH(CO)(TPPTS)3]9- (with triphenylphosphine trisulfonated TPPTS3- ligands) sits in water, but the less charged [RhH(CO)(TPPTS)2]6- catalyst and the [RhH(CO)(TPPTS)2(alkene)]6- reaction intermediate are clearly surface active. The TPPTS3- anions also concentrate at the interface, where they adopt an amphiphilic conformation, forming an electrical double layer with their Na+ counterions. Thus, the most important key partners involved in the hydroformylation reaction concentrate at the interface, thereby facilitating the reaction, a process which may be further facilitated upon complexation by CDs. These results point to the importance of adsorption at the liquid-liquid interface in the two-phase hydroformylation reaction of olefins promoted by beta-CDs and provide microscopic pictures of this peculiar region of the solution.

Journal Article↗
PubMed2006

Excitation energy transfer in ion pairs of polymethine cyanine dyes: efficiency and dynamics.

The present work deals with singlet excitation energy transfer (EET) occurring in contact ion pairs (CIPs) of several anionic oxonol analogues (acting as EE donors) and cationic cyanines (acting as acceptors) characterized by off resonance individual transitions. Combining conductometric and spectroscopic measurements with decreasing solvent polarity, we were able to observe a progressive ion pairing leading first to solvent-separated ion pairs (SSIPs) and then to CIPs. Analysis of the absorption spectra of three selected salts (A2,C1, A2,C2, and A1,C4) in chloroform-toluene mixtures showed that the transformation of SSIP into CIP involves the appearance of a certain exciton coupling, the extent of which decreases regularly with increasing gap between the local excitation energies. Fluorescence excitation spectra showed that EET occurs in CIP, and EET efficiencies were evaluated with a procedure expressly devised for weakly emitting donors. These were between 0.2 and 0.65 for the examined ion pairs involving anions A1 and A2. The spectroscopic study was complemented by a theoretical investigation aimed at establishing the dynamic regime of the observed EET. From classical MD simulations and local full geometry optimizations, A2,C1 and A2,C2 were found to form rather stable sandwich-type CIP structures with interchromophore distances (R) of about 0.45-0.50 nm. The donor-acceptor electronic coupling was calculated in terms of Coulombic interactions between atomic transition charges. For CIP, the electronic coupling was decidedly beyond the limit of the weak coupling required for an incoherent Förster-type mechanism. Thus, we tried to arrange the EET dynamics within the theory developed by Kimura, Kakitani, and Yamato (J. Phys. Chem. B 2000, 104, 9276) for the intermediate coupling case, which provides analytical expressions of time-dependent occupation probability, EET rate, and coherency in terms of two basic quantities: the electronic coupling and a correlation time related to the Franck-Condon factor. The latter was shown to be primarily modulated by Förster's spectral overlap integral (related in turn to the excitation energy gap). Calculations were carried out for the three sample systems using three values of the electronic coupling roughly corresponding to CIP, 1.0, and 2.0 nm interchromophore distances. At the CIP distance, EET in both A2,C1 and A2,C2 was predicted to occur with a partial exciton mechanism, very short transfer times (about 10 fs), and high degree of coherence. In A1,C4 (having the largest energy gap), EET was found to occur with a hot-transfer mechanism. More or less hot-transfer dynamics appeared to be retained by all three systems at R = 1.0 nm. Fully incoherent EET appeared to become operative only at distances larger than 2.0 nm.

Journal Article↗
PubMed2006

Surface segregation of dissolved salt ions.

Surface segregation of iodide, but not of fluoride or cesium ions, is observed by a combination of metastable impact electron spectroscopy (MIES) and ultraviolet photoelectron spectroscopy (UPS(HeI)) of amorphous solid water exposed to CsI or CsF vapor. The same surface ionic behavior is also derived from molecular dynamics (MD) simulations of the corresponding aqueous salt solutions. The MIES results show the propensity of iodide, but not fluoride, for the surface of the amorphous solid water film, providing thus strong evidence for the suggested presence of heavier halides (iodide, bromide, and to a lesser extent chloride) at the topmost layer of aqueous surfaces. In contrast, no appreciable surface segregation of ions is observed in methanol, neither in the experiment nor in the simulation. Furthermore, the present results indicate that, as far as the thermodynamic aspects of solvation of alkali halides are concerned, amorphous solid water and methanol surfaces behave similarly as surfaces of the corresponding liquids.

Ions↗
PubMed2006

Inertial suppression of protein dynamics in a binary glycerol-trehalose glass.

The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples. The amount of glycerol added to a trehalose glass coincides with the maximal recovery of biological activity in a separate study using similar binary glass samples. In this study, we use molecular dynamics (MD) simulations to investigate the dynamics of a hydrated protein encased in glycerol, unary trehalose and binary glycerol-trehalose glasses. We have found that we are able to reproduce the rigidification of the glycerol-trehalose glassy matrix and that there is a direct correlation between bulk glass dynamics and the extent of atomic fluctuation of protein atoms. The detailed microscopic picture that emerges is that protein dynamics are suppressed mainly by inertia of the bulk glass and to a lesser extent specific interactions at the protein-solvent interface. Thus, the inertia of the glassy matrix may be an influential factor in the determination of pharmaceutically relevant formulations.

Glass↗
PubMed2006

Entropy of water in the hydration layer of major and minor grooves of DNA.

Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex are known to be different from those in the bulk. Here, we use a recently developed theoretical scheme to compute the entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. The scheme requires as input both translational and rotational velocity autocorrelation function (C(V)(t) and C(omega)(t), respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulation of a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy of water at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and that in the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS value is 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TDeltaS) of transferring a minor groove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is 0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We also calculate the energy of interaction of each water molecule with the rest of the atoms in the system and hence calculate the chemical potential (Helmholtz free energy per water molecule, A = E - TS) in the different domains. The identical free energy value of water molecules in the different domains proves the robustness of the scheme. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or microviscosity) of water molecules in a given domain.

Biophysics↗
PubMed2006

The [BMI][Tf2N] ionic liquid/water binary system: a molecular dynamics study of phase separation and of the liquid-liquid interface.

We report molecular dynamics (MD) simulations of the aqueous interface of the hydrophobic [BMI][Tf2N] ionic liquid (IL), composed of 1-butyl-3-methylimidazolium cations (BMI+) and bis(trifluoromethylsulfonyl)imide anions (Tf2N-). The questions of water/IL phase separation and properties of the neat interface are addressed, comparing different liquid models (TIP3P vs TIP5P water and +1.0/-1.0 vs +0.9/-0.9 charged IL ions), the Ewald vs the reaction field treatments of the long range electrostatics, and different starting conditions. With the different models, the "randomly" mixed liquids separate much more slowly (in 20 to 40 ns) than classical water-oil mixtures do (typically, in less than 1 ns), finally leading to distinct nanoscopic phases separated by an interface, as in simulations which started with a preformed interface, but the IL phase is more humid. The final state of water in the IL thus depends on the protocol and relates to IL heterogeneities and viscosity. Water mainly fluctuates in hydrophilic basins (rich in O(Tf2N) and aromatic CH(BMI) groups), separated by more hydrophobic domains (rich in CF3(Tf2N) and alkyl(BMI) groups), in the form of monomers and dimers in the weakly humid IL phase, and as higher aggregates when the IL phase is more humid. There is more water in the IL than IL in water, to different extents, depending on the model. The interface is sharper and narrower (approximately 10 A) than with the less hydrophobic [BMI][PF6] IL and is overall neutral, with isotropically oriented molecules, as in the bulk phases. The results allow us to better understand the analogies and differences of aqueous interfaces with hydrophobic (but hygroscopic) ILs, compared to classical organic liquids.

Journal Article↗
PubMed2006

Role of aspartic acid in collagen structure and stability: A molecular dynamics investigation.

A molecular dynamics (MD) simulation study has been carried out to understand the stability of the triple helical collagen models. The calculations show that the presence of the aspartic acid residue in different positions leads to the local variation in the structure. Analyses of root-mean-square deviation (RMSD), radial distribution function (RDF), puckering effect, dihedral angle variation, hydrogen bond (H-bond), and conformational changes during molecular dynamics simulation reveal that the local perturbation in the sequences, increase in chain flexibility due to removal of five membered rings in the collagen by aspartic acid, change of intermolecular H-bonding pattern, and differences in the association of water are mainly influencing the nature of stabilization of collagen by aspartic acid.

Amino Acid Sequence↗
PubMed2006

Molecular dynamics study of surfactant monolayers adsorbed at the oil/water and air/water interfaces.

Atomistic molecular dynamics (MD) simulations have been carried out to investigate the physical properties of monolayers of monododecyl diethylene glycol (C(12)E(2)) surfactants adsorbed at the oil/water and air/water interfaces. The study shows that the surfactant molecules exhibit more extended conformations with a consequent increase of the thickness of the monolayer in the presence of the oil medium. It is noticed that the hydrocarbon tails of the surfactants are more vertically oriented at the oil/water interface. Interestingly, we notice that the presence of the oil medium has a strong influence in restricting both the translational and reorientational motions of the water molecules present in the hydration layer close to the surfactant headgroups.

Journal Article↗
PubMed2006

Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin.

The potential energy change during the M --> N process in bacteriorhodopsin has been evaluated by ab initio quantum chemical and advanced quantum chemical calculations following molecular dynamics (MD) simulations. Many previous experimental studies have suggested that the proton transfer from Asp96 to the Schiff base occurs under the following two conditions: (1) the hydrogen bond between Thr46 and Asp96 breaks and Thr46 is detached from Asp96 and (2) a stable chain of four water molecules spans an area from Asp96 --> Schiff base. In this work, we successfully reproduced the proton-transfer process occurring under these two conditions by molecular dynamics and quantum chemical calculations. The quantum chemical computation revealed that the proton transfer from Asp96 to Shiff base occurs in two-step reactions via an intermediate in which an H(3)O(+) appears around Ala215. The activation energy for the proton transfer in the first reaction was calculated to be 9.7 kcal/mol, which enables fast and efficient proton pump action. Further QM/MM (quantum mechanical/molecular mechanical) and FMO (fragment molecular orbital) calculations revealed that the potential energy change during the proton transfer is tightly regulated by the composition and the geometry of the surrounding amino acid residues of bacteriorhodopsin. Here, we report in detail the Asp96 --> Schiff base proton translocation mechanism of bacteriorhodopsin. Additionally, we discuss the effectiveness of combining quantum chemical calculations with truncated cluster models followed by advanced quantum chemical calculations applied to a whole protein to elucidate its reaction mechanism.

Aspartic Acid↗