Influence of 1,2-alkanediols on the structure of their intercalates with strontium phenylphosphonate solved by molecular simulation and experimental methods

Strontium phenylphosphonate intercalates with 1,2-diols (from 1,2-ethanediol to 1,2-hexanediol) were synthesized and characterized by X-ray diffraction, thermogravimetry, chemical analysis, and molecular simulation methods. Prepared samples exhibit a very good stability at ambient conditions. Structural arrangement calculated by simulation methods suggested formation of cavities surrounded by six benzene rings. Each cavity contained one molecule of diol and one molecule of water for the 1,2-ethanediol to 1,2-butanediol intercalates. In the case of 1,2-pentanediol two types of cavities alternated: one with diol molecules and another one with two water molecules. In the 1,2-hexanediol intercalate the benzene rings created two types of cavities containing one or two diol molecules, respectively, and this conformational variability led to a more disordered arrangement with respect to the models with shorter alkyl chains. Coordination of the oxygen atoms of the diols to the strontium atoms of the host follows the same pattern for all 1,2-diol intercalates except the 1,2-hexanediol intercalate, where these oxygen atoms can be mutually exchanged at their positions. The calculated basal spacings and structural models are in good agreement with experimental basal spacings obtained from X-ray powder diffraction and with other experimental results.     

Theoretical investigation of tautomerism in N-hydroxy amidines

A DFT study with QST3 approach method is used to calculate kinetic, thermodynamic, spectral and structural data of tautomers and transition state structures of some N-hydroxy amidines. All tautomers and transition states are optimized at the B3LYP/6-311++g** and B3LYP/aug-cc-pvtz level, with good agreement in energetic result with energies obtained from CBS-QB3, a complete basis set composite energy method. The result shows that the tautomer a (amide oxime) is more stable than the tautomer b (imino hydroxylamine) as is reported in the literature. In addition, our finding shows that, the energy difference between two tautomers is only in about 4–10 kcal/mol but the barrier energy found in traversing each tautomer to another one is in the range of 33–71 kcal/mol. Therefore, it is impossible to convert these two tautomers to each other at room temperature. Additionally, transition state theory is applied to estimate the barrier energy and reaction rate constants of the hydrogen exchange between tautomers in presence of 1–3 molecules of water. The computed activation barrier shows us that the barrier energy of solvent assisted tautomerism is about 9–20 kcal/mol and lower than simple tautomerism and this water-assisted tautomerism is much faster than simple tautomerism, especially with the assisting two molecules of water.     

A computer-aided quantum chemical study of the N<Stack><Subscript>15</Subscript><Superscript>−</Superscript></Stack> cluster

Ab initio (RHF, MP2) and Density Functional Theory (DFT) methods have been used to examine six isomers of the N15m cluster with the 6-31+G* basis set. Different from the known odd-numbered anionic N7m, N9m, and N11m clusters, in which the open-chain structures are the most stable species, the most stable N15m isomer is structure 1 (C1), which may be considered as a complex between the fragments cyclic N5m (D5h) and staggered N10 (D2d). The decomposition pathways of structure 2 (CS), containing two aromatic N5 rings connected by a N5 chain, and the open-chain structure 3 (C2v) were studied at the B3LYP/6-31+G* level of theory. Relative energies were refined at the level of B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G*+ZPE (B3LYP/6-31+G*). The barriers for N2 and N5m (D5h) fission reactions for structure 2 are predicted to be 18.2 and 14.2 kcal x mol(-1), respectively. The corresponding N2+N3m fission barrier for structure 3 is predicted to be 11.2 kcal x mol(-1). Supplementary material is available for this article if you access the article at http://dx.doi.org/10.1007/s00894-003-0118-0. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Structure 1 of the N15m cluster, showing bond distances in A and bond angles in degrees     

Monolayers of long chain lecithins at the air/water interface and their hydrolysis by phospholipase A2

The behavior of phosphatidylcholine monolayers at the air/water interface was studied by measuring their surface isotherm, surface potential, surface viscosity, and rate of hydrolysis by the dimeric phospholipase A2 from the venom of Crotalus atrox. The monolayers showed typical liquid-expanded behavior. In this phase, the surface potential was linearly dependent on surface concentration and extrapolated at zero concentration to a value characteristic of a liquid hydrocarbon/water interface. The rate of the reaction was measured by monitoring changes in area at constant surface pressure for 1,2-dioctanoyl- and 1,2-didecanoyl-3-sn-phosphatidylcholines, and by monitoring changes in surface potential for 1,2-dimyristoyl-, 1,2-dipalmitoyl-, 1-palmitoyl-2-oleoyl-, and 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholines. The enzymatic hydrolysis is first order with respect to the enzyme-calcium complex which forms with a Kd = 1.5 mM. A mechanism is proposed to account for the dependency of the reaction rates on the surface concentration of the substrate. We postulate that the rate-limiting step is the decomposition of a quaternary complex formed from two phospholipid molecules, one calcium ion and one dimeric enzyme. The rate is independent of the surface pressure per se; addition of inert lipids to a monolayer at constant area, and hence constant surface concentration of the substrate, increases the surface pressure without changing the surface density of the substrate yielding maximal enzymatic rate. The enzyme is specific for loosely packed substrate molecules in the liquid-expanded state: transition into the liquid-condensed state or compression of the liquid-expanded layer beyond 80 A2/phospholipid strongly inhibits the enzymatic reaction. Our results show that surface recognition is a direct consequence of a bifunctional active site since it is only at a phospholipid surface that the distance between two substrate molecules is optimal for forming a catalytically competent enzyme-Ca2+-(substrate)2 complex.     

Monte-Carlo simulation of hydration of nucleic acid fragments

Monte-Carlo simulation of the systems containing a stack of 6 complementary base pairs and 180 water molecules has been performed. Characteristic of the hydration shell structure in major and minor grooves has been found for the stacks of repeating A : U and G : C base pairs as well as alternating (A : U, U : A) and (G : C, C : G) ones. Probabilities of the formation of bridges, formed by 1, 2 and 3 water molecules, between hydrophilic centres of the bases have been estimated. One water molecule forms an H-bonded bridge between two adjacent hydrophilic centres with high probability if N...N, N...O or O...O distance between these centres is close to 4.3 A. Hydration shell structure was found to depend significantly on the stack sequence and configuration, while global hydration characteristics (average energy, the number of water-water and water-base H-bonds) are only slightly dependent on the stack sequence and configuration. For the stacks in A conformation the number of water molecules forming more than one H-bonds with the bases is greater in comparison with the stacks in B-like conformation. This result is discussed in connection with the concept of hydration economy during B to A transition.     

Tetraethylorthosilicate as molecular precursor to the formation of amorphous silica networks. A DFT-SCRF study of the base catalyzed hydrolysis

Quantum chemical calculations using density functional theory have been carried out to investigate two chemical pathways for the last step of the hydrolysis of tetraethylorthosilicate (TEOS) in basic catalyzed environment. The two models that are introduced in this study depend on the number of water molecules involved at the base catalyzed hydrolysis. Solution equilibrium geometries of the molecules involved in the transition states, reactants and product complexes of the two chemical pathways were fully optimized at B3LYP level of theory with the standard 6-31+G(d) basis set, modeling solvent effects using a polarizable continuum solvation model (PCM). Both models predict relative low activation energies. However, the model with two water molecules seems to be more adequate to describe the basic hydrolysis. A natural bond orbital (NBO) analysis seems to show that the proton transfer from water to ethoxy group would occur through a large hyperconjugative interaction, LP(O) → σ*(O-H), which is related to the nonbonding oxygen lone pair orbital from ethoxy group with the vicinal σ*(O-H) anti bonding orbital O-H of a water molecule.     

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.     

Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain

The folding thermodynamics of the src-SH3 protein domain were characterized under refolding conditions through biased fully atomic molecular dynamics simulations with explicit solvent. The calculated free energy surfaces along several reaction coordinates revealed two barriers. The first, larger barrier was identified as the transition state barrier for folding, associated with the formation of the first hydrophobic sheet of the protein. phi values calculated from structures residing at the transition state barrier agree well with experimental phi values. The microscopic information obtained from our simulations allowed us to unambiguously assign intermediate phi values as the result of multiple folding pathways. The second, smaller barrier occurs later in the folding process and is associated with the cooperative expulsion of water molecules between the hydrophobic sheets of the protein. This posttransition state desolvation barrier cannot be observed through traditional folding experiments, but is found to be critical to the correct packing of the hydrophobic core in the final stages of folding. Hydrogen exchange and NMR experiments are suggested to probe this barrier.     

Exploring the gating mechanism in the ClC chloride channel via metadynamics

Computer simulations have been used to probe the gating mechanism in the Salmonella serovar typhimurium chloride channel (st-ClC). Specifically, the recently developed metadynamics methodology has been exploited to construct free energy surfaces as a function of the positions of either one or two chloride ions inside the pore, the position and protonation state of the key E148 residue, and the number of water molecules coordinating the translocating ions. The present calculations confirm the multi-ion mechanism in which an ion-push-ion effect lowers the main barriers to chloride ion translocation. When a second anion is taken into account, the barrier for chloride passage through the E148 narrow region is computed to be 6 kcal/mol in the wild-type channel, irrespective of the protonation state of the E148 residue, which is shown to only affect the entrance barrier. In the E148A mutant, this barrier is much lower, amounting to 3 kcal/mol. The metadynamics calculations reported herein also demonstrate that before reaching the periplasmic solution, chloride ions have to overcome an additional barrier arising from two different effects, namely the rearrangement of their solvation shell and a flip in the backbone angles of the residues E148 and G149, which reside at the end of the alphaF helix.     

RNA hydrolysis via an oxyphosphorane intermediate.

From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis, a pentacoodinate dianionic intermediate 2a (Storer, et al., J. Am. Chem. Soc., 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. Although the intermediate, which has the well depth on the order of kBT, is unlikely to be kinetically significant, the overall rate-limiting transition state structure TS2 obtained at 3-21G* level is very close to the corresponding structure at the STO-3G level; it has an extended P-O(5') bond breaking character. These gas-phase calculation results are used to qualitatively interpret mutagenesis results of Barnase and RNase T1 where water molecules are absent from the active site.     

Unexpected formation of complex bridged tetrazoles via intramolecular 1,3-dipolar cycloaddition of 1,2-O-cyanoalkylidene derivatives of 3-azido-3-deoxy-D-allose

An unexpected and interesting intramolecular side reaction occurred during the attempted synthesis of glycosyl cyanides upon treatment of 1-O-acetyl-3-azido-3-deoxyallose derivatives with TMSCN and different Lewis acids. Exo-1,2-O-cyanoalkylidene derivatives formed by neighboring group participation and attack of cyanide underwent, after Lewis-acid mediated isomerization to the endo-isomer, intramolecular azide-cyanide cycloaddition leading to the formation of tetrazoles embedded in bridged tetracyclic ring systems. The efficiency of cycloaddition is dependent on the ring structure of the sugar (pyranose or furanose). Of the studied molecules, 3-azido-1,2-O-cyanoethylidene-3-deoxy-allopyranose provides the most suitable scaffold for intramolecular [2+3] cycloaddition under exceptionally mild conditions. Our results highlight the capability of carbohydrates to act as scaffolds for the precise positioning of functional groups productive for a specific chemical reaction.     

Molecular structure of deoxycytidyl-3''-methylphosphonate (RP) 5''-deoxyguanidine, d[Cp(CH3)G]. A neutral dinucleotide with Watson-Crick base pairing and a right handed helical twist.

The crystal structure of d[Cp(CH3)G] has been determined as part of a project to study the mechanism of the B----Z transition in DNA. The asymmetric unit contains two dinucleotides and the equivalent of 7.5 water molecules, partially disordered over 12 definable positions. The two symmetry-independent dinucleotides form a duplex with Watson-Crick base-pairing and a right-handed helical sense. Comparison with previously determined structures of the B and A conformation showed that this duplex is closer to B than to A but significantly different from B. It corresponds to a stretched out helix with a 4 A rise per base pair and a helical twist of 32 degrees. This structure may serve as a model for the bending of DNA in certain situations. The configuration at the methyl phosphonate is RP, and a mechanism, based on this assignment, is presented for the B----Z transition in DNA.     

An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability

An all-atom Gō model of Trp-cage protein is simulated using discontinuous molecular dynamics in an explicit minimal solvent, using a single, contact-based interaction energy between protein and solvent particles. An effective denaturant or osmolyte solution can be constructed by making the interaction energy attractive or repulsive. A statistical mechanical equivalence is demonstrated between this effective solvent model and models in which proteins are immersed in solutions consisting of water and osmolytes or denaturants. Analysis of these studies yields the following conclusions: 1), Osmolytes impart extra stability to the protein by reducing the entropy of the unfolded state. 2), Unfolded states in the presence of osmolyte are more collapsed than in water. 3), The folding transition in osmolyte solutions tends to be less cooperative than in water, as determined by the ratio of van 't Hoff to calorimetric enthalpy changes. The decrease in cooperativity arises from an increase in native structure in the unfolded state, and thus a lower thermodynamic barrier at the transition midpoint. 4), Weak denaturants were observed to destabilize small proteins not by lowering the unfolded enthalpy, but primarily by swelling the unfolded state and raising its entropy. However, adding a strong denaturant destabilizes proteins enthalpically. 5), The folding transition in denaturant-containing solutions is more cooperative than in water. 6), Transfer to a concentrated osmolyte solution with purely hard-sphere steric repulsion significantly stabilizes the protein, due to excluded volume interactions not present in the canonical Tanford transfer model. 7), Although a solution with hard-sphere interactions adds a solvation barrier to native contacts, the folding is nevertheless less cooperative for reasons 1–3 above, because a hard-sphere solvent acts as a protecting osmolyte.     

Hydration of carbon dioxide by carbonic anhydrase: internal proton transfer of Zn2+-bound HCO3-

Proton transfer within HCO3- has been examined under various conditions through molecular orbital methods: partial retention of diatomic differential overlap and 4-31G self-consistent field programs. These conditions include the absence or presence of Zn2+, Zn2+(NH3)3, or a water ligand on Zn2+. In addition, 4-31G+ and some MP2/4-31G results are obtained. The use of Be2+ to simulate Zn2+ reproduces reaction pathways and energy barriers, except for marginal cases. The barrier of 35.6 kcal/mol for direct internal proton transfer is reduced to 3.5 kcal/mol when one water molecule, not bound to Zn2+, is included for proton relay and to 1.4 kcal/mol when two such water molecules are included. In the enzyme, either Thr-199 or solvent molecules could perform this relay function. Our results favor this facilitated proton transfer over a mechanism in which Zn2+-bound OH- attacks CO2, a bidentate intermediate forms, and the OH moiety of the resulting HCO3- dissociates from Zn2+, thus leaving one of the oxygens of the original CO2 as a ligand to Zn2+.     

Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model

The src SH3 domain has been known to be a two-state folder near room temperature. However, in a previous study with an all-atom model simulation near room temperature, the transition state of this protein was not successfully detected on a free-energy profile using two axes: the radius of gyration (R(g)) and native contact reproduction ratio (Q value). In this study, we focused on an atom packing effect to characterize the transition state and tried another analysis to detect it. To explore the atom packing effect more efficiently, we introduced a charge-neutralized all-atom model, where all of the atoms in the protein and water molecules were treated explicitly, but their partial atomic charges were set to zero. Ten molecular dynamics simulations were performed starting from the native structure at 300 K, where the simulation length of each run was 90 ns, and the protein unfolded in all runs. The integrated trajectories (10 x 90 = 900 ns) were analyzed by a principal component analysis (PCA) and showed a clear free-energy barrier between folded- and unfolded-state conformational clusters in a conformational space generated by PCA. There were segments that largely deformed when the conformation passed through the free-energy barrier. These segments correlated well with the structural core regions characterized by large phi-values, and the atom-packing changes correlated with the conformational deformations. Interestingly, using the same simulation data, no significant barrier was found in a free-energy profile using the R(g) and Q values for the coordinate axes. These results suggest that the atom packing effect may be one of the most important determinants of the transition state.     

Biosynthesis of (R)-phenyl-1,2-ethanediol from racemic styrene oxide by using bacterial and marine fish epoxide hydrolases

Enantio-convergent hydrolysis of racemic styrene oxides was achieved to prepare enantiopure (R)-phenyl-1,2-ethanediol by using two recombinant epoxide hydrolases (EHs) of a bacterium, Caulobacter crescentus, and a marine fish, Mugil cephalus. The recombinant C. crescentus EH primarily attacked the benzylic carbon of (S)-styrene oxide, while the M. cephalus EH preferentially attacked the terminal carbon of (R)-styrene oxide, thus leading to the formation of (R)-phenyl-1,2-ethanediol as the main product. (R)-Phenyl-1,2-ethanediol was obtained with 90% enantiomeric excess and yield as high as 94% from 50 mM racemic styrene oxides in a one-pot process.     

Schiff bases or glycosylamines: crystal and molecular structures of four derivatives of D-mannose

Crystal and molecular structures of four derivatives of D-mannose are described. Each could exist as either an open-chain Schiff base or as a glycosylamine in the solid state. The derivative formed upon reaction of D-mannose with hydroxylamine is an open-chain oxime, but those formed upon reaction with semicarbazide, aniline, and p-chloroaniline are glycosylamines. The oxime, which crystallizes as the syn-(E) isomer, has a fully extended carbon chain. The glycosylamines are all beta-pyranoses. The packing arrangement of the oxime involves 'head-to-tail' hydrogen bonding. The semicarbazide derivative, which crystallizes as a dihydrate, features a hydrogen-bonded intramolecular bridge formed by the two water molecules and linking O-6 to the carbonyl oxygen atom. The packing arrangements of the aniline and p-chloroaniline derivatives differ from each other but are nevertheless closely related by similar hydrogen-bonding interactions.     

Chiroptical properties of lecithin reverse micelles and organogels

The ultraviolet absorbance and circular dichroism (CD) spectra of lecithin reverse micelles and gels were investigated in order to establish whether the formation of these noncovalent macromolecular aggregates, which was induced by the addition of water to solutions of lecithin in organic solvents, was accompanied by specific spectroscopic changes. Systems containing the synthetic short-chain lecithins, 1,2-hexanoyl-, 1,2-diheptanoyl-, 1,2-dioctanoyl-, and 1,2-dinonaoyl-sn-glycero-3-phosphatidylcholines were used as models for the long-chain lecithins, soybean phosphatidylcholine and palmitoyl-oleoyl-phosphatidylcholine. All the molecules studied had asymmetric centres, formed reverse micelles under appropriate conditions, and, while both the long-chain lecithins also formed gels, none of the short-chain molecules did. As well as having CD spectra that were simpler to interpret, spectroscopic observations on solutions of the short-chain lecithins could be carried out over a large water content range. The ester chromophore of these compounds was shown to be highly sensitive to variation in both the solvent environment and the temperature, and components of both direct solvent effects and conformational change upon the addition of water were detected in the spectra. The spectra of the longer chain lecithins were complicated by the presence of double bonds although, here again, it was found that significant changes occurred as the water content increased, as monitored by the ester chromophore. However, no specific effect that could be ascribed to gelation alone was detected. The overall picture that emerged was that the ester chromophore of anhydrous micelles gave rise to a specific negative band in the CD spectrum (λ_max ≈ 210 nm) whereas a positive CD signal (λ_max ≈ 233 nm) was associated with the same chromophore in filled (i.e., hydrated) micelles. The two signals correspond to two different conformational states of the lecithin molecule, the hydrated state being not only more conformationally restricted but also providing a less polar environment for the ester groups, while the addition of water to the system shifts the conformational equilibrium. These observations have been interpreted as showing that only a limited range of lecithin conformation is compatible with the formation of the micellar structure and that it is this constraint, together with those introduced by the overall geometry of the aggregated state, that gives rise to the changes observed in the CD spectrum.     

Solvation of the folding-transition state in Pseudomonas aeruginosa azurin is modulated by metal: Solvation of azurin's folding nucleus

The role of water in protein folding, specifically its presence or not in the transition-state structure, is an unsolved question. There are two common classes of folding-transition states: diffuse transition states, in which almost all side chains have similar, rather low phi (phi) values, and polarized transition states, which instead display distinct substructures with very high phi-values. Apo-and zinc-forms of Pseudomonas aeruginosa azurin both fold in two-state equilibrium and kinetic reactions; while the apo-form exhibits a polarized transition state, the zinc form entails a diffuse, moving transition state. To examine the presence of water in these two types of folding-transition states, we probed the equilibrium and kinetic consequences of replacing core valines with isosteric threonines at six positions in azurin. In contrast to regular hydrophobic-to-alanine phi-value analysis, valine-to-threonine mutations do not disrupt the core packing but stabilize the unfolded state and can be used to assess the degree of solvation in the folding-transition state upon combination with regular phi-values. We find that the transition state for folding of apo-azurin appears completely dry, while that for zinc-azurin involves partially formed interactions that engage water molecules. This distinct difference between the apo-and holo-folding nuclei can be rationalized in terms of the shape of the free-energy barrier.