OH Group Of Side Chain Research Articles

NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups.

Hydrogen bonds between protein side-chain hydroxyl (OH) and phosphate groups are one of the most common types of intermolecular hydrogen bonds in protein-DNA/RNA complexes. Using NMR spectroscopy, we identified and characterized the hydrogen bonds between tyrosine side-chain OH and DNA phosphate groups in a protein-DNA complex. These OH groups exhibited relatively slow hydrogen-exchange rates and sizable scalar couplings between hydroxyl 1H and DNA phosphate 31P nuclei across the hydrogen bonds. Information about intermolecular hydrogen bonds facilitates investigations of the DNA/RNA recognition by the protein.

Investigating the behaviors of corticosterone hormone in different solvents by using DFT calculations and experimental data

In this work, structural, electronic, topological and vibrational properties of corticosterone hormone have been investigated in aqueous, ethanol and methanol solutions by using DFT calculations and experimental available infrared, attenuated total reflectance (ATR), Raman and Ultraviolet spectra. The properties predicted in the different solvents at the B3LYP/6-31G* level of theory were compared with those obtained in gas phase and, with others reported for steroids species at the same level of theory. The universal solvation model has evidenced higher solvation energy for corticosterone in aqueous solution and a higher value in methanol, as compared with the corresponding values to equilenin, equilin and estrone steroids in the same medium. Higher Mulliken charges on O atoms of C=O group of side chain are observed in the three solvents than the corresponding to C=O group of ring A while the MK charges on O atoms of OH group of ring C present higher values than the corresponding to O atoms of OH group of side chain. The natural bond orbital (NBO) studies have revealed a low stability of corticosterone in aqueous solution, as compared with the values in ethanol and methanol solutions, in total agreement with the higher solvation energy and dipole moment in this medium. On the other hand, the atoms in molecules (AIM) analyses support the lower stabilities of corticosterone in the three solutions because only five H bonds interactions different from of gas phase where six interactions are observed. The gap values suggests that corticosterone is most reactive in aqueous solution than the other solutions, as supported by the low stability and higher solvation energy and dipole moment values in this medium. This study shows clearly that the steroid species most reactive, equilenin and corticosterone, are characterized by a high global electrophilicity index value and low nucleophilicity index. Reasonable correlations in the predicted IR, Raman and UV spectra were observed, as compared with the corresponding experimental ones. Additionally, the complete vibrational assignments of all 159-vibration modes of corticosterone together with the harmonic force fields and force constants in the different media are for the first time presented.

Acetylation of Bombyx mori silk fibroin and their characterization in the dry and hydrated states using 13C solid-state NMR

Acetylation of Bombyx mori silk fibroin (SF) was accomplished by chemical reaction of the side chain OH groups in Ser and Tyr residues with acetic anhydrate to increase hydrophobic character of SF. A combination of three kinds of 13C solid-state NMR techniques was used to elucidate the effect of acetylation in the dry and hydrated states for [3-13C]Ser, [3-13C]Tyr and [3-13C]Ala enriched-SF powder. The mobilities of Tyr and Ala residues in the amorphous region of acetylated 13C-labeled SF powder increased slightly and only very small amounts of the Ala residue with high mobility was observed by hydration. On the other hand, there are essentially no effect of water on the β-sheet region of these residues and acetylated Ser residues. A similar tendency toward the effect of hydration for acetylated SF powder was observed for acetylated SF fiber. The remarkable improvement of the dimensional stability in water was attained although the tensile strengths of fibers were slightly lower by the acetylation of SF fiber. Thus, acetylation proved very effective to achieve water-proofing of SF materials and the effect of acetylation on the local structure and dynamics of SF could be clarified using 13C solid-state NMR.

Quantitative chiral analysis of amino acids in solution using enantiomer-selective photodissociation of cold gas-phase tryptophan via chiral recognition

To explore the origin of biomolecule homochirality in interstellar molecular clouds, enantiomer-selective photodissociation via chiral recognition between amino acids in the gas phase was examined using a tandem mass spectrometer containing an electrospray ionization source and a cold ion trap. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of sodiated l-tryptophan ion, Na+(l-Trp), with an amino acid such as serine (Ser), threonine (Thr), or alanine (Ala) were obtained by the photo-excitation of l-Trp in the noncovalent complexes. Dissociation of l-Trp via CO2 loss occurred when it was noncovalently complexed with d-Ser or d-Thr in the presence of Na+. For the l-enantiomers, the energy absorbed by l-Trp was released through evaporation of l-Ser or l-Thr, and dissociation of the amino acids was suppressed. In contrast, the enantiomer-selective phenomenon was not observed in the noncovalent complex with Ala, suggesting that a side-chain OH group plays an important role in chiral recognition and enantiomer-selective photodissociation. The enantiomer-selective photodissociation was applied to the quantitative chiral analysis of amino acids. The enantiomeric excess of Ser and Thr in solution could be determined by measuring the relative abundance ratio of the enantiomer-selective photodissociation of Trp to amino acid evaporation in a single photodissociation mass spectrum obtained by photo-excitation of l-Trp used as a chiral probe in cold gas-phase noncovalent complexes with the analyte amino acids, and by referring to the linear relationships established in this work.

Introduction of a Hydrogen Bond between Phylloquinone PhQA and a Threonine Side-Chain OH Group in Photosystem I

The phylloquinone acceptor PhQ(A) in photosystem I binds to the protein through a single H-bond to the backbone nitrogen of PsaA-L722. Here, we investigate the effect of this H-bond on the electron transfer (ET) kinetics by substituting threonine for PsaA-L722. Room temperature spin-polarized transient EPR measurements show that in the PsaA-L722T mutant, the rate of PhQ(A)(-) to F(X) ET increases and the hyperfine coupling to the 2-methyl group of PhQ(A) is much larger than in the wild type. Molecular dynamics simulations and ONIOM type electronic structure calculations indicate that it is possible for the OH group of the Thr side chain to form an H-bond to the carbonyl oxygen atom, O(4) of the phylloquinone, and that this results in an increase in the 2-methyl hyperfine couplings as observed in the transient EPR data. The Arrhenius plot of the PhQ(A)(-) to F(X) ET in the PsaA-L722T mutant suggests that the increased rate is probably the result of a slight change in the electronic coupling between PhQ(A)(-) and F(X). The strong deviation from Arrhenius behavior observed at ∼200 K can be reproduced using a semiclassical model, which takes the zero-point energy of the mode coupled to the ET into account. However, since the change in slope of the Arrhenius plot occurs at the protein glass transition temperature, it is argued that it could be the result of a change in the protein relaxation dynamics at this temperature rather than quantum mechanical effects.

Modified synthesis scheme for N,N´-dimethyl-N,N´-dioctyl-2,(2´-hexyloxyethyl) malonamide (DMDOHEMA) and its comparison with proposed solvents for actinide partitioning

Abstract N,N´-dimethyl-N,N´-dioctyl-2,(2´-hexyloxyethyl) malonamide (DMDOHEMA) has been synthesized by a relatively simpler route with a better yield than the conventional procedures for the synthesis of pentaalkyl substituted diamides. The proposed route replaces the use of acid chlorides and brominating agents (corrosive in nature) by acid diester and p-toluene sulphonyl (tosyl) chloride, respectively. The later easily replaces hydrogen from primary OH group of the 3-oxanonyl side chain and relatively less corrosive. The synthesized product has been tested for the extraction behavior of 241Am, Np, Pu as pure tracers as well as under Pressurized Heavy Water Reactor (PHWR) Simulated High-Level Waste (SHLW) conditions. The stoichiometries of extracted species of Np(IV), Pu(IV), and Am(III) from 3 M HNO3 using varying concentrations of DMDOHEMA in n-dodecane has been determined. The effect of the nature of mineral acid (viz. HCl, HNO3, and HClO4) on the extraction of Am(III) has also been investigated employing DMDOHEMA and N,N´-dimethyl-N,N´-dibutyl-tetradecyl malonamide (DMDBTDMA) as extractants and explained in terms of the aggregation behavior of diamides. The performance of DMDOHEMA has been evaluated vis-à-vis other proposed extractants for actinide partitioning under PHWR-SHLW conditions.

IR spectra of stigmastane series brassinosteroids differing in configuration and number of diol groups

IR spectra of steroid phytohormones of the stigmastane series (22R, 23R)-28-homocastasterone and (22R,23R)-28-homosecasterol and their isomers (22S,23S)-28-homocastasterone and (22S,23S)-28-homosecasterol have been analyzed. The 28-homocastasterone molecule contains diol groups in ring A and in the side chain whereas that of 28-homosecasterol has one diol group in the side chain. The lack of two OH groups in ring A of homosecasterol compared to homocastasterone results in the appearance of stretching vibrational bands of H-C= (ν max = 3025 cm -1 ) and -C=C (ν max = 1656 cm -1 ) groups of ring A. Substantial changes are observed in the area of OH stretching vibrations. Homocastasterones pressed in KBr possess twice as many OH groups as homosecasterols such that absorption band total intensities in IR spectra of both isomers caused by H-bonds of the diol groups in the side chain amount to 65% whereas the share of the 2α,3α group is only 35% of the total intensity. Hence the contribution from the side-chain OH groups of the studied brassinosteroids to the integral optical density of the bands exceeds that from the ring-A OH groups. In dilute CHCl3 solutions of the brassinosteroids, the conformations of the brassinosteroid side chains are not the same. As a result, intramolecular H-bonds of different energy are created. The optical density D max in band maxima of free OH groups for homocastasterones is three times higher than that for the corresponding band maxima of homosecasterol. This implies that D max for bands of free OH groups of the homocastasterone ring-A diol group is greater, in contrast with the relatively greater D max for bands of homosecasterol side-chain OH groups bound by an intermolecular H-bond. The homocastasterone diol groups also form intramolecular Hbonds more actively. The lack of the diol group in ring A of the homosecasterols does not affect the frequencies of the C=O stretching vibrations. This leads to the conclusion that the C=O group forms intermolecular H-bonds only with the side-chain OH groups of brassinosteroids pressed in KBr.

Effect of pyridyl nitrogen on the conformational landscape of 7-azaserotonin: A computational study

The conformational topology of gaseous neutral 7-azaserotonin has been investigated by employing systematic ab initio calculations. The whole conformational landscape has been explored by varying four dihedral angles which define the position of ethyl amine side chain and phenolic OH group with respect to the 7-azaindole plane. A total of 22 local minima have been located by geometry optimization of 216 possible trial structures at the B3LYP/6-31+G * level of theory. With the exception of a few conformers, in most cases the OH- syn conformers were more stable than their OH- anti counterparts. Vibrational frequency analysis for all 22 conformers computed at B3LYP/6-31+G * shows some interesting features in the pyrrole and pyridine C H stretches. In some of the conformers the presence of intramolecular blue shifted H-bonding is confirmed using the atoms in molecules (AIM) analysis. The AIM analysis explains the differences in the relative energy order of various conformers compared to that observed in the case of serotonin. It also explains the behavior of the pyrrole and pyridine C H stretches observed for some of the conformers. The conformational distribution of 7-azaserotonin at various temperatures is computed based on simple thermodynamic principle. At lower temperature of about 100 K only six conformers were significantly populated according to their electronic energies while at higher temperature of about 400 K the populations were determined by their vibrational partition functions.

Complexation of boric acid with vitamin C

Mono-chelate (1 : 1) and bis-chelate (1 : 2) anionic complexes of boric acid with vitamin C (L-ascorbic acid, H2A) were isolated from aqueous solutions in salt form with Li+, Na+ and Ca2+ ions. The complexes were characterized by FTIR, 13C and 11B MAS (magic angle spinning) NMR techniques. The spectral data agreed with the calculated structures that H2A complexes with boric acid through its cis-enediol groups by forming five-membered chelate rings. Side-chain OH groups do not participate in complexation as corroborated by the results of the test experiments conducted with iso-propylideneascorbic acid (i-H2A) where the side chain is blocked. Empirical relations, that can be used as diagnostics for the 1 : 1 and 1 : 2 ascorbatoborate complexes, were derived from the observed chemical shift values. Bis-chelate complexes were found to have higher thermal and hydrolytic stabilities than their mono-chelate homologs. The effect of the cation on the stabilization of the complexes was also investigated. The observed relative stability of the 1 : 1 Na–ascorbatoborate complex with respect to the analogous Ca complex, correlated with the recent reports about the role of alkali metal ions in the stabilization of ribose in the prebiotic world.

Roles of adenine anchoring and ion pairing at the coenzyme B12-binding site in diol dehydratase catalysis

The X-ray structure of the diol dehydratase-adeninylpentylcobalamin complex revealed that the adenine moiety of adenosylcobalamin is anchored in the adenine-binding pocket of the enzyme by hydrogen bonding of N3 with the side chain OH group of Seralpha224, and of 6-NH(2), N1 and N7 with main chain amide groups of other residues. A salt bridge is formed between the epsilon-NH(2) group of Lysbeta135 and the phosphate group of cobalamin. To assess the importance of adenine anchoring and ion pairing, Seralpha224 and Lysbeta135 mutants of diol dehydratase were prepared, and their catalytic properties investigated. The Salpha224A, Salpha224N and Kbeta135E mutants were 19-2% as active as the wild-type enzyme, whereas the Kbeta135A, Kbeta135Q and Kbeta135R mutants retained 58-76% of the wild-type activity. The presence of a positive charge at the beta135 residue increased the affinity for cobalamins but was not essential for catalysis, and the introduction of a negative charge there prevented the enzyme-cobalamin interaction. The Salpha224A and Salpha224N mutants showed a k(cat)/k(inact) value that was less than 2% that of the wild-type, whereas for Lysbeta135 mutants this value was in the range 25-75%, except for the Kbeta135E mutant (7%). Unlike the wild-type holoenzyme, the Salpha224N and Salpha224A holoenzymes showed very low susceptibility to oxygen in the absence of substrate. These findings suggest that Seralpha224 is important for cobalt-carbon bond activation and for preventing the enzyme from being inactivated. Upon inactivation of the Salpha224A holoenzyme during catalysis, cob(II)alamin accumulated, and a trace of doublet signal due to an organic radical disappeared in EPR. 5'-Deoxyadenosine was formed from the adenosyl group, and the apoenzyme itself was not damaged. This inactivation was thus considered to be a mechanism-based one.

Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

An extremely low-field signal (at approximately 18 p.p.m.) in the (1)H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental (1)H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 A resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 A) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor-acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK(a) values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins.

2-(3-Hydroxypropyl)isoindoline-1,3-dione: competition among hydrogen-bond acceptors

The title compound, C(11)H(11)NO(3), has two molecules in the asymmetric unit, which differ in the orientation of their side-chain OH groups, allowing them to form intermolecular O-H...O hydrogen bonds to different acceptors. In one case, the acceptor is the OH group of the other molecule, and in the other case it is an imide O=C group. This is the first example in the N-substituted phthalimide series in which independent molecules have different types of acceptor. Molecular-orbital calculations place the greatest negative charge on the OH group.

Quantifying the Intrinsic Effects of Two Point Mutation Models of Pro-Pro-Pro Triamino Acid Diamide. A First-Principle Computational Study

Stabilities and conformational properties of two Pro --> Thr point mutation models were computed at the B3LYP/6-31G(d) level of theory for the parent triamino acid diamide Pro-Pro-Pro (HCO-Pro-Pro-Pro-NH2). Geometrical parameters for the amino acid sequences, used in the molecular orbital computations for Pro-Pro-Thr and Pro-Thr-Pro, were retrieved from the Protein Data Bank. Thermodynamic functions (S, H, G) were computed for the fully optimized geometries. To assess the stabilization energetics of these mutant models, relative to the parent Pro-Pro-Pro reference conformer epsilon(L) epsilon(L) gamma(L), isodesmic reactions were constructed to calculate DeltaS, DeltaH, and DeltaG. The importance of intramolecular hydrogen bonds involving the -OH group of the Thr side chain, which emerged after the point mutations, was also examined to determine the internal stabilization of these peptide models. This study describes an approach to analyzing a point mutation at the center of a peptide chain and compares its stability to that of a point mutation at a terminal end in a small peptide model.

Low-Calcemic, Highly Antiproliferative, 23-Oxa Ether Analogs of the Natural Hormone 1α,25-Dihydroxyvitamin D3: Design, Synthesis, and Preliminary Biological Evaluation

Eight new side-chain allylic, benzylic, and propargylic ether analogs of the natural hormone calcitriol have been rationally designed and easily synthesized. Three of these 23-oxa ether analogs lacking the typical side-chain OH group are more antiproliferative in vitro and desirably less calcemic in vivo than the natural hormone. One of these three 23-oxa analogs has transcriptional potency almost as high as that of calcitriol, even though it binds to the human vitamin D receptor only about 1% as well as calcitriol.

Quantifying the Intrinsic Effects of Two Point Mutation Models of Proline−Proline Diamino Acid Diamide: A First-Principle Computational Study

Two sites of a Pro-Pro diamide were subjected to individual Pro --> Thr point mutations. The parent diamide Pro-Pro as well as selected conformers of the Pro-Thr and Thr-Pro mutant models were subjected to molecular computations at the B3LYP/6-31G(d) level of theory. At the optimized geometries, thermodynamic functions (S, H, and G) were computed. In order to assess relative stabilities of the mutant models, isodesmic reactions were constructed to calculate DeltaS, DeltaH, and DeltaG, relative to the initial Pro-Pro state. The importance of intramolecular hydrogen bonds, involving the -OH group of the Thr side chain, which emerged after the point mutations were also examined. Our findings suggest a novel approach to analyzing the stability of point mutants in peptide models through the analysis of thermodynamic functions.

Competitive H-bonds in vacuo and in aqueous solution for N-protonated adrenaline and its monohydrated complexes

The conformational landscape of the N-protonated form of adrenaline (epinephrine in the U.S.) has been considered at both the B3LYP/6-31G* and 6-311++G** levels, with full geometry optimization in the gas phase and in aqueous solution, using the integral equation formalism for the polarizable continuum model (IEF-PCM). All stable orientations of the two catecholic hydroxy groups as well as the interconversion pathways between them have been taken into account. The dependence of the potential energy profile for the −[NH 2CH 3] + group rotation on the catechol ring and side-chain OH group orientation has been also examined. B3LYP/6-31G* stationary points have been confirmed with frequency calculations (at 310 K and 1 atm) allowing thermal corrections and IR spectra to be evaluated. Basis set effects do not alter the relative stability of the various forms that is maintained also when MP2 correlation corrections are included. The role of the internal structures either embedding in aqueous solution the conformers kept rigid at their in vacuo geometries or allowing the structure to relax has been examined at the IEF-PCM/B3LYP/6-31G* and 6-311++G** levels and compared to the IEF-PCM/MP2/6-31G* results. In vacuo the G1 conformers are favored with respect to the T and G2 ones, while in water the stability ordering changes, T becoming significantly more stable than both gauche forms. This occurs even for the gas-phase structures, including or not thermal corrections. The addition of a single water molecule to N-protonated adrenaline caused the intramolecular H-bond within the side chain to weaken till formation of two H-bonds with water. This fact, coupled to the strain relaxation, further stabilized the G1 and T conformers. The maximum intensity of the IR spectra increases in solution, especially for monohydrated adducts, where a significant red shift in the vibration of the NH involved in a H-bond to the water O is found.

Structural Scaffold of 18-Crown-6 Tetracarboxylic Acid for Optical Resolution of Chiral Amino Acid: X-Ray Crystal Analyses of Complexes of D- and L-Isomers of Serine and Glutamic Acid

(+)-18-crown-6 tetracarboxylic acid (18C6H4) has been used as a chiral selector for D/L-amino acids in HPLC, where L-isomer is usually eluted prior to D-isomer, except for the case of serine. To clarify why serine exhibits the reverse order for the elusion, the chiral interactions of D- and L-serines with (+)-18C6H4 were investigated by the X-ray single crystal analyses, together with the case of D- and L-glutamic acids, which exhibit the usual elution order in HPLC. The backbone structures (amino, Calpha-H and carboxyl groups) of these four amino acids showed the nearly same interaction with (+)-18C6H4 despite their different chirality. In contrast, the hydroxyl group of L-serine side chain formed a hydrogen bond with the carboxyl group of (+)-18C6H4, whereas such a interaction was not formed for the side chain of D-serine and D- and L-glutamic acids. Thus, it was shown that the exception of D/L-serine from the first elution rule of L-isomer in HPLC is due to the presence and absence of a hydrogen bond formation of its side chain OH group.

Model studies on p-hydroxybenzoate hydroxylase. The catalytic role of Arg-214 and Tyr-201 in the hydroxylation step.

A model C-(4a)-flavinhydroperoxide (FlHOOH) is described that contains the tricyclic isoalloxazine moiety, the C-4a-hydroperoxide functionality, and a beta-hydroxyethyl group to model the effect of the 2'-OH group of the ribityl side chain of native FADHOOH. The electronic structures of this reduced flavin (H(3)()Fl(red)()), its N1 anion (H(2)()Fl(red)()(-)()), oxidized flavin (HFl(ox)()), and FlHOOH have been fully optimized at the B3LYP/ 6-31+G(d,p) level of theory. This model C-4a-flavinhydroperoxide is used to describe the transition state for the key step in the paradigm aromatic hydroxylase, p-hydroxybenzoate hydroxylase (PHBH): the oxidation of p-hydroxybenzoate (p-OHB). The Tyrosine-201 residue in PHBH is modeled by phenol, and Arginine-214 is modeled by guanidine. Electrophilic aromatic substitution proceeds by an S(N)2-like attack of the aromatic sextet of p-OHB phenolate anion on the distal oxygen of FlHOOH 3. The transition structure for oxygen atom transfer is fully optimized [B3LYP/6-31+G(d,p)] and has a classical activation barrier of 24.9 kcal/mol. These data suggest that the role of the Tyr-201 is to orient the p-OHB substrate and to properly align it for the oxygen transfer step. Although the negatively charged phenolate oxygen does activate the C-3 carbon of p-OHB phenolate anion toward oxidation relative to ortho oxidation of the carboxylate anion, it appears that H-bonding the Tyr-201 residue to this phenolic oxygen stabilizes both the ground state (GS) and the transition state (TS) approximately equally and therefore plays only a minor role, if any, in lowering the activation barrier. Complexation of p-OHB with guanidine has only a modest effect upon the oxidation barriers. When the complex is in the form of a salt-bridge (10a), the barrier is only slightly reduced. When the TSs are placed in THF solvent (COSMO) with full geometry optimization, salt-bridge TS-A is slightly favored (DeltaDeltaE() = 2.3 kcal/mol).

Interplay of intra‐ and intermolecular H‐bonds for the addition of a water molecule to the neutral and N‐protonated forms of noradrenaline

AbstractThe conformational flexibility of noradrenaline in its N‐protonated and neutral forms was considered at the Hartree–Fock (HF)/6‐31G* level, taking into account the orientation of the two hydroxy groups located on the catechol ring and the interconversion pathways between their stable arrangements. The difference in stability among the various forms of N‐protonated noradrenaline was maintained including either more diffuse functions on the heteroatoms or Møller–Plesset second order (MP2) correlation corrections. The embedding in aqueous solution, in the polarizable continuum model framework, of the conformers kept rigid at their in vacuo geometries favored the T conformers with respect to the G ones at the HF level (for neutral noradrenaline at the MP2 level as well). The addition of a single water molecule to noradrenaline (either N‐protonated or not) caused the intramolecular H‐bond within the side chain to weaken until formation of one or two intermolecular H‐bonds with water. This fact, coupled to the intramolecular H‐bond strain relaxation, further stabilized the G1 and T conformers. Continuum solvation of the hydrated clusters of neutral noradrenaline favored significantly the Twater adducts at the HF level, but only slightly at the MP2 level, because of their large energy gap in vacuo with respect to G1water, even enhanced by MP2 geometry optimizations. The dependence of the potential energy profile for the NH2 group rotation on the catechol ring and side chain OH group orientation was examined in noradrenaline and compared to the trend shown by dopamine. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Redox thermodynamics of mutant forms of the rubredoxin from Clostridiumpasteurianum: identification of a stable FeIII(S-Cys)3(OH) centre in the C6S mutant

Redox thermodynamic data provide a detailed insight into control of the reduction potential E degrees' of the [Fe(S-Cys)4] site in rubredoxin. Mutant forms were studied in which specific structural changes were made in both the primary and secondary coordination spheres. Those changes have been probed by resonance Raman spectroscopy. The decrease of approximately 200 mV in E degrees' observed for the [Fe(S-Cys)3(O-Ser)]-/2- couples in the surface ligand mutants C9S and C42S is essentially enthalpic in origin and associated with the substitution of ligand thiolate by ligand olate. However, the pH dependence of the potentials below characteristic pKa(red) approximately equals 7 is an entropic contribution, plausibly associated with increased conformational flexibility induced by a longer Fe(II)-O(H)-Ser bond in the reduced form. The presence of a second surface Ser ligand in the new double mutant protein C9S/C42S affects the enthalpic term primarily for pH>pKa(red) > or = 9.3, but for pH<pKa(red) the entropic term again becomes significant. The available data for the internal ligand mutant C39S appear to follow those for the surface ligand mutants. A longer Fe(III)-O-Ser link in the oxidized form is expected from structural considerations and a smaller decrease of approximately 100 mV in E degrees' is observed for this particular [Fe(S-Cys)3(O-Ser)]/2- couple. The reduced form is particularly susceptible to hydrolysis with consequent irreversible electrochemistry, an apparent consequence of an even longer Fe(II)-O(H)-Ser bond. The second internal ligand mutant C6S exhibits starkly different behaviour. The cause was traced to the presence of a Fe(III)(S-Cys)3(OH)- centre in the oxidized form. Resonance Raman spectroscopy on 54Fe-, H2 18O- and D2O-enriched samples supports the presence of an iron hydroxyl group that donates a hydrogen bond to the OH group of the free S6 side chain and/or a cluster of bound water molecules. The thermodynamic parameters can then be rationalized in terms of the following processes: pH>pKa approximately 9: [Fe(III)(S-Cys)3(OH)]- + e- --> [Fe(II)(S-Cys)3(OH)]2-. pH<pKa: [Fe(III)(S-Cys)3(OH)]- +H+ e- --> [Fe(II)(S-Cys)3(OH2)]-.