A quantum chemical survey of metalloporphyrin-nitrosyl linkage isomers: insights into the observation of multiple FeNO conformations in a recent crystallographic determination of nitrophorin 4

Using density functional theory-based geometry optimizations, we have searched for eta(1)-NO, eta(1)-ON (isonitrosyl), and eta(2)-NO (side-on bound NO) linkage isomers of a number of metalloporphyrin-NO complexes, M(Por)(NO)(L), where Por = porphinato dianion, M = Mn(II), Fe(II), Fe(III), Ru(II), Ru(III), Co(II), and Rh(II), and L = no ligand, SMe, Ph, and imidazole. The eta(1)-NO isomer had the lowest energy in all cases, and the isonitrosyl isomer was also located as a higher energy potential energy minimum in a number of cases. The eta(2)-NO isomer was only located as a minimum for Mn(II) (L = no ligand), Fe(III) (L = no ligand), and Ru(III) (L = Ph, imidazole, pyrdine), suggesting that an [MNO](6) electron count is important for stabilization of the eta(2) mode of ligation. However, in the presence of axial ligands L, the side-on isomers of [FeNO](6) complexes were not stable and opened up to an unusual geometry where the FeN(O) and NO vectors were tilted in opposite directions relative to the heme normal. Exactly such a geometry, as well as a "normal" upright geometry, has been observed in a recent crystallographic determination of nitrophorin 4 (Nature Struct. Biol. 2000, 7, 551), a salivary protein from the blood-sucking insect Rhodnius prolixus. Together, the calculated and experimental result illustrate the extreme softness of the FeNO potential energy surface toward various forms of tilting and bending deformations.     

Solid state conformations of symmetrical aromatic biheterocycles: an X-ray crystallographic investigation

Accurate, low temperature X-ray crystal structure determinations show that 3,3'-biquinoline (6), 2,2'-biquinazoline (7), 2,2'-biquinoxaline (8), 2,2'-bibenzoxazole (10) and 2,2'-bibenzothiazole (11) all exist in the solid state in centrosymmetric, planar conformations that minimise their dipole moments and maximise both conjugation between the rings and various types of attractive intermolecular associations. In contrast, 4,4'-biquinazoline (9) and 1,1'-bibenzotriazole (12) display non-planar conformations due to repulsive intramolecular interactions.     

Communication between the active site and the allosteric site in class A beta-lactamases

Bacterial production of beta-lactamases, which hydrolyze beta-lactam type antibiotics, is a common antibiotic resistance mechanism. Antibiotic resistance is a high priority intervention area and one strategy to overcome resistance is to administer antibiotics with beta-lactamase inhibitors in the treatment of infectious diseases. Unfortunately, beta-lactamases are evolving at a rapid pace with new inhibitor resistant mutants emerging every day, driving the design and development of novel beta-lactamase inhibitors. Here, we examined the inhibitor recognition mechanism of two common beta-lactamases using molecular dynamics simulations. Binding of beta-lactamase inhibitor protein (BLIP) caused changes in the flexibility of regions away from the binding site. One of these regions was the H10 helix, which was previously identified to form a lid over an allosteric inhibitor binding site. Closer examination of the H10 helix using sequence and structure comparisons with other beta-lactamases revealed the presence of a highly conserved Trp229 residue, which forms a stacking interaction with two conserved proline residues. Molecular dynamics simulations on the Trp229Ala mutants of TEM-1 and SHV-1 resulted in decreased stability in the apo form, possibly due to loss of the stacking interaction as a result of the mutation. The mutant TEM-1 beta-lactamase had higher H10 fluctuations in the presence of BLIP, higher affinity to BLIP and higher cross-correlations with BLIP. Our results suggest that the H10 helix and specifically W229 are important modulators of the allosteric communication between the active site and the allosteric site.     

Chromophoric spin-labeled beta-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C beta-lactamases

The chromophoric spin-label substrate 6-N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M(-1) cm(-1) at 275 nm compared to 670 M(-1) cm(-1) at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/KM, determined under initial velocity conditions, were 637 +/- 36 s(-1) and 13.8 +/- 1.4 x 10(6) M(-1) s(-1), respectively, for hydrolysis catalyzed by TEM-1 beta-lactamase of E. coli, and 0.5 +/- 0.04 s(-1) and 3.9 +/- 0.4 x 10(4) M(-1) s(-1) for hydrolysis catalyzed by the beta-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 beta-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H2O (30:70, v:v) cryosolvent mixtures buffered to pH* 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 degrees C was > or = 3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 beta-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme.     

Role of protein flexibility in enzymatic catalysis: quantum mechanical-molecular mechanical study of the deacylation reaction in class A beta-lactamases

We present a theoretical study of a mechanism for the hydrolysis of the acyl-enzyme complex formed by a class A beta-lactamase (TEM1) and an antibiotic (penicillanate), as a part of the process of antibiotic's inactivation by this type of enzymes. In the presented mechanism the carboxylate group of a particular residue (Glu166) activates a water molecule, accepting one of its protons, and afterward transfers this proton directly to the acylated serine residue (Ser70). In our study we employed a quantum mechanics (AM1)-molecular mechanics partition scheme (QM/MM) where all the atoms of the system were allowed to relax. For this purpose we used the GRACE procedure in which part of the system is used to define the Hessian matrix while the rest is relaxed at each step of the stationary structures search. By use of this computational scheme, the hydrolysis of the acyl-enzyme is described as a three-step process: The first step corresponds to the proton transfer from the hydrolytic water molecule to the carboxylate group of Glu166 and the subsequent formation of a tetrahedral adduct as a consequence of the attack of this activated water molecule to the carbonyl carbon atom of the beta-lactam. In the second step, the acyl-enzyme bond is broken, obtaining a negatively charged Ser70. In the last step this residue is protonated by means of a direct proton transfer from Glu166. The large mobility of Glu166, a residue that is placed in a Ohms-loop, is essential to facilitate this mechanism. The geometry of the acyl-enzyme complex shows a large distance between Glu166 and Ser70 and thus, if protein coordinates were kept frozen during the reaction path, it would be difficult to get a direct proton transfer between these two residues. This computational study shows how a flexible treatment suggests the feasibility of a mechanism that could have been discounted on the basis of crystallographic positions.     

Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin

Herein, we present results from molecular dynamics MD simulations ( approximately 1 ns) of the TEM-1 beta-lactamase in aqueous solution. Both the free form of the enzyme and its complex with benzylpenicillin were studied. During the simulation of the free enzyme, the conformation of the Omega loop and the interresidue contacts defining the complex H-bond network in the active site were quite stable. Most interestingly, the water molecule connecting Glu166 and Ser70 does not exchange with bulk solvent, emphasizing its structural and catalytic relevance. In the presence of the substrate, Ser130, Ser235, and Arg244 directly interact with the beta-lactam carboxylate via H-bonds, whereas the Lys234 ammonium group has only an electrostatic influence. These interactions together with other specific contacts result in a very short distance ( approximately 3 A) between the attacking hydroxyl group of Ser70 and the beta-lactam ring carbonyl group, which is a favorable orientation for nucleophilic attack. Our simulations also gave insight into the possible pathways for proton abstraction from the Ser70 hydroxyl group. We propose that either the Glu166 carboxylate-Wat1 or the substrate carboxylate-Ser130 moieties could abstract a proton from the nucleophilic Ser70.     

A coordination polymer of cobalt(II)-glutarate: two-dimensional interlocking structure by dicarboxylate ligands with two different conformations

A novel Co-glutarate, Co[O(2)C(CH(2))(3)CO(2)] (1), was synthesized as single crystals by the hydrothermal reaction of CoCl(2) with glutaric acid in the presence of KOH and characterized by single-crystal X-ray diffraction analysis, TGA, IR, UV-vis reflectance spectrometry, and SQUID measurements. The dark purple Co-glutarate crystallizes in the monoclinic system in the space group P2/c, with a = 14.002(3) A, b = 4.8064(10) A, c = 9.274(3) A, beta = 90.5(2)degrees, and Z = 4. The Co(2+) centers are tetrahedrally coordinated to four oxygen atoms from the dicarboxylate ligands. The anhydrous-pillared three-dimensional structure consists of infinite Co-CO(2)-Co inorganic layers, which are stacked by the coordinated glutarate alkyl chain along the a-axis. There are two different conformations for glutarate ligands, i.e., the gauche- and the anti-forms. These ligands reside between the inorganic layers alternatively to separate each layer by 7.01 A (gauche) and 6.99 A (anti). Magnetic measurement reveals that the predominant magnetic interactions are antiferromagnetic below 14 K.     

Sesquiterpenoids—27: X-ray crystallographic analysis of istanbulin-B,A 1-oxo-eremophilenolide

The stereochemistry of istanbulin-B has been defined by X-ray crystal-structure analysis. Rings A and B are transfused, with the Me groups at C(4) and C(5) cis. The α,β-unsaturated,γ -lactone ring is essentially planar. Crystals of istanbulin-B are orthorhombic, space group P2₁2₁,2₁, with a = 6.729(2), b = 13.447(3), c = 14.721(3)Â,and Z = 4. The crystal structure was determined by direct phasing and the atomic parameters were subsequently adjusted by least-squares calculations that converged at R 38% over 1179 diffractometer |F_a| values     

Relationship between chiroptical properties, structural changes and interactions in enzymes: a computational study on beta-lactamases from class A

Enzyme functions such as catalysis, binding and regulation are directly related to a variety of conformational changes. A sensitive and useful method for their investigation is circular dichroism (CD) and a rotational strength (R) is its fundamental characteristic. In this study, we show how the sensitivity of the mechanisms of rotational strengths to important conformational changes depends on the chromophore environment in two beta-lactamases from class A (from Escherichia coli and B. licheniformis). Rotational strengths have been calculated using the matrix method and including the effects of local environment (LE). X-ray structures (of protein components) of several enzyme-ligand complexes from the catalytic cycle of the TEM-1 enzyme and for both crystallographic monomers of the enzyme from B. licheniformis were used. An analysis of the relative degree of perturbation of the rotational strengths upon local interactions is performed.     

DME构象的ADF研究

用ＡＤＦ方法对游离状态下的１,２－二甲氧基乙烷（ＤＭＥ）的构象进行了研究。结果表明,能量最低的３种构象ｔｇｇ,’ｔｇｔ,ｔｔｔ的能量相近,其中ｔｔｔ不是能量最低的构象,而且说明ＤＭＥ在气态、液态、固态和游离状态下分别采用哪种构象为最优构象,除了与构象的能量有关外,还受分子间相互作用及分子的对称性是否适合于紧密堆积的影响。     

1-Aminoadamantane as guest molecule in dodecasil 1H: an X-ray crystallographic study

Dodecasil 1H, 34SiO₂ · 3M¹² · 2M¹² · 1M²⁰ with M¹², M¹²=N₂ and M²⁰=1-aminoadamantane, is hexagonal witha=13.825(2) Å,c=11.189(2) Å and crystallizes in space groupP6/mmm. With 767 unique reflexions the structure has been refined to a weighted reliability factorR _w =0.054. The three-dimensional four-connected host framework is built by corner sharing [SiO₄] tetrahedra and shows three types of cagelike voids, [5¹²] cages, [4³5⁶6³] cages and [5¹²6⁸] cages, the latter housing the 1-aminoadamantane guest molecule. Difference Fourier synthesis (obs)-(calc(Si,O)) delineate the guest molecules within the different types of cage. Residual electron densities reveal positional disorder of the 1-aminoadamantane guest molecule. Four crystallographically different preferred orientations for the 1-aminoadamantane guest molecule are found.     

Synthesis and structure of two tetranuclear osmium carbonyl isotopomers: a crystallographic isotope effect

A synthetic route to [Os4(mu-H)(mu-OH)(mu-CO)(CO)12] ( 1) has been devised through the activation of [Os4(CO)14] with Me3NO. The pyrolysis and photolysis of the reactant in the presence of a trace amount of water produces 1 in low yield. The solid-state structure of [Os4(mu-H)(mu-OH)(mu-CO)(CO)12 x H2O] (1 x H2O) reveals a butterfly Os4 skeleton with bridging H, OH and CO ligands as well as hydrogen-bonded molecules of water in the crystal lattice. A low-temperature 13C{1H} NMR spectroscopic study revealed a merry-go-round exchange of CO ligands around the Os3 plane containing the asymmetric bridging CO. The exposure of 1 x H2O to D2O yielded [Os4(mu-H)(mu-OD)(mu-CO)(CO)12]2. Although the solid-state, intramolecular structure of 2 closely matched that of 1 x H2O, the intermolecular structure did not: its crystal lattice contained no water of crystallization, a previously unreported crystallographic isotope effect.     

Azolium-linked cyclophanes: a comprehensive examination of conformations by 1H NMR spectroscopy and structural studies

The synthesis and characterization of a series of azolium-linked cyclophanes are reported. The cyclophanes consist of two azolium groups (17 examples) or three imidazolium groups (1 example) linked to two benzenoid units (benzene, naphthalene, p-xylene, mesitylene, 1,2,3,4- and 1,2,4,5-tetramethylbenzene, 2,6-pyridine, and p-tert-butylphenol) via methylene groups. Cyclophanes containing ortho-, meta-, and para-substitution patterns in the benzenoid units were examined. The conformations of the cyclophanes were examined in solution by variable-temperature NMR studies and in the solid state by crystallographic studies. The p-cyclophanes and mesitylene-based m- and o/m-cyclophanes are rigid on the NMR time scale, as indicated by sharp (1)H NMR spectra at all accessible temperatures. The non-mesitylene-based m-cyclophanes and the o-cyclophanes are fluxional on the NMR time scale at high temperatures, but in most cases, specific conformations can be "frozen out" at low temperatures. Many structures deduced from solution studies were consistent with those in the solid state.     

A model for describing the conformations of flexible 6-membered rings—I : The non-chair conformations

An empirical model for calculating the torsional angles for flexible 6-membered rings is presented in terms of three independent parameters, two geometrical and one pseudorotation angle. The rings are classified according to four estimators, the fit of the model depending upon their values. Equations are given for defining any conformation by a point in a 2-dimensional pathway. Some examples have been examined in the light of this model.     

Ring conformations of d-glucose derivatives possessing two bulky silyl protecting groups at the 3,4-positions; the first observation of a stable full-axial chair conformer without bridge structures

The ring conformations of 3,4-bis-O-tert-butyldimethylsilyl- and 3,4-bis-O-tert-butyldiphenylsilyl-d-glucopyranoses as well as the corresponding phenyl 1-thio-d-glucopyranosides were investigated. Observations showed that the introduction of the two tert-butyldiphenylsilyl groups can flip the pyranose-ring into the ¹C₄ conformation possessing more axial substituents. All the substituents of the 3,4-bis-O-tert-butyldiphenylsilyl-β-d-glucopyranose were axially oriented.     

Twisted amides: X-ray crystallographic and theoretical study of two acylated glycolurils with aromatic substituents

X-ray crystallography and theoretical analysis were applied to explore the molecular basis for the efficient and selective Claisen-like condensations of diacylglycolurils. The crystal structures of 1-acetyl-6-benzoyl-3,4,7,8-tetramethylglycoluril (4b), and of 1-(3′-oxo-3′-phenylpropionyl)-3,4,7,8-tetramethylglycoluril (5b), the product of base-promoted intramolecular condensation of 4b, were obtained by X-ray diffraction. The acetyl (Ac) group in 4b is essentially coplanar with the attached tetrahydroimidazolone ring of the glycoluril core (τ=7°), while the benzoyl (Bz) group is twisted by τ=45° relative to a plane through the ring to which it is bonded. Product 5b contains a flat amide (τ=7°). Ab initio energy optimizations of the experimental structures for 4b and 5b give optimized geometries which are not dramatically altered, suggesting that crystal packing effects are small. An atoms-in-molecules study of the delocalization of the Fermi hole reveals that electrons in the Bz C=O group of 4b are delocalized into the phenyl ring as well as into the urea moiety of the glycoluril core. This effect stabilizes the Bz over the Ac carbonyl group, and accounts for selective twisting of the Bz group. The Laplacian of the electron density reveals a non-bonded valence shell charge concentration at O of the Ac group, corresponding to a lone-pair region, aligned with a charge depletion in the valence shell of the Bz C=O carbon [(C15–O16C18)=113°]. The angle of approach [(O16C18=O19)] is 100°, equal to the angle for ideal nucleophilic attack on a carbonyl group. Oxygen atom O16 is thus poised to attack C18; only the O16C18 distance (3.248 Å) seems to prevent reaction. These results suggest that the same distance restraint may prevent O-acylation in the enolate intermediate 6b derived from4b. By contrast, the transition state for C-acylation, leading from 6b towards product 5b requires a different geometry, which may explain the observed selectivity for C-acylation in this enolate. The results show that, as 4b is converted to 5b, amide torsional strain is relieved, which may account for the high reactivity of 4b and the efficiency and irreversibility of this condensation process. This study provides a starting point for quantitative correlation of substrate structure in diacylglycolurils with kinetic data for the rearrangement reaction.     

The two components of the crystallographic transition in VO2

Two distinguishable mechanisms of the monoclinic-to-tetragonal transition in VO₂ are identified: an antiferroelectric-to-paraelectric transition at a temperature T_t as well as a change from homopolar to metallic VV bonding at a temperature T_t′. In pure VO₂ at atmospheric pressure, the two transitions occur at the same temperature, T_t′ = T_t = 340°K. However, a T_t′ < T_t may be induced by atomic substitutions; and in the intermediate temperature range the structure is orthorhombic, the antiferroelectric distortions being somewhat different in the absence of homopolar VV bonding. From energy-band considerations, the semiconductor-to-metal transition is to be associated with the transition at T_t; but below T_t′ the semiconducting energy gap should be larger and the charge-carrier mobilities should be smaller. The existence of two transition temperatures in doped VO₂ is distinguished from the claim of two transition temperatures in the Magnéli phases V_nO_2n−1. In this latter case, the appearance of two transitions reflects a two-phase region consisting of two adjoining Magnéli phases.