Hysteresis in clay swelling induced by hydrogen bonding: accurate prediction of swelling states

We perform grand-canonical molecular simulations to study the molecular mechanism of clay swelling hysteresis as a function of the relative humidity. In particular, we focus on the transition from the one- to the two-layer hydrate and the influence of three types of counterions (Li+, Na+, and K+). Our results cover the experimental relative humidity region where swelling and shrinking usually occur. We show that the thermodynamic origin of swelling hysteresis is a free-energy barrier separating the layered hydrates. This free-energy barrier is dominated by breaking and formation of hydrogen bonds between and within water layers. This network of water molecules is similar for all counterions, but the positions of these counterions depend upon their size. The relatively large K+ counterions show more affinity for clay surface adsorption, which increases the free-energy barrier and inhibits swelling. On the other hand, the relatively small Li+ counterions are quite well-accommodated in the water network, and thereby, they can form a new swelling state with a basal spacing of approximately 13.5 A. This new swelling state is an alternative explanation for the widely accepted simultaneous occurrence of two or more swelling phases.     

Effect of aluminum on the nature of the iron species in Fe-SBA-15

We report the preparation of highly ordered mesoporous Fe-Al-SBA-15 with isolated extraframework Fe species under acidic conditions. The materials were characterized by means of UV resonance Raman spectroscopy, in conjunction with BET, XRD, TEM, UV-vis, H2-TPR, FT-IR, and 27Al MAS NMR spectroscopy. The addition of both Fe and Al to the synthesis gel of SBA-15 results in the formation of isolated extraframework Fe species located close to the framework Al ions and the Fe content an order of magnitude higher than that in Fe-SBA-15 synthesized without Al. The existence of anchored extraframework Fe species was confirmed by the presence of a strong absorption band at 270 nm, hydrogen reduction at relatively low temperature, and the presence of a resonance Raman band at 1140 cm(-1). The location of Fe in close proximity to framework Al nuclei is further supported by 27Al MAS NMR measurements. Two characteristic UV Raman bands at 510 cm(-1) and 1090 cm(-1) excited by 244-nm laser are assigned to Fe-O-Si symmetric and asymmetric stretching modes of isolated tetrahedral Fe ions in the silica framework for Fe-SBA-15. The resonance Raman band at 1140 cm(-1) excited by 325-nm laser is attributed to the asymmetric stretching mode of the isolated extraframework iron species in Fe-Al-SBA-15. The isolated Fe species close to framework Al species are stable in acidic HCl solution, whereas the majority of Fe species in Fe-SBA-15 can be easily removed.     

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Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin

Understanding the mechanisms by which beta-lactamases destroy beta-lactam antibiotics is potentially vital in developing effective therapies to overcome bacterial antibiotic resistance. Class A beta-lactamases are the most important and common type of these enzymes. A key process in the reaction mechanism of class A beta-lactamases is the acylation of the active site serine by the antibiotic. We have modeled the complete mechanism of acylation with benzylpenicillin, using a combined quantum mechanical and molecular mechanical (QM/MM) method (B3LYP/6-31G+(d)//AM1-CHARMM22). All active site residues directly involved in the reaction, and the substrate, were treated at the QM level, with reaction energies calculated at the hybrid density functional (B3LYP/6-31+Gd) level. Structures and interactions with the protein were modeled by the AM1-CHARMM22 QM/MM approach. Alternative reaction coordinates and mechanisms have been tested by calculating a number of potential energy surfaces for each step of the acylation mechanism. The results support a mechanism in which Glu166 acts as the general base. Glu166 deprotonates an intervening conserved water molecule, which in turn activates Ser70 for nucleophilic attack on the antibiotic. This formation of the tetrahedral intermediate is calculated to have the highest barrier of the chemical steps in acylation. Subsequently, the acylenzyme is formed with Ser130 as the proton donor to the antibiotic thiazolidine ring, and Lys73 as a proton shuttle residue. The presented mechanism is both structurally and energetically consistent with experimental data. The QM/MM energy barrier (B3LYP/ 6-31G+(d)//AM1-CHARMM22) for the enzymatic reaction of 9 kcal mol(-1) is consistent with the experimental activation energy of about 12 kcal mol(-1). The effects of essential catalytic residues have been investigated by decomposition analysis. The results demonstrate the importance of the "oxyanion hole" in stabilizing the transition state and the tetrahedral intermediate. In addition, Asn132 and a number of charged residues in the active site have been identified as being central to the stabilizing effect of the enzyme. These results will be potentially useful in the development of stable beta-lactam antibiotics and for the design of new inhibitors.     

Quantenmechanische Behandlung von tief liegenden elektronischen Zuständen des Ammonium-Radikals mit der Methode der Einzentrumentwicklung

Zusammenfassung Mit der Methode der Einzentrumentwicklung (OCE) werden der Grundzustand und einige tief liegende angeregte Zustände des NH₄-Radikals unter Verwendung einer minimalen Basis von wasserstoffartigen bzw. Slaterschen Funktionen berechnet. Zur Kontrolle der Brauchbarkeit der Modellrechnungen bei der Interpretation experimenteller Ergebnisse werden zusätzlich die Alkaliatome Lithium und Natrium behandelt. Es ergibt sich eine deutliche Uberlegenheit der Funktionen vom Slater-Typ. Das Ammoniumradikal erweist sich gegenüber Autoionisation als stabil, während der Grundzustand bezüglich des Zerfalls in NH₃+H in der Nähe der Stabilitätsgrenze liegt. Einige Eigenschaften von metallammoniakalischen Lösungen werden mit den hier vorgelegten Ergebnissen in Zusammenhang gebracht.

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OCE-calculations of the ground state and some low lying excited states of NH₄

The ground state and some low lying excited states of NH₄ are calculated using the one-center expansion method (OCE) with a minimum basis set of hydrogen- resp. Slater-type functions. To check the validity of the method calculations are done for the alkali atoms lithium and sodium; comparison with experimental results shows that Slater-type functions are much more suitable. NH₄ comes out to be stable against autoionization. Concerning the dissociation into NH₃+H the ground state of NH₄ is very close to the limit of stability. Some properties of solutions of metals in liquid ammonia are correlated with the presented results.

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Résumé Calcul de l'état fondamental et d'états excités inférieurs de NH₄ avec emploi d'une base minimale de fonctions hydrogénoïdes (ou de Slater) dans une méthode avec développement par rapport à un centre (OCE). Des calculs sont effectués sur les atomes de lithium et de sodium afin de tester la valeur de la méthode; la comparaison avec les résultats expérimentaux montre que les fonctions de Slater donnent de meilleurs résultats. NH₄ apparait comme stable par rapport à l'autoionisation. L'état fondamental de NH₄ est trés prés de la limite de stabilité en ce qui concerne la dissociation selon NH₃+H. Les résultats obtenus sont mis en rapport avec certaines propriétés des solutions métalliques dans l'ammoniac liquide.

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Für die Mlichkeit, die numerischen Rechnungen mit der elektronischen Rechenanlage CD 6600 im Regionalen Rechenzentrum der Universität Stuttgart ausführen zu dürfen, sind wir Herrn Prof. Dr. J. H. Argyris und der Deutschen Forschungsgemeinschaft zu Dank verpflichtet. Herrn Dr. H. Dorada von der Firma Control Data GmbH danken wir für tatkräftige Hilfe bei der Ausführung der numerischen Rechnungen. Einer von uns (W. Sarholz) dankt der Deutschen Forschungsgemeinschaft für finanzielle Unterstützung.