A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.     

Diastereoselective Spirocyclization of C-(Alkyloxycarbonyl)formimines of 2-Substituted 1HIndole-3-ethanamines (= Tryptamines): Basic Studies. 5th Communication on Indoles,Indolenines, and Indolines

C-(Alkoxycarbonyl)formimines of type 15–18 were derived from the 2-substituted tryptamines 2 , 9 , 10 , and 11 and transformed with tosyl chloride into tricyclic 3-spiroindoles of types 19–22 (Scheme 3). The influence of the homochiral alkoxy moieties A–D on the stereochemical outcome of this reaction was studied. Good-to-excellent diastereoselectivities were observed with the (?)-8-(phenylmenth-3-yl)oxy group ( B ) as homochiral auxiliary. The structures of the tricycles 4 , (2′R,3S)- 19B , and (2′S,3R) 20C were established by X-ray analysis, the structures of the others by NOE and CD studies, and by chemical correlation. Possibilities to explain the steric course of the spirocyclizations are discussed.     

Nordesferriferrithiocin. Comparative Coordination Chemistry of a Prospective Therapeutic Iron Chelating Agent(1)

Nordesferriferrithiocin, NDFFTH(2), is a derivative of the siderophore desferriferrithiocin, DFFTH(2), in which the methyl group is substituted by a hydrogen atom. Both compounds show high oral activity as possible drugs for the treatment of iron overload. While DFFTH(2) is significantly toxic, NDFFTH(2) exhibits a lower toxicity and offers a much better therapeutic window than other orally active iron chelators. In this study, complexes of DFFTH(2) and NDFFTH(2) with various trivalent metals have been synthesized and characterized. Five isomers (the maximum possible) have been observed in the case of [Co(DFFT)(2)](-) in solution, as proved by (1)H-NMR measurements. Although normally labile, complexes of Al(3+) ([Al(DFFT)(2)](-)) have been separated by HPLC. In general, DFFTH(2) forms kinetically inert complexes whereas complexes of NDFFTH(2) tend to isomerize quickly in solution, as indicated by CD spectroscopy of separated HPLC fractions of [Cr(NDFFT)(2)](-). The most stable isomers of the aluminum complexes of both ligands have been characterized by X-ray crystallography; K[Al(DFFT)(2)] crystallizes from methanol/diethyl ether in the orthorhombic space group P2(1)2(1)2 with a = 11.238(3) ?, b = 31.719(11) ?, c = 7.684(2) ?, V = 2739.2(24) ?(3), and Z = 4. This isomer has the mer-(N,O-Lambda)(S,S) configuration, while K[Al(NDFFT)(2)] crystallizes from methanol/diethyl ether in the space group P6(1) (a = 21.269(8) ?, c = 9.643(3) ?, V = 3777.8(42) ?(3), Z = 6) and has the same coordination geometry. The solution thermodynamics of the Al(3+), Ga(3+), and Fe(3+) complexes have been studied by spectrophotometric titration. The stability constants (log K) are 23.6(1), 29.2(3), and 31.04(3), respectively, for the DFFTH(2) complexes and 22.0(1), 27.8(2), and 29.09(3), respectively, for the NDFFTH(2) complexes. Cyclic voltammograms of both iron complexes have been recorded in water at a carbon disk working electrode and in DMF at a graphite working electrode. The reduction waves measured in DMF indicate no reversibility whereas in water a quasi-reversible reduction is observed. The reduction potentials (E(1/2)'s) in water are -166 mV for [Fe(DFFT)(2)](-) and -97 mV for [Fe(NDFFT)(2)](-) versus NHE. These potentials are well in the range for biological reductants, which makes possible an in vivo reduction mechanism for the iron removal from the siderophore.     

Vesicle Phases with Semipolar Additives

We examined the influence of semipolar additives on the phase behavior of mixed zwitterionic surfactant/consurfactant systems. It is shown that in these systems with increasing concentration esters like hexylacetate (HA) and ketones like hexylmethylketone (HMK) can behave both like consurfactants and like hydrocarbons. In solutions of 200 mM tetradecyldimethylamineoxide (TDMAO)/cosurfactant the additives cause first a phase transformation from the micellar L(1) phase to a lamellar L(alpha) phase. Upon further increasing concentration, the L(alpha) phase is transformed into a microemulsion. The L(alpha) phase consists of densely packed multilamellar vesicles. The vesicles are shown by electron microscopy. The multilamellar character of the vesicles is also reflected in the conductivity of the phase. It is up to 10 times lower than the conductivity of the L(1) phase. In some systems the vesicles are transformed on rest into a multidomain stacked L(alpha) phase. It is furthermore demonstrated that the two-phase L(1)/L(alpha) region in these systems is very narrow. In situations where enough HA is added to be close to the boundary of the L(1) phase, it is shown that very small amounts of cosurfactant can transform the L(1) phase into the L(alpha) phase. In extreme situations 1 mM cosurfactant is sufficient for transforming the L(1) phase with 200 mM TDMAO into the L(alpha) phase. In the investigated systems the L(alpha) phase is a highly viscoelastic fluid in which the storage modulus is 1 order of magnitude larger than the loss modulus. Besides the conventional way to prepare samples by adding all ingredients and stirring the solution intensively, all investigated systems were additionally prepared without applying any shear forces. In a surfactant/cosurfactant solution the additive was brought into the sample by diffusion. The phase behavior of both types of samples showed fundamental differences in some cases, which give insight into the influence of shear forces on these systems. Copyright 2001 Academic Press.     

Die Kristallstrukturen von KNdTe4, RbPrTe4 und RbNdTe4 — Untersuchungen zur thermischen Stabilität von KNdTe4 sowie Bemerkungen zu einigen anderen Vertretern der Zusammensetzung ALnTe4 (A = K,Rb, Cs und Ln = Seltenerd‐Metall)

Crystal Structures of KNdTe₄, RbPrTe₄, and RbNdTe₄ — Investigations concerning the Thermal Stability of KNdTe₄ as well as some Remarks concerning Additional Representatives of the Composition ALnTe₄ (A = K, Rb, Cs and Ln = Rare Earth Metal) Of the compounds ALnQ₄ (A = Na, K, Rb, Cs; Ln = Lanthanoid; Q = S, Se and Te) the crystal structures of the three new tellurides KNdTe₄, RbPrTe₄ and RbNdTe₄ were determined by X‐ray single‐crystal structure analysis and of the three additional new ones KCeTe₄, KPrTe₄ and CsNdTe₄ by X‐ray powder diffraction experiments. All six new compounds are isotypic with KCeSe₄. Characteristic for the crystal structure of the compounds mentioned above are layers built from (Q₂)^2— dumbbells in form of 4.3².4.3 nets with embedded cations A⁺ and Ln³⁺ between them, which are coordinated eightfold in form of square‐shaped antiprisms by Q ions. The distances Te‐Te within the dumbbells were found to be 277.8(2) pm for all investigated tellurides. By combination of X‐ray diffraction and DTA measurements it was shown that the compound KNdTe₄ is metastable at ambient temperature with a limited existence range between the temperatures 260 and 498 °C.     

Novel open-chain and cyclic conformationally constrained (R)- and (S)-α,α-disubstituted tyrosine analogues

A series of novel open-chain and cyclic conformationally constrained (R)- and (S)-α,α-disubstituted tyrosine analogues 1a–e were synthesized in good yields and high optical purities (Schemes 1 and 2). The absolute configurations of these tyrosine analogues were unambiguously determined based on the X-ray structures of the precursor diastereoisomeric peptides of type 4 and 5 . Four of these structures are described (Figs. 1–4), showing β-turn type-I geometries for dipeptides 4a, 5b , and 4c and an extended conformation for peptide 5c (Table 3). The conversion of the free amino acids 1a–c into suitably protected building blocks 11a–d and 15d,e for peptide synthesis is discussed (Schemes 3 and 4).     

1,3-Cycloaddition von alkinen an hetero-1,3-diene 1-aminopyrrole aus 1,2-diazabuta-1,3-dienen und 1-diethylaminopropin

1-Aminopyrroles (4) are obtained by reaction of 1,2-diazabuta-1,3-dienes (1) and ynamines (2). This reaction represents one of the very rare examples of 1,3-cycloaddition processes of alkynes and hetero-1,3-dienes.     

A convenient synthesis of 1,3-oxazolidin-4-ones and 1,3-oxazin-4-ones

1,3-Oxazolidin-4-ones and 1,3-oxazin-4-ones were synthesized by formal cyclocondensation of imines with α- or β-hydroxy acids.