ASYM20: a program for force constant and normal coordinate calculations, with a critical review of the theory involved

The theory of harmonic force constant refinement calculations is reviewed, and a general-purpose program for force constant and normal coordinate calculations is described. The program, called ASYM20. is available through Quantum Chemistry Program Exchange. It will work on molecules of any symmetry containing up to 20 atoms and will produce results on a series of isotopomers as desired. The vibrational secular equations are solved in either nonredundant valence internal coordinates or symmetry coordinates. As well as calculating the (harmonic) vibrational wavenumbers and normal coordinates, the program will calculate centrifugal distortion constants, Coriolis zeta constants, harmonic contributions to the α′s. root-mean-square amplitudes of vibration, and other quantities related to gas electron-diffraction studies and thermodynamic properties. The program will work in either a predict mode, in which it calculates results from an input force field, or in a refine mode, in which it refines an input force field by least squares to fit observed data on the quantities mentioned above. Predicate values of the force constants may be included in the data set for a least-squares refinement. The program is written in FORTRAN for use on a PC or a mainframe computer. Operation is mainly controlled by steering indices in the input data file, but some interactive control is also implemented.

Characterization of a gamma-aminobutyric acid transport system of rhizobium leguminosarum bv. viciae 3841

Spontaneous mutants of Rhizobium leguminosarum bv. viciae 3841 were isolated that grow faster than the wild type on gamma-aminobutyric acid (GABA) as the sole carbon and nitrogen source. These strains (RU1736 and RU1816) have frameshift mutations (gtsR101 and gtsR102, respectively) in a GntR-type regulator (GtsR) that result in a high rate of constitutive GABA transport. Tn5 mutagenesis and quantitative reverse transcription-PCR showed that GstR regulates expression of a large operon (pRL100242 to pRL100252) on the Sym plasmid that is required for GABA uptake. An ABC transport system, GtsABCD (for GABA transport system) (pRL100248-51), of the spermidine/putrescine family is part of this operon. GtsA is a periplasmic binding protein, GtsB and GtsC are integral membrane proteins, and GtsD is an ATP-binding subunit. Expression of gtsABCD from a lacZ promoter confirmed that it alone is responsible for high rates of GABA transport, enabling rapid growth of strain 3841 on GABA. Gts transports open-chain compounds with four or five carbon atoms with carboxyl and amino groups at, or close to, opposite termini. However, aromatic compounds with similar spacing between carboxyl and amino groups are excellent inhibitors of GABA uptake so they may also be transported. In addition to the ABC transporter, the operon contains two putative mono-oxygenases, a putative hydrolase, a putative aldehyde dehydrogenase, and a succinate semialdehyde dehydrogenase. This suggests the operon may be involved in the transport and breakdown of a more complex precursor to GABA. Gts is not expressed in pea bacteroids, and gtsB mutants are unaltered in their symbiotic phenotype, suggesting that Bra is the only GABA transport system available for amino acid cycling.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Molecular structure of 2,5-dihydropyrrole (C4NH7), obtained by gas-phase electron diffraction and theoretical calculations

The structure of 2,5-dihydropyrrole (C4NH7) has been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing third-order Moller-Plesset (MP3) level of theory and the 6-311+G(d,p) basis set. Several theoretical calculations were performed. From theoretical calculations using MP3/6-311+G(d,p) evidence was obtained for the presence of an axial (63%) (N-H bond axial to the CNC plane) and an equatorial conformer (37%) (N-H bond equatorial to the CNC plane). The five-membered ring was found to be puckered with the CNC plane inclined at 21.8 (38)&DEG; to the plane of the four carbon atoms.

Copper complexes of new benzodioxotetraaza macrocycles with potential applications in nuclear medicine

Two novel benzodioxotetraaza macrocycles [2,9-dioxo-1,4,7,10-tetraazabicyclo[10.4.0]1,11-hexadeca-1(11),13,15-triene (H(2)L1) and 2,10-dioxo-1,4,8,11-tetraazabicyclo[11.4.0]1,12-heptadeca-1(12),14,16-triene (H(2)L2)] were synthesized by a [1 + 1] crablike cyclization. The protonation constants of both ligands were determined by H-1 NMR titration and by potentiometry at 25.0 degrees C in 0.10 M ionic strength in KNO3. The latter method was also used to ascertain the stability constants of their copper(II) complexes. These studies showed that the CuL1 complex has a much lower thermodynamic stability than the CuL2, and the H(2)L2 displays an excellent affinity for copper(II), due to the good fit of copper(II) into its cavity. The copper complexes of the novel ligands were characterized by electronic spectroscopy in solution and by crystal X-ray diffraction. These studies indicated that the copper center in the CuL1 complex adopts a square-pyramidal geometry with the four nitrogen atoms of the macrocycle forming the equatorial plane and a water molecule at axial position, and the copper in the CuL2 complex is square-planar. Several labeling conditions were tested, and only H(2)L2 could be labeled with Cu-67 efficiently (> 98%) in mild conditions (39 degrees C, 15 min) to provide a slightly hydrophilic radioligand (log D = -0.19 +/- 0.03 at pH 7.4). The in vitro stability was studied in the presence of different buffers or with an excess of diethylenetriamine-pentaethanoic acid. Very high stability was shown under these conditions for over 5 days. The incubation of the radiocopper complex in human serum showed 6% protein binding.

Equilibrium studies on mixed ligand complex formation of Co(II), Ni(II), Cu(II) and Zn(II) with N-(2-hydroxybenzyl)-L-histidine (H(2)hb-L-his) and typical N,N donor ligands: Crystal structure of [Ni(hb-L-his)(bipyridine)]center dot H2O complex

Equilibrium study on complex formation of Co(II), Ni(II), Cu(II) and Zn(II), hereafter M(II), with the quadridentate (O-, N, O-, N) donor ligand, N-(2-hydroxybenzyl)-L-histidine (H(2)hb-L-his, hereafter H2L), in the absence and in the presence of typical (N, N) donor bidentate ligands, 1,10 phenanthroline(phen), 2, 2'-bipyridine(bipy), ethylenediamine(en), hereafter B, in aqueous solution at 25 +/- 1 degrees C was done at a fixed ionic strength, I = 0.1 mol dm(-3) (NaNO3) by combined pH-metric, UV-Vis and EPR measurements provide evidence for the formation of mononuclear and dinuclear binary and mixed ligand complexes of the types: M(L), M(L)(2)(2-), M-2(L)(2+), M-2(H-1L)(+), M(L)(B), (B)M(H-1L)M(B)(+). The imidazole moiety of the ligand is found to act as a bridging bidentate ligand in the dinuclear M-2(L)(2+), M-2(H-1L)(+) and (B)M(H-1L)M(B)(+) complexes, using its N-3 atom and N1-H deprotonated moiety. Stability constants of the complexes provide evidence of discrimination of Cu(II) from the other M(II) ions by this ligand. Solid complexes: [Ni(L)(H2O)(2)] (1), [Cu(L)(H2O)] (2), and [Ni(L)(bipy)] (.) H2O (3) have been isolated and characterized by various physicochemical studies. Single crystal X-ray diffraction of the ternary complex, 3, shows an octahedral [(O-,N,N,O-)(N,N)] geometry with extensive pi-pi stacking of the aromatic rings and H-bonding with imidazole (N1-H), secondary amino N-atom, the lattice H2O molecule, and the carboxylate and phenolate O-atoms. (c) 2006 Elsevier B.V. All rights reserved.

Construction of coordination polymers of cadmium(II) with mixed hexamethylenetetramine and terephthalate or thiocyanate ligands

Three new polymeric complexes [Cd(hmt)(SCN)(2)(H2O)(2)](n) (1), [Cd-3(mu(2)-hmt)(2)(SCN)(6)(H2O)(2)](n) (2), and [Cd-2(hmt)(2)(tP)(2)(H2O)(6)](n) (3) [hmt = hexamethylenetetramine, tp = terephthalate] have been synthesized and characterized by single crystal X-ray diffraction. Both the compounds 1 and 2 are 1-D polymers where Cd units are linked by double end-to-end thiocyanate bridges but in 2 the chain is wider containing three cadmium atoms instead of one as found in 1. In both compounds the coordination environment around cadmium atom is distorted octahedral. Compound 3 is a three-dimensional polymer having water-filled microporous channels. Both tp and brut are mu(2)-bridged. One of the acid groups of tp is coordinated in chelating bidentate and the other in monodentate fashion. Half of its Cd atoms are hexa-coordinated and the rest are hepta-coordinated. Thermogravimetric analysis and X-ray diffraction study of 3 show that its framework remains intact upon removal of water molecules. The flexibility of coordination number around cadmium atoms (six or seven) probably plays an important role in establishing the rigidity of the framework. (C) 2003 Elsevier Ltd. All rights reserved.

Dinuclear complexes of M-II thiocyanate (M = Ni and Cu) containing a tridentate Schiff-base ligand: synthesis, structural diversity and magnetic properties

A dinuclear Ni-II complex, [Ni-2(L)(2)(H2O)(NCS)(2)]center dot 3H(2)O (1) in which the metal atoms are bridged by one water molecule and two mu(2)-phenolate ions, and a thiocyanato-bridged dimeric Cull complex, [Cu(L)NCS](2) (2) [L = tridentate Schiff-base ligand, N-(3-aminopropyl)salicylaldimine, derived from 1:1 condensation of salicylaldehyde and 1,3-diaminopropane], have been synthesized and characterized by IR and UV/Vis spectroscopy, cyclic voltammetry and single-crystal X-ray diffraction studies. The structure of 1 consists of dinuclear units with crystallographic C-2 symmetry in which each Ni-II atom is in a distorted octahedral environment. The Ni-O distance and the Ni-O-Ni angle, through the bridged water molecule, are 2.240(11) angstrom and 82.5(5)degrees, respectively. The structure of 2 consists of dinuclear units bridged asymmetrically by di-mu(1,3)-NCS ions; each Cull ion is in a square-pyramidal environment with tau = 0.25. Variable-temperature magnetic susceptibility studies indicate the presence of dominant ferromagnetic exchange coupling in complex 1 with J = 3.1 cm(-1), whereas complex 2 exhibits weak antiferromagnetic coupling between the Cu-II centers with J = -1.7 cm(-1). ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

Ring-chain interconversion in high-performance polymer systems. 3. Cyclodepolymerization of poly(m-phenylene isophthalamide) (Nomex) and entropically driven ring-opening polymerization of the macrocyclic oligomers so produced

A homologous series of macrocyclic oligoamides has been prepared in high yield by reaction of isophthaloyl chloride with m-phenylenediamine under pseudo-high-dilution conditions. The products were characterized by infrared and H-1 NMR spectroscopies, matrix assisted laser desorption-ionization time-of-flight mass spectrometry, and gel permeation chromatography (GPC). A series of linear oligomers was prepared for comparison. The macrocycles ranged in size from the cyclic trimer up to at least the cyclic nonamer (90 ring atoms). The same homologous series of macrocyclic oligomers was prepared in high yield by the cyclodepolymerization of poly(m-phenylene isophthalamide) (Nomex). Cyclodepolymerization was best achieved by treating a 1% w/v solution of the polymer in dimethyl sulfoxide containing calcium chloride or lithium chloride with 3-4 mol % of sodium hydride or the sodium salt of benzanilide at 150 degreesC for 70 h. Treatment of a concentrated solution of the macrocyclic oligomers (25% w/v) with 4 mol % of sodium hydride or the sodium salt of benzanilide in a solution of lithium chloride in dimethyl sulfoxide at 170 degreesC for 6 h resulted in efficient entropically driven ring-opening polymerizations to give poly(m-phenylene isophthalamide), characterized by infrared and H-1 NMR spectroscopies and by GPC. The molecular weights obtained were comparable with those of the commercial polymer.

Anion-pi, Lone-Pair-pi, pi-pi and Hydrogen-Bonding Interactions in a Cu-II Complex of 2-Picolinate and Protonated 4,4 '-Bipyridine: Crystal Structure and Theoretical Studies

A Cu-II complex of protonated 4,4'-bipyridine (Hbyp) and 2-picolinate (pic), [Cu-2(pic)(3)(Hbyp)(H2O)(ClO4)(2)], has been synthesised and characterised by single-crystal X-ray analysis. The structure consists of two copper atoms that have different environments, bridged by a carboxylate group. The equatorial plane is formed by the two bidentate picolinate groups in one Cu-II, and one picolinate, one monodentate 4,4'-bipyridyl ligand and a water molecule in the other. Each copper atom is also weakly bonded to a perchlorate anion in an axial position. One of the coordinated perchlorate groups displays anion-pi interaction with the coordinated pyridine ring. The noncoordinated carboxylate oxygen is involved in lone-pair (l.p.)-pi interaction with the protonated pyridine ring. In addition there are pi-pi and H-bonding interactions in the structure. Bader's theory of "atoms in molecules" (AIM) is used to characterise the anion-pi and l.p.-pi interactions observed in the solid state. A high-level ab initio study (RI-MP2/aug-cc-pVTZ level of theory) has been performed to analyse the anion-pi binding affinity of the pyridine ring when it is coordinated to a transition metal and also when the other pyridine ring of the 4,4'-bipyridine moiety is protonated. Theoretical investigations support the experimental findings of an intricate network of intermolecular interactions, which is characterised in the studied complex, and also indicate that protonation as well as coordination to the transition metal have important roles in influencing the pi-binding properties of the aromatic ring. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Stabilization of a helical water chain in a metal-organic host of a trinuclear Schiff base complex

Three heterometallic trinuclear Schiff base complexes, [{GuL(1)(H2O)}(2)Ni(CN)(4)]center dot 4H(2)O (1), [{CuL2(H2O)}(2)Ni(CN)(4)] (2), and [{CuL3(H2O)}(2)Ni(CN)(4)] (3) (HL1 = 7-amino-4-methyl-5-azahept-3-en-2-one, HL2 = 7-methylamino-4-methyl-5-azahept-3-en-2-one, and HL3 = 7-dimethylamino-4-methyl-5-azahept-3-en-2-one), were synthesized. All three complexes were characterized by elemental analysis, IR and UV spectroscopies, and thermal analysis. Two of them (1 and 3) were also characterized by single crystal X-ray crystallography. Complex 1 forms a hydrogen-bonded one-dimensional metal-organic framework that stabilizes a helical water chain into its cavity, but when any of the amine hydrogen atoms of the Schiff base are replaced by methyl groups, as in L 2 and L 3, the water chain, vanishes, showing explicitly the importance of the host-guest H-bonding interactions for the stabilization of a water cluster.

Anion-directed synthesis of metal-organic frameworks based on 2-picolinate Cu(II) complexes: a ferromagnetic alternating chain and two unprecedented ferromagnetic fish backbone chains

Three new polynuclear copper(II) complexes of 2-picolinic acid (Hpic), {[Cu-2(pic)(3)(H2O)]ClO4}(n) (1), {[Cu-2(pic)(3)(H2O)]BF4}(n) (2), and [Cu-2(pic)3(H2O)(2)(NO3)](n) (3), have been synthesized by reaction of the "metalloligand" [Cu-(pic)(2)] with the corresponding copper(II) salts. The compounds are characterized by single-crystal X-ray diffraction analyses and variable-temperature magnetic measurements. Compounds 1 and 2 are isomorphous and crystallize in the triclinic system with space group P (1) over bar, while 3 crystallizes in the monoclinic system with space group P2(1)/n. The structural analyses reveal that complexes 1 and 2 are constructed by "fish backbone" chains through syn-anti (equatorial-equatorial) carboxylate bridges, which are linked to one another by syn-anti (equatorial-axial) carboxylate bridges, giving rise to a rectangular grid-like two-dimensional net. Complex 3 is formed by alternating chains of syn-anti carboxylate-bridged copper(II) atoms, which are linked together by strong H bonds involving coordinated nitrate ions and water molecules and uncoordinated oxygen atoms from carboxylate groups. The different coordination ability of the anions along with their involvement in the H-bonding network seems to be responsible for the difference in the final polymeric structures. Variable-temperature (2-300 K) magnetic susceptibility measurement shows the presence of weak ferromagnetic coupling for all three complexes that have been fitted with a fish backbone model developed for 1 and 2 (J = 1.74 and 0.99 cm(-1); J' = 0.19 and 0.25 cm(-1), respectively) and an alternating chain model for 3 (J = 1.19 cm(-1) and J' = 1.19 cm(-1)).

Cascade dicopper architectures of a dibenzodioxatetraazamacrocycle

The dibenzodioxatetraazamacrocycle [26]pbz(2)N(4)O(2) was characterised by single crystal X-ray diffraction and the protonation constants of this compound and the stability constants of its copper(II) and lead(II) complexes were determined by potentiometry in water at 298.2 K in 0.10 mol dm(-3) in KNO3. Mono- and dinuclear complexes were found for both metal ions, the dinuclear complexes being the main species in the 5-7.5 pH range for copper(II) and 7.5-8.5 for lead(II). As expected the values of the stability constants for the copper(II) complexes are lower than those for related macrocycles containing only nitrogen atoms. The presence of mono- and dinuclear copper complexes was also confirmed by electrospray ionization mass spectrometry. These results suggest that the symmetric macrocyclic cavity of [26]pbZ(2)N(4)O(2) has enough space for the coordination of two metal ions. Additionally, NMR spectroscopy showed that the dinuclear complex of lead(II) has high symmetry. The equilibrium constants of the dinuclear copper(II) complexes and dicarboxylate anions (oxalate, malonate and succinate) were also determined in 0.10 mol dm-3 aqueous KNO3 solution. Only species containing one anion, Cu(2)H(h)LA((2+h)), were found, strongly suggesting that the anion bridges the two copper(II) ions. The binding constants of the cascade species formed by [Cu-2[26]pbZ(2)N(4)O(2)(H2O)(4+) with dicarboxylate anions decrease with the increase in length of the alkyl chain of the anion, a fact which was attributed to a higher conformational energy necessary for the rearrangement of the macrocycle to accommodate the larger anions bridging the two copper(II) centres. The variation of the magnetic susceptibility with temperature Of [Cu-2(H-2[26]pbz(2)N(4)O(2))(oxa)(3)]-4H(2)O and [Cu-2([26]pbz(2)N(4)O(2))(suc)Cl-2] were measured and the two complexes showed different behaviour. (c) 2007 Elsevier Ltd. All rights reserved.

Hydrothermal synthesis and structural characterization of novel alpha-Keggin unit-supported Cu(II)- and Mn(II)-bipyridine complexes from a tri-lacunary precursor

Blue [{Cu(2,2'-bipy)(2)}(2){alpha-SiW12O40}] (bipy = bipyridyl) (1) and pale yellow [Mn(2,2'-bipy)(3)](2)[alpha-SiW12O40] (2) have been synthesized hydrothermally and characterized by IR spectroscopy and single crystal X-ray structure analysis. In 1, the [alpha-SiW12O40](4-) ion acts as a bridge between the two [{Cu(2,2'-bipy)(2)](2+) moieties via coordination through the terminal oxygen atoms, while in 2, the [Mn(2,2'-bipy)(3)](2+) ion balances the charge on the polyoxo anion without forming any covalent bond. To the best of our knowledge, this is the first example of transition metal-mediated transformation of [alpha-SiW9O34](10-) to [alpha-SiW12O40](4-).