How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers?

We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95 + + (d,p) basis sets at both the Hartree-Fock and second-order Møller-Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone

Destabilizing Mutations Alter the Hydrogen Exchange Mechanism in Ribonuclease A

The effect of strongly destabilizing mutations, I106A and V108G of Ribonuclease A (RNase A), on its structure and stability has been determined by NMR. The solution structures of these variants are essentially equivalent to RNase A. The exchange rates of the most protected amide protons in RNase A (35ºC), the I106A variant (35ºC), and the V108G variant (10ºC) yield stability values of 9.9, 6.0, and 6.8 kcal/mol, respectively, when analyzed assuming an EX2 exchange mechanism. Thus, the destabilization induced by these mutations is propagated throughout the protein. Simulation of RNase A hydrogen exchange indicates that the most protected protons in RNase A and the V108G variant exchange via the EX2 regime, whereas those of I106A exchange through a mixed EX1 1 EX2 process. It is striking that a single point mutation can alter the overall exchange mechanism. Thus, destabilizing mutations joins high temperatures, high pH and the presence of denaturating agents as a factor that induces EX1 exchange in proteins. The calculations also indicate a shift from the EX2 to the EX1 mechanism for less protected groups within the same protein. This should be borne in mind when interpreting exchange data as a measure of local stability in less protected regions

Analysis of chemical bonding and aromaticity from electronic delocalization descriptors

Interactions between electrons determine the structure and properties of matter from molecules to solids. Therefore, the understanding of the electronic structure of molecules will enable us to extract relevant chemical information. In the first part of this thesis, we focus our attention on the analysis of chemical bonding by means of the Electron Localization Function (ELF) and the Domain-Averaged Fermi Hole analysis (DAFH). In the second part, we assess the performance of some indicators of aromaticity by analyzing their advantages and drawbacks. We propose a series of tests based on well-known aromaticity trends that can be applied to evaluate the aromaticity of current and future indicators of aromaticity in both organic and inorganic species. Moreover, we investigate the nature of electron delocalization in both aromatic and antiaromatic systems in the light of Hückel’s (4n + 2) rule. Finally, we analyze the phenomenon of multiple aromaticity in all-metal clusters.

GDASH: a grid-enabled program for structure solution from powder diffraction data

The simulated annealing approach to structure solution from powder diffraction data, as implemented in the DASH program, is easily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can therefore be achieved by distributing individual DASH runs over a network of computers. The GDASH program achieves this by packaging DASH in a form that enables it to run under the Univa UD Grid MP system, which harnesses networks of existing computing resources to perform calculations.

MDASH: a multi-core-enabled program for structure solution from powder diffraction data

The simulated annealing approach to structure solution from powder diffraction data, as implemented in the DASH program, is easily amenable to parallelization at the individual run level. Modest increases in speed of execution can therefore be achieved by executing individual DASH runs on the individual cores of CPUs.

Preparation and properties of gallaborane, GaBH6: structure of the gaseous molecule H2Ga(μ-H)2BH2 as determined by vibrational, electron diffraction, and ab initio studies, and structure of the crystalline solid at 110 K as determined by x-ray diffraction``

Gallaborane (GaBH6, 1), synthesized by the metathesis of LiBH4 with [H2GaCl]n at ca. 250 K, has been characterized by chemical analysis and by its IR and 1H and 11B NMR spectra. The IR spectrum of the vapor at low pressure implies the presence of only one species, viz. H2Ga(μ-H)2BH2, with a diborane-like structure conforming to C2v symmetry. The structure of this molecule has been determined by gas-phase electron diffraction (GED) measurements afforced by the results of ab initio molecular orbital calculations. Hence the principal distances (rα in Å) and angles ( α in deg) are as follows: r(Ga•••B), 2.197(3); r(Ga−Ht), 1.555(6); r(Ga−Hb), 1.800(6); r(B−Ht), 1.189(7); r(B−Hb), 1.286(7); Hb−Ga−Hb, 71.6(4); and Hb−B−Hb, 110.0(5) (t = terminal, b = bridging). Aggregation of the molecules occurs in the condensed phases. X-ray crystallographic studies of a single crystal at 110 K reveal a polymeric network with helical chains made up of alternating pseudotetrahedral GaH4 and BH4 units linked through single hydrogen bridges; the average Ga•••B distance is now 2.473(7) Å. The compound decomposes in the condensed phases at temperatures exceeding ca. 240 K with the formation of elemental Ga and H2 and B2H6. The reactions with NH3, Me3N, and Me3P are also described.

Barley oxalate oxidase is a hexameric protein related to seed storage proteins: evidence from X-ray crystallography

The oxalate oxidase enzyme expressed in barley roots is a thermostable, protease-resistant enzyme that generates H2O2. It has great medical importance because of its use to assay plasma and urinary oxalate, and it has also been used to generate transgenic, pathogen-resistant crops. This protein has now been purified and three types of crystals grown. X-ray analysis shows that the symmetry present in these crystals is consistent with a hexameric arrangement of subunits, probably a trimer of dimers. This structure may be similar to that found in the related seed storage proteins.

Germin and germin-like proteins: evolution, structure, and function

Germin and germin-like proteins (GLPs) are encoded by a family of genes found in all plants. They are part of the cupin superfamily of biochemically diverse proteins, a superfamily that has a conserved tertiary structure, though with limited similarity in primary sequence. The subgroups of GLPs have different enzyme functions that include the two hydrogen peroxide-generating enzymes, oxalate oxidase (OxO) and superoxide dismutase. This review summarizes the sequence and structural details of GLPs and also discusses their evolutionary progression, particularly their amplification in gene number during the evolution of the land plants. In terms of function, the GLPs are known to be differentially expressed during specific periods of plant growth and development, a pattern of evolutionary subfunctionalization. They are also implicated in the response of plants to biotic (viruses, bacteria, mycorrhizae, fungi, insects, nematodes, and parasitic plants) and abiotic (salt, heat/cold, drought, nutrient, and metal) stress. Most detailed data come from studies of fungal pathogenesis in cereals. This involvement with the protection of plants from environmental stress of various types has led to numerous plant breeding studies that have found links between GLPs and QTLs for disease and stress resistance. In addition the OxO enzyme has considerable commercial significance, based principally on its use in the medical diagnosis of oxalate concentration in plasma and urine. Finally, this review provides information on the nutritional importance of these proteins in the human diet, as several members are known to be allergenic, a feature related to their thermal stability and evolutionary connection to the seed storage proteins, also members of the cupin superfamily.

A benchmark method for global optimization problems in structure determination from powder diffraction data

Quasi-Newton-Raphson minimization and conjugate gradient minimization have been used to solve the crystal structures of famotidine form B and capsaicin from X-ray powder diffraction data and characterize the chi(2) agreement surfaces. One million quasi-Newton-Raphson minimizations found the famotidine global minimum with a frequency of ca 1 in 5000 and the capsaicin global minimum with a frequency of ca 1 in 10 000. These results, which are corroborated by conjugate gradient minimization, demonstrate the existence of numerous pathways from some of the highest points on these chi(2) agreement surfaces to the respective global minima, which are passable using only downhill moves. This important observation has significant ramifications for the development of improved structure determination algorithms.

Structure of the snake-venom toxin convulxin

Snake venoms contain a number of proteins that interact with components of the haemostatic system that promote or inhibit events leading to blood- clot formation. The snake- venom protein convulxin ( Cvx) binds glycoprotein ( GP) VI, the platelet receptor for collagen, and triggers signal transduction. Here, the 2.7 Angstrom resolution crystal structure of Cvx is presented. In common with other members of this snake-venom protein family, Cvx is an alphabeta- heterodimer and conforms to the C- type lectin- fold topology. Comparison with other family members allows a set of Cvx residues that form a concave surface to be putatively implicated in GPVI binding. Unlike other family members, with the exception of flavocetin- A ( FL- A), Cvx forms an (alphabeta)(4) tetramer. This oligomeric structure is consistent with Cvx clustering GPVI molecules on the surface of platelets and as a result promoting signal transduction activity. The Cvx structure and the location of the putative binding sites suggest a model for this multimeric signalling assembly.

Synthesis and crystal structure of the thiophene-3-acetonitrile complex fac-[Mo(CO)(3){NCCH2(C4H3S-3)}(3)]

Reaction of fac-[ Mo( CO)(3)( NCMe)(3)] with three equivalents of NCCH2(C4H3S- 3) in acetonitrile gives the tris(thiophene- 3- acetonitrile) complex, fac-[Mo(CO)(3){NCCH2(C4H3S-3)}(3)] (1) in 7% yield. Complex 1 crystallizes out in the orthorhombic space group Pnma with a = 12.714( 17), b = 16.41( 2), c = 11.304(16) Angstrom, Z = 4. The structure has crystallographic m symmetry and the metal is in an almost perfect octahedral environment, with a facial arrangement of carbonyl and thiophene- 3- acetonitrile groups. The thiophene rings are disordered.

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.

Rhodium assisted C-H activation of N-(2 '-hydroxyphenyl)benzaldimines. Synthesis, structure and electrochemical properties of a group of organorhodium complexes

Reaction of a group of N-(2'-hydroxyphenyl)benzaldimines, derived from 2-aminophenol and five para-substituted benzaldehydes (the para substituents are OCH3, CH3, H, Cl and NO2), with [Rh(PPh3)(3)Cl] in refluxing toluene in the presence of a base (NEW afforded a family of organometallic complexes of rhodium(III). The crystal structure of one complex has been determined by X-ray crystallography. In these complexes the benzaldimine ligands are coordinated to the metal center, via dissociation of the phenolic proton and the phenyl proton at the ortho position of the phenyl ring in the imine fragment, as dianionic tridentate C,N,O-donors, and the two PPh3 ligands are trans. The complexes are diamagnetic (low-spin d(6), S = 0) and show intense MLCT transitions in the visible region. Cyclic voltammetry shows a Rh(III)-Rh(IV) oxidation within 0.63-0.93 V vs SCE followed by an oxidation of the coordinated benzaldimine ligand. A reduction of the coordinated benzaldimine is also observed within -0.96 to -1.04 V vs SCE. Potential of the Rh(Ill)-Rh(IV) oxidation is found to be sensitive to the nature of the para-substituent. (c) 2006 Elsevier B.V. All rights reserved.

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.

Low-temperature determination of theophylline dimethyl sulfoxide solvate

The title solvate, C7H8N4O2 center dot C2H6OS, was obtained unintentionally from a cocrystal screen involving theophylline and isophthalic acid. One molecule each of theophylline and dimethyl sulfoxide is present in the asymmetric unit. The packing consists of molecular sheets lying parallel to the ( 040) series of lattice planes, in which each theophylline molecule is hydrogen bonded to one dimethyl sulfoxide molecule through an N-H center dot center dot center dot O [2.7658 (15) angstrom] hydrogen bond. This particular hydrogen-bond donor was found to be used in this type of interaction in a variety of other crystal structures of theophylline.