Monomer–Dimer Control and Crystal Engineering in TASPs

We have reported a template assembled synthetic protein (cavitein Q4) as an unexpected dimer in the solid state and as a monomer–dimer equilibrium in solution. We have since reported an ability to bias a cavitein’s monomer–dimer equilibrium in solution by sequence design involving histidine metal chelation or disulfide incorporation. However, little remains known about the forces contributing to dimeric cavitein crystal nucleation and lattice stabilization. We, therefore, designed glutamine variants to probe factors involved in dimeric cavitein crystallization. It was found that a key glutamate hydrogen-bonding interaction between dimers is integral to crystal formation and stabilization. Additionally, we obtained a crystal structure of a cavitein (Q4-E3H) designed to bias the dimeric structure via histidine metal coordination. The resolved structure indicates a histidine cluster interaction that likely accounts for the biased dimeric form observed in solution.     

Conformationally constrained sequence designs to bias monomer-dimer equilibriums in TASP systems

We have designed template-assembled synthetic proteins (TASPs) with the intent of controlling their oligomeric state by stabilizing specific helical tertiary structures via histidine metal ion chelation or disulfide incorporation. In solution, cavitein Q4 was previously determined to interconvert between a four-helix bundle monomer and an eight-helix bundle dimer. In this paper, we show that judicious mutation of cavitein Q4 can stabilize either the monomeric parallel four-helix bundle or the dimeric antiparallel eight-helix bundle structure. Cavitein Q4-E3H, designed to be dimeric, is indeed biased toward dimerization as a result of incorporation of histidines. Moreover, the addition of nickel was found to further increase the association constant of dimerization. Similarly, a cavitein designed to stabilize the monomeric structure via histidine metal ion chelation (Q4-H) was found to favor a monomer in solution upon addition of nickel. Lastly, a cavitein intended to stabilize a monomeric structure via disulfide incorporation (Q4-C2) is reported. Surprisingly, this disulfide cavitein yielded two products upon oxidation suggesting disulfide formation both above the cavitand template and below may be possible. Nevertheless, the two disulfide caviteins were shown to exist as monomers as per their design.     

Li(CH(Me)P(Ph)2(NCO2Me))2(THF)2]: crystal,solution, and calculated structure of a N-delocalized lithium phosphazene

The first crystal structure of the lithium complex of a P-alkyl-P,P-diphenyl(N-methoxycarbonyl)phosphazene has been characterized. It is dimeric, with the anion chelating the lithium in an unusual six-membered ring. A monomer-dimer equilibrium has been identified in THF solution. Ab initio calculations indicated that the six-membered ring is electronically favored over an alternative Li-C-P-N four-membered ring.     

A comparative study of pi-arene-bridged lanthanum arylamide and aryloxide dimers. Solution behavior, exchange mechanisms, and X-ray crystal structures of La2(NH-2,6-iPr2C6H3)6, La(NH-2,6-iPr2C6H3)3(THF)3, and La(NH-2,6-iPr2C6H3)3(py)2

Reaction of 3 equiv of 2,6-diisopropylaniline with La[N(SiMe(3))(2)](3) produces the dimeric species La(2)(NHAr)(6) (1). X-ray crystallography reveals a centrosymmetric structure, where the dimeric unit is bridged by intermolecular eta(6)-arene interactions of a unique arylamide ligand attached to an adjacent metal center. Exposure of 1 to THF results in formation of the monomeric tris-THF adduct La(NHAr)(3)(THF)(3) (2), which was shown by X-ray crystallography to maintain a fac-octahedral structure in the solid state. (1)H NMR spectroscopy illustrates that the binding of THF to 1 to form 2 is reversible and removal of THF under vacuum regenerates dimeric 1. Addition of pyridine to 1 yields the monomeric bis-pyridine adduct La(NHAr)(3)(py)(2) (3), which exhibits a distorted trigonal-bipyramidal La metal center. Solution (1)H NMR, IR, and Raman spectroscopy indicate that the pi-arene-bridged dimeric structure of 1 is maintained in solution. Variable-temperature (1)H NMR spectroscopic investigations of 1 are consistent with a monomer-dimer equilibrium at elevated temperature. In contrast, variable-temperature (1)H NMR spectroscopic investigations of the aryloxide analogue La(2)(OAr)(6) (4) show that the bridging and terminal aryloxide groups exchange by a mechanism in which the dimeric nature of the compound is retained. Density functional theory (DFT) calculations were carried out on model compounds La(2)(OC(6)H(5))(6), La(2)(NHC(6)H(5))(6), and (C(6)H(5)R)La(XC(6)H(5))(3), where X = O or NH and R = H, OH, or NH(2). The formation of eta(6)-arene interactions is energetically favored over monomeric LaX(3) (X = OPh or NHPh) with the aryloxide pi-arene interaction being stronger than the arylamide pi-arene interaction. Calculation of vibrational frequencies reveals the origin of the observed IR spectral behavior of both La(2)(OC(6)H(5))(6) and La(2)(NHC(6)H(5))(6), with the higher energy nu(C=C) stretch due to terminal ligands and the lower energy stretch associated with the bridging ligands.     

Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.     

Dipoles-dipole association of mesogenic molecules in solution

The dielectric polarization has been used to study dipolar association of 4-n-pentyl-4'-cyanobiphenyl in benzene solution. The results have been interpreted with the assumption of a monomer-dimer equilibrium. To explain the relatively high effective dipole moment of the dimers, a new structure has been proposed for them.     

A spectroscopic study of dyes: mechanism of detection of nonabsorbing analytes in reverse-phase chromatography with the aid of chromophores

In order to understand the mechanism by which dyes assist chromatographic detection in reverse-phase systems, absorption spectra of brilliant green and methylene blue were investigated. It is shown that dye-assisted chromatographic detection depends on the ability of the analyte to shift the monomer-dimer equilibrium of the dyes toward greater monomer concentrations. Monomers have higher molar absorptivities than dimers. Equilibrium constants and molar absorptivities for monomeric and dimeric forms of the dyes are reported.     

Fluorescent detection of nitroaromatics and 2,3-dimethyl 2,3-dinitrobutane (DMNB) by a zinc complex: (salophen)Zn

Fluorescent sensors for the detection of chemical explosives are in great demand. It is shown herein that the fluorescence of ZnL* (H2L=N,N'-phenylene-bis-(3,5-di-tert-butylsalicylideneimine)) is quenched in solution by nitroaromatics and 2,3-dimethyl-2,3-dinitrobutane (DMNB), chemical signatures of explosives. The relationship between the structure and fluorescence of ZnL is explored, and crystal structures of three forms of ZnL(base), (base=ethanol, tetrahydrofuran, pyridine) are reported, with the base=ethanol structure exhibiting a four-centered hydrogen bonding array. Solution structures are monitored by 1H NMR and molecular weight determination, revealing a dimeric structure in poor donor solvents which converts to a monomeric structure in the presence of good donor solvents or added Lewis bases to form five-coordinate ZnL(base). Fluorescence wavelengths and quantum yields in solution are nearly insensitive to monomer-dimer interconversion, as well as to the identity of the Lewis base; in contrast, the emission wavelength in the solid state varies for different ZnL(base) due to pi-stacking. Nitroaromatics and DMNB are moderately efficient quenchers of ZnL*, with Stern-Volmer constants KSV=2-49 M-1 in acetonitrile solution.     

Synthesis and spectroscopic and structural characterization of two novel photoactivatable Ca2+ compounds

Two novel photoactivatable Ca(2+) compounds were synthesized to achieve a fast concentration jump of calcium ions in solution; this is of paramount importance for investigating the physiological cellular response. The light-sensitive ligands 4-(2-nitrophenyl)-3,6-dioxaoctane dioic acid (H2L1) and 4-(4,5-dimethoxy-2-nitrophenyl)-3,6-dioxaoctane dioic acid (H2L2) were generated by multistep syntheses, and the corresponding calcium complexes, Ca1 and Ca2, were isolated and characterized. The solution equilibria of H2L1 and H2L2 with Ca2+ were investigated; for both ligands, the formation of a 1:2 Ca2+/ligand species is detected and the complete characterization is presented. The crystal structures of Ca1 and Ca2 were determined. In Ca1 the solid state assembly is attained by a polymeric association of [(CaL1(H2O))2(mu-OH2)] dimeric units. Each calcium ion coordinates four oxygen atoms of one ligand (two ethereal, one carboxylic, and one bridging carboxylic oxygen atom), one water molecule, one bridging water molecule, and a carboxylate group of the other ligand within the dimer. The octacoordination of the metal is completed by an interaction with the adjacent dimeric unit. The crystal structure of the complex Ca2 does not show a polymeric nature, but it is a centrosymmetric dimer. The coordination number of the metal ion is still 8:4 oxygen atoms of the ligand; 3 water molecules; 1 bridging carboxylate group. A preliminary study of the photochemical features of the complexes Ca1 and Ca2 is reported: photoexcitation by a nanosecond pulsed UV laser induces the cleavage of the ligand. This drastically reduces the affinity of the ligand toward Ca2+, which is then released in solution.     

二甲基甲酰胺的变温付立叶变换红外光谱研究

DMF是一种具有优异性能的常用溶剂。根据FT-IR的高分辨率和高灵敏度的特点,研究了液体DMF的20-120℃的变温红外光谱,不同浓度的CCl₄溶液光谱和气体光谱。结果表明在液体DMF中存在着聚合分子,它们是以分子中醛基的C-H键与另一分子的羰基生成C-H…O式氢键而相互作用的。这种以C-H健与O所形成的氢键,已有报导的实例很少。     

Some observations on the NOE effect in 1H NMR spectroscopy

The NOE enhancement factor in ¹H NMR spectroscopy is shown to be a function of dipole-dipole interaction of the solute. The NOE increases with increasing concentration if a monomer-dimer equilibrium exists in solution.     

Lanthanide complexes based on a 1,7-diaza-12-crown-4 platform containing picolinate pendants: a new structural entry for the design of magnetic resonance imaging contrast agents

We have synthesized a new macrocyclic ligand, N,N'-Bis[(6-carboxy-2-pyridyl)methyl]-1,7-diaza-12-crown-4 (H 2bp12c4), designed for complexation of lanthanide ions in aqueous solution. The X-ray crystal structure of the Gd (III) complex shows that the metal ion is directly bound to the eight donor atoms of the bp12c4 ligand, the ninth coordination site being occupied by an oxygen atom of a carboxylate group of a neighboring [Gd(bp12c4)] (+) unit, while the structure of the Lu (III) analogue shows the metal ion being only eight-coordinate. The hydration numbers obtained from luminescence lifetime measurements in aqueous solution of the Eu (III) and Tb (III) complexes suggest an equilibrium in aqueous solution between a dihydrated ( q = 2), ten-coordinate and a monohydrated ( q = 1), nine-coordinate species. This has been confirmed by a variable temperature UV-vis spectrophotometric study on the Eu (III) complex. The structure of the complexes in solution has been investigated by (1)H and (13)C NMR spectroscopy, as well as by theoretical calculations performed at the DFT (B3LYP) level. The results indicate that the change in hydration number occurring around the middle of the lanthanide series is accompanied by a change in the conformation adopted by the complexes in solution [Delta(lambdalambdalambdalambda) for q = 2 and Lambda(deltalambdadeltalambda) for q = 1]. The structure calculated for the Yb (III) complex (Lambda(deltalambdadeltalambda)) is in good agreement with the experimental structure in solution, as demonstrated by the analysis of the Yb (III)-induced paramagnetic (1)H shifts.     

Designed high affinity Cu2+-binding alpha-helical foldamer

The design, synthesis, and characterization of a folded high-affinity metal-binding peptide is described. Based on the previously described folded peptide NTH-18, in which an alpha-helix was constrained through two disulfide bonds to a C-terminal extension of noncanonical secondary structure, a peptide (1) was designed to contain two histidine residues in positions 3 and 7. Air oxidation of 1 led to the formation of peptide 2, which contained two intramolecular disulfide bonds. The presence of the two histidines significantly destabilized the alpha-helical structure of 2 when compared to NTH-18. However, CD spectroscopy revealed that the addition of certain transition metal ions allowed the reformation of a stable alpha-helix. CD, NMR, and EPR spectroscopy as well as MALDI-TOF mass spectrometry indicated that 2 bound to Cu2+ to form a 1:1 complex via the imidazoles of the two histidine side chains. A glycine displacement assay revealed a dissociation constant for this complex of 5 nM at pH 8, which is the lowest reported value for a designed Cu2+-binding peptide. This peptide displayed more than 100-fold selectivity for Cu2+ over Zn2+, Ni2+, and Co2+. The 1.05 A crystal structure of the Cu(II)-complex of 2 revealed a square-pyramidal coordination geometry and confirmed that 2 bound to copper in an alpha-helical conformation via its two histidine side chains. The high affinity metal binding of peptide 2 demonstrates that metals can be used for the selective nucleation of alpha-helices.     

Gold Behaves as Hydrogen in the Intermolecular Self‐Interaction of Metal Aurides MAu4 (M=Ti,Zr, and Hf)

We performed density functional calculations to examine the intermolecular self‐interaction of metal tetraauride MAu₄ (M=Ti, Zr, and Hf) clusters. We found that the metal auride clusters have strong dimeric interactions (2.8–3.1 eV) and are similar to the metal hydride analogues with respect to structure and bonding nature. Similarly to (MH₄)₂, the (μ‐Au)₃ C_s structures with three three‐center two‐electron (3c–2e) bonds were found to be the most stable. Natural orbital analysis showed that greater than 96 % of the Au 6s orbital contributes to the 3c–2e bonds, and this predominant s orbital is responsible for the similarity between metal aurides and metal hydrides (>99 % H 1s). The favorable orbital interaction between occupied Au 6s and unoccupied metal d orbitals leads to a stronger dimeric interaction for MAu₄‐MAu₄ than the interaction for MH₄‐MH₄. There is a strong relationship between the dimeric interaction energy and the chemical hardness of its monomer for (MAu₄)₂ and (MH₄)₂.     

The π-Molecular Complex of Biphenylene and Tetracyanoethylene

The investigation of the biphenylene (BP)-tetracyanoethylene (TCNE) π-molecular complex is reported. The first study on this complex appeared in 1961 and was considered as a charge transfer complex with a symmetric, co-planar arrangement of the components. Moreover, it was assumed that this arrangement is not only dictated by the formation of a Mulliken-type donor-acceptor complex, but also by the electronic stabilization of the ‘cyclobutadieneoid’ central ring of biphenylene through complex formation. Yet, crystal structure and associated computational analysis have not verified these predictions so far. We found that factors other than charge-transfer interactions are most influential in the crystal formation. The low association constant in solution, and the weak interaction between the components in the 1 : 1 crystal structure point towards the low contribution of charge transfer interactions to their binding. Nevertheless, the presence of these interaction is hinted by the color of its solution and verified by theoretical calculations. Furthermore, Nucleus Independent Chemical Shift (NICS) calculations were carried out to characterize potential changes in the (anti)aromatic character of BP upon complex formation. The NICS(0) values of the rings of BP exhibit tiny changes both in the BP-TCNE dimer and in the crystal, which also suggests weak electronic interactions between them.     

UV-Vis spectroscopic and chemometric study on the aggregation of ionic dyes in water

The monomer-dimer equilibrium in several ionic dyes (Methylene Blue, Acridine Orange, Nile Blue A, Neutral Red, Rhodamine 6G and Safranine O) has been investigated by means of UV-Vis spectroscopy. The data have been processed by a recently developed method for quantitative analysis of undefined mixtures, based on simultaneous resolution of the overlapping bands in the whole set of absorption spectra. In the cases of Acridine Orange a second chemometric approach has been used as a reference. It is based on a decomposition of the recorded spectra into a product of target and projection matrices using non iterative partial least squares (NIPALS). The matrices are then rotated to give the correct concentrations, spectral profiles of the components and the equilibrium constant. The dimeric constants determined by the two methods were in excellent agreement, evidencing the accuracy of the analysis. From the calculated dimeric constant and monomer and dimer spectra, the structures of the dimeric forms of the studied dyes are estimated.     

Supramolecular hydrogen-bonded liquid crystals

The role of hydrogen-bonding interactions in the formation and/or stabilization of liquid crystalline phases has been recognized in recent years and significant work has been conducted. Following the first and well-established examples of liquid crystal formation through the dimerization of aromatic carboxylic acids, several classes of compounds have been prepared by the interaction of complementary molecules, the liquid crystalline behaviour of which is crucially dependent on the structure of the resulting supramolecular systems. In this review the main classes of liquid crystals prepared through hydrogen-bonding interactions are presented, with the aim of establishing, in the first place, the diversity of organic compounds that can be used as building elements in the process of liquid crystal formation. Rigid-rod anisotropic or amphiphilic-type molecules, appropriately functionalized with recognizable moieties, interact in the melt or in solution and lead to the formation of supramolecular complexes that may exhibit thermotropic liquid crystalline character. Depending on the nature, number and position of the groups able to form hydrogen bonds, a diversity of supramolecular structures, both dimeric and polymeric, have been obtained, affording in turn various liquid crystalline phases. The structure and stability of these hydrogen-bonded supramolecular complexes and their relation to the observed liquid crystalline phases are the main topics of this review.     

Supramolecular hydrogen-bonded liquid crystals

The role of hydrogen-bonding interactions in the formation and/or stabilization of liquid crystalline phases has been recognized in recent years and significant work has been conducted. Following the first and well-established examples of liquid crystal formation through the dimerization of aromatic carboxylic acids, several classes of compounds have been prepared by the interaction of complementary molecules, the liquid crystalline behaviour of which is crucially dependent on the structure of the resulting supramolecular systems. In this review the main classes of liquid crystals prepared through hydrogen-bonding interactions are presented, with the aim of establishing, in the first place, the diversity of organic compounds that can be used as building elements in the process of liquid crystal formation. Rigid-rod anisotropic or amphiphilic-type molecules, appropriately functionalized with recognizable moieties, interact in the melt or in solution and lead to the formation of supramolecular complexes that may exhibit thermotropic liquid crystalline character. Depending on the nature, number and position of the groups able to form hydrogen bonds, a diversity of supramolecular structures, both dimeric and polymeric, have been obtained, affording in turn various liquid crystalline phases. The structure and stability of these hydrogen-bonded supramolecular complexes and their relation to the observed liquid crystalline phases are the main topics of this review.     

Adsorption of myoglobin to Cu(II)-IDA and Ni(II)-IDA functionalized langmuir monolayers: study of the protein layer structure during the adsorption process by neutron and X-ray reflectivity

The structure and orientation of adsorbed myoglobin as directed by metal-histidine complexation at the liquid-film interface was studied as a function of time using neutron and X-ray reflectivity (NR and XR, respectively). In this system, adsorption is due to the interaction between iminodiacetate (IDA)-chelated divalent metal ions Ni(II) and Cu(II) and histidine moieties at the outer surface of the protein. Adsorption was examined under conditions of constant area per lipid molecule at an initial pressure of 40 mN/m. Adsorption occurred over a time period of about 15 h, allowing detailed characterization of the layer structure throughout the process. The layer thickness and the in-plane averaged segment volume fraction were obtained at roughly 40 min intervals by NR. The binding constant of histidine with Cu(II)-IDA is known to be about four times greater than that of histidine with Ni(II)-IDA. The difference in interaction energy led to significant differences in the structure of the adsorbed layer. For Cu(II)-IDA, the thickness of the adsorbed layer at low protein coverage was < or = 20 A and the thickness increased almost linearly with increasing coverage to 42 A. For Ni(II)-IDA, the thickness at low coverage was approximately 38 A and increased gradually with coverage to 47 A. The in-plane averaged segment volume fraction of the adsorbed layer independently confirmed a thinner layer at low coverage for Cu(II)-IDA. These structural differences at the early stages are discussed in terms of either different preferred orientations for isolated chains in the two cases or more extensive conformational changes upon adsorption in the case of Cu(II)-IDA. Subphase dilution experiments provided additional insight, indicating that the adsorbed layer was not in equilibrium with the bulk solution even at low coverages for both IDA-chelated metal ions. We conclude that the weight of the evidence favors the interpretation based on more extensive conformational changes upon adsorption to Cu(II)-IDA.     

Role of long-range intermolecular forces in the formation of inorganic nanoparticle clusters

An understanding of the role played by intermolecular forces in terms of the electron density distribution is fundamental to the understanding of the self-assembly of molecules in the formation of a molecular crystal. Using ab initio methods capable of describing both short-range intramolecular interactions and long-range London dispersion interactions arising from electron correlation, analyses of inorganic dimers of As(4)S(4) and As(4)O(6) molecules cut from the structures of realgar and arsenolite, respectively, reveal that the molecules adopt a configuration that closely matches that observed for the crystal. Decomposition of the interaction energies using symmetry-adapted perturbation theory reveals that both model dimers feature significant stabilization from electrostatic forces as anticipated by a Lewis acid/Lewis base picture of the interaction. London dispersion forces also contribute significantly to the interaction, although they play a greater role in the realgar structure near equilibrium than in arsenolite.