Aggregation of chlorophylls in monolayers. Part IV. The reorganisation of chlorophyll a in multilayer array

The nature of the interaction between the chlorophyll a molecules in multilayer arrays obtained by the Langmuir-Blodgett technique is examined by electronic and infrared spectroscopies. Following the deposition of the multilayers, we observed a blue shift with time in the electronic spectra. This effect is monitored by infrared spectroscopy. The intensity of the coordinated ketone band is decreased while the intensity of the free ketone band is increased. These modifications are explained by the reorganization of the chlorophyll a molecules from an organized to a less organized one. The influence of H2O, D2O and SO2 vapors on the chlorophyll a multilayers give some informations on the role of water molecules in the aggregation of chlorophyll a in this ordered system. From these observations, a model is proposed for the multilayer arrangement implying two molecules of water per molecule of chlorophyll a.     

Phosphatidylcholine and cholesterol interactions in model membranes

Various phosphatidylcholines differing either in the stereochemistry around their chiral center or in the position of a cis double bond along the acyl chains were synthesized in order to study critical contact regions in the phospholipid molecule with adjacent cholesterol in model membranes. Microviscosities calculated from fluorescence depolarization of diphenylhexatriene and chain order from spin label studies were measured to monitor physical membrane properties. The enhancing effect of cholesterol on the microviscosity of membranes containing phosphatidylcholines with comparable acyl chain length was largest when the two acyl chains were saturated and smallest when both were unsaturated. Membranes prepared from phosphatidylcholines having a single cis double bond at different positions along the sn-2 acyl chain showed roughly the same changes of microviscosity or chain order upon incorporation of cholesterol. No discrimination was evident in the interaction between cholesterol and enantiomeric phosphatidylcholines or between the enantiomeric phosphatidylcholine molecules themselves. We conclude that the rigidifying effect of cholesterol in membranes does not depend on specific sites of interaction and that with respect to physical membrane properties phosphatidylcholine behaves as an achiral molecule.     

Experimental and theoretical investigations on the folding modes of depsipeptide molecules

The coupling of N-acyl-α-amino-acids with α-hydroxyacid-methyl amides results in depsipeptide molecules containing two chiral centers and one ester function inserted between two amide functions. Their conformational features have been investigated by IR spectroscopy, proton magnetic resonance, X-ray diffraction, and theoretical P.C.I.L.O. calculations. It is shown that most of these molecules are folded by an intramolecular 4 → 1 hydrogen bonding. Two folded conformations, similar to the well known β turn in peptides, are described, the stability of which depends on the configurational sequence in the investigated molecule. LL and LD species are folded in two different ways whereas LG sequences containing an achiral hydroxy-acid residue accommodate both of them. The presence of a N-terminal achiral amino acid noticeably decreases the folding ratio. The above conclusions are then compared with the conformational features of homologous tripeptide molecules.     

Optical Properties of DNA in Aqueous Solution

In the study of DNA electric birefringence, it is usual to use theories that consider that molecules in solution are small in relation to the light wavelength. In this work, we study the DNA electric birefringence using a broken-rod macroion (BRM) model composed of two cylindrical arms which does not restrict the size of the molecules. To achieve this, we include the inhomogeneity effect of the light electric field through the molecule and the interaction between its different parts. To analyze the interaction between a molecule and the incident beam of light, we apply the discrete dipole approximation (DDA), according to which each molecule is described as a finite array of electronic coupled oscillators. The electric birefringence is calculated from the oscillator polarizability. This is obtained from experimental data of electric birefringence saturation and from the increment of the solution refraction index in relation to that of the solvent. Furthermore, the oscillator polarizability is also estimated from DNA absorption spectrum using the Kronig–Kramers relations. This allows us to analyze the contributions of the different absorption bands of DNA to the electric birefringence. We analyze the influence of the inhomogeneity of the light electric field and of the intramolecular interactions in the characterization of DNA optical properties using electric birefringence measurements.     

Sensing behavior of Al-rich AlN nanotube toward hydrogen cyanide

In order to explore a sensor for detection of toxic hydrogen cyanide (HCN) molecules, interaction of pristine and defected Al-rich aluminum nitride nanotubes (AlNNT) with a HCN molecule has been investigated using density functional theory calculations in terms of energetic, geometric, and electronic properties. It has been found that unlike the pristine AlNNT, the Al-rich AlNNT can effectively interact with the HCN molecule so that its conductivity changes upon the exposure to this molecule. The adsorption energies of HCN on the pristine and defected AlNNTs have been calculated to be in the range of ?0.16 to ?0.62 eV and ?1.75 to ?2.21 eV, respectively. We believe that creating Al-rich defects may be a good strategy for improving the sensitivity of these tubes toward HCN molecules, which cannot be trapped and detected by the pristine AlNNT.     

An extension of the tersoff-hamann model for a molecule on a graphite support: STM-image construction

A method is proposed for the theoretical construction of STM images of adsorbates on a graphite support. Tunnel current is taken to be proportional to the local density of graphite electronic states perturbed by the interaction with the adsorbed molecule. The coefficients of mixing of the graphite states with the adsorbate MOs are found by first-order perturbation theory, using the CNDO-S² method to calculate the adsorbate electronic structure together with analytical expressions for the graphite states. The long-distance behavior of adsorbate MOs is taken into account by means of energy-dependent MO asymptotics. As an example of the implications of this technique, the theoretical STM images of benzene and butane molecules on a graphite surface are presented and discussed.     

Reactivity of phosphorene with a 3d element trioxide (CrO<Subscript>3</Subscript>) considering van der Waals molecular interactions: a DFT-D2 study

First-principle calculations are performed to investigate the interaction between clean black phosphorene and the CrO₃ molecule which is known to be a powerful oxidizer and a suspected carcinogen. Van der Waals forces are included in all calculations through empirical corrections. Energetics studies are first done to determine the structural stability. Then charge density, Löwdin population analysis and electronic states are evaluated. Results show that the CrO₃ molecule, with an acceptor electron character, is chemisorbed on the phosphorene surface inducing minimal geometrical distortions, however, after adsorption, a partial charge gradient is produced between the P atoms located at the phosphorene upper and lower planes. Furthermore, variations on the CrO₃ concentration causes different interaction strengths. At high concentrations of adsorbed CrO₃ molecules, the interaction with the surface becomes stronger due to an increased steric effect between neighboring molecules. Nevertheless, this effect along with the geometrical distortions produced on the phosphorene structure, due to the large number of molecules adsorbed, leads to a decrement on the adsorption energy. It is expected that the reported results may render phosphorene as a promising material for application as a gas sensor.     

Structure-activity studies of a series of dipyrazolo[3,4-b:3',4'-d]pyridin-3-ones binding to the immune regulatory protein B7.1

The interaction of co-stimulatory molecules on T cells with B7 molecules on antigen presenting cells plays an important role in the activation of naive T cells. Consequently, agents that disrupt these interactions should have applications in treatment of transplant rejection as well as autoimmune diseases. To this end, specific small molecule inhibitors of human B7.1 were identified and characterized. Herein, we report the identification of potent small molecule inhibitors of the B7.1-CD28 interaction. In a high-throughput screen we identified several leads that prevented the interaction of B7.1 with CD28 with activities in the nanomolar to low micromolar range. One of these, the dihydrodipyrazolopyridinone 1, was subsequently shown to bind the V-like domain of human B7.1 at equimolar stoichiometry. With this as a starting point, we report here the synthesis and initial in vitro structure-activity relationships of a series of these compounds.     

Molecular recognition of human CD1b antigen complexes: evidence for a common pattern of interaction with alpha beta TCRs

Ag-specific T cell recognition is mediated through direct interaction of clonotypic TCRs with complexes formed between Ag-presenting molecules and their bound ligands. Although characterized in substantial detail for class I and class II MHC encoded molecules, the molecular interactions responsible for TCR recognition of the CD1 lipid and glycolipid Ag-presenting molecules are not yet well understood. Using a panel of epitope-specific Abs and site-specific mutants of the CD1b molecule, we showed that TCR interactions occur on the membrane distal aspects of the CD1b molecule over the alpha1 and alpha2 domain helices. The location of residues on CD1b important for this interaction suggested that TCRs bind in a diagonal orientation relative to the longitudinal axes of the alpha helices. The data point to a model in which TCR interaction extends over the opening of the putative Ag-binding groove, making multiple direct contacts with both alpha helices and bound Ag. Although reminiscent of TCR interaction with MHC class I, our data also pointed to significant differences between the TCR interactions with CD1 and MHC encoded Ag-presenting molecules, indicating that Ag receptor binding must be modified to accommodate the unique molecular structure of the CD1b molecule and the unusual Ags it presents.     

Si-doped graphene: an ideal sensor for NO- or NO<Subscript>2</Subscript>-detection and metal-free catalyst for N<Subscript>2</Subscript>O-reduction

Exploring and evaluating the potential applications of two-dimensional graphene is an increasingly hot topic in graphene research. In this paper, by studying the adsorption of NO, N₂O, and NO₂ on pristine and silicon (Si)-doped graphene with density functional theory methods, we evaluated the possibility of using Si-doped graphene as a candidate to detect or reduce harmful nitrogen oxides. The results indicate that, while adsorption of the three molecules on pristine graphene is very weak, Si-doping enhances the interaction of these molecules with graphene sheet in various ways: (1) two NO molecules can be adsorbed on Si-doped graphene in a paired arrangement, while up to four NO₂ molecules attach to the doped graphene with an average adsorption energy of −0.329 eV; (2) the N₂O molecule can be reduced easily to the N₂ molecule, leaving an O-atom on the Si-doped graphene. Moreover, we find that adsorption of NO and NO₂ leads to large changes in the electronic properties of Si-doped graphene. On the basis of these results, Si-doped graphene can be expected to be a good sensor for NO and NO₂ detection, as well as a metal-free catalyst for N₂O reduction.     

A new type of semi-empirical molecular orbital method for large molecules.

A new type of molecular orbital method is proposed. It is applicable to large molecules containing large conjugated substructures. Only π-electrons in the conjugated part, but all-valence electrons in the non-conjugated part of a molecule, are taken into account explicitly. The Fock matrix elements are evaluated from the semi-empirical values employed in the existing all-valence-electron methods. The examples presented here suggest that the new type of MO method predicts electronic structures which are quite similar to those obtained by complete semi-empirical MO calculations. This new method may make it possible to reasonably well describe the electronic structure of, and interaction between, large molecules using considerably less computation time and core storage than the complete calculation analogs.     

Circular dichroism study of the interaction of mitoxantrone, ametantrone and their Pd(II) complexes with deoxyribonucleic acid

The interaction of mitoxantrone, ametantrone and their Pd(II) complexes with DNA have been studied using absorption and circular dichroism spectroscopy. We have shown that mitoxantrone forms with Pd(II) a complex in which two Pd(II) ions are bound to two molecules of drug (D1 and D2). One Pd(II) ion is bound to the two nitrogens of the side chain on C-5 of molecule D1 and to the two nitrogens of the side chain on C-5 of molecule D2, whereas the second Pd(II) ion is bound to the nitrogens of the side chain on C-8 of molecule D1 and of molecule D2. The same complex is formed between Pd(II) and ametantrone. The stability constants for these complexes are, respectively, beta M = (1.4 +/- 0.5).10(19) and beta A = (2.5 +/- 0.5).10(18). They display antitumor activity against P 388 leukemia which compares with that of the free drugs. Interactions of the free drugs with DNA have been studied. Mitoxantrone and ametantrone are not optically active by themselves. However, through interaction with DNA, there is an induction of optical activity within the electronic transitions of both drugs. At a nucleotide/drug molar ratio lower than about 5 a CD signal of the couplet type is observed, suggesting that there is a coupling between the pi----pi transitions of the molecules of drugs intercalated between the base pairs. This coupling disappears when the molar ratio is increased. The interactions of the Pd(II) complexes with DNA do not give rise to induction of optical activity within the electronic transition of the drugs, indicating that the presence of the metal ion prevents the intercalation of the drugs between the base pairs.     

Using small molecules to study big questions in cellular microbiology

High-throughput screening of small molecules is used extensively in pharmaceutical settings for the purpose of drug discovery. In the case of antimicrobials, this involves the identification of small molecules that are significantly more toxic to the microbe than to the host. Only a small percentage of the small molecules identified in these screens have been studied in sufficient detail to explain the molecular basis of their antimicrobial effect. Rarer still are small molecule screens undertaken with the explicit goal of learning more about the biology of a particular microbe or the mechanism of its interaction with its host. Recent technological advances in small molecule synthesis and high-throughput screening have made such mechanism-directed small molecule approaches a powerful and accessible experimental option. In this article, we provide an overview of the methods and technical requirements and we discuss the potential of small molecule approaches to address important and often otherwise experimentally intractable problems in cellular microbiology.     

Cutting edge: molecular analysis of the negative regulatory function of lymphocyte activation gene-3

Lymphocyte activation gene (LAG)-3 (CD223) is a CD4-related activation-induced cell surface molecule that binds to MHC class II molecules with high affinity and negatively regulates T cell expansion and homeostasis. In this study, we show that LAG-3 inhibits CD4-dependent, but not CD4-independent, T cell function via its cytoplasmic domain. Although high affinity interaction with MHC class II molecules is essential for LAG-3 function, tailless LAG-3 does not compete with CD4 for ligand binding. A single lysine residue (K468) within a conserved "KIEELE" motif is essential for interaction with downstream signaling molecules. These data provide insight into the mechanism of action of this important T cell regulatory molecule.     

The anomalous variation of successive molecular ionization energies and the electron-vibrational interaction

In this work we point out the conditions which determine the anomalous variation of successive molecular ionization energies. It is shown that this variation arises when the strong electronvibrational interaction coming from the change of the number of electrons in a molecule exceeds the Coulomb electronic repulsion. The interrelation between this effect and the mechanism of the disproportionation reaction is discussed.     

Viewing and Inducing Symmetry Breaking at the Single‐Molecule Limit

Symmetry breaking by photons, electrons, and molecular interactions lies at the heart of many important problems as varied as the origin of homochiral life to enantioselective drug production. Herein we report a system in which symmetry breaking can be induced and measured in situ at the single‐molecule level using scanning tunneling microscopy. We demonstrate that electrical excitation of a prochiral molecule on an achiral surface produces large enantiomeric excesses in the chiral adsorbed state of up to 39%. The degree of symmetry breaking was monitored as a function of scanning probe tip state, and the results revealed that enantiomeric excesses are correlated with the intrinsic chirality in scanning probe tips themselves, as evidenced by height differences between single molecule enantiomers. While this work has consequences for the study of two‐dimensional chirality, more importantly, it offers a new method for interrogating the coupling of photons, electrons, and combinations of physical fields to achiral starting systems in a reproducible manner. This will allow the mechanism of chirality transfer to be studied in a system in which enantiomeric excesses are quantified accurately by counting individual molecules. Chirality 24:1051–1054, 2012. © 2012 Wiley Periodicals, Inc.     

Stretching Submicron Biomolecules with Constant-Force Axial Optical Tweezers

Optical tweezers have become powerful tools to manipulate biomolecular systems, but are increasingly difficult to use when the size of the molecules is <1 μm. Many important biological structures and processes, however, occur on the submicron length scale. Therefore, we developed and characterized an optical manipulation protocol that makes this length scale accessible by stretching the molecule in the axial direction of the laser beam, thus avoiding limiting artifacts from steric hindrances from the microscope coverslip and other surface effects. The molecule is held under constant mechanical tension by a combination of optical gradient forces and backscattering forces, eliminating the need for electronic feedback. We demonstrate the utility of this method through a measurement of the force-extension relationship of a 1298 bp ds-DNA molecule.     

Towards a circular bis-peptide nucleic acid

En route to a circular bis-PNA molecule, we have synthesized and characterized the DNA binding of several "clamp"-type bis-PNAs. In order to incorporate charge into a circular PNA, a new linker based on the achiral 2-aminoethylglycine has been used.