Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer

The polyamidoamine (PAMAM) dendrimer prevents HIV-1 entry into target cells in vitro. Its mechanism of action, however, remains unclear and precludes the design of potent dendrimers targeting HIV-1 entry. We employed steered molecular dynamics simulations to examine whether the HIV-1 gp120-CD4 complex is a target of PAMAM. Our simulations mimicked single molecule force spectroscopy studies of the unbinding of the gp120-CD4 complex under the influence of a controlled external force. We found that the complex dissociates via complex pathways and defies the standard classification of adhesion molecules as catch and slip bonds. When the force loading rate was large, the complex behaved as a slip bond, weakening gradually. When the loading rate was small, the complex initially strengthened, akin to a catch bond, but eventually dissociated over shorter separations than with large loading rates. PAMAM docked to gp120 and destabilized the gp120-CD4 complex. The rupture force of the complex was lowered by PAMAM. PAMAM disrupted salt bridges and hydrogen bonds across the gp120-CD4 interface and altered the hydration pattern of the hydrophobic cavity in the interface. In addition, intriguingly, PAMAM suppressed the distinction in the dissociation pathways of the complex between the small and large loading rate regimes. Taken together, our simulations reveal that PAMAM targets the gp120-CD4 complex at two levels: it weakens the complex and also alters its dissociation pathway, potentially inhibiting HIV-1 entry.

Definition of the halogen bond (IUPAC Recommendations 2013)

This recommendation proposes a definition for the term ``halogen bond'', which designates a specific subset of the inter- and intramolecular interactions involving a halogen atom in a molecular entity.

Linear and nonlinear optical properties of expanded porphyrins: a DMRG study

We study absorption spectra and two photon absorption coefficient of expanded porphyrins (EPs) by the density matrix renormalization group (DMRG) technique. We employ the Pariser-Parr-Pople (PPP) Hamiltonian which includes long-range electron-electron interactions. We find that, in the 4n+2 EPs, there are two prominent low-lying one-photon excitations, while in 4n EPs, there is only one such excitation. We also find that 4n+2 EPs have large two-photon absorption cross sections compared to 4n EPs. The charge density rearrangement in the one-photon excited state is mostly at the pyrrole nitrogen site and at the meso carbon sites. In the two-photon states, the charge density rearrangement occurs mostly at the aza-ring sites. In the one-photon state, the C-C bond length in aza rings shows a tendency to become uniform. In the two-photon state, the bond distortions are on C-N bonds of the pyrrole ring and the adjoining C-C bonds which connect the pyrrole ring to the aza or meso carbon sites.

Layerwise decomposition of water dynamics in reverse micelles: A simulation study of two-dimensional infrared spectrum

We present computer simulation study of two-dimensional infrared spectroscopy (2D-IR) of water confined in reverse micelles (RMs) of various sizes. The present study is motivated by the need to understand the altered dynamics of confined water by performing layerwise decomposition of water, with an aim to quantify the relative contributions of different layers water molecules to the calculated 2D-IR spectrum. The 0-1 transition spectra clearly show substantial elongation, due to in-homogeneous broadening and incomplete spectral diffusion, along the diagonal in the surface water layer of different sized RMs. Fitting of the frequency fluctuation correlation functions reveal that the motion of the surface water molecules is sub-diffusive and indicate the constrained nature of their dynamics. This is further supported by two peak nature of the angular analogue of van Hove correlation function. With increasing system size, the water molecules become more diffusive in nature and spectral diffusion almost completes in the central layer of the larger size RMs. Comparisons between experiments and simulations establish the correspondence between the spectral decomposition available in experiments with the spatial decomposition available in simulations. Simulations also allow a quantitative exploration of the relative role of water, sodium ions, and sulfonate head groups in vibrational dephasing. Interestingly, the negative cross correlation between force on oxygen and hydrogen of O-H bond in bulk water significantly decreases in the surface layer of each RM. This negative cross correlation gradually increases in the central water pool with increasing RMs size and this is found to be partly responsible for the faster relaxation rate of water in the central pool. (C) 2013 AIP Publishing LLC.

Conformational Diversity in Contryphans from Conus Venom: cis-trans Isomerisation and Aromatic/Proline Interactions in the 23-Membered Ring of a 7-Residue Peptide Disulfide Loop

Conformational diversity or shapeshifting in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds.

Synergistic Lewis base and anion-binding catalysis for the enantioselective vinylogous addition of deconjugated butenolides to allenoates

An enantioselective vinylogous umpolung addition of deconjugated butenolides to allenoates has been developed for the first time with the help of synergistic combination of an achiral phosphine and a chiral squaramide, and represents the first example of a catalytic enantioselective C gamma-C gamma bond formation between two different carbonyl partners.

Computational Study of the Migration of Rhenium from One Enantioface of an Olefin to the Other Facilitated by (C-H)center dot center dot center dot Re Interactions

The migration of a metal atom in a metal olefin complex from one pi face of the olefin to the opposite pi face has been rarely documented. Gladysz and co-workers showed that such a movement is indeed possible in monosubstituted chiral Re olefin complexes, resulting in diastereomerization. Interestingly, this isomerization occurred without dissociation, and on the basis of kinetic isotope effects, the involvement of a trans C-H bond was indicated. Either oxidative addition or an agostic interaction of the vinylic C-H(D) bond with the metal could account for the experimentally observed kinetic isotope effect. In this study we compute the free energy of activation for the migration of Re from one enantioface of the olefin to the other through various pathways. On the basis of DFT calculations at the B3LYP level we show that a trans (C-H)center dot center dot center dot Re interaction and trans C-H oxidative addition provide a nondissociative path for the diastereomerization. The trans (C-H)center dot center dot center dot Re interaction path is computed to be more favorable by 2.3 kcal mol(-1) than the oxidative addition path. While direct experimental evidence was not able to discount the migration of the metal through the formation of a eta(2)-arene complex (conducted tour mechanism), computational results at the B3LYP level show that it is energetically more expensive. Surprisingly, a similar analysis carried out at the M06 level computes a lower energy path for the conducted tour mechanism and is not consistent with the experimental isotope effects observed. Metal-(C-H) interactions and oxidative additions of the metal into C-H bonds are closely separated in energy and might contribute to unusual fluxional processes such as this diastereomerization.

Some Themes in Chemical Crystallography Pertinent to the Indian Contribution

It is particularly appropriate that the Journal of the Indian Institute of Science is bringing out a commemorative issue to mark the International Year of Crystallography 2014 (IYCr2014). India has had a strong crystallographic tradition, and the earliest work in what may be described as structural crystallography from this country is the work of K. Banerjee on the determination of the crystal structure of naphthalene in 1930. The Indian Institute of Science itself has played no small part in establishing and sustaining the subject of crystallography in this country. A large number of papers in this special issue are written by authors who have either have been trained in the Institute or who have some kind of professional association with this organization. In this article I will try to capture some unique features that characterize the intersection of the crystallographic and the chemical domains, mostly as they pertain to the Indian contribution to this subject. Crystallography is of course is as old as chemistry itself, and some would say it is even older. The relationships between chemistry and crystallography go back to much before the discovery of diffraction of X-rays by crystals.The discovery of polymorphism by Mitscherlisch in 1822, Haüy’s formulation of the molecule integrante, and the work of Fedorov and Groth on the identification of crystals from their morphology alone, are well known examples of such relationships.A very early article by Tutton speaks of “crystallo-chemical analysis”. In this article, I shall, however, be dealing with the interplay of chemistry and crystallography only in the post diffraction era, that is, after 1912. Much had been written and said about chemical crystallography, and even within the context of the present special issue, there is a review of chemical crystallography in India including some futuristic trends. This topic was also reviewed by Nangia in a special publication brought out by Indian Academy of Sciences in 2009,and by Desiraju in a special publication brought out by the Indian National Science Academy in 2010. A rather detailed account of crystallography in India appeared in 2007 in the newsletter of the International Union of Crystallography (IUCr) in which chemical crystallography was detailed. Since all these publications are fairly recent there is little need for me to attempt a comprehensive coverage of chemical crystallography in India in this short review

ENDOR studies of hydrogen bonding of the AsO44- centre in x-ray irradiated KH2AsO4

We here report what we believe to be an important method for studying hydrogen bonding in systems containing a paramagnetic centre. The technique of electron-nuclear double resonance ( ENDOR) has been applied to study the hydrogen-bond network around the AsO44-. centre in X-ray irradiated KH2AsO4. ENDOR transitions from several sets of hydrogen nuclei surrounding the centre were observed at 4.2 degrees K and the spectra for two sets of neighbouring nuclei are identified. The angular dependences for these spectra are fitted with a spin-Hamiltonian to obtain the isotropic and anisotropic magnetic hyperfine constants. The results are discussed in terms of the available spectroscopic and crystallographic data on KH2AsO4 and the order-disorder model of ferroelectrictricity in this class of crystals.

Carbon nanoflake growth from carbon nanotubes by hot filament chemical vapor deposition

We report the growth of carbon nanoflakes (CNFs) on Si substrate by the hot filament chemical vapor deposition without the substrate bias or the catalyst. CNFs were grown using the single wall carbon nanotubes and the multiwall carbon nanotubes as the nucleation center, in the Ar-rich CH4-H-2-Ar precursor gas mixture with 1% CH4, at the chamber pressure and the substrate temperature of 7.5 Ton and 840 degrees C, respectively. In the H-2-rich condition, CNF synthesis failed due to severe etch-removal of carbon nanotubes (CNTs) while it was successful at the optimized Ar-rich condition. Other forms of carbon such as nano-diamond or mesoporous carbon failed to serve as the nucleation centers for the CNF growth. We proposed a mechanism of the CNF synthesis from the CNTs, which involved the initial unzipping of CNTs by atomic hydrogen and subsequent nucleation and growth of CNFs from the unzipped portion of the graphene layers. (C) 2013 Elsevier Ltd. All rights reserved.

Chemical vapor detection using nonlinear electrical properties of carbon nanotube bundles

We demonstrate the electrical transport behavior of carbon nanotubes (CNTs) upon exposure to organic analytes (namely ethanol, benzene, acetone and toluene). The resulting nonlinear current-voltage characteristics revealed a power law dependence of the differential conductivity on the applied bias voltage. Moreover, suppression of differential conductivity at zero bias is found to be dependent on different selective analytes. The power law exponent values have been monitored before, during and after exposure to the chemicals, which revealed a reversible change in the number of electron conducting channels. Therefore, the reduction in the number of conductive paths can be attributed to the interaction of the chemical analyte on the CNT surfaces, which causes a decrease in the differential conductivity of the CNT sample. These results demonstrate chemical selectivity of CNTs due to varying electronic interaction with different chemical analytes.

Calculation of Chemical Potentials and Occupancies in Clathrate Hydrates through Monte Carlo Molecular Simulations

The flexibility of the water lattice in clathrate hydrates and guest-guest interactions has been shown in previous studies to significantly affect the values of the thermodynamic properties, such as chemical potentials and free energies. Here we describe methods for computing occupancies, chemical potentials, and free energies that account for the flexibility of water lattice and guest-guest interactions in the hydrate phase. The methods are validated for a wide variety of guest molecules, such as methane, ethane, carbon dioxide, and tetrahydrodfuran by comparing the predicted occupancy values of guest molecules with those obtained from isothermal isobaric semigrand Monte Carlo simulations. The proposed methods extend the van der Waals and Platteuw theory for clathrate hydrates, and the Langmuir constant is calculated based on the structure of the empty hydrate lattice. These methods in combination with development of advanced molecular models for water and guest molecules should lead to a more thermodynamically consistent theory for clathrate hydrates.