Structure and stability of the sH binary hydrate cavity and host-guest versus guest-guest interactions therein: A DFT approach.

The intrinsic ability of clathrate hydrates to encage gaseous molecules is explored. Encapsulation ability depends on the cavity size and the type of guest gaseous species in addition to the physical parameters, temperature and pressure. Here we have reported the structure, stability and nature of interaction in dissimilar guest occupied sH hydrate cavity. Diatomic gas molecules and small polyatomic hydrocarbons are considered as guests. The irregular icosahedron (512 68 ) cavity of sH hydrate is the host. Different thermodynamic parameters for the guest molecules encapsulation were calculated using three different hybrid DFT functionals, B3LYP, M05-2X, M06, and moreover using dispersion correction (PBE0-D3). With the consideration of large H-bonded systems the 6-31G* and cc-pVTZ basis sets were used for two set of computations. To disclose the nature of interaction between the host-guest systems as well as the interaction between the guest molecules inside the host the non-covalent interaction (NCI) indices and energy decomposition analysis (EDA) were done. Impact of host-guest and guest-guest interactions are discussed.

Intriguing structural, bonding and reactivity features in some beryllium containing complexes.

Although the toxicity of beryllium compounds causes impediments in experiments involving them, beryllium chemistry has seen a recent upsurge of interest and considerable progress. Computations play a very important complementary role in analyzing the structure, stability and bonding of these compounds. In this perspective article, we highlighted our contribution to beryllium chemistry which is either completely through theoretical results or sometimes supported by experimental findings. It starts with the smallest 2π aromatic system, Be32-, which also exhibits rare bond-stretch isomerism. Furthermore, its reactivity towards different transformations is mentioned. Because of the ability of beryllium to attain a high ionic potential, the beryllium center in an appropriate situation can act as an excellent Lewis acid which is utilized to bind noble gas (Ng) atoms, carbon monoxide and dinitrogen through donor-acceptor types of interactions. We made several efforts to have strong Ng-Be bonds which led us to NgBeNCN that is recorded to have the strongest Ng-Be bond among the neutral Ng-Be complexes reported so far. Significant dinitrogen activation was also achieved in (NN)2Be(η2-N2) and OCBeNN complexes. In the latter case, a complete cleavage of the N-N bond producing the most stable NBeNCO molecule has occurred. We also found viable M2(NHBMe)2 (M = Be, Mg) complexes having unusual bonding where the interacting fragments are best described as the neutral M2 and (NHBMe)2 but M2 still possesses a single bond. We finally discussed the complex comprising an unusual Be(i) oxidation state, [BeI(cAACAr)2]+˙ and di-ortho-beryllated carbodiphosphorane exhibiting Be⇇C double dative bonds.

Discovery of isoquinolinone and naphthyridinone-based inhibitors of poly(ADP-ribose) polymerase-1 (PARP1) as anticancer agents: Structure activity relationship and preclinical characterization.

The exploitation of GLU988 and LYS903 residues in PARP1 as targets to design isoquinolinone (I & II) and naphthyridinone (III) analogues is described. Compounds of structure I have good biochemical and cellular potency but suffered from inferior PK. Constraining the linear propylene linker of structure I into a cyclopentene ring (II) offered improved PK parameters, while maintaining potency for PARP1. Finally, to avoid potential issues that may arise from the presence of an anilinic moiety, the nitrogen substituent on the isoquinolinone ring was incorporated as part of the bicyclic ring. This afforded a naphthyridinone scaffold, as shown in structure III. Further optimization of naphthyridinone series led to identification of a novel and highly potent PARP1 inhibitor 34, which was further characterized as preclinical candidate molecule. Compound 34 is orally bioavailable and displayed favorable pharmacokinetic (PK) properties. Compound 34 demonstrated remarkable antitumor efficacy both as a single-agent as well as in combination with chemotherapeutic agents in the BRCA1 mutant MDA-MB-436 breast cancer xenograft model. Additionally, compound 34 also potentiated the effect of agents such as temozolomide in breast cancer, pancreatic cancer and Ewing's sarcoma models.

The role of viscosity in various dynamical processes of different fluorophores in ionic liquid-cosolvent mixtures: a femtosecond fluorescence upconversion study.

Literature reports provide ample evidence of the dynamical studies of various fluorophores in different room-temperature ionic liquid (RTIL)-cosolvent mixtures. However, most of the experimental and simulation studies reveal that ∼50% of the spectral relaxation dynamics is fast and cannot be resolved using traditional time correlated single photon counting (TCSPC) measurements. Our group has also investigated the dynamics of a solvatochromic probe coumarin 153 (C153) in a RTIL-cosolvent mixture using a TCSPC setup (S. Sarkar, R. Pramanik, C. Ghatak, P. Setua and N. Sarkar, J. Phys. Chem. B, 2010, 114, 2779-2789). Consequently, a major portion of the solvation dynamics remained undetected and moreover we could not monitor the dynamics beyond 0.4 mole fraction of the cosolvents. Thus in this study, we have rekindled our interest to sufficiently capture the rotational anisotropy and solvation dynamics of C153 beyond 0.4 mole fraction of the cosolvents in the RTIL-cosolvent mixture employing femtosecond fluorescence upconversion measurements. Additionally, we have utilized another RTIL with a higher alkyl chain length and viscosity to obtain a comprehensive and quantitative picture of the role of viscosity on the dynamics of the probe molecule. The most interesting observation of the present work is that the viscosities of different RTIL-cosolvent mixtures can efficiently control the cis-trans isomerization kinetics of the anionic fluorophore merocyanine 540 (MC 540) and the translational diffusion of a hydrophobic probe. The optimization of geometrical structures of [EmimOs]- and [EmimOs]-cosolvent mixtures followed by frequency analyses in both gas and solution phases have been carried out using quantum chemical calculations with the aid of density functional theory (DFT) methods. The computation based on the bond distances, electron densities and non-covalent interactions (NCI) has also been used to investigate the existence of the hydrogen-bond (H-bond). Again to comprehend van der Waals interactions and the conventional hydrogen-bond, the evolution of NCI plots are simulated. Therefore, the detailed experimental and theoretical studies presented in this manuscript lead to the inference that addition of the conventional solvents finely tunes the physicochemical properties of RTILs and broadens their scope of applications in the fields of chemistry and biology.

Noble-Noble Strong Union: Gold at Its Best to Make a Bond with a Noble Gas Atom.

This Review presents the current status of the noble gas (Ng)-noble metal chemistry, which began in 1977 with the detection of AuNe+ through mass spectroscopy and then grew from 2000 onwards; currently, the field is in a somewhat matured state. On one side, modern quantum chemistry is very effective in providing important insights into the structure, stability, and barrier for the decomposition of Ng compounds and, as a result, a plethora of viable Ng compounds have been predicted. On the other hand. experimental achievement also goes beyond microscopic detection and characterization through spectroscopic techniques and crystal structures at ambient temperature; for example, (AuXe4)2+(Sb2F11 -)2 have also been obtained. The bonding between two noble elements of the periodic table can even reach the covalent limit. The relativistic effect makes gold a very special candidate to form a strong bond with Ng in comparison to copper and silver. Insertion compounds, which are metastable in nature, depending on their kinetic stability, display an even more fascinating bonding situation. The degree of covalency in Ng-M (M=noble metal) bonds of insertion compounds is far larger than that in non-insertion compounds. In fact, in MNgCN (M=Cu, Ag, Au) molecules, the M-Ng and Ng-C bonds might be represented as classical 2c-2e σ bonds. Therefore, noble metals, particularly gold, provide the opportunity for experimental chemists to obtain sufficiently stable complexes with Ng at room temperature in order to characterize them by using experimental techniques and, with the intriguing bonding situation, to explore them with various computational tools from a theoretical perspective. This field is relatively young and, in the coming years, a lot of advancement is expected experimentally as well as theoretically.

Noble Gas Inserted Metal Acetylides (Metal = Cu, Ag, Au).

Metal acetylides (MCCH, M = Cu, Ag, Au) were already experimentally detected in molecular form. Herein, we investigate the possibility of noble gas (Ng) insertion within the C-H bond of MCCH and their stability is compared with those of the reported MNgCCH and HCCNgH molecules. Our coupled-cluster-level computations show that MCCNgH (Ng = Kr, Xe, Rn) systems are local minima on the corresponding potential energy surfaces, whereas their lighter analogues do not remain in the chemically bound form. Further, their stability is analyzed with respect to all possible dissociation channels. The most favorable dissociation channel leads to the formation of free Ng and MCCH. However, there exists a high free energy barrier (29.3-46.9 kcal/mol) to hinder the dissociation. The other competitive processes against their stability include two-body and three-body neutral dissociation channels, MCCNgH → MCC + NgH and MCCNgH → MCC + Ng + H, respectively, which are slightly exergonic in nature at 298 K for Ng = Kr, Xe and M = Cu, Ag, and for AuCCKrH. However, the Xe analogues for Cu and Ag and AuCCKrH would be viable at a lower temperature. AuCCNgH (Ng = Kr-Rn) molecules are the best candidates for experimental realization, since they have higher dissociation energy values and higher kinetic protection in the case of feasible dissociation channels compared to the Cu and Ag systems. A detailed bonding analysis indicates that the Ng-H bonds are genuine covalent bonds and there is also a substantial covalent character in Ng-C contacts of these molecules. Moreover, the possibility of insertion of two Xe atoms in AuCCH resulting in AuXeCCXeH and the stability of XeAuXeCCXeH are also tested herein.

Cyanide-isocyanide isomerization: stability and bonding in noble gas inserted metal cyanides (metal = Cu, Ag, Au).

The internal isomerization, MNC ↔ MCN (M = Cu, Ag, Au), is investigated through quantum chemical computations. CuNC and AgNC are shown to be neither thermochemically nor kinetically stable against transformation to MCN. The free energy barrier (ΔG‡) for AuNC is somewhat considerable (7.1 kcal mol-1), indicating its viability, particularly at low temperature. Further, the Ng inserted analogues, MNgCN (M = Cu, Ag, Au; Ng = Xe, Rn) turn out to be thermochemically stable with respect to all possible dissociation channels but for two two-body dissociation channels, viz., MNgCN → Ng + MCN and MNgCN → Ng + MNC, which are connected to the internal isomerization processes, MNgCN → NgMCN and MNgCN → NgMNC, respectively. However, they are kinetically protected by substantial ΔG‡ values (11.8-15.4 kcal mol-1 for Cu, 9.8-13.6 kcal mol-1 for Ag, and 19.7-24.7 kcal mol-1 for Au). The pathways for such internal conversion are explored in detail. A thorough inspection of the bonding situation of the studied molecules, employing natural bond order, electron density, adaptive natural density partitioning, and energy decomposition analyses indicates that the M-Ng bonds in MNgCN and Ng-C bonds in AuNgCN can be represented as an electron-shared covalent bond. For the other Ng-C bonds, although an ionic description is better suited, the degree of covalent character is also substantial therein.

Stable NCNgNSi (Ng=Kr, Xe, Rn) Compounds with Covalently Bound C-Ng-N Unit: Possible Isomerization of NCNSi through the Release of the Noble Gas Atom.

Although the noble gas (Ng) compounds with either Ng-C or Ng-N bonds have been reported in the literature, compounds containing both bonds are not known. The first set of systems having a C-Ng-N bonding unit is predicted herein through the analysis of stability and bonding in the NCNgNSi (Ng=Kr-Rn) family. While the Xe and Rn inserted analogues are thermochemically stable with respect to all dissociation channels, but for the one producing CNSiN and free Ng, NCKrNSi has another additional three-body dissociation channel, NCKrNSi→CN+Kr+NSi, which is exergonic by -9.8 kcal mol-1 at 298 K. This latter dissociation can be hindered by lowering the temperature. Moreover, the NCNgNSi→Ng+CNSiN dissociation is also kinetically prohibited by a quite high free energy barrier ranging from 25.2 to 39.3 kcal mol-1 , with a gradual increase in going from Kr to Rn. Therefore, these compounds are appropriate candidates for experimental realization. A detailed bonding analysis by employing natural bond orbital, electron density, energy decomposition, and adaptive natural density partitioning analyses indicates that both Ng-N and C-Ng bonds in the title compounds are covalent in nature. In fact, the latter analysis indicates the presence of delocalized 3c-3e σ-bond within the C-Ng-N moiety and a totally delocalized 5c-2e σ-bond in these compounds. This is an unprecedented bonding characteristic in the sense that the bonding pattern in Ng inserted compounds is generally represented as the presence of covalent bond in one side of Ng, and the ionic interaction in the other side. Further, the dissociation of Ng from NCNgNSi facilitates the formation of a higher energy isomer of NCNSi, CNSiN, which cannot be formed from bare NCNSi as such, because of the very high free energy barrier associated with the isomeric transformation. Therefore, in the presence of Ng atoms it might be possible to detect the high energy isomer.

Endohedral gas adsorption by cucurbit[7]uril: a theoretical study.

The selectivity of cucurbit[7]uril (CB[7]) towards adsorbing a series of 14 molecules encompassing four hydrocarbons (C2H2, C2H4, C2H6, and CH4), diatomic molecules of halogens (F2 and Cl2), nitrogen oxides (NO2 and NO), carbon oxides (CO2 and CO), SO2, H2S, N2, and H2 is explored via a density functional theory based study. CB[7] is noted to have high selectivity towards adsorbing SO2 over the other considered molecules, highlighting its probable utility to separate SO2 from flue gas or other gas mixtures containing these molecules. The nature of bonding is deciphered via the computations of non-covalent interaction indices and energy decomposition analysis. Although in all cases the dispersion interaction turns out to be the most dominating contributor in stabilizing these complexes, the electrostatic contribution is also considerable. In fact, the combined effect of these two energy terms in SO2@CB[7] is responsible for the obtained selectivity.

Binding of Small Gas Molecules by Metal-Bipyridyl Monocationic Complexes (Metal = Cu, Ag, Au) and Possible Bond Activations Therein.

The viability of a series of small gas molecules (H2, N2, CO, CO2, H2O, H2S, C2H2, CH4, CH3Cl, C2H4, and C2H6) bound [M-(bipy)]+ (bipy = bipyridyl; M = Cu, Ag, Au) complexes is investigated at the PBE0/cc-pVTZ/cc-pVTZ-PP level with a special emphasis on the possible bond activation within the bound ligands. While the bond dissociation energy, enthalpy change, and free energy change are computed to show the stability of the complexes with respect to the dissociation into [M-(bipy)]+ and free gas molecule (L), natural bond orbital, electron density, and energy decomposition analyses in conjunction with natural orbitals for chemical valence are carried out to characterize the nature of L-M bonds. For a given L, the L binding ability is the highest for Au followed by Cu and Ag complexes, except for quite loosely bound CO2. For all ligand cases, the dissociation processes from the respective bound complexes are endergonic in nature at room temperature, except for the H2-, CH4-, and C2H6-bound Ag complexes and CO2-bound Ag and Au complexes. The interaction between L and M centers is supported by orbital and ionic interactions with latter being more dominant over the former. The delocalization index and local energy density values support the covalent character in L-M bonds in most of the cases. These M centers can act as a mild bond activation agent for L, Au being the best candidate in this series for this purpose. Particularly, the H-H bond in H2, C═C bond in C2H4, C≡C bond in C2H2, and C-H bonds in CH4 and C2H6 (the last two are for Au) are elongated along with a significant red-shift in the corresponding stretching frequency, compared to those in free molecules. These can be explained by the significant π-back-donation populating the lowest unoccupied antibonding molecular orbital of L in these complexes.