Structural characterization of the (MeSH)4 potential energy surface

A random walk on the PES for (MeSH)₄ clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

Ammonium adsorption on Brønsted acidic centers on low-index vanadium pentoxide surfaces

Vanadium-based catalysts are used in many technological processes, among which the removal of nitrogen oxides (NO_x) from waste gases is one of the most important. The chemical reaction responsible for this selective catalytic reaction (SCR) is based on the reduction of NO_x molecules to N₂, and a possible reductant in this case is pre-adsorbed NH₃. In this paper, NH₃ adsorption on Brønsted OH acid centers on low-index surfaces of V₂O₅ (010, 100, 001) is studied using a theoretical DFT method with a gradient-corrected functional (RPBE) in the embedded cluster approximation model. The results of the calculations show that ammonia molecules are spontaneously stabilized on all low-index surfaces of the investigated catalyst, with adsorption energies ranging from ?0.34 to ?2 eV. Two different mechanisms of ammonia adsorption occur: the predominant mechanism involves the transfer of a proton from a surface OH group and the stabilization of ammonia as an NH₄ ⁺ cation bonded to surface O atom(s), while an alternative mechanism involves the hydrogen bonding of NH₃ to a surface OH moiety. The latter binding mode is present only in cases of stabilization over a doubly coordinated O(2) center at a (100) surface. The results of the calculations indicate that a nondirectional local electrostatic interaction with ammonia approaching a surface predetermines the mode of stabilization, whereas hydrogen-bonding interactions are the main force stabilizing the adsorbed ammonia. Utilizing the geometric features of the hydrogen bonds, the overall strength of these interactions was quantified and qualitatively correlated (R?=?0.93) with the magnitude of the stabilization effect (i.e., the adsorption energy).

Boron nitride nanotube based nanosensor for acetone adsorption: a DFT simulation

We have investigated the adsorption properties of acetone on zigzag single-walled BNNTs using density functional theory (DFT) calculations. The results obtained show that acetone is strongly bound to the outer surface of a (5,0) BNNT on the top site directly above the boron atom, with a binding energy of ?96.16 kJ?mol^?1 and a B–O binding distance of 1.654 Å. Our first-principles calculations also predict that the ability of zigzag BNNTs to adsorb acetone is significantly stronger than the corresponding ability of zigzag CNTs. A comparative investigation of BNNTs with different diameters indicated that the ability of the side walls of the tubes to adsorb acetone decreases significantly for nanotubes with larger diameters. Furthermore, the stability of the most stable acetone/BNNT complex was tested using ab initio molecular dynamics simulation at room temperature.

Conformational entropy of a polymer chain grafted to rough surfaces

A polymer molecule (represented by a statistical chain) end-grafted to a topologically rough surface was studied by static MC simulations. A modified self-avoiding walk on a cubic lattice was used to model the polymer in an athermal solution. Different statistical models of surface roughness were applied. Conformational entropies of chains attached to uncorrelated Gaussian, Brownian, and fractional Brownian surfaces were calculated. Results were compared with the predictions of a simple analytical model of a macromolecule end-grafted to a fractal surface.

Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies

We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

Theoretical study of hydrogen bonding interactions on MDI-based polyurethane

Hydrogen bonding among hard–hard segments and hard–soft segments in 4,4′-diphenylmethane diisocyanate (MDI)-based polyurethane was investigated theoretically by density functional theory (DFT). Both B3LYP/6-31G* and B3PW91/6-31G* methods gave good structures, reasonable Mulliken charges, binding energies, dipole moments, and good infrared (IR) spectra trends in predicting hydrogen bonding. Bond distances R(N–H?O), which were in the range of 3.005–3.028 Å for the carbonyl bonded hydrogen-bond, and 3.074–3.075 Å for the ester bonded hydrogen-bond, are in reasonable agreement with experimental values. Most of the carbonyl oxygen in polyurethane exists in a hydrogen-bonded form. Complex (c), with two carbonyl hydrogen bonds, features the largest dipole moment, while complex (d) with two ester hydrogen bonds, possesses the smallest dipole moment, i.e., lower than that of the isolated monomer, which may be due to the symmetry of the two monomers. These results confirm that the DFT method is a good tool with which to study weak interactions, and indicate that hydrogen bonds are indeed formed between carbonyl and N-H, or ester and N-H, with the former being stronger.

Theoretical study of the triangular bonding complex formed by carbon tetrabromide, a halide, and a solvent molecule in the gas phase

MP2(full)/aug-cc-pVDZ(-PP) computations predict that new triangular bonding complexes (where X^? is a halide and H–C refers to a protic solvent molecule) consist of one halogen bond and two hydrogen bonds in the gas phase. Carbon tetrabromide acts as the donor in the halogen bond, while it acts as an acceptor in the hydrogen bond. The halide (which commonly acts as an acceptor) can interact with both carbon tetrabromide and solvent molecule (CH₃CN, CH₂Cl₂, CHCl₃) to form a halogen bond and a hydrogen bond, respectively. The strength of the halogen bond obeys the order CBr₄???Cl^? > CBr₄???Br^? > CBr₄???I^?. For the hydrogen bonds formed between various halides and the same solvent molecule, the strength of the hydrogen bond obeys the order C-H???Cl^? > C-H???Br^? > C-H???I^?. For the hydrogen bonds formed between the same halide and various solvent molecules, the interaction strength is proportional to the acidity of the hydrogen in the solvent molecule. The diminutive effect is present between the hydrogen bonds and the halogen bond in chlorine and bromine triangular bonding complexes. Complexes containing iodide ion show weak cooperative effects.

Relativistic theoretical studies on hydrogen bonds and the electronic structure of aqueous solvated bis(uranyl) complex: an insight into explicit and/or implicit solvent effects

To understand the chemical behavior of uranyl complexes in water, a bis-uranyl [(phen)(UO₂)(μ₂–F)(F)]₂ (A; phen?=?phenanthroline, μ₂?=?doubly bridged) and its hydrated form A?·?(H₂O)_n (n?=?2, 4 and 6) were examined using scalar relativistic density functional theory. The addition of water caused the phen ligands to deviate slightly from the U₂(μ₂–F)₂ plane, and red-shifts the U–F-terminal and U?=?O stretching vibrations. Four types of hydrogen bonds are present in the optimized hydrated A?·?(H₂O)_n complexes; their energies were calculated to fall within the range 4.37–6.77 kcal mol^-1, comparable to the typical values of 5.0 kcal mol^-1 reported for hydrogen bonds. An aqueous environment simulated by explicit and/or implicit models lowers and re-arranges the orbitals of the bis-uranyl complex.

Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study

Extensive DFT and ab initio calculations were performed to characterize the conformational space of pamidronate, a typical pharmaceutical for bone diseases. Mono-, di- and tri-protic states of molecule, relevant for physiological pH range, were investigated for both canonical and zwitterionic tautomers. Semiempirical PM6 method were used for prescreening of the single bond rotamers followed by geometry optimizations at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. For numerous identified low energy conformers the final electronic energies were determined at the MP2/6-311++G(2df,2p) level and corrected for thermal effects at B3LYP level. Solvation effects were also considered via the COSMO and C-PCM implicit models. Reasonable agreement was found between bond lengths and angle values in comparison with X-ray crystal structures. Relative equilibrium populations of different conformers were determined from molecular partition functions and the role of electronic, vibrational and rotational degrees of freedom on the stability of conformers were analyzed. For no level of theory is a zwitterionic structure stable in the gas-phase while solvation makes them available depending on the protonation state. Geometrically identified intramolecular hydrogen bonds were analyzed by QTAIM approach. All conformers exhibit strong inter-phosphonate hydrogen bonds and in most of them the alkyl-amine side chain is folded on the P-C-P backbone for further hydrogen bond formation.

A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes

The potential energy surfaces of the reactions of organometallic arene complexes of the type [(η ⁶-arene)M^II(pic)Cl] (where pic = 2-picolinic acid, M = Ru or Os) were examined by a DFT computational study. Among the seven density functional methods, hybrid exchange functional B3LYP outperforms the others to explain the aquation of the complexes. The reactions and binding energies of Ru^II and Os^II arene complexes with both 9EtG and 9EtA were studied to gain insight into the reactivity of these types of organometallic complexes with DNA. The obtained data rationalize experimental observation, contributing to partly understanding the potential biological and medical applications of organometallic complexes.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

Plasmonic Heating-Assisted Transformation of SiO2/Au Core/Shell Nanospheres (Au Nanoshells): Caveats and Opportunities for SERS and Direct Laser Writing

The selective modification of silica/gold nanospheres (gold nanoshells) driven by plasmonic heating is demonstrated. Direct laser writing and reshaping of nanoshell assemblies can be easily controlled and exploited for nanofabrication purposes. The modified nanoshells exhibit improved surface enhanced Raman scattering, allowing to settle most of the issues related to nanoshell stability under working conditions.

Why tazobactam and sulbactam have different intermediates population with SHV-1 β-lactamase: a molecular dynamics study

The imine intermediates of tazobactam and sulbactam bound to SHV-1 β-lactamase were investigated by molecular dynamics (MD) simulation respectively. Hydrogen bond networks around active site were found different between tazobactam and sulbactam acyl-enzymes. In tazobactam imine intermediate, it was observed that the triazolyl ring formed stable hydrogen bonds with Asn170 and Thr167. The results suggest that conformation of imine determined the population of intermediates. In imine intermediate of tazobactam, the triazolyl ring is trapped in Thr_Asn pocket, and it restricts the rotation of C5-C6 bond so that tazobactam can only generate trans enamine intermediate. Further, conformational cluster analyses are performed to substantiate the results. These findings provide an explanation for the corresponding experimental results, and will be potentially useful in the development of new inhibitors.

Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers

O-H…X and O-H…O H-bonds as well as C-X…X dihalogen and C-X…O halogen bonds have been investigated in halomethanol dimers (bromomethanol dimer, iodomethanol dimer, difluorobromomethanol…bromomethanol complex and difluoroiodomethanol…iodomethanol complex). Structures of all complexes were optimized at the counterpoise-corrected MP2/cc-pVTZ level and single-point energies were calculated at the CCSD(T)/aug-cc-pVTZ level. Energy decomposition for the bromomethanol dimer complex was performed using the DFT-SAPT method based on the aug-cc-pVTZ basis set. OH…O and OH…X H-bonds are systematically the strongest in all complexes investigated, with the former being the strongest bond. Halogen and dihalogen bonds, being of comparable strength, are weaker than both H-bonds but are still significant. The strongest bonds were found in the difluoroiodomethanol…iodomethanol complex, where the O-H…O H-bond exceeds 7 kcal mol^-1, and the halogen and dihalogen bonds exceed 2.5 and 2.3 kcal mol^-1, respectively. Electrostatic energy is dominant for H-bonded structures, in halogen bonded structures electrostatic and dispersion energies are comparable, and, finally, for dihalogen structures the dispersion energy is clearly dominant.

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

Interplay between halogen bonds and hydrogen bonds in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes

The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y―H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller?Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials (V _S,min) and the most positive electrostatic potentials (V _S,max) on the electron density contours of the individual species. The greater the V _S,max values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V _S,max of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species.

Exploration of various electronic properties along the reaction coordinate for hydration of Pt(II) and Ru(II) complexes; the CCSD, MPx, and DFT computational study

In the study behavior of molecular electrostatic potential, averaged local ionization energy, and reaction electronic flux along the reaction coordinate of hydration process of three representative Ru(II) and Pt(II) complexes were explored using both post-HF and DFT quantum chemical approximations. Previously determined reaction mechanisms were explored by more detailed insight into changes of electronic properties using ωB97XD functional and MP2 method with 6–311++G(2df,2pd) basis set and CCSD/6–31(+)G(d,p) approach. The dependences of all examined properties on reaction coordinate give more detailed understanding of the hydration process.

Molecular simulation study of PAMAM dendrimer composite membranes

Pure polysulfone (PSF) and its composites with chitosan (CST), hyaluronic acid (HA), conventional poly(amidoamine), and hydroxyl poly(amidoamine) dendrimers as the membranes for separation of the gases, methane, carbon dioxide, hydrogen sulfide, nitrogen, and oxygen have been studied by molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. The transport properties (solubility, diffusivity, and permeability) of pure and gas mixtures in the membranes were calculated and the results of the simulations were compared with the available experimental data. The simulated structural properties of the pure and composite PSF membranes including occupied volume, free volume, surface area, fractional free volume (FFV), and radius of gyration (R _g ) were evaluated and their effects on the separability of the gases by the membranes were analyzed and interpreted by the obtained results.

A theoretical study on the hydrogen adducts of diamidocarbenes and diaminocarbenes

The hybrid-meta GGA DFT functional M06-2X was used to examine the potential of N,N′-diamidocarbenes for use as hydrogen storage materials. We previously discovered that borylene, which is isoelectronic with an Arduengo-type carbene, was a suitable candidate for a hydrogen storage material. We compared the capabilities of N,N′-diamidocarbenes and N-heterocyclic carbenes as hydrogen storage materials. The results indicate that diamidocarbenes are not suitable hydrogen storage materials because the removal of H₂ is more endothermic for diamidocarbenes than for diaminocarbenes.