What Stabilizes the LinPn Inorganic Double Helices?

Chiral Jahn-Teller Distortion in Quasi-Planar Boron Clusters

In this work, we have observed that some chiral boron clusters (B16-, B20-, B24-, and B28-) can simultaneously have helical molecular orbitals and helical spin densities; these seem to be the first compounds discovered to have this intriguing property. We show that chiral Jahn-Teller distortion of quasi-planar boron clusters drives the formation of the helical molecular spin densities in these clusters and show that elongation/enhancement in helical molecular orbitals can be achieved by simply adding more building blocks via a linker. Aromaticity of these boron clusters is discussed. Chiral boron clusters may find potential applications in spintronics, such as molecular magnets.

Lithiation of phosphorus at the nanoscale: a computational study of LinPm clusters

Systematic structure prediction of LinPm nanoclusters was performed for a wide range of compositions (0 ≤ n ≤ 10, 0 ≤ m ≤ 20) using the evolutionary global optimization algorithm USPEX coupled with density functional calculations. With increasing Li concentration, the number of P-P bonds in the cluster reduces and the phosphorus backbone undergoes the following transformations: elongated tubular → multi-fragment (with mainly P5 rings and P7 cages) → cyclic topology → branched topology → P-P dumbbells → isolated P ions. By applying several stability criteria, we determined the most favorable LinPm clusters and found that they are located in the compositional area between m ≈ n/3 and m ≈ n/3 + 6. For instance, the Li3P7 cluster has the highest stability and is known to be the structural basis of the corresponding bulk crystal. The obtained results provide valuable insights into the lithiation mechanism of nanoscale phosphorus which is of interest for development of novel phosphorus-based anode materials.

Boron-Based Chiral Helix Be6 B10 2- and Be6 B11 - Clusters: Structures, Chemical Bonding, and Formation Mechanism

Boron forms a rich variety of low-dimensional nanosystems, including the newly discovered helix Be₆ B₁₀ ^2- (1) and Be₆ B₁₁ ^- (2) clusters. We report herein on the elucidation of chemical bonding in clusters 1/2, using the modern quantum chemistry tools of canonical molecular orbital analyses and adaptive natural density partitioning (AdNDP). It is shown that clusters 1/2 contain a chiral helix Be₂ B₁₀ Be₂ or Be₂ B₁₁ Be₂ skeleton with a total of 11 and 12 segments, respectively, which effectively curve into "helical pseudo rings" and chemically consist of two "quasicircles" as defined by their anchoring Be centers. The helix skeleton is connected via Lewis-type B-B and Be-B-Be σ bonds, being further stabilized by island π/σ bonds and a loose π bond at the junction. The Be₆ component in 1/2 assumes a distorted prism shape only physically, and it is fragmented into four parts: two terminal Be₂ dimers and two isolated Be centers. A Be₂ dimer at the far end manages to bend over and cap a quasicircle from one side of B plane. Consequently, each quasicircle of a helical pseudo ring is capped from opposite sides by two Be₂ /Be units, facilitating intramolecular charge-transfers of 5 electrons from Be to B. Overall, the folding of B helix involves as many as 10 electrons. The enormous electrostatics offers the ultimate driving forces for B helix formation.

Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions

Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized.

Double-helix PnLin chains: novel potential nonlinear optical materials

The structures, circular dichroism (CD) spectra and nonlinear optical (NLO) responses of a series of inorganic double-helix chains, P_nLi_n (n = 6–12), have been investigated using the quantum chemistry method.

Exploring Ultrashort Hydrogen-Hydrogen Nonbonded Contacts in Constrained Molecular Cavities

Confined molecular chambers such as macrocycle bridged E₁-H···H-E₂ (E₁(E₂) = Si(Si), 1) exhibit rare ultrashort H···H nonbonded contacts (d(H···H) = 1.56 Å). In this article, on the basis of density functional theory and ab initio molecular dynamics simulations, we propose new molecular motifs where d(H···H) can be reduced to 1.44 Å (E₁(E₂) = Si(Ge), 3). Further tuning the structure of the macrocycle by replacing the bulky phenyl groups by ethylenic spacers and substitution of the H-atoms by -CN groups makes the cavity more compact and furnishes even shorter d(H···H) = 1.38 Å (E₁(E₂) = Ge(Ge), 8). These unusually close H···H nonbonded contacts originate from the strong attractive noncovalent interactions between them, which are evident from various computational indicators, namely, NCI, Wiberg bond index, relaxed force constant, quantum theory of atoms in molecules, and natural orbitals for chemical valence combined with the extended transition state method analyses. Substantial stabilization of the in,in-configuration (exhibiting short H···H contacts) compared with the out,out-configuration (by ∼5.7 kcal/mol) and statistically insignificant fluctuations in ⟨d(H···H)⟩ and ⟨θ_av⟩(θ(E₁(E₂)-H···H = 152°) at room temperature confirm that the ultrashort H···H distances in these molecules are thermodynamically stable and would be persistent under ambient experimental conditions.

Computational studies on the interactions of glycine amino acid with graphene, h-BN and h-SiC monolayers

In the present work, the adsorption of glycine amino acid and its zwitterionic form onto three different hexagonal sheets, namely graphene, boron-nitride (h-BN) and silicon carbide (h-SiC), has been investigated within the framework of density functional theory (DFT) calculations.

Fluorescence from an H-aggregated naphthalenediimide based peptide: photophysical and computational investigation of this rare phenomenon

Fluorescence associated with J-aggregated naphthalenediimides (NDIs) is common. However, in this study an NDI based synthetic peptide molecule is found to form a fluorescent H-aggregate in a chloroform (CHCl3)-methylcyclohexane (MCH) mixture. An attempt has been made to explain the unusual fluorescence property of this H-aggregated NDI derivative. Time correlated single photon counting (TCSPC) shows that the average lifetime of the NDI based molecule is on the order of a few nanoseconds. It is revealed from the computational study that the transition from the second exited state (S2) to the ground energy state (S0) is responsible for the fluorescence as S1 is a dark state. Such rare violation of Kasha's rule accounts for the unusual fluorescence properties of this type of NDI molecule in the H-aggregated state.

Nanoscale stabilization of zintl compounds: 1D ionic Li-P double helix confined inside a carbon nanotube

One-dimensional (1D) ionic nanowires are extremely rare materials due to the difficulty in stabilizing 1D chains of ions under ambient conditions. We demonstrate here a theoretical prediction of a novel hybrid material, a nanotube encapsulated 1D ionic lithium monophosphide (LiP) chain, featuring a unique double-helix structure, which is very unusual in inorganic chemistry. This nanocomposite has been investigated with density functional theory, including molecular dynamics simulations and electronic structure calculations. We find that the formation of the LiP double-helical nanowire is facilitated by strong interactions between LiP and CNTs resulting in a charge transfer. This work suggests that nanostructured confinement may be used to stabilize other polyphosphide 1D chains, thus opening new ways to study the chemistry of zintl compounds at the nanoscale.

First-principles investigation of the lattice vibrational properties of inorganic double helical XY (X = Li, Na, K, Rb, Cs; Y = P, As, Sb)

The vibrational frequencies of the newly discovered inorganic double helical compounds XY (X = Li, Na, K, Rb, Cs; Y = P, As, Sb) are sensitive to either cation or anion or both of them.

Metal Free Azide-Alkyne Click Reaction: Role of Substituents and Heavy Atom Tunneling

Metal free click reactions provide an excellent noninvasive tool to modify and understand the processes in biological systems. Release of ring strain in cyclooctynes on reaction with azides on the formation of triazoles results in small activation energies for various intermolecular Huisgen reactions (1-9). Substitution of difluoro groups at the α, α' position of the cyclooctyne ring enhances the rates of cycloadditions by 10 and 20 times for methyl azide and benzyl azide respectively at room temperature. The computed rate enhancement on difluoro substitution using direct dynamical calculations using the canonical variational transition state theory (CVT/CAG) with small curvature tunneling (SCT) corrections are in excellent agreement with the experimental results. For the intramolecular click reaction (10) notwithstanding its much higher activation energy, quantum mechanical tunneling (QMT) enhances the rate of cycloaddition significantly and increases the N(14)/N(15) primary kinetic isotope effect at 298 K. QMT is shown to be rather efficient in 10 due to a thin barrier of ∼2.4 Å. The present study shows that tunneling effects can be significant for intramolecular click reactions.

Mechanistic insights into the synergistic catalysis by Au(i), Ga(iii), and counterions in the Nakamura reaction

DFT calculations explain the origin of Au/Ga dual catalyzed regioselectivity of Nakamura reactions. The role of the counterions and the triazole ligand is shown to be significant.

Emerging double helical nanostructures

As one of the most important and land-mark structures found in nature, a double helix consists of two congruent single helices with the same axis or a translation along the axis. This double helical structure renders the deoxyribonucleic acid (DNA) the crucial biomolecule in evolution and metabolism. DNA-like double helical nanostructures are probably the most fantastic yet ubiquitous geometry at the nanoscale level, which are expected to exhibit exceptional and even rather different properties due to the unique organization of the two single helices and their synergistic effect. The organization of nanomaterials into double helical structures is an emerging hot topic for nanomaterials science due to their promising exceptional unique properties and applications. This review focuses on the state-of-the-art research progress for the fabrication of double-helical nanostructures based on 'bottom-up' and 'top-down' strategies. The relevant nanoscale, mesoscale, and macroscopic scale fabrication methods, as well as the properties of the double helical nanostructures are included. Critical perspectives are devoted to the synthesis principles and potential applications in this emerging research area. A multidisciplinary approach from the scope of nanoscience, physics, chemistry, materials, engineering, and other application areas is still required to the well-controlled and large-scale synthesis, mechanism, property, and application exploration of double helical nanostructures.