Chalcogen Atom Size: A Key Parameter in Modulating Carbonyl Compound Properties.

Exchanging oxygen in the functional group C=O (i. e., carbonyl) for the less electronegative Group 16 elements, sulfur or selenium, unexpectedly enhances the electronegativity of the C=X group in π-conjugated molecules and reduces the molecular π HOMO-LUMO energy gap. Quantum-chemical analyses revealed that the steric size of the chalcogen atom X is at the origin of this seemingly counterintuitive behavior. This tuning of the chemical properties of carbonyl compounds by varying the chalcogen atom size in the C=X bond can be applied in many fields of chemistry. This concept article delineates several useful applications in the fields of organocatalysis, supramolecular chemistry, and photo(electro)chemistry.

Multiple hydrogen-bonded dimers: are only the frontier atoms relevant?

Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.

More Electropositive is More Electronegative: Atom Size Determines C=X Group Electronegativity.

Opposite to what one might expect, we find that the C=X group can become effectively more, not less, electronegative when the Pauling electronegativity of atom X decreases down Groups 16, 15, and 14 of the Periodic Table. Our quantum-chemical analyses, show that, and why, this phenomenon is a direct consequence of the increasing size of atom X down a group. These findings can be applied to tuning and improving the hydrogen-bond donor strength of amides H2 NC(=X)R by increasingly withdrawing density from the NH2 group. A striking example is that H2 NC(=SiR2 )R is a stronger hydrogen-bond donor than H2 NC(=CR2 )R.

Understanding chemistry with the symmetry-decomposed Voronoi deformation density charge analysis.

The symmetry-decomposed Voronoi deformation density (VDD) charge analysis is an insightful and robust computational tool to aid the understanding of chemical bonding throughout all fields of chemistry. This method quantifies the atomic charge flow associated with chemical-bond formation and enables decomposition of this charge flow into contributions of (1) orbital interaction types, that is, Pauli repulsive or bonding orbital interactions; (2) per irreducible representation (irrep) of any point-group symmetry of interacting closed-shell molecular fragments; and now also (3) interacting open-shell (i.e., radical) molecular fragments. The symmetry-decomposed VDD charge analysis augments the symmetry-decomposed energy decomposition analysis (EDA) so that the charge flow associated with Pauli repulsion and orbital interactions can be quantified both per atom and per irrep, for example, for σ, π, and δ electrons. This provides detailed insights into fundamental aspects of chemical bonding that are not accessible from EDA.

Chalcogen Atom Size Dictates Stability of Benzene-1,3,5-triamide Polymers: Overlooked Role of Geometrical Fit for Enhanced Hydrogen Bonding.

Our quantum chemical analyses elucidated how the replacement of O in the amide bonds of benzene-1,3-5-tricarboxamides (OBTAs) with the larger chalcogens S and Se enhances the intermolecular interactions and thereby the stability of the obtained hydrogen-bonded supramolecular polymers due to two unexpected reasons: i) the SBTA and SeBTA monomers have a better geometry for self-assembly and ii) induce stronger covalent (hydrogen-bond) interactions besides enhanced dispersion interactions. In addition, it is shown that the cooperativity in benzene-1,3,5-triamide (BTA) self-assembly is caused by charge separation in the σ-electronic system following the covalency in the hydrogen bonds.

How the Chalcogen Atom Size Dictates the Hydrogen-Bond Donor Capability of Carboxamides, Thioamides, and Selenoamides.

Invited for the cover of this issue are Celine Nieuwland and Célia Fonseca Guerra of the Vrije Universiteit Amsterdam. The image depicts how the increasing atom size of the chalcogen from O to S to Se elongates the carbon-chalcogen bond in amides due to the increase in the steric Pauli repulsion and thereby enhances the amide hydrogen-bond donor strength. Read the full text of the article at 10.1002/chem.202200755.

Polycyclic Aromatic Hydrocarbons (PAHs) in Interstellar Ices: A Computational Study into How the Ice Matrix Influences the Ionic State of PAH Photoproducts.

It has been experimentally observed that water-ice-embedded polycyclic aromatic hydrocarbons (PAHs) form radical cations when exposed to vacuum UV irradiation, whereas ammonia-embedded PAHs lead to the formation of radical anions. In this study, we explain this phenomenon by investigating the fundamental electronic differences between water and ammonia, the implications of these differences on the PAH-water and PAH-ammonia interaction, and the possible ionization pathways in these complexes using density functional theory (DFT) computations. In the framework of the Kohn-Sham molecular orbital (MO) theory, we show that the ionic state of the PAH photoproducts results from the degree of occupied-occupied MO mixing between the PAHs and the matrix molecules. When interacting with the PAH, the lone pair-type highest occupied molecular orbital (HOMO) of water has poor orbital overlap and is too low in energy to mix with the filled π-orbitals of the PAH. As the lone-pair HOMO of ammonia is significantly higher in energy and has better overlap with filled π-orbitals of the PAH, the subsequent Pauli repulsion leads to mixed MOs with both PAH and ammonia character. By time-dependent DFT calculations, we demonstrate that the formation of mixed PAH-ammonia MOs opens alternative charge-transfer excitation pathways as now electronic density from ammonia can be transferred to unoccupied PAH levels, yielding anionic PAHs. As this pathway is much less available for water-embedded PAHs, charge transfer mainly occurs from localized PAH MOs to mixed PAH-water virtual levels, leading to cationic PAHs.

How the Chalcogen Atom Size Dictates the Hydrogen-Bond Donor Capability of Carboxamides, Thioamides, and Selenoamides.

The amino groups of thio- and selenoamides can act as stronger hydrogen-bond donors than of carboxamides, despite the lower electronegativity of S and Se. This phenomenon has been experimentally explored, particularly in organocatalysis, but a sound electronic explanation is lacking. Our quantum chemical investigations show that the NH2 groups in thio- and selenoamides are more positively charged than in carboxamides. This originates from the larger electronic density flow from the nitrogen lone pair of the NH2 group towards the lower-lying π*C=S and π*C=Se orbitals than to the high-lying π*C=O orbital. The relative energies of the π* orbitals result from the overlap between the chalcogen np and carbon 2p atomic orbitals, which is set by the carbon-chalcogen equilibrium distance, a consequence of the Pauli repulsion between the two bonded atoms. Thus, neither the electronegativity nor the often-suggested polarizability but the steric size of the chalcogen atom determines the amide's hydrogen-bond donor capability.

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.

Invited for this month's cover are the groups of Célia Fonseca Guerra at the Vrije Universiteit Amsterdam and Leiden University, Giampaolo Barone from the Università degli Studi di Palermo, and F. Matthias Bickelhaupt at Vrije Universiteit Amsterdam and Radboud University Nijmegen. The cover picture shows the four primary interaction components (hydrogen bonding, cross-terms, base stacking, and solvation) that determine the stability of B-DNA duplexes. Quantum chemical analyses identify an interplay between the stabilizing hydrogen bonds between nucleotides that drive the formation of the DNA double-strand, and the destabilizing loss of stacking interactions within individual strands combined with partial desolvation. The sequence-dependence in the duplex stability originates mainly from the cross-terms, which can be attractive or repulsive. Read the full text of their Research Article at 10.1002/open.202100231.

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes.

The front cover artwork is provided by the TheoCheM group of the Vrije Universiteit Amsterdam. The image shows that guanine quadruplexes have a stronger binding affinity for divalent cations than monovalent cations. Read the full text of the Article at 10.1002/cphc.202100529.

How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes.

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+ , Ca2+ , Sr2+ , and Ba2+ ), and (post-)transition metal (Zn2+ , Cd2+ , Hg2+ , and Pb2+ ) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+ ). Importantly, we establish the nature of the cation-GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations' unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.

Enhancement of Oxygen Evolution Activity of Nickel Oxyhydroxide by Electrolyte Alkali Cations.

Herein, the effect of the alkali cation (Li+ , Na+ , K+ , and Cs+ ) in alkaline electrolytes with and without Fe impurities is investigated for enhancing the activity of nickel oxyhydroxide (NiOOH) for the oxygen evolution reaction (OER). Cyclic voltammograms show that Fe impurities have a significant catalytic effect on OER activity; however, both under purified and unpurified conditions, the trend in OER activity is Cs+ > Na+ > K+ > Li+ , suggesting an intrinsic cation effect of the OER activity on Fe-free Ni oxyhydroxide. In situ surface enhanced Raman spectroscopy (SERS), shows this cation dependence is related to the formation of superoxo OER intermediate (NiOO- ). The electrochemically active surface area, evaluated by electrochemical impedance spectroscopy (EIS), is not influenced significantly by the cation. We postulate that the cations interact with the Ni-OO- species leading to the formation of NiOO- -M+ species that is stabilized better by bigger cations (Cs+ ). This species would then act as the precursor to O2 evolution, explaining the higher activity.