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The hydrogen-bond donor strength of ureas, widely used in hydrogen-bond donor catalysis, molecular recognition, and self-assembly, can be enhanced by increasing the size of the chalcogen X in the C＝X bond from O to S to Se and by introducing more electron-withdrawing substituents because both modifications increase the positive charge on the NH groups which become better hydrogen-bond donors. However, in 1,3-diaryl X-ureas, a steric mechanism disrupts the positive additivity of these two tuning factors, as revealed by our quantum-chemical analyses. This leads to an enhanced hydrogen-bond donor strength, despite a lower NH acidity, for 1,3-diaryl substituted O-ureas compared to the S- and Se-urea analogs. In addition, we provide a strategy to overcome this steric limitation using a predistorted urea-type hydrogen-bond donor featuring group 14 elements in the C＝X bond so that the hydrogen-bond donor strength of X-urea derivatives bearing two aryl substituents can be enhanced upon varying X down group 14. [ABSTRACT FROM AUTHOR]

We have quantum chemically analyzed the closed-shell d8–d8 metallophilic interaction in dimers of square planar [M(CO)2X2] complexes (M = Ni, Pd, Pt; X = Cl, Br, I) using dispersion-corrected density functional theory at ZORA-BLYP-D3(BJ)/TZ2P level of theory. Our purpose is to reveal the nature of the [X2(CO)2M]⋯[M(CO)2X2] bonding mechanism by analyzing trends upon variations in M and X. Our analyses reveal that the formation of the [M(CO)2X2]2 dimers is favored by an increasingly stabilizing electrostatic interaction when the M increases in size and by more stabilizing dispersion interactions promoted by the larger X. In addition, there is an overlooked covalent component stemming from metal–metal and ligand–ligand donor–acceptor interactions. Thus, at variance with the currently accepted picture, the d8–d8 metallophilicity is attractive, and the formation of [M(CO)2X2]2 dimers is not a purely dispersion-driven phenomenon. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The formation of Co(III)–thiolate complexes from Co(II)–disulfide complexes using the anionic ligand 8-quinolinolate (quin−) has been studied experimentally and quantum chemically. Two Co(II)–disulfide complexes [Co2(LxSSLx)(Cl)4] (x = 1 or 2; L1SSL1 = 2,2′-disulfanediylbis(N,N-bis(pyridin-2-ylmethyl)ethan-1-amine; L2SSL2 = 2,2′-disulfanedylbis (N-((6-methylpyridin-2-yl)methyl)-N-(pyridin-2-ylmethyl) ethan-1-amine) have been successfully converted with high yield to their corresponding Co(III)–thiolate complexes upon addition of the ligand 8-quinolinolate. Using density functional theory (DFT) computations the d-orbital splitting energies of the cobalt–thiolate compounds [Co(L1S)(quin)]+ and [Co(L2S)(quin)]+ were estimated to be 3.10 eV and 3.07 eV, indicating a slightly smaller ligand-field strength of ligand L2SSL2 than of L1SSL1. Furthermore, the orientation of the quin− ligand in the thiolate compounds determines the stability of the thiolate complex. DFT computations show that the thiolate structure benefits from more electrostatic attraction when the oxygen atom of the quin− ligand is positioned trans to the sulfur atom of the [Co(L1S)]2+ fragment. Quin− is the first auxiliary ligand with which it appeared possible to induce the redox-conversion reaction in cobalt(II) compounds of the relatively weak-field ligand L2SSL2. [ABSTRACT FROM AUTHOR]

We discuss the fundamental aspects of the EDA-NOCV method and address some critical comments that have been made recently. The EDA-NOCV method unlike most other methods focuses on the process of bond formation between the interacting species and not just only on the analysis of the finally formed bond. This is demonstrated using LiF as an example. There is a difference between the interactions between the initial species which form the bond and are also the final product of bond cleavage, and the interactions between the fragments in the eventually formed molecule. The flexibility of the method allows the choice of the interacting fragments which helps to identify the charge and electron configuration of the fragments which describe the bond. This is very helpful in cases where the bond may be described with several Lewis structures. We reject the idea that it would be a disadvantage to have "bond path functions" as the energy components in the EDA, which actually indicate the variability of the method. The bonding analysis in a different sequence of the bond formation gives important results for the various questions that can be asked. This is demonstrated by using CH2, CO2 and the formation of a guanine quartet as examples. The fact that a bond is always defined by the bound molecule, the fragments, and their states is universal and deeply physical, as we show here again for various examples. The results of the EDA-NOCV method are in full accordance with the physical mechanism of the chemical bond as revealed by Ruedenberg. [ABSTRACT FROM AUTHOR]

The redox-conversion reaction of cobalt(II)-disulfide to cobalt(III)-thiolate complexes triggered by addition of the bidentate ligand 2,2′-bipyridine has been investigated. Reaction of the cobalt(II)-disulfide complex [Co2(L1SSL1)(X)4] (L1SSL1 = di-2-(bis(2-pyridylmethyl)amino)-ethyldisulfide; X = Cl or Br) [1X] with 2,2′-bipyridine (bpy) resulted in the formation of two different products, namely the cobalt(III)-thiolate complex [Co(L1S)(bpy)]X2 and the unexpected side product [Co2(L1SSL1)(bpy)2(X)2]X2. Crystals of [Co2(L1SSL1)(bpy)2(Cl)2](BPh4)2 [2Cl](BPh4)2 obtained after anion exchange showed the cobalt(II) ions to be in octahedral geometries with the nitrogen donors of the disulfide ligand arranged in a facial conformation and the chloride ion trans to the tertiary amine nitrogen. Remarkably, this side product cannot be converted to the cobalt(III)-thiolate compound [Co(L1S)(bpy)](SbF6)2 [3](SbF6)2 by removal of the chloride ion with use of a silver salt, as this causes scrambling of the ligands, resulting in the formation of [Co(bpy)3]n+. [Co(L1S)(bpy)](SbF6)2 was obtained in a pure form by addition of bpy to a solution in acetonitrile of the compound [Co(L1S)(MeCN)2]2+ [4]2+. Addition of NEt4Cl to [3](SbF6)2 regenerates the cobalt(II)-disulfide complex [1Cl] as confirmed spectroscopically. DFT studies revealed that the conversion from [1Cl] to [3]2+ most likely occurs via the hypothetical intermediate species [2Cl]2+mer, in which the nitrogen atoms of the disulfide ligand are arranged in a meridional conformation. Interestingly, the estimated d-orbital splitting energy of [3]2+ is lower than that of [4]2+, indicating that the ligand-field strength of bpy is lower than anticipated, which hampers clean conversion in the redox-conversion reaction. This study shows that the redox-conversion reaction between cobalt(II)-disulfide and cobalt(III)-thiolate complexes is intricate rather than straightforward. [ABSTRACT FROM AUTHOR]

The concept of dipolar repulsion has been widely used to explain several phenomena in organic chemistry, including the conformational preferences of carbonyl compounds. This model, in which atoms and bonds are viewed as point charges and dipole moment vectors, respectively, is however oversimplified. To provide a causal model rooted in quantitative molecular orbital theory, we have analyzed the rotational isomerism of haloacetaldehydes OHC–CH2X (X = F, Cl, Br, I), using relativistic density functional theory. We have found that the overall trend in the rotational energy profiles is set by the combined effects of Pauli repulsion (introducing a barrier around gauche that separates minima at syn and anti), orbital interactions (which can pull the anti minimum towards anticlinal to maximize hyperconjugation), and electrostatic interactions. Only for X = F, not for X = Cl–I, electrostatic interactions push the preference from syn to anti. Our bonding analyses show how this trend is related to the compact nature of F versus the more diffuse nature of the heavier halogens. [ABSTRACT FROM AUTHOR]

A new organometallic alkynyl–gold(I) complex capable of exhibiting aggregation induced emission was designed and synthesized. The linear complex structure possesses a central Au(I) atom, bearing two axial ligands: (1) 1,3,5-triaza-7-phosphaadamantane and (2) 2-acetamido-7-ethynyl-1,8-naphthyridine. While the former accounts for its partial solubility in an aqueous environment, the latter acts as a receptor unit for binding guanosine nucleotides and derivatives via multiple hydrogen bonding interactions. At high concentrations, aggregation of the complex was observed by the formation of new absorption (λmax ∼ 400 nm) and emission bands (550–700 nm). Formation of aggregates of ca. 60 nm diameter was confirmed by Small Angle X-ray Scattering (SAXS). Disruption of the aggregates in the presence of guanosine derivatives resulted in a ratiometric signal with apparent association constants in the order of 105 M−1 and high sensitivity (around 63% signal change) which are, to the best of our knowledge, in line with the highest values recorded for nucleotide sensors based on hydrogen bonding and capable of working in water. Computational studies indicate the presence of additional hydrogen bonding interactions that account for the strong binding of the Au(I) complex to phosphorylated guanosine nucleotides. [ABSTRACT FROM AUTHOR]

For a series of organonitrile [RCN (R = Me, CF3, Ph, CH3Ph, CF3Ph)] ligands, the nature of the N–Pt bond in the related cis-/trans-(RCN)2PtCl2 complexes has been computationally investigated by Density Functional Theory. A fragment based bond analysis has been performed in the canonical Kohn–Sham molecular orbitals framework, and it has been ultimately assessed that this bond is characterized both by N→Pt σ and by N←Pt π contributions. Voronoi Deformation Density charges further confirms the occurrence of N←Pt π interactions. Moreover, the Energy Decomposition Analysis-Natural Orbital for Chemical Valence (EDA-NOCV) method shows that the strength of the N←Pt π interaction is not negligible by contributing to about 30–40% of the total orbital interaction. Finally, the well-known νC≡N blue-shift occurring upon coordination to PtII, has been thoroughly investigated by exploiting the EDA-NOCV and by evaluating νC≡N and force constants. The origin of the νC≡N blue-shift in these systems has been discussed on the basis of the CN bond polarization. N←Pt π backbonding causes only a systematic decrease of the observed νC≡N blue-shift when compared to the one calculated for RCN–X (X = H+, alkaline, Lewis acids) herein reported (X = purely σ acceptors). [ABSTRACT FROM AUTHOR]

The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity. [ABSTRACT FROM AUTHOR]

Our quantum chemical activation strain analyses demonstrate how Mg2+ lowers the barrier of the enzymatic triphosphate hydrolysis through two distinct mechanisms: (a) weakening of the leaving-group bond, thereby decreasing activation strain; and (b) transition state (TS) stabilization through enhanced electrophilicity of the triphosphate PPP substrate, thereby strengthening the interaction with the nucleophile. [ABSTRACT FROM AUTHOR]

We have computationally analyzed a comprehensive series of Watson–Crick and mismatched B-DNA base pairs, in the gas phase and in several solvents, including toluene, chloroform, ammonia, methanol and water, using dispersion-corrected density functional theory and implicit solvation. Our analyses shed light on how the molecular-recognition machinery behind life's genetic code depends on the medium, in order to contribute to our understanding of the possibility or impossibility for life to exist on exoplanetary bodies. Calculations show how a common non-terran environment like ammonia, less polar than water, exhibits stronger hydrogen-bonding affinities, although showing reduced selectivities towards the correct incorporation of Watson–Crick base pairs into the backbone. Thus, we prove the viability of DNA replication in a non-terran environment. [ABSTRACT FROM AUTHOR]

We have observed the 1-bond 199Hg–15N J-coupling (1J(199Hg,15N) = 1050 Hz) within the HgII-mediated thymine–thymine base pair (T–HgII–T). This strikingly large 1J(199Hg,15N) is the first one for canonical sp2-nitrogen atoms, which can be a sensitive structure-probe of N-mercurated compounds and a direct evidence for N-mercuration. [ABSTRACT FROM AUTHOR]

The control over the formation of a bi-component porous network was attained by the self-assembly at a solid–liquid interface by exploiting both primary and secondary non-covalent interactions between melamine and N3-alkylated xanthine modules. [ABSTRACT FROM AUTHOR]

The hydrogen-bond donor strength of ureas, widely used in hydrogen-bond donor catalysis, molecular recognition, and self-assembly, can be enhanced by increasing the size of the chalcogen X in the CX bond from O to S to Se and by introducing more electron-withdrawing substituents because both modifications increase the positive charge on the NH groups which become better hydrogen-bond donors. However, in 1,3-diaryl X-ureas, a steric mechanism disrupts the positive additivity of these two tuning factors, as revealed by our quantum-chemical analyses. This leads to an enhanced hydrogen-bond donor strength, despite a lower NH acidity, for 1,3-diaryl substituted O-ureas compared to the S- and Se-urea analogs. In addition, we provide a strategy to overcome this steric limitation using a predistorted urea-type hydrogen-bond donor featuring group 14 elements in the CX bond so that the hydrogen-bond donor strength of X-urea derivatives bearing two aryl substituents can be enhanced upon varying X down group 14.

Secondary interactions, such as hydrogen bonding or phase separation, can enhance the stability of dynamic covalent materials without compromising on desired dynamic properties. Here, we investigate the combination of multiple secondary interactions in dynamic covalent materials based on acylsemicarbazides (ASCs), with the aim of achieving tunable material properties. The effects of different ASC substituents on the dynamic covalent and hydrogen bonding capabilities were investigated in a small molecule study using a combined experimental and theoretical approach, and revealed the presence of cooperative hydrogen-bonding interactions in 2 directions in one of the derivatives. The different motifs were subsequently incorporated into polymeric materials. Combining ASC motifs capable of strong, multiple hydrogen bonding with a polydimethylsiloxane backbone introduces structure-dependent, ordered nanophase separation in polymeric materials. The thermo-mechanical properties of the materials reveal a strong dependance on the hydrogen-bonding structure and exact nature of the ASC bond. The dynamic behavior in bulk shows that bond exchange depends on the dissociation rate obtained from ASC model compounds, as well as the strength of the secondary interactions in these materials. Differences in hydrogen-bonding structures of the ASC motifs also cause differences in creep resistance of the materials. Interestingly, the materials with strong, ordered and cooperative hydrogen-bonded clusters show the highest creep resistance. Our results demonstrate that tuning both the dissociation rate and the secondary interactions by molecular design in dynamic covalent materials is important for controlling their thermal stability and creep resistance., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

We have quantum chemically analyzed the closed-shell d 8 -d 8 metallophilic interaction in dimers of square planar [M(CO) 2 X 2 ] complexes (M = Ni, Pd, Pt; X = Cl, Br, I) using dispersion-corrected density functional theory at ZORA-BLYP-D3(BJ)/TZ2P level of theory. Our purpose is to reveal the nature of the [X 2 (CO) 2 M]⋯[M(CO) 2 X 2 ] bonding mechanism by analyzing trends upon variations in M and X. Our analyses reveal that the formation of the [M(CO) 2 X 2 ] 2 dimers is favored by an increasingly stabilizing electrostatic interaction when the M increases in size and by more stabilizing dispersion interactions promoted by the larger X. In addition, there is an overlooked covalent component stemming from metal-metal and ligand-ligand donor-acceptor interactions. Thus, at variance with the currently accepted picture, the d 8 -d 8 metallophilicity is attractive, and the formation of [M(CO) 2 X 2 ] 2 dimers is not a purely dispersion-driven phenomenon.

The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.

Our dispersion-corrected DFT computations reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide.