Biological noncovalent N/O⋯V interactions: insights from theory and protein data bank analyses

Computations at the PBE0-D3/def2-TZVP level of theory in conjunction with a Protein Data Bank (PDB) survey have provided first time evidence of favorable noncovalent interactions between ADP metavanadate (VO4) and ADP orthovanadate (VO5) and electron rich atoms. These involve a σ-hole present in the V atom and the lone pairs belonging to (i) protein residues (e.g., serine (SER), glutamate (GLU) or histidine (HIS)), (ii) backbone carbonyl groups and (iii) water molecules. A computational study has been carried out to rationalize the physical nature and directionality of the interaction in addition to its plausible biological role. The results reported herein are expected to have an impact in the fields of medicinal chemistry, bioinorganic chemistry and chemical biology.

Tuning the Nucleophilicity and Electrophilicity of Group 10 Elements through Substituent Effects: A DFT Study

In this study, a series of electron donor (-NH2, -NMe2 and -tBu) and electron-withdrawing substituents (-F, -CN and -NO2) were used to tune the nucleophilicity or electrophilicity of a series of square planar Ni2+, Pd2+ and Pt2+ malonate coordination complexes towards a pentafluoroiodobenzene and a pyridine molecule. In addition, Bader's theory of atoms in molecules (AIM), noncovalent interaction plot (NCIplot), molecular electrostatic potential (MEP) surface and natural bond orbital (NBO) analyses at the PBE0-D3/def2-TZVP level of theory were carried out to characterize and discriminate the role of the metal atom in the noncovalent complexes studied herein. We hope that the results reported herein may serve to expand the current knowledge regarding these metals in the fields of crystal engineering and supramolecular chemistry.

Enzymatic reversion of Pt(II) nucleophilicity through charge dumping: the case of Pt(CN)42

Combining computations and X-ray structure analysis we have demonstrated that [Pt(CN4)]2- can behave as a Lewis acid inside an enzyme's cavity. The nature of a counterintuitive contact found between a catalytically active GLN residue belonging to a mitochondrial synthase and the Pt(II) center was investigated by combining molecular dynamics and quantum mechanics calculations. Results confirm the electron acceptor role of [Pt(CN4)]2-, serving as an inspiration for the design of biomolecular cages able to tweak the nucleophilic/electrophilic character of an organometallic compound.

Hg(II)⋅d8 [M] Interactions: Are they Metallophilic Interactions or Spodium Bonds?

Some literature reports have shown the existence of short Hg(II)⋅⋅⋅d8 [M] (M=Pd, Pt) contacts between linear Hg(II) and square planar d8 [M] complexes that have been defined as heterometallophilic interactions. Linear L-Hg(II)-L complexes exhibit a π-hole or positive belt of electrostatic potential at the Hg atom, whereas late transition metals can serve as effective electron donors through their filled dz 2 orbitals. This study provides compelling evidence that Hg(II)⋅⋅⋅d8 [M] interactions should be more appropriately termed spodium bonds.

On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.

Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work

Understanding the molecular interactions that drive peptide folding is crucial to chemistry and biology. In this study, we analyzed the role of CO···CO tetrel bonding (TtB) interactions in the folding mechanism of three different peptides (ATSP, pDIQ, and p53), which exhibit a different propensity to fold in an α helix motif. To achieve this goal, we used both a recently developed Bayesian inference approach (MELDxMD) and Quantum Mechanics (QM) calculations at the RI-MP2/def2-TZVP level of theory. These techniques allowed us to study the folding process and to evaluate the strength of the CO···CO TtBs as well as the synergies between TtBs and hydrogen-bonding (HB) interactions. We believe that the results derived from our study will be helpful for those scientists working in computational biology, peptide chemistry, and structural biology.

Tetrel bonds involving a CF3 group participate in protein-drug recognition: a combined crystallographic and computational study

In this study, the ability of CF₃ groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF₃ group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF₃⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.

Structural predictions of protein-DNA binding: MELD-DNA

Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein-DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein-DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein-DNA interactions).

Importance of Cu and Ag regium-π bonds in supramolecular chemistry and biology: a combined crystallographic and ab initio study

Identifying and characterizing new binding events between electron donor and acceptor counterparts represents a crucial step to complete the molecular recognition and aggregation picture, which is key to chemistry and biology. In this study we interrogated both the PDB (Protein Data Bank) and CSD (Cambridge Structural Database) for the presence of Cu and Ag regium-π (Rg-π) bonds (an attractive noncovalent force between elements from group 11 and π-systems). Concretely, we found evidence of the plausible biological role of the interaction in protein-DNA systems, bacterial Ag extrusion processes and Heme group redox functionality. Furthermore, we also highlighted the implications of Rg-π bonds in the crystal packing of two host-guest systems, where this interaction is key for the binding and recognition of small organic molecules as well as for the encapsulation of organometallic complexes. Theoretical models were used to analyse the strength of the interaction (RI-MP2/def2-TZVP level of theory) together with QTAIM (Quantum Theory of Atoms in Molecules), NBO (Natural Bonding Orbital) and NCIplot (Non Covalent Interactions plot) analyses, which further assisted in the characterization of the regium-π interactions described herein. We expect the results from this study will be useful to attract the attention of chemical biologists as well as to expand the potential of the interaction to the supramolecular chemistry and crystal engineering communities.

Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors

In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal‐ligand interaction). We provide evidence of the existence of this interaction by inspecting the X‐ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf‐Ligand orbital involved) are also analyzed by means of ab initio calculations (RI‐MP2/def2‐TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.

Direct conversion of white phosphorus to versatile phosphorus transfer reagents via oxidative onioation

The main feedstock for the value-added phosphorus chemicals used in industry and research is white phosphorus (P₄), from which the key intermediate for forming P(III) compounds is PCl₃. Owing to its high reactivity, syntheses based on PCl₃ are often accompanied by product mixtures and laborious work-up procedures, so an alternative process to form a viable P(III) transfer reagent is desirable. Our concept of oxidative onioation, where white phosphorus is selectively converted into triflate salts of versatile P₁ transfer reagents such as [P(L_N)₃][OTf]₃ (L_N is a cationic, N-based substituent; that is, 4-dimethylaminopyridinio), provides a convenient alternative for the implementation of P-O, P-N and P-C bonds while circumventing the use of PCl₃. We use p-block element compounds of type R_nE (for example, Ph₃As or PhI) to access weak adducts between nitrogen Lewis bases L_N and the corresponding dications [R_nEL_N]²⁺. The proposed equilibrium between [R_nEL_N]²⁺ + L_N and [R_nE(L_N)₂]²⁺ allows for the complete oxidative onioation of all six P-P bonds in P₄ to yield highly reactive and versatile trications [P(L_N)₃]³⁺.

Substituent effects in π-hole regium bonding interactions between Au(p-X-Py)2 complexes and Lewis bases: an ab initio study

For the first time, long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated. The Au(I) atom is coordinated to two para -substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide some experimental support to the existence of regium π-hole bonding in [Au(Py) 2 ] + derivatives.

Frustrated Lewis Pairs Based on Carbon⋅⋅⋅Carbon+ Tetrel Bonds: A DFT Study

The ability of Triangulenium (TA⁺ ) compounds to form Frustrated Lewis Pairs (FLPs) with N-HeteroCycle Carbenes (NHCs) is analysed in this manuscript at the PBE0-D3/def2-TZVP level of theory. We have used six TA⁺ -based moieties, three presenting similar bridging groups (O (trioxo), -CH₂ (triaryl) and -NH (triaza)) and another three mixing, O, -CH₂ and NH moieties. In addition, several aryl-substituted NHCs have been used as electron donor moieties to undergo carbon⋅⋅⋅carbon⁺ tetrel bonds with the TA⁺ derivatives. More precisely, -Me,-iPr, -tBu and -Ph groups were used. Finally, we have used Bader's quantum theory of "atoms in molecules" (QTAIM) and Natural Bonding Analysis (NBO) to characterize the carbon⋅⋅⋅carbon⁺ tetrel bonds described herein. We expect the results gathered herein will be useful for further exploitation of carbon⋅⋅⋅carbon⁺ bonds in the formation of FLPs as well as to expand the current knowledge of tetrel bonds to the fields of synthetic chemistry and catalysis.

Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study

In this study, we demonstrate that anion−π interactions (an attractive noncovalent force between electron deficient π-systems and anions) are involved in the stabilization of GAAA and GGAG RNA tetraloops. Using the single recognition particle (SRP)–RNA complexes as a case of study, we combined molecular dynamics (MD) and quantum mechanics (QM) calculations to shed light on the structural influence of phosphate–G anion−π interactions and hydrogen bonds (HBs) involving K⁺/Mg²⁺ water clusters. In addition, the RNA assemblies herein were further characterized by means of the “atoms in molecules” (AIM) and noncovalent interactions plot (NCIplot) methodologies. We believe the results derived from this study might be important in the fields of chemical biology (RNA folding and engineering) and supramolecular chemistry (anion−π interactions) as well as to further expand the current knowledge regarding RNA structural motifs.

Bifunctional Fluorophosphonium Triflates as Intramolecular Frustrated Lewis Pairs: Reversible CO2 Sequestration and Binding of Carbonyls, Nitriles and Acetylenes

Electrophilic fluorophosphonium triflates bearing pyridyl (3[OTf]) or imidazolyl (4[OTf])-substituents act as intramolecular frustrated Lewis pairs (FLPs) and reversibly form 1 : 1 adducts with CO₂ (5⁺ and 6⁺ ). An unusual and labile spirocyclic tetrahedral intermediate (7²⁺ ) is observed in CO₂ -pressurized (0.5-2.0 bar) solutions of cation 4⁺ at low temperatures, as demonstrated by variable-temperature NMR studies, which were confirmed crystallographically. In addition, cations 3⁺ and 4⁺ actively bind carbonyls, nitriles and acetylenes by 1,3-dipolar cycloaddition, as shown by selected examples.

Glutamate carboxypeptidase II as a model system for designing host-guest units: a theoretical approach

Through the combination of X-ray structure analysis and density functional theory (DFT) theoretical calculations at the B3LYP-D3/def2-TZVP level of theory, we designed and investigated two novel host units for the recognition of neutral (e.g. halobenzenes) and charged (e.g. chloride and nitrate) guests inspired by a glutamate carboxypeptidase II (GCPII) system and its inhibitors.

Selenium chalcogen bonds are involved in protein-carbohydrate recognition: a combined PDB and theoretical study

In this manuscript the ability of selenium carbohydrates to undergo chalcogen bonding (ChB) interactions with protein residues has been studied at the RI-MP2/def2-TZVP level of theory. An inspection of the Protein Data Bank (PDB) revealed SeA (A = O, C and S) intermolecular contacts involving Se-pyranose ligands and ASP, TYR, SER and MET residues. Theoretical models were built to analyse the strength and directionality of the interaction together with "Atoms in Molecules" (AIM), Natural Bonding Orbital (NBO) and Non Covalent Interactions plot (NCIplot) analyses, which further assisted in the characterization of the ChBs described herein. We expect that the results from this study will be useful to expand the current knowledge regarding biological ChBs as well as to increase the visibility of the interaction among the carbohydrate chemistry community.

Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases

In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.

Theoretical study of spodium bonding in the active site of three Zn-proteins and several model systems

In this manuscript, three examples retrieved from the PDB are selected to demonstrate the existence and relevance of spodium bonding (SpB) in biological systems. SpB is defined as an attractive noncovalent interaction between elements of group 12 of the periodic table acting as a Lewis acid and any atom or group of atoms acting as an electron donor. The utilization of this term (SpB) is convenient to differentiate classical coordination bonds from noncovalent interactions. In the latter, the distance between the electron rich and the spodium atoms is longer than the sum of the covalent radii but shorter than the sum of the van der Waals radii. In most Zn-dependent metalloenzymes, the spodium atom is bonded to three imidazole moieties belonging to the side chains of histidine amino-acids. Herein, in addition to the investigation of the SpB in the active site of three exemplifying enzymes, theoretical models where the Zn(ii) atom is bonded either to three imidazole or triazole ligands are used in order to investigate the strength of the SpB and its competition with hydrogen bonding. A series of Lewis bases and anions have been used as SpB acceptors combined with six SpB donors (receptors) of general formula [ZnY3X]+ (Y = imidazole and triazole and X = Cl, N3 and SCH3). In addition to the investigation of the energetic and geometric features of the complexes, the SpB interactions have been further characterized using the natural bond orbital (NBO) method, quantum theory of "atoms-in-molecules" and the noncovalent interaction plot (NCI plot).

Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function

Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X–X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X–X···N with the chloride of N-chlorosuccinimide lead to Cl–X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (−11.2 to −12.5 kcal/mol) are smaller than the values for (imide)I···N (−8.4 to −29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N–I covalent bond and I···N non-covalent bond of a (saccharin)N–I···N motif signify the covalent character for I···N halogen bonding.

Spodium bonding in five coordinated Zn(ii): a new player in crystal engineering?

This highlight evidences the existence and importance of spodium bonds (SpB) in solid state structures involving five-coordinated square-pyramidal Zn(ii) spodium atom.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X-X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X-X···N with the chloride of N-chlorosuccinimide lead to Cl-X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔE_int). The calculated ΔE_int values for (imide)Br···N (-11.2 to -12.5 kcal/mol) are smaller than the values for (imide)I···N (-8.4 to -29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N-I covalent bond and I···N non-covalent bond of a (saccharin)N-I···N motif signify the covalent character for I···N halogen bonding.

Toward N,P-Doped π-Extended PAHs: A One-Pot Synthesis to Diannulated 1,4,2-Diazaphospholium Triflate Salts

A novel method for the one-pot synthesis of diannulated 1,4,2-diazaphospholium triflate salts by a Me₃SiOTf-mediated self-condensation of dichlorophosphaneyl aza-(poly)cyclic aromatic hydrocarbons (aza-(P)AHs; namely, pyridine, quinoline, phenanthridine, and benzo[d]thiazole) is reported. The diannulated 1,4,2-diazaphospholium triflate salts are characterized by multinuclear NMR spectroscopy, X-ray analysis, as well as their calculated NICS values, underlining their aromatic character. Quantum mechanical calculations shed light on the intermolecular reaction mechanism. Follow up chemistry, such as the halogenation reaction with XeF₂ or SO₂Cl₂ with the dipyridinium derivative selectively yields the respective dihalo-σ⁴,λ⁵- and tetrahalo-σ⁵,λ⁶-diazaphospholium triflate salts. The dihalo-σ⁴,λ⁵-diazaphospholium triflate salt serves well as a surrogate for the introduction of the cationic 2-(1,2'-bipyridin)-1-iumyl ligand (1,2'-bipyl), the monocationic structural isomer of the prototypical 2,2'-bipyridine ligand (2,2'-bipy).

Regium-π Bonds Are Involved in Protein-Gold Binding

The regium-π interaction is an attractive noncovalent force between group 11 elements (Cu, Ag, and Au) acting as Lewis acids and aromatic surfaces. Herein, we report for the first time experimental (Protein Data Bank analysis) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of regium-π bonds involving Au(I) and aromatic amino acids (Phe, Tyr, Trp, and His). These findings might be important in the field of drug design and for retrospectively understanding the role of gold in proteins.

Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study

In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements

The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.

Halogen Bonds in Protein Nucleic Acid Recognition

Identifying new binding forces between electron donor and acceptor entities is key to properly understanding molecular recognition and aggregation phenomena, which are of inmense importance to biology. For decades, the halogenation of DNA/RNA bases has been routinely carried out to solve solid state structures of nucleic acids (NA). However, the effects of this modification might be deeper than just a simple atom substitution since halogens are also known to undergo noncovalent binding (halogen bonding). Herein we show that halogenated NAs with either Br or I atoms are able to establish halogen bonds with properly disposed protein residues. An inspection of the Protein Data Bank (PDB) reveals several examples involving 5-iodo/5-bromouracil, 8-bromoadenine, and 5-iodocytosine bases that are consistent with the halogen bond geometry features. Computations reveal the favorable and moderately strong nature of this interaction, thus confirming the ability of halogenated bases to actively participate in protein-NA binding.

Binuclear and tetranuclear Zn(ii) complexes with thiosemicarbazones: synthesis, X-ray crystal structures, ATP-sensing, DNA-binding, phosphatase activity and theoretical calculations

Two Zinc(ii) complexes [Zn₄(L¹)₄]·2H₂O (1) and [Zn₂(L²)₂]·2H₂O (2) of pyruvaldehydethiosemicarbazone ligands are reported. The complexes were characterized by elemental analysis, IR, NMR, UV-vis spectroscopy and by single-crystal X-ray crystallography. X-ray crystal structure determinations of the complexes show that though Zn : ligand stoichiometry is 1 : 1 in both the complexes, the molecular unit is tetranuclear for 1 and binuclear for 2. Both the complexes show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH₃CN–H₂O (9 : 1) medium in the presence of other anions like AcO⁻, NO₃⁻, F⁻, Cl⁻, H₂PO₄⁻, HPO₄²⁻ and P₂O₇²⁻. The UV-titration experiments of complexes 1 and 2 with ATP results in binding constants of 2.0(±0.07) × 10⁴ M⁻¹ and 7.1(±0.05) × 10³ M⁻¹ respectively. The calculated detection limits of 6.7 μM and 1.7 μM for 1 and 2 respectively suggest that the complexes are sensitive detectors of ATP. High selectivity of the complexes is confirmed by the addition of ATP in presence of an excess of other anions. DFT studies confirm that the ATP complexes are more favorable than those with the other inorganic phosphate anions, in agreement with the experimental results. Phosphatase like activity of both complexes is investigated spectrophotometrically using 4-nitrophenylphosphate (NPP) as a substrate, indicating the complexes possess significant phosphate ester hydrolytic efficiency. The kinetics for the hydrolysis of the substrate NPP was studied by the initial rate method at 25 °C. Michaelis–Menten derived kinetic parameters indicate that rate of hydrolysis of the P–O bond by complex 1 is much greater than that of complex 2, the k_cat values being 212(±5) and 38(±2) h⁻¹ respectively. The DNA binding studies of the complexes were investigated using electronic absorption spectroscopy and fluorescence quenching. The absorption spectral titrations of the complexes with DNA indicate that the CT-DNA binding affinity (K_b) of complex 1 (2.10(±0.07) × 10⁶ M⁻¹) is slightly greater than that of 2 (1.11(±0.04) × 10⁶ M⁻¹). From fluorescence spectra the apparent binding constant (K_app) values were calculated and they are found to be 5.41(±0.01) × 10⁵ M⁻¹ for 1 and 3.93(±0.02) × 10⁵ M⁻¹ for 2. The molecular dynamics simulation demonstrates that the Zn(ii) complex 1 is a good intercalator of DNA.

A binuclear and a tetranuclear zinc(ii) of pyruvaldehyde thiosemicarbazone show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH₃CN–H₂O (9 : 1) medium. The DNA binding and phosphatase activities of the complexes are also reported.

On the supramolecular properties of neutral, anionic and cationic cadmium complexes harvested from dithiolate–polyamine binary ligand systems

Three Cd(ii) complexes [Cd(i-mnt)(DMSO)₂]_n (1), {[Cd(i-mnt)pn]·2H₂O} (2), and [Cd(i-mnt)₃][Cd(tren)₂]₂ (3) harvested from 1,1-dicyanoethylene-2,2-dithiolate (i-mnt²⁻) and polyamine ligand systems have been designed, synthesized and structurally characterized.

Biological promiscuity of a binuclear Cu(ii) complex of aminoguanidine Schiff base: DNA binding, anticancer activity and histidine sensing ability of the complex

A binuclear Cu(ii) complex of aminoguanidine shows strong DNA binding activity and encouraging anti-cancer activity against HCT-16 cells. The complex can also be used for selective spectrophotomteric or fluorometric determination of histidine.

Supramolecular assemblies involving salt bridges: DFT and X-ray evidence of bipolarity

Three new aminopyridinium/4,4′-oxydibenzoate salts have been synthesized and structurally characterized. A common feature of these compounds is the formation of antiparallel π-stacked salt bridges.

Halogen⋯halogen interactions in decahalo-closo-carboranes: CSD analysis and theoretical study

We theoretically (PBE0-D3/def2TZVP) and experimentally (CSD analysis) demonstrate the importance of “like–like” halogen interactions for the stability of several decahalo-closo-carborane dimers.

Halogen and Chalcogen Bond Energies Evaluated Using Electron Density Properties

Halogen (X-bond) and chalcogen bond (Ch-bond) energies for 36 complexes have been obtained at the RI-MP2/def2-TZVP level of theory, involving the heavier halogen and chalcogen atoms (Br, I, Se, Te). We have explored the existence of linear relationships between the interaction energies and the local kinetic energy densities at the bond critical points that characterize the σ-hole interactions (both electronic G(r) and potential V(r) energy densities). Interestingly, we have found strong relationships for halogen and chalcogen bonding energies, especially for the V(r) energy density, thus allowing to estimate the interaction energy without computing the separate monomers. This is also useful to estimate the interaction in monomeric systems (intramolecular X/Ch-bonds), as illustrated using several examples. Remarkably, we have also found a good relationship when in the same representation both halogen and chalcogen atoms are included, thus allowing to use the same empirical correlation for both interactions.

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.

Exploiting 1,4-naphthoquinone and 3-iodo-1,4-naphthoquinone motifs as anion binding sites by hydrogen or halogen-bonding interactions

We describe here the utilization of 1,4-naphthoquinone and 3-iodo-1,4-naphthoquinone motifs as new anion binding sites by hydrogen- or halogen-bonding interactions, respectively. These binding sites have been integrated in bidentate ester based receptors. Emission experiments reveal that both receptors selectively recognize sulfate anions, which induced a remarkable increase of a new emission band attributed to the formation of π-stacking interactions between two 1,4-naphthoquinone units. Absorption spectroscopy and mass spectrometry indicate the disruption of the ester group of the 1,4-naphthoquinone based receptor in the presence of HP₂O₇^3-, H₂PO₄^-, F^-, AcO^- and C₆H₅CO₂^- and in the halogenated receptor with HP₂O₇^3-, F^- and AcO^- anions, while the presence of sulfate anions showed the clasical complexation behaviour. The ¹H-NMR experiment showed a slow exchange process of the receptors with their sulfate complexes. The binding mode of the receptors with sulfate has been studied by DFT calculations along with the Molecular Electrostatic Potential (MEP) surface computational tool that reveals those parts of the receptors which are more suitable for interacting with anions.

Formation of an imidazoliumyl-substituted [(LC)4P4]4+ tetracation and transition metal mediated fragmentation and insertion reaction (LC = NHC)

Tetracationic cyclo-tetraphosphane [(L_C)₄P₄]⁴⁺ as triflate salt (3[OTf]₄) (L_C = 4,5-dimethyl-1,3-diisopropyl-imidazol-2-yl) is obtained in high yield from the reduction of [L_CPCl₂]⁺ (4[OTf]) with 1,4-bis(trimethylsilyl)-1,4-dihydropyrazine (6) and represents the first salt of the cationic cyclo-phosphane series with the general formula [L _n P _n ] ⁿ⁺. Theoretical calculations reveal the electrophilic nature of the P atoms within the P₄-ring due to the influence of the imidazoliumyl-substituents. Further reduction of 3[OTf]₄ with 6 affords the unexpected formation of the notricyclane P₇-type cation [(L_C)₃P₇]³⁺ (9[OTf]₃). Selective transition metal mediated [2 + 2]-fragmentation of 3 ⁴⁺ is achieved when 3[OTf]₄ is reacted with Fe₂(CO)₉, Pd(PPh₃)₄ and Pt(PPh₃)₄ leading to the formation of the dicationic diphosphene complexes [(η²-L_CP[double bond, length as m-dash]PL_C)Fe(CO)₄]²⁺ (12[OTf]₂) and [(η²-L_CP[double bond, length as m-dash]PL_C)M(PPh₃)₂]²⁺ (13[OTf]₂ for M = Pd; 14[OTf]₂ for M = Pt). In contrast, the reaction of 3[OTf]₄ with an excess of AuCl(tht) gives rise to the formation of the five-membered ring complex [((L_C)₄P₄)AuCl₂]³⁺ (15[OTf]₃), where the Au(i) atom reductively inserts into a P-P bond of 3 ⁴⁺.

An inorganic–organic hybrid supramolecular framework based on the γ-[Mo8O26]4− cluster and cobalt complex of aspartic acid: X-ray structure and DFT study

A new inorganic–organic hybrid based on an aspartate functionalized polyoxomolybdate, [pentaaquacobalt(II)]-μ-aspartate-[γ-octamolybdate]-μ-aspartate-[pentaaquacobalt(II)] tetrahydrate, [Co2(C4H6NO4)2(γ-Mo8O26)(H2O)10]·4H2O (1), has been synthesized under hydrothermal conditions from the reaction of an Evans–Showell-type polyoxometalate, (NH4)6[Co2Mo10H4O38], and L-aspartic acid. The complex exhibits a supramolecular three-dimensional framework structure in the crystal lattice. Compound 1 was structurally characterized by elemental analyses, IR and UV–Vis (diffuse reflectance) spectroscopy and single-crystal X-ray diffraction. In this compound, aspartic acid acts as a bridge between the two Co atoms and the Mo centres, with the –CH2COOH side chain directly linked to the Mo centre in γ-[Mo8O26]4− and the α-carboxylate side chain bound to the Co centre. Commonly, the binding of transition-metal complexes to POMs involves coordination of the metal to a terminal O atom of the POM so that 1, with a bridging ligand between Mo and Co atoms, belongs to a separate class of hybrid materials. While the starting materials are both chiral and one might expect them to form a chiral hybrid, the decomposition of the chiral Evans–Showell-type POM and its conversion to the centrosymmetric γ-octamolybdate POM, plus the presence of two aspartate ligands centrosymmetrically placed on either side of the POM, leads to the formation of an achiral hybrid. We have studied energetically by means of density functional theory (DFT) calculations and using the Bader's `atoms-in-molecules' analysis the electrostatically enhanced hydrogen bonds (EEHBs) observed in the solid state of 1, which are crucial for the formation of one-dimensional supramolecular assemblies.

The role of π-π stacking and hydrogen-bonding interactions in the assembly of a series of isostructural group IIB coordination compounds

This article describes the syntheses, crystal structures and theoretical calculations of six group IIB coordination compounds containing a 2-{[(2-meth­oxy­phen­yl)imino]­meth­yl}phenol ligand to provide further insight into the role of π-stacking and hydrogen bonding in metallo­supra­molecular assembly.

The supra­molecular chemistry of coordination compounds has become an im­portant research domain of modern inorganic chemistry. Herein, six iso­structural group IIB coordination compounds containing a 2-{[(2-meth­oxy­phen­yl)imino]­meth­yl}phenol ligand, namely di­chlorido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)zinc(II), [ZnCl₂(C₂₈H₂₆N₂O₄)], 1, di­iodido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)zinc(II), [ZnI₂(C₂₈H₂₆N₂O₄)], 2, di­bromido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­n­iumyl­idene]meth­yl}pheno­lato-κO)cadmium(II), [CdBr₂(C₂₈H₂₆N₂O₄)], 3, di­iodido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)cadmium(II), [CdI₂(C₂₈H₂₆N₂O₄)], 4, di­chlorido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)mercury(II), [HgCl₂(C₂₈H₂₆N₂O₄)], 5, and di­iodido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)mercury(II), [HgI₂(C₂₈H₂₆N₂O₄)], 6, were synthesized and characterized by X-ray crystallography and spectroscopic techniques. All six compounds exhibit an infinite one-dimensional ladder in the solid state governed by the formation of hydrogen-bonding and π–π stacking inter­actions. The crystal structures of these compounds were studied using geometrical and Hirshfeld surface analyses. They have also been studied using M06-2X/def2-TZVP calculations and Bader’s theory of ‘atoms in mol­ecules’. The energies associated with the inter­actions, including the contribution of the different forces, have been evaluated. In general, the π–π stacking inter­actions are stronger than those reported for conventional π–π complexes, which is attributed to the influence of the metal coordination, which is stronger for Zn than either Cd or Hg. The results reported herein might be useful for understanding the solid-state architecture of metal-containing materials that contain M^IIX₂ subunits and aromatic organic ligands.

closo-Carboranes as dual CH⋯π and BH⋯π donors: theoretical study and biological significance

In this manuscript the ability ofcloso-carboranes to establish CH⋯π and BH⋯π interactions with several aromatic moieties exhibiting different electronic natures has been evaluated at the PBE0-D3/def2-TZVP level of theory.

Solid-state supramolecular architectures of a series of Hg(ii) halide coordination compounds based on hydroxyl-substituted Schiff base ligands

Herein, six Hg(ii) coordination compounds containing Schiff base ligands were synthesized, characterized and studied using geometrical and Hirshfeld analyses as well as theoretical calculations.