Dihydrogen bonding: structures, energetics, and dynamics

Theoretical Insights into the Effect of Different Numbers of Thiophene Groups on Hydrogen Bond Interaction and Excited-State Intramolecular Proton-Transfer Process for Flavonoid Derivatives

In this study, we systematically explored the impact of varying the number of thiophene groups on the hydrogen bond interaction and excited-state intramolecular proton-transfer (ESIPT) processes in flavonoid derivatives (STF, DTF, and TTF) using the density functional theory and time-dependent density functional theory methods. Initially, a thorough analysis of the optimized geometric structures revealed that the intramolecular hydrogen bond in the S1 state is enhanced and gradually weakened as the number of thiophene groups increases. To gain a deeper understanding of the hydrogen bond interaction, topological analysis, interaction region indicator scatter plots, and isosurface plots were employed. These images provide further insights that align with the structural analysis. Additionally, we observed a red-shift in the electronic spectra (absorption and fluorescence spectra), which is primarily attributed to the narrowing of the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, as elucidated by the frontier molecular orbitals. Furthermore, a combined analysis between the hole-electron distribution and the transition density matrix heat map shows that electron excitation involves the unidirectional charge-transfer mechanism. In the end, by conducting relaxed potential energy curve scans, we found that an increase in the number of thiophene groups elevates the energy barrier for ESIPT, making it more challenging for the reaction. In summary, our study underscores the vital effect of thiophene-substituted numbers in modulating the ESIPT process, which is able to provide valuable insights for the design and synthesis of desired organic fluorescent probes in the future.

B(C6F5)3-Catalyzed Dehydrogenation of Pyrrolidines to Form Pyrroles

Pyrroles are important N-heterocycles found in medicines and materials. The formation of pyrroles from widely accessible pyrrolidines is a potentially attractive strategy but is an underdeveloped approach due to the sensitivity of pyrroles to the oxidative conditions required to achieve such a transformation. Herein, we report a catalytic approach that employs commercially available B(C6F5)3 in an operationally simple procedure that allows pyrrolidines to serve as direct synthons for pyrroles. Mechanistic studies have revealed insights into borane-catalyzed dehydrogenative processes.

Location of the Shared Proton in Proton-Bound Dimer Compound of Hydrogen Sulfate and Formate: Path Integral Molecular Dynamics Study

The structure of the proton-bound dimer compound of hydrogen sulfate and formate has been studied by considering nuclear quantum effects (NQEs) using the path integral molecular dynamics method. This study unveiled the location of the shared proton and answered the following question: "Is the shared proton localized on either an anion or located around the center of two anions?" We have elucidated that the shared proton is distributed in the region beyond the transition state due to the NQEs, even though the shared proton did not completely overcome the transition state for the proton shuttle.

Bispidine as a Versatile Scaffold: From Topological Hosts to Transmembrane Transporters

The development of designer topological structures is a synthetically challenging endeavor. We present herein bispidine as a platform for the design of molecules with various topologies and functions. The bispidine-based acyclic molecule, which shows intriguing S-shape topology, is discussed. Single-crystal X-ray diffraction studies revealed that this molecule exists in the solid state as two conformational enantiomers. In addition, bispidine-based designer macrocycles were synthesized and investigated for ionophoric properties. Patch clamp experiments revealed that these macrocycles transport both anions and cations non-specifically with at least tenfold higher chloride conductance over the cations under the given experimental conditions. Ultramicroscopy and single-crystal X-ray crystallographic studies indicated that the self-assembling macrocycle forms a tubular assembly. Our design highlights the use of unconventional dihydrogen interactions in nanotube fabrication.

Effect of Substituents on the Intramolecular n→π* Interaction in 3-[2-(Dimethylamino) phenyl] propanal: A Computational Study

n→π* non-covalent interaction (NCI) and hydrogen bond have similarity in terms of delocalization of the electron density between the two orbitals involved in the interaction. Hydrogen bond (X-H···Y) involves delocalization of the lone pair electrons (n) on the Y atom into the σ* orbital of the X-H bond. In contrast, the n→π* interaction deals with delocalizing the lone pair electrons (n) on the N, O, or S atom into the π* orbital of a C═O group or aromatic ring. Herein, we have shown a resemblance of this weak n→π* interaction with the relatively stronger hydrogen bond in terms of folding the side chains in flexible molecules. This work reports the study of folding of the flexible side-chain in 3-[2-(dimethylamino) phenyl] propanal (DMAPhP) through a N···C═O n→π* interaction using various computational approaches such as NBO, QTAIM, and NCI analyses. The folding of the molecule by the n→π* interaction observed in this study is found to be similar to that present in the secondary structures of peptides or proteins through hydrogen bonding interactions. Interestingly, the stabilization of the global minimum conformer of DMAPhP by the n→π* interaction demonstrates the importance of this NCI in providing conformational preferences in molecular systems. Another important finding of this study is that the theoretical redshift obtained in the C═O stretching frequency of the most stable conformer of the DMAPhP is contributed mostly by the n→π* interaction as the C═O group is not involved in hyperconjugation with any neighboring heteroatom, which is a common phenomenon in any ester or amide. We have also demonstrated here that the strength of the intramolecular n→π* interaction can be modulated by varying the electronic substituents at the para position of the donor group involved in the interaction.

Photoinduced Dehydrogenative Borylation via Dihydrogen Bond Bridged Electron Donor and Acceptor Complexes

Air-stable amine- and phosphine-boranes are discovered as donors to integrate with pyridinium acceptor for generating photoactive electron-donor-acceptor (EDA) complexes. Experimental results and DFT calculations suggest a dihydrogen bond bridging the donor and acceptor. Irradiating the EDA complex enables an intra-complex single electron transfer to give a boron-centered radical for dehydrogenative borylation with no need of external photosensitizer and radical initiator. The deprotonation of Wheland-like radical intermediate rather than its generation is believed to determine the good ortho-selectivity based on DFT calculations. A variety of α-borylated pyridine derivatives have been readily synthesized with good functional group tolerance.

B-H⋯π and C-H⋯π interactions in protein-ligand complexes: carbonic anhydrase II inhibition by carborane sulfonamides

Among non-covalent interactions, B-H⋯π and C-H⋯π hydrogen bonding is rather weak and less studied. Nevertheless, since both can affect the energetics of protein-ligand binding, their understanding is an important prerequisite for reliable predictions of affinities. Through a combination of high-resolution X-ray crystallography and quantum-chemical calculations on carbonic anhydrase II/carborane-based inhibitor systems, this paper provides the first example of B-H⋯π hydrogen bonding in a protein-ligand complex. It shows that the B-H⋯π interaction is stabilized by dispersion, followed by electrostatics. Furthermore, it demonstrates that the similar C-H⋯π interaction is twice as strong, with a slightly smaller contribution of dispersion and a slightly higher contribution of electrostatics. Such a detailed insight will facilitate the rational design of future protein ligands, controlling these types of non-covalent interactions.

Dihydrogen Bonding-Seen through the Eyes of Vibrational Spectroscopy

In this work, we analyzed five groups of different dihydrogen bonding interactions and hydrogen clusters with an H3+ kernel utilizing the local vibrational mode theory, developed by our group, complemented with the Quantum Theory of Atoms-in-Molecules analysis to assess the strength and nature of the dihydrogen bonds in these systems. We could show that the intrinsic strength of the dihydrogen bonds investigated is primarily related to the protonic bond as opposed to the hydridic bond; thus, this should be the region of focus when designing dihydrogen bonded complexes with a particular strength. We could also show that the popular discussion of the blue/red shifts of dihydrogen bonding based on the normal mode frequencies is hampered from mode-mode coupling and that a blue/red shift discussion based on local mode frequencies is more meaningful. Based on the bond analysis of the H3+(H2)n systems, we conclude that the bond strength in these crystal-like structures makes them interesting for potential hydrogen storage applications.

Stereochemistry Controls Dihydrogen Bonding Strengths in Chiral Amine Boranes Adducts

The growing interest in exploiting novel concepts of non-covalent interactions in catalysts and supramolecular chemistry made us revisit a special kind of hydrogen bonding: the dihydrogen bond (DHB), formed between a classical hydrogen bond donor and a hydridic hydrogen as acceptor. Herein, we investigate how the strength of the N-H^δ+ ⋅⋅⋅^δ- H-B interaction and hence the DHB-driven self-aggregation of amine-borane adducts is governed by steric effects by comparing the structures and binding enthalpies of various chiral derivatives. For a diastereomeric pair of amine-boranes prepared from a chiral secondary amine, we show that the stereochemistry at the nitrogen has significant influence on the interaction enthalpy. Based on this finding, N-chiral amine boranes can be envisioned to become interesting building blocks in supramolecular chemistry to fine-tune the formation dynamics of assemblies.

Theory of Borazine-Derived Nanothreads: Enumeration, Reaction Pathways, and Piezoelectricity

Nanothreads are one-dimensional macromolecules formed by pressure-induced polymerization along stacks of multiply unsaturated (or highly strained) molecules such as benzene (or cubane). Borazine is isoelectronic to benzene yet with substantial bond polarity, thus motivating a theoretical examination of borazine-derived nanothreads with degrees of saturation of 2, 4, and 6 (defined as the number of four-coordinated boron and nitrogen atoms per borazine formula unit). The energy increases upon going from molecular borazine to degree-2 borazine-derived threads and then decreases for degree-4 and degree-6 nanothreads as more σ bonds are formed. With the constraint of no more than two borazine formula units within the repeat unit of the framework's bonding topology, there are only 13 fully saturated (i.e., degree-6) borazine-derived nanothreads that avoid energetically costly homopolar bonds (as compared to more than 50 such candidates for benzene-derived threads). Only two of these are more stable than borazine. Hypothetical pathways from molecular borazine to these two degree-6 borazine-derived nanothreads are discussed. This relative paucity of outcomes may assist in kinetic control of reaction products. Beyond the high mechanical strength also predicted for carbon-based threads, properties such as piezoelectricity and flexoelectricity may be accessible to the polar lattice of borazine-derived nanothreads, with intriguing prospects for expression in these extremely thin yet rigid objects.

Dehydropolymerization of H3B·NMeH2 Mediated by Cationic Iridium(III) Precatalysts Bearing κ3-iPr-PNRP Pincer Ligands (R = H, Me): An Unexpected Inner-Sphere Mechanism

The dehydropolymerization of H₃B·NMeH₂ to form N-methylpolyaminoborane using neutral and cationic catalysts based on the {Ir(ⁱPr-PN^HP)} fragment [ⁱPr-PN^HP = κ³-(CH₂CH₂PⁱPr₂)₂NH] is reported. Neutral Ir(ⁱPr-PN^HP)H₃ or Ir(ⁱPr-PN^HP)H₂Cl precatalysts show no, or poor and unselective, activity respectively at 298 K in 1,2-F₂C₆H₄ solution. In contrast, addition of [NMeH₃][BAr^F₄] (Ar^F = 3,5-(CF₃)₂C₆H₃) to Ir(ⁱPr-PN^HP)H₃ immediately starts catalysis, suggesting that a cationic catalytic manifold operates. Consistent with this, independently synthesized cationic precatalysts are active (tested between 0.5 and 2.0 mol % loading) producing poly(N-methylaminoborane) with M_n ∼ 40,000 g/mol, Đ ∼1.5, i.e., dihydrogen/dihydride, [Ir(ⁱPr-PN^HP)(H)₂(H₂)][BAr^F₄]; σ-amine-borane [Ir(ⁱPr-PN^HP)(H)₂(H₃B·NMe₃)][BAr^F₄]; and [Ir(ⁱPr-PN^HP)(H)₂(NMeH₂)][BAr^F₄]. Density functional theory (DFT) calculations probe hydride exchange processes in two of these complexes and also show that the barrier to amine-borane dehydrogenation is lower (22.5 kcal/mol) for the cationic system compared with the neutral system (24.3 kcal/mol). The calculations show that the dehydrogenation proceeds via an inner-sphere process without metal–ligand cooperativity, and this is supported experimentally by N–Me substituted [Ir(ⁱPr-PN^MeP)(H)₂(H₃B·NMe₃)][BAr^F₄] being an active catalyst. Key to the lower barrier calculated for the cationic system is the outer-sphere coordination of an additional H₃B·NMeH₂ with the N–H group of the ligand. Experimentally, kinetic studies indicate a complex reaction manifold that shows pronounced deceleratory temporal profiles. As supported by speciation and DFT studies, a key observation is that deprotonation of [Ir(ⁱPr-N^HP)(H)₂(H₂)][BAr^F₄], formed upon amine-borane dehydrogenation, by the slow in situ formation of NMeH₂ (via B–N bond cleavage), results in the formation of essentially inactive Ir(ⁱPr-PN^HP)H₃, with a coproduct of [NMeH₃]⁺/[H₂B(NMeH₂)₂]⁺. While reprotonation of Ir(ⁱPr-PN^HP)H₃ results in a return to the cationic cycle, it is proposed, supported by doping experiments, that reprotonation is attenuated by entrainment of the [NMeH₃]⁺/[H₂B(NMeH₂)₂]⁺/catalyst in insoluble polyaminoborane. The role of [NMeH₃]⁺/[H₂B(NMeH₂)]⁺ as chain control agents is also noted.

Hydration of Nitriles Catalyzed by Ruthenium Complexes: Role of Dihydrogen Bonding Interactions in Promoting Base-Free Catalysis

Ru(II) complexes of amide-phosphine-based tridentate ligands additionally containing pyridine, isoquinoline, and quinoline rings have been synthesized, and their catalytic utility for the selective hydration of nitriles to amides is explored under the base-containing as well as base-free conditions. The chloride-ligated complexes 1-3 exhibited significant catalytic activity in the presence of a base, whereas hydride-ligated complexes 4-6 carried out the hydration of nitrile without the requirement of any base. The mechanistic studies revealed the involvement of [Ru-H] species as the active catalyst in the catalytic cycle. The [Ru-H] species assisted in the polarization of an incoming water molecule through [Ru-H···H-OH] dihydrogen bonding interaction and consequently aided in the attack of a positioned water molecule to a nitrile coordinated to a ruthenium center. Substrate binding studies and kinetic experiments further supported the mechanism. A wide variety of aromatic nitriles containing both electron-withdrawing and electron-releasing groups as well as other substrates including aliphatic nitriles, base-sensitive nitriles, and a few biologically relevant nitriles were employed for the selective hydration.

Hydrogen-bonded aromatic amide macrocycles: synthesis, properties and functions

As a classic example of nearly planar cyclic compounds, hydrogen-bonded aromatic amide (H-bonded aramide) macrocycles, consisting of consecutive intramolecular hydrogen bonds and aromatic residues, receive considerable research attention due to their rich host-guest chemistry. This review provides a detailed summary of the synthesis, properties and functions of H-bonded aramide macrocycles and their derivatives. Herein, the constitutional patterns of these macrocycles are divided into two subcategories: interior hydrogen bonding motifs and exterior hydrogen bonding motifs. Based on these two motifs, we summarize the facile synthesis, self-assembly, host-guest interaction complexation of H-bonded aramide macrocycles and the resulting applications such as molecular recognition, artificial ion channels, soft materials, supramolecular catalysis, and artificial molecular machines. The development of H-bonded aramide macrocycles is still in its infancy, although a considerable number of examples have been reported. We hope that this review will provide useful information and unlock new opportunities in this field.

The roles of charge transfer and polarization in non-covalent interactions: a perspective from ab initio valence bond methods

Noncovalent interactions are ubiquitous and have been well recognized in chemistry, biology and material science. Yet, there are still recurring controversies over their natures, due to the wide range of noncovalent interaction terms. In this Essay, we employed the Valence Bond (VB) methods to address two types of interactions which recently have drawn intensive attention, i.e., the halogen bonding and the CH‧‧‧HC dihydrogen bonding. The VB methods have the advantage of interpreting molecular structures and properties in the term of electron-localized Lewis (resonance) states (structures), which thereby shed specific light on the alteration of the bonding patterns. Due to the electron localization nature of Lewis states, it is possible to define individually and measure both polarization and charge transfer effects which have different physical origins. We demonstrated that both the ab initio VB method and the block-localized wavefunction (BLW) method can provide consistent pictures for halogen bonding systems, where strong Lewis bases NH₃, H₂O and NMe₃ partake as the halogen bond acceptors, and the halogen bond donors include dihalogen molecules and XNO₂ (X = Cl, Br, I). Based on the structural, spectral, and energetic changes, we confirm the remarkable roles of charge transfer in these halogen bonding complexes. Although the weak C-H∙∙∙H-C interactions in alkane dimers and graphene sheets are thought to involve dispersion only, we show that this term embeds delicate yet important charge transfer, bond reorganization and polarization interactions.

A path integral molecular dynamics study on the NH4+ rotation in NH4+⋯XH2 (X = Be or Mg) dihydrogen bond systems

The nuclear quantum effects (NQEs) in dihydrogen bond (DHB) complexes, i.e., NH₄⁺⋯BeH₂ and NH₄⁺⋯MgH₂, have been investigated using multicomponent quantum mechanics (MC_QM) calculations and path integral molecular dynamics (PIMD) simulation. The MC_QM method considers the NQEs, whereas PIMD considers both the NQEs and the thermal effects. The linear C_3v structure is maintained in the optimized structures obtained by the static MP2 and MC_MP2 calculations, whereas the average structures obtained by the PIMD simulation are nonlinear. The strong DHB interaction in NH₄⁺⋯MgH₂ suppresses the fluctuation in the H^δ+NMg and H^δ-MgN angles, and hence, the NH₄⁺ rotation did not occur in the simulation of NH₄⁺⋯MgH₂. The analysis of the radius of gyration revealed that the nuclear quantum fluctuation in the perpendicular direction is suppressed by the formation of the DHB complex, whereas that in the parallel direction is slightly enhanced in both the H^δ+ and H^δ- nuclei.

Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines

Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as "P₂N₂" ligands, have profound effects on the reactivity of many catalysts. The resulting [Ni(P^R₂N^R'₂)₂]²⁺ complexes are electrocatalysts for both the oxidation and production of H₂. Achieving the optimal benefit of the pendant amine requires that it has suitable basicity and is properly positioned relative to the metal center. In addition to the catalytic efficacy demonstrated with [Ni(P^R₂N^R'₂)₂]²⁺ complexes for the oxidation and production of H₂, catalysts with diphosphine ligands containing pendant amines have also been demonstrated for several metals for many different reactions, both in solution and immobilized on surfaces. The impact of pendant amines in catalyst design continues to expand.

The CON−H…+NH2 Blue-Shifting H-Bond Stabilizing Effect on Z Secondary Amides and Cyclic System Conformational Rearrangement through an Alkylamine-Chain Migration Pathway

The paper is focusing on the amide linkage exceptional properties and usage of chemistry (conformational rearrangement, geometrical stereoisomers, spectroscopic blue shift phenomenon, protonation and deprotonation reactions, synthetic scope, and mechanistic implications). Hydrogen-bond-stabilized acylation reactions of a diamine with thioamides or nitriles reveal how substituents influence both the outcome of stereoselectivity and interactions. Inferring the chemical mechanism from the structures of reactants is dissimilar to the appropriate E isomers, the Z form becomes more favored in the secondary amides obtained. One conclusion from the estimation of Z structures, based on the 1H-15N 2D NMR spectra in comparison with the references, is the existence of the intramolecular, blue shifting CON−H…+NH2CH3 hydrogen bonds. The rearrangement of a methylamino residue provided the free base stabilized in the CH3N−H…O=CNH after deprotonation. An essential part of the publication describes systems in a highly stereoselective fashion, so the stereochemical outcome of the product is predictable now.

Complex Metal Borohydrides: From Laboratory Oddities to Prime Candidates in Energy Storage Applications

Despite being the lightest element in the periodic table, hydrogen poses many risks regarding its production, storage, and transport, but it is also the one element promising pollution-free energy for the planet, energy reliability, and sustainability. Development of such novel materials conveying a hydrogen source face stringent scrutiny from both a scientific and a safety point of view: they are required to have a high hydrogen wt.% storage capacity, must store hydrogen in a safe manner (i.e., by chemically binding it), and should exhibit controlled, and preferably rapid, absorption–desorption kinetics. Even the most advanced composites today face the difficult task of overcoming the harsh re-hydrogenation conditions (elevated temperature, high hydrogen pressure). Traditionally, the most utilized materials have been RMH (reactive metal hydrides) and complex metal borohydrides M(BH₄)_x (M: main group or transition metal; x: valence of M), often along with metal amides or various additives serving as catalysts (Pd²⁺, Ti⁴⁺ etc.). Through destabilization (kinetic or thermodynamic), M(BH₄)_x can effectively lower their dehydrogenation enthalpy, providing for a faster reaction occurring at a lower temperature onset. The present review summarizes the recent scientific results on various metal borohydrides, aiming to present the current state-of-the-art on such hydrogen storage materials, while trying to analyze the pros and cons of each material regarding its thermodynamic and kinetic behavior in hydrogenation studies.

Carbon-Centered Hydrogen Bonds in Proteins

Hydrogen bonding (H-bonding) without lone pair(s) of electrons and π-electrons is a concept developed 2-3 years ago. H-bonds involving less electronegative tetrahedral carbon are beyond the classical concept of H-bonds. Herein, we present the first report on H-bonds with tetravalent carbons in proteins. A special bonding arrangement is needed to increase the negative charge density around the sp³-hybridized carbon atom. Therefore, less electronegative elements such as As and Mg, when bonded to sp³-C, enable the C-atoms as H-bond acceptors. Careful protein structure analysis aided by several quantum chemical calculations suggests that these H-bonds are weak to moderate in strength. We developed an empirical equation to estimate the C-H···C H-bond energy in proteins from the distances between the C- and H-atoms. In proteins, the binding energies range from -5.4 to -14.0 kJ/mol. The C-H···C H-bonds assist the substrate binding in proteins. We also explored the potential role of these carbon-centered H-bonds in C-H bond activation through σ-bond metathesis. To our surprise, contribution from these H-bonds is almost of similar magnitude as that from C-H···π H-bonds for C-H bond activation.

Catechin Derivatives as Inhibitor of COVID-19 Main Protease (Mpro): Molecular Docking Studies Unveil an Opportunity Against CORONA

BACKGROUND

A newly emergent strain of coronavirus (COVID-19) has affected almost the whole of the world's population. Currently, there is no specific vaccine or drug against COVID-19. Xu et al. (2020) built a homolog model of SARS-CoV-2 Mpro based on SARS-CoV Mpro, which is considered as a target to inhibit the replication of CoV.

OBJECTIVE

The aim of the current study was to find potential inhibitors of COVID-19 Mpro using docking analysis.

METHODS

Autodockvina was used to carry out Protein-Ligand docking. COVID-19 main protease Mpro was docked with catechin and its different synthetic derivatives. Nelfinavir, an antiretroviral drug belonging to protease inhibitors, was taken as the standard.

RESULTS

According to the result obtained, it was found that Compound (4) and Compound (1) have more affinity than nelfinavir.

CONCLUSION

Compounds were found to have a great potential to become COVID-19 main protease Mpro inhibitor. Nevertheless, for their medicinal use, further investigation is necessary.

Unraveling hydridic-to-protonic dihydrogen bond predominance in monohydrated dodecaborate clusters

Hydridic-to-protonic dihydrogen bonds (DHBs) are involved in comprehensive structural and energetic evolution, and significantly affect reactivity and selectivity in solution and solid states. Grand challenges exist in understanding DHBs’ bonding nature and strength, and how to harness DHBs. Herein we launched a combined photoelectron spectroscopy and multiscale theoretical investigation using monohydrated closo-dodecaborate clusters B₁₂X₁₂²⁻·H₂O (X = H, F, I) to address such challenges. For the first time, a consistent and unambiguous picture is unraveled demonstrating that B–H⋯H–O DHBs are superior to the conventional B–X⋯H–O HBs, being 1.15 and 4.61 kcal mol⁻¹ stronger than those with X = F and I, respectively. Energy decomposition analyses reveal that induction and dispersion terms make pronounced contributions resulting in a stronger B–H⋯H–O DHB. These findings call out more attention to the prominent roles of DHBs in water environments and pave the way for efficient and eco-friendly catalytic dihydrogen production based on optimized hydridic-to-protonic interactions.

A joint gas-phase ion spectroscopic and multiscale theoretical study reveals unequivocally the predominance of the hydridic-to-protonic dihydrogen bond over the prototypical strong hydrogen bond in monohydrated dodecaborate clusters.

Structures and reaction dynamics of N2 and H2 binding at FeMo-co, the active site of nitrogenase

The chemical reactions occurring at the Fe₇MoS₉C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N₂ → NH₃), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N₂ and H₂, each with more than one type of reactivity. This paper reports investigations of the binding of H₂ and N₂ at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H₂ and/or N₂ bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H₂/N₂ are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H₂ or N₂, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol^-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N₂ structures and three H₂ structures have negative binding free energies, which include the estimated entropy penalties for binding of N₂, H₂ from proximal protein. These favoured structures have N₂ bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H₂ bound at the endo-Fe2 position. Various postulated structures with N₂ bridging Fe2 and Fe6 revert to end-on-N₂ at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H₂ range from 1 to 20 kcal mol^-1 and barriers to dissociation of H₂ range from 3 to 18 kcal mol^-1. Barriers to the binding of N₂, in either side-on or end-on mode, range from 2 to 18 kcal mol^-1, while dissociation of bound N₂ encounters barriers of 3 to 8 kcal mol^-1 for side-on bonding and 7 to 18 kcal mol^-1 for end-on bonding. These results allow formulation of mechanisms for the H₂/N₂ exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.

Vibrational Perturbation of the [FeFe] Hydrogenase H-Cluster Revealed by 13C2H-ADT Labeling

[FeFe] hydrogenases are highly active catalysts for the interconversion of molecular hydrogen with protons and electrons. Here, we use a combination of isotopic labeling, ⁵⁷Fe nuclear resonance vibrational spectroscopy (NRVS), and density functional theory (DFT) calculations to observe and characterize the vibrational modes involving motion of the 2-azapropane-1,3-dithiolate (ADT) ligand bridging the two iron sites in the [2Fe]_H subcluster. A -¹³C²H₂- ADT labeling in the synthetic diiron precursor of [2Fe]_H produced isotope effects observed throughout the NRVS spectrum. The two precursor isotopologues were then used to reconstitute the H-cluster of [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1), and NRVS was measured on samples poised in the catalytically crucial H_hyd state containing a terminal hydride at the distal Fe site. The ¹³C²H isotope effects were observed also in the H_hyd spectrum. DFT simulations of the spectra allowed identification of the ⁵⁷Fe normal modes coupled to the ADT ligand motions. Particularly, a variety of normal modes involve shortening of the distance between the distal Fe-H hydride and ADT N-H bridgehead hydrogen, which may be relevant to the formation of a transition state on the way to H₂ formation.

Bifurcated Dihydrogen Bonding in the Uptake of Gas-Phase Diborane on Silica

The interfacial chemistry of diborane (B₂H₆) with hydroxylated silica was investigated via in situ Fourier-transform infrared spectroscopy and temperature-programmed desorption. During exposure of silica to B₂H₆ under ultrahigh vacuum conditions, a decline in infrared band intensity assigned to excitation of the interfacial silanol O-H vibration at 3750 cm^-1 and the associated appearance of a feature at 3687 cm^-1 revealed hydrogen-bonding interactions between B₂H₆ and interfacial silanol groups. The IR spectrum for silica was completely recovered following desorption of the adsorbates, indicating that interactions between B₂H₆ and clean silica are reversible, in contrast to other reports on this system. During temperature-programmed desorption of diborane from silica, B₂H₆ was observed to desorb between 80 and 150 K, evidence for weak interactions between B₂H₆ and the surface. Electronic-structure calculations revealed that these interactions were due to bifurcated dihydrogen bonds between two terminal B-H groups of the adsorbate and interfacial silanol groups.

Observation of Dihydrogen Bonds in High-Pressure Phases of Ammonia Borane by X-ray and Neutron Diffraction Measurements

High-pressure X-ray and neutron diffraction analyses of an ambient-pressure phase (AP) and two high-pressure phases (HP1 and HP2) of ammonia borane (i.e., NH₃BH₃ and ND₃BD₃) were conducted to investigate the relationship between their crystal structures and dihydrogen bonds. It was confirmed that the hydrogen atoms in AP formed dihydrogen bonds between adjacent molecules, and the H-H distance between the hydrogen atoms forming this interaction was shorter than 2.4 Å, which was nearly 2 times larger than the van der Waals radius of hydrogen. In the case of half of the hydrogen bonds, a phase transition from AP to the first high-pressure phase (HP1) at ∼1.2 GPa resulted in an increase in the H-H distances, which suggested that the dihydrogen bonds were broken. However, when HP1 was further pressurized to ∼4 GPa, all of the H-H distances became shorter than 2.4 Å again, which implied the occurrence of pressure-induced re-formation of the dihydrogen bonds. It was speculated that the re-formation was consistent with a second-order phase transition suggested in previous studies by Raman spectroscopy and X-ray diffraction measurement. Furthermore, at ∼11 GPa, HP1 transformed to the second high-pressure phase (HP2), and its structure was determined to be P2₁ (Z = 2). In this phase transition, the inclination of the molecule axis became larger, and the number of types of dihydrogen bonds increased from 6 to 11. At 18.9 GPa, which was close to the upper pressure limit of HP2, the shortest dihydrogen bond decreased to ∼1.65 Å. Additionally, the X-ray diffraction results suggested another phase transition to the third high-pressure phase (HP3) at ∼20 GPa. The outcomes of this study confirmed experimentally for the first time that the structural change under pressure causes the breakage and re-formation of the dihydrogen bonds of NH₃BH₃.

Trends in the Series of Ammine Rare-Earth-Metal Borohydrides: Relating Structural and Thermal Properties

Ammine metal borohydrides display extreme structural and compositional diversity and show potential applications for solid-state hydrogen and ammonia storage and as solid-state electrolytes. Thirty-two new compounds are reported in this work, and trends in the full series of ammine rare-earth-metal borohydrides are discussed. The majority of the rare-earth metals (RE) form trivalent RE(BH₄)₃·xNH₃ (x = 7-1) compounds, which possess an intriguing crystal chemistry changing with the number of ammonia ligands, varying from structures built from complex ions (x = 5-7), to molecular structures (x = 3, 4), one-dimensional chains (x = 2), and structures built from two-dimensional layers (x = 1). Divalent RE(BH₄)₂·xNH₃ (x = 4, 2, 1) compounds are observed for RE²⁺ = Sm, Eu, Yb, with structures varying from molecular structures (x = 4) to two-dimensional layered (x = 2, 1) and three-dimensional structures (Yb(BH₄)₂·NH₃). The crystal structure and composition of the compounds depend on the volume of the rare-earth ion. In all structures, NH₃ coordinates to the metal, while BH₄^- has a more flexible coordination and is observed as a bridging and terminal ligand and as a counterion. RE(BH₄)₃·xNH₃ (x = 7-5, 4) releases NH₃ stepwise during thermal treatment, while mainly H₂ is released for x ≤ 3. In contrast, only NH₃ is released from RE(BH₄)₂·xNH₃ due to the lower charge density on the RE²⁺ ion and higher stability of RE(BH₄)₂. The thermal stability of RE(BH₄)₃·xNH₃ increase with increasing cation charge density for x = 5, 7, while it decreases for x = 4, 6. For x = 3, the thermal stability decreases with increasing charge density, due to the destabilization of the BH₄^- group, making it more reactive toward NH₃. This research provides a large number of novel compounds and new insight into trends in the crystal chemistry of ammine metal borohydrides and reveals a correlation between the local metal coordination and the thermal stability.

Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study

Splitting of molecular hydrogen (H₂) into bridging and terminal hydrides is a common step in transition metal chemistry. Herein, we propose a novel organometallic platform for cleavage of multiple H₂ molecules, which combines metal centers capable of stabilizing multiple oxidation states, and ligands bearing positioned pendant basic groups. Using quantum chemical modeling, we show that low-valent, early transition metal diniobium(ii) complexes with diphosphine ligands featuring pendant amines can favorably uptake up to 8 hydrogen atoms, and that the energetics are favored by the formation of intramolecular dihydrogen bonds. This result suggests new possible strategies for the development of hydrogen scavenger molecules that are able to perform reversible splitting of multiple H₂ molecules.

Modeling Hydrogen Release from Water with Borane and Alane Catalysts: A Unified Reaction Valley Approach

The unified reaction valley approach combined with the local vibrational mode and ring puckering analysis is applied to investigate the hydrogen evolution from water in the presence of small hydrides such as BH₃, metal hydrides as AlH₃, and their derivatives. We studied a series of reactions involving BH₃, AlH₃, B₂H₆, Al₂H₆, and AlH₃BH₃ with one- and two-water molecules, considering multiple reaction paths. In addition, the influence of the aqueous medium was examined. A general reaction mechanism was identified for most of the reactions. Those that deviate could be associated with unusually high reaction barriers with no hydrogen release. The charge transfer along the reaction path suggests that a viable hydrogen release is achieved when the catalyst adopts the role of a charge donor during the chemical processes. The puckering analysis showed that twistboat and boat forms are the predominant configurations in the case of an intermediate six-membered ring formation, which influences the activation barrier. The local mode analysis was used as a tool to detect the H-H bond formation as well as to probe catalyst regenerability. Based on the correlation between the activation energy and the change in the charge separation for cleaving O-H and B(Al)-H bonds, two promising subsets of reactions could be identified along with prescriptions for lowering the reaction barrier individually with electron-donating/withdrawing substituents.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

Assessing the structure and first hyperpolarizability of Li@B10H14 in solution: a sequential QM/MM study using the ASEC-FEG method

The structure and electronic properties of the lithium decahydroborate (Li@B₁₀H₁₄) complex in chloroform and water in normal thermodynamic conditions have been investigated using sequential QM/MM calculations by means of the average solvent electrostatic configuration (ASEC) and the Free Energy Gradient (FEG) methods. To obtain the structure of the Li@B₁₀H₁₄ complex in each of the solvents considered, we have performed geometry optimizations in solution using the ASEC-FEG method. The results show, for the first time with a realistic model of the molecular environment, that this alkali-metal-borane cluster is stable in chloroform but unstable in water. We have also explored the role of the electronic polarization of the solute due to solvent in the static first hyperpolarizability. The results show that, despite the reduction due to the effect of electrostatic polarization in chloroform, the Li@B₁₀H₁₄ complex still exhibits a large electronic first hyperpolarizability, with potential for application as a second-order nonlinear optical (NLO) material. In water, in contrast, the contribution of the excess electron for NLO responses is significantly affected by the electrostatic polarization effects. Therefore our results reveal that the influence of the environment must be considered in the design of new stable NLO materials.

Raman studies of hydrogen trapped in As4O6·2H2 at high pressure and low temperature

Raman spectroscopic measurements of the arsenolite-hydrogen inclusion compound As₄O₆·2H₂ were performed in diamond anvil cells at high pressure and variable temperature down to 80 K. The experimental results were complemented by ab initio molecular dynamics simulations and phonon calculations. Observation of three hydrogen vibrons in As₄O₆·2H₂ is reported in the entire temperature and pressure range studied (up to 24 GPa). While the experiments performed with protium and deuterium at variable temperatures allowed for the assignment of two vibrons as Q₁(1) and Q₁(0) transitions of ortho and para spin isomers of hydrogen trapped in the inclusion compound, the origin of the third vibron could not be unequivocally established. Low-temperature spectra revealed that the lowest-frequency vibron is actually composed of two overlapping bands of A_g and T_2g symmetries dominated by H₂ stretching modes as predicted by our previous density functional theory calculations. We observed low-frequency modes of As₄O₆·2H₂ vibrations dominated by H₂ "librations," which were missed in a previous study. A low-temperature fine structure was observed for the J = 0 → 2 and J = 1 → 3 manifolds of hydrogen trapped in As₄O₆·2H₂, indicating the lifting of degeneracy due to an anisotropic environment. A non-spherical distribution was captured by molecular dynamics simulations, which revealed that the trajectory of H₂ molecules is skewed along the crystallographic ⟨111⟩ direction. Last but not least, low-temperature synchrotron powder x-ray diffraction measurements on As₄O₆·2H₂ revealed that the bulk structure of the compound is preserved down to 5 K at 1.6 GPa.

Hydrogen bond design principles

Hydrogen bonding principles are at the core of supramolecular design. This overview features a discussion relating molecular structure to hydrogen bond strengths, highlighting the following electronic effects on hydrogen bonding: electronegativity, steric effects, electrostatic effects, π-conjugation, and network cooperativity. Historical developments, along with experimental and computational efforts, leading up to the birth of the hydrogen bond concept, the discovery of nonclassical hydrogen bonds (C-H…O, O-H…π, dihydrogen bonding), and the proposal of hydrogen bond design principles (e.g., secondary electrostatic interactions, resonance-assisted hydrogen bonding, and aromaticity effects) are outlined. Applications of hydrogen bond design principles are presented.

Dihydrogen Bonds in Aqueous NaBD4 Solution by Neutron and X-ray Diffraction

Neutron diffraction, X-ray diffraction, and empirical potential structure refinement modeling were employed to study the structure of alkaline aqueous NaBD₄ solutions at different NaBD₄ concentrations and temperatures. In 1.0 mol·dm^-3 NaBD₄ aqueous solutions, about 5.6 ± 1.6 water molecules bond to BD₄^- via tetrahedral edges or tetrahedral corners without a very specific hydration geometry; that is, each hydrogen atom of BD₄^- bonds to 2.2 ± 1.0 water molecules through dihydrogen bonds with the D(B)···D(W) distance of 1.95 Å. The number of dihydrogen bonds decreases with increasing concentration and increases with temperature. Dihydrogen bonding is a predominantly electrostatic interaction which shows relatively lower directionality and saturability in comparison with the regular hydrogen bonds between water molecules. The water orientation around BD₄^- shows that the proportion of tetrahedral-edge dihydrogen bonds increases with temperature and decreases with concentration.

On Prediction of a Novel Chiral Material Y2H3O(OH): A Hydroxyhydride Holding Hydridic and Protonic Hydrogens

Examination of possible pathways of how oxygen atoms can be added to a yttrium oxyhydride system allowed us to predict new derivatives such as hydroxyhydrides possessing the composition M₂H₃O(OH) (M = Y, Sc, La, and Gd) in which three different anions (H^-, O²-, and OH^-) share the common chemical space. The crystal data of the solid hydroxyhydrides obtained on the base of DFT modeling correspond to the tetragonal structure that is characterized by the chiral space group P 4 1 . The analysis of bonding situation in M₂H₃O(OH) showed that the microscopic mechanism governing chemical transformations is caused by the displacements of protons which are induced by interaction with oxygen atoms incorporated into the crystal lattice of the bulk oxyhydride. The oxygen-mediated transformation causes a change in the charge state of some adjacent hydridic sites, thus forming protonic sites associated with hydroxyl groups. The predicted materials demonstrate a specific charge ordering that is associated with the chiral structural organization of the metal cations and the anions because their lattice positions form helical curves spreading along the tetragonal axis. Moreover, the effect of spatial twisting of the H^- and H⁺ sites provides additional linking via strong dihydrogen bonds. The structure-property relationships have been investigated in terms of structural, mechanical, electron, and optical features. It was shown that good polar properties of the materials make them possible prototypes for the design of nonlinear optical systems.