Why are Hydrogen Bonds Directional?

Modulating Hydrogen Shuttling in Ammonia by Neutral and Cationic Boron-Containing Frustrated Lewis Pairs (FLPs)

Xanthene-backbone FLPs featuring secondary borane functions -B(ArX)H (where ArX=C6F5 (ArF) or C6Cl5 (ArCl)) have been targeted through reactions of the dihydroboranes Me2S ⋅ BArXH2 with [4,5-xanth(PR2)Li]2 (R=Ph, iPr), and investigated in the synthesis of related cationic systems via hydride abstraction. The reactivity of these systems (both cationic and charge neutral) with ammonia have been probed, with a view to probing the potential for proton shuttling via N-H bond 'activation.' We find that in the case of four-coordinate boron systems (cationic or change neutral), the N-H linkage remains intact, supported by a NH⋅⋅⋅P hydrogen bond which is worth up to 17 kcal mol-1 thermodynamically, and enabled by planarization of the flexible xanthene scaffold. For cationic three coordinate systems, N-to-P proton transfer is viable, driven by the ability of the boron centre to stabilise the [NH2]- conjugate base through N-to-B π bonding. This proton transfer can be shown to be reversible in the presence of excess ammonia, depending on the nature of the B-bound ArX group. It is viable in the case of C6F5 substituents, but is prevented by the more sterically encumbering and secondary donor-stabilising capabilities of the C6Cl5 substituent.

Hydrogen-Bonded Mesoporous Frameworks with Tunable Pore Sizes and Architectures from Nanocluster Assembly Units

Construction of mesoporous frameworks by noncovalent bonding still remains a great challenge. Here, we report a micelle-directed nanocluster modular self-assembly approach to synthesize a novel type of two-dimensional (2-D) hydrogen-bonded mesoporous frameworks (HMFs) for the first time based on nanoscale cluster units (1.0-3.0 nm in size). In this 2-D structure, a mesoporous cluster plate with ∼100 nm in thickness and several micrometers in size can be stably formed into uniform hexagonal arrays. Meanwhile, such a porous plate consists of several (3-4) dozens of layers of ultrathin mesoporous cluster nanosheets. The size of the mesopores can be precisely controlled from 11.6 to 18.5 nm by utilizing the amphiphilic diblock copolymer micelles with tunable block lengths. Additionally, the pore configuration of the HMFs can be changed from spherical to cylindrical by manipulating the concentration of the micelles. As a general approach, various new HMFs have been achieved successfully via a modular self-assembly of nanoclusters with switchable configurations (nanoring, Keggin-type, and cubane-like) and components (titanium-oxo, polyoxometalate, and organometallic clusters). As a demonstration, the titanium-oxo cluster-based HMFs show efficient photocatalytic activity for hydrogen evolution (3.6 mmol g-1h-1), with a conversion rate about 2 times higher than that of the unassembled titanium-oxo clusters (1.5 mmol g-1h-1). This demonstrates that HMFs exhibited enhanced photocatalytic activity compared with unassembled titanium-oxo clusters units.

Fabrication strategies for chiral self-assembly surface

Chiral self-assembly is the spontaneous organization of individual building blocks from chiral (bio)molecules to macroscopic objects into ordered superstructures. Chiral self-assembly is ubiquitous in nature, such as DNA and proteins, which formed the foundation of biological structures. In addition to chiral (bio) molecules, chiral ordered superstructures constructed by self-assembly have also attracted much attention. Chiral self-assembly usually refers to the process of forming chiral aggregates in an ordered arrangement under various non-covalent bonding such as H-bond, π-π interactions, van der Waals forces (dipole-dipole, electrostatic effects, etc.), and hydrophobic interactions. Chiral assembly involves the spontaneous process, which followed the minimum energy rule. It is essentially an intermolecular interaction force. Self-assembled chiral materials based on chiral recognition in electrochemistry, chiral catalysis, optical sensing, chiral separation, etc. have a broad application potential with the research development of chiral materials in recent years.

Structure, Vibrational Spectra, and Cryogenic MatrixPhotochemistry of 6-Bromopyridine-2-carbaldehyde: From the Single Molecule of the Compound to the Neat Crystalline Material

6-Bromopyridine-2-carbaldehyde (abbreviated as BPCA) is used both as a building block in supramolecular chemistry and as a ligand for transition metal catalysts and luminescent complexes. In this study, the structure and vibrational spectra of BPCA were investigated in both the room temperature neat crystalline phase and for the compound isolated in cryogenic Ar, Kr and Xe matrices. The experimental studies were complemented by quantum chemical DFT(B3LYP)/6-311++G(d,p) calculations. For the crystalline compound, infrared and Raman spectra were obtained and interpreted. Comparison of the obtained infrared spectrum of the crystal with those obtained for the isolated molecules of BPCA in the studied cryomatrices helped to conclude that the intermolecular interactions in the crystal do not significantly perturb the intramolecular vibrational potential. Structural analysis further supports the existence of weak coupling between the intermolecular interactions and the structure of the constituting molecular units in crystalline state. The intermolecular interactions in the BPCA crystal were also evaluated by means of Hirshfeld analysis, which revealed that the most important interactions are weak and of the H^…N, H^…O, H^…H, H^…Br and Br^…Br types. The conformer of BPCA present in the crystal was found to correspond to the most stable form of the isolated molecule (trans), which bears stabilizing C-H^…O=C and C(=O)H^…N interactions. This conformer was shown to be the single conformer present in the as-deposited cryogenic matrices prepared from the room temperature gaseous compound. Broadband UV irradiation of matrix-isolated BPCA (λ ≥ 235 nm) resulted in the conversion of the trans conformer into the higher-energy cis conformer, where repulsive C-H^…H-C(=O) and C=O_LP^…_LPN (where LP designates a lone electron pair) interactions are present, and decarbonylation of the compound with formation of 2-bromopyridine (plus CO). The decarbonylation reaction was found to be more efficient in the more polarizable Xe matrix, indicating stabilization of the radicals initially formed upon breaking of the C-C(HO) and C-H (aldehyde) bonds in this medium, and testifying the occurrence of the decarbonylation reaction with involvement of radical species. TD-DFT calculations were used to access the nature of the excited states associated with the observed UV-induced reactions. As a whole, this study provides fundamental data to understand the physicochemical behavior of the compound, bridging the properties of the isolated molecule to those of the neat crystalline com-pound. Such information is of fundamental importance for the understanding of the role of BPCA in supramolecular chemistry and to potentiate its applications in synthesis and as a ligand for transition metal catalysts and luminescent complexes.

QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin

Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.

pH-Dependent physicochemical properties of ornithine lipid in mono- and bilayers

In certain bacteria, phosphatidylethanolamine lipids (PEL) get largely replaced by phosphate-free ornithine lipids (OL) under conditions of phosphate starvation. It has so far been unknown how much these two lipid types deviate in their physicochemical properties, and how strongly bacteria thus have to adapt in order to compensate for the difference. Here, we use differential scanning calorimetry, X-ray scattering, and X-ray fluorescence to investigate the properties of OL with saturated C14 alkyl chains in mono- and bilayers. OL is found to have a greater tendency than chain-analogous PEL to form ordered structures and, in contrast to PEL, even a molecular superlattice based on a hydrogen bonding network between the headgroups. This superlattice is virtually electrically uncharged and persists over a wide pH range. Our results indicate that OL and PEL behave very differently in ordered single-component membranes but may behave more similarly in fluid multicomponent membranes.

Enhancing Effects of the Cyano Group on the C-X∙∙∙N Hydrogen or Halogen Bond in Complexes of X-Cyanomethanes with Trimethyl Amine: CH3−n(CN)nX∙∙∙NMe3, (n = 0–3; X = H, Cl, Br, I)

In this paper, density functional theory and wave function theory calculations are carried out to investigate the strength and nature of the intermolecular C-X∙∙∙N bond interaction as a function of the number of cyano groups, CN, in the X-bond donor while maintaining the X-bond acceptor as fixed. Specifically, complexes of X-cyanomethanes with trimethyl amine CH_3−n(CN)_nX∙∙∙NMe₃ (n = 0–3; X = H, Cl, Br, I) are used as model systems. Geometrical parameters and vibrational C-X-stretching frequencies as well as interaction energies are used as relevant indicators to gauge hydrogen or halogen bond strength in the complexes. Additional characteristics of interactions that link these complexes, i.e., hydrogen or halogen bonds, are calculated with the use of the following theoretical tools: the atoms in molecules (AIM) approach, the natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The results show that, for the specified X-center, the strength of C-X∙∙∙N interaction increases significantly and in a non-additive fashion with the number of CN groups. Moreover, the nature (noncovalent or partly covalent) of the interactions is revealed via the AIM approach.

Theoretical study on L-H+-L with identical donors: short strong hydrogen bond or not?

Short strong hydrogen bonds (SSHBs) play crucial role in many chemical processes. Recently, as the representative of SSHBs, [F-H-F]- was experimentally observed. [F-H-F]- has a symmetric structure, which can be described as a H+ acid shared by two terminal F- donors (F--H+-F-). To explore whether two identical donors are bound to result in SSHBs, we performed theoretical studies on a series of compounds (L-H+-L) with two identical electron donors (L corresponds to donors containing group 14, 15, 16 and 17 elements). The results show that identical donors do not definitely lead to SSHBs. Instead, typical hydrogen bonds also exist. We found that both electronegativity and basicity contribute to the patterns of hydrogen bonds, where more electronegative and weaker donors benefit to SSHBs. Besides, it was found that zero-point energies also respond to the hydrogen bonding systems. This systemic work is expected to provide more insights into SSHBs.

Electrostatics, Charge Transfer, and the Nature of the Halide-Water Hydrogen Bond

Binary halide-water complexes X^-(H₂O) are examined by means of symmetry-adapted perturbation theory, using charge-constrained promolecular reference densities to extract a meaningful charge-transfer component from the induction energy. As is known, the X^-(H₂O) potential energy surface (for X = F, Cl, Br, or I) is characterized by symmetric left and right hydrogen bonds separated by a C_2v-symmetric saddle point, with a tunneling barrier height that is <2 kcal/mol except in the case of F^-(H₂O). Our analysis demonstrates that the charge-transfer energy is correspondingly small (<2 kcal/mol except for X = F), considerably smaller than the electrostatic interaction energy. Nevertheless, charge transfer plays a crucial role determining the conformational preferences of X^-(H₂O) and provides a driving force for the formation of quasi-linear X··· H-O hydrogen bonds. Charge-transfer energies correlate well with measured O-H vibrational redshifts for the halide-water complexes and also for OH^-(H₂O) and NO₂^-(H₂O), providing some indication of a general mechanism.

When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins

Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction.

Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.

Mutation of an atypical oxirane oxyanion hole improves regioselectivity of the α/β-fold epoxide hydrolase Alp1U

Epoxide hydrolases (EHs) have been characterized and engineered as biocatalysts that convert epoxides to valuable chiral vicinal diol precursors of drugs and bioactive compounds. Nonetheless, the regioselectivity control of the epoxide ring opening by EHs remains challenging. Alp1U is an α/β-fold EH that exhibits poor regioselectivity in the epoxide hydrolysis of fluostatin C (compound 1) and produces a pair of stereoisomers. Herein, we established the absolute configuration of the two stereoisomeric products and determined the crystal structure of Alp1U. A Trp-186/Trp-187/Tyr-247 oxirane oxygen hole was identified in Alp1U that replaced the canonical Tyr/Tyr pair in α/β-EHs. Mutation of residues in the atypical oxirane oxygen hole of Alp1U improved the regioselectivity for epoxide hydrolysis on 1. The single site Y247F mutation led to highly regioselective (98%) attack at C-3 of 1, whereas the double mutation W187F/Y247F resulted in regioselective (94%) nucleophilic attack at C-2. Furthermore, single-crystal X-ray structures of the two regioselective Alp1U variants in complex with 1 were determined. These findings allowed insights into the reaction details of Alp1U and provided a new approach for engineering regioselective epoxide hydrolases.

Charting Hydrogen Bond Anisotropy

A hydrogen bond (HB) is an essential interaction in countless phenomena, regulating the chemistry of life. HBs are characterized by two features, strength and directionality, with a high degree of heterogeneity across different chemical groups. These characteristics are dependent on the electronic configuration of the atoms involved in the interaction, which, in turn, is influenced strongly by the local molecular environment. Studies based on the analysis of HB in the solid phase, such as X-ray crystallography, suffer from significant biases due to packing forces. These will tend to better describe strong HBs at the expenses of weak ones, which will be either distorted or under-represented. Using quantum mechanics (QM), we calculated interaction energies for about a hundred acceptors and donors in a rigorously defined set of geometries. We performed 180,000 independent QM calculations, covering all relevant angular components, mapping strength and directionality in a context free from external biases, with both single-site and cooperative HBs. By quantifying directionality, we show that there is no correlation with strength; therefore, these two components need to be addressed separately. Results demonstrate that there are very strong HB acceptors (e.g., dimethyl sulfoxide) with nearly isotropic interactions and weak ones (e.g., thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity but be very distant in the strength spectrum (e.g., thioacetone and pyridine). Results provide a new perspective on the way HB directionality is described, with implications for biophysics and molecular recognition that ultimately can influence chemical biology, protein engineering, and drug design.

Structural and molecular bases of angiotensin-converting enzyme inhibition by bovine casein-derived peptides: an in silico molecular dynamics approach

The angiotensin-converting enzyme (ACE) plays a key role in blood pressure regulation process, and its inhibition is one of the main drug targets for the treatment of hypertension. Though various peptides from milk proteins are well-known for their ACE-inhibitory capacity, research devoted to understand the molecular bases of such property remain scarce, specifically for such peptides. Therefore, in this work, computational molecular docking and molecular dynamics calculations were performed to enlighten the intermolecular interactions involved in ACE inhibition by six different casein-derived peptides (FFVAPFPEVFGK, FALPQYLK, ALNEINQFYQK, YLGYLEQLLR, HQGLPQEVLNENLLR and NAVPITPTLNR). Two top ranked docking poses for each peptide (one with N- and the other C-terminal peptide extremity oriented towards the ACE active site) were selected for dynamic simulations (50 ns; GROMOS53A6 force field), and the results were correlated to in vitro ACE inhibition capacity. Two molecular features appeared to be essential for peptides to present high ACE inhibition capacity in vitro: i) to interact with the S1 active site residues (Ala354, Glu384, and Tyr523) by hydrogen bonds; ii) to interact with Zn²⁺ coordinated residues (His383, His387, and Glu411) by short-lenght hydrogen bonds, as observed in the cases of ALNEINQFYQK (IACE = 80.7%), NAVPITPTLNR (IACE = 80.7%), and FALPQYLK (IACE = 79.0%). Regardless of the temporal stability of these strong interactions, they promoted some disruption of Zn²⁺ tetrahedral coordination during the molecular dynamics trajectories, and were pointed as the main reason for the greatest ACE inhibition by these peptides. On the other hand, peptides with intermediate inhibition capacity (50% < I_ACE < 45%) interacted mainly by weaker interactions (e.g.: electrostatic and hydrophobic) with the Zn²⁺ coordinated residues, and were not able to change significantly its tetrahedral coordination structure. These findings may: i) assist the discrimination in silico of "good" and "bad" ACE-inhibitory peptides from other food sources, and/or ii) aid in designing de novo new molecules with ACE-inhibitory capacity. Communicated by Ramaswamy Sarma.

Computational Analysis of Non-covalent Interactions in Phycocyanin Subunit Interfaces

Protein-protein interactions are an important phenomenon in biological processes and functions. We used the manually curated non-redundant dataset of 118 phycocyanin interfaces to gain additional insight into this phenomenon using a robust inter-atomic non-covalent interaction analyzing tool PPCheck. Our observations indicate that there is a relatively high composition of hydrophobic residues at the interfaces. Most of the interface residues are clustered at the middle of the range which we call "standard-size" interfaces. Furthermore, the multiple interaction patterns founded in the present study indicate that more than half of the residues involved in these interactions participate in multiple and water-bridged hydrogen bonds. Thus, hydrogen bonds contribute maximally towards the stability of protein-protein complexes. The analysis shows that hydrogen bond energies contribute to about 88 % to the total energy and it also increases with interface size. Van der Waals (vdW) energy contributes to 9.3 %±1.7 % on average in these complexes. Moreover, there is about 1.9 %±1.5 % contribution by electrostatic energy. Nevertheless, the role by vdW and electrostatic energy could not be ignored in interface binding. Results show that the total binding energy is more for large phycocyanin interfaces. The normalized energy per residue was less than -16 kJ mol^-1 , while most of them have energy in the range from -6 to -14 kJ mol^-1 . The non-covalent interacting residues in these proteins were found to be highly conserved. Obtained results might contribute to the understanding of structural stability of this class of evolutionary essential proteins with increased practical application and future designs of novel protein-bioactive compound interactions.

Exploring the Role of Consecutive Addition of Nitrogen Atoms on Stability and Reactivity of Hydrogen-Bonded Azine-Water Complexes

The second-order Møller-Plesset perturbation theory (MP2) and density functional theory with dispersion function calculations have been applied to investigate the hydrogen-bonding interaction between azines and water. The study suggests that the ability of nitrogen present in azine to act as a hydrogen-bond acceptor decreases in the order of pyridine (PY) > diazine (DZ) > triazine (TZ) > tetrazine (TTZ) > pentazine (PZ) > hexazine (HZ). Natural bond orbital (NBO) analysis, atoms in molecules, symmetry-adapted perturbation theory (SAPT), and molecular electrostatic potential studies reflect the factors important for hydrogen-bond strength as well as for the structural, electronic, and vibrational changes occurring during complexation. NBO analysis reflects that upon gradual addition of nitrogen atoms, hyperconjugation leads to an increase in the population of antibonding O-H bond, thus causing elongation and weakening of O-H bond in complexes incorporating N···H-O_W interaction, whereas rehybridization leads to an increase in the s character of the carbon hybrid orbital in C-H bond, thus causing contraction and shortening of C-H bond in complexes having C-H···O_W interactions. From the topological analysis, an excellent linear correlation is found to exist between stabilization energy (ΔE _BSSE), electron density (ρ_c), and its Laplacian (∇²ρ_c) at the bond critical points.

Expanding reversible chalcogenide binding: supramolecular receptors for the hydroselenide (HSe-) anion

Synthetic supramolecular receptors have been widely used to study reversible solution binding of anions; however, few systems target highly-reactive species. In particular, the hydrochalcogenide anions hydrosulfide (HS^-) and hydroselenide (HSe^-) have been largely overlooked despite their critical roles in biological systems. Herein we present the first example of reversible HSe^- binding in two distinct synthetic supramolecular receptors, using hydrogen bonds from N-H and aromatic C-H moieties. The arylethynyl bisurea scaffold 1 ^{t Bu} achieved a binding affinity of 460 ± 50 M^-1 for HSe^- in 10% DMSO-d ₆/CD₃CN, whereas the tripodal-based receptor 2^CF₃ achieved a binding affinity of 290 ± 50 M^-1 in CD₃CN. Association constants were also measured for HS^-, Cl^-, and Br^-, and both receptors favored binding of smaller, more basic anions. These studies contribute to a better understanding of chalcogenide hydrogen bonding and provide insights into further development of probes for the reversible binding, and potential quantification, of HSe^- and HS^-.

Electrostatics for probing lone pairs and their interactions

The value of the molecular electrostatic potential minimum (V_min ) and its topographical features (position, as well as the eigenvalues and eigenvectors of the corresponding Hessian matrix) are recently proposed as the criteria for characterizing a lone pair (Kumar A. et al., J. Phys. Chem. 2014, A118, 526). This electrostatic characterization of lone pairs is examined for a large number of small molecules employing MP4/6-311++G(d,p)//MP2/6-311++G(d,p) theory. The eigenvector of the Hessian matrix corresponding to its largest eigenvalue (λ_max ), is found to be directed toward the lone pair-bearing-atom, with λ_max showing a strong linear correlation with V_min . Large magnitudes of V_min and λ_max indicate a charge-dense lone pair. The topographical features of V_min are seen to provide insights into the interactive behavior of the molecules with model electrophiles, viz. HF, CO₂ , and Li⁺ . In all the complexes of HF and majority of the other complexes, the interaction energy (E_int ) correlates well with the respective V_min, value, but for some deviations occurring due to other competing secondary interactions. The electrostatic interactions are found to be highly directional in nature as the orientation of interacting atom correlates strongly to the position of lone pair. In summary, the present study on a large number of test molecules shows that electrostatics is able to probe lone pairs in molecules and offers a simple interpretation of chemical reactivity. © 2017 Wiley Periodicals, Inc.