Strengthening of hydrogen bonding with the push-pull effect

Positive and Negative Impacts of Interfacial Hydrogen Bonds on Photocatalytic Hydrogen Evolution

Understanding the behavior of water molecules at solid-liquid interfaces is crucial for various applications such as photocatalytic water splitting, a key technology for sustainable fuel production and chemical transformations. Despite extensive studies conducted in the past, the impact of the microscopic structure of interfacial water molecules on photocatalytic reactivity has not been directly examined. In this study, using real-time mass spectrometry and Fourier-transform infrared spectroscopy, we demonstrated the crucial role of hydrogen bond (H-bond) networks on the photocatalytic hydrogen evolution in thickness-controlled water adsorption layers on various TiO2 photocatalysts. Under controlled water vapor environments with relative humidity (RH) below 70%, we observed a monotonic increase in the H2 formation rate with increasing RH, indicating that reactive water molecules were present not only in the first adsorbed layer but also in several overlying layers. In contrast, at RH > 70%, when more than three water layers covered the catalyst surface, the H2 formation rate turned to decrease dramatically because of the structural rearrangement and hardening of the interfacial H-bond network induced during further water adsorption. This unique many-body effect of interfacial water was consistently observed for various TiO2 particles with different crystalline structures, including brookite, anatase, and a mixture of anatase and rutile. Our results demonstrated that depositing several water layers in a water vapor environment with RH ∼ 70% is optimal for photocatalytic hydrogen evolution rather than liquid-phase reaction conditions in aqueous solutions. This study provides molecular-level insights into designing interfacial water conditions to enhance photocatalytic performance.

Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study

Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.

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.

Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study

Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) cause serious public health problems, with nearly 390 million people affected and 20,000 deaths per year in tropical and subtropical countries. Despite numerous attempts, no antiviral drug or vaccine is currently available to combat the manifestation. The challenge of discovering an efficient vaccine is enhanced by the surplus presence of efficient vectors and drug resistance from the virus. For centuries, papaya (Carica papaya) extracts have been traditionally used to treat DF, DHF, and DSS. In the present study, we systematically investigated seven compounds isolated from papaya leaf extract with regard to their potential as inhibitors for non-structural (NS) proteins, NS3 and NS5, which play a crucial role in viral RNA replication. The computational tools applied stretched across classical molecular docking, molecular dynamics (MD) simulations and SwissADME used to calculate binding affinities; binding free energies; Absorption, Distribution, Metabolism, and Excretion (ADME); and drug-likeness properties, thus, identifying Kaempferol, Chlorogenic acid, and Quercetin as potential candidates, with Kaempferol and Quercetin scoring best. Therefore, for the Kaempferol and Quercetin complexes, hybrid quantum mechanical/molecular mechanical (QM/MM) geometry and frequency calculations were performed, followed by the local mode analysis developed in our group to quantify Kaempferol-NS and Quercetin-NS hydrogen bonding. Given the non-toxic nature and the wide availability of the Kaempferol and Quercetin papaya extract in almost all of the susceptible regions, and our results showing high NS3 and NS5 binding affinities and energies, strong hydrogen bonding with both NS3 and NS5, and excellent ADME properties, we suggest Kaempferol and Quercetin as a strong NS3 and NS5 inhibitor to be further investigated in vitro.

Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study

In this work, we investigated the catalytic effects of a Sharpless dimeric titanium (IV)–tartrate–diester catalyst on the epoxidation of allylalcohol with methyl–hydroperoxide considering four different orientations of the reacting species coordinated at the titanium atom (reactions R1–R4) as well as a model for the non-catalyzed reaction (reaction R0). As major analysis tools, we applied the URVA (Unified Reaction Valley Approach) and LMA (Local Mode Analysis), both being based on vibrational spectroscopy and complemented by a QTAIM analysis of the electron density calculated at the DFT level of theory. The energetics of each reaction were recalculated at the DLPNO-CCSD(T) level of theory. The URVA curvature profiles identified the important chemical events of all five reactions as peroxide OO bond cleavage taking place before the TS (i.e., accounting for the energy barrier) and epoxide CO bond formation together with rehybridization of the carbon atoms of the targeted CC double bond after the TS. The energy decomposition into reaction phase contribution phases showed that the major effect of the catalyst is the weakening of the OO bond to be broken and replacement of OH bond breakage in the non-catalyzed reaction by an energetically more favorable TiO bond breakage. LMA performed at all stationary points rounded up the investigation (i) quantifying OO bond weakening of the oxidizing peroxide upon coordination at the metal atom, (ii) showing that a more synchronous formation of the new CO epoxide bonds correlates with smaller bond strength differences between these bonds, and (iii) elucidating the different roles of the three TiO bonds formed between catalyst and reactants and their interplay as orchestrated by the Sharpless catalyst. We hope that this article will inspire the computational community to use URVA complemented with LMA in the future as an efficient mechanistic tool for the optimization and fine-tuning of current Sharpless catalysts and for the design new of catalysts for epoxidation reactions.

Bonding in Nitrile Photo-dissociating Ruthenium Drug Candidates --A Local Vibrational Mode Study

In this work, we investigated bonding features 15 ruthenium complexes of the type [Ru(tpy)(L)-(CH3CN)]n+, containing the tridentate tpy ligand (tpy = 2,2':6',2'--terpyridine) and various bidentate ancillary ligands, 12 compounds originally synthesized by Loftus et al. (J. Phys. Chem. C 123, 10291-10299 (2019)) complemented with three additional complexes. The main focus of our work was to relate these local features to the experimental data of Loftus et al. which assess the efficiency of nitrile release in an indirect way via observed quantum yields for ruthenium water association after nitrile release. As a tool to quantitatively assess Ru-NC and Ru-L bonding we utilized the local vibrational mode analysis complemented by the topological analysis of the electron density and the natural bond orbital analysis. Interestingly, the stronger Ru-NC bonds have the greater observed quantum yields, leading to the conclusion that the observed quantum yields are a result of a complex interplay of several processes excluding a direct relationship between QY and Ru-NC or Ru-L bond strengths. We identified the ST splitting as one of the key players and not the Ru-NC bond strength, as one may have thought. In summary, this work has presented a modern computational tool set for the investigation of bonding features applied to nitrile photo-dissociating ruthenium drug candidates forming a valuable basis for future design and fine tuning of nitrile releasing ruthenium compounds, as well as for the understanding of how local properties affect overall experimental outcomes.

Uranium: The Nuclear Fuel Cycle and Beyond

This review summarizes the recent developments regarding the use of uranium as nuclear fuel, including recycling and health aspects, elucidated from a chemical point of view, i.e., emphasizing the rich uranium coordination chemistry, which has also raised interest in using uranium compounds in synthesis and catalysis. A number of novel uranium coordination features are addressed, such the emerging number of U(II) complexes and uranium nitride complexes as a promising class of materials for more efficient and safer nuclear fuels. The current discussion about uranium triple bonds is addressed by quantum chemical investigations using local vibrational mode force constants as quantitative bond strength descriptors based on vibrational spectroscopy. The local mode analysis of selected uranium nitrides, N≡U≡N, U≡N, N≡U=NH and N≡U=O, could confirm and quantify, for the first time, that these molecules exhibit a UN triple bond as hypothesized in the literature. We hope that this review will inspire the community interested in uranium chemistry and will serve as an incubator for fruitful collaborations between theory and experimentation in exploring the wealth of uranium chemistry.

BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.

LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis

The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0-3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is cross-platform, open-source and freely available on GitHub: https://github.com/smutao/LModeA-nano.

Thermodynamically Stable Cationic Dimers in Carboxyl-Functionalized Ionic Liquids: The Paradoxical Case of "Anti-Electrostatic" Hydrogen Bonding

We show that carboxyl-functionalized ionic liquids (ILs) form doubly hydrogen-bonded cationic dimers (c⁺=c⁺) despite the repulsive forces between ions of like charge and competing hydrogen bonds between cation and anion (c⁺–a⁻). This structural motif as known for formic acid, the archetype of double hydrogen bridges, is present in the solid state of the IL 1−(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC−CH₂−py][NTf₂]. By means of quantum chemical calculations, we explored different hydrogen-bonded isomers of neutral (HOOC–(CH₂)_n–py⁺)₂(NTf₂⁻)₂, single-charged (HOOC–(CH₂)_n–py⁺)₂(NTf₂⁻), and double-charged (HOOC– (CH₂)_n−py⁺)₂ complexes for demonstrating the paradoxical case of “anti-electrostatic” hydrogen bonding (AEHB) between ions of like charge. For the pure doubly hydrogen-bonded cationic dimers (HOOC– (CH₂)_n−py⁺)₂, we report robust kinetic stability for n = 1–4. At n = 5, hydrogen bonding and dispersion fully compensate for the repulsive Coulomb forces between the cations, allowing for the quantification of the two equivalent hydrogen bonds and dispersion interaction in the order of 58.5 and 11 kJmol⁻¹, respectively. For n = 6–8, we calculated negative free energies for temperatures below 47, 80, and 114 K, respectively. Quantum cluster equilibrium (QCE) theory predicts the equilibria between cationic monomers and dimers by considering the intermolecular interaction between the species, leading to thermodynamic stability at even higher temperatures. We rationalize the H-bond characteristics of the cationic dimers by the natural bond orbital (NBO) approach, emphasizing the strong correlation between NBO-based and spectroscopic descriptors, such as NMR chemical shifts and vibrational frequencies.

Capturing Individual Hydrogen Bond Strengths in Ices via Periodic Local Vibrational Mode Theory: Beyond the Lattice Energy Picture

Local stretching force constants derived from periodic local vibrational modes at the vdW-DF2 density functional level have been employed to quantify the intrinsic hydrogen bond strength of 16 ice polymorphs, ices Ih, II, III, IV, V, VI, VII, VIII, IX, XI, XII, XIII, XIV, XV, XVII, and XIX, that are stable under ambient to elevated pressures. Based on this characterization on 1820 hydrogen bonds, relationships between local stretching force constants and structural parameters such as hydrogen bond length and angle were identified. Moreover, different bond strength distributions, from uniform to inhomogeneous, were observed for the 16 ices and could be explained in relation to different local structural elements within ices, that is, rings, that consist of different hydrogen bond types. In addition, criteria for the classification of hydrogen bonds as strong, intermediate, and weak were introduced. The latter was used to explore a different dimension of the water-ice phase diagram. These findings will provide important guidelines for assessing the credibility of new ice structures.

Classical Electrostatics Remains the Driving Force for Interanion Hydrogen and Halogen Bonding

Interanion hydrogen bonding (IAHB) and halogen bonding (IAXB) have emerged as a counterintuitive linker in a range of fascinating applications. Despite the overall repulsive (positive) binding energy, anions are trapped in a local minimum with its corresponding transition state (TS) preventing dissociation. In other words, the adduct of anions is metastable. Seemingly, the electrostatic paradigm and force field description of hydrogen/halogen bonding (HB/XB) are challenged, because of the preconceived Coulombic repulsion. Aiming at an insightful understanding of these interanion phenomena, we employed the energy decomposition approach based on the block-localized wavefunction method (BLW-ED) to investigate a series of exemplary interanion complexes. As expected, the key distinction from the conventional HB/XB lies in the electrostatic interaction, which is not increasingly repulsive as anions gradually approach to each other. Rather, there is a Coulombic barrier at a certain point. After this point, the electrostatic repulsion diminishes with the decreasing distance between anions. Differently, other energy components vary monotonically just like in conventional cases. The nonmonotonic characteristic of the electrostatic interaction in interanion complexes was reproduced using the multipole expansion in AMOEBA polarizable force field in which the state-specified atomic multipoles were adopted. This suggests that the nonmonotonicity can be well interpreted by classical electrostatic theory and there is no conceptual difference between conventional HB/XB and IAHB/IAXB. The stability of IAHB/IAXB depends on the competition between the local attractive HB/XB and the global Coulombic repulsion of net charges, though there is cooperativity between these two contrasting forces. This concise model was supported by the attractive IAHB/IAXB in modified molecular capsules, which exhibit strong quadruple HB/XBs and a considerable distance between charged substituents.

The effect of hydrogen-bonding on flavin's infrared absorption spectrum

Cluster and continuum solvation computational models are employed to model the effect of hydrogen bonding interactions on the vibrational modes of lumiflavin. Calculated spectra were compared to experimental Fourier-transform infrared (FTIR) spectra in the diagnostic 1450-1800 cm^-1 range, where intense ν_C=C, ν_C=N, [Formula: see text] , and [Formula: see text] stretching modes of flavin's isoalloxazine ring are found. Local mode analysis is used to describe the strength of hydrogen-bonding in cluster models. The computations indicate that ν_C=C and ν_C=N mode frequencies are relatively insensitive to intermolecular interactions while the [Formula: see text] and [Formula: see text] modes are sensitive to direct (and also indirect for [Formula: see text] ) hydrogen-bonding interactions. Although flavin is neutral, basis sets without the diffuse functions provide incorrect relative frequencies and intensities. The 6-31+G* basis set is found to be adequate for this system, and there is limited benefit to considering larger basis sets. Calculated vibrational mode frequencies agree with experimentally determined frequencies in solution when cluster models with multiple water molecules are used. Accurate simulation of relative FTIR band intensities, on the other hand, requires a continuum (or possibly quantum mechanical/molecular mechanical) model that accounts for long-range electrostatic effects. Finally, an experimental peak at ca. 1624 cm^-1 that is typically assigned to the [Formula: see text] vibrational stretching mode has a complicated shape that suggests multiple underlying contributions. Our calculations show that this band has contributions from both the C₆-C₇ and C₂ = O stretching vibrations.

Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study

Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.

Assessing the Intrinsic Strengths of Ion–Solvent and Solvent–Solvent Interactions for Hydrated Mg2+ Clusters

Information resulting from a comprehensive investigation into the intrinsic strengths of hydrated divalent magnesium clusters is useful for elucidating the role of aqueous solvents on the Mg2+ ion, which can be related to those in bulk aqueous solution. However, the intrinsic Mg–O and intermolecular hydrogen bond interactions of hydrated magnesium ion clusters have yet to be quantitatively measured. In this work, we investigated a set of 17 hydrated divalent magnesium clusters by means of local vibrational mode force constants calculated at the ωB97X-D/6-311++G(d,p) level of theory, where the nature of the ion–solvent and solvent–solvent interactions were interpreted from topological electron density analysis and natural population analysis. We found the intrinsic strength of inner shell Mg–O interactions for [Mg(H2O)n]2+ (n = 1–6) clusters to relate to the electron density at the bond critical point in Mg–O bonds. From the application of a secondary hydration shell to [Mg(H2O)n]2+ (n = 5–6) clusters, stronger Mg–O interactions were observed to correspond to larger instances of charge transfer between the lp(O) orbitals of the inner hydration shell and the unfilled valence shell of Mg. As the charge transfer between water molecules of the first and second solvent shell increased, so did the strength of their intermolecular hydrogen bonds (HBs). Cumulative local vibrational mode force constants of explicitly solvated Mg2+, having an outer hydration shell, reveal a CN of 5, rather than a CN of 6, to yield slightly more stable configurations in some instances. However, the cumulative local mode stretching force constants of implicitly solvated Mg2+ show the six-coordinated cluster to be the most stable. These results show that such intrinsic bond strength measures for Mg–O and HBs offer an effective way for determining the coordination number of hydrated magnesium ion clusters.

Substituent Effects on Excited-State Intramolecular Proton Transfer Reaction of 2-Aryloxazoline Derivatives

Different substituents and benzene ring numbers had significant effects on the fluorescence phenomenon of 2-aryloxazoline derivatives as observed in an experiment. Here, we select five 2-aryloxazoline derivatives with different substituents and benzene ring numbers (2u, 2ad, 2af, 2ai, and 2ah) to analyze the effects on the fluorescence phenomena. For 2ad, 2ah, and 2ai, first, the geometric structures are optimized based on the density functional theory and time-dependent density functional theory methods. The analysis of the obtained bond parameters reveals the variation of hydrogen bond interactions from S₀ to S₁ states. Second, the calculated absorption and emission spectra are consistent with the experimental values, which proves that the theoretical method is feasible. Finally, through the analysis of the infrared vibrational spectrum, reduced density gradient isosurfaces, frontier molecular orbitals, and potential energy curves, the strengthening mechanism of the hydrogen bond interaction and the ability of the excited-state intramolecular proton transfer (ESIPT) reaction to occur are further explained. Since the proton transfer reactions of 2u and 2af occur spontaneously under photoexcitation, they have no stable structures in the S₁ state. In conclusion, due to the different substituents, 2u is more prone to the proton transfer reaction than 2ad. For 2af, 2ai, and 2ah with different benzene ring numbers, the ESIPT reaction is more difficult to occur as the number of benzene rings increases. The ability of the ESIPT reaction to occur follows the order 2af → 2ah → 2ai. For 2-aryloxazoline derivatives with different substituents or different benzene ring numbers, the hydrogen bond strengthening mechanism has been authenticated, which promotes the occurrence of the ESIPT reactions.

Complexes of Formaldehyde and α-Dicarbonyls with Hydroxylamine: FTIR Matrix Isolation and Theoretical Study

The interactions of formaldehyde (FA), glyoxal (Gly) and methylglyoxal (MGly) with hydroxylamine (HA) isolated in solid argon and nitrogen were studied using FTIR spectroscopy and ab initio methods. The spectra analysis indicates the formation of two types of hydrogen-bonded complexes between carbonyl and hydroxylamine in the studied matrices. The cyclic planar complexes are stabilized by O–H⋯O(C), and C–H⋯N interactions and the nonplanar complexes are stabilized by O–H⋯O(C) bond. Formaldehyde was found to form with hydroxylamine, the cyclic planar complex and methylglyoxal, the nonplanar one in both argon and nitrogen matrices. In turn, glyoxal forms with hydroxylamine the most stable nonplanar complex in solid argon, whereas in solid nitrogen, both types of the complex are formed.

Quantifying bond strengths via a Coulombic force model: application to the impact sensitivity of nitrobenzene, nitrogen-rich nitroazole, and non-aromatic nitramine molecules

The quantification of bond strengths is a useful and general concept in chemistry. In this work, a Coulombic force model based on atomic electric charges computed using the accurate distributed multipole analysis (DMA) partition of the molecular charge density was employed to quantify the weakest N-NO₂ and C-NO₂ bond strengths of 19 nitrobenzene, 11 nitroazole, and 10 nitramine molecules. These bonds are known as trigger linkages because they are usually related to the initiation of an explosive. The three families of explosives combine different types of molecular properties and structures ranging from essentially aromatic molecules (nitrobenzenes) to others with moderate aromaticity (nitroazoles) and non-aromatic molecules with cyclic and acyclic skeletons (nitramines). We used the results to investigate the impact sensitivity of the corresponding explosives employing the trigger linkage concept. For this purpose, the computed Coulombic bond strength of the trigger linkages was used to build four sensitivity models that lead to an overall good agreement between the predicted values and available experimental sensitivity values even when the model included the three chemical families simultaneously. We discussed the role of the trigger linkages for determining the sensitivity of the explosives and rationalized eventual discrepancies in the models by examining alternative decomposition mechanisms and features of the molecular structures.

Comment on "Exploring nature and predicting strength of hydrogen bonds: A correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory"

We evaluate the correlation between binding energy (BE) and electron density ρ(r) at the bond critical point for 28 neutral hydrogen bonds, recently reported by Emamian and co-workers (J. Comput. Chem., 2019, 40, 2868). As an efficient tool, we use local stretching force constant k HB a derived from the local vibrational mode theory of Konkoli and Cremer. We compare the physical nature of BE versus k HB a , and provide an important explanation for cases with significant deviation in the BE- k HB a relation as well as in the BE-ρ(r) correlation. We also show that care has to be taken when different hydrogen bond strength measures are compared. The BE is a cumulative hydrogen bond strength measure while k HB a is a local measure of hydrogen bond strength covering different aspects of bonding. A simplified and unified description of hydrogen bonding is not always possible and needs an in-depth understanding of the systems involved.

Local vibrational mode analysis of ion-solvent and solvent-solvent interactions for hydrated Ca2+ clusters

Hydrated calcium ion clusters have received considerable attention due to their essential role in biological processes such as bone development, hormone regulation, blood coagulation, and neuronal signaling. To better understand the biological role of the cation, the interactions between the Ca²⁺ ions and water molecules have been frequently investigated. However, a quantitative measure for the intrinsic Ca-O (ion-solvent) and intermolecular hydrogen bond (solvent-solvent) interactions has been missing so far. Here, we report a topological electron density analysis and a natural population analysis to analyze the nature of these interactions for a set of 14 hydrated calcium clusters via local mode stretching force constants obtained at the ωB97X-D/6-311++G(d,p) level of theory. The results revealed that the strength of inner Ca-O interactions for Ca(H₂O)_n ²⁺ (n = 1-8) clusters correlates with the electron density. The application of a second hydration shell to Ca(H₂O)_n ²⁺ (n = 6-8) clusters resulted in stronger Ca-O interactions where a larger electron charge transfer between lp(O) of the first hydration shell and the lower valence of Ca prevailed. The strength of the intermolecular hydrogen bonds, formed between the first and second hydration shells, became stronger when the charge transfers between hydrogen bond (HB) donors and HB acceptors were enhanced. From the local mode stretching force constants of implicitly and explicitly solvated Ca²⁺, we found the six-coordinated cluster to possess the strongest stabilizations, and these results prove that the intrinsic bond strength measures for Ca-O and hydrogen bond interactions form new effective tools to predict the coordination number for the hydrated calcium ion clusters.

PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology

Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)_n clusters, for n = 3-7; various clusters of HF and H₂O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H₂O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.

Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors

11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.

Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.

In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ-hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n→σ∗(X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol^-1 . This value increases by ca. 1 kcal mol^-1 on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol^-1 depending on the structure of the β-diketone in question.

Theoretical Description of R-X⋯NH3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion

In the present work, a number of R–X⋯NH₃ (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme’s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R–Br⋯NH₃ complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback–Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R–X bond is significantly polarized due to the presence of the NH₃ molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br—CN]_n system (n = 1–8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.

Metal-Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy

Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y₂)(NC₅H₄X-3)₂ with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC₅H₄X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.

Water in protein hydration and ligand recognition

This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.

Interplay of Ring Puckering and Hydrogen Bonding in Deoxyribonucleosides

The Cremer-Pople ring puckering analysis and the Konkoli-Cremer local mode analysis supported by the topological analysis of the electron density were applied for the first comprehensive analysis of the interplay between deoxyribose ring puckering and intramolecular H-bonding in 2'-deoxycytidine, 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxyguanosine. We mapped for each deoxyribonucleoside the complete conformational energy surface and the corresponding pseudorotation path. We found only incomplete pseudorotation cycles, caused by ring inversion, which we coined as pseudolibration paths. On each pseudolibration path a global and a local minimum separated by a transition state were identified. The investigation of H-bond free deoxyribonucleoside analogs revealed that removal of the H-bond does not restore the full conformational flexibility of the sugar ring. Our work showed that ring puckering predominantly determines the conformational energy; the larger the puckering amplitude, the lower the conformational energy. In contrast no direct correlation between conformational energy and H-bond strength was found. The longest and weakest H-bonds are located in the local minimum region, whereas the shortest and strongest H-bonds are located outside the global and local minimum regions at the turning points of the pseudolibration paths, i.e., H-bonding determines the shape and length of the pseudolibration paths. In addition to the H-bond strength, we evaluated the covalent/electrostatic character of the H-bonds applying the Cremer-Kraka criterion of covalent bonding. H-bonding in the puric bases has a more covalent character whereas in the pyrimidic bases the H-bond character is more electrostatic. We investigated how the mutual orientation of the CH₂OH group and the base influences H-bond formation via two geometrical parameters describing the rotation of the substituents perpendicular to the sugar ring and their tilting relative to the ring center. According to our results, rotation is more important for H-bond formation. In addition we assessed the influence of the H-bond acceptor, the lone pair (N, respectively O), via the delocalization energy. We found larger delocalization energies corresponding to stronger H-bonds for the puric bases. The global minimum conformation of 2'-deoxyguanosine has the strongest H-bond of all conformers investigated in this work with a bond strength of 0.436 which is even stronger than the H-bond in the water dimer (0.360). The application of our new analysis to DNA deoxyribonucleotides and to unnatural base pairs, which have recently drawn a lot of attention, is in progress.

A Continuum from Halogen Bonds to Covalent Bonds: Where Do λ3 Iodanes Fit?

The intrinsic bonding nature of λ 3 -iodanes was investigated to determine where its hypervalent bonds fit along the spectrum between halogen bonding and covalent bonding. Density functional theory with an augmented Dunning valence triple zeta basis set ( ω B97X-D/aug-cc-pVTZ) coupled with vibrational spectroscopy was utilized to study a diverse set of 34 hypervalent iodine compounds. This level of theory was rationalized by comparing computational and experimental data for a small set of closely-related and well-studied iodine molecules and by a comparison with CCSD(T)/aug-cc-pVTZ results for a subset of the investigated iodine compounds. Axial bonds in λ 3 -iodanes fit between the three-center four-electron bond, as observed for the trihalide species IF 2 − and the covalent FI molecule. The equatorial bonds in λ 3 -iodanes are of a covalent nature. We explored how the equatorial ligand and axial substituents affect the chemical properties of λ 3 -iodanes by analyzing natural bond orbital charges, local vibrational modes, the covalent/electrostatic character, and the three-center four-electron bonding character. In summary, our results show for the first time that there is a smooth transition between halogen bonding → 3c–4e bonding in trihalides → 3c–4e bonding in hypervalent iodine compounds → covalent bonding, opening a manifold of new avenues for the design of hypervalent iodine compounds with specific properties.

Theoretical Prediction of Robust Second-Row Oxyanion Clusters in the Metastable Domain of Antielectrostatic Hydrogen Bonding

We provide ab initio and density functional theory evidence for a family of surprisingly robust like-charged clusters of common HSO₄^- and H₂PO₄^- oxyanions, ranging up to tetramers of net charge 4-. Our results support other recent theoretical and experimental evidence for "antielectrostatic" hydrogen-bonded (AEHB) species that challenge conventional electrostatic conceptions and force-field modeling of closed-shell ion interactions. We provide structural and energetic descriptors of the predicted kinetic well-depths (in the range 3-10 kcal/mol) and barrier widths (in the range 2-4 Å) for simple AEHB dimers, including evidence of extremely strong hydrogen bonding in the fluoride-bisulfate dianion. For more complex polyanionic species, we employ natural-bond-orbital-based descriptors to characterize the electronic features of the cooperative hydrogen-bonding network that are able to successfully defy Coulomb explosion. The computational results suggest a variety of kinetically stable AEHB species that may be suitable for experimental detection as long-lived gas-phase species or structural units of condensed phases, despite the imposing electrostatic barriers that oppose their formation under ambient conditions.

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc.

Characterizing Chemical Similarity with Vibrational Spectroscopy: New Insights into the Substituent Effects in Monosubstituted Benzenes

A novel approach is presented to assess chemical similarity based the local vibrational mode analysis developed by Konkoli and Cremer. The local mode frequency shifts are introduced as similarity descriptors that are sensitive to any electronic structure change. In this work, 59 different monosubstituted benzenes are compared. For a subset of 43 compounds, for which experimental data was available, the ortho-/para- and meta-directing effect in electrophilic aromatic substitution reactions could be correctly reproduced, proving the robustness of the new similarity index. For the remaining 16 compounds, the directing effect was predicted. The new approach is broadly applicable to all compounds for which either experimental or calculated vibrational frequency information is available.