Charged versus Neutral Hydrogen‐Bonded Complexes: Is There a Difference in the Nature of the Hydrogen Bonds?

A theoretical study on some carboxylic acid dimers formed by positively or negatively charged molecules has been carried out by using DFT methods. The resulting dimers possess either a charge of +2 or ?2. In addition, the corresponding neutral complexes have also been considered. The electron density distribution described by the atoms in molecules and the natural bond orbital methods, as well as the electric field maps of the systems, have been analyzed and compared without finding significant differences between the neutral and ionic complexes. The interaction energy along the dissociation path of the charged dimers shows both a local minimum and a local maximum, defining a stability region between them. When this energetic profile is recalculated by removing the repulsion between the charged groups, it resembles to those of the neutral molecules. Hence, the characteristics of the charged dimers are similar to those of the neutral ones: the addition of a repulsion term for the charged groups permits to retrieve the energetic profiles dependence with the distance in the charged system. The interacting quantum atom (IQA) method has been used to calculate the interaction energy terms, including the classic Coulombic term between the whole molecules and the corresponding of the carboxylic acid groups. The IQA results show repulsive electrostatic interactions when the whole molecules are considered in the ionic complexes, but attractive ones between the carboxylic groups in both neutral and ionic complexes.     

Photodissociation of carboxylic acids: dynamics of OH formation

In this review article, recent studies on the photodissociation dynamics of carboxylic acids carried out in our laboratory are presented. The dynamics are investigated by mapping the energy partitioning in the nascent photoproduct OH using laser-induced fluorescence spectroscopy. To understand the effect of the nature of the CC bond on the dissociation dynamics, both saturated (acetic) as well as unsaturated (acrylic and propiolic) carboxylic acids are investigated. In all of the carboxylic acids studied, a high percentage of the available energy is partitioned into the product translational state, indicating the presence of an exit barrier in the dissociative potential energy surface. Based on the energy partitioning, the quantum yield and the OH formation rate, the photoexcitation dynamics of carboxylic acids are revealed.     

Anion-Anion Complexes Established between Aspartate Dimers

Stable dimers aspartate-aspartate have been studied in aqueous and gas phase through theoretical simulations. The polarizable continuum model (PCM) has been applied to simulate the effect of the hydration on monomers and complexes. The quantum theory of atoms in molecules (QTAIM) and the interacting quantum atoms (IQA) scheme has been used to inquire into if, in the aqueous phase, individual hydrogen bonds have attractive electrostatic components. In all cases a spontaneous formation of the complexes in the aqueous phase are observed, while in the gas phase a considerable energy barrier must be overcome (between 100.8 to 263.2 kJ mol⁻¹). The intermolecular distance at which this barrier is indicates when the hydrogen-bond interactions begin to take importance between the dimers and the corresponding molecular recognition among them. The IQA analysis shows that in aqueous phase, the hydrogen bonds N−H⋅⋅⋅O are mainly electrostatic in nature with a certain covalent character which increases linearly with the decrease of internuclear distances H⋅⋅⋅O. The H⋅⋅⋅H interactions observed are stabilizing and they are mainly quantum in nature.     

Infrared intensity analysis of hydroxyl stretching modes in carboxylic acid dimers by means of the charge–charge flux–dipole flux model

The Charge‑Charge Flux‑Dipole Flux (CCFDF) model in terms of multipoles from the quantum theory of atoms in molecules (QTAIM) was used to investigate the variations in infrared intensities of hydroxyl (O H) stretching modes during the dimerization of carboxylic acids. The hydrogen bond formation in these systems results into bathochromic shifts of vibrational frequencies for all the O H stretching modes along with huge infrared intensity increments for some of them. These bands become more intense on dimerization due mainly to changes in the cross-term contribution between charge and charge flux. In addition, interaction energies for the pair of atoms directly involved in individual hydrogen bonds (O…H) are linearly correlated to electron densities at their bond critical points (BCPs). Therefore, the hydrogen bonds between the carbonyl group (CO) of acetic acid and the hydroxyl group of halogenated monomers show the largest electron density values at their BCPs. The formation of these intermolecular interactions is also accompanied by ionic character enhancements of O H bonds and electron density decrements at their BCPs. We finally noticed that the hydrogen atom belonging to the hydroxyl group loses electronic charge, while the oxygen from the CO end becomes more negatively charged during dimerization. © 2019 Wiley Periodicals, Inc.     

In-silico exploration of noble gas dimer enforced by noncovalent interaction

Density functional calculations have been carried out to investigate the possibility of trapping of noble gas dimers by cyclo[18]carbon dimer. Parallel-displaced conformation of the cyclo[18]carbon dimer is found to be the minimum energy structure. Noncovalent interaction is found to hold the noble gas dimers. The lighter noble gases (He, Ne) posses weaker attractive interactions while the heavier one (Ar, Kr) are held by stronger attractive interactions forming genuine bonds. Each of the noble gas atoms in turn forms noncovalent interaction with the cyclo[18]carbon monomers. The bond dissociation energy of the noble gas dimers dramatically increases inside the cyclo[18]carbon dimer. Energy decomposition analysis reveals that dispersion plays the major role toward the stabilization energy.     

Direct assessment of quantum nuclear effects on hydrogen bond strength by constrained-centroid ab initio path integral molecular dynamics

The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)(2) is about 30% weaker when quantum nuclear effects are included, while that in (H(2)O)(2) is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.     

Interpreting geometric preferences in π‐stacking interactions through molecular orbital analysis

The preference of π‐stacking interactions for parallel‐displaced (PD) and twisted (TW) conformations over the fully eclipsed sandwich (S) in small π‐stacked dimers of benzene, pyridine, pyrimidine, 1,3,5‐trifluorobenzene, and hexafluorobenzene are examined in terms of enhancement of the inter‐ring density through mixing of the monomer orbitals (MOs). PD and/or TW conformations are consistent with a non‐zero “stack bond order” (SBO), defined in analogy to the bond order of conventional MO theory, as the difference in the occupation of bonding and antibonding π‐type dimer MOs. In the S conformation, the equal number of bonding and antibonding MOs cancel overall stack bonding character between the monomers for an SBO of zero and an overall repulsive interaction. PD from the S shifts the character of at least one antibonding combination of monomer π‐type MOs with nodes perpendicular to the coordinate for PD to bonding, leading to an attractive nonzero SBO. The inter‐ring density measured through the Wiberg bond index analysis shows an enhancement at the PD conformations consistent with greater interpenetration of the monomer densities. This intuitive bonding model for π‐stacking interactions is complementary to highly accurate calculations of π‐stacking energies and allows a predictive understanding of relative stability using cheaper quantum chemical methods.     

Recurrence of carboxylic acid-pyridine supramolecular synthon in the crystal structures of some pyrazinecarboxylic acids.

X-ray crystal structures of pyrazinic acid 1 and isomeric methylpyrazine carboxylic acids 2-4 are analyzed to examine the occurrence of carboxylic acid-pyridine supramolecular synthon V in these heterocyclic acids. Synthon V, assembled by (carboxyl)O-H...N(pyridine) and (pyridine)C-H...O(carbonyl) hydrogen bonds, controls self-assembly in the crystal structures of pyridine and pyrazine monocarboxylic acids. The recurrence of acid-pyridine heterodimer V compared to the more common acid-acid homodimer I in the crystal structures of pyridine and pyrazine monocarboxylic acids is explained by energy computations in the RHF 6-31G* basis set. Both the O-H.N and the C-H...O hydrogen bonds in synthon V result from activated acidic donor and basic acceptor atoms in 1-4. Pyrazine 2,3- and 2,5-dicarboxylic acids 10 and 11 crystallize as dihydrates with a (carboxyl)O-H...O(water) hydrogen bond in synthon VII, a recurring pattern in the diacid structures. In summary, the carboxylic acid group forms an O-H...N hydrogen bond in pyrazine monocarboxylic acids and an O-H...O hydrogen bond in pyrazine dicarboxylic acids. This structural analysis correlates molecular features with supramolecular synthons in pyridine and pyrazine carboxylic acids for future crystal engineering strategies.     

Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases

The strongest gas-phase MP2/6-31G*(0.25) stacking energies between the aromatic amino acids and the natural or methylated nucleobases were considered. The potential energy surfaces of dimers were searched as a function of the vertical separation, angle of rotation and horizontal displacement between monomers stacked according to their centers of mass. Our calculations reveal that the stacking interactions of adducts for a given nucleobase are dependent on the methylation site (by up to 20 kJ mol(-1)), where the relative magnitudes of the interactions are determined by the dipole moments of the adducts and the proton affinities of nucleobase methylation sites. Nevertheless, the differences in the (gas-phase) stacking of methylated adducts are small compared with the differences between the stacking of the corresponding natural and methylated nucleobases. Indeed, methylation increases the stacking energy by up to 40 kJ mol(-1) (or 135%). Although immersing the dimers in different solvents decreases the gas-phase stacking energies with an increase in the polarity of the environment, base methylation still has a significant effect on the nucleobase stacking ability in solvents with large dipole moments, and, perhaps more importantly, environments that mimic enzyme active sites. Our results shed light on the workings of DNA repairs enzymes that selectively remove a wide variety of alkylated nucleobases over the natural bases.     

Photodissociation dynamics of hydroxybenzoic acids

Aromatic amino acids have large UV absorption cross-sections and low fluorescence quantum yields. Ultrafast internal conversion, which transforms electronic excitation energy to vibrational energy, was assumed to account for the photostability of amino acids. Recent theoretical and experimental investigations suggested that low fluorescence quantum yields of phenol (chromophore of tyrosine) are due to the dissociation from a repulsive excited state. Radicals generated from dissociation may undergo undesired reactions. It contradicts the observed photostability of amino acids. In this work, we explored the photodissociation dynamics of the tyrosine chromophores, 2-, 3- and 4-hydroxybenzoic acid in a molecular beam at 193 nm using multimass ion imaging techniques. We demonstrated that dissociation from the excited state is effectively quenched for the conformers of hydroxybenzoic acids with intramolecular hydrogen bonding. Ab initio calculations show that the excited state and the ground state potential energy surfaces change significantly for the conformers with intramolecular hydrogen bonding. It shows the importance of intramolecular hydrogen bond in the excited state dynamics and provides an alternative molecular mechanism for the photostability of aromatic amino acids upon irradiation of ultraviolet photons.     

Weak interactions in furan dimers

Dimers of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran were investigated with the use of theoretical methods to determine the interactions that keep the molecules together. The QTAIM and NCI methods confirmed that for furan dimers the C–H?O hydrogen bond and stacking interactions can form the dimers with similar energy. For 2,3-dihydrofuran, 2,5-dihydrofuran and tetrahydrofuran, the decisive mechanism of dimer formation is the stacking interaction between the furan rings.     

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.     

核酸碱基的非谐性振动:Ⅲ,DNA叠加二聚体的一维和二维红外光谱

用量子化学计算方法研究了DNA碱基单体及其15个B型和2个G-四链体的叠加二聚体的非谐性振动光谱特征.研究发现,从碱基单体到二聚体,C=O伸缩模式之间的相互作用很强,表现在其非谐性振动频率和非谐性常数都发生了明显的改变,特别是在含碱基G的叠加体中.这些变化能在一维和二维红外光谱中很好地表现出来.利用振动模式的势能分布和非谐性常数的组成分析,讨论了叠加二聚体中C=O模式的离域化程度.     

Hydrogen-bonding interactions in 2-thiophen-3-ylmalonic acid

Formation of intra- and intermolecular hydrogen bonds in 2-thiophen-3-ylmalonic acid, the precursor of a polythiophene derivative bearing two carboxylic acid groups in the side chain, have been examined by Fourier transform infrared (FTIR) spectroscopy and ab initio quantum mechanical calculations. Interactions found in the FTIR spectra recorded for the melted and solid states are in good agreement with results provided by MP2/6-31+G(d,p) calculations on monomers and dimers, respectively. Specifically, inter- and intramolecular hydrogen bonds were detected in the solid and melted states, respectively. Calculations on dimers stabilized by intermolecular hydrogen bonds exclusively and by both intra- and intermolecular interactions indicated that the former structures are significantly more stable than the latter ones, which is fully consistent with experimental observations. On the other hand, intramolecular interactions in isolated monomers are favored in the melted state, which is dominated by a thermally driven entropic process.     

The nature of bond critical points in dinuclear copper(I) complexes

Closed-shell contacts between two copper(I) ions are expected to be repulsive. However, such contacts are quite frequent and are well documented. Crystallographic characterization of such contacts in unsupported and bridged multinuclear copper(I) complexes has repeatedly invited debates on the existence of cuprophilicity. Recent developments in the application of Bader's theory of atoms-in-molecules (AIM) to systems in which weak hydrogen bonds are involved suggests that the copper(I)-copper(I) contacts would benefit from a similar analysis. Thus the nature of electron-density distributions in copper(I) dimers that are unsupported, and those that are bridged, have been examined. A comparison of complexes that are dimers of symmetrical monomers and those that are dimers of two copper(I) monomers with different coordination spheres has also been made. AIM analysis shows that a bond critical point (BCP) between two Cu atoms is present in most cases. The nature of the BCP in terms of the electron density, ρ, and its Laplacian is quite similar to the nature of critical points observed in hydrogen bonds in the same systems. The ρ is inversely correlated to Cu-Cu distance. It is higher in asymmetrical systems than what is observed in corresponding symmetrical systems. By examining the ratio of the local electron potential-energy density (V(c)) to the kinetic energy density (G(c)), |V(c)|/G(c) at the critical point suggests that these interactions are not perfectly ionic but have some shared nature. Thus an analysis of critical points by using AIM theory points to the presence of an attractive metallophilic interaction similar to other well-documented weak interactions like hydrogen bonding.     

Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials

Noncovalent interactions involving aromatic rings, such as π‐stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion‐corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene???methane and cyclohexane???methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel‐displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non‐additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

6-甲基-4-羟基嘧啶单体及二聚体质子转移过程的理论研究

应用密度泛函理论的B3LYP/6-311+G(d)方法研究了6-甲基-4-羟基嘧啶单体及二聚体质子转移的异构化反应.对反应势能面的研究发现,该化含物可能存在9种单体异构体,对其最稳定的单体构型进行分析.各单体间异构化反应的过渡态共有9种,反应的活化能最小为22.06 kJ/mol,最大为356.55 kJ/mol,最可能的反应路径在室温下即可进行. 研究了2种二聚体及其异构化反应的过渡态,发现二聚体均比其对应的单体稳定,而且质子转移所需要的活化能仅为20.13 kJ/mol,比单体低很多. 氢键在这种变化中起了主要作用,由单体和二聚体的总能量计算了氢键的键能.     

Thermodynamics and kinetics of aggregation for the GNNQQNY peptide

The energy landscape of the monomer and dimer are explored for the amyloidogenic heptapeptide GNNQQNY from the N-terminal prion-determining domain of the yeast protein Sup35. The peptide is modeled by a united-atom potential and an implicit solvent representation. Replica exchange molecular dynamics is used to explore the conformational space, and discrete path sampling is employed to investigate the pathways that interconvert the most populated minima on the free energy surfaces. For the monomer, we find a rapid fluctuation between four different conformations, where a geometry intermediate between compact and extended structures is the most thermodynamically favorable. The GNNQQNY dimer forms three stable sheet structures, namely in-register parallel, off-register parallel, and antiparallel. The antiparallel dimer is stabilized by strong electrostatic interactions resulting from interpeptide hydrogen bonds, which restrict its conformational flexibility. The in-register parallel dimer, which is close to the amyloid beta-sheet structure, has fewer interpeptide hydrogen bonds, making hydrophobic interactions more important and increasing the conformational entropy compared to the antiparallel sheet. The estimated two-state rate constants indicate that the formation of dimers from monomers is fast and that the dimers are kinetically stable against dissociation at room temperature. Interconversions between the different dimers are feasible processes and are more likely than dissociation.     

Molecular Structure of 1-Germatrahol and its Complex With Chloroform

The crystal structures of anhydrous 1-germatranol and its complex with HCCl₃ are centrosymmetrical dimers because of their intermolecular hydrogen bonds. In the germatranol crystal, the axial and equatorial oxygen atoms of its two molecules are hydrogen bonded into an eight-membered coordination cycle. In the complex with HCCl₃, the two molecules of germatranol are likewise linked in dimers, and both axial oxygen atoms are H bonded with HCCl₃. In the investigated structures, the axial Ge—O bond is shorter than the equatorial ones. Depending on the number and strength of the hydrogen bonds, the interatomic Ge—O and Ge ← N distances change markedly. The quantitative estimates of the H bond energy are obtained from quantum chemical calculations of the model systems containing 1-germatranol and HCCl₃ molecules.