On the electron-pair nature of the hydrogen bond in the framework of the atoms in molecules theory

Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mn+-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H ⋯ D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H ⋯ D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H ⋯ D interaction in the GC base pair, becomes the weakest in the Mn+-GC complexes. A broader perspective on the stability of GC and Mn+-GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mn+-GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mn+-GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

Deciphering the chemical bonding of the trivalent oxygen atom in oxygen doped graphene

Recently, planar and neutral tricoordinated oxygen embedded in graphene has been imaged experimentally (Nat. Commun., 2019, 10, 4570-4577). In this work, this unusual chemical species is studied utilizing a variety of state-of-the-art methods and combining periodic calculations with a fragmental approach. Several factors influencing the stability of trivalent oxygen are identified. A σ-donation and a π-backdonation mechanism between graphite and oxygen is established. π-Local aromaticity, with a delocalized 4c-2e bond involving the oxygen atom and the three nearest carbon atoms aids in the stabilization of this system. In addition, the framework in which the oxygen is embedded is crucial too to the stabilization, helping to delocalize the "extra" electron pair in the virtual orbitals. Based on the understanding gathered in this work, a set of organic molecules containing planar and neutral trivalent oxygen is theoretically proposed for the first time.

Exploring the Non-Covalent Bonding in Water Clusters

QTAIM and source function analysis were used to explore the non-covalent bonding in twelve different water clusters (H2O)n obtained by considering n = 2–7 and various geometrical arrangements. A total of seventy-seven O−H⋯O hydrogen bonds (HBs) were identified in the systems under consideration, and the examination of the electron density at the bond critical point (BCP) of these HBs revealed the existence of a great diversity of O−H⋯O interactions. Furthermore, the analysis of quantities, such as |V(r)|/G(r) and H(r), allowed a further description of the nature of analogous O−H⋯O interactions within each cluster. In the case of 2-D cyclic clusters, the HBs are nearly equivalent between them. However, significant differences among the O−H⋯O interactions were observed in 3-D clusters. The assessment of the source function (SF) confirmed these findings. Finally, the ability of SF to decompose the electron density (ρ) into atomic contributions allowed the evaluation of the localized or delocalized character of these contributions to ρ at the BCP associated to the different HBs, revealing that weak O−H⋯O interactions have a significant spread of the atomic contributions, whereas strong interactions have more localized atomic contributions. These observations suggest that the nature of the O−H⋯O hydrogen bond in water clusters is determined by the inductive effects originated by the different spatial arrangements of the water molecules in the studied clusters.

Cocrystals; basic concepts, properties and formation strategies

Cocrystallization is an old technique and remains the focus of several research groups working in the field of Chemistry and Pharmacy. This technique is basically in field for improving physicochemical properties of material which can be active pharmaceutical ingredients (APIs) or other chemicals with poor profile. So this review article has been presented in order to combine various concepts for scientists working in the field of chemistry, pharmacy or crystal engineering, also it was attempt to elaborate concepts belonging to crystal designing, their structures and applications. A handsome efforts have been made to bring scientists together working in different fields and to make chemistry easier for a pharmacist and pharmacy for chemists pertaining to cocrystals. Various aspects of chemicals being used as co-formers have been explored which predict the formation of co-crystals or molecular salts and even inorganic cocrystals.

Matrix effects on hydrogen bonding and proton transfer in fluoropyridine - HCl complexes

We report an extensive computational and spectroscopic study of several fluoropyridine-HCl complexes, and the parent, pyridine-HCl system. Matrix-IR spectra for pentafluoropyridine-HCl, 2,6-difluororpyridine-HCl, and 3,5-difluororpyridine-HCl in solid neon exhibit shifts for the H-Cl stretching band that parallel the effects of fluorination on hydrogen-bond strength. Analogous spectral shifts observed across various host environments (solid neon, argon, and nitrogen) for pentafluoropyridine-HCl and 2,6-difluororpyridine-HCl convey a systematically varying degree of matrix stabilization on the hydrogen bonds in these complexes. An extended quantum-chemical study of pyridine-HCl and eight fluorinated analogs, including 2-, 3-, and 4-fluoropyridine-HCl, 2,6- and 3,5-difluororpyridine-HCl, 2,4,6- and 3,4,5-trifluropyridine-HCl, as well as pentafluoropyridine-HCl, was also performed. Equilibrium structures and binding energies for the gas-phase complexes illustrate two clear trends in how fluorine substitution affects hydrogen bond strength; increasing fluorination weakens these interactions, yet substitution at the 2- and 6-positions has the most pronounced effect. Bonding analyses for a select subset of these systems reveal shifts in electron density that accompany hydrogen bonding, and most notably, the values of the electron density at the N-H bond critical points among the stronger systems in this subset significantly exceed those typical for moderately strong hydrogen-bonds. We also explored the effects of dielectric media on the structural and bonding properties of these systems. For pyridine-HCl, 3-fluoropyridine-HCl, and 3,5-difluororpyridine-HCl, a transition to proton transfer-type structures is observed at ε-values of 1.2, 1.5, and 2.0, respectively. This is signaled by key structural changes, as well as an increase in the negative charge on the chorine, and dramatic shifts in topological properties of the H-Cl and N-H bonds. In the case of pentafluoropyridine-HCl, and 2,6-difluororpyridine-HCl, we do not predict proton transfer in dielectric media up to ε = 20.0. However, there are clear indications that the media enhance hydrogen-bond strength, and moreover, these observations are completely consistent with the experimental IR spectra.

Strength of the [Z-I···Hal]- and [Z-Hal···I]- Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z-I···Hal]- and [Z-Hal···I]- types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06-4.76 kcal/mol.

Tuning the Binding Strength of Even and Uneven Hydrogen-Bonded Arrays with Remote Substituents

We investigated the tunability of hydrogen bond strength by altering the charge accumulation around the frontier atoms with remote substituents. For pyridine···H2O with NH2 and CN substituted at different positions on pyridine, we find that the electron-withdrawing CN group decreases the negative charge accumulation around the frontier atom N, resulting in weakening of the hydrogen bond, whereas the electron-donating NH2 group increases the charge accumulation around N, resulting in strengthening of the hydrogen bond. By applying these design principles on DDAA-AADD, DADA-ADAD, DAA-ADD, and ADA-DAD hydrogen-bonded dimers, we find that the effect of the substituent is delocalized over the whole molecular system. As a consequence, systems with an equal number of hydrogen bond donor (D) and acceptor (A) atoms are not tunable in a predictable way because of cancellation of counteracting strengthening and weakening effects. Furthermore, we show that the position of the substituent and long-range electrostatics can play an important role as well. Overall, the design principles presented in this work are suitable for monomers with an unequal number of donor and acceptor atoms and can be exploited to tune the binding strength of supramolecular building blocks.

Effect of Alkali Metal Cations on Length and Strength of Hydrogen Bonds in DNA Base Pairs

For many years, non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases, and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and the delocalization index from QTAIM calculations. The aromaticity changes were determined by a HOMA index.

Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs

The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods-DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)-are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers-e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on π-electron delocalization are also documented.

Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY-X···X-Z(B)m] Type (X = Cl, Br, I)

Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY-X···X-Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as -Eint = 0.128Gb2 - 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.

Secondary Electrostatic Interaction Model Revised: Prediction Comes Mainly from Measuring Charge Accumulation in Hydrogen-Bonded Monomers

The secondary electrostatic interaction (SEI) model is often used to predict and explain relative hydrogen bond strengths of self-assembled systems. The SEI model oversimplifies the hydrogen-bonding mechanisms by viewing them as interacting point charges, but nevertheless experimental binding strengths are often in line with the model’s predictions. To understand how this rudimentary model can be predictive, we computationally studied two tautomeric quadruple hydrogen-bonded systems, DDAA-AADD and DADA-ADAD. Our results reveal that when the proton donors D (which are electron-donating) and the proton acceptors A (which are electron-withdrawing) are grouped together as in DDAA, there is a larger accumulation of charge around the frontier atoms than when the proton donor and acceptor groups are alternating as in DADA. This accumulation of charge makes the proton donors more positive and the proton acceptors more negative, which enhances both the electrostatic and covalent interactions in the DDAA dimer. The SEI model is thus predictive because it provides a measure for the charge accumulation in hydrogen-bonded monomers. Our findings can be understood from simple physical organic chemistry principles and provide supramolecular chemists with meaningful understanding for tuning hydrogen bond strengths and thus for controlling the properties of self-assembled systems.

Tuning the Strength of the Resonance-Assisted Hydrogen Bond in o-Hydroxybenzaldehyde by Substitution in the Aromatic Ring1

Intramolecular resonance-assisted hydrogen bonds (RAHBs) are stronger than conventional hydrogen bonds (HBs) thanks to the extra stabilization connected with the partial delocalization of the π-electrons within the HB motif containing conjugated formally single and double bonds. When these conjugated bonds are part of an aromatic ring, there is an interplay between resonance-assisted hydrogen bonding and the aromaticity of the ring. The main aim of the present work is to analyze the changes in RAHB strength by substitution in the aromatic ring. For this purpose, we use density functional theory methods to study all possible mono- and disubstitutions in the four free positions of the aromatic ring of o-hydroxybenzaldehyde. As substituents, we consider three π-electron donating groups (EDG: NH₂, OH, and F) and three π-electron withdrawing groups (EWG: NO₂, NO, and CN). We show that it is possible to tune the HB bond distance in the RAHB by locating different substituents in given positions of the aromatic ring. Indeed, certain combinations of EDG and EWD result in a reduction or increase of the HB distance by up to 0.05 Å. Results found can be explained by considering the existence of a resonance effect of the π-electrons within the HB motif.

Nature of Intramolecular Resonance Assisted Hydrogen Bonding in Malonaldehyde and Its Saturated Analogue

The nature of resonance-assisted hydrogen bonds (RAHB) is still subject of an ongoing debate. We therefore analyzed the σ and π charge redistributions associated with the formation of intramolecular hydrogen bonds in malonaldehyde (MA) and its saturated analogue 3-hydroxypropanal (3-OH) and addressed the question whether there is a resonance assistance phenomenon in the sense of a synergistic interplay between the σ and π electron systems. Our quantum chemical calculations at the BP86/TZ2P level of theory show that the π charge flow is indeed in line with the Lewis structure as proposed by the RAHB model. This typical rearrangement of charge is only present in the unsaturated system, and not in its saturated analogue. Resonance in the π electron system assists the intramolecular hydrogen bond by reducing the hydrogen bond distance, and by providing an additional stabilizing component to the net bonding energy. The σ orbital interaction plays an important role in the enhanced hydrogen bond strength in MA as well. However, there is no resonance assistance in the sense of an interplay between σ charge transfer and π polarization; σ and π contribute independently from each other.

Hydrogen-Bond Strength of CC and GG Pairs Determined by Steric Repulsion: Electrostatics and Charge Transfer Overruled

Theoretical and experimental studies have elucidated the bonding mechanism in hydrogen bonds as an electrostatic interaction, which also exhibits considerable stabilization by charge transfer, polarization, and dispersion interactions. Therefore, these components have been used to rationalize the differences in strength of hydrogen‐bonded systems. A completely new viewpoint is presented, in which the Pauli (steric) repulsion controls the mechanism of hydrogen bonding. Quantum chemical computations on the mismatched DNA base pairs CC and GG (C=cytosine, G=guanine) show that the enhanced stabilization and shorter distance of GG is determined entirely by the difference in the Pauli repulsion, which is significantly less repulsive for GG than for CC. This is the first time that evidence is presented for the Pauli repulsion as decisive factor in relative hydrogen‐bond strengths and lengths.

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇²ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)₄ with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

Tuning diastereoisomerism in platinum(ii) phosphino- and aminothiolato hydrido complexes

Tuning between the cis and trans Pt(ii) based complexes bearing phosphinothiolato and aminothiolato ligands.

Fmoc–RGDS based fibrils: atomistic details of their hierarchical assembly

We describe the 3D supramolecular structure of Fmoc–RGDS fibrils, where Fmoc and RGDS refer to the hydrophobic N-(fluorenyl-9-methoxycarbonyl) group and the hydrophilic Arg-Gly-Asp-Ser peptide sequence, respectively.

Hydrogen-hydrogen bonding: the current density perspective

Current density plots of closed-shell intermolecular H-H interactions characterized by a bond critical point (BCP) show two vortices separated by a saddle, a pattern which allows for a clear definition of a pair current strength. This H-H current strength turns out to be roughly related to the potential energy density at the BCP and then to the dissociation energy. The same pattern is also recognizable, at least for an azimuthal orientation of a field perpendicular to the H-H line, for the intramolecular interactions previously investigated to propose the H-H bonding. In the case of the H atoms of the bay region of polycyclic aromatic hydrocarbons, the current of the H-H delocalized diatropic vortex gives a quantitative indication of stabilization; however, on rotation of the field and the subsequent onset of a bay-delocalized paratropic vortex (a typical signature of antiaromaticity), the diatropic vortex can be reshaped or it can even disappear, consistently with its smallness, and thus showing the effect of other more relevant interactions.

A fuzzy-atom analysis of electron delocalization on hydrogen bonds

The extent of electron delocalization is quantified for set of cyclic complexes exhibiting two or more hydrogen bonds (HBs). In particular, the delocalization index (DI) between the atoms directly involved in the HB, and the ING (a normalized n-center delocalization index) have been evaluated using several fuzzy-atom schemes, namely Becke, Becke-ρ, Hirshfeld, and Hirshfeld-Iterative. The results have been compared with the widely used Quantum Theory of Atoms in Molecules (QTAIM) atomic definition. The DI values are found to correlate very well with geometrical or topological descriptors widely used in the literature to characterize HB systems. Among all fuzzy-atom methods, the ones that can better accommodate the different partial ionic character of the bonds perform particularly well. The best performing fuzzy-atom scheme for both pairwise and n-center electron delocalization is found to be the Becke-ρ method, for which similar results to QTAIM model are obtained with a much reduced computational cost. These results open up a wide range of applications of such electron delocalization descriptors based on fuzzy-atoms for noncovalent interactions in more complex and larger systems.

The hydrogen bond – practice and QTAIM theory

IR intensities in the spectra of H-complexes as a source of electron-density data ρ(r_c) (e a⁻³) = 10⁻²(ΔA^1/2) (A, 10⁻⁴ cm mmol^−1/2).

Electron density distribution in tetralithium hypodiphosphate hexahydrate, Li4P2O6·6H2O

Tetralithium hypodiphosphate hexahydrate, Li4P2O6·6H2O, forms a highly symmetrical crystal structure, where hypodiphosphate anions have \bar 3m (D3d) symmetry. Analysis of the charge distribution (experimental and theoretically calculated) shows that the charges of the P atoms are lower than in phosphates and phosphonates, whereas the O charges are similar. Values of both ρc and ∇(2)ρc suggest that the P-P bond is a weak covalent one, while the P-O one is polarized covalent, with topological parameters similar to those of P-O bonds in phosphates or phosphonates. Theoretical calculations show that the hypodiphosphate anion is relatively insensitive to its coordination environment; this is brought about by the vicinity of cationic P atoms. The localization and delocalization indices have been computed and discussed.

Different zeroes of interaction energies as the cause of opposite results on the stabilizing nature of C-H···O intramolecular interactions

The interaction energy of the C-H···O intramolecular interaction is estimated by several methods for a large group of systems possessing a quasi-cyclic six-membered ring. In the case of the geometry corrected method (GCM), the related rotamers method (RRM), and Espinosa's method (EM), the linear correlations between interaction energies and the electron density at the bond critical point have close slopes. The first and the last two methods yield almost systematically opposite results concerning the stabilizing/destabilizing character of the interaction, and their main difference is their zero of the interaction energy. An investigation on the limitations of reference energies has led to the introduction of the geometry corrected related rotamers method (GCRRM), estimating both stabilizing and destabilizing C-H···O interactions. An extension of EM is proposed.

Influence of confinement on hydrogen bond energy. The case of the FH···NCH dimer

The influence of the external pressure on the energy of the intermolecular hydrogen bond is investigated by modeling the pressure effects with helium atoms located at fixed points in space around the hydrogen bonded dimer. Several methods of estimating the energy of the H···N hydrogen bond in the He···FH···NCH···He model system are proposed. They show that the energy of the H···N hydrogen bond in this confined dimer decreases continuously with the reduction of the He···He distance, thus with the increase of the pressure effect exerted on the confined dimer.

Beryllium Bonds, Do They Exist?

The complexes between BeX2 (X = H, F, Cl, OH) with different Lewis bases have been investigated through the use of B3LYP, MP2, and CCSD(T) approaches. This theoretical survey showed that these complexes are stabilized through the interaction between the Be atom and the basic center of the base, which are characterized by electron densities at the corresponding bond critical points larger than those found in conventional hydrogen bonds (HBs). Actually, all bonding indices indicate that, although these interactions that we named "beryllium bonds" are in general significantly stronger than HBs, they share many common features. Both interactions have a dominant electrostatic character but also some covalent contributions associated with a non-negligible electron transfer between the interacting subunits. This electron transfer, which in HBs takes place from the HB acceptor lone-pairs toward the σYH* antibonding orbital of the HB donor, in beryllium bonds goes from the lone pairs of the Lewis base toward the empty p orbital of Be and the σBeX* antibonding orbital. Accordingly, a significant distortion of the BeX2 subunit, which in the complex becomes nonlinear, takes place. Concomitantly, a significant red-shifting of the X-Be-X antisymmetric stretching frequencies and a significant lengthening of the X-Be bonds occur. The presence of the beryllium bond results in a significant blue-shifting of the X-Be-X symmetric stretch.

Dihydrogen bonding: donor-acceptor bonding (AH...HX) versus the H2 molecule (A-H2-X)

Dihydrogen bonds (DHBs) play a role in, among others, crystal packing, organometallic reaction mechanisms, and potential hydrogen-storage materials. In this work we have analyzed the central H-H bond in linear H(4), LiH...HX, BH(4)(-)...HX, and AlH(4)(-)...HX complexes with various X by using the quantitative molecular orbital model contained in Kohn-Sham density functional theory at the BP86/TZ2P level of theory. First, we address the questions of if and how one can distinguish, in principle, between a H...H donor-acceptor DHB and the formation of an H(2) molecule by using the simple H(4) model system. The results of these analyses have been used to gain an understanding of the bonding in more realistic model systems (some of which have been studied experimentally), and how this differs from the bonding in H(4).

Watson-crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA

We have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H···O hydrogen bonds are replaced by N-H···S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a slight weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many, and in particular, on which hydrogen bonds AT and GC are substituted.. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the hydrogen bonds involved in the mimics, using a quantitative bond energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these hydrogen bonds is found to contribute more than 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction.

Nanoswitches based on DNA base pairs: why adenine-thymine is less suitable than guanine-cytosine

Substituted Watson-Crick guanine-cytosine (GC) base pairs were recently shown to yield robust three-state nanoswitches. Here, we address the question: Can such supramolecular switches also be based on Watson-Crick adenine-thymine (AT) base pairs? We have theoretically analyzed AT pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X=NH(-), NH(2), NH(3) (+) (N series), O(-), OH or OH(2) (+) (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. Thus, we explore the trend in geometrical shape and hydrogen bond strengths in AT pairs along a series of stepwise protonations of the substituents. Introducing a charge on the substituents leads to substantial and characteristic changes in the individual hydrogen bond lengths when compared to the neutral AT pair. However, the trends along the series of negative, neutral, and positive substituents are less systematic and less pronounced than for GC. In certain instances, internal proton transfer from thymine to adenine occurs. Our results suggest that AT is a less suitable candidate than GC in the quest for chemically controlled nanoswitches.

Electron density topological properties are useful to assess the difference between hydrogen and dihydrogen complexes

B3LYP/6-31++G(d,p) and MP2/6-31++G(d,p) calculations for a series of hydrogen- and dihydrogen-bonded systems have been carried out in order to analyze the topology of the electron density and the energy densities at the respective energy-optimized bond critical points. Even though there are no significant differences when these properties are represented as a function of the dimerization energy, they can be separated into two well-defined sets if those properties are correlated with intermolecular distances. When analyzing the dependence of various properties with equilibrium bond lengths, the specific trends of dihydrogen bond systems consist of (a) lower electron density at the bond critical point, and (b) lower concentration/depletion of that density which can be translated in a different behavior for the Laplacian components. Furthermore, the sets of molecules form two different plots which allow for a valuable classification between hydrogen- and dihydrogen-bonded systems.

The nature of the hydrogen bond: A synthesis from the interacting quantum atoms picture

The interacting quantum atoms approach [IQA, as presented by Blanco et al., J. Chem. Theory Comput. 1, 1096 (2005)] is applied to standard hydrogen bonded dimers. IQA is an interpretation tool based on a real space energy decomposition scheme fully consistent with the quantum theory of atoms in molecules. It provides a partition of every physical term present in the Hamiltonian into atomic and interatomic contributions. The procedure is orbital-free and self-contained, needing neither external references nor artificial intermediate states. Binding is the result of a competition between the destabilizing deformations suffered by the interacting fragments upon interaction and the stabilizing interaction energy itself. According to IQA, there is no incompatibility between the prevalent electrostatic image of hydrogen bonded systems and that favoring important covalent contributions. Depending on how we gather the different energetic terms, we may recover electrostatic or covalent pictures from the same underlying quantum mechanical description. Our results show that the nonclassical contributions to hydrogen bonding are spatially localized, involving only the H atom and its two nearest neighbors. IQA is well suited as a comparative tool. Its thin energetic decomposition allows us to recover exactly (or to a very good approximation) the quantities of the most widely used energy decomposition schemes. Such a comparison sheds light on the virtues and faults of the different methods and on the origin of the 50 years old debate regarding the covalent/electrostatic nature of the hydrogen bond.

Supramolecular Switches Based on the Guanine–Cytosine (GC) Watson–Crick Pair: Effect of Neutral and Ionic Substituents

We have theoretically analyzed Watson-Crick guanine-cytosine (GC) base pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X = NH(-), NH(2), NH(3) (+) (N series), O(-), OH, or OH(2) (+) (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. The purpose is to study the effects on structure and hydrogen-bond strength if X= H is substituted by an anionic, neutral, or cationic substituent. We found that replacing X = H by a neutral substituent has relatively small effects. Introducing a charged substituent, on the other hand, led to substantial and characteristic changes in hydrogen-bond lengths, strengths, and hydrogen-bonding mechanism. In general, introducing an anionic substituent reduces the hydrogen-bond-donating and increases the hydrogen-bond-accepting capabilities of a DNA base, and vice versa for a cationic substituent. Thus, along both the N and O series of substituents, the geometric shape and bond strength of our DNA base pair can be chemically switched between three states, thus yielding a chemically controlled supramolecular switch. Interestingly, the orbital-interaction component in some of these hydrogen bonds was found to contribute to more than 49 % of the attractive interactions and is thus virtually equal in magnitude to the electrostatic component, which provides the other (somewhat less than) 51 % of the attraction.

A trinuclear Pt(ii) compound with short Pt–Pt–Pt contacts. An analysis of the influence of π–π stacking interactions on the strength and length of the Pt–Pt bond

In this work we report the first example of a trinuclear Pt(II) complex with Pt-Pt-Pt bonds that are not facilitated by direct intervention of bridging ligands but are partially held by the attractive pi-pi stacking interaction between the phenyl units of the 4,4'-dimethyl-2,2'-bipyridyl ligands. The effect of the pi-pi stacking interactions on the strength and length of the Pt-Pt bond has been discussed using reduced models of the interacting moieties in which the aromatic rings have been removed. The nature of the Pt-Pt bonds has been studied through energy decomposition and atoms-in-molecules analyses. The results indicate that the relatively strong (about 40 kcal mol(-1)) Pt-Pt metallic bond has similar covalent and ionic contributions.