Exploring fundamental differences between red- and blue-shifted intramolecular hydrogen bonds using FAMSEC,FALDI, IQA and QTAIM

We have discovered, using developed by us recently FALDI and FAMSEC computational techniques, fundamentally distinct mechanisms of intramolecular red- and blue-shifted H-bond formation that occurred in different conformers of the same molecule (amino-acid β-alanine) involving the same heteroatoms (O–H???N and N–H???O). Quantitative topological, geometric and energetic data of both H-bonds obtained with well-known QTAIM and IQA methodologies agree with what is known regarding H-bonding in general. However, the FALDI charge and decomposition scheme for calculating in real space 3D conformational deformation densities provided clear evidence that the process of electron density redistribution taking place on the formation of the stronger red-shifted H-bond is fundamentally distinct from the weaker blue-shifted H-bond. Contributions made by atoms of the X–H???Y–Z fragment (IUPAC notation) as well as distinct atoms on the H-bond formation were fully explored. The FAMSEC energy decomposition approach showed that the atoms involved in formation of the red-shifted H-bond interact in a fundamentally different fashion, both locally and with the remainder of the molecule, as compared with those of the blue-shifted H-bond. Excellent correlations of trends obtained with QTAIM, IQA, FAMSEC and FALDI techniques were obtained. Commentary regarding IUPAC recommended definition of an H-bond and validity of observed AILs (or bond paths) of the two H-bond kinds is also discussed.     

FALDI‐based decomposition of an atomic interaction line leads to 3D representation of the multicenter nature of interactions

Atomic interaction lines (AILs) and the QTAIM's molecular graphs provide a predominantly two‐center viewpoint of interatomic interactions. While such a bicentric interpretation is sufficient for most covalent bonds, it fails to adequately describe both formal multicenter bonds as well as many non‐covalent interactions with some multicenter character. We present an extension to our Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) electron density (ED) decomposition scheme, with which we can measure how any atom‐pair's delocalized density concentrates, depletes or reduces the electron density in the vicinity of a bond critical point. We apply our method on five classical bonds/interactions, ranging from formal either two‐ or three‐center bonds, a non‐covalent interaction (an intramolecular hydrogen bond) to organometallic bonds with partial multicenter character. By use of 3D representation of specific atom‐pairs contributions to the delocalized density we (i) fully recover previous notion of multicenter bonding in diborane and predominant bicentric character of a single covalent C C bond, (ii) reveal a multicenter character of an intramolecular H‐bond and (iii) illustrate, relative to a Schrock carbene, a larger degree of multicenter M C interaction in a Fischer carbene (due to a presence of a heteroatom), whilst revealing the holistic nature of AILs from multicenter ED decomposition. © 2018 Wiley Periodicals, Inc.     

Exact and exclusive electron localization indices within QTAIM atomic basins

Novel measures of electron (de)localization within the Quantum Theory of Atoms in Molecules (QTAIM) atomic basins are presented which, unlike orthodox localization indices (LIs), are fully exclusive and can be easily visualized. This work shows that QTAIM‐defined LIs describe a portion of interatomic delocalized electrons; hence, the chemical/physical interpretation of orthodox LIs is misleading. Using the recently introduced Fragment, Atomic, Localized, Delocalized, and Interatomic (FALDI) density decomposition technique we derive two novel sets of LIs and delocalization indices (DIs), by accounting for the overlap between localized and delocalized density functions. The FALDI‐based LIs and DIs perfectly recover chemically expected core and bonded electron count. Usefulness of new (de)localization indices and their 3D representations were demonstrated on a number of examples, including formamide and benzene. We therefore expect that the scheme reported in this work will provide a valuable stepping stone between classical conceptual chemistry and quantum chemical topology. © 2018 Wiley Periodicals, Inc.     

Characterization of bonding modes in metal complexes through electron density cross-sections

Qualitative inspection of molecular orbitals (MOs) remains one of the most popular analysis tools used to describe the electronic structure and bonding properties of transition metal complexes. In symmetric coordination complexes, the use of group theory and the symmetry-adapted linear combination (SALC) of fragment orbitals allows for a very accurate and informative interpretation of MOs, but the same procedure cannot be performed for asymmetric complexes, such as Schrock and Fischer carbenes. In this work, we present a straight-forward approach for classifying and quantifying MO contributions to a particular metal–ligand interaction. Our approach utilizes the topology of MO density contributions to a cross-section of an inter-nuclear region, and is computationally inexpensive and applicable to symmetric and asymmetric complexes alike. We also apply the same approach with similar decompositions using Natural Bond Orbitals (NBO) and the recently developed Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) density decomposition scheme. In particular, FALDI analysis provides additional insights regarding the multi-centric nature of metal-carbene bonds without resorting to expensive multi-reference calculations.     

Solvent‐Modulated Influence of Intramolecular Hydrogen‐Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study

Intramolecular hydrogen‐bonding (H‐bonding) is commonly regarded as a major determinant of the conformation of (bio)molecules. However, in an aqueous environment, solvent‐exposed H‐bonds are likely to represent only a marginal (possibly adverse) conformational driving as well as steering force. For example, the hydroxymethyl rotamers of glucose and galactose permitting the formation of an intramolecular H‐bond with the adjacent hydroxyl group are not favored in water but, in the opposite, least populated. This is because the solvent‐exposed H‐bond is dielectrically screened as well as subject to intense H‐bonding competition by the water molecules. In the present study, the effect of a decrease in the solvent polarity on this rotameric equilibrium is probed using molecular dynamics simulation. This is done by considering six physical solvents (H₂O, DMSO , MeOH , CHC l₃, CC l₄, and vacuum), along with 19 artificial water‐like solvent models for which the dielectric permittivity and H‐bonding capacity can be modulated independently via a scaling of the O–H distance and of the atomic partial charges. In the high polarity solvents, the intramolecular H‐bond is observed, but arises as an opportunistic consequence of the proximity of the H‐bonding partners in a given rotameric state. Only when the polarity of the solvent is decreased does the intramolecular H‐bond start to induce a conformational pressure on the rotameric equilibrium. The artificial solvent series also reveals that the effects of the solvent permittivity and of its H‐bonding capacity mutually enhance each other, with a slightly larger influence of the permittivity. The hydroxymethyl conformation in hexopyranoses appears to be particularly sensitive to solvent‐polarity effects because the H‐bond involving the hydroxymethyl group is only one out of up to five H‐bonds capable of forming a network around the ring.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Substituent effect on structure,electron density,and intramolecular hydrogen bonding in nitroso‐oxime methane

Density functional calculations with Beck's three‐parameter hybrid method using the correlation functional of Lee, Yang, and Parr (B3LYP) were carried out for investigation of the intramolecular hydrogen bond strength in Nitroso‐oxime methane and its derivatives. Also, vibrational frequencies for them were calculated at the same level of theory. The π‐electron delocalization parameter (Q) and as a geometrical indicator of a local aromaticity, the geometry‐based harmonic oscillator measure of aromaticity index has been applied. Additionally, the linear correlation coefficients between substituent constants and selected parameters in R position have calculated. The obtained results show that the hydrogen bond strength is mainly governed by the resonance variations inside the chelate ring induced by the substituent groups. The topological properties of the electron density distributions for O? H ··· O intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Correlations between the H‐bond strength and topological parameters have been also studied. The electron density (ρ) and Laplacian (?²ρ) properties, estimated by AIM calculations, show that O ··· H bond have low ρ and negative (?²ρ) values (consistent with covalent character of the HBs), whereas O? H bond have positive (?²ρ) Furthermore, the analysis of hydrogen bond in this molecule and its derivatives by quantum theory of natural bond orbital (NBO) methods fairly support the ab initio results. Natural population analysis data, the electron density, and Laplacian properties as well as υ(O? H) and γ(O? H) were further used for estimation of the hydrogen bonding interactions and the forces driving their formation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Intramolecular hydrogen bonding in structural conformers of 2‐amino methylene malonaldehyde: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energies of 44 conformers of 2‐Amino methylene malonaldehyde were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set and AIM and NBO analysis. The calculated geometrical parameters and conformational analysis in gas phase show that the closed ring via intramolecular hydrogen bonded conformers of this compound are more stable than the other ones. Hydrogen bond energies for H‐bonded conformers were obtained from the related rotamers method (RRM) and Schuster method, and also the nature of H‐bonding of them has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. Delocalization effects can be identified from the presence of off diagonal elements of the Fock matrix in the NBO basis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Experimental and Theoretical Charge Density Study on Di‐2‐pyrazylamine (Hdpza) Molecule in Crystal

Electron density distribution of Di‐2‐pyrazylamine ( Hdpza ) is studied both by single‐crystal X‐ray diffraction method at 100K and theoretical calculation. Structural determination reveals that Hdpza molecules crystalize in a syn‐anti conformation with an intramolecular C? H?N hydrogen bond between two pyrazine rings and then gather together via two intermolecular N? H?N and C? H?N hydrogen interaction and π? π stacking interaction between pyrazine rings. Charge density analysis is made in terms of deformation density (Δπ), Laplacian distribution and topological analysis of total electron density based on multipole model and theoretical calculation. The agreement between experiment and theory is good. The topological properties at bond critical points of C? C and C? N bonds reveal a covalent bond character, and those of intermolecular interactions, such as hydrogen bonds and π? π stacking interactions, reveal a closed‐shell interaction. The potential energy curve of Hdpza molecule shows that the syn‐anti conformation is the most stable one (global minima) than the other two of syn‐syn and anti‐anti conformations.     

A new approach to counterpoise correction to BSSE

In the present work the intermolecular BSSE, associated to the A-B interaction, is obtained by subtracting the intramolecular BSSE of the fragments from the intramolecular BSSE of the supermolecule, and considering every atom as a fragment in the calculation of each intramolecular BSSE. This atom by atom scheme (CP(aa)) is based on the consideration that the proximity of the fragments may affect the intramolecular BSSE of every involved species, and artificially influences the value of the BSSE associated to the supermolecule formation. It drastically decreases the reported counterpoise overcorrection of the A-B interaction, even though it does not deal with all the overcorrection because it includes all the orbitals, and not only the unoccupied ones. This new approach has been tested on the water dimer, some hydrogen fluoride weakly bonded complexes, the conformational analysis of 1,2-dichloroethane, and the reaction profile of formaldehyde + OH reaction.     

A theoretical investigation on the structures,densities, detonation properties,and pyrolysis mechanism of the nitro derivatives of phenols

The nitro derivatives of phenols are optimized to obtain their molecular geometries and electronic structures at the DFT‐B3LYP/6‐31G* level. Detonation properties are evaluated using the modified Kamlet–Jacobs equations based on the calculated densities and heats of formation. It is found that there are good linear relationships between density, detonation velocity, detonation pressure, and the number of nitro and hydroxy groups. Thermal stability and pyrolysis mechanism of the title compounds are investigated by calculating the bond dissociation energies (BDEs) at the unrestricted B3LYP/6‐31G* level. The activation energies of H‐transfer reaction is smaller than the BDEs of all bonds and this illustrates that the pyrolysis of the title compounds may be started from breaking O? H bond followed by the isomerization reaction of H transfer. Moreover, the C? NO₂ bond with the smaller bond overlap population and the smaller BDE will also overlap may be before homolysis. According to the quantitative standard of energetics and stability as a high‐energy density compound, pentanitrophenol essentially satisfies this requirement. In addition, we have discussed the effect of the nitro and hydroxy groups on the static electronic structural parameters and the kinetic parameter. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Hydroxy‐Directed,Fluoride‐Catalyzed Epoxide Hydrosilylation for the Synthesis of 1,4‐Diols

A novel highly regioselective, fluoride‐catalyzed hydrosilylation of β‐hydroxy epoxides has been developed. The reaction is modular and applicable to the synthesis of a broad range of 1,4‐diols. Fluoride is crucial for two reasons: First, it promotes the formation of a silyl ether (which contains a Si‐H bond) and, second, it enables ring opening by an intramolecular S_N2 reaction through activation of the silane. The reaction can be performed under air.     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

F···HO intramolecular hydrogen bond as the main transmission mechanism for 1hJF,H(O) coupling constant in 2′‐fluoroflavonol

Flavonoids are useful compounds in medicinal chemistry and exhibit conformational isomerism, which is ruled by intramolecular interactions. One of the main intramolecular forces governing the stability of conformations is the hydrogen bond. Hydrogen bond involving fluorine covalently bonded to carbon has been found to be rare, but it appears in 2′‐fluoroflavonol, although the F···HO hydrogen bond cannot be considered the main effect governing the conformational stability of this compound. Because ¹⁹F is magnetically active and suitable for NMR studies, the ^1hJ_F,H(O) coupling constant can be used as a probe for such an interaction in 2′‐fluoroflavonol. In fact, the ^1hJ_F,H(O) coupling was computationally analyzed in this work, and the F···HO hydrogen bond was found to be its main transmission mechanism, which modulates this coupling in 2′‐fluoroflavonol, rather than overlap of proximate electronic clouds, such as in 2‐fluorophenol. Copyright © 2012 John Wiley & Sons, Ltd.     

Reinvestigation of intramolecular hydrogen bond in malonaldehyde derivatives: An ab initio,AIM and NBO study

The RAHB systems in malonaldehyde and its derivatives at MP2/ 6‐311++G(d,p) level of theory were studied and their intramolecular hydrogen bond energies by using the related rotamers method was obtained. The topological properties of electron density distribution in O? H···O intramolecular hydrogen bond have been analyzed in term of quantum theory of atoms in molecules (QTAIM). Correlations between the H‐bond strength and topological parameters are probed. The results of QTAIM clearly showed that the linear correlation between the electron density distribution at HB critical point and RAHB ring critical point with the corresponding hydrogen bond energies was obtained. Moreover, it was found a linear correlation between the electronic potential energy density, V(r_cp), and hydrogen bond energy which can be used as a simple equation for evaluation of HB energy in complex RAHB systems. Finally, the similar linear treatment between the geometrical parameters, such as O···O or O? H distance, and Lp(O)→σ*_OH charge transfer energy with the intramolecular hydrogen bond energy is observed. © 2010 Wiley Periodicals, Inc., Int J Quantum Chem, 2011     

An approach to estimate the energy and strength of the intramolecular hydrogen bond in different conformers of 4‐methylamino‐3‐penten‐2‐one

The molecular structure and intramolecular hydrogen bond energy of 32 conformers of 4‐methylamino‐3‐penten‐2‐one were investigated at MP2 and B3LYP levels of theory using the standard 6–31G** basis set and AIM analyses. Furthermore, calculations for all the possible conformations of 4‐methylamino‐3‐penten‐2‐one in water solution were also carried out at B3LYP/6–31G** level of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the ketoamine conformers of this compound are more stable than the other conformers (i.e., enolimine and ketoimine). This stability is mainly due to the formation of a strong N? H···O intramolecular hydrogen bond, which is assisted by π‐electrons resonance. Hydrogen bond energies for all conformers of 4‐methylamino‐3‐penten‐2‐one were obtained from the related rotamers method. The nature of intramolecular hydrogen bond existing within 4‐methylamino‐3‐penten‐2‐one has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. The results of these calculations support the results which obtained by related rotamers method. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Insights into the excited state intramolecular proton transfer process and mechanism of the novel 3‐hydroxythioflavone system: A theoretical study

It is well known that the molecular excited state dynamical process plays important roles in designing and developing novel applications. In this work, based on density functional theory and time‐dependent density functional theory methods, we theoretically explored a novel 3‐hydroxythioflavone (3HTF). Through calculating the electrostatic potential surface of the 3HTF structure, we confirm the formation of intramolecular hydrogen bonding O2‐H3···O4. Our theoretically obtained dominating bond lengths and bond angles involved in hydrogen bonds demonstrate that the intramolecular hydrogen bonds should be strengthened in the S₁ state. Coupling with the simulated infrared vibrational spectra, we further verify the enhanced hydrogen bonding O2‐H3···O4 in the S₁ state. Upon photoexcitation, we found that the charge transfer characteristics around hydrogen bonding moieties play important roles in facilitating the excited state intramolecular proton transfer (ESIPT) process. Via constructing potential energy curves in both S₀ and S₁ states, we confirm the almost nonbarrier ESIPT reaction should be an ultrafast process that further explains the previous experimental phenomenon. At last, we search the S₁‐state transition state (TS) structure along with ESIPT path, based on which we simulate the intrinsic reaction coordinate path that further confirms the ESIPT mechanism. We hope that our theoretical work could guide novel applications based on the 3HTF system in future.     

Tracing the Fingerprint of Chemical Bonds within the Electron Densities of Hydrocarbons: A Comparative Analysis of the Optimized and the Promolecule Densities

The equivalence of the molecular graphs emerging from the comparative analysis of the optimized and the promolecule electron densities in two hundred and twenty five unsubstituted hydrocarbons was recently demonstrated [Keyvani et al. Chem. Eur. J. 2016 , 22, 5003]. Thus, the molecular graph of an optimized molecular electron density is not shaped by the formation of the C?H and C?C bonds. In the present study, to trace the fingerprint of the C?H and C?C bonds in the electron densities of the same set of hydrocarbons, the amount of electron density and its Laplacian at the (3, ?1) critical points associated with these bonds are derived from both optimized and promolecule densities, and compared in a newly proposed comparative analysis. The analysis not only conforms to the qualitative picture of the electron density build up between two atoms upon formation of a bond in between, but also quantifies the resulting accumulation of the electron density at the (3, ?1) critical points. The comparative analysis also reveals a unified mode of density accumulation in the case of 2318 studied C?H bonds, but various modes of density accumulation are observed in the case of 1509 studied C?C bonds and they are classified into four groups. The four emerging groups do not always conform to the traditional classification based on the bond orders. Furthermore, four C?C bonds described as exotic bonds in previous studies, for example the inverted C?C bond in 1,1,1‐propellane, are naturally distinguished from the analysis.     

A metal-free approach to the synthesis of indoline derivatives by a phenyliodine(III) bis(trifluoroacetate)-mediated amidohydroxylation reaction

A novel approach to the synthesis of indoline derivatives is presented. The key cyclization step features the phenyliodine(III) bis(trifluoroacetate)- (PIFA-) mediated formation of a N-acylnitrenium ion and its succeeding intramolecular trapping by the olefin fragment. In addition, difunctionalization of the alkene moiety is achieved since the in situ generation of an additional hydroxy group at the terminal position of the original double bond accompanies the intramolecular C-N bond formation.     

Comparing Long‐Chain Branching Mechanisms for Ethylene Polymerization with Metallocenes and Other Single‐Site Catalysts: What Simulated Microstructures Can Teach Us

Three different long‐chain branch (LCB) formation mechanisms for ethylene polymerization with metallocenes in solution polymerization semi‐batch and continuous stirred‐tank reactors are modeled to predict the microstructure of the resulting polymer. The three mechanisms are terminal branching, C–H bond activation, and intramolecular random incorporation. Selected polymerization parameters are varied to observe how each mechanism affects polymer microstructure. Increasing the ethylene concentration during semi‐batch polymerization reduces the LCB frequency of polymers made with the terminal branching and intramolecular mechanisms, but has no effect on those made with the C–H bond activation mechanism, which disagrees with most previous data published in the literature. The intramolecular mechanism predicts that LCB frequencies hardly depend on polymerization time or ethylene conversion, which also disagrees with the published experimental data for these systems. For continuous polymerization reactors, experimental data relating polydispersity to LCB frequency can be well described with the terminal branching mechanism, but both C–H bond activation and intramolecular models fail to describe this experimental relationship. Therefore, detailed simulations confirm that the terminal branching mechanism is indeed the most likely mechanism for LCB formation when ethylene is polymerized with single‐site coordination catalysts such as metallocenes in solution polymerization reactors.