Intramolecular Interactions in 2-Aminoethanol and 3-Aminopropanol

Reactivity of Monoethanolamine at the Air-Water Interface and Implications for CO2 Capture

The development of CO2-capture technologies is key to mitigating climate change due to anthropogenic greenhouse gas emissions. These cover a number of technologies designed to reduce the level of CO2 emitted into the atmosphere or to eliminate CO2 from ambient air. In this context, amine-based sorbents in aqueous solutions are broadly used in most advanced separation techniques currently implemented in industrial applications. It has been reported that the gas/liquid interface plays an important role in the early stages of the capture process, but how the interface influences the chemistry is still a matter of debate. With the help of first-principles molecular dynamics simulations, we show that monoethanolamine (MEA), a prototypical sorbent molecule, has a weak affinity for the air-water interface, where in addition it exhibits a lower nucleophilicity compared to bulk solution. The change in reactivity is due to the combination of structural and electronic factors, namely, the shift of the conformational equilibrium and the stabilization of the N-atom lone pair. Based on these results, strategies for improving the efficiency of alkanolamine sorbents are proposed.

Dependence of Intramolecular Hydrogen Bond on Conformational Flexibility in Linear Aminoalcohols

Intramolecular hydrogen bonds (H-bonds) are abundant in physicochemical and biological processes. The strength of such interaction is governed by a subtle balance between conformational flexibility and steric effect that are often hard to predict. Herein, using linear aminoalcohols NH2(CH2)nOH (n = 2-5) as a model system, we demonstrated the dependence of intramolecular H-bond on the backbone chain length. With sensitive photoacoustic Raman spectroscopy (PARS), the gas-phase Raman spectra of aminoalcohols were measured in both N-H and O-H stretching regions at 298 and 338 K and explained with the aid of quantum chemistry calculations. For n = 2-4, two conformers corresponding to the O-H···N intramolecular H-bond and free OH were identified, whereas for n = 5, only the free-OH conformer was identified. Compared to free OH, a striking spectral dependence was observed for the intramolecular H-bonded conformer. According to the red shift of the OH-bonded band, the strongest intramolecular H-bond yields in n = 4, but the favorable chain length to form an intramolecular hydrogen bond at room temperature was observed in n = 3, which corresponds to a six-membered-ring in 3-aminopropanol. This is in good agreement with statistical analysis from the Cambridge Structural Database (CSD) that the intramolecular hydrogen bond is preferred when the six-membered ring is formed. Furthermore, combined with the calculated thermodynamic data at the MP2/aug-cc-pVTZ//M062X/6-311++G(d,p) level, the origin of decrease in intramolecular hydrogen-bond formation was ascribed to an unfavorable negative entropy contribution when the backbone chain is further getting longer, which results in the calculated Gibbs free energy optimum changing with increasing temperature from n = 4 (0-200 K) to n = 3 (200-400 K) and to n = 2 (above 400 K). These results will provide new insight into the nature of intramolecular hydrogen bonds at the molecular level and the application of intramolecular hydrogen bonds in rational drug design and supramolecular assembly.

Inductive Effects on Intramolecular Hydrogen Bond Strength: An Investigation of the Effect of an Electron-Withdrawing CF3 Group Adjacent to an Alcohol Hydrogen Bond Donor

This combined experimental and theoretical study seeks to determine the role that inductive effects have on hydrogen bonds by an investigation into the change in intramolecular hydrogen bond strength in 2-amino-1-trifluoromethylethanol (2ATFME) relative to that in 2-aminoethanol (2AE). Toward this end, the rotational spectra of the normal, 13C, and 15N isotopologues have been measured using Fourier transform microwave spectroscopy and fit to the rotational, quadrupole coupling, and centrifugal distortion constants of the Watson A-reduction Hamiltonian. Structural parameters used to characterize the strength of the intramolecular hydrogen bond have been determined from the experimental structures of both 2ATFME and 2AE as well as from MP2/6-311++G(d,p) calculations. A comparison of these parameters in 2ATFME with those of 2AE indicates that the electron-withdrawing trifluoromethyl CF3 group strengthens the hydrogen bond. These include a 4% decrease in the distance between the donor and acceptor heavy atoms of the hydrogen bond, a 6% increase toward linearity of the OH···N angle, and a 23% decrease of the COH···N torsional angle toward planarity in 2ATFME relative to 2AE. This trend toward increased intramolecular hydrogen bond strength in 2ATFME is also observed within the ab initio structures.

Tetrel Bonding in Anion Recognition: A First Principles Investigation

Twenty-five molecule-anion complex systems [I₄Tt···X^-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I₄Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I₄C···X^-] series and [I₄Tt···X^-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol^-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I₄Tt···X^-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.

Non-covalent interactions in molecular systems: thermodynamic evaluation of the hydrogen bond strength in aminoalcohols

In molecules with two functional groups that form hydrogen bonds, the structure-property relationship can depend significantly on the strength of intra-molecular hydrogen bonding. This bonding can cause a substantial conformational change that is accompanied by a frequency shift in the infrared spectrum, which provides the basis for experimental studies. Despite its great importance in biological systems, the available literature data for the strength of this bonding are scarce and not in agreement. In this work, we present the results of four thermodynamic methods for the determination of the strength of intramolecular hydrogen bonds. Comprehensive thermochemical analysis of 1-amino-2-alcohols and 2-amino-1-alcohols was performed with Fourier-transform infrared spectroscopy, high-level G4 quantum-chemical calculations, the homomorph scheme with enthalpies of vaporization and a group contribution method. With the combination of these four thermodynamic methods, the strength of intramolecular hydrogen bonding in 1,2-aminoalcohols and 2,1-aminoalcohols was evaluated quantitatively. The results were correlated with NBO parameters to find an explanation for the different strengths of intramolecular hydrogen bonds in total charge transfer and second order stabilization energies.

Lactic Acid Spectroscopy: Intra- and Intermolecular Interactions

Lactic acid, a relevant molecule in biology and the environment, is an α-hydroxy acid with a high propensity to form hydrogen bonds, both internally and to other hydrogen-bond-accepting molecules. This work includes the novel recording of infrared spectra of gas-phase lactic acid using Fourier transform infrared spectroscopy, and the vibrational absorption features of lactic acid are assigned with the aid of computationally simulated vibrational spectra with anharmonic corrections. Theoretical chemistry methods are used to relate intramolecular hydrogen-bond strengths to the relative stability of lactic acid conformers. The formation of hydrogen-bonded lactic acid dimers and 1:1 water complexes is investigated by simulated vibrational spectra and calculated thermodynamic parameters for the lactic acid monomer and dimer and its water complex in the gas phase. The results of this study are discussed in the context of environmental chemistry with an emphasis on indoor environments.

The Volumetric Source Function: Looking Inside van der Waals Interactions

The study of van der Waals interactions plays a central role in the understanding of bonding across a range of biological, chemical and physical phenomena. The presence of van der Waals interactions can be identified through analysis of the reduced density gradient, a fundamental parameter at the core of Density Functional Theory. An extension of Bader’s Quantum Theory of Atoms in Molecules is developed here through combination with the analysis of the reduced density gradient. Through this development, a new quantum chemical topological tool is presented: the volumetric source function. This technique allows insight into the atomic composition of van der Waals interactions, offering the first route towards applying the highly successful source function to these disperse interactions. A new algorithm has been implemented in the open-source code, CRITIC2, and tested on acetone, adipic and maleic acids molecular crystals, each stabilized by van der Waals interactions. This novel technique for studying van der Waals interactions at an atomic level offers unprecedented opportunities in the fundamental study of intermolecular interactions and molecular design for crystal engineering, drug design and bio-macromolecular processes.

Insight into the factors controlling the equilibrium of allylic azides

Several allylic azides with different double bond substitutions were studied to understand the factors, governing their equilibrium using density functional theory along with the quantum theory of atoms in molecules, non-covalent interactions and natural bond orbital approaches. The results showed that the hydroxyl group or heteroatoms in allylic azides interact with the molecule through an electrostatic weak interaction in each pair of regioisomers. The equilibrium shifts of substituted allylic azides, compared to non-substituted allylic azides, were not attributed to the presence of specific interactions, such as hydrogen bonds. The observed equilibrium shifts stemmed mainly from the strengthening and weakening of negative hyperconjugative interactions, which were affected by the weak interaction involving the proximal substituent in each regioisomer. A good linear correlation was obtained between the hyperconjugative energies of πC Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> C→σ*Z_b interactions and the calculated percentages of the secondary azide and tertiary azide in the equilibrium mixture. Also, the effect of the aromatic ring substituent was analysed using such approaches. This study not only provides insights into the factors controlling the stabilities of the substituted allylic azides, but also settles the basis to predict the regioisomer predominance in the equilibrium mixture.

The factors controlling the allyl azides equilibrium has been studied by different theoretical approaches setting the basis to predict the regioisomers predominance in the equilibrium mixture.

Interactions, electronic and optical properties of nanographene–peptide complexes: a theoretical study

We studied the interaction of planar phenylalanine (phe), tryptophan (try), tyrosine (tyr); amide asparagine (asn) and glutamine (gln); arginine (arg) side-chains, charged histidine (his-c) and charged lysine (lys-c) side-chains on a nanographene (g) surface by Density Functional theory (DFT) and Time Dependent Density Functional Theory (TDDFT). The occupied number of states by the system at each energy level and relative contribution of a particular atom/orbital has been studied by Density of States (DOS) and Partial Density of States (PDOS) respectively. Atom-in Molecules (AIM) analysis and non-covalent interaction (NCI) PLOT are used to study the interactions in these complexes. The absorption spectra and HOMO–LUMO (HL) gaps are quantitatively analysed to study the correlation between the optical properties of the studied complexes. The HL gap of peptides is larger than the HL gap of graphene–peptide complexes, indicating strong interactions. All the peptides interact from the above the nanographene surfaces. garg, glys-c, gtry and gtyr complexes have smaller bond distance as compared to gasn, ggln, ghis-c and gphe complexes. AIM analysis and (NCI) PLOT showed noncovalent interactions for these complexes. TDDFT calculations indicated the applicability of these complexes as biosensors.

We studied interactions of planar phenylalanine, tryptophan, tyrosine; amide asparagine and glutamine; arginine side-chains, charged histidine and charged lysine side-chains on a nanographene surface by density functional theory and time dependent density functional theory.

Dealing with Hydrogen Bonding on the Conformational Preference of 1,3-Aminopropanols: Experimental and Molecular Dynamics Approaches

This study expands the knowledge on the conformational preference of 1,3-amino alcohols in the gas phase and in solution. By employing Fourier transform infrared spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, density functional theory (DFT) calculations, quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) analysis, and molecular dynamics (MD), the compounds 3-aminopropan-1-ol (1), 3-methylaminopropan-1-ol (2), and 3-dimethylaminopropan-1-ol (3) are evaluated. The results show that the most stable conformation of each compound in the gas phase and in nonpolar solvents exhibited an O-H···N intramolecular hydrogen bond (IHB). Based on the experimental and theoretical OH-stretching frequencies, the IHB becomes stronger from 1 to 3. In addition, from the experimental NMR J-couplings, the IHB conformers are predominant in nonbasic solvents, representing 70-80% of the conformational equilibrium, while in basic solvents, such conformers only represent 10%. DFT calculations and QTAIM analysis in the gas phase support the occurrence of IHBs in these compounds. The MD simulation indicates that the non-hydrogen-bonded conformers are the lowest energy conformations in the solution because of molecular interactions with the solvent, while they are absent in the implicit solvation model based on density. NBO analysis suggests that methyl groups attached on the nitrogen atom affect the charge transfer energy involved in the IHB. This effect occurs mostly because of a decrease in the s-character of the LPN orbital along with weakening of the charge transfer from LPN to σ*OH, which is caused by an increase in the C-C-N bond angle.

Cis/Trans Energetics in Epoxide, Thiirane, Aziridine and Phosphirane Containing Cyclopentanols: Effects of Intramolecular OH⋯O, S, N and P Contacts

A recent computational analysis of the stabilizing intramolecular OH⋯O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the cis isomers are lowered by roughly 3 to 4 kcal mol⁻¹ when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. The results also suggest that S and P can participate in these stabilizing intramolecular interactions as effectively as O and N in constrained molecular environments. The stabilizing intramolecular OH⋯O, OH⋯S, OH⋯N and OH⋯P contacts also increase the covalent OH bond length and significantly decrease the OH stretching vibrational frequency in every system with shifts typically on the order of −41 cm⁻¹.

The chalcogen bond: can it be formed by oxygen?

This study theoretically investigates the possibility of oxygen-centered chalcogen bonding in several complexes. Shown in the graph is such a bonding scenario formed between the electrophile on O in OF₂ and the nucleophile on O in H₂CO.

Competing Intramolecular Hydrogen Bond Strengths and Intermolecular Interactions in the 4-Aminobutanol-Water Complex

We seek to determine the effect of competing intermolecular hydrogen bonds from water on the preferred conformation of 4-aminobutanol (4AB) monomers stabilized by intramolecular hydrogen bonds. Toward this end, the rotational spectrum of the 4-aminobutanol-H₂O complex was recorded using Fourier transform microwave spectroscopy and fit to the rotational, quadrupole coupling, and centrifugal distortion constants of the Watson S-reduction Hamiltonian. The experimental results are consistent with a 4AB-water complex that preserves the intramolecular hydrogen bond within the 4AB monomer and forms a single intermolecular bond with water acting as a donor. The experimental monomer structure agrees well with the lowest energy conformation calculated at the MP2/6-311++G(d,p) level of theory. Upon complex formation and the introduction of competing intermolecular bonds from water, only small changes in the OH···N intramolecular hydrogen bond and backbone torsional angles of the 4-aminobutanol monomer are observed. Similar small changes were observed for the shorter chain 3-aminopropanol amino alcohol monomer when complexed with water, in contrast to the 2-aminoethanol-H₂O complex. In the latter, a large change in the backbone torsional angle and a breaking of the intramolecular hydrogen bond were observed. Thus, extending the methylene chain results in an increase in the strength of the intramolecular hydrogen bond in unbranched amino alcohols.

A DFT assessment of some physical properties of iodine-centered halogen bonding and other non-covalent interactions in some experimentally reported crystal geometries

A set of six binary complexes that feature iodine-centered halogen bonding, extracted from structures deposited in the Cambridge Structure Database, has been examined computationally using density functional theory calculations with the M06-2X global hybrid, and dispersion corrected B3LYP-D3 and B97-D3, to determine their equilibrium geometries, binding energies and electronic properties. The results show that gas phase calculations are very informative in evaluating what occurs in the solid state, even though these calculations ignore the importance of lattice packing and counter ion effects. The calculated binding energies for the non-covalent interactions responsible for these complexes lie between -4.15 and -7.48 kcal mol-1 (M06-2X), which enables us to characterize them as weak-to-moderate in strength. The basis set superposition error energies are calculated to vary between 0.60 and 2.42 kcal mol-1 for all the complexes examined, even though an all-electron QZP basis set used in the analysis was of quadrupole-ζ (plus polarization) quality. Dispersion is found to have a profound effect on the binding energy of some of these complexes, and was estimated to be as large as 5.0 kcal mol-1. For one complex, the crystal geometry could not be precisely reproduced using a gas phase calculation. While both halogen- and hydrogen-bonding interactions were found competitive, they cooperate with each other to determine the stable configuration of the binary complex. The molecular electrostatic surface potential, quantum theory of atoms in molecules, and reduced density gradient non-covalent Interaction models were utilized to arrive at a fundamental understanding of the various inter- and intra-molecular molecular interactions involved, as well as some other previously-overlooked non-covalent interactions that emerge in the modelling.

Stereochemistry-dependent structure of hydrogen-bonded protonated dimers: the case of 1-amino-2-indanol

Stereochemistry effects on the structure of molecular aggregates are studied in the prototypical 1-amino-2-indanol. Conformer-selective IR-UV double resonance spectroscopy reveals how stereochemistry shapes its dimers.

Mechanistic Duality in Tertiary Amine Additions to Thermally Generated Hexadehydro-Diels-Alder Benzynes

Reported here are studies directed at understanding the mechanism of tertiary amine addition to hexadehydro-Diels-Alder (HDDA)-generated benzynes. Tertiary amines are presumed to engage benzynes by generation of a zwitterionic intermediate. Simple trialkylamines undergo intermolecular protonation by a protic nucleophile to give an aryl ammonium intermediate that is then dealkylated. Amines containing acidified β-protons undergo an intramolecular elimination to give the aniline and an alkene. Finally, amino alcohols react at either of their N- or O atoms, depending upon the extent of internal hydrogen bonding.

Trends of intramolecular hydrogen bonding in substituted alcohols: a deeper investigation

NBO analyses were used to perform a deeper investigation on the effects that drive IAHB strength in substituted acyclic alcohols.

Exploring short intramolecular interactions in alkylaromatic substrates

From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.

Absorption intensity changes and frequency shifts of fundamental and first overtone bands for OH stretching vibration of methanol upon methanol–pyridine complex formation in CCl4: analysis by NIR/IR spectroscopy and DFT calculations

The first overtone of the OH stretching mode of the OH–N hydrogen bond of the methanol–pyridine complex was observed.

Viscosity minima in binary mixtures of ionic liquids + molecular solvents

The viscosity (η) of four binary mixtures (ionic liquids plus molecular solvents, ILs+MSs) was measured in the 283.15 < T/K < 363.15 temperature range. Different IL/MS combinations were selected in such a way that the corresponding η(T) functions exhibit crossover temperatures at which both pure components present identical viscosity values. Consequently, most of the obtained mixture isotherms, η(x), exhibit clear viscosity minima in the studied T-x range. The results are interpreted using auxiliary molecular dynamics (MD) simulation data in order to correlate the observed η(T,x) trends with the interactions in each mixture, including the balance between electrostatic forces and hydrogen bonding.

Understanding the azeotropic diethyl carbonate-water mixture by structural and energetic characterization of DEC(H2O)(n) heteroclusters

Diethyl carbonate (DEC) is an oxygenated fuel additive. During its synthesis through a promising green process, a DEC-water azeotrope is formed, which decreases DEC production efficiency in the gas phase. Molecular information about this system is scarce but could be of benefit in understanding (and potentially improving) the synthetic process. Therefore, we report a detailed computational study of the conformers of DEC, and their microsolvation with up to four water molecules, with the goal of understanding the observed 1:3 DEC:H2O molar ratio. The most stable DEC conformers (with mutual energy differences < 1.5 kcal mol(-1)) contribute to the energetic and structural properties of the complexes. An exhaustive stochastic exploration of each potential energy surface of DEC-(H2O)n, (where n = 1, 2, 3, 4) heteroclusters discovered 3, 8, 7, and 4 heterodimers, heterotrimers, heterotetramers, and heteropentamers, respectively, at the MP2/6-311++G(d,p) level of theory. DEC conformers and energies of the most stable structures at each heterocluster size were refined using CCSD(T)/6-311++G(d,p). Energy decomposition, electron density topology, and cooperative effects analyses were carried out to determine the relationship between the geometrical features of the heteroclusters and the non-covalent interaction types responsible for their stabilization. Our findings show that electrostatic and exchange energies are responsible for heterocluster stabilization, and also suggest a mutual weakening among hydrogen bonds when more than three water molecules are present. All described results are complementary and suggest a structural and energetic explanation at the molecular level for the experimental molar ratio of 1:3 (DEC:H2O) for the DEC-water azeotrope.