Symmetry-adapted Perturbation Theory Analysis Research Articles

New Aspects of Alcohol-Alcohol and Alcohol-Water Interactions: Crystallographic and Quantum Chemical Studies of Antiparallel O-H/O-H Interactions.

New modes of interaction, antiparallel O-H/O-H interactions of alcohol-alcohol dimers and alcohol-water dimers, were studied by analyzing data in the Cambridge Structural Database (CSD) and by calculating potential energy surfaces at a very accurate quantum chemical CCSD(T)/CBS level. The data reveal the existence of antiparallel interactions in crystal structures and significant interaction energies. Data from the CSD for alcohol-alcohol dimers show 49.2% of contacts with classical hydrogen bonds and 10.1% of contacts with antiparallel interactions, while for alcohol-water dimers, 59.4% of contacts are classical hydrogen bonds and only 0.6% of contacts are antiparallel interactions. The calculations were performed on methanol, ethanol, and n-propanol dimers. Classical hydrogen-bonded alcohol-alcohol and alcohol-water dimers have interaction energies of up to -6.2 kcal/mol and up to -5.5 kcal/mol, respectively. Antiparallel interactions in alcohol-alcohol and alcohol-water dimers have interaction energies of up to -4.7 kcal/mol and up to -4.4 kcal/mol, respectively. Symmetry-adapted perturbation theory analysis for antiparallel interactions shows their electrostatic nature.

Binary conformers of a flexible, long-chain fluoroalcohol: dispersion controlled selectivity and relative abundances in a jet.

The complex conformational panorama of binary 4,4,4-trifluoro-1-butanol (TFB) aggregates was investigated using chirped-pulse Fourier transform microwave spectroscopy, aided by conformational searches using CREST (Conformer-Rotamer Ensemble Sampling Tool) and quantum chemistry calculations. From nearly 1500 initial dimer geometries, 16 most stable binary candidates were obtained within a relative energy window of ∼4 kJ mol-1. Rotational spectra of five binary conformers were experimentally observed in supersonic expansion and assigned. Interestingly, three out of the five observed binary conformers are composed solely of monomer conformers, which were not observed in their isolated gas phase forms in jet expansion. In addition, an observed dimer that is made exclusively of the most stable TFB monomer subunits does not correspond to the global minimum. The intricate kinetically and thermodynamically controlled dimer formation mechanisms are discussed, and a modified kinetic-thermodynamic model was developed, providing conformational abundances that are in good agreement with the experiment. Subsequent non-covalent interaction analyses reveal that the observed conformers are held together by one primary O-H⋯O hydrogen bond and secondary intermolecular C-H⋯O, C-H⋯F, and/or O-H⋯F interactions, as well as C-H⋯H-C London dispersion interactions between the methylene groups. Further symmetry-adapted perturbation theory analyses of the TFB dimer conformers and related alcohol dimers reveal a considerable rise in dispersion contributions with increasing n-alkyl carbon chain length and highlight the role of dispersion interactions in preferentially stabilizing the global minimum of the TFB dimer.

Rotational Spectroscopy Probes Lone Pair···π-Hole Interactions in Hexafluorobenzene-Tertiary Alkylamines Complexes.

We employed microwave spectroscopy to investigate the 1:1 complexes of hexafluorobenzene with trimethylamine and quinuclidine, respectively. These complexes exhibit a C3v symmetry and are stabilized by nitrogen lone pair···π-hole interactions along the C3 axes. The N···π-center distances were determined to be 3.110(1) and 3.040(2) Å, respectively, which are shorter than that of hexafluorobenzene-ammonia at 3.2685(3) Å. Additionally, the strength of the intermolecular interaction increases with cluster size. While it was initially expected that the electron-donating effect of alkyl groups was responsible for changing the N···π interaction, the symmetry-adapted perturbation theory analysis revealed that, from hexafluorobenzene-ammonia to both hexafluorobenzene-alkylamines, electrostatic interaction actually decreases while dispersion interaction increases and becomes dominant. Interestingly, dispersion interaction decreases while electrostatic interaction increases from C6F6-N(CH3)3 to C6F6-NC7H13. The splitting pattern of the spectra indicates hexafluorobenzene rotates freely relative to its partners along the axis of the N···π-hole interactions.

Probing the n → π* carbonyl-carbonyl interactions in the formaldehyde-trifluoroacetone dimer by rotational spectroscopy.

The non-covalent bonding features of carbonyl-carbonyl interactions have been investigated in the dimer of formaldehyde and trifluoroacetone using high resolution rotational spectroscopy combined with quantum chemical calculations. The observation of all possible isotopic substitutions for the heavy atoms in the complex enabled the determination of the accurate structure, characterized by the antiparallel arrangement of the two C=O bonds. The two moieties are connected through a dominant n → π* interaction enhanced by one weak C-H⋯O hydrogen bond, as revealed by supporting natural bond orbital analysis and symmetry-adapted perturbation theory analysis. Further computational investigations on 17 related adducts stabilized by carbonyl-carbonyl n → π* interactions show how the interaction strength is regulated by the incorporation of either electron-donating or withdrawing functional groups.

Conformations and non-covalent interactions of cyclohexyl isothiocyanate and its water complex

The conformational equilibria of cyclohexyl isothiocyanate and its complex with water were studied by microwave spectroscopy combined with theoretical calculations. For the bare cyclohexyl isothiocyanate, the rotational spectra of the two conformers, namely a-trans and e-trans, were measured and analyzed. Additional mono-substituted isotopologues of two 13C and one 34S of a-trans and e-trans were also measured, which result in an accurate structural determination of the two conformers. For the binary complex with water, the rotational spectra were measured for the monohydrates of both a-trans and e-trans conformers. Water isotopologues were also detected for the monohydrates. All the measured rotational spectra show 14N quadrupole coupling hyperfine structures. Water molecule prefers linking to the isothiocyanate group through a OwH⋯S hydrogen bond and forming two CH⋯Ow hydrogen bonds with the oxygen atom of water acting as a proton acceptor. The non-covalent bonding features of the monohydrates were revealed by natural bond orbital analysis and symmetry-adapted perturbation theory analysis.

Energy property and covalency of H2S···X (X = N2, CO, CS and SiO) hydrogen bond

CCSD(T) calculations on H2S…X (X = N2, CO, CS and SiO) series provide reliable structures, energy properties and covalency of hydrogen bonds (HB). Symmetry adapted perturbation theory analysis demonstrates the dominant role of electrostatic interactions for the relative stronger HBs; and the dispersion demonstrates the attraction of the very weak HB of H2S…N2. Upon formation of HBs, the electrostatic and dispersion energies play important role. The covalent character is analyzed by AIM theory and topological analysis on electron density functions; and it suggests the very weak strength of HBs with non-covalent character.

A Theoretical Study of the Halogen Bond between Heteronuclear Halogen and Benzene.

Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied using density functional theory. The structures of the complexes between heteronuclear halogen and benzene have Cs symmetry. The interaction energies of the complexes between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene range from -27.80 to -37.18 kJ/mol, increasing with the increases in the polarity between the atoms of X and D, and are proportional to the angles of a between the Z axis and the covalent bond of heteronuclear halogen. The electron density (ρ) and corresponding Laplacian (∇2ρ) values indicate that the interaction of the heteronuclear halogen and benzene is a typical long-range weak interaction similar to a hydrogen bond. Independent gradient model analysis suggests that the van der Waals is the main interaction between the complexes of heteronuclear halogen and benzene. Symmetry-adapted perturbation theory analysis suggests that the electrostatic interaction is the dominant part in the complexes of C6H6⋯ClF, C6H6⋯ICl, C6H6⋯BrF and C6H6⋯IF, and the dispersion interaction is the main part in the complexes of C6H6⋯BrCl, C6H6⋯IBr.

Noncovalent Interactions between Aromatic Heterocycles and Carboxylic Acids: Rotational Spectroscopy of the Furan-Formic Acid and Thiophene-Formic Acid Complexes.

The binary molecular complexes formed between the aromatic heterocycles furan and thiophene with formic acid were investigated using pulsed-jet Fourier transform microwave spectroscopy and quantum chemical computations. For both of the complexes, rotational spectra of the lowest energy isomer were detected and assigned. Rotational spectroscopic results and density functional theory calculations support that the preferred conformation of the furan-formic acid complex is characterized by a relatively strong O-H···O and a weak C-H···O hydrogen bonds while the O-H···π and C-H···O hydrogen bonds stabilize the thiophene-formic acid complex. Natural bond orbital analysis further proves the experimental observation, suggesting that the strength of the O-H···O(furan) interaction is about two times stronger than that of O-H···π(thiophene). The symmetry adapted perturbation theory analysis reveals that electrostatic interaction is dominant in stabilizing the two complexes and that dispersion becomes significant in the thiophene-formic acid complex compared to furan-formic acid.

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives.

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car–Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion—the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.

Theoretical investigations of the interaction between B9N9 ring and nine adamantane derivatives

Nine adamantane derivatives’ interaction on B9N9 was systematically studied by using quantum chemistry techniques at the ωb97xd/def2tzvp level. We investigated the effect of the interaction of nine unimolecular and dimolecular adamantane derivatives on B9N9 in both vacuum and solvent (water, CCl4) environments by calculating bond distance, interaction energy, density of states, and frontier molecular orbitals and by performing charge and electrostatic-potential analyses. The most notable feature is the different interaction behaviors between the B9N9 ring and the nine adamantane derivatives. Second-order symmetry-adapted perturbation theory analysis was performed to quantify the nature of interactions. Our investigations establish the high potential of boron nitride ring compounds for use in drug transport.

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids.

The lone-pair···π (lp···π) (deoxy)ribose···nucleobase stacking is a recurring interaction in Z-DNA and RNAs that is characterized by sub-van der Waals lp···π contacts (<3.0 Å). It is a part of the structural signature of CpG Z-step motifs in Z-DNA and r(UNCG) tetraloops that are known to behave poorly in molecular dynamics (MD) simulations. Although the exact origin of the MD simulation issues remains unclear, a significant part of the problem might be due to an imbalanced description of nonbonded interactions, including the characteristic lp···π stacking. To gain insights into the links between lp···π stacking and MD, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the nonbonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, and U). Among other differences, we found that the AFF overestimates the DHDF-D3 lp···π distances by ∼0.1-0.2 Å, while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule polarizabilities and symmetry-adapted perturbation theory analysis, we inferred that the DHDF-D3 versus AFF differences partly originate in identical nucleobase carbon atom Lennard-Jones (LJ) parameters despite the presence/absence of connected electron-withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp···π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.

Prediction of the Liquid-Liquid Extraction Properties of Imidazolium-Based Ionic Liquids for the Extraction of Aromatics from Aliphatics.

Liquid-liquid extraction (LLE) is an important technique to separate aromatics from aliphatics since these compounds have very similar boiling points and cannot be separated by distillation. Ionic liquids (ILs) are considered as potential extractants to extract aromatics from aliphatics. In this paper, molecular dynamics (MD) simulations were used to predict the extraction property (i.e., capacity and selectivity) of ILs for the LLE of aromatics from aliphatics. The extraction properties of seven different ILs including [C2mim][Tf2N], [C2mim][TFO], [C2mim][SCN], [C2mim][DCA], [C2mim][TCM], [C4mim][Tf2N], and [C8mim][Tf2N] were investigated. Results show that ILs with shorter alkyl chain cations and [Tf2N]- anion exhibit better extraction efficiency than other ILs, which is in agreement with previously reported experimental data on the extraction of toluene from aliphatics and further validated the reliability of the proposed model. The binding energies between ILs and organic molecules were calculated by the density functional theory, which help explain the different extraction behaviors of different ILs. The symmetry-adapted perturbation theory analysis was performed to further understand the interaction mechanisms between ILs and organics. Our study shows that the [Tf2N]- anion also has the best extraction capability for heavier aromatics (o-xylene, m-xylene, and p-xylene) from common aliphatics (heptane and octane). The MD modeling approach can be a low-cost in silico tool for the high-throughput fast screening of ILs for the LLE of aromatics from aliphatics.

Characterization of Large-Amplitude Motions and Hydrogen Bonding Interactions in the Thiophene-Water Complex by Rotational Spectroscopy.

The rotational fingerprint of the thiophene-water complex was investigated for the first time using Fourier transform microwave spectroscopy (7-20 GHz) aided by quantum mechanical calculations. Transitions for a single species were observed, and the rotational constants for the parent and 18O isotopomers are consistent with a geometry that is highly averaged over a barrierless large-amplitude motion of water that interconverts two equivalent forms corresponding to the global minimum (B2PLYP-D3(BJ)/def2-TZVP). In this effective geometry, the water lies above the thiophene ring close to its σv plane of symmetry. The observed transitions are split by a second water-centered tunneling motion that exchanges its two protons by internal rotation about its C2 axis with a calculated barrier of ∼2.7 kJ mol-1 (B2PLYP-D3(BJ)/def2-TZVP). Based on quantum theory of atoms in molecules, noncovalent interaction, and symmetry-adapted perturbation theory analyses, the observed geometry enables two intermolecular interactions (O-H···π and O-H···S) whose electrostatic and dispersive contributions favor formation of the thiophene-water complex.

Van der Waals interactions of the disulfide bond revealed: A microwave spectroscopic study of the diethyl disulfide-argon complex.

The van der Waals complex formed between diethyl disulfide (DEDS) and an argon atom was investigated by pulsed-jet Fourier transform microwave spectroscopy in conjunction with quantum chemical computations. One set of transition lines belonging to the configuration of the global potential energy minimum was measured and assigned. The rotational constants A, B, and C were accurately determined to be 1262.5758(1) MHz, 845.402 12(9) MHz, and 574.006 38(8) MHz, respectively. The distance between the argon atom and the center of mass of the DEDS subunit is 4.075(16) Å. Quantum theory of atoms in molecules and non-covalent interaction analyses reveal that the interactions take place between the argon atom and four sites of the DEDS subunit. Furthermore, the usage of the energy decomposition analysis approach provides further understanding of the characteristics of the van der Waals interactions. Additionally, ab initio calculations and symmetry-adapted perturbation theory analysis of the binary complexes of DEDS with He, Ne, Kr, and Xe atoms were carried out to get further insight into the characteristics of the van der Waal interactions of the disulfide bond.

On the nature of inter- and intramolecular interactions involving benzo[h]quinoline and 10-hydroxybenzo[h]quinoline: Electronic ground state vs excited state study

The inter- and intramolecular interactions of benzo[h]quinoline and 10-hydroxybenzo[h]quinoline have been studied using quantum-chemical methods. Here, we report on results of monomeric and dimeric forms obtained on the basis of Density Functional Theory (DFT) in its classical formulation as well as using its Time-Dependent extension (TD-DFT). The simulations were performed in the gas phase and with solvent reaction field using toluene and acetonitrile as solvents. Symmetry-Adapted Perturbation Theory (SAPT) and Atoms in Molecules (AIM) were employed to characterize interactions and forces present in the studied compounds with special attention paid to the presence of inter- and intramolecular hydrogen bonds. It was found that spontaneous proton transfer phenomenon was not preferable in the electronic ground state. However it was noticed in the excited electronic state. The presence of the polar environment lowers the energy profile of the proton reaction path and slightly influences the electronic structure and aromaticity of the compounds. The results of the SAPT analysis showed that the O-H... N intermolecular hydrogen bond in the dimer 1 is only ca. twice stronger than the C-H... O and C-H... π contact present in the dimers formed by 10-hydroxybenzo[h]quinoline.

The nature of the intermolecular interaction in (H2X)2 (X = O, S, Se).

Hydrogen bonds (HBs) are crucial non-covalent interactions in chemistry. Recently, the occurrence of an HB in (H2S)2 has been reported (Arunan et al., Angew. Chem., Int. Ed., 2018, 57, 15199), challenging the textbook view of H2S dimers as mere van der Waals clusters. We herein try to shed light on the nature of the intermolecular interactions in the H2O, H2S, and H2Se dimers via correlated electronic structure calculations, Symmetry Adapted Perturbation Theory (SAPT) and Quantum Chemical Topology (QCT). Although (H2S)2 and (H2Se)2 meet some of the criteria for the occurrence of an HB, potential energy curves as well as SAPT and QCT analyses indicate that the nature of the interaction in (H2O)2 is substantially different (e.g. more anisotropic) from that in (H2S)2 and (H2Se)2. QCT reveals that the HB in (H2O)2 includes substantial covalent, dispersion and electrostatic contributions, while the last-mentioned component plays only a minor role in (H2S)2 and (H2Se)2. The major contributions to the interactions of the dimers of H2S and H2Se are covalency and dispersion as revealed by the exchange-correlation components of QCT energy partitions. The picture yielded by SAPT is somewhat different but compatible with that offered by QCT. Overall, our results indicate that neither (H2S)2 nor (H2Se)2 are hydrogen-bonded systems, showing how the nature of intermolecular contacts involving hydrogen atoms evolves in a group down the periodic table.

Weak hydrogen bonds between alkyl halides and amides: The microwave spectroscopic and theoretical study of the difluoromethane⋯formamide complex.

The pure rotational spectrum of the complex of difluoromethane with formamide was investigated by means of microwave spectroscopy supplemented with theoretical calculations. The hyperfine structure arising from the 14N nuclear quadrupole coupling effect was completely resolved. The most stable isomer that displays the Cs symmetry with the ∠HCH angle of difluoromethane being bisected by the ab-plane of formamide was detected. The two moieties in the detected isomer are connected via one N-H⋯F and one bifurcated CH2⋯O weak hydrogen bonds confirmed by the non-covalent interaction plot and natural bond orbital analyses. The distances of the NH⋯F and CH2⋯O interactions were determined to be 2.140(14) Å and 2.749(14) Å, respectively. The NH⋯F bond angle was determined to be 150.7°. Symmetry-adapted perturbation theory analysis indicates that the electrostatic component is the largest contributor to the total attractive interaction energy of the difluoromethane⋯formamide complex.

The rotational spectrum of acetophenone-CO2: Preferred non-covalent interactions.

The rotational spectrum of the acetophenone-CO2 complex was investigated by pulsed jet-expansion Fourier transform microwave spectroscopy combined with ab initio calculations. In the supersonically cooled jet, only one isomer has been observed which is characterized by a dominant (CO2)C···O tetrel bond and a secondary (C-H)methyl∙∙∙O weak hydrogen bond. Johnson's non-covalent interaction, Bader's quantum theory of atoms in molecules and Symmetry-Adapted Perturbation Theory analyses have been applied to understand better the nature of non-covalent interactions in the acetophenone-CO2 complex.

Cooperativity of hydrogen bonding network in microsolvated biotin, the ligand of avidin class proteins.

Biotin is well known to be bound with exceptional strength by the avidin class of proteins. This ability comes from a match between the biotin-binding pocket of the protein and the structural elements of biotin, including its ureido and thiolane rings. Here we investigate the solvation shell of biotin in water as revealed by classical force field molecular dynamics with GAFF force field. Snapshots from the classical molecular dynamics were then used to generate microsolvated structures. Details of hydrogen bonding patterns present in these microsolvated structures were studied by symmetry-adapted perturbation theory (SAPT). Interaction energy values for small models of biotin hydrated by 5 or 6 water molecules show that the cooperativity constitutes 15-22% of the total interaction energy and corresponds roughly to formation of one additional hydrogen bond to biotin. The SAPT analysis shows the differences underlying hydrogen bonds of similar strength (with oxygen or sulfur atoms as the hydrogen bond acceptors, and with nitrogen atom playing a dual role of the donor and acceptor).

Structure and non-covalent interactions of 1,3-difluoropropane and its complex with water explored by rotational spectroscopy and quantum chemical calculations.

1,3-difluoropropane and its complex with water were characterized by using Fourier transform microwave spectroscopy with the aid of quantum chemical calculations. Rotational spectra of the monomer were extended to the 13C isotopologues which lead to a precise structural determination of the two observed conformers. For the 1,3-difluoropropane-water complex, the most stable isomer has been observed and assigned in the supersonic jet expansion. In the observed isomer, water acts as a proton donor and a proton acceptor forming one O-H⋯F weak hydrogen bond and two C-H⋯O weak hydrogen bonds, respectively. The measurements on the three 13C, 18O, and deuterated water allowed determination of the skeleton structure and evaluation of the weak hydrogen bond parameters. Quantum theory of atoms in molecules, non-covalent interaction, and symmetry-adapted perturbation theory analyses were performed to reveal the nature of the intermolecular non-covalent interactions.