Molecular Electron Density Topography Research Articles

Deconvolution of conformational equilibria in methimazolium-based ionic liquid ion pair: Infrared spectroscopic and computational study

Deconvolution of conformational equilibria in ionic liquids is a challenging task. Infrared spectroscopy coupled with computational simulations is a powerful tool to characterize the interactions and conformational equilibria in ionic liquids. Herein, this approach is employed to study methimazolium-based ionic liquids. Electronic, structural and vibrational properties of the ion pair consisting of a methimazolium cation and a bis(trifluoromethanesulfonyl)imide (Tf2N) anion are analyzed via the density functional theory (DFT) method using the hybrid B3LYP functional, while experimental IR study is performed for the corresponding bulk ionic liquid. DFT predicts that two lowest energy conformers are nearly degenerate in energy, suggesting that both structures are present in the bulk phase. Two intense peaks at 2848 cm−1 and 2915 cm−1 in the IR spectrum—which are assigned to the cation NH stretching vibrations of the two lowest-energy conformers—lend experimental support to this interpretation. Natural bond analysis and molecular electron density topography are used to understand the frequency shifts of the normal vibrations, especially those of the anion.

Structure and electronic properties of ion pairs accompanying cyclic morpholinium cation and alkylphosphite anion based ionic liquids

Molecular insights for the formation of ion pairs accompanying the cyclic ammonium cation based room temperature ionic liquids (RTILs) composed of alkyl substituted N-methylmorpholinium (RMMor) and alkylphosphite [(RO)2PHO] (Rethyl, butyl, hexyl, octyl) anion have been derived from the M06-2x level of theory. Electronic structures, binding energies, and spectral characteristics of the ion pairs underlying these RTILs have been characterized. The ion pair formation is largely governed by CH⋯O and other intermolecular interactions. Calculated binding energies increase with the increasing alkyl chain on either cation or alkylphosphite anion. The cation-anion binding reveals signature in the frequency down-(red) shift of the characteristic anionic PO stretching whereas the PH stretching exhibits a shift in the opposite direction in vibrational spectra which has further been rationalized through molecular electron density topography. Correlations of measured electrochemical stability with the separation of frontier orbital energies and binding energies in the ion pairs have further been established.

A computational study on structure and bonding in ion pairs accompanying pyrrolidinium and piperidinium based ionic liquids

Noncovalent interactions accompanying the cyclic ammonium based ionic liquids composed of alkyl substituted N-methylpyrrolidium (RMPyr) or N-methylpiperidium (RMPip) cations and alkylphosphite [(R–O)2PH=O] (R=ethyl, butyl, hexyl, octyl) anion have been analyzed employing the dispersion corrected density functional theory. Electronic structures, binding energies, vibrational as well as 1H NMR spectra of the ion pairs underlying these room temperature ionic liquids (RTILs) are characterized. It has been demonstrated that ion pair formation is largely governed by C–H⋯O interactions between the anionic oxygens and methylene or alkyl group protons of the cation as well as other weak intermolecular interactions. Calculated binding energies increase with the increasing alkyl chain (from ethyl to octyl) on either cation or alkylphosphite anion. The cation-anion binding reveals signature in the frequency down-(red) shift of characteristics P=O stretching whereas the P–H stretching exhibits a shift in the opposite direction in their vibrational spectra. A largest downshift of 52cm−1 was predicted for the P=O stretching in ethyl substituted [MPyr] ion pairs. The direction of such frequency shifts has been rationalized through molecular electron density topography and corroborated further by natural bond orbital analyses. It has been demonstrated that the separation of frontier orbital energies in the ion pairs correlate well with ionic conductivities measured from the experiments.

TfOH Catalyzed [3+2] Cycloaddition of Cyclopropane 1,1‐Diesters with Nitriles: A Density Functional Study

AbstractThe mechanistic pathways for TfOH catalyzed [3+2] cycloaddition reaction between cyclopropane 1, 1 diesters and MeCN has been investigated using density functional theory. The study sheds light on selective synthesis of 1‐pyrroline or γ‐lactone derivatives in two different reaction conditions. Analysis of global reactivity descriptors in the solvent free medium predicts the protonated cyclopropane 1,1 diesters and MeCN as strong electrophile and nucleophile respectively, favoring intermolecular reaction to give 1‐pyrroline derivative as the product. On the other hand, the presence of solvent environment with DCM solvent significantly supresses this nature of the two molecules to undergo intermolecular reaction. Protonated cyclopropane 1,1 diester, therefore, prefers intramolecular rearrangement to yield γ‐lactone. While the synthesis of 1‐pyrroline derivative follows pathway involving a transition state showing weak interaction between two reactants, γ‐lactone synthesis undergo mechanism preferring initial cyclopropane ring opening transition state. Molecular electron density topography yield support to the proposed mechanism.

Hydrogen Bonding, (1)H NMR, and Molecular Electron Density Topographical Characteristics of Ionic Liquids Based on Amino Acid Cations and Their Ester Derivatives.

Amino acid ionic liquids (AAILs) have attracted significant attention in the recent literature owing to their ubiquitous applications in diversifying areas of modern chemistry, materials science, and biosciences. The present work focuses on unraveling the molecular interactions underlying AAILs. Electronic structures of ion pairs consisting of amino acid cations ([AA(+)], AA = Gly, Ala, Val, Leu, Ile, Pro, Ser, Thr) and their ester substituted derivatives [AAE(+)] interacting with nitrate anion [NO3(-)] have been obtained from the dispersion corrected M06-2x density functional theory. The formation of ion pair is accompanied by the transfer of proton from quaternary nitrogen to anion facilitated via hydrogen bonding. The [Ile], [Pro], [Ser], and [Thr] and their esters reveal relatively strong inter- as well as intramolecular hydrogen-bonding interactions. Consequently, the hierarchy in binding energies of [AA][NO3] ion pairs and their ester analogues turns out to be [Gly] > [Ala] > [Ser] ∼ [Val] ∼ [Ile] > [Leu] ∼ [Thr] > [Pro]. The work underlines how the interplay of intra- as well as intermolecular hydrogen-bonding interactions in [AA]- and [AAE]-based ILs manifest in their infrared and (1)H NMR spectra. Substitution of -OCH3 functional group in [AA][NO3] ILs lowers the melting point attributed to weaker hydrogen-bonding interactions, making them suitable for room temperature applications. As opposed to gas phase structures, the presence of solvent (DMSO) does not bring about any proton transfer in the ion pairs or their ester analogues. Calculated (1)H NMR chemical shifts of the solvated structures agree well with those from experiment. Correlations of decomposition temperatures in [AA]- and [AAE]-based ILs with binding energies and electron densities at the bond critical point(s) in molecular electron density topography, have been established.

Encapsulation of alkyl and aryl derivatives of quaternary ammonium cations within cucurbit[n]uril (n = 6,7) and their inverted diastereomers: density functional investigations

Electronic structure, vibrational frequencies, and ¹H chemical shifts of inclusion complexes between CB[n] (n = 6,7) or their inverted iCB[n] diastereomer hosts and quaternary diammonium viz., 1,6-hexyldiammonium (HDA) or p-xylyldiammonium (XYL) cationic guests are obtained from the density functional calculations. The interaction of CB[n] or iCB[n] with HDA (guest) conduce inclusion complexes in which the guest attains gauche conformation within the host cavity. The lowest energy XYL complexes of CB[6] or iCB[6] are comprised of one ammonium group orienting parallel to aromatic ring. The CB[7] or iCB[7] complexes of XYL on the other hand, reveal ammonium group(s) perpendicular to aromatic ring of the guest. The ureido C=O and N--H stretching vibrations on complexation engender frequency down-shift in the calculated spectra. This can be attributed to C--H-- --O and N--H-- --O interactions in the complex. The inverting of glycouril unit in iCB[n] renders a frequency shift (12 cm⁻¹) for the C=O stretching in the opposite direction. Molecular electron density topography and natural bond orbital analyses have been used to explain the direction of frequency shifts. Calculated ¹H NMR reveal that guest protons within the host cavity not participating in hydrogen bonding interactions, exhibit shielded signals compared to isolated XYL or HDA. Likewise the inverted protons in the iCB[6]-XYL complex led to up-field signals in calculated ¹H NMR as a result of C-H-- -π interactions.

Hydrogen bond studies in substituted imino-acetaldehyde oxime

The intramolecular hydrogen bond, molecular structure and vibrational frequencies of imino-acetaldehyde oxime and its twelve derivatives have been investigated by means of density functional (DFT) method with 6-311++G∗∗ basis set. The nature of these interactions, known as resonance assisted hydrogen bonds, has been discussed. As a geometrical indicator of a local aromaticity, the geometry-based HOMA index has been applied. Additionally the linear correlation coefficients between substituent constants and selected parameters in R position have been calculated. The 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 OH⋯N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIMs). Furthermore, calculated 1H NMR chemical shifts (δH) correlate well with the hydrogen-bond distance as well as electron density at the bond and ring critical points in the molecular electron density topography. Finally, the natural population analysis method has been used to evaluate the hydrogen bonding interactions.

Electronic Structure and Normal Vibrations of the 1-Ethyl-3-methylimidazolium Ethyl Sulfate Ion Pair

Electronic and structural properties of the ion pair 1-ethyl-3-methylimidazolium ethyl sulfate are studied using density functional methods. Three locally stable conformers of the ion pair complex are considered to analyze molecular interactions between its cation and anion. Manifestations of these interactions in the vibrational spectra are discussed and compared with experimental IR and Raman spectroscopy data. NBO analysis and difference electron density coupled with molecular electron density topography are used to interpret the frequency shifts of the normal vibrations of the ion pair, compared to the free anion and cation. Excitation energies of low-lying singlet excited states of the conformers are also studied. The density functional theory results are found to be in a reasonable agreement with experimental UV/vis absorption spectra.

Structure and normal vibrations in xanthine and its methyl derivatives from first principle calculations

Structure and vibrational characteristics of biologically important 3,7-dihydro-purine-2,6-dione (xanthine) and its 7- or 9-substituted methyl derivatives derived from the second order MØller–Plesset perturbation theory have been analyzed using the molecular electron density (MED) topography. Successive substitution of methyl group at 9 position engender carbonyl stretching vibrations at higher wavenumber compared to those in X 7 tautomer along the series. The C–O bond distance in 7-substituted xanthine tautomers correlate well to electron density at the bond critical point (bcp) in the MED topography.

Electronic Structure and Normal Vibrations in (+)-Catechin and (−)-Epicatechin Encapsulated β-Cyclodextrin

Host-guest interactions between beta-cyclodextrin (beta-CD) and flavan-3-Ol enantiomers (guest) namely, (+)-catechin (CA) or (-)-epicatechin (EC), have been analyzed within the framework of density functional theory. Both CA and EC consist of two phenol rings, I and II, and a pyran ring, III, which facilitate a variety of binding patterns with the host, beta-CD. The minimum energy beta-CD-CA complex reveals that ring II of CA interacts with primary hydroxyls of the upper rim and the phenol ring I engenders hydrogen-bonded interactions with secondary hydroxyl from the lower rim of CD. On the other hand, the O-H...O interactions between ring I and primary hydroxyls of beta-CD along with those between one of hydroxyl of ring II and secondary hydroxyl of the host render large stability to the beta-CD-EC complex. Structures of both beta-CD-CA and beta-CD-EC complexes thus obtained are in consonant with those inferred from the experimental NMR data and exhibit distinct features in infrared spectra. The frequency shifts of characteristic vibrations in infrared spectra of these complexes compared to the unbound individual host or guest in its free state have been analyzed with the use of natural bond orbital analyses and combining difference electron density maps with bond critical points in molecular electron density topography.

Structure and vibrational spectra of sulfur hexafluoride encapsulated α-cyclodextrin

Density functional calculations have been utilized to understand the interactions of sulfur hexafluoride (SF 6) with α-cyclodextrin (α-CD) host. An encapsulation of SF 6 (guest) within the host cavity and its binding to primary as well as secondary hydroxyl rims of α-CD exhibiting different hydrogen bonding patterns have been analyzed. The present calculations have shown that interactions between the guest and protons within the host cavity yield the minimum energy complex wherein guest penetrates from secondary hydroxyl end of the host. Calculated vibrational spectra reveal frequency downshift of S–F stretching in the guest molecule on complexation. Frequency shift in opposite direction has been noticed for O–H vibrations of secondary hydroxyls of the host those facilitate relatively strong hydrogen bonded interactions. These inferences have been supported by mapping difference molecular electron density on the bond critical points in molecular electron density topography. The electronic structure and vibrational spectra derived from the density functional calculations based on the B3LYP and the X3LYP functional are similar. Use of X3LYP functional however, predicts shortening of O6H⋯O6′ as well as CH⋯F hydrogen bonds and thus points to the strengthened host–guest interactions and in turn binding energies of SF 6 within these complexes employing the X3LYP functional turn out to be nearly ∼35–40% higher compared to those obtained within the framework of B3LYP theory.

Alkali metals (Li, Na, and K) in methyl phosphodiester hydrolysis

The phosphodiester linkage central to biological systems has been modeled by methyl phosphodiester (MPDE) in various theoretical and experimental studies. Under physiological conditions, hydrolysis of the phosphodiester is negligible, however this process can be catalyzed in the presence of metal ions. To understand the role of alkali metals in MPDE hydrolysis and, in particular, how it influences the reaction pathway and the associated energetics, density functional calculations employing the 6-31+G(d,p) basis set have been carried out. Different pathways that include the reactant, intermediates and the products have been investigated for MPDE hydrolysis catalyzed by one or two lithium ions, characterized as stationary point geometries on the potential energy surface. The pathways A and B incorporate a single lithium ion bonded to different oxygens of the diester functionality. In pathway C, a six-membered ring was noticed wherein the nucleophile bridges two lithium ions interacting with different oxygens of the phosphoryl group. Furthermore, in the pathway (D) incorporating two lithium ions, one of the lithium ions interacts with the hydroxyl group and another with the methoxy oxygen; both metal ions are coordinated by the same phosphoryl oxygen. In addition to this, yet another pathway (E), where the metal ions are bound to different oxygens of the phosphoryl group, has also been dealt with. The calculations have shown that the A and B pathways lead to a single step reaction. A three-step mechanism including the nucleophilic (hydroxyl) attack, rotation of a methyl group and, finally, departure of the methoxy group has been predicted for the D and E profiles. Both D and E pathways are favored equally (with a marginal difference of 0.3 kJ mol(-1) in their activation energies) in the gas phase and a transition state corresponding to nucleophilic attack with an energy barrier of 32.5 kJ mol(-1) was located when lithium was used. A penta-coordinated phosphorous intermediate on the potential energy surface was characterized along these pathways. MPDE hydrolysis yielded a lower energy barrier for lithium than those for the remaining alkali metal ions. This agrees well with the experimentally observed trend for the hydrolysis rates: Li > Na > K. Self consistent reaction field (SCRF) calculations reveal the lower energy barrier between the reactant and the transition state for the nucleophilic attack in nonpolar solvents. The extent of bond formation (or cleavage) in different stationary point structures along the reaction path as estimated from the electron density at the bond critical point in the molecular electron density topography, has proven useful in distinguishing the associative or dissociative reaction pathways.

Molecular electrostatic potentials in aromatic substituted 4-hydroxyquino-2-lones: Glycine/NMDA receptor antagonists

Hydroxyquinolone derivatives have proven to be useful for inhibition at the glycine binding site of N-methyl-D-aspartate (NMDA) receptor. In this work the electronic structure, molecular electrostatic potential (MESP) and vibrational characteristics of a set of C(3) substituted 4-hydroxyquino-2-lone (HQ) derivatives, which act as Glycine/NMDA receptor antagonists, have been investigated using the density functional calculations. In the optimized structures a substituent at the C(3) site of HQ tends to adopt a helical structure. MESP investigations reveal that the ligands showing better inhibition activity should possess electron-rich regions extending over the substituent and carbonyl group of HQ. A correlation of inhibitory activity to the molecular electrostatic potential topography at the carbonyl oxygen as well as to the molecular electron density topography turns out to be a significant output of the investigation.

Electrostatic guidelines and molecular tailoring for density functional investigation of structures and energetics of (Li)n clusters

A molecular electrostatic potential (MESP)-guided method for building metal aggregates is proposed and tested on prototype lithium (Li)(n) clusters from n=4 to 58. The smaller clusters are subsequently subjected to direct density functional theory based geometry optimization, while the larger ones are optimized via molecular tailoring approach (MTA). The calculations are performed using PW91-PW91 as well as B3LYP functionals, and the trends in the interaction energies are found to be similar. The MESP-guided model for building metal clusters is validated by comparing the resulting cluster geometries with the ones reported in the literature up to n=20. A comparison of the ionization potential and polarizability (up to n=22) with their experimental counterparts shows a fairly good agreement. A new MTA-based scheme for calculating the ionization potential and polarizability values of large metal clusters is proposed and tested on Li(40) and Li(58) clusters. Further, the existence of "magic numbered clusters" up to n=22 is justified in terms of "maximum hardness principle" as well based on molecular electron density topography and distance descriptors.

Theoretical studies on the electronic structure, charge distribution and vibrational spectra of diglyme–M +-AsF 6− (M = Li, Na, K)

Electronic structure and the vibrational spectra of CH 3(OCH 2CH 2) 2OCH 3–M +-AsF 6 − (M = Li, Na, K) have been obtained using the density functional theory. Lithium ion exhibits a pentavalent coordination via 3 oxygens from diglyme and two fluorines of AsF 6 − whereas Na + and K + exhibit coordinate number 6 with 3 fluorines of the anion binding to alkali metal in these complexes. Analysis of calculated spectra reveal that the CH 2 wag (840–1120 cm −1) vibrations in the complex are sensitive to metal ion coordination. A frequency downshift relative to the free anion has been predicted for the vibrations of AsF 6 − anion when the fluorines are directly bonded (denoted by F*) to metal ion. Consequent reorganization of electron density in the complex engenders a frequency shift in the opposite direction for As–F vibrations wherein the fluorine atoms are not coordinating to the alkali metal ion. An approach based on the molecular electron density topography coupled with the difference electron density map explains the direction of the frequency shifts of C–O–C and the As–F stretchings compared to those of free diglyme or AsF 6 anion. A new method, which includes the color-mapping function for the difference molecular electron density (MED), superimposed on the bond critical points in MED topography has been suggested to explain the direction of the frequency shifts in a single attempt.

Theoretical Studies on Hydrogen Bonding, NMR Chemical Shifts and Electron Density Topography in α, β and γ-Cyclodextrin Conformers

Hydrogen-bonded interactions in alpha-, beta-, and gamma-CD conformers are investigated from the molecular electron density topography and chemical shift in the nuclear magnetic resonance (NMR) spectra calculated by using the Gauge Invariant Atomic Orbital (GIAO) method within the framework of density functional theory. For the lowest-energy CD conformers in the gas phase, the O3-H...O2' hydrogen-bonding interactions are present. Calculated 1H NMR chemical shifts (delta H) correlate well with the hydrogen-bond distance as well as electron density at the bond critical point in the molecular electron density (MED) topography. The conformers of beta- and gamma-CD comprised of relatively strong secondary hydroxyl interactions are stabilized by solvation from polar solvents.

Molecular interactions in 1,3-dimethylimidazolium-bis(trifluromethanesulfonyl)imide ionic liquid

Molecular interactions in 1,3-dimethylimidazolium-bis(trifluromethanesulfonyl)imide ionic liquids are studied by employing the ab initio Hartree–Fock and density functional methods. Different conformers are simulated with respect to molecular interactions between cation and anion. Manifestation of these molecular interactions in the vibrational spectra is discussed. Direction of frequency shifts of the normal vibrations relative to those in free anion and cations are explained by calculating difference electron density coupled with molecular electron density topography.

Electronic Structure and Normal Vibrations of CH3(OCH2CH2)nOCH3−M+−CF3SO3- (n = 2−4, M = Li, Na, and K)

Electronic structure and the vibrational frequencies of CH(3)(OCH(2)CH(2))(n)OCH(3)-M(+)-CF(3)SO(3)(-) (n = 2-4, M = Li, Na, and K) complexes have been derived from ab initio Hartree-Fock calculations. The metal ion shows varying coordination from 5 to 7 in these complexes. In tetraglyme-lithium triflate, Li(+) binds to one of the oxygens of CF(3)SO(3)(-) (triflate or Tf(-)) unlike for potassium or sodium ions, which possess bidentate coordination. Structures of glyme-MTf complexes thus derived agree well with those determined from X-ray diffraction experiments. The metal ion binds more strongly to ether oxygens of tetraglyme than its di- or triglyme analogues and engenders contraction of SO (for oxygens binding to metal ion) bonds with consequent frequency upshift for the corresponding vibration in the complex relative to those in the free MTf ion pairs. Complexation of the diglyme with LiTf engenders the largest downshift (91 cm(-1)) for the SO(2) stretching vibration of the free anion, which suggests stronger binding of lithium to the diglyme than the tri- (79 cm(-1)) or tetraglyme (70 cm(-1)). A frequency shift in the opposite direction for the SO (where oxygens do not coordinate to the metal) and CF(3) stretchings, which stems from the ion-polymer and anion-ion interactions, has been noticed. These frequency shifts have been analyzed using natural bond orbital analysis and difference electron density maps coupled with molecular electron density topography.

Molecular electrostatic potentials and electron densities in nitrotriprismanes

Molecular electrostatic potential and Electron density topography in a series of nitrotriprismanes (C 6H 6− α (NO 2) α , α=1–6) have been analyzed using the Hartree–Fock and hybrid density functional methods. Weak, electrostatic C–H⋯O interactions, which render more stability to the isomers of nitroprismane, manifest in the shallow minima of the nitro groups along a series. As revealed from the molecular electron density topography the critical points of the X–N (X=C or N) bonds correlate well with the heat of formation derived from the isodesmic reaction approach.