DFT study of the monomers and dimers of 2-pyrrolidone: equilibrium structures, vibrational, orbital, topological, and NBO analysis of hydrogen-bonded interactions

A computational study of the monomers and hydrogen-bonded dimers of 2-pyrrolidone was executed at different DFT levels and basis sets. The above dimeric complexes were treated theoretically to elucidate the nature of the intermolecular hydrogen bonds, geometry, thermodynamic parameters, interaction energies, and charge transfer. The processes of dimer formation from monomers and concerted reactions of double proton transfer were considered. The evolution of geometry, vibrational frequencies, charge distribution, and AIM properties in going from monomers to dimers was systematically followed. The solvent effects upon dimer formation were investigated in terms of the self-consistent reaction field (SCRF Onsager model). For the monomers and three dimers, vibrational frequencies were calculated and the changes in frequencies of the vibrations most sensitive to complexation were discussed. The orbital interactions were shown to lengthen the X-H (X = N, O) bond and lower its vibrational frequency (a red shift). To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis. Topological analysis of electron density at bond critical points (BCP) was executed for complex molecules using the Bader's atoms in molecules (AIM) theory. The interaction energies were calculated, and the basis set superposition errors (BSSE) were estimated systematically. Satisfactory correlations between the structural parameters, interaction energies, and electron density characteristics at BCP were found.     

How short can the H...H intermolecular contact be? New findings that reveal the covalent nature of extremely strong interactions

Ab initio calculations at the MP2/6-311++G(d,p) and MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ levels have been performed for the following complexes: H2OH+...HBeH, H2OH+...HBeBeH, H2OH+...HBeF, HClOH+...HBeH, Cl2OH+...HBeH, and Cl2OH+...HBeF. For all dimers considered, extremely short H...H intermolecular contacts (1.0-1.3 A) were obtained. These are the shortest intermolecular distances which have ever been reported, with binding energies within the range of 13.7-24.3 kcal/mol (MP2/aug-cc-pVDZ//MP2/aug-cc-pVTZ level). The interaction energies of the complexes analyzed were also extrapolated to the complete basis set (CBS) limit. To explain the nature of such strong interactions, the Bader theory was applied, and the characteristics of the bond critical points (BCPs) were analyzed. It was pointed out that for the major part of the H...H contacts considered here the Laplacian of the electron density at H...H BCP is negative indicating the partly covalent nature of such a connection. The term "covalent character of the hydrogen bond" used sometimes in recent studies is discussed. An analysis of the interaction energy components for dihydrogen bonded systems considered indicates that in contrast to conventional hydrogen bonded systems the attractive electrostatic term is outweighed by the repulsive exchange energy term and that the higher order delocalization energy term is the most important attractive term.     

Hydrogen bonding in substituted formic acid dimers

The hydrogen-bonded dimers of formic acid derivatives XCOOH (X = H, F, Cl, and CH3) have been investigated using density functional theory (B3LYP) and second-order M?ller-Plesset perturbation (MP2) methods, with the geometry optimization carried out using 6-311++G(2d,2p) basis set. The dimerization energies calculated using aug-cc-pVXZ (with X = D and T) basis have been extrapolated to infinite basis set limit using the standard methodology. The results indicate that the fluorine-substituted formic acid dimer is the most stable one in comparison to the others. Topological analysis carried out using Bader's atoms in molecules (AIM) theory shows good correlation of the values of electron density and its Laplacian at the bond critical points (BCP) with the hydrogen bond length in the dimers. Natural bond orbital (NBO) analysis carried out to study the charge transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes reveals that most of the dimers are associated with conventional H-bonding except a few, where improper blue-shifting hydrogen bonds are found to be present.     

The possible covalent nature of N-H...O hydrogen bonds in formamide dimer and related systems: an ab initio study

The N-H...O hydrogen bonds are analyzed for formamide dimer and its simple fluorine derivatives representing a wide spectrum of more or less covalent interactions. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. To explain the nature of such interactions, the Bader theory was also applied, and the characteristics of the bond critical points (BCPs) were analyzed: the electron density at BCP and its Laplacian, the electron energy density at BCP and its components, the potential electron energy density, and the kinetic electron energy density. These parameters are used to justify the statement that some of the interactions analyzed are partly covalent in nature. An analysis of the interaction energy components for the systems considered indicates that the covalent character of the hydrogen bond is manifested by a markedly increased contribution of the delocalization term relative to the electrostatic interaction energy. Moreover, the ratio of stabilizing the delocalization/electrostatic contributions grows linearly with the decreasing lengths of the hydrogen bond.     

Self-discrimination of enantiomers in hydrogen-bonded dimers

The homochiral and heterochiral hydrogen-bonded (HB) dimers of a set of small model molecules (alpha-amino alcohols) have been studied by means of ab initio methods. The gas-phase calculations have been carried out with the hybrid HF/DFT B3LYP method and the 6-311++G** basis set. The electron density of the complexes has been analyzed using the atoms in molecules (AIM) methodology, which allows characterization of the HB interactions and additional intermolecular contacts. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the Delta G(solv). The gas-phase results show that the heterochiral dimers are the most stable ones for each case studied, while in solution for several cases, the relative stability is reversed and the homochiral dimers become more stable. The AIM analysis shows the typical bond critical points characteristic of the HB and additional bond critical points denoting, in this case, destabilization of intermolecular interaction as CF(3)...F(3)C and CH(3)...H(3)C contacts.     

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.     

Partial hydrogen bonds: structural studies on thioureidoalkylphosphonates

X-ray crystal and molecular structures of the following compounds are investigated: diphenyl 1-(3-phenylthioureido)propylphosphonate (I), diphenyl 1-(3-phenylthioureido)methylthio-propylphosphonate (II), and diphenyl [2-methyl-1-(3-methylthioureido)propyl]phosphonate (III). Additionally single point density functional theory calculations at the B3LYP/6-311+G(d) level of theory are performed on dimers whose geometries are taken from the crystal structures. The additional diffuse and polarization components are included on H-atoms which participate in H-bonds. The obtained wave functions are applied later to study theoretical electron densities for these species. Bond critical points are determined for dimers investigated to characterize the nature of interactions, especially bifurcated acceptor hydrogen bonds. The characteristics of bond critical points are investigated in terms of the electron densities and their Laplacians.     

Strength and nature of hydrogen bonding interactions in mono- and di-hydrated formamide complexes

In this work, mono- and di-hydrated complexes of the formamide were studied. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. The atoms in molecules theory (AIM), based on the topological properties of the electronic density distribution, was used to characterize the different types of bonds. The analysis of the hydrogen bonds (H-bonds) in the most stable mono- and di-hydrated formamide complexes shows a mutual reinforcement of the interactions, and some of these complexes can be considered as "bifunctional hydrogen bonding hydration complexes". In addition, we analyzed how the strength and the nature of the interactions, in mono-hydrated complexes, are modified by the presence of a second water molecule in di-hydrated formamide complexes. Structural changes, cooperativity, and electron density redistributions demonstrate that the H-bonds are stronger in the di-hydrated complexes than in the corresponding mono-hydrated complexes, wherein the σ- and π-electron delocalization were found. To explain the nature of such interactions, we carried out the atoms in molecules theory in conjunction with reduced variational space self-consistent field (RVS) decomposition analysis. On the basis of the local Virial theorem, the characteristics of the local electron energy density components at the bond critical points (BCPs) (the 1/4? (2)ρ(b) component of electron energy density and the kinetic energy density) were analyzed. These parameters were used in conjunction with the electron density and the Laplacian of the electron density to analyze the characteristics of the interactions. The analysis of the interaction energy components for the systems considered indicates that the strengthening of the hydrogen bonds is manifested by an increased contribution of the electrostatic energy component represented by the kinetic energy density at the BCP.     

Hydrogen Bonding Properties of the Complexes of Formaldehyde and its Derivatives with HF and HCl

 The complexes of formaldehyde and some of its derivatives with HF and HCl were investigated at HF/6-311 + +G^** and MP2/6-311 + +G^** levels of theory. Interaction energies were corrected for the basis set superposition error (BSSE). The full optimizations of dimers and monomers were performed during calculations. The Bader theory of atoms-in-molecules (AIM) was also applied for the localization of bond critical points (BCP) and for the calculation the electron densities and their Laplacians at these points. The relationships between H-bond energy and parameters obtained from calculations were also studied.     

Ligand‐Unsupported Cuprophilicity in the Preparation of Dodecacopper(I) Complexes and Raman Studies

Synthesis and characterization of two dodecacopper(I) extended metal atom chains (EMAC) assembled by two hexadentate bis(pyridylamido)amidinate‐supported hexacopper(I) string complexes (monomers) via the ligand‐unsupported cuprophilicity are described. In addition to short unsupported Cu?Cu contacts, two hexacopper fragments in these two dodecacopper EMACs show a bent conformation based on X‐ray crystallography. Compared with their THF‐bound hexacopper(I) monomers and protonated ligands, these ligand‐unsupported cuprophilic interactions are shown to be weak by Raman spectroscopy. DFT calculations suggest the ligand‐unsupported cuprophilicity originate from weak attractive orbital interactions, and the strength is estimated to be 2.4 kcal mol^?1.     

Hydrogen Bonding Properties of the Complexes of Formaldehyde and its Derivatives with HF and HCl

Summary.  The complexes of formaldehyde and some of its derivatives with HF and HCl were investigated at HF/6-311 + +G^** and MP2/6-311 + +G^** levels of theory. Interaction energies were corrected for the basis set superposition error (BSSE). The full optimizations of dimers and monomers were performed during calculations. The Bader theory of atoms-in-molecules (AIM) was also applied for the localization of bond critical points (BCP) and for the calculation the electron densities and their Laplacians at these points. The relationships between H-bond energy and parameters obtained from calculations were also studied. Received June 29, 2001. Accepted (revised) October 29, 2001     

Modeling the protein-nucleic acid base interactions through hydrogen-bonded complexes of N-heterocyclic analogs of Indene with amino acid side-chain mimics

A series of hydrogen-bonded complexes between N-heterocyclic analogs of Indene and amino acid side-chain mimics have been analyzed employing second-order Møller-Plesset perturbation (MP2) theory and density functional theory with dispersion function (DFT-D) calculations with the aim of gaining greater insight in to the nature of intermolecular interactions in these systems. In this study, the hydrogen bonding ability of N-heterocyclic analogs of Indene towards amino acid side-chain mimics follows the sequence Azaindazole (AIND) > Indazole (IND) > Azaindole (AIN) > Indole (IN) whereas the hydrogen bonding ability of amino acid side-chain mimics towards N-heterocyclic analogs of Indene follows the sequence AcOH > MeNH₂ > MeOH > MeSH. Bader’s theory of atoms in molecules (AIM) and natural bond orbitals (NBO) analyses are employed to elucidate the interaction characteristics in the complexes under study. The purpose of conducting these studies is to measure the relative strength of hydrogen bonding interactions such as N-H···O=C, N-H···O, N-H···S, N-H···N, and O-H···N in these complexes and their role in providing stability to the complexes. The AIM theory shows good correlation of the electron density and its Laplacian at the bond critical points (BCP) with the computed stabilization energy for all the complexes under study.

     

Intra- and intermolecular interactions in the crystals of 3,4-diamino-1,2,4-triazole and its 5-methyl derivative. Experimental and theoretical investigations of charge density distribution

In this paper intra- and intermolecular interactions in crystals of 3,4-diamino-1,2,4-triazole (DAT) and its 5-methyl derivative (DAMT) were investigated in details by experimental (high-resolution X-ray diffraction) and theoretical (ab initio quantum chemistry (MP2/aug-cc-pvdz), AIM, and NBO) methods. Influence of n-π conjugation and n→σ* hyperconjugation on the geometry of DAT and DAMT molecules was shown. All intermolecular interactions in crystals of the DAT and DAMT including weak X-H···π and mixed X-H···N/X-H···π hydrogen bonds were considered. Comparison of BCP characteristics of these interactions from experimental and theoretical charge density distribution demonstrates systematic increase of bonding in isolated dimers compared with dimers in the crystal phase. The ability of amino groups in both crystals serve as proton acceptors in hydrogen bonding was confirmed.     

Effect of dimerization and racemization processes on the electron density and the optical rotatory power of hydrogen peroxide derivatives

The variation of the electron density properties and optical rotatory power of the monomers and dimers of seven monosubstituted hydrogen peroxide derivatives, HOOX (X = CCH, CH(3), CF(3), t-Bu, CN, F, Cl), upon racemization has been studied using DFT (B3LYP/6-31+G) and MP2 (MP2/6-311+G) methods. The geometrical results have been rationalized on the basis of natural bond orbital (NBO) analysis. The atomic partition of the electron density properties within the atoms in molecules (AIM) methodology has allowed investigating the energy and charge redistribution in the different structures considered. The calculated optical rotatory power (ORP) of the dimers are, in general, twice of the values obtained for the monomers.     

Bonding trends of thiosemicarbazones in mononuclear and dinuclear copper(I) complexes: syntheses, structures, and theoretical aspects

Reactions of copper(I) halides with a series of thiosemicarbazone ligands (Htsc) in the presence of triphenylphosphine (Ph(3)P) in acetonitrile have yielded three types of complexes: (i) monomers, [CuX(eta1-S-Htsc)(Ph3P)2] [X, Htsc = I (1), Br (2), benzaldehyde thiosemicarbazone (Hbtsc); I (5), Br (6), Cl (7), pyridine-2-carbaldehyde thiosemicarbazone (Hpytsc)], (ii) halogen-bridged dimers, [Cu2(mu2-X)2(eta1-S-Htsc)2(Ph3P)2] [X, Htsc = Br (3), Hbtsc; I (8), furan-2-carbaldehyde thiosemicarbazone (Hftsc); I (11), thiophene-2-carbaldehyde thiosemicarbazone (Httsc)], and (iii) sulfur-bridged dimers, [Cu2X2(mu2-S-Htsc)2(Ph3P)2] [X, Htsc = Cl (4), Hbtsc; Br (9), Cl (10), pyrrole-2-carbaldehyde thiosemicarbazone (Hptsc); Br (12), Httsc]. All of these complexes have been characterized with the help of elemental analysis, IR, 1H, 13C, or 31P NMR spectroscopy, and X-ray crystallography (1-12). In all of the complexes, thiosemicarbazones are acting as neutral S-donor ligands in eta()S or mu2-S bonding modes. The Cu...Cu separations in the Cu(mu2-X)2Cu and Cu(mu2-S)2Cu cores lie in the ranges 2.981(1)-3.2247(6) and 2.813(1)-3.2329(8) Angstroms, respectively. The geometry around each Cu center in monomers and dimers may be treated as distorted tetrahedral. Ab initio density functional theory calculations on model monomeric and dimeric complexes of the simplest thiosemicarbazone [H2C=N-NH-C(S)-NH2, Htsc] have revealed that monomers and halogen-bridged dimers have similar stability and that sulfur-bridged dimers are stable only when halogen atoms are engaged in hydrogen bonding with the solvent of crystallization or H2O molecules.     

Theoretical study of dihydrogen bonds between (XH)2, X = Li, Na, BeH, and MgH, and weak hydrogen bond donors (HCN, HNC, and HCCH)

The dihydrogen-bonded (DHB) complexes formed by (XH)2, with X = Li, Na, BeH, and MgH, with one, two, and four protonic molecules (HCN, HNC, and HCCH) have been studied. These complexes have been compared to those of the XH monomers with the same hydrogen bond donor molecules. The energetic results have been rationalized based on the electrostatic potential of the isolated hydridic systems. The electron density properties have been analyzed within the AIM methodology, both at the bond critical points and the integrated values at the atomic basins. Exponential relationships between several properties calculated at the bond critical points (rho,nabla2rho, lambdai, G, and V) and variation of integrated properties (energy, charge, and volume) vs the DHB distance have been obtained.     

Bond Characterization of the 3-D Framework Structure of the Copper(Ⅱ) Isonicotinic Acid Complex Formed by Hydrogen Bonding

The crystal of qudra-aquabis(isonicotinato-N)copper(Ⅱ),Cu[(NC5H4COO)]2 . 4H2O was synthesized via hydrothermal method. Single crystal X-ray analysis at 100K (Siemens SmartCCD) and 25K (Nonius KappaCCD) are performed. The results reveal that the Cu atom is octahedrally coordinated by two Nitrogen atoms of pyridine rings in the axial positions and the four Oxygen atoms of the four water molecules in an equatorial orientation. The octahedral Cu(lI) center shows a large Jahn-Teller distortion with the distances of the Cu-N 2.0253(6)A, Cu-O(3)2.0124(6)~, Cu-O(4) 2.4304(7)A. By means of the hydrogen bonding connections, this compound is formed a 3D framework. In addition, the thermal displacement of each atom at 25K is about three-times smaller than that at 100K. Electron density distribution of this compound at 25K and 100K is also analyzed and compared in terms of multipole model. All topological properties based on X-ray diffraction result and theoretical calculation including the bond critical points (BCP), Laplacian of the electron density and electron density at the BCP will be presented.     

Identification of the monoanions and of their complexes with lithium salts possibly formed in solution during the alkylation of lithiated phenylacetonitrile dianions: infrared spectroscopy and density functional theory calculations

The carbanionic species possibly formed during the first alkylation step of phenylacetonitrile lithiated anion by CH(3)I and PhCH(2)Cl in THF-hexane solution and their complexes with the lithium salt formed have been observed by infrared spectrometry and characterized by density functional theory calculations. The spectra of alkylated phenylacetonitrile lithiated anion monomers and dimers have been identified in good agreement with calculations. The wave numbers of the vibrational modes of the alkylated species differ significantly from those of PhCHCNLi species, but do not depend appreciably on the substituent nature. Nevertheless with the methyl substituent, the isomerization equilibrium of the monomer is noticeably shifted toward the bridged (C-lithiated) species. The formation of a heterodimer at the expense of the dimer after addition of LiCl has been confirmed by experiment.     

Evaporation of Lennard-Jones fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.     

聚吡咯并[3,4-c]吡咯的电子结构及导电性研究

采用密度泛函(DFT)方法在6-31g(d)水平下研究了聚吡咯和聚吡咯并[3,4-c]吡咯, 以及它们的单体和低聚物的电子结构. 对中心键的键长、电荷密度以及Weberg键级的研究表明, 随着主链聚合度的增加, 其共轭性增强. 对聚合物还进行了能带结构和态密度分析. 结果发现, 在3位聚合的并环化合物具有最优的导电性能, 其能隙仅有0.25 eV, 可以作为潜在的导电聚合物材料.