Effect of hydrogen‐bonded interactions on the energetics and spectral properties of the astromolecule aminoacetonitrile

A detailed and systematic electronic structure calculation has been performed to analyze the hydrogen‐bonded interaction of aminoacetonitrile (H₂NCH₂CN) with hydrogen cyanide (HCN) and Glycine (H₂NCH₂COOH). Both HCN and aminoacetonitrile have already been detected in the interstellar medium (ISM) and their active role in the molecular mechanisms of glycine production has already been recognized. Four different density functional models have been used to study the effect of hydrogen bond formation on the energetic stability and vibrational spectra of the aminoacetonitrile‐HCN and aminoacetonitrile‐glycine complexes in gas phase. The aminoacetonitrile‐glycine dimer is energetically far more stable than all forms of aminoacetonitrile‐HCN dimers. Elastic and inelastic scattering of light off the hydrogen‐bonded clusters have been investigated in details via Rayleigh and Raman spectroscopic parameters. The dipole moments and depolarization ratios are found to be sensitive on the type of hydrogen‐bond network. The mean polarizabilty show appreciable dependence on the choice of the DFT‐model. In general, all the chemical groups (OH, CN, NH₂, and CH) that participate directly in the hydrogen bond formation suffer appreciable variation in the intensity of vibration.     

Theoretical study on the interlay of hydrogen bonds in the trimers involving HCN and water

In this study, the hydration of hydrogen cyanide (HCN) has been investigated by means of quantum chemical ab initio calculations at the MP2/6‐311++G(3df,2p) level. Various HCN· · ·( H₂O)₂ and (HCN)₂· · ·H₂O complexes were optimized. Geometrics and energetics in these complexes have been analyzed. The hydration of the H atom leads to an elongation of the N?C and C? H bonds, whereas the hydration of the N atom results in a contraction of the N?C bond and a little elongation of the C? H bond. The interaction energy between each molecule pair in the trimers (except in HCN? H₂O? H₂O trimer) is increased relative to that in the respective dimer. The cooperativity of hydrogen bond in HCN? H₂O? H₂O trimer plays a negative contribution to the total interaction energy of the complex, whereas that in the other trimers is a positive contribution. Geometry and energy in H₂O? H₂OO? HCN? H₂O tetramer have also been analyzed. The binding energies in the trimers and tetramer have been studied by means of many‐body interaction analysis. The mechanism of HCN hydration was suggested. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Treatment of hydrogen bonding in SINDO1

For the treatment of hydrogen bonding in SINDO1, 2p orbitals are introduced on hydrogen. The optimization of the orbital exponent together with the generation of approximate formulas for the core attraction integrals is sufficient to obtain good geometries and binding energies in hydrogen bonded systems. The method is applied to the dimers (H₂O)₂, (NH₃)₂, (HF)₂, (HCOOH)₂, (HCN)₂, (H₂S)₂, and (HCI)₂, mixed dimers NH₃ · H₂O and H₂O · HCN, and cyclic polymers (HF)_n(n = 3, 4, 6). © 1993 John Wiley & Sons, Inc.     

Theoretical Studies on the Hydrogen‐bonding and π‐Stacking Interactions in the m‐Nisoldipine Polymorphism Dimers

The intermolecular interactions in the dimers of m‐nisoldipine polymorphism were studied by B3LYP calculations and quantum theory of "atoms in molecules" (QTAIM) studies. Four geometries of dimers were obtained: dimer I (a‐dimer, O···H? N), dimer II (b‐dimer, O···H? N), dimer III (b‐dimer, π‐stacking‐c), and dimer IV (b‐dimer, π‐stacking‐p). The interaction energies of the four dimers are along the sequence of II>I>III>IV. The intermolecular distance of the interactions follows the order: I (O···H? N)II>III>IV, and the electrostatic character decreases along the sequence: I>II>III>IV.     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

HNO(H<Subscript>2</Subscript>O)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–4) clusters: a theoretical study

The geometrical structure, binding energy, and vibrational spectra of small clusters of nitrosyl hydride (HNO) and water molecules, HNO(H₂O) _n , where (n = 1–4), have been investigated at the MP2 level of theory, using 6-311++G(2d,2p) basis set. We located three dimers, six trimers, nine tetramers, and three pentamers at the MP2/6-311++G(2d,2p) computational level. Particular attention is given to existence and magnitude of NH···O blue-shifting hydrogen bonds. Blue shifts of the NH stretching frequency upon complex formation in the ranges between 28 and 151 cm⁻¹ is predicted. Cooperative effect in terms of stabilization energy along with the many-body interaction energies analysis was performed for the studied clusters. The Atoms in Molecules (AIM) theory was also applied to explain the nature of the complexes.     

Hydrogen bonding characterization of XH2NH2···HNO(X = B,Al, Ga) complexes: A theoretical investigation

The complexes of XH₂NH₂···HNO(X = B, Al, Ga) are characterized as head to tail with hydrogen bonding interactions. The structural characteristics can be confirmed by atoms in molecules (AIM) analysis, which also provide comparisons of hydrogen bonds strengths. The calculated interaction energies at G2MP2 level show that stability of complexes decrease as BH₂NH₂···HNO > AlH₂NH₂···HNO > GaH₂NH₂···HNO. On the basis of the vibrational frequencies calculations, there are red‐shifts for ν(X1? H) and blue‐shifts for ν(N? H) in the complexes on dihydrogen bonding formations (X1? H···H? N). On hydrogen bonding formations (N? H···O), there are red‐shifts for ν(N? H) compared to the monomers. Natural bond orbital (NBO) analysis is used to discuss the reasons for the ν(X1? H) and ν(N? H) stretching vibrational shifts by hyperconjugation, electron density redistribution, and rehybridization. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Fluorines in tetrafluoromethane as halogen bond donors: Revisiting address the nature of the fluorine's σhole

It has been demonstrated in several instances that the 0.001 a.u. (electrons per bohr³) isodensity mapped electrostatic surface potentials on the fluorines along the outermost extensions of the C? F covalent bonds in tetrafluoromethane (CF₄) are entirely negative, they are thereby unable to engage in σ_hole bonding interactions with the negative sites on another molecules. In this study, we have attempted at resolving this controversy by performing various high‐level electronic structure calculations with Quadratic Configuration Integrals of Singles and Doubles QCISD(full), second‐order Møller–Plesset MP2(full), and 12 other Density Functional Theory (DFT) based functionals with and without dispersion corrections, all in conjunction with the 6–311++G(2d,2p) basis set. The results achieved with all the levels of theory utilized suggest that the fluorine's σ_holes in CF₄ are positive regardless of the 0.001‐, 0.0015‐, and 0.002‐a.u. isodensity mapped electrostatic surfaces examined. Because of this specific quality, the fluorines in CF₄ have displayed their capacities to form not only 1:1 clusters with the Lewis bases such as water (H₂O), ammonia (NH₃), formaldehyde (H₂C?O), hydrogen fluoride (HF), and hydrogen cyanide (HCN), but also 1:2, 1:3, and 1:4 clusters with the latter three randomly chosen Lewis bases. Various topological and nontopological features obtained from applications of atoms in molecules, noncovalent interaction reduced‐density‐gradient and natural bond orbital analytical tools reveal that the N···F, O···F, and F···F long‐ranged interactions developed between the interacting monomers in H₃N···FCF₃, H₂O···FCF₃, and (Y? D)_n=1–4···F₄C (Y? D = H₂C?O, HCN, and HF) are reminiscent of halogen bonding. The nonadditive cooperative and anticooperative energetic effects emerged on cluster formations are discussed in detail. © 2015 Wiley Periodicals, Inc.     

Molecular dynamics of cis‐1‐(2‐hydroxy‐5‐ methylphenyl)ethanone oxime and N‐(2‐hydroxy‐4‐methylphenyl)acetamide in solution studied by NMR spectroscopy

The formation of hydrogen bonds and molecular dynamics for the molecules cis‐1‐(2‐hydroxy‐5‐methylphenyl)ethanone oxime ( I ) and N‐(2‐hydroxy‐4‐methylphenyl)acetamide ( II ) have been investigated in solution using NMR. The results confirm the formation of O? H···O, O? H···N and O···H? N type inter‐ and intramolecular hydrogen bonds. Spin‐lattice relaxation times (T₁), activation energy of molecular dynamics and energy of intramolecular hydrogen bonds have been determined. Copyright © 2010 John Wiley & Sons, Ltd.     

Conformational isomers of the [(5‐methyl‐2‐pyridinio)aminomethylene]diphosphonate dianion and [(5‐methyl‐2‐pyridyl)aminomethylene]diphosphonate trianion in salts with 4‐aminopyridine and ammonia

The crystal structures of two salts, products of the reactions between [(5‐methyl‐2‐pyridyl)aminomethylene]bis(phosphonic acid) and 4‐aminopyridine or ammonia, namely bis(4‐aminopyridinium) hydrogen [(5‐methyl‐2‐pyridinio)aminomethylene]diphosphonate 2.4‐hydrate, 2C₅H₇N₂⁺·C₇H₁₀N₂O₆P₂²⁻·2.4H₂O, (I), and triammonium hydrogen [(5‐methyl‐2‐pyridyl)aminomethylene]diphosphonate monohydrate, 3NH₄⁺·C₇H₉N₂O₆P₂³⁻·H₂O, (II), have been determined. In (I), the Z configuration of the ring N—C and amino N—H bonds of the bisphosphonate dianion with respect to the C_ring—N_amino bond is consistent with that of the parent zwitterion. Removing the H atom from the pyridyl N atom results in the opposite E configuration of the bisphosphonate trianion in (II). Compound (I) exhibits a three‐dimensional hydrogen‐bonded network, in which 4‐aminopyridinium cations and water molecules are joined to ribbons composed of anionic dimers linked by O—H...O and N—H...O hydrogen bonds. The supramolecular motif resulting from a combination of these three interactions is a common phenomenon in crystals of all of the Z‐isomeric zwitterions of 4‐ and 5‐substituted (2‐pyridylaminomethylene)bis(phosphonic acid)s studied to date. In (II), ammonium cations and water molecules are linked to chains of trianions, resulting in the formation of double layers.     

Lenalidomide,an antineoplastic drug,and its hemihydrate

The crystal structures of lenalidomide [systematic name: (RS)‐3‐(4‐amino‐1‐oxoisoindolin‐2‐yl)piperidine‐2,6‐dione], C₁₃H₁₃N₃O₃, (I), an antineoplastic drug, and its hemihydrate, C₁₃H₁₃N₃O₃·0.5H₂O, (II), have been determined by single‐crystal X‐ray diffraction analysis. The overall conformation of the molecule defined by the orientation of the two ring portions, viz. pyridinedione and isoindolinone, is twisted in both structures. The influence of the self‐complementary pyridinedione ring is seen in the crystal packing of both structures through its involvement in forming hydrogen‐bonded dimers, although alternate dione O atoms are utilized. An extensive series of N—H...O hydrogen bonds link the dimers into two‐dimensional supramolecular arrays built up from infinite chains. The water molecule in (II) has a cohesive function, connecting three lenalidomide molecules by hydrogen bonds. The significance of this study lies in the analysis of the interactions in these structures and the aggregations occurring via hydrogen bonds in the hydrated and dehydrated crystalline forms of the title compound.     

A polarizable electrostatic model of the N‐methylacetamide dimer

Our previously developed polarizable electrostatic model is applied to isolated N‐methylacetamide (NMA) and to three hydrogen‐bonded configurations of the NMA dimer. Two versions of the model are studied. In the first one (POL1), polarizability along the valence bonds is described by induced bond charge increments, and polarizability perpendicular to the bonds is described by cylindrically isotropic induced atomic dipoles. In the other version (POL2), the induced bond charge increments are replaced by induced atomic dipoles along the bonds. The parameterization is done by fitting to ab initio MP2/6‐31++G(d,p) electric potentials. The polarizability parameters are determined by subjecting the NMA molecule to various external electric fields. POL1 turns out to be easier to optimize than POL2. Both models reproduce well the ab initio electric potentials, molecular dipole moments, and molecular polarizability tensors of the monomer and the dimers. Nonpolarizable models are also investigated. The results show that polarization is very important for reproducing the electric potentials of the studied dimers, indicating that this is also the case in hydrogen bonding between peptide groups in proteins. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1933–1943, 2001     

Interaction of thiamine with anions in the triclinic form of thiamine iodide: 3‐[(4‐amino‐2‐methylpyrimidin‐5‐yl)methyl]‐5‐(2‐hydroxyethyl)‐4‐methyl‐1,3‐thiazol‐3‐ium iodide 1.25‐hydrate

The asymmetric unit of the title compound, C₁₂H₁₇N₄OS⁺·I⁻·1.25H₂O, contains two crystallographically independent molecules. Both formula units assume the usual F conformation and have the hydroxyethyl group disordered over two sites, each with half occupation. Two thiamine cations are linked by hydrogen bonds into a cyclic dimer. These dimers are further connected by base‐pairing hydrogen bonds into a chain along [010]. The stacked dimers form channels, which are occupied by iodide anions. The cations and anions are associated by N—H...I hydrogen bonds, C—H...I interactions and I...thiazolium ring close contacts. The interactions between thiamine and the iodide anions are similar to those observed in monoclinic thiamine iodide 1.5‐hydrate [Hu & Zhang (1993). J. Inclusion Phenom. Mol. Recognit. Chem. 16 , 273–281].     

A new polymorph and two pseudopolymorphs of pyrimethamine

Due to its donor–acceptor–donor site, the antimalarial drug pyrimethamine [systematic name: 5‐(4‐chlorophenyl)‐6‐ethylpyrimidine‐2,4‐diamine] is a potential component of a supramolecular synthon. During a cocrystallization screen, one new polymorph of solvent‐free pyrimethamine, C₁₂H₁₃ClN₄, (I), and two pseudopolymorphs, pyrimethamine dimethyl sulfoxide monosolvate, C₁₂H₁₃ClN₄·C₂H₆OS, (Ia), and pyrimethamine N‐methylpyrrolidin‐2‐one monosolvate, C₁₂H₁₃ClN₄·C₅H₉NO, (Ib), were obtained. In (I), (Ia), (Ib) and the previously reported polymorph, the pyrimethamine molecules exhibit similar conformations and form R²₂(8) dimers stabilized by a pair of N—H...N hydrogen bonds. However, the packing arrangements are completely different. In (I), the dimers are connected by two additional N—H...N hydrogen bonds to form ribbons and further connected into a two‐dimensional network parallel to (100), while layers containing N—H...Cl hydrogen‐bonded pyrimethamine ribbons are observed in the packing of the known polymorph. In the two pseudopolymorphs, two pyrimethamine molecules are linked to form R²₂(8) dimers and the solvent molecules are connected to the dimers by R²₃(8) interactions involving two N—H...O hydrogen bonds. These arrangements are connected to form zigzag chains by N—H...Cl interactions in (Ia) and to form ribbons by N—H...N interactions in (Ib). Unexpectedly, a reaction between pyrimethamine and N‐methylpyrrolidin‐2‐one occurred during another cocrystallization experiment from a solvent mixture of N‐methylpyrrolidin‐2‐one and dimethyl sulfoxide, yielding solvent‐free 5,5′‐{[5‐(4‐chlorophenyl)‐6‐ethylpyrimidine‐2,4‐diyl]bis(azanediyl)}bis(1‐methylpyrrolidin‐2‐one), C₂₂H₂₇ClN₆O₂, (II). In the packing of (II), the pyrimethamine derivatives are N—H...O hydrogen bonded to form ribbons. A database study was carried out to compare the molecular conformations and hydrogen‐bonding interactions of pyrimethamine.     

A novel crystal form of metacetamol: the first example of a hydrated form

We report the crystal structure and crystallization conditions of a first hydrated form of metacetamol (a hemihydrate), C₈H₉NO₂·0.5H₂O. It crystallizes from metacetamol‐saturated 1:1 (v/v) water–ethanol solutions in a monoclinic structure (space group P2₁/n) and contains eight metacetamol and four water molecules per unit cell. The conformations of the molecules are the same as in polymorph II of metacetamol, which ensures the formation of hydrogen‐bonded dimers and R₂²(16) ring motifs in its crystal structure similar to those in polymorph II. Unlike in form II, however, these dimers in the hemihydrate are connected through water molecules into infinite hydrogen‐bonded molecular chains. Different chains are linked to each other by metacetamol–water and metacetamol–metacetamol hydrogen bonds, the latter type being also present in polymorph I. The overall noncovalent network of the hemihydrate is well developed and several types of hydrogen bonds are responsible for its formation.     

Hydrogen Cyanide Exchange on [Al(HCN)6]3+ – A DFT Study

The hydrogen cyanide exchange mechanism of [Al(HCN)₆]³⁺ has been investigated by DFT calculations (B3LYP/6‐311+G**). The calculations provide theoretical evidence that the hydrogen cyanide exchange proceeds via a limiting dissociative (D) mechanism involving a stable five‐coordinate intermediate [Al(HCN)₅ · (HCN)₂]³⁺. The activation energy for the D‐mechanism is 23.4 kcal · mol^–1, which is 2.8 kcal · mol^–1 lower than for the seven‐coordinate transition state [Al(HCN)₇]^3+? for the alternative associative (A) pathway. The difference in stability between the two intermediates [Al(HCN)₅ · (HCN)₂]³⁺ (12.1 kcal · mol^–1) and [Al(HCN)₇]³⁺ (25.7 kcal · mol^–1) in comparison to [Al(HCN)₆ · (HCN)]³⁺ is much more pronounced and further supports a limiting dissociative mechanism.     

Quantum chemical investigation of linear hydrogen bonding in ONCCN···HX (X = F,Cl, Br) dimers

Linear hydrogen bonding formed between the nitrogen end of cyanogen‐N‐oxide (ONCCN) and hydrogen halides HX (X = F, Cl, Br) has been observed in their ground Σ states. The order of agreement of energetic stabilities between the correlated functionals used in this calculation is: B3LYP < PBE0 < PBE < PW91 in conjunction with the 6–311++G(3df,3pd) basis set. Analysis of various parameters describing the existence of H‐bonds in these dimers follows the conventional trend: ONCCN···HF > ONCCN···HCl > ONCCN···HBr in the series, except H‐bond lengths and static dipole polarizabilities which are in reverse order. The atomic charges obtained from the Mulliken and natural population analysis is used to assess the charge transfer effects that accompany the dimer formation. It is found from the investigation that the dimers having highest binding energy are accompanied by the highest transfer of charge. The ¹⁴N nuclear quadrupole coupling constants of the monomer ON¹CCN² are found to be decreased upon complection and in the series it increases from F through Br. We observed enhancements in the values of the dimer dipole moment and intrinsic dipole polarizabilities compared with the sum of the monomer values by intermolecular electrical interaction. Investigation reveals vibrational spectral shifts of HX and CN stretching modes similar to the conventional red‐shifted H‐bonded dimers; for the former case, the infrared band intensity increases significantly. Finally, the new vibrational modes originated from the intermolecular interaction are outlined. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Novel Hydrogen-bonded Three-dimensional Supramolecular Architectures Containing 2D Honeycomb Networks or 2D Grids

Two new supramolecular complexes,[Cu(H_2dhbd)(3-pyOH)(H_2O)]_2·3-pyOH·2H_2O(1)and[Cu_2(dhbd)(dpa)_2-(H_2O)]·6H_2O(2)(H_4dhbd=2,3-dihydroxybutanedioic acid,3-pyOH=3-hydroxypyddine,dpa=2,2'-dipyridylamine),have been synthesized in aqueous solution and characterized by single-crystal X-ray diffraction,elemental analyses,UV-Vis and IR spectra,and TGA analysis.X-ray structural analysis revealed that,through four pairs of strong O…H—O hydrogen bonds,the cyclic dinuclear units in 1 together with four adjacent neighbors are connected into a 2Dhoneycomb network encapsulating free 3-pyOH ligands.Unexpectedly,the water-dimers are fixed in interlayers of2D honeycomb network and act as hydrogen-bond bridging to further extend these 2D networks into 3D hydro-gen-bonded framework.Complex 2 includes interesting 2D grids constructed from chiral dinuclear units throughstrong O…H—O and O…H—N hydrogen bonding,which are extended through other crystallization water mole-cules into three dimension with channels.Variable-temperature magnetic susceptibility measurements for bothcomplexes indicate the presence of weak antiferromagnetic exchange interactions between adjacent copper(Ⅱ)ions.     

Channel‐forming solvate crystals and isostructural solvent‐free powder of 5‐hydroxy‐6‐methyl‐2‐pyridone

Crystals of 5‐hydroxy‐6‐methyl‐2‐pyridone, (I), grown from a variety of solvents, are invariably trigonal (space group R); these are 5‐hydroxy‐6‐methyl‐2‐pyridone acetone 0.1667‐solvate, C₆H₇NO₂·0.1667C₃H₆O, (Ia), and 6‐methyl‐5‐hydroxy‐2‐pyridone propan‐2‐ol 0.1667‐solvate, C₆H₇NO₂·0.1667C₃H₈O, (Ib), and the forms from methanol, (Ic), water, (Id), benzonitrile, (Ie), and benzyl alcohol, (If). They incorporate channels running the length of the c axis that contain extensively disordered solvent molecules. A solvent‐free sublimed powder of 5‐hydroxy‐6‐methyl‐2‐pyridone microcrystals is essentially isostructural. Inversion‐related host molecules interact via pairs of N—H...O hydrogen bonds to form R₂²(8) dimers. Six of these dimers form large R₁₂⁶(42) puckered rings, in which the O atom of each N—H...O hydrogen bond is also the acceptor in an O—H...O hydrogen bond that involves the 5‐hydroxy group. The large R₁₂⁶(42) rings straddle the axes and form stacked columns viaπ–π interactions between inversion‐related molecules of (I) [mean interplanar spacing = 3.254 Å and ring centroid–centroid distance = 3.688 (2) Å]. The channels are lined by methyl groups, which all point inwards to the centre of the channels.     

A combined computational and experimental approach for investigating a hydrogen‐bonded supermolecular compound comprising benzimidazole and malonic acid

A hydrogen‐bonded tetramer supramolecular motif of 2:2 benzimidazole (BIZ) and malonic acid (MLA) has been synthesized and characterized by elemental analysis, infrared (IR), and X‐ray single crystal diffraction. Thermal stability analyses demonstrate that this supramolecular adduct is a new material and it is not the ordinary superposition of the original monomers. Density function theory (DFT) calculations for the models of dimers, trimers, and tetramer comprising BIZ and MLA have been carried out at B3LYP/6‐31G* and PBE1PBE/6‐31G* levels of theory, respectively. By comparing the calculated results with the experiments (single crystal structure, IR spectra, and thermal analysis) and based on the statistic thermodymnamic calculations, it is concluded that the dimers cannot exist at room temperature and the tetramer can simulate the title supramolecular complex better than the two trimers. Further studies on the model of tetramer indicate that the hydrogen bond of N···H? O is stronger than that of O···H? N. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008