Calculation of molecular crystals within the PCILOCC framework

Stabilization energies and equilibrium distances of one-dimensional (HF)_n and (H₂O)_n chains have been calculated by means of the PCILO method for finite chain length and by the PCILOCC method for infinite chain length. Both types of calculation are compared with corresponding CNDO /2-MO and CNDO /2-CO calculations. Further we have performed an analysis of the individual contributions of the stabilization energies per monomer of the PCILO and PCILOCC calculations. The results show that the PCILOCC method is well suited for the calculation of molecular associations with translational symmetry.     

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.     

Molecular orbital theory of the hydrogen bond.: XVI. A comparative study of pyridine and the diazines as proton acceptors in ground and excited n → π* states

Ab initio LCAO MO SCF calculations with a minimal STO-3G basis set have been performed to determine the structures and energies of dimers having pyridazine, pyrimidine, and pyrazine as proton acceptor molecules, with HF and H₂O as proton donors. The structures of these dimers are consistent with structures anticipated from the General Hybridization Model. Differences in the relative stabilities of dimers in the two series which have HF and H₂O as proton donors and pyridine and the diazines as proton acceptors are attributed to different weightings of secondary effects which influence dimer stabilities. These azabenzeme molecules form stronger hydrogen bonds than HCN and weaker hydrogen bonds than NH₃ whether HF or H₂O is the proton donor. Configuration interaction calculations indicate that vertical excitation to n → π* states of these proton aceptor molecules results in various degrees of destabilization of hydrogen bonded dimers and trimers, depending upon the excited state electron densities at the nitrogen atoms and the excited state dipole moments. With respect to the proton acceptor molecule, computed blue shifts of the n → π* bands increase in the order pyrazine < pyradizine < pyrimidine < pyridine.     

Electronic structures of large,extended, nonperiodic systems by using the elongation method: Model calculations for the cluster series of a polymer and the molecular stacking on a surface

The elongation method based on the molecular orbital (MO ) theory, which enables us to extend a polymer with any molecular fragments theoretically, has recently been developed by our group. As the next step, we introduced an approach based on the crystal orbital (CO ) theory into above treatment. In the present work, the elongation method was developed at the Hartree–Fock level with CNDO /2 parameters and applied to model systems composed of the cluster series of a polymer and the molecular stacking on a surface. In the cluster-series calculations, the hydrogen molecule [(H₂)_n], hydrogen fluoride [(HF)_n], polyethylene, and polyacetylene were created successively to approximate their one-dimensional periodic polymers by using the MO -based elongation method. In the molecular-stacking models, we described the hypothetical surface of crystal as periodically arranged hydrogen molecules by the CO s, and several hydrogen molecules were stacked up on the surface one after another with the elongation procedure. Furthermore, the lattice defect on surface in which a part of stacked layer is lacking was dealt with by our approach. We also treated carbon monoxide chemisorption on a periodic magnesium chain as a more realistic model. Results for these systems support the applicability of our method for nonperiodic interactions in one- and two-dimensional large systems. © 1995 John Wiley & Sons, Inc.     

Structure of associates in tetramethylurea aqueous solutions from the data of Raman scattering spectroscopy

The results from investigating interactions between tetramethylurea (TMU) and water molecules by means of Raman light scattering spectroscopy (RS) are presented. It is established that spectroscopic manifestations of association of TMU and H₂O molecules are observed for the TMU molecule valence vibration band ν(CO) 1638 cm⁻¹. By means of quantum-chemical calculations, it is shown that the band sensitivity to molecular environment is defined by the number of 5–6 H₂O molecules. It is found that in a pure TMU medium, chain dimers are formed due to the interactions of molecular dipoles arranged in parallel and hydrogen bonds of the C-H…O type. Ground state geometries of TMU, TMU-TMU, H₂O molecules and TMU · (H₂O) _n complexes (n = 1−14) are optimized by the density functional B3LYP procedure, using the 6–31++G(d, p) basis set. The main vibration frequencies are calculated in the harmonic approximation. Associate formation energies are calculated with allowance for the basis set superposition error (BSSE).     

Theoretical study on intermolecular interactions in BrF/HnX adducts

Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and H_nX (HF, H₂O, and NH₃) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions.     

Ab initio studies of peroxynitrite anion-water complexes

Quantum mechanical methods have been applied to thecis-ONOO^–-H₂O,cis-ONOO^–-(H₂O)₂ andtrans- ONOO^–-H₂O complexes. Equilibrium geometries, binding energies, net atomic charges and vibrational frequencies are presented for several different arrangements. The MØller-Plessett second-order perturbation (MP2) method predicted shorter hydrogen bonds than the SCF method, but the computed Hartree-Fock (HF) binding energies are similar to counterpoise corrected MP2 values. The geometry changes of ONOO^– and water after solvation are examined. The ONOO^– and H₂O bond length changes follow typical hydrogen bond structural trends, whereas bond angles in ONOO^– are unaffected when the hydrogen bond is formed, similar to the conclusions from NO ₂ ^– -(H₂O) _n HF/6-31G studies and Monte Carlo simulations. Thecis-ONOO^–-(H₂O) _n frequencies are compared with the solution Raman spectrum and with calculations on isolated ONOO^–.     

Ab initio studies on infinite linear hydrogen fluoride chains

Ab initio crystal orbital calculations on linear infinite chains of hydrogen fluoride and MO calculations on HF and the linear dimer have been performed. Equilibrium geometries, force constants, band structures, densities of states and longitudinal phonon dispersions are presented, and compared with the available data. In agreement with experiment the most common features of hydrogen bonding, elongation of HX bond length (ΔR_HX and decrease in HF stretching force constants, are much more pronounced in the solid state than in the isolated dimer.     

Potential curves for proton motion in H-bonded systems: HF and H2O polymers

The presence of long range coupling between hydrogen atoms is shown for the HF and H₂O hydrogen bonded systems. The coupling of H atoms critically depends on the spatial orientation of the H atoms being considered. Explicit calculations of the potential curves of the protons are performed using as a model a ring of six HF, or H₂O, molecules. The method of calculation is the CNDO/2. The strong similarities of the results for H₂O and HF polymers supports the conclusion that the coupling is essentially due to factors such as the asymmetric equilibrium position of the H atoms, the high electronic polarizability of the system, etc.     

Molecular orbital theory of the hydrogen bond. VIII. Hydrogen bonding in H2OH2CO in relaxed singlet and triplet n → π* states

Ab initio SCF CI calculations with a minimal STO-3G basis set have been performed on the hydrogen bonded dimers in which H₂O is the proton donor to H₂CO in its relaxed singlet and triplet n→π^* states. Two dimers which are easily interconverted are found in the singet n→π^* state with hydrogen bond energies of 1.82 and 1.71 kcal/mole. The equilibrium dimer in the triplet state has a hydrogen bond energy of 2.97 kcal/mole. In both states, hydrogen bond formation occurs at the carbon atom. The structures of the dimers and the nature of the intermolecular surfaces in the regions of hydrogen bond formation are examined. Electron densities and distributions are also discussed.     

Orbital relaxation and the third-order induction energy in symmetry-adapted perturbation theory

Theoretical investigations of the induction interaction between closed-shell molecules which fully account for the orbital relaxation effects are presented. Explicit expressions for the third-order induction energy in terms of molecular integrals and orbital energies are given and implemented within the sapt2008 program for symmetry-adapted perturbation theory (SAPT) calculations. Numerical investigations for the He–He, He–LiH, Ar–Ar, H₂–CO, H₂O–H₂O, and H₂O–NH₃ model dimers show that the orbital relaxation increases the third-order induction interaction by 15 to 50% at near-equilibrium geometries, with the largest effect observed for complexes involving highly polar monomers. At large intermonomer separations, the relaxed third-order induction energy perfectly recovers the difference $\delta E^{\rm HF}_{\rm int}$ between the Hartree–Fock interaction energy and the sum of the uncorrelated SAPT contributions through second order in the intermolecular interaction operator. At the near-equilibrium geometries, the sum of the relaxed third-order induction and exchange-induction energies reproduces, however, only a small fraction (6 to 15%) of $\delta E^{\rm HF}_{\rm int}$ for the nonpolar systems and about 40 to 60% for the polar ones. A comparison of the complete SAPT calculations with the coupled-cluster treatment with single, double, and noniterative triple excitations [CCSD(T)] suggests that the pure SAPT approach with all the available third-order corrections is more accurate for nonpolar systems while for the polar ones the hybrid approach including $\delta E^{\rm HF}_{\rm int}$ gives better results.     

Ab initio investigation of water clusters (H2O)n (n = 2–34)

Various properties of typical structures of water clusters in the n = 2–34 size regime with the change of cluster size have been systematically explored. Full optimizations are carried out for the structures presented in this article at the Hartree–Fock (HF) level using the 6‐31G(d) basis set by taking into account the positions of all atoms within the cluster. The influence of the HF level on the results has been reflected by the comparison between the binding energies of (H₂O)_n (n = 2–6, 8, 11, 13, 20) calculated at the HF level and those obtained from high‐level ab initio calculations at the second‐order Møller–Plesset (MP2) perturbation theory and the coupled cluster method including singles and doubles with perturbative triples (CCSD(T)) levels. HF is inaccurate when compared with MP2 and CCSD(T), but it is more practical and allows us to study larger systems. The computed properties characterizing water clusters (H₂O)_n (n = 2–34) include optimal structures, structural parameters, binding energies, hydrogen bonds, charge distributions, dipole moments, and so on. When the cluster size increases, trends of the above various properties have been presented to provide important reference for understanding and describing the nature of the hydrogen bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Calculation of periodic molecular systems with perturbed periodicity within the PCILO framework. II. Model systems

The energetic behavior of one-dimensional (HF)_n and (H₂O)_n chains with added or inserted H₂O or HF was studied by means of the PCILOPSI method presented in Part I. The results were compared with the ones by the original PCILO method. The stabilization energies are in good qualitative agreement; energy differences due to impurity effects even quantitatively agree. The results show that the PCILOPSI method is well suited for the study of perturbed periodic molecular systems.     

Density Functional Theory Study on Hydrogen Bonding Interaction of Catechin-(H2O)n

Density functional theory B3LYP method with 6‐31G* basis set has been used to optimize the geometries of the catechin, water and catechin‐(H₂O)_n complexes. The vibrational frequencies have been studied at the same level to analyze these complexes. Six and eleven stable structures for the catechin‐H₂O and catechin‐(H₂O)₂ have been found, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are from ?13.27 to ?83.56 kJ/mol. All calculations also indicate that there are strong hydrogen‐bonding interactions in catechin‐water complexes. The strong hydrogen‐bonding contributes to the interaction energies dominantly. The O–H stretching motions in all the complexes are red‐shifted relative to that of the monomer.     

Cooperativity between the Halogen Bond and the Hydrogen Bond in H3N⋅⋅⋅XY⋅⋅⋅HF Complexes (X,Y=F,Cl, Br)

Ab initio calculations are used to provide information on H₃N???XY???HF triads (X, Y=F, Cl, Br) each having a halogen bond and a hydrogen bond. The investigated triads include H₃N???Br₂‐HF, H₃N???Cl₂???HF, H₃N???BrCI???HF, H₃N???BrF???HF, and H₃N???ClF???HF. To understand the properties of the systems better, the corresponding dyads are also investigated. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads are studied at the MP2 level of theory with the 6‐311++G(d,p) basis set. Because the primary aim of this study is to examine cooperative effects, particular attention is given to parameters such as cooperative energies, many‐body interaction energies, and cooperativity factors. The cooperative energy ranges from ?1.45 to ?4.64 kcal mol^?1, the three‐body interaction energy from ?2.17 to ?6.71 kcal mol^?1, and the cooperativity factor from 1.27 to 4.35. These results indicate significant cooperativity between the halogen and hydrogen bonds in these complexes. This cooperativity is much greater than that between hydrogen bonds. The effect of a halogen bond on a hydrogen bond is more pronounced than that of a hydrogen bond on a halogen bond.     

DFT study on the intermolecular interactions between Aun (n = 2–4) and thymine

Density functional B3LYP method with 6-31++G** basis set is applied to optimize the geometries of the luteolin, water and luteolin–(H₂O)_n complexes. The vibrational frequencies are also studied at the same level to analyze these complexes. We obtained four steady luteolin–H₂O, nine steady luteolin–(H₂O)₂ and ten steady luteolin–(H₂O)₃, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) are used to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are within −13.7 to −82.5 kJ/mol. The strong hydrogen bonding mainly contribute to the interaction energies, Natural bond orbital analysis is performed to reveal the origin of the interaction. All calculations also indicate that there are strong hydrogen bonding interactions in luteolin–(H₂O)_n complexes. The OH stretching modes of complexes are red-shifted relative to those of the monomer.     

Molecular orbital studies of polyethylene deformation

Young's modulus E for polyethylene in the chain direction is calculated with molecular orbital theory applied to n-alkanes C₃H₈ through n-C₁₃H₂₈ and analyzed with the cluster-difference method. Semiempirical CNDO, MNDO, and AM1 models and ab initio HF/STO-3G, HF/6-31G, HF/6-31G*, and MP2/6-31G* models are used. Cluster-difference results, when extrapolated to infinite chain length, give E in good agreement with moduli evaluated with molecular cluster or crystal orbital methods, provided minimal basis sets are employed. E decreases from 495 GPa (CNDO) to 336 GPa (MP2/6-31G*) as the level of theory is improved, consistent with established behaviors of the various models. Our calculations do not reproduce earlier molecular cluster or crystal orbital results, which gave E < 330 GPa. The most rigorous MP2/6-31G* model is known to overestimate force constants by ∼ 11%; the scaled modulus E = 299 GPa is in good accord with E = 306 GPa from recent calculations based on experimental vibration frequencies. © 1996 John Wiley & Sons, Inc.     

A theoretical investigation of electronic reorganizations accompanying core and valence ionization in simple hydrogen bonded systems

Non-empirical LCAO MO SCF calculations have been carried out on the ground state and core ionized states of some hydrogen bonded dimers, and in the particular case of H₂O the trimer has also been investigated. Comparison of absolute and relative binding energies and relaxation energies with respect to the corresponding monomers reveals that substantial changes occur in going to the associated species. The relaxation energies for a given core hole are shown to increase on going from monomer to dimer indicating that intermolecular contributions to relaxation energies are of the same sign irrespective of the sign for the shift in core binding energy. Creation of a core hole in the dimer species is shown to give rise to substantial changes in hydrogen bond energies compared with the neutral species. In the particular case of valence holes dominantly of 2s and 2p character it is shown that trends in shifts and relaxation energies parallel those for the core hole states.     

Minimal basis sets in calculations of intermolecular interaction energies

Several minimal (7, 3/3) Gaussian basis sets have been used to calculate the energies and some other properties of CH₄ and H₂O. Improved basis sets developed for these molecules have been extended to NH₃ and HF and employed to H₂CO and CH₃OH. Interaction energies between XH_n molecules have been calculated using the old and the new minimal basis sets. The results obtained with the new basis sets are comparable in accuracy to those calculated with significantly more extended basis sets involving polarization functions. Binding energies calculated using the counterpoise method are not much different for the new and the old minimal basis sets, and are likely to be more accurate than the results of much more extended calculations.