Structure of the ammonia dimer studied by density functional theory

Self-consistent Kohn–Sham density functional calculations have been carried out to study the structure of the ammonia dimer. The local-density approximation yields unusually large binding energy and short internitrogen distance compared with the experimental and more accurate theoretical data. The results from the Becke–Perdew gradient-corrected functionals are generally in good agreement with those at the SCF MP 2 level when the geometry is fully optimized with various large basis sets. With our best estimation, the staggered quasi-linear structure (C_s) is 0.6 kcal/mol lower in energy than the symmetric cyclic one (C_2h). The hydrogen-bonded N—H bond in the staggered quasi-linear structure is found to be 0.008 Å longer than the N—H bond in ammonia. In our calculations, we could not find the minima on the energy surface corresponding to the two asymmetric cyclic structures suggested by microwave spectra and coupled pair functional calculations. © 1994 John Wiley & Sons, Inc.     

A comparison of Hartree—Fock,MP2, and DFT results for the HCN dimer and crystal

A number of hydrogen-bond related quantities—geometries, interaction energies, dipole moments, dipole moment derivatives, and harmonic vibrational frequencies—were calculated at the Hartree—Fock, MP2, and different DFT levels for the HCN dimer and the periodic HCN crystal. The crystal calculations were performed with the Hartree—Fock program CRYSTAL92, which routinely allows an a posteriori electron-correlation correction of the Hartree—Fock obtained lattice energy using different correlation-only functionals. Here, we have gone beyond this procedure by also calculating the electron-correlation energy correction during the structure optimization, i.e., after each CRYSTAL92 Hartree—Fock energy evaluation, the a posteriori density functional scheme was applied. In a similar manner, we optimized the crystal structure at the MP2 level, i.e., for each Hartree—Fock CRYSTAL92 energy evaluation, an MP2 correction was performed by summing the MP2 pair contributions from all HCN molecules within a specified cutoff distance. The crystal cell parameters are best reproduced at the Hartree—Fock and the nongradient-corrected HF + LDA and HF + VWN levels. The BSSE-corrected MP2 method and the HF + P91, HF + LDA, and HF + VWN methods give lattice energies in close agreement with the ZPE-corrected experimental lattice energy. The (HCN)₂ dimer properties are best reproduced at the MP2 level, at the gradient-corrected DFT levels, and with the B3LYP and BHHLYP methods. © 1996 John Wiley & Sons, Inc.     

Molecular orbital theory of the hydrogen bond. XXX. Water-cytosine complexes

Ab initio SCF and SCF -CI calculations with the STO -3G basis set have been performed to investigate the structures and energies of water–cytosine complexes and the intermolecular water–cytosine surface in the cytosine molecular plane. Although there are six nominal hydrogen-bonding sites in this plane, only three dimers are distinguishable in the ground state. The most stable has an energy of ?10.7 kcal/mol, and is found in the N₁? H and O₂ region. An asymmetric cyclic structure in which the water molecule bridges adjacent N₁? H and O₂ sites is the preferred form of this dimer. The dimer in the region between O₂ and N₄? H′ of the amino group is slightly less stable at ?10.4 kcal/mol, and also has an asymmetric cyclic structure as the preferred structure, with the water molecule bridging amino N₄? H′ and N₃ hydrogen-bonding sites. The third dimer has the amino group as the proton donor to water through the hydrogen cis to C₅, and a stabilization energy of ?7.0 kcal/mol. The water-cytosine surface is characterized by deeper minima and higher barriers than the water-thymine surface and by a decreased mobility of the water molecule between adjacent hydrogen-bonding sites. Absorption of energy by the C₂?O group leads to the first n → π* excited state in which interactions of water with O₂ are broken. The water-cytosine dimers remain bound in this state, but may change structurally. In the second n → π* state interactions between water and N₃ are no longer stabilizing. As a result, the dimer in the O₂ and N₄? H′ region collapses to either a dimer with water the proton donor to O₂, or one with N₄? H′ the proton donor to water. The other two dimers remain bound. All excited dimers are destabilized on vertical excitation relative to the ground state.     

Investigation of the Benzene–Naphthalene and Naphthalene–Naphthalene Potential Energy Surfaces: DFT/CCSD(T) Correction Scheme

The potential energy surfaces of the naphthalene dimer and benzene–naphthalene complexes are investigated using the recently developed DFT/CCSD(T) correction scheme [J. Chem. Phys. 2008 , 128, 114 102]. One and three minima are located on the PES of the benzene–naphthalene and the naphthalene dimer complexes, respectively, all of which are of the parallel‐displaced type. The stabilities of benzene–naphthalene and the naphthalene dimer are ?4.2 and ?6.2 kcal mol^?1, respectively. Unlike the benzene dimer, where the T‐shaped complex is the global minimum, the lowest‐energy T‐shaped structure is about 0.2 and 1.6 kcal mol^?1 above the global minimum on the benzene–naphthalene and the naphthalene dimer potential energy surfaces, respectively.     

A First‐Principles Examination of the Asymmetric Induction Model in the Binap/RhI‐Catalysed 1,4‐Addition of Phenylboronic Acid to Cyclic Enones by Density Functional Theory Calculations

First‐principles modelling of the diastereomeric transition states in the enantiodiscrimination stage of the catalytic cycle can reveal intimate details about the mechanism of enantioselection. This information can be invaluable for further improvement of the catalytic protocols by rational design. Herein, we present a density functional theory (IEFPCM/PBE0/DGDZVP level of theory) modelling of the carborhodation step for the asymmetric 1,4‐arylation of cyclic α,β‐unsaturated ketones mediated by a [(binap)Rh^I] catalyst. The calculations completely support the older, qualitative, pictorial model predicting the sense of the asymmetric induction for both the chelating diphosphane (binap) and the more recent chiral diene (Phbod) ligands, while also permitting quantification of the enantiomeric excess (ee). The effect of dispersion interaction correction and basis sets has been also investigated. Dispersion‐corrected functionals and solvation models significantly improve the predicted ee values.     

Structure of Cyclic Aryl Thiosester Dimer Based on o—Phthaloyl Dichloride and Bis（4—mercaptophenyl）Sulfide

A Cyclic aryl thioester dimer was prepared by the reaction of o-phthaloyl dichloride and bis(4-mercaptophenyl)sulfide in good yield under pseudo-high dilution conditions via interfacial polycondensation.The structure of the cyclic dimer was confirmed by a conmbination of MALDI-TOF-Ms,FTIR,gel permeation chromatography and NMR analyses.The X-ray diffraction study of the single crystal of cyclic thioester dimer obtained form two sotutions reveals no severe internal strain on the cyclic structure.     

Molecular orbital theory of the hydrogen bond. 24. Ground-state water–uracil complexes

Ab initio SCF calculations with the STO -3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water–uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N₁? H and O₂, N₃? H and O₂, and N₃? H and O₄. Open structures form at O₄, N₁? H, and N₃? H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N₁? H and the cyclic one at N₁? H and O₂. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N₃? H and a cyclic structure at N₃? H and O₄. The third cyclic structure at N₃? H and O₂ collapses to the “wobble” dimer at N₃? H and O₄. The two “wobble” dimers are significantly more stable than the open dimer formed at O₄, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N₁? H than N₃? H, owing to a more favorable molecular dipole moment alignment when association occurs through H₁. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water–uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.     

Hydro­gen bonds and C—H⋯O interactions in 2‐(2‐methyl­benzyl)­malonic acid at 150 K

The title compound, C₁₁H₁₂O₄, crystallized in the centrosymmetric space group Pbca with one mol­ecule as the asymmetric unit. The two hydrogen bonds have O_D?O_A distances of 2.667 (2) and 2.628 (2) Å, and O—H?O angles of 179 (2) and 177 (2)°. Each hydrogen bond forms an R(8) cyclic dimer about a center of symmetry. The leading intermolecular C—­H?O interaction has an H?O distance of 2.66 Å and a C—H?O angle of 160°. Taken together with the hydrogen bonds, it results in a three‐dimensional network of inter­actions. The structure is compared with that of a close analog, benzyl­malonic acid.     

Assessment of new meta and hybrid meta density functionals for predicting the geometry and binding energy of a challenging system: the dimer of H2S and benzene

Noncovalent interactions of a hydrogen bond donor with an aromatic pi system present a challenge for density functional theory, and most density functionals do not perform well for this kind of interaction. Here we test seven recent density functionals from our research group, along with the popular B3LYP functional, for the dimer of H 2S with benzene. The functionals considered include the four new meta and hybrid meta density functionals of the M06 suite, three slightly older hybrid meta functionals, and the B3LYP hybrid functional, and they were tested for their abilities to predict the dissociation energies of three conformations of the H 2S-benzene dimer and to reproduce the key geometric parameters of the equilibrium conformation of this dimer. All of the functionals tested except B3LYP correctly predict which of the three conformations of the dimer is the most stable. The functionals that are best able to reproduce the geometry of the equilibrium conformation of the dimer with a polarized triple-zeta basis set are M06-L, PWB6K, and MPWB1K, each having a mean unsigned relative error across the two experimentally verifiable geometric parameters of only 8%. The success of M06-L is very encouraging because it is a local functional, which reduces the cost for large simulations. The M05-2X functional yields the most accurate binding energy of a conformation of the dimer for which a binding energy calculated at the CCSD(T) level of theory is available; M05-2X gives a binding energy for the system with a difference of merely 0.02 kcal/mol from that obtained by the CCSD(T) calculation. The M06 functional performs well in both categories by yielding a good representation of the geometry of the equilibrium structure and by giving a binding energy that is only 0.19 kcal/mol different from that calculated by CCSD(T). We conclude that the new generation of density functionals should be useful for a variety of problems in biochemistry and materials where aromatic functional groups can serve as hydrogen bond acceptors.     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Difluoroamine Complex

Introduction　　ApplicationsofabinitiocalculationstointermolecularinteractionsincludingeitherweakvanderWaalsorstrongerhydrogenbondinghavedrawnmuchattentioninthepastdecadesbecausetheyareimportantinawiderangeofphysical,chemicalandbiologicalfields .1 5Inre centyears ,wehaveappliedtheintermolecularinteractionstoenergeticsystemsandobtainedsomemeaningfulinfor mationthatisvaluableforthestudyofenergeticmateri als .6 14 Thebehaviorofmolecularcomplexesisusuallybe tweentwoextremes :thegasphaseandthecrys…     

Molecular dynamics simulation of liquid water: hybrid density functionals

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.     

Sensitivity of the properties of ruthenium "blue dimer" to method, basis set, and continuum model

The ruthenium "blue dimer" [(bpy)(2)Ru(III)OH(2)](2)O(4+) is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structure of "blue dimer" using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.     

Comparison of Hydrogen Bonds in FH—CO and FH—OC Weakly Bound Dimer Complexes

Weakly bound dimer complexes FH—CO and FH—OC were investigated using various ab initio and density function theory (DFT) methods. This study compares the strengths of the H—C H‐bond in FH—CO and the H—O H‐bond in FH—OC. The energy difference between dimers, the H‐bond energy, the inter‐monomer distance, the inter‐monomer vibration frequencies, the red shift of the HF stretching frequency, and the elongation of HF bond, all demonstrate that the H—C H‐bond is stronger than the related H—O H‐bond, according to all methods. The calculated Gibbs energies of the formation of the two dimers show that the weakly bound complexes are unstable at room temperature (T = 298 K) and ordinary pressure (P = 1 atm). However, decreasing T or increasing P monotonically decreases ΔG and increases the related equilibrium constant, K, of their dimer formation.     

Preparation and photocrosslinking behaviors of polyesters derived from trans-2,2′-dihydroxystilbene

The monomer, trans-2,2′-dihydroxystilbene (DHS), has been prepared by asymmetric photocleavage (254 nm) of coumarin dimer acid derived from coumarin dimer. Four new polyesters are successfully synthesized by interfacial polycondensation of the DHS with adipoyl chloride, azelaoyl chloride, sebacoyl chloride, and dodecanedioyl dichloride, respectively. The reduced viscosities of the polyesters decrease from 0.32 to 0.11 dL/g as the number of methylene unit in diacid chlorides increases from 4 to 10. From DSC investigation, it is found that the polyesters are semi-crystalline polymers with T_m = 39–192°C. Under 350 nm light, photocrosslinking behavior in solution and film-state is investigated by UV spectral change with irradiation time (350 nm). The photoreactive stilbene chromophores in the main chain dimerize to form cyclobutane derivatives, and lead to crosslinking of the polyesters. Photosensitivity in the film state has also been evaluated by their characteristic curves. Polyester from dodecanedioyl dichloride ( 5d ) exhibits the highest initial reaction rate and ultimate crosslinking ratio. © 1995 John Wiley & Sons, Inc.     

Calculation of the Vibrationally Resolved,Circularly Polarized Luminescence of d‐Camphorquinone and (S,S)‐trans‐β‐Hydrindanone

Circularly polarized luminescence (CPL), the differential emission of left‐ and right‐handed circularly polarized light from a molecule, is modeled by using time‐dependent density functional theory. Calculations of the CPL spectra for the first electronic excited states of d‐camphorquinone and (S,S)‐trans‐β‐hydrindanone under the Franck–Condon approximation and using various functionals are presented, as well as calculations of absorption, emission, and circular dichroism spectra. The functionals B3LYP, BHLYP, and CAM‐B3LYP are employed, along with the TZVP and aug‐cc‐pVDZ Gaussian‐type basis sets. For the lowest‐energy transitions, all functionals and basis sets perform comparably, with the long‐range‐corrected CAM‐B3LYP better reproducing the excitation energy of camphorquinone but leading to a blue shift with respect to experiment for hydrindanone. The vibrationally resolved spectra of camphorquinone are very well reproduced in terms of peak location, widths, shapes, and intensities. The spectra of hydrindanone are well reproduced in terms of overall envelope shape and width, as well as the lack of prominent vibrational structure in the emission and CPL spectra. Overall the simulated spectra compare well with experiment, and reproduce the band shapes, emission red shifts, and presence or absence of visible vibrational fine structure.     

A Nove Asymmetric ent—Kauranoid Dimer from Isodon enanderianus

Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer,enanderi-nanin J(1).The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR tecniques ),Enanderinanin J was a dimer of xerophilusin A and probably formed by [4 2] cycloaddition.     

An HF and DFT ab initio Study on the Mechanism of ortho‐Directed Lithiation of Hydric and Nonhydric Aromatic Compounds Incorporating Aggregation and Discrete Solvation: The Role of N,N,N′,N′‐Tetramethylethane‐1,2‐diamine (TMEDA) in Lithiation Reactions

An HF and DFT ab initio study was set up to decipher the roles of aggregation and solvation in the ortho‐directed lithiation of aromatics (hydric and nonhydric), as well as to shed light on the much debated question of precomplexation in the mechanism of lithiation. Ab initio (HF/6‐31‐G*) calculations on the lithiation of non‐hydric aromatics have uncovered several competitive routes operating as a function of the aggregation state of the organolithium base used. Specifically, two competitive routes were found for the lithiation of the anisole model 2 by organolithium dimers 1‐dim , namely the so‐called cyclic‐dimer and open‐dimer routes, whereas, for organolithium tetramers 1‐tet , the corresponding cyclic route is the only one operative, and, for monomers 1‐mon , several optional routes seem to be available. Precomplexation is, in all cases, a requirement. According to the computational data presented, the mysterious rate acceleration experimentally observed for lithiations carried out in TMEDA can be assigned to an aggregation effect on the intermediate open‐dimer species, which subsidiarily give rise to several so‐called s‐monomer routes, of which the dimerization‐driven s‐monomer route s‐m_3b is the one having the lowest energy barrier. The relevant species characteristic of both the open‐dimer and s‐monomer routes are the so‐called open dimers, i.e., high‐energy intermediates (actually, spiro dimeric aggregates), resulting from cleavage‐induced associative complexation of the aromatic substrate upon the fully solvated organolithium dimer. DFT calculations (B3LYP/6‐31+G*) also revealed that the peri‐lithiation (i.e., Li at C(8)) of 1‐naphthol model 3 is a slow process taking place preferentially through the open‐dimer route.     

2,2′‐Bi[benzo[b]thiophene]: an unexpected isolation of the benzo[b]thiophene dimer

The crystal structure of 2,2′‐bi[benzo[b]thiophene], C₁₆H₁₀S₂, at 173 K has triclinic (P) symmetry. It is of interest with respect to its apparent mode of synthesis, as it is a by‐product of a Stille cross‐coupling reaction in which it was not explictly detected by spectroscopic methods. It was upon crystal structure analysis of a specimen isolated from the mother liquor that this reaction was determined to give rise to the title compound, which is a dimer arising from the starting material. Two independent half‐molecules of this dimer comprise the asymmetric unit, and the full molecules are generated via inversion centers. Both molecules in the unit cell exhibit ring disorder, and they are essentially identical because of their rigidity and planarity.