Structures and stabilities of diacetylene-expanded polyhedranes by quantum mechanics and molecular mechanics

The structures, heats of formation, and strain energies of diacetylene (buta-1,3-diynediyl) expanded molecules have been computed with ab initio and molecular mechanics calculations. Expanded cubane, prismane, tetrahedrane, and expanded monocyclics and bicyclics were optimized at the HF/6-31G(d) and B3LYP/6-31G(d) levels. The heats of formation of these systems were obtained from isodesmic equations at the HF/6-31G(d) level. Heats of formation were also calculated from Benson group equivalents. The strain energies of these expanded molecules were estimated by several independent methods. An adapted MM3 molecular mechanics force field, specifically parametrized to treat conjugated acetylene units, was employed for one measure of strain energy and as an additional method for structural analysis. Expanded dodecahedrane and icosahedrane were calculated by this method. Expanded molecules were considered structurally in the context of their potential material applications.     

Saturated hydrocarbon-benzene complexes: theoretical study of cooperative CH/pi interactions

High-level ab initio calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug(d,p)-6-311G(d,p) level were employed to investigate the cooperative CH/pi effects between the pi face of benzene and several modeled saturated hydrocarbons, propane, isobutane, cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclopentane, cyclooctane, and bicyclo[2.2.2]octane. In all cases, multiple C-H groups (2-4) are found to interact with the pi face of benzene, with one C-H group pointing close to the center of the benzene ring. The geometries of these complexes are governed predominantly by electrostatic interaction between the interacting systems. The calculated interaction energies (10-14 kJ mol(-1)) are 2-3 times larger than that of the prototypical methane-benzene complex. The trends of geometries, interaction energies, binding properties, as well as electron-density topological properties were analyzed. The calculated interaction energies correlate well with the polarizabilities of the hydrocarbons. AIM analysis confirms the hydrogen-bonded nature of the CH/pi interactions. Significant changes in proton chemical shift and stretching frequency (blue shift) are predicted for the ring C-H bond in these complexes.     

The effect of carbonyl substitution on the strain energy of small ring compounds and their six-member ring reference compounds

High level ab initio calculations have been applied to the estimation of ring strain energies (SE) of a series of three- and six-member ring compounds. The SE of cyclohexane has been estimated to be 2.2 kcal/mol at the CBS-APNO level of theory. The SE of cyclopropane has been increased to 28.6 kcal/mol after correction for the one-half of the SE of cyclohexane. The SEs of a series of carbonyl-containing three-member ring compounds have been estimated at the CBS-Q level by their combination with cyclopropane to produce a six-member ring reference compound. The SEs of cyclopropanone (5), the simplest alpha-lactone (6) [oxiranone], and alpha-lactam (7) [aziridinone] have been predicted to be 49, 47, and 55 kcal/mol, respectively, after correction for the SE of the corresponding six-member ring reference compound. The SEs of cyclohexanone, delta-valerolactone, and delta-valerolactam have been estimated to be 4.3, 11.3, and 5.1 kcal/mol, respectively. Marked increases in the SE of silacyclopropane and siladioxirane have been established, while significant decreases in the SEs of phosphorus, sulfur, dioxa- and diaza-containing three-member ring compounds were observed. The ring strain energies of the hydrocarbons (but not heterocycles) exhibit a strong correlation with their C-H bond dissociation energies.     

Sigma-antiaromaticity in cyclobutane,cubane, and other molecules with saturated four-membered rings

Dissected nucleus-independent chemical shift (NICS) analyses of cycloalkanes and cage hydrocarbons reveal contrasting ring current effects, diatropic in three- and five-membered and paratropic in four-membered ring systems. The large shielding effects of the C-C bonds of the archetypal sigma-aromatic, cyclopropane, are magnified in tetrahedrane and related structures. The remarkable deshielding effect of the cyclobutane C-C(sigma) bonds is general: cubane and cages with four-membered rings are strongly deshielding (i.e., sigma-antiaromatic).[structure--see text]     

传统氢键(X—H…Y)还是X—H…π相互作用？ ——无机苯与卤化氢相互作用本质的量子化学研究

在MP2/6-311＋＋G**水平对无机苯(B3N3H6)与卤化氢HX (X＝F, Cl, Br, I)相互作用体系进行了系统研究. 结果表明在B3N3H6-HX (X＝F, Cl, Br, I)体系的平衡几何结构中, HX的H原子倾向于指向B3N3H6环上的N原子, 且从HF到HI相互作用强度依次减弱. 与苯-卤化氢体系比较, 除与HF相互作用B3N3H6较C6H6强外, 其余体系B3N3H6均较C6H6弱(结合能数值相差4 kJ/mol左右). 对称匹配微扰理论(SAPT)能量分解结果说明静电、诱导和色散力对描述B3N3H6-卤化氢体系的相互作用都很重要, 从HF到HI静电能占总吸引作用能的百分比逐渐减少, 色散能占总吸引作用能的百分比逐渐增加, 这种变化趋势与苯-卤化氢体系比较类似, 表明B3N3H6与卤化氢的相互作用随着卤素原子序数的递增, 传统氢键作用趋势减弱, X—H…π相互作用趋势增强.     

Theoretical investigation of the He-I2(E3Πg) ion-pair state: ab initio intermolecular potential and vibrational levels

We present a theoretical study on the potential energy surface and vibrational bound states of the E electronic excited state of the HeI(2) van der Waals system. The interaction energies are computed using accurate ab initio methods and large basis sets. Relativistic small-core effective core potentials in conjunction with a quintuple-zeta quality basis set are employed for the heavy iodine atoms in multireference configuration interaction calculations for the (3)A' and (3)A" states. For the representation of the potential energy surface we used a general interpolation technique for constructing potential surfaces from ab initio data based on the reproducing kernel Hilbert space method. The surface presents global and local minima for T-shaped configurations with well-depths of 33.2 and 4.6 cm(-1), respectively. Vibrational energies and states are computed through variational quantum mechanical calculations. We found that the binding energy of the HeI(2)(E) T-shaped isomer is 16.85 cm(-1), in excellent agreement with recent experimental measurements. In lieu of more experimental data we also report our predictions on higher vibrational levels and we analyze the influence of the underlying surface on them. This is the first attempt to represent the potential surface of such a highly excited electronic state of a van der Waals complex, and it demonstrates the capability of the ab initio technology to provide accurate results for carrying out reliable studies to model experimental data.     

Strain Energies in Homoatomic Nitrogen Clusters N(4), N(6), and N(8)

Strain energies and resonance energies can be obtained as the energy changes for appropriate homodesmotic reactions using ab initio calculated total energies as the energies of the reactants and products involved. Homodesmotic reactions conserve bond types and preserve valence environments at all atoms, requirements that favor the cancellation of basis set and electron correlation errors in the ab initio energies. In this paper we calculate strain energies and resonance energies for N(4), N(6), and N(8) clusters in a number of chemically significant but, for nitrogen, hypothetical structural forms. The nitrogen cluster strain energies are generally of the same order of magnitude as those of isostructural hydrocarbon clusters, and individual differences can be explained by using the ring strain additivity rule and recognizing the effect of the presence of lone pairs of electrons on nitrogen clusters but not on the hydrocarbons. Resonance energies of the nitrogen clusters are much smaller than those of the comparable aromatic hydrocarbons. The differences can be rationalized by considering the relative strengths of CC and NN single and double bonds. Strain and resonance energies of nitrogen clusters are compared with those previously reported for homoatomic clusters of phosphorus and arsenic. Trends through the series are remarkably similar, but strain energies for clusters from lower periods are progressively smaller. Strain and resonance have been important organizing concepts in organic chemistry for many years. Estimates of corresponding parameters for inorganic analogs are only now becoming available.     

G3(MP2) ring strain in bicyclic phosphorus heterocycles and their hydrocarbon analogues

[Figure: see text] The ring strain present in 2-aza-1-phosphabicyclo[n.1.0]alka(e)nes (n = 1-5) is calculated at the G3(MP2) level using homodesmotic reactions. The influence of cyclopropa(e)nation and heteroatom substitution is analyzed by a comparison with the corresponding bicyclic hydrocarbons and separate ring systems. It is shown that the strain caused by fusion with a cyclopropane is the sum of the separate rings, whereas the strain resulting from fusion with cyclopropene leads to strain energies much larger than the sum of rings, as a result of the inverted nature of the bridgehead carbon. In all ring structures but one, cyclohexane, substitution by nitrogen and phosphorus is favorable and the effect is most pronounced for the most condensed structures. The calculated strain energies correlate very well with the experimental stability and reactivity of the bicyclic iron-amino phosphirane and phosphirene complexes.     

CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule

The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed.     

Complexes of ammonia with propane and cyclopropane: electrostatic guidelines for ab initio treatment

A model based on the molecular electrostatic potential (MESP) is employed for the investigation of structures and energies of complexes of ammonia with propane and cyclopropane. The electrostatic model geometries are employed as starting points for an ab initio investigation at the self-consistent field and second-order M?ller-Plesset (MP2) levels. The most stable structures of C₃H₆..NH₃ and C₃H₈..NH₃ complexes have the interaction energies of 10.07 kJ/mol and 8.15 kJ/mol, respectively, at the MP2/6-31G(d,p) level. The energy rank order of the structures is not altered with the use of the 6-31++G(d,p) basis set, and the basis␣set superposition error has little effect. The interaction energy decomposition analysis shows that the electrostatic component is dominant over the other ones. MESP topography thus seems to offer valuable hints for predicting the structures of weakly bonded complexes. Received: 8 July 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method

We analyzed the interaction energies between residues (fragments) in an oligopeptide occurring during dynamic simulations by using the fragment molecular orbital-Hamiltonian algorithm (FMO-HA) method, an ab initio MO-molecular dynamics technique. The FMO method enables not only calculation of large molecules based on ab initio MO but also easy evaluation of interfragment interaction energies. The glycine pentamer [(Gly)(5)] and decamer [(Gly)(10)] were divided into five and ten fragments, respectively. alpha-helix structures of (Gly)(5) and (Gly)(10) were stabilized by attractive interaction energies owing to intramolecular hydrogen bonds between fragments n and n+3 (and n+4), and beta-strand structures were characterized by repulsive interaction energies between fragments n and n+2. We analyzed interfragment interaction energies during dynamics simulations as the peptides' geometries changed from alpha helix to beta strand. Intramolecular hydrogen bonds between fragments 2-4 and 2-5 control the geometrical preference of (Gly)(5) for the beta-strand structure. The pitch of one turn of the alpha helix of (Gly)(10) elongated and thus weakened during dynamics due to a shifting of the intramolecular hydrogen bonds, and enabled the beta-strand structure to form. Changes in interaction energies due to the intramolecular hydrogen bonds controlled the tendency toward alpha-helix or beta-strand structure of (Gly)(5) and (Gly)(10). Evaluation of interfragment interaction energies during dynamics simulations thus enabled detailed analysis of the process of the geometrical changes occurring in oligopeptides.     

Computational study of the interaction of indole-like molecules with water and hydrogen sulfide

The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H···π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH(2) ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.     

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.     

Theoretical analysis of the hydrogen bond of imidazolium C(2)-H with anions

The intermolecular interaction energies of ion pairs of imidazolium-based ionic liquids were studied by MP2/6-311G level ab initio calculations. Although the hydrogen bond between the C(2) hydrogen atom of an imidazolium cation and anion has been regarded as an important interaction in controlling the structures and physical properties of ionic liquids as in the cases of conventional hydrogen bonds, the calculations show that the nature of the C(2)-H...X interaction is considerably different from that of conventional hydrogen bonds. The interaction energies of the imidazolium cation with neighboring anions in the four crystals of ionic liquids were calculated. The size of the interaction is determined mainly by the distance between the imidazolium ring and anion. The calculated interaction energy is nearly inversely proportional to the distance, which shows that the charge-charge interaction is the dominant interaction in the attraction. The orientation of the anion relative to the C(2)-H bond does not greatly affect the size of the interaction energy. Calculated interaction energy potentials of 1,3-dimethylimidazolium tetrafluoroborate ([dmim][BF(4)]) complexes show that the C(2)-H bond does not prefer to point toward a fluorine atom of the BF(4). This shows that the C(2)-H...X hydrogen bond is not essential for the attraction.     

Ab initio studies of structural features not easily amenable to experiment. 17. The molecular structures of some strained cyclic hydrocarbons and estimates of their strain energies

The molecular structures of tricyclohexane, norbornane, quadricyclane, and cubane were completely refined by standard ab initio force relaxation on the 4-21G level. The results can be used as a basis to interpret some contradictory experimental reports found in the literature and to establish some hitherto unobserved structural trends involving the C? C and C? H bond distances of the cases studied. Group Delta;E values for C? (H)₃(C), C? (H)₂(C)₂, and C? (H)(C)₃ (Benson's notation) derived from the total energies of the completely relaxed 4-21G geometries of a number of unstrained hydrocarbons are also listed. The values are used to estimate the strain energies of the systems studied and of the optimized 4-21G geometries of cyclopropane, cyclobutane, cyclohexane, and bicyclo (2.1.0)pentane. Cooperative effects in the strain energies are discussed.     

Prediction of Vapor–Liquid Equilibria for Pb–Pd and Pb–Pt Alloys Using Ab Initio Methods in Vacuum Distillation

The vapor–liquid equilibrium (VLE) phase diagrams of Pb–Pd and Pb–Pt alloy systems in vacuum distillation were obtained based only on pure-component properties and the structures of the atoms. The interaction energies between pairs of atoms were calculated from ab initio methods and were used as the input energy parameters for the Wilson equation. The calculated activity data of the components, using energy parameters which were obtained by ab initio methods, are in good agreement with the experimental data. It is revealed that a cluster size of eight atoms, optimized using the NVT ensemble at 300 K, a time step of 1 femtosecond, and the simulation time 10 ps gives a good representation of the liquid phase systems. This approach can be used to obtain accurate VLE predictions for alloy systems in vacuum distillation. The VLE phase diagram has a significant advantage in guiding experiment and industrial production in vacuum metallurgy.     

Site charge models for molecular electrostatic potentials of cycloalkanes and tetrahedrane

The molecular structures of cycloalkanes (from cyclopropane to cyclodecane) and tetrahedrane were optimized at the Hartree–Fock/6–31G** level and their molecular electric potentials (MEPs) were calculated using a geodesic grid. The MEPs were fitted using net atomic charges and several site charge models. The net atomic charge model gave very poor fits to the MEPs in every case. A model with additional methylene bisector charge sites, similar to one successfully used previously for linear alkanes, greatly improved the fits to the MEPs of these cycloalkanes. The MEPs of the highly strained molecules cyclopropane and tetrahedrane were further studied using ring center and displaced bond charge sites. The fitting of the MEP of cyclopropane was consistent with a banana bond model with asymmetrically displaced electron density in the C C bonds. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 579–585, 1999     

从头算和ABEEMσπ/MM对(CH_3OH)_n(n=3～12)和[Na(CH_3OH)_n]~+(n=3～6)体系的研究

采用从头算方法(ab initio)和原子-键电负性均衡浮动电荷分子力场方法(ABEEMσπ/MM),对甲醇团簇(CH_3OH)n(n=3~12)和[Na(CH_3OH)_n]~+(n=3~6)体系的结构、电荷分布和结合能进行研究.依据从头算结果构建上述体系的ABEEMσπ/MM浮动电荷势能函数,并确定相关参数.结果表明,ABEEMσπ/MM所获得的结构和结合能等均优于OPLS/AA力场,并与从头算结果相符,其中键长的平均绝对偏差(AAD)小于0.004 nm,键长、键角和结合能的相对均方根偏差(RRMSD)分别小于3.8%,1.7%和6.8%;电荷分布与从头算结果的线性相关系数均大于0.99.