A theoretical study of bond energies in model Si–H–Cl molecules using density functional approaches for representing Si surface chemistry

The reliability of density functional theory (DFT) methods for calculating Si(SINGLE BOND)2H, Si(SINGLE BOND)Cl, and Si(SINGLE BOND)Si bond energies is examined in reactions involving molecules and small clusters representing various surface sites appropriate for Si surface chemistry. Results are presented for systematic studies using a valence double-zeta polarization basis for both all-electron calculations and valence–electron calculations employing effective core potentials (ECPs). All-electron DFT results are comparable to much more demanding MP4, G2, and MC–SCF–CI calculations for computed bond energies. Whereas the use of ECPs introduces systematic energy differences of ca. 3–5 kcal/mol compared to AE results, depending on the type of bond involved, the use of ECPs for carrying out calculations on larger clusters is discussed where AE calculations become more computationally demanding. The convergence of Si bond energies as a function of replacing hydrogens with silyl groups is examined. In constructing models to describe etching processes involving Cl species on Si surfaces, the need for incorporating differences in thermochemistries for one-, two-, and three-coordinate Si surface sites is emphasized. Comparisons of semiempirical approaches for thermochemistries of Si-containing species find these methods somewhat less reliable for obtaining reliable bond energies compared to computationally more demanding DFT and ab initio correlated models. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2075–2085, 1997     

尿素晶体介电性能的量子化学计算

利用量子化学的第一性原理,在自洽场理论水平上对尿素晶体的线性和非线性光学介电性质进行了定量计算,获得了与实验值相符的理论计算结果.提供了一种解决分子晶体量子化学理论计算的新思路.     

Polarization charge densities provide a predictive quantification of hydrogen bond energies

A systematic density functional theory based study of hydrogen bond energies of 2465 single hydrogen bonds has been performed. In order to be closer to liquid phase conditions, different from the usual reference state of individual donor and acceptor molecules in vacuum, the reference state of donors and acceptors embedded in a perfect conductor as simulated by the COSMO solvation model has been used for the calculation of the hydrogen bond energies. The relationship between vacuum and conductor reference hydrogen bond energies is investigated and interpreted in the light of different physical contributions, such as electrostatic energy and dispersion. A very good correlation of the DFT/COSMO hydrogen bond energies with conductor polarization charge densities of separated donor and acceptor atoms was found. This provides a method to predict hydrogen bond strength in solution with a root mean square error of 0.36 kcal mol(-1) relative to the quantum chemical dimer calculations. The observed correlation is broadly applicable and allows for a predictive quantification of hydrogen bonding, which can be of great value in many areas of computational, medicinal and physical chemistry.     

Removing critical errors for DFT applications to transition-metal nanoclusters: correct ground-state structures of Ru clusters

As ruthenium plays an important role in heterogeneous catalysis, understanding the structural and electronic properties of Ru clusters is crucial to advancement of technology. Because of its efficiency, density functional theory (DFT) calculations are often utilized in nanoscience, but careful validation is necessary. Recently, small, nonmetallic Ru(n) clusters were reported by Zhang et al. [J. Phys. Chem. B 2004, 108, 2140] to form unusual square and cubic ground-state structures within DFT by treating the exchange-correlation (XC) functional at the level of general-gradient-corrected approximation (GGA). For such clusters, we show that the calculated, energetically preferred structures are sensitive to which XC functional is used and whether relativistic effects are included. We find that a hybrid XC functional with partially exact exchange, such as PBE0, corrects the Ru2 magnetic moment, bond length, and dissociation energy in agreement with experiment and high-level quantum chemistry calculations and changes the Ru4 ground-state structure to a tetrahedron, instead of a square. The change in structural preference is explained by the corrections to the electronic structure of a Ru atom, where the relative position of majority spin s level is shifted with respect to e(g) levels. We also find that standard nonrelativistic DFT-GGA gives similar results to relativistic DFT-PBE0, i.e., relative shifting of s level, but not for the right reasons. Our results again stress the need to validate an XC functional before application to transition-metal nanoclusters.     

共价键稳定性的影响因素

虽然小分子中的共价键强度可以很方便地通过高斯计算而相当准确地得到,一些手册和数据库中也可以直接查出部分键能/离解能数据,但共价键的强弱变化的影响因素分析在化学教学中仍然显得非常重要。共价键的强弱与成键原子及其环境密切相关,其中成键原子因素主要包括原子半径、成键类型、成键轨道类型、相对论效应、电负性、成键数量、反馈效应和孤电子对效应,而成键环境因素包括键间张力效应、离域效应、次级化学键效应、诱导效应和位阻效应。在教学中,我们可以通过对化学键影响因素的分析帮助学生理解共价键键能的变化规律。本文分析了影响共价键强弱的主要因素,并介绍了这种分析思路在化学教学中的应用。     

New insights into oxidation properties and band structure of fluorescein dyes from ab initio calculations

During recent years, several publications have investigated the electrical bistability of spin cast films of halogenated fluorescein dyes. In the present contribution, we simulate the excited states of single fluorescein dyes with time-dependent density functional theory (TD-DFT) and we analyzed the band structure of the corresponding molecular crystals with DFT. More precisely, the molecules examined are fluorescein, erythrosine B, and rose bengal. We consider the molecular crystals of fluorescein in salt and lactone forms as well as erythrosine B. Rose bengal showed high quantum yield of the triplet state and high electronic affinity. Therefore, the rose bengal has very strong oxidation properties and it is able to form electrically bistable thin oxide layer. The poor crystal order and small bandwidths of fluorescein in salt form and erythrosine B indicated high resistivity for both crystals.     

A partial proton transfer in hydrogen bond O-H···O in crystals of anhydrous potassium and rubidium complex chloranilates

Hydrogen bonding and proton transfer in the solid state are studied on the crystals of isostructural anhydrous potassium and rubidium complex chloranilates by variable-temperature single crystal X-ray diffraction, solid state (1)H NMR and IR spectroscopies, and periodic DFT calculations of equilibrium geometries, proton potentials, and NMR chemical shifts. Their crystal structures reveal neutral molecules of chloranilic acid and its dianions connected into a chain by O-H···O hydrogen bond. A strong hydrogen bond with a large-amplitude movement of the proton with NMR shift of 13-17 ppm and a broad continuum in IR spectra between 1000 and 500 cm(-1) were observed. Periodic DFT calculations suggest that proton transfer is energetically more favorable if it occurs within a single pair of chloranilate dianion and chloranilic acid molecule but not continuously along the chains of long periodicity. The calculated chemical shifts confirm the assumption that the weak resonance signals observed at lower magnetic fields pertain to the case when the proton migrates to the acceptor side of the hydrogen bond. The detected situation can be described by a partial proton transfer.     

Understanding thermodynamic properties at the molecular level: multiple temperature charge density study of ribitol and xylitol

X-ray diffraction data of high quality measured to high resolution on crystals of the two pentitol epimers ribitol (centric) and xylitol (acentric) at 101, 141, and 181 K and data on the two compounds previously recorded at 122 K have formed the basis for multipole refinements with the VALRAY system. Our analysis showed that it is possible to obtain a reliable crystal electron density for an acentric compound (xylitol) from X-ray diffraction data and that the thermal motion can be deconvoluted from the static density in this temperature range. The Bader-type topological analysis of the static electron densities revealed virtually identical intramolecular interactions as well as very similar hydrogen bond interactions of ribitol and xylitol; the only minor differences are found in the weaker intermolecular interactions. The high-level periodic DFT calculations are in accordance with the thermodynamic measurements that show that the two pentitols have identical sublimation energies. A rigid body normal coordinate analysis was performed on the atomic displacement parameters obtained at the four different temperatures. The translational and librational mean square deviations derived through this analysis were used in a quantum statistical approach to derive frequencies of the corresponding harmonic oscillators. The analysis showed a consistent vibrational model for all temperatures. The frequencies were subsequently used to calculate crystal entropies assuming an Einstein-type behavior. These calculations show that the crystal entropy of ribitol is 8 J K(-1) mol(-1) higher than the crystal entropy of xylitol, confirming that it is a difference in the entropy of the two compounds that causes the difference in their free energy. Our results presented in this Article show the potential to use X-ray diffraction data to obtain physicochemical properties of crystals.     

Enabling Control over Mechanical Conformity and Luminescence in Molecular Crystals: Interaction Engineering in Action

Molecular crystals of π-conjugated molecules are of great interest as the highly ordered dense packing offers superior charge and exciton transport compared with its amorphous counterparts. However, integration into optoelectronic devices remains a major challenge owing to its inherently brittle nature. Herein, control over the mechanical conformity in single crystals of pyridine-appended thiazolothiazole derivatives is reported by modulating the molecular packing through interaction engineering. Two polymorphs were prepared by achieving control over the thermodynamic/kinetic factors of crystallization; one of the polymorphs exhibits elastic bending whereas the other is brittle. The control over the bending ability was achieved by forming co-crystals with hydrogen/halogen bond donors. A seamless extended crisscross pattern with respect to the bend plane through a ditopic hydrogen-bonding motif showed the highest compliance towards mechanical bending, whereas the co-crystals with a layered crisscross arrangement with segregated layers of co-formers exhibit slightly lower bending conformity. These results update the rationale behind the plastic/elastic bending in molecular crystals. The co-crystals of ditopic halogen bond co-assemblies are particularly appealing for waveguiding applications as the co-crystals blend high mechanical flexibility and luminescence properties. The hydrogen bonded co-crystals are non-emissive in nature owing to excited state proton transfer dynamics. The rationale behind the fluorescence properties of these materials was also established from DFT calculations in a quantum mechanics/molecular mechanics (QM/MM) framework.     

Mechanically induced generation of highly reactive excited-state oxygen molecules in cluster scattering

Molecular electronic excitation in (O(2))(n) clusters induced by mechanical collisions via the "chemistry with a hammer" is investigated by a combination of molecular dynamics simulations and quantum chemistry calculations. Complete active space self-consistent field augmented with triple-zeta polarizable basis set quantum chemistry calculations of a compressed (O(2))(2) cluster model in various configurations reveal the emergence of possible pathways for the generation of electronically excited singlet O(2) molecules upon cluster compression and vibrational excitation, due to electronic curve-crossing and spin-orbit coupling. Extrapolation of the model (O(2))(2) results to larger clusters suggests a dramatic increase in the population of electronically excited O(2) products, and may account for the recently observed cluster-catalyzed oxidation of silicon surfaces, via singlet oxygen generation induced by cluster impact, followed by surface reaction of highly reactive singlet O(2) molecules. Extensive molecular dynamics simulations of (O(2))(n) clusters colliding onto a hot surface indeed reveal that cluster compression is sufficient under typical experimental conditions for nonadiabatic transitions to occur. This work highlights the importance of nonadiabatic effects in the "chemistry with a hammer."     

Ab initio study of the electronic and structural properties of the crystalline polyethyleneimine polymer

Polyethyleneimine is a very interesting polymer, not only for its extensive use in biological applications, but also for its crystal structure as a double-stranded helix in the anhydrous state. In order to elucidate the electronic bulk properties of the crystalline (or linear) polyethyleneimine built from ethylenediamine molecules in anhydrous conditions, we performed ab initio density functional theory calculations on water-free molecular crystal structures. The resulting polymer is a semiconductor with a small band gap: Eg = 0.40 eV.     

COSMOfrag: a novel tool for high-throughput ADME property prediction and similarity screening based on quantum chemistry

The COSMO-RS (Continuum Solvation Model for Real Solvents) method has proven its broad applicability for the accurate prediction of thermodynamic, environmental, or physiological properties. On the basis of quantum chemical calculations with COSMO, COSMO-RS calculations were unavoidably restricted to small- to medium-sized compound sets, because of the time demand of the COSMO calculations. The COSMOfrag method, presented here, overcomes this restriction by replacing the costly quantum chemistry step with a selection of suitable fragments from a database of, presently, 40,000 DFT/COSMO precalculated molecules. Since, in the COSMO-RS picture, any molecular information is gathered in the so-called sigma profiles, COSMOfrag replaces the single sigma profile with a composition of partial sigma profiles, selected by the use of extensive similarity searching algorithms. On five representative datasets, the accuracy loss of COSMOfrag versus full COSMO-RS calculations has been shown to be only in the range of 0.05 log units. From the performance point of view, it is now possible to carry out COSMO-RS property calculations for more than 100,000 compounds a day per standard PC CPU.     

The effective fragment potential: small clusters and radial distribution functions

The effective fragment potential (EFP) method for treating solvent effects provides relative energies and structures that are in excellent agreement with the analogous fully quantum [i.e., Hartree-Fock (HF), density functional theory (DFT), and second order perturbation theory (MP2)] results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. The resulting radial distribution functions (RDF) suggest that as the underlying quantum method is improved from HF to DFT to MP2, the agreement with the experimental RDF also improves. The MP2-based EFP method yields a RDF that is in excellent agreement with experiment.     

Fast quantum crystallography

Typical contemporary X-ray crystallography delivers the geometries and, at best, the electron densities of molecules or periodic systems in the crystalline phase. Energies, electron momentum densities, and information relating to the pair density such as electron delocalization measures—all crucial to chemistry—are simply missed. Quantum crystallography (QCr) is an emerging line of research aimed at filling this gap by solving the crystallographic problem under the constraints of quantum mechanics. In this way, not only geometries and electron densities become experimentally accessible but also the entire panoply of quantum mechanical properties that are in the output of any quantum chemical software package. However, QCr remains limited to smaller systems (small molecules or small unit cells) due to the exponential bottleneck that plagues quantum mechanical calculations. When combined with a fragmentation technique, termed the “kernel energy method (KEM)”, QCr's reach to larger molecules is extended considerably to almost “any size”, that is, systems of up to many hundreds of thousands of atoms. KEM has made this doable with any chemical model and is capable of providing the entire quantum mechanics of large molecular systems. The smallness of the R-factor adjudicates the accuracy of the quantum mechanics extracted from the crystallography.     

Symbasis Between Formation Entalpies,Activation Energies of the Electrical Conductivity in Wüstite and in the Clusters of Its Crystal Lattice

It is shown that formation enthalpy and activation energy of the electrical conductivity in stoichiometric wüstite can be estimated with the methods of quantum chemistry using the properties of its clusters. The clusters are represented by crystal lattice fragments with fixed or optimized geometric parameters. The formation enthalpy is determined by extrapolating the energy of clusters according to the formulas of simple theories of clusters. The activation energy of electrical conductivity is calculated from relative total energies of formula units for various spin states of wüstite clusters. Calculations were performed with efficient quantum chemical methods PM7 and PBE/sbk which were chosen according to test calculations of bonding and ionization energies for the ground states of the iron atom, its ions, and some of its compounds. The results are in satisfactory agreement with experimental literature data.