ER-BOC calculations of crystal bulk properties from smallest-cluster models

Ab initio calculation of bulk properties of crystals with a high accuracy, which is a long-time goal of solid chemistry and physics, is still difficult and expensive because a large cluster is required as a crystal structure model. This article proposes a model based on density functional theory (DFT) quantum chemistry calculations and the assumption that the bond order of a given atom with its nearest atoms in a compound is conserved over the entire range from its diatomic molecules to clusters and further to crystals. This entire range bond order conservation (ER-BOC) provides an effective way to correlate bulk properties of crystals with those of the corresponding molecules and small clusters. By combining this ER-BOC principle with hybrid DFT quantum chemistry calculations, accurate predictions of the bulk bond lengths of a crystal can be made using calculations on small clusters.     

Is There a Single Ideal Parameter for Halogen-Bonding-Based Lewis Acidity?

Halogen-bond donors (halogen-based Lewis acids) have now found various applications in diverse fields of chemistry. The goal of this study was to identify a parameter obtainable from a single DFT calculation that reliably describes halogen-bonding strength (Lewis acidity). First, several DFT methods were benchmarked against the CCSD(T) CBS binding data of complexes of 17 carbon-based halogen-bond donors with chloride and ammonia as representative Lewis bases, which revealed M05-2X with a partially augmented def2-TZVP(D) basis set as the best model chemistry. The best single parameter to predict halogen-bonding strengths was the static σ-hole depth, but it still provided inaccurate predictions for a series of compounds. Thus, a more reliable parameter, Ω_σ*, has been developed through the linear combination of the σ-hole depth and the σ*(C−I) energy, which was further validated against neutral, cationic, halogen- and nitrogen-based halogen-bond donors with very good performance.     

Coupled‐cluster reaction barriers of : An application of the coupled‐cluster//Kohn–Sham density functional theory model chemistry

In this work, we report a theoretical investigation concerning the use of the popular coupled‐cluster//Kohn‐Sham density functional theory (CC//KS‐DFT) model chemistry, here applied to study the entrance channel of the reaction, namely by comparing CC//KS‐DFT calculations with KS‐DFT, MRPT2//CASSCF, and CC//CASSCF results from our previous investigations. This was done by performing single point energy calculations employing several coupled cluster methods and using KS‐DFT geometries optimized with six different functionals, while conducting a detailed analysis of the barrier heights and topological features of the curves and surfaces here obtained. The quality of this model chemistry is critically discussed in the context of the title reaction and also in a wider context. © 2013 Wiley Periodicals, Inc.     

Synthetic studies on the solanacol ABC ring system by cation-initiated cascade cyclization: implications for strigolactone biosynthesis

We report a new method for constructing the ABC ring system of strigolactones, in a single step from a simple linear precursor by acid-catalyzed double cyclization. The reaction proceeds with a high degree of stereochemical control, which can be qualitatively rationalized using DFT calculations. Our concise synthetic approach offers a new model for thinking about the (as yet) unknown chemistry that is employed in the biosynthetic pathways leading to this class of plant hormones.     

Computational molecular characterization of Coumarin-102

In this work, we make use of a model chemistry within Density Functional Theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of 8-methyl-2,3,5,6-tetrahydro-1H,4H-11-oxa-3a-aza-benzo(de)anthracen-10-one (Coumarin-102), as well to predict its infrared (IR), ultraviolet (UV–vis) and fluorescence (Fluo) spectra, the dipole moment and polarizability, and the HOMO and LUMO orbitals as a possible indication of its usefulness for Organic Photovoltaics applications.     

Perceiving molecular themes in the structures and bonding of intermetallic phases: the role of Hückel theory in an ab initio era

Qualitative molecular orbital theory is central to our understanding of the bonding and reactivity of molecules and materials across chemistry. Advances in computational technology and methodology, however, have made ab initio or density functional theory calculations a simpler alternative, offering reliable results on increasingly large systems in a reasonable time-scale without the need for concerns about the approximations and parameterization of semi-empirical one-electron based methods. In this perspective, we illustrate how the availability of higher-level computational results can augment, rather than supplant, the insights provided by approaches such as the simple and extended Hückel methods. We begin by describing a way to parameterize Hückel-type Hamiltonians against DFT results for intermetallic systems. The potential for chemical understanding embodied by such orbital-based models is then demonstrated with two schemes of bonding analysis that originated in them (but can be extended to DFT results): the μ(3)-acid/base model and the μ(2)-Hückel chemical pressure analysis, which translate the molecular concepts of acidity and electronic/steric competition, respectively, into the context of intermetallic chemistry.     

Recent performance improvements to the DFT and TDDFT in GAMESS

The general atomic and molecular electronic structure system (GAMESS) is a quantum chemistry package used in the first-principles modeling of complex molecular systems using density functional theory (DFT) as well as a number of other post-Hartree-Fock methods. Both DFT and time-dependent DFT (TDDFT) are of particular interest to the materials modeling community. Millions of CPU hours per year are expended by GAMESS calculations on high-performance computing systems; any substantial reduction in the time-to-solution for these calculations represents a significant saving in CPU hours. As part of this work, three areas for improvement were identified: (1) the exchange-correlation (XC) integration grid, (2) profiling and optimization of the DFT code, and (3) TDDFT parallelization. We summarize the work performed in these task areas and present the resulting performance improvement. These software enhancements are available in 12JAN2009R3 or later versions of GAMESS.     

The interdependence of defects, electronic structure and surface chemistry

In this article we present three diverse applications of first-principles simulations to problems of materials chemistry and chemical physics. Their common characteristic is that they are essentially problems of the relationships among atomic structures and the properties they promote in real materials and real applications. The studies are on transition-metal oxide surface chemistry, the reactivity and electronic structure of sp(2)-bonded carbon systems, and defects and electrochromic properties in WO(3). In these demanding applications we must have concern for how realistic our model systems are and how well current implementations of DFT perform, and we comment on both.     

Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models

The conductor-like polarizable continuum model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in quantum chemistry. We have previously implemented C-PCM solvation for Hartree-Fock (HF) and density functional theory (DFT) on graphical processing units (GPUs), enabling the quantum mechanical treatment of large solvated biomolecules. Here, we first propose a GPU-based algorithm for the PCM conjugate gradient linear solver that greatly improves the performance for very large molecules. The overhead for PCM-related evaluations now consumes less than 15% of the total runtime for DFT calculations on large molecules. Second, we demonstrate that our algorithms tailored for ground state C-PCM are transferable to excited state properties. Using a single GPU, our method evaluates the analytic gradient of the linear response PCM time-dependent density functional theory energy up to 80× faster than a conventional central processing unit (CPU)-based implementation. In addition, our C-PCM algorithms are transferable to other methods that require electrostatic potential (ESP) evaluations. For example, we achieve speed-ups of up to 130× for restricted ESP-based atomic charge evaluations, when compared to CPU-based codes. We also summarize and compare the different PCM cavity discretization schemes used in some popular quantum chemistry packages as a reference for both users and developers.     

Theoretical investigation of substituted anthraquinone dyes

We have investigated with computational chemistry techniques the visible spectra of substituted anthraquinones. A wide panel of theoretical methods has been used, with various basis sets and density functional theory (DFT) functionals, in order to assess a level of theory that would lead to converged excitation energies. It turns out that the hybrid Becke-Lee-Yang-Parr and Perdew-Burke-Erzenrhof functionals with the 6-31G (d,p) atomic basis set provide reliable lambda(max) when the solvent effects are included in the model. Combining the results of both DFT schemes allows the prediction of lambda(max) with a standard deviation limited to 13 nm.     

Understanding the Woodward-Hoffmann rules by using changes in electron density

The Woodward-Hoffmann rules for pericyclic reactions are explained entirely in terms of directly observable physical properties of molecules (specifically changes in electron density) without any recourse to model-dependent concepts, such as orbitals and aromaticity. This results in a fundamental explanation of how the physics of molecular interactions gives rise to the chemistry of pericyclic reactions. This construction removes one of the key outstanding problems in the qualitative density-functional theory of chemical reactivity (the so-called conceptual DFT). One innovation in this paper is that the link between molecular-orbital theory and conceptual DFT is treated very explicitly, revealing how molecular-orbital theory can be used to provide "back-of-the-envelope" approximations to the reactivity indicators of conceptual DFT.     

Electronic structures and spectra of porphyrin with fused benzoheterocycles: DFT and TDDFT‐PCM investigations

Density functional theory (DFT) and time‐dependent DFT (TDDFT) are applied to study seven asymmetric π‐conjugated porphyrins with extended benzoheterocycles: quinoline, indole, benzoimidazole, benzothiazole, benzooxazole, 2,1,3‐benzothiadiazole, and 2,1,3‐benzoxadiazole. The solvation effects on the excitation energies for these porphyrin derivatives in chloroform are taken into account by using the continuum model (C‐PCM) combined with TDDFT, and this method makes a closer agreement with the experimental values, especially for the B‐bands of these objects. Great efforts have been made on investigating the influences of the fused aromatic units of the porphyrins on the absorption properties as these can be particularly important for many applications. Benzoheterocycle introduction and solvent effects have been systemically investigated, and close agreement is obtained between calculated and measured UV–vis spectra. These theoretical data could shed light on future synthetic chemistry. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Comparison of model chemistry and density functional theory thermochemical predictions with experiment for formation of ionic clusters of the ammonium cation complexed with water and ammonia; atmospheric implications

The G2, G3, CBS-QB3, and CBS-APNO model chemistry methods and the B3LYP, B3P86, mPW1PW, and PBE1PBE density functional theory (DFT) methods have been used to calculate deltaH(o) and deltaG(o) values for ionic clusters of the ammonium ion complexed with water and ammonia. Results for the clusters NH4(+) (NH3)n and NH4(+) (H2O)n, where n = 1-4, are reported in this paper and compared against experimental values. Agreement with the experimental values for deltaH(o) and deltaG(o) for formation of NH4(+) (NH3)n clusters is excellent. Comparison between experiment and theory for formation of the NH4(+) (H2O)n clusters is quite good considering the uncertainty in the experimental values. The four DFT methods yield excellent agreement with experiment and the model chemistry methods when the aug-cc-pVTZ basis set is used for energetic calculations and the 6-31G* basis set is used for geometries and frequencies. On the basis of these results, we predict that all ions in the lower troposphere will be saturated with at least one complete first hydration shell of water molecules.     

Density functional studies of the hydrolysis of aluminum (chloro)hydroxide in water with CPMD and COSMO

Car-Parrinello molecular dynamics (CPMD) and the static density functional method (DFT) with a conductor-like screening model (COSMO) were used to investigate the chemistry of aluminum (chloro)hydroxide in water. With these methods, the stability, reactivity, and acidic nature of the chosen chlorohydrate were able to be determined. Constrained molecular dynamics simulations were used to investigate the binding of chlorine in an aquatic environment. According to the results, aluminum preferred to be 5-fold-coordinated. In addition, the activation energy barriers for the dissociation of chlorine atoms from the original chlorohydrate structure were able to be determined. The actual values for the barriers were 14 +/- 3 and 40 +/- 5 kJ mol (-1). The results also revealed the acidity of the original cationic dimer. DFT with COSMO was used to determine free energy differences for the reactions detected in the molecular dynamic simulations. In conclusion, new results and insight into the aquatic chemistry of the aluminum (chloro)hydroxides are provided.     

Anticorrelation between Surface and Subsurface Point Defects and the Impact on the Redox Chemistry of TiO2(110)

By using a combination of scanning tunneling microscopy (STM), density functional theory (DFT), and secondary‐ion mass spectroscopy (SIMS), we explored the interplay and relative impact of surface versus subsurface defects on the surface chemistry of rutile TiO₂. STM results show that surface O vacancies (V_O) are virtually absent in the vicinity of positively charged subsurface point defects. This observation is consistent with DFT calculations of the impact of subsurface defect proximity on V_O formation energy. To monitor the influence of such lateral anticorrelation on surface redox chemistry, a test reaction of the dissociative adsorption of O₂ was employed and was observed to be suppressed around them. DFT results attribute this to a perceived absence of intrinsic (Ti), and likely extrinsic interstitials in the nearest subsurface layer beneath inhibited areas. We also postulate that the entire nearest subsurface region could be devoid of any charged point defects, whereas prevalent surface defects (V_O) are largely responsible for mediation of the redox chemistry at the reduced TiO₂(110).     

Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.     

Toward the complete range separation of non‐hybrid exchange–correlation functional

In this study, we use a very simple scheme to achieve range separation of a total exchange–correlation functional. We have utilized this methodology to combine a short‐range pure density functional theory (DFT) functional with a corresponding long‐range pure DFT, leading to a “Range‐separated eXchange–Correlation” (RXC) scheme. By examining the performance of a range of standard exchange–correlation functionals for prototypical short‐ and long‐range properties, we have chosen B‐LYP as the short‐range functional and PBE‐B95 as the long‐range counterpart. The results of our testing using a more diverse range of data sets show that, for properties that we deem to be short‐range in nature, the performance of this prescribed RXC‐DFT protocol does resemble that of B‐LYP in most cases, and vice versa. Thus, this RXC‐DFT protocol already provides meaningful numerical results. Furthermore, we envisage that the general RXC scheme can be easily implemented in computational chemistry software packages. This study paves a way for further refinement of such a range‐separation technique for the development of better performing DFT procedures. © 2015 Wiley Periodicals, Inc.     

Constitutional Dynamics of Metal–Organic Motifs on a Au(111) Surface

Constitutional dynamic chemistry (CDC), including both dynamic covalent chemistry and dynamic noncovalent chemistry, relies on reversible formation and breakage of bonds to achieve continuous changes in constitution by reorganization of components. In this regard, CDC is considered to be an efficient and appealing strategy for selective fabrication of surface nanostructures by virtue of dynamic diversity. Although constitutional dynamics of monolayered structures has been recently demonstrated at liquid/solid interfaces, most of molecular reorganization/reaction processes were thought to be irreversible under ultrahigh vacuum (UHV) conditions where CDC is therefore a challenge to be achieved. Here, we have successfully constructed a system that presents constitutional dynamics on a solid surface based on dynamic coordination chemistry, in which selective formation of metal–organic motifs is achieved under UHV conditions. The key to making this reversible switching successful is the molecule–substrate interaction as revealed by DFT calculations.