Dispersion corrections to density functionals for water aromatic interactions

Molecular dynamics simulation studies of 1,3-dimethyl imidazolium nitrate ionic liquid with water

The fundamental understanding of intermolecular interactions of ionic liquids (ILs) with water is essential in predicting IL-water thermodynamic properties. In this study, intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium [DMIM]⁺ cation and nitrate [NO₃]^- anion with water, employing quantum mechanics and molecular dynamics simulations. Molecular dynamics simulations were performed using a revised multipolar polarizable force field. The effect of water on ionic liquids was evaluated in terms of thermodynamic and dynamic properties. Thermodynamic properties included liquid densities ρ, excess molar volumes ΔV^E, and liquid structures gr. Dynamic properties included self-diffusion coefficients D of mixture constituents as a function of water concentration. The density of ionic liquid-water mixtures monotonically decrease with increasing concentration of water. A negative excess volume was obtained for low and high water concentrations, demonstrating strong intermolecular interactions of water with ionic liquid components. Liquid structures of ionic liquid-water mixtures revealed a tendency for anions to interact with cations at shorter intermolecular distances when the water concentration is increased. Diffusion rates were found to increase for all mixture components with increase in the fraction of water. A significant change in the diffusion rate was found at ∼0.3 weight fraction of water. However, the water self-diffusion coefficient was dominant at all concentrations. The ratio of water/anion and anion/cation self-diffusion coefficients was found to decrease linearly with increasing concentration of water molecules.

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution-Insight from Experiment and Computations

An isotope fractionation analysis of organic groundwater pollutants can assess the remediation at contaminated sites yet needs to consider physical processes as potentially confounding factors. This study explores the predictability of water–air partitioning isotope effects from experiments and computational predictions for benzene and trimethylamine (both H-bond acceptors) as well as chloroform (H-bond donor). A small, but significant, isotope fractionation of different direction and magnitude was measured with ε = −0.12‰ ± 0.07‰ (benzene), ε_C = 0.49‰ ± 0.23‰ (triethylamine), and ε_H = 1.79‰ ± 0.54‰ (chloroform) demonstrating that effects do not correlate with expected hydrogen-bond functionalities. Computations revealed that the overall isotope effect arises from contributions of different nature and extent: a weakening of intramolecular vibrations in the condensed phase plus additional vibrational modes from a complexation with surrounding water molecules. Subtle changes in benzene contrast with a stronger coupling between intra- and intermolecular modes in the chloroform–water system and a very local vibrational response with few atoms involved in a specific mode of triethylamine. An energy decomposition analysis revealed that each system was affected differently by electrostatics and dispersion, where dispersion was dominant for benzene and electrostatics dominated for chloroform and triethylamine. Interestingly, overall stabilization patterns in all studied systems originated from contributions of dispersion rather than other energy terms.

New Charge Transfer Complexes of K+-Channel-Blocker Drug (Amifampridine; AMFP) for Sensitive Detection; Solution Investigations and DFT Studies

UV-Vis spectroscopy was used to investigate two new charge transfer (CT) complexes formed between the K⁺-channel-blocker amifampridine (AMFP) drug and the two π-acceptors 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and tetracyanoethylene (TCNE) in different solvents. The molecular composition of the new CT complexes was estimated using the continuous variations method and found to be 1:1 for both complexes. The formed CT complexes' electronic spectra data were further employed for calculating the formation constants (K_CT), molar extinction coefficients (ε_CT), and physical parameters at various temperatures, and the results demonstrated the high stability of both complexes. In addition, sensitive spectrophotometric methods for quantifying AMFP in its pure form were proposed and statistically validated. Furthermore, DFT calculations were used to predict the molecular structures of AMFP-DDQ and AMFP-TCNE complexes in CHCl₃. TD-DFT calculations were also used to predict the electronic spectra of both complexes. A CT-based transition band (exp. 399 and 417 nm) for the AMFP-TCNE complex was calculated at 411.5 nm (f = 0.105, HOMO-1 → LUMO). The two absorption bands at 459 nm (calc. 426.9 nm, f = 0.054) and 584 nm (calc. 628.1 nm, f = 0.111) of the AMFP-DDQ complex were theoretically assigned to HOMO-1 → LUMO and HOMO → LUMO excitations, respectively.

Computational modelling of Pd-catalysed alkoxycarbonylation of alkenes and alkynes

This perspective highlights the computational modelling of alkene and alkyne alkoxycarbonylation at palladium catalysts. We cover studies on Pd-catalysed alkoxycarbonylation of alkenes with bidentate diphosphine ligands, which reveal a hydride pathway is operating with an intermolecular alcoholysis step, where explicit solvation is mandatory to estimate the overall barriers correctly and model alcoholysis/copolymerisation selectivities. Subsequently, we discuss Pd-catalysed alkyne alkoxycarbonylation with P,N-chelating ligands, where an in situ base mechanism is operating involving ketene-type intermediates. We also discuss catalyst poisoning due to allene and designing a potential new catalyst tolerant towards allene poisoning.

X-ray Photoionization Cross Section Spectra of Water and Ammonia Bonded on Polycyclic Aromatic Hydrocarbons: A Quantum Mechanical Interpretation to the Absorption Spectra on Graphene

A theoretical study of the K-shell total photoabsorption and photoionization cross section spectra of water and ammonia bonded to benzene (C₆H₆) and the polycyclic aromatic hydrocarbons (PAHs) naphthalene (C₁₀H₈), coronene (C₂₄H₁₂) and circumcoronene (C₅₄H₁₈) by van der Waals (vdW) forces is presented. The discretized electronic pseudospectra at the oxygen and nitrogen K-edges, covering the discrete and the continuum spectral regions, were obtained at the time-dependent density functional theory (TDDFT) level with dispersion correction. An analytic continuation procedure based on the Padé approximants was used in order to obtain the K-shell cross sections of the structures at the discrete and the continuum regions of the spectra. By examining the electronic spectra of water and ammonia bonded to coronene and circumcoronene, we observed that our results agree well with the experiments performed with graphene. This work provides a quantum mechanical interpretation to the NEXAFS experiments of water and ammonia adsorbed on graphene in terms of a physisorption model of these molecules by van der Waals forces.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Theoretical Study of the Potential Energy Profile of the HBr+ + CO2 → HOCO+ + Br· Reaction

Recent guided ion beam experiments have revealed interesting reaction dynamics of the HBr⁺ + CO₂ → HOCO⁺ + Br· reaction under different conditions. The hypothesis is that the predominant reaction mechanism depends on the collision energy between two reactants, the angular momentum of HBr⁺, and the spin-orbit coupling state of the system. The potential energy profile of the HBr⁺ + CO₂ → HOCO⁺ + Br· reaction is studied in this research to lay the groundwork for an ab initio molecular dynamics simulation. First, a benchmark potential energy profile of this reaction is identified using coupled-cluster theory extrapolated to the complete basis set limit. A transition state connecting the previously reported intermediates is found, making the potential energy surface of the HBr⁺ + CO₂ → HOCO⁺ + Br· reaction double-welled. Second, various single reference ab initio methods are compared with the benchmark potential energy profile to search for the most suitable ab initio method for the dynamics simulation. Two combinations of double-ζ basis sets (with effective core potentials) with MP2 and density functional theory have been identified to accurately represent the potential energy profile of this reaction.

Halogen and Chalcogen Binding Dominated by Density-Driven Errors

Dispersion corrections of various kinds usually improve DFT energetics of weak noncovalent interactions. However, in some cases involving molecules or halides, especially those with σ-hole interactions, the density-driven errors of uncorrected DFT are larger than the dispersion corrections. In these abnormal situations, HF-DFT (using Hartree-Fock densities instead of self-consistent densities) greatly improves bond energies, while dispersion corrections can even worsen the results. On the other hand, pnictogen bonds and the S22 data set are normal and are not improved by this procedure. Such effects should be accounted for when parametrizing dispersion interactions.

Extension of the D3 dispersion coefficient model

A new model, termed D4, for the efficient computation of molecular dipole-dipole dispersion coefficients is presented. As in the related, well established D3 scheme, these are obtained as a sum of atom-in-molecule dispersion coefficients over atom pairs. Both models make use of dynamic polarizabilities obtained from first-principles time-dependent density functional theory calculations for atoms in different chemical environments employing fractional atomic coordination numbers for interpolation. Different from the D3 model, the coefficients are obtained on-the-fly by numerical Casimir-Polder integration of the dynamic, atomic polarizabilities α(iω). Most importantly, electronic density information is now incorporated via atomic partial charges computed at a semi-empirical quantum mechanical tight-binding level, which is used to scale the polarizabilities. Extended statistical measures show that errors for dispersion coefficients with the proposed D4 method are significantly lower than with D3 and other, computationally more involved schemes. Alongside, accurate isotropic charge and hybridization dependent, atom-in-molecule static polarizabilities are obtained with an unprecedented efficiency. Damping function parameters are provided for three standard density functionals, i.e., TPSS, PBE0, and B3LYP, allowing evaluation of the new DFT-D4 model for common non-covalent interaction energy benchmark sets.

On the structure of superbasic (MgO)n sites solvated in a faujasite zeolite

Theory and experiment reveal the structure of magnesium oxide nanoclusters in a superbasic faujasite zeolite.

First-Principles Models for van der Waals Interactions in Molecules and Materials: Concepts, Theory, and Applications

Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches). Particular attention is paid to the intriguing nature of many-body vdW interactions, whose fundamental relevance has recently been highlighted in several landmark experiments. The performance of these models in predicting binding energetics as well as structural, electronic, and thermodynamic properties is connected with the theoretical concepts and provides a numerical summary of the state-of-the-art in the field. We conclude with a roadmap of the conceptual, methodological, practical, and numerical challenges that remain in obtaining a universally applicable and truly predictive vdW method for realistic molecular systems and materials.

Evaluating dispersion forces for optimization of van der Waals complexes using a non-empirical functional

Modelling dispersion interactions with traditional density functional theory (DFT) is a challenge that has been extensively addressed in the past decade. The exchange-dipole moment (XDM), among others, is a non-empirical add-on dispersion correction model in DFT. The functional PW86+PBE+XDM for exchange, correlation and dispersion, respectively, compromises an accurate functional for thermochemistry and for van der Waals (vdW) complexes at equilibrium and non-equilibrium geometries. To use this functional in optimizing vdW complexes, rather than computing single point energies, it is necessary to evaluate accurate forces. The purpose of this paper is to validate that, along the potential energy surface, the distance at which the energy is minimum is commensurate with the distance at which the forces vanish to zero. This test was validated for 10 rare gas diatomic molecules using various integration grids and different convergence criteria. It was found that the use of either convergence criterion, 10^-6 or 10^-8, in Gaussian09, does not affect the accuracy of computed optimal distances and binding energies. An ultra-fine grid needs to be used when computing accurate energies using generalized gradient approximation functionals.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics

Protonation by carbonic acid H2CO3 of the strong base methylamine CH3NH2 in a neutral contact pair in aqueous solution is followed via Car-Parrinello molecular dynamics simulations. Proton transfer (PT) occurs to form an aqueous solvent-stabilized contact ion pair within 100 fs, a fast time scale associated with the compression of the acid-base hydrogen-bond (H-bond), a key reaction coordinate. This rapid barrierless PT is consistent with the carbonic acid-protonated base pKa difference that considerably favors the PT, and supports the view of intact carbonic acid as potentially important proton donor in assorted biological and environmental contexts. The charge redistribution within the H-bonded complex during PT supports a Mulliken picture of charge transfer from the nitrogen base to carbonic acid without altering the transferring hydrogen's charge from approximately midway between that of a hydrogen atom and that of a proton.

Why Is MP2-Water "Cooler" and "Denser" than DFT-Water?

Density functional theory (DFT) with a dispersionless generalized gradient approximation (GGA) needs much higher temperature and pressure than the ambient conditions to maintain water in the liquid phase at the correct (1 g/cm(3)) density during first-principles simulations. Conversely, ab initio second-order many-body perturbation (MP2) calculations of liquid water require lower temperature and pressure than DFT/GGA to keep water liquid. Here we present a unifying explanation of these trends derived from classical water simulations using a polarizable force field with different sets of parameters. We show that the different temperatures and pressures between DFT/GGA and MP2 at which the simulated water displays the experimentally observed liquid structure under the ambient conditions can be largely explained by their differences in polarizability and dispersion interaction, respectively. In DFT/GGA, the polarizability and thus the induced dipole moments and the hydrogen-bond strength are all overestimated. This hinders the rotational motion of molecules and requires a higher temperature for DFT-water to be liquid. MP2 gives a stronger dispersion interaction and thus shorter intermolecular distances than dispersionless DFT/GGA, which is why MP2-water is denser than DFT-water under the same external pressure.

Empirical Correction to Molecular Interaction Energies in Density Functional Theory (DFT) for Methane Hydrate Simulation

A general and empirical method is proposed for correction of London dispersion and other deficiencies in density functional theory (DFT). This method is based on the existing Lennard-Jones (L-J) equation and van der Waals parameters. The benchmark of energy correction is set as the energy difference between DFT and more accurate methods, for example CCSD(T). The energy correction includes all differences between CCSD(T) and DFT, dispersion energy, configuration interaction, induction interaction, residual correlation, and other effects. The energy correction is expressed as a linear combination of van der Waals potentials of nonbonded atomic pairs. The combination coefficients are determined using a least-squares approach in a training set of molecular pairs. The coefficients then can be used for the energy corrections in DFT calculations in a molecular family. Three correction equations of molecular pair interaction energy, water-water, water-methane, and methane-methane, are derived for methane hydrate simulation. The correction equation of the water-water pair is applied in the DFT calculation of water pentamer, yielding good intermolecular potential energy surfaces (PES), very close to the results of CCSD(T) over the active interaction range from 2.1 Å to 8.0 Å.

Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches

The work involves an experimental ((1)H NMR) and theoretical (MD, MM-PBSA and DFT) investigation of the molecular recognition and discrimination properties of a chiral aza-15-crown-5 against methyl esters of alanine, phenylalanine and valine hydrochloride salts. The results indicate that the receptor binds enantiomers with moderate binding constants (88-1,389 M(-1)), with phenylalanine being more discriminated. The difference in experimental binding free energies (ΔG(R) - ΔG(S)) for alanine, phenylalanine and valine enantiomers were calculated as -0.36, -1.58 and 0.80 kcal mol(-1), respectively. The differences in theoretical binding energies were calculated by MM-PBSA (ΔE(R)PB - ΔE(S)PB=) as -0.30, -1.45 and 0.88, by B3LYP/6-31+G(d) as -1.17, -0.84 and 0.74 and by M06-2X/6-31+G(d) as -1.40, -3.26 and 1.66 kcal mol(-1). The data obtained give valuable information regarding the molecular recognition mode of the organoammonium complexes of chiral aza-crown ether with C 1 symmetry, which may be relevant to biological systems.

Properties of noncovalent tetraphenylporphine⋯C60 dyads as studied by different long-range and dispersion-corrected DFT functionals

The exceptional ability of M05-2X/6-31G(d,p) calculations to describe binding energies and separation distances in porphyrin–fullerene complexes.

Exploring energy landscapes: from molecular to mesoscopic systems

We review a comprehensive computational framework to survey the potential energy landscape for systems composed of rigid or partially rigid molecules. Illustrative case studies relevant to a wide range of molecular clusters and soft and condensed matter systems are discussed.

Modelling excited states of weakly bound complexes with density functional theory

Different dispersion correction parameters are required to describe the interaction when the molecule is in an excited Rydberg state.

B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)₂ <d(CpA)₂ <d(ApT)₂ <d(ApA)₂ <d(GpT)₂ <d(GpA)₂ <d(ApG)₂ <d(CpG)₂ <d(GpG)₂ <d(GpC)₂, where the energy differences between the last four dimers, d(ApG)₂, d(CpG)₂, d(GpG)₂ and d(GpC)₂, is within 4.0 kcal mol⁻¹, and the energy between the most and the least stable isomers is 13.4 kcal mol⁻¹. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.

Intermolecular Interactions in Dye-Sensitized Solar Cells: A Computational Modeling Perspective

We present a unified overview of our recent activity on the modeling of relevant intermolecular interactions occurring in dye-sensitized solar cells (DSCs). The DSC is an inherent complex system, whose efficiency is essentially determined by the interrelated phenomena occurring at the multiple molecular-semiconductor-electrolyte heterointerfaces. In this Perspective, we illustrate the basic methodology and selected applications of computational modeling of dye-dye and dye-coadsorbent intermolecular interactions taking place at the dye-sensitized interface. We show that the proposed methodology offers a realistic picture of aggregation phenomena among surface-adsorbed dyes and nicely describes semiconductor surfaces cosensitized by different dyes. The information acquired from this type of studies might constitute the basis for an integrated multiscale computational description of the device functioning, including all of the possible interdependencies among the device constituents, which may further boost the DSCs efficiency. We believe that this direction should be the target of future computational research in the DSC field.

The multiple roles of histidine in protein interactions

Background

Among the 20 natural amino acids histidine is the most active and versatile member that plays the multiple roles in protein interactions, often the key residue in enzyme catalytic reactions. A theoretical and comprehensive study on the structural features and interaction properties of histidine is certainly helpful.

Results

Four interaction types of histidine are quantitatively calculated, including: (1) Cation-π interactions, in which the histidine acts as the aromatic π-motif in neutral form (His), or plays the cation role in protonated form (His⁺); (2) π-π stacking interactions between histidine and other aromatic amino acids; (3) Hydrogen-π interactions between histidine and other aromatic amino acids; (4) Coordinate interactions between histidine and metallic cations. The energies of π-π stacking interactions and hydrogen-π interactions are calculated using CCSD/6-31+G(d,p). The energies of cation-π interactions and coordinate interactions are calculated using B3LYP/6-31+G(d,p) method and adjusted by empirical method for dispersion energy.

Conclusions

The coordinate interactions between histidine and metallic cations are the strongest one acting in broad range, followed by the cation-π, hydrogen-π, and π-π stacking interactions. When the histidine is in neutral form, the cation-π interactions are attractive; when it is protonated (His⁺), the interactions turn to repulsive. The two protonation forms (and pK_a values) of histidine are reversibly switched by the attractive and repulsive cation-π interactions. In proteins the π-π stacking interaction between neutral histidine and aromatic amino acids (Phe, Tyr, Trp) are in the range from -3.0 to -4.0 kcal/mol, significantly larger than the van der Waals energies.

Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory

Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals, and many other systems. However, an accurate description of dispersion is highly challenging, with the most widely used electronic structure technique, density functional theory (DFT), failing to describe them with standard approximations. Therefore, applications of DFT to systems where dispersion is important have traditionally been of questionable accuracy. However, the last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods. Here we discuss, classify, and evaluate some of the promising schemes to emerge in recent years. A brief perspective on the outstanding issues that remain to be resolved and some directions for future research are also provided.

Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry

The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries.

Long-Range Corrected Hybrid Density Functionals with Improved Dispersion Corrections

By incorporating the improved empirical atom-atom dispersion corrections from DFT-D3 [Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys.2010, 132, 154104], two long-range corrected (LC) hybrid density functionals are proposed. Our resulting LC hybrid functionals, ωM06-D3 and ωB97X-D3, are shown to be accurate for a very wide range of applications, such as thermochemistry, kinetics, noncovalent interactions, frontier orbital energies, fundamental gaps, and long-range charge-transfer excitations, when compared with common global and LC hybrid functionals. Relative to ωB97X-D [Chai, J.-D.; Head-Gordon, M. Phys. Chem. Chem. Phys.2008, 10, 6615], ωB97X-D3 (reoptimization of ωB97X-D with improved dispersion corrections) is shown to be superior for nonbonded interactions, and similar in performance for bonded interactions, while ωM06-D3 is shown to be superior for general applications.

Factors that distort the heme structure in Heme-Nitric Oxide/OXygen-Binding (H-NOX) protein domains. A theoretical study

DFT and dispersion-corrected DFT calculations were carried out to probe the factors that distort the heme structure in Heme-Nitric oxide/OXygen-binding (H-NOX) protein domains. Various model systems that include heme, heme+surrounding residues, and heme+surrounding residues+additional protein environment were examined; the latter system was calculated with a quantum mechanics/molecular mechanics (QM/MM) method. The computations were extended to a myoglobin (Mb) protein, in which the heme structure is quite planar, in contrast to that in H-NOX. The natural tendency of the heme is to be planar. The strong structural distortion in H-NOX is mainly brought about by the intermolecular interactions between the whole heme molecule (heme ring plus its peripheral substituents) and the surrounding residues, among which the polar residues (Tyr140, Pro115, Mse98) play major roles in distorting the heme structure. The two peripheral propionate substituents that are oriented on the same side of the heme plane can also make the molecule distort, but the distortion caused by this factor is not significant. In Mb, the surrounding residues considered are all nonpolar and do not cause a structural distortion. The different structural features of the heme macrocycle in the different proteins (H-NOX and Mb) are reproduced by the calculations. The dispersion correction is necessary, since it improves the calculated structures. The effects of the distortion on the binding affinity of the axial ligand to the heme were also examined.

A Density Functional with Spherical Atom Dispersion Terms

A new hybrid density functional, APF, is introduced, which avoids the spurious long-range attractive or repulsive interactions that are found in most density functional theory (DFT) models. It therefore provides a sound baseline for the addition of an empirical dispersion correction term, which is developed from a spherical atom model (SAM). The APF-D empirical dispersion model contains nine adjustable parameters that were selected based on a very small training set (15 noble gas dimers and 4 small hydrocarbon dimers), along with two computed atomic properties (ionization potential and effective atomic polarizability) for each element. APF-D accurately describes a large portion of the potential energy surfaces of complexes of noble gas atoms with various diatomic molecules involving a wide range of elements and of dimers of small hydrocarbons, and it reproduces the relative conformational energies of organic molecules. The accuracy for these weak interactions is comparable to that of CCSD(T)/aug-cc-pVTZ calculations. The accuracy in predicting the geometry of hydrogen bond complexes is competitive with other models involving DFT and empirical dispersion.

Dynamical screening of the van der Waals interaction between graphene layers

The interaction between graphene layers is analyzed combining local orbital DFT and second order perturbation theory. For this purpose we use the linear combination of atomic orbitals-orbital occupancy (LCAO-OO) formalism, that allows us to separate the interaction energy as the sum of a weak chemical interaction between graphene layers plus the van der Waals interaction (Dappe et al 2006 Phys. Rev. B 74 205434). In this work, the weak chemical interaction is calculated by means of corrected-LDA calculations using an atomic-like sp(3)d(5) basis set. The van der Waals interaction is calculated by means of second order perturbation theory using an atom-atom interaction approximation and the atomic-like-orbital occupancies. We also analyze the effect of dynamical screening in the van der Waals interaction using a simple model. We find that this dynamical screening reduces by 40% the van der Waals interaction. Taking this effect into account, we obtain a graphene-graphene interaction energy of 70 ± 5 meV/atom in reasonable agreement with the experimental evidence.