Water-benzene interactions: an effective fragment potential and correlated quantum chemistry study

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree-Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. The accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, Rcut. Rcut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small Rcut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

A Simple Electron-Density Based Force Field Model for High-Energy Interactions between Atoms and Molecules

In high-energy molecular dynamics or Monte Carlo simulations, standard force fields optimized for simulations at ambient temperatures are inadequate. This is largely because their repulsive parts have been regarded as not very significant, even well below zero interaction energies. It is, therefore, not obvious which force fields to resort to for simulating hot gases or plasmas. A force field model that uses the electronic densities of noninteracting atoms or molecules within the pair approximation is introduced. We start by deriving a naïve model that neglects any exchange and correlation effects between the electronic clouds and then correct this model by adding a term calibrated from ab initio calculations using the CCSD(T)/cc-pVTZ level of theory. The resulting expression for this term can be regarded as a simple exchange-correlation function. We compare the results for the repulsive part of the potential energy hypersurfaces with the force fields commonly used on some dimers of small molecules.

R-8 Dispersion Interaction: Derivation and Application to the Effective Fragment Potential Method

The anisotropic and isotropic R-8 dispersion contributions (disp8) are derived and implemented within the framework of the effective fragment potential (EFP) method formulated with imaginary frequency-dependent Cartesian polarizability tensors distributed at the centroids of the localized molecular orbitals (LMOs). Two forms of damping functions, intermolecular overlap-based and Tang-Toennies, are extended for disp8. To obtain LMO polarizability tensors centered at LMO centroids, an origin-shifting transformation is derived and implemented for the dipole-octopole polarizability tensor and the quadrupole-quadrupole polarizability tensor. The analytic gradient is derived and implemented for the isotropic disp8 contribution. Relative to the previously implemented empirical EFP disp8 energy, the isotropic disp8 component of the interaction energy improves the overall agreement of the EFP dispersion energies with the symmetry-adapted perturbation theory (SAPT) benchmarks, reducing the mean absolute errors (MAEs) and mean absolute percentage errors for most of the databases examined in this work. While the anisotropic disp8 can further enhance the accuracy of the EFP dispersion energy and yield smaller MAEs, significantly overbound dispersion energies are predicted by the anisotropic disp8 when the maximum element in the intermolecular overlap matrix is greater than 0.1, possibly due to the breakdown of the approximations made in the EFP dispersion derivation at a short range. For potential energy scan databases, the newly developed EFP dispersion model with isotropic disp8 yields the overall correct curvature and good agreement with SAPT benchmarks around equilibrium and longer but overestimates the dispersion interactions at a short range. While the overlap-based dispersion-damping functions produce better MAEs than Tang-Toennies damping functions, further improvement is needed to better screen the large attractive dispersion energies at a short range (overlap >0.1).

The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies

The thermodynamic parameters of host-guest binding can be used to describe, understand, and predict molecular recognition events in aqueous systems. However, interpreting binding thermodynamics remains challenging, even for these relatively simple molecules, as they are determined by both direct and solvent-mediated host-guest interactions. In this contribution, we focus on the contributions of water to binding by studying binding thermodynamics, both experimentally and computationally, for a series of nearly rigid, electrically neutral host-guest systems and report the temperature-dependent thermodynamic binding contributions ΔGb(T), ΔHb(T), ΔSb(T), and ΔCp,b. Combining isothermal titration calorimetry (ITC) measurements with molecular dynamics (MD) simulations, we provide insight into the binding forces at play for the macrocyclic hosts cucurbit[n]uril (CBn, n = 7-8) and β-cyclodextrin (β-CD) with a range of guest molecules. We find consistently negative changes in heat capacity on binding (ΔCp,b) for all systems studied herein - as well as for literature host-guest systems - indicating increased enthalpic driving forces for binding at higher temperatures. We ascribe these trends to solvation effects, as the solvent properties of water deteriorate as temperature rises. Unlike the entropic and enthalpic contributions to binding, with their differing signs and magnitudes for the classical and non-classical hydrophobic effect, heat capacity changes appear to be a unifying and more general feature of host-guest complex formation in water. This work has implications for understanding protein-ligand interactions and other complex systems in aqueous environments.

Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening

The results of electronic and vibrational structure simulations are an invaluable support for interpreting experimental absorption/emission spectra, which stimulates the development of reliable and cost-effective computational protocols. In this work, we contribute to these efforts and propose an efficient first-principle protocol for simulating vibrationally-resolved absorption spectra, including nonempirical estimations of the inhomogeneous broadening. To this end, we analyze three key aspects: (i) a metric-based selection of density functional approximation (DFA) so to benefit from the computational efficiency of time-dependent density function theory (TD-DFT) while safeguarding the accuracy of the vibrationally-resolved spectra, (ii) an assessment of two vibrational structure schemes (vertical gradient and adiabatic Hessian) to compute the Franck-Condon factors, and (iii) the use of machine learning to speed up nonempirical estimations of the inhomogeneous broadening. In more detail, we predict the absorption band shapes for a set of 20 medium-sized fluorescent dyes, focusing on the bright ππ^★ S₀ → S₁ transition and using experimental results as references. We demonstrate that, for the studied 20-dye set which includes structures with large structural variability, the preselection of DFAs based on an easily accessible metric ensures accurate band shapes with respect to the reference approach and that range-separated functionals show the best performance when combined with the vertical gradient model. As far as band widths are concerned, we propose a new machine-learning-based approach for determining the inhomogeneous broadening induced by the solvent microenvironment. This approach is shown to be very robust offering inhomogeneous broadenings with errors as small as 2 cm^-1 with respect to genuine electronic-structure calculations, with a total CPU time reduced by 98%.

Uptake of Hydrogen Bonding Molecules by Benzene Nanoparticles

The uptake of molecules on nanometer-size clusters of polyaromatic hydrocarbons (PAHs) is important for the condensation of water on PAH aerosols in the atmosphere and for ice mantle growth on nanoparticles in the interstellar medium. We generate benzene clusters Bz_N of mean size N̅ ≈ 300 (radius R̅ ≈ 2.2 Å) as a model system for the PAH nanoparticles. Using molecular beams and mass spectrometry detection, we investigate the uptake of water, methanol, and ethanol by these clusters. All picked up molecules are highly mobile on Bz_N and generate clusters within <3 ms. The relative uptakes for the different investigated molecules can be directly compared and quantified. Water molecules exhibit the lowest relative pickup probability that is ∼30% lower than those for methanol and ethanol, which are approximately the same.

Molecular interactions in diffusion-controlled aldol condensation with mesoporous silica nanoparticles

The aldol reaction of p-nitrobenzaldehyde in amino-catalyzed mesoporous silica nanoparticles (MSN) has revealed varying catalytic activity with the size of the pores of MSN. The pore size dependence related to the reactivity indicates that the diffusion process is important. A detailed molecular-level analysis for understanding diffusion requires assessment of the noncovalent interactions of the molecular species involved in the aldol reaction with each other, with the solvent, and with key functional groups on the pore surface. Such an analysis is presented here based upon the effective fragment potential (EFP). The EFP method can calculate the intermolecular interactions, decomposed into Coulomb, polarization, dispersion, exchange-repulsion, and charge-transfer interactions. In this study, the potential energy surfaces corresponding to each intermolecular interaction are analyzed for homo- and hetero-dimers with various configurations. The monomers that compose dimers are five molecules such as p-nitrobenzaldehyde, acetone, n-hexane, propylamine, and silanol. The results illustrate that the dispersion interaction is crucial in most dimers.

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.

Exploring amino acid functions in a deep mutational landscape

Amino acids fulfil a diverse range of roles in proteins, each utilising its chemical properties in different ways in different contexts to create required functions. For example, cysteines form disulphide or hydrogen bonds in different circumstances and charged amino acids do not always make use of their charge. The repertoire of amino acid functions and the frequency at which they occur in proteins remains understudied. Measuring large numbers of mutational consequences, which can elucidate the role an amino acid plays, was prohibitively time-consuming until recent developments in deep mutational scanning. In this study, we gathered data from 28 deep mutational scanning studies, covering 6,291 positions in 30 proteins, and used the consequences of mutation at each position to define a mutational landscape. We demonstrated rich relationships between this landscape and biophysical or evolutionary properties. Finally, we identified 100 functional amino acid subtypes with a data-driven clustering analysis and studied their features, including their frequencies and chemical properties such as tolerating polarity, hydrophobicity or being intolerant of charge or specific amino acids. The mutational landscape and amino acid subtypes provide a foundational catalogue of amino acid functional diversity, which will be refined as the number of studied protein positions increases.

Dispersion-induced structural preference in the ultrafast dynamics of diphenyl ether

Dispersion interactions are omnipresent in large aromatic systems and influence the dynamics as intermolecular forces. The structural preference induced by dispersion interactions is demonstrated to influence the excited state dynamics of diphenyl ether (DPE) using femtosecond time-resolved transient absorption (TA) associated with quantum chemical calculations. The experimental results in aprotic solvents show that the S₁ state is populated upon irradiation at 267 nm with excess vibrational energy dissipating to solvent molecules in several picoseconds, and then decays via internal conversion (IC) within 50 ps as well as intersystem crossing (ISC) and fluorescence with a lifetime of nanoseconds. The polarity of the solvent disturbs the excited state energies and enhances the energy barriers of the ISC channel. Furthermore, the intermolecular dispersion interactions with protic solvents result in the OH–π isomer dominating in methanol and the OH–O isomer is slightly preferred in t-butanol in the ground state. The hydrogen bonded isomer measurements show an additional change from OH–O to OH–π geometry in the first 1 ps besides the relaxation processes in aprotic solvents. The time constants measured in the TA spectra suggest that the OH–O isomer facilitates IC. The results show that the OH–π isomer has a more rigid structure and a higher barrier for IC, making it harder to reach the geometric conical intersection through conformer rearrangement. This work enables us to have a good knowledge of how the structural preference induced by dispersion interactions affects excited state dynamics of the heteroaromatic compounds.

Dispersion interactions are omnipresent in large aromatic systems and influence the dynamics as intermolecular forces.

Hydration of Aromatic Heterocycles as an Adversary of π-Stacking

Hydration is one of the key players in the protein-ligand binding process. It not only influences the binding process per se, but also the drug's absorption, distribution, metabolism, and excretion properties. To gain insights into the hydration of aromatic cores, the solvation thermodynamics of 40 aromatic mono- and bicyclic systems, frequently occurring in medicinal chemistry, are investigated. Thermodynamics is analyzed with two different methods: grid inhomogeneous solvation theory (GIST) and thermodynamic integration (TI). Our results agree well with previously published experimental and computational solvation free energies. The influence of adding heteroatoms to aromatic systems and how the position of these heteroatoms impacts the compound's interactions with water is studied. The solvation free energies of these heteroaromatics are highly correlated to their gas phase interaction energies with benzene: compounds showing a high interaction energy also have a high solvation free energy value. Therefore, replacing a compound with one having a higher gas phase interaction energy might not result in the expected improvement in affinity. The desolvation costs counteract the higher stacking interactions, hence weakening or even inverting the expected gain in binding free energy.

An Accurate Quantum-Based Approach to Explicit Solvent Effects: Interfacing the General Effective Fragment Potential Method with Ab Initio Electronic Structure Theory

An interface between ab initio quantum mechanics (QM) methods and the general effective fragment potential (EFP2) method, QM-EFP2, is implemented in which the intermolecular interactions between a QM molecule and EFP fragments consist of Coulomb, polarization, exchange repulsion (exrep), and dispersion components. In order to ensure accuracy in the QM-EFP2 exrep interaction energy, the EFP2-EFP2 spherical Gaussian overlap (SGO) approximation is abandoned and replaced with the exact electron repulsion integrals (ERI) that are evaluated with a direct method to reduce disk usage. A Gaussian damping function for the QM-EFP2 Coulomb component damps both the EFP nuclear and electronic charges. A new overlap damping function has been implemented for the QM-EFP2 dispersion component. The current QM-EFP2 implementation has been benchmarked with the S22 and S66 data sets and demonstrates excellent agreement with symmetry-adapted perturbation theory (SAPT) for component energies and with coupled cluster theory [CCSD(T)] for the total interaction energies. Water clusters of various sizes (up to 256 water molecules) have been tested; it is shown that the QM-EFP2 method has an accuracy that is comparable to that of EFP2-EFP2. It has been shown previously that the accuracy of EFP2-EFP2 intermolecular interactions is comparable to that of second-order perturbation theory (MP2) or better. The implementation of the distributed data interface (DDI) parallelization scheme significantly improves the efficiency of QM-EFP2 calculations. The time to form the QM-EFP2 Fock operator per SCF iteration for water clusters scales linearly with the number EFP basis functions.

An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute

Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.

Long-lived water clusters in hydrophobic solvents investigated by standard NMR techniques

Unusual physical characteristics of water can be easier explained and understood if properties of water clusters are revealed. Experimental investigation of water clusters has been reported by highly specialized equipment and/or harsh experimental conditions and has not determined the properties and the formation processes. In the current work, we used standard ¹H-NMR as a versatile and facile tool to quantitatively investigate water clusters in the liquid phase under ambient conditions. This approach allows collection of data regarding the formation, long lifetime, stability, and physical properties of water clusters, as a cubic octamer in the liquid phase.

Effects of pore surfaces on the electronic states of metal complexes formed on bipyridine periodic mesoporous organosilica

A combined experimental–theoretical study clarifies correlations between the pore-surface structures and the electronic properties of metal complexes on BPy-PMO.

Surface Water Structure and Hygroscopic Properties of Light Absorbing Secondary Organic Polymers of Atmospheric Relevance

Hygroscopic properties and chemical reactivity of secondary organic aerosols (SOA) influence their overall contribution to the indirect effect on the climate. In this study, we investigate the hygroscopic properties of organic and organometallic polymeric particles, namely polycatechol, polyguaiacol, Fe-polyfumarte, and Fe-polymuconate. These particles efficiently form in iron-catalyzed reactions with aromatic and aliphatic dicarboxylic acid compounds detected in field-collected SOA. The structure of surface water was studied using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and the uptake of gas water was quantified using quartz crystal microbalance (QCM) as a function of relative humidity. Spectroscopic data show that water bonding with organic functional groups acting as hydrogen bond acceptors causes shifts in their vibrational modes. Analysis of the hydroxyl group stretching region revealed weak and strong hydrogen bonding networks that suggest cluster formation reflecting water-water and water-organics interactions, respectively. A modified Type II multilayer Brunauer-Emmett-Teller adsorption model described the adsorption isotherm on the nonporous materials, polycatechol, polyguaiacol, and Fe-polymuconate. However, water adsorption on porous Fe-polyfumarate was best described using a Type V adsorption model, namely the Langmuir-Sips model that accounts for condensation in pores. The data revealed that organometallic polymers are more hygroscopic than organic polymers. The implications of these investigations are discussed in the context of the chemical reactivity of these particles relative to known SOA.

Co-operativity in non-covalent interactions in ternary complexes: a comprehensive electronic structure theory based investigation

The structure and stability of various ternary complexes in which an extended aromatic system such as coronene interacts with ions/atoms/molecules on opposite faces of the π-electron cloud were investigated using ab initio calculations. By characterizing the nature of the intermolecular interactions using an energy decomposition analysis, it was shown that there is an interplay between various types of interactions and that there are co-operativity effects, particularly when different types of interactions coexist in the same system. Graphical abstract Weak OH-π, π-π and van der Waals-π ternary systems are stabilized through dispersion interactions. Cation-π ternary systems are stabilized by through-space electrostatic interactions.

Dynamics of water in conical solvation shells around a benzene solute under different thermodynamic conditions

Water molecules in different parts of the anisotropic hydration shell of an aromatic molecule experience different interactions. In the present study, we investigate the anisotropic dynamics of water molecules in different non-overlapping conical shells around a benzene solute at sub- and supercritical conditions by means of molecular dynamics simulations using both non-polarizable and polarizable models. In addition to the dynamical properties, the effects of polarizability on the hydration structure of benzene at varying thermodynamic conditions are also investigated in the current study. The presence of πH-bonding in the solvation shell is found to be an important factor that influences the anisotropic dynamics of the benzene hydration shell. The water molecules located axial to the benzene plane are found to be maximally influenced by the πH-bonding. The extent of πH-bonding is found to be somewhat reduced on inclusion of polarizability. The πH-bonded water molecules are found to reorient through large-amplitude angular jumps where the jump-angle amplitude increases at higher temperatures and lower densities. For both non-polarizable and polarizable models, it is found that the water molecules in the axial conical shells possess faster orientational and hydrogen bond dynamics compared to those in the equatorial plane. Water molecules in the axial conical shells are also found to diffuse at a faster rate than bulk molecules due to the relatively weaker benzene-water πH-bonding interactions in the axial region of the hydration shell. The residence dynamics of water molecules in different conical solvation shells around the solute is also investigated in the current study.

Supramolecular Aggregates of Tetraphenylethene-Cored AIEgen toward Mechanoluminescent and Electroluminescent Devices

Luminescent materials possessing both the mechanoluminescence (MCL) and electroluminescence (EL) properties are the quest for sensing and optoelectronic applications. We report on the synthesis of a new tailor-made luminogen, 1,2-bis(4-(1-([1,1'-biphenyl]-4-yl)-2,2-diphenylvinyl)phenyl)-1,2-diphenylethene (TPE 5), using Suzuki coupling reaction with high yield. An aggregation-induced emission (AIE) active complex TPE 5 forms supramolecular spherical aggregates at the air-water interface of a Langmuir trough. As a consequence, a large enhancement of luminescence is obtained from the mono- and multilayer Langmuir-Blodgett films of TPE 5 owing to the AIE effect. The luminogen TPE 5 exhibits a reversible MCL response, displaying photoluminescence switching due to change in the crystalline states under external stimuli. The unique feature of luminescence enhancement upon aggregate formation is utilized for the fabrication of light-emitting diodes with low threshold voltage using supramolecular aggregates as the active layer. This work demonstrates an efficient strategy for obtaining controlled supramolecular aggregates of AIEgen with a potential in the dual applications of MCL and EL.

Benchmarking the Effective Fragment Potential Dispersion Correction on the S22 Test Set

The usual modeling of dispersion interactions in density functional theory (DFT) is often limited by the use of empirically fitted parameters. In this study, the accuracies of the popular empirical dispersion corrections and the first-principles derived effective fragment potential (EFP) dispersion correction are compared by computing the DFT-D and HF-D equilibria interaction energies and intermolecular distances of the S22 test set dimers. Functionals based on the local density approximation (LDA) and generalized gradient approximation (GGA), as well as hybrid functionals, are compared for the DFT-D calculations using coupled cluster CCSD(T) at the complete basis set (CBS) limit as the reference method. In general, the HF-D(EFP) method provides accurate equilibrium dimerization energies and intermolecular distances for hydrogen-bonded systems compared to the CCSD(T)/CBS reference data without using any empirical parameters. For dispersion-dominant and mixed systems, the structures and interaction energies obtained with the B3LYP-D(EFP) method are similar to or better than those obtained with the other DFT-D and HF-D methods. Overall, the first-principles derived -D(EFP) correction presents a robust alternative to the empirical -D corrections when used with the B3LYP functional for dispersion-dominant and mixed systems or with Hartree-Fock for hydrogen-bonded systems.

Dispersion Interactions in QM/EFP

The dispersion energy term between quantum-mechanical (QM) and classical (represented by effective fragment potentials, EFP) subsystems is developed and implemented. A new formulation is based on long-range perturbation theory and uses dynamic polarizability tensors of the effective fragments and electric field integrals and orbital energies of the quantum-mechanical subsystem. No parametrization is involved. The accuracy of the QM-EFP dispersion energy is tested on a number of model systems; the average mean unsigned error is 0.8 kcal/mol or 13% with respect to the symmetry adapted perturbation theory on the S22 data set of noncovalent interactions. The computational cost of the dispersion energy computation is low compared to the self-consistent field calculation of the QM subsystem. The dispersion energy is sensitive to the level of theory employed for the QM part and to the electrostatic interactions in the system. The latter means that the dispersion interactions in the QM/EFP method are not purely two-body but have more complex many-body behavior.

Capturing Many-Body Interactions with Classical Dipole Induction Models

The nonadditive many-body interactions are significant for structural and thermodynamic properties of condensed phase systems. In this work we examined the many-body interaction energy of a large number of common organic/biochemical molecular clusters, which consist of 18 chemical species and cover nine common organic elements, using the Møller-Plesset perturbation theory to the second order (MP2) [ Møller et al. Phys. Rev. 1934 , 46 , 618 . ]. We evaluated the capability of Thole-based dipole induction models to capture the many-body interaction energy. Three models were compared: the original model and parameters used by the AMOEBA force field, a variation of this original model where the damping parameters have been reoptimized to MP2 data, and a third model where the damping function form applied to the permanent electric field is modified. Overall, we find the simple classical atomic dipole models are able to capture the 3- and 4-body interaction energy across a wide variety of organic molecules in various intermolecular configurations. With modified Thole models, it is possible to further improve the agreement with MP2 results. These models were also tested on systems containing metal/halogen ions to examine the accuracy and transferability. This work suggests that the form of damping function applied to the permanent electrostatic field strongly affects the distance dependence of polarization energy at short intermolecular separations.

Quantum Chemical Methods for the Prediction of Energetic, Physical, and Spectroscopic Properties of Ionic Liquids

The accurate prediction of physicochemical properties of condensed systems is a longstanding goal of theoretical (quantum) chemistry. Ionic liquids comprising entirely of ions provide a unique challenge in this respect due to the diverse chemical nature of available ions and the complex interplay of intermolecular interactions among them, thus resulting in the wide variability of physicochemical properties, such as thermodynamic, transport, and spectroscopic properties. It is well understood that intermolecular forces are directly linked to physicochemical properties of condensed systems, and therefore, an understanding of this relationship would greatly aid in the design and synthesis of functionalized materials with tailored properties for an application at hand. This review aims to give an overview of how electronic structure properties obtained from quantum chemical methods such as interaction/binding energy and its fundamental components, dipole moment, polarizability, and orbital energies, can help shed light on the energetic, physical, and spectroscopic properties of semi-Coulomb systems such as ionic liquids. Particular emphasis is given to the prediction of their thermodynamic, transport, spectroscopic, and solubilizing properties.

Non-covalent interaction of benzene with methanol and diethyl ether solid surfaces

We have investigated the interactions involved at the interface of binary, layered ices (benzene on methanol and on diethyl ether) by means of laboratory experiments and ab initio calculations on model clusters.

Efficient electron-promoted desorption of benzene from water ice surfaces

We study the desorption of benzene from solid water surfaces during irradiation of ultrathin solid films with low energy electrons.

Modulating intramolecular P⋯N pnictogen interactions

The strength of P⋯N intramolecular pnictogen interactions can be modulated, enhanced or diminished upon substitution of different electron withdrawing or donor groups.

Isomer-Specific Spectroscopy of Benzene-(H2O)n, n = 6,7: Benzene's Role in Reshaping Water's Three-Dimensional Networks

The water hexamer and heptamer are the smallest sized water clusters that support three-dimensional hydrogen-bonded networks, with several competing structures that could be altered by interactions with a solute. Using infrared-ultraviolet double resonance spectroscopy, we record isomer-specific OH stretch infrared spectra of gas-phase benzene-(H2O)(6,7) clusters that demonstrate benzene's surprising role in reshaping (H2O)(6,7). The single observed isomer of benzene-(H2O)6 incorporates an inverted book structure rather than the cage or prism. The main conformer of benzene-(H2O)7 is an inserted-cubic structure in which benzene replaces one water molecule in the S4-symmetry cube of the water octamer, inserting itself into the water cluster by engaging as a π H-bond acceptor with one water and via C-H···O donor interactions with two others. The corresponding D(2d)-symmetry inserted-cube structure is not observed, consistent with the calculated energetic preference for the S4 over the D(2d) inserted cube. A reduced-dimension model that incorporates stretch-bend Fermi resonance accounts for the spectra in detail and sheds light on the hydrogen-bonding networks themselves and on the perturbations imposed on them by benzene.

Effect of spacer chain length on the liquid structure of aqueous dicationic ionic liquid solutions: molecular dynamics studies

Cations in an aqueous [C₁₆(MIm)₂][2Br] solution aggregate spontaneously to form micelles, with a hydrophobic core composed of spacer alkyl chains and a hydrophilic surface composed of imidazolium head groups.

What are preferred water-aromatic interactions in proteins and crystal structures of small molecules?

The distribution of water molecules around aromatic rings in the protein structures and crystal structures of small molecules shows quite a small number of the strongest OH-π interactions, a larger number of parallel interactions, and the largest number of the weakest CH-O interactions.

Parallel water/aromatic interactions of non-coordinated and coordinated water

The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one OH bond is parallel to the aromatic ring, whereas the other OH bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1) . The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.

Density functional theory based generalized effective fragment potential method

We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

The structure and UV spectroscopy of benzene–water (Bz–W6) clusters using time-dependent density functional theory

MP2, DFT and TD-DFT applied to benzene–(water)₆ clusters show how both perturb the electronic spectra of each other and give rise to new charge transfer features from the benzene to the water cluster.

Molecular recognition of aromatic rings by flavin: electrostatics and dispersion determine ring positioning above isoalloxazine

Aromatic stacking interactions between isoalloxazine (ISA) of flavin and three prototypical aromatics (benzene, pyridine, chlorobenzene) were investigated using electronic structure calculations with Monte Carlo simulated annealing. The Effective Fragment Potential (EFP) method was used to locate the low-energy equilibrium configurations for the three dimer systems. These structures were further characterized through DFT (M06-2X) and MP2 calculations. One equilibrium configuration exists for ISA-benzene; characterizing the stacked dimer surface revealed a steep, single-welled potential that funnels benzene directly between rings II and III, positioning a substituent hydrogen adjacent to the redox-active N5. ISA-pyridine and ISA-chlorobenzene minimum-energy structures contain the aromatic ring in very similar position to that in ISA-benzene. However, the added rotational degree of freedom leads to two distinct binding motifs, having approximately antiparallel or parallel dipole moment alignment with ISA. The existence of the latter binding configuration was unexpected but is explained by the shape of the ISA electrostatic potential. Dispersion is the primary noncovalent interaction driving the positioning of aromatic rings above ISA, while electrostatics determine the orientation in dipole-containing substituted benzenes. The interplay of these interactions can be used to tune molecular recognition properties of synthetic redox cofactors, including positioning desired functional groups adjacent to the redox-active N5.

Accurate first principles model potentials for intermolecular interactions

The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

Open-shell pair interaction energy decomposition analysis (PIEDA): formulation and application to the hydrogen abstraction in tripeptides

An open-shell extension of the pair interaction energy decomposition analysis (PIEDA) within the framework of the fragment molecular orbital (FMO) method is developed. The open-shell PIEDA method allows the analysis of inter- and intramolecular interactions in terms of electrostatic, exchange-repulsion, charge-transfer, dispersion, and optional polarization energies for molecular systems with a radical or high-spin fragment. Taking into account the low computational cost and scalability of the FMO and PIEDA methods, the new scheme provides a means to characterize the stabilization of radical and open-shell sites in biologically relevant species. The open-shell PIEDA is applied to the characterization of intramolecular interactions in capped trialanine upon hydrogen abstraction (HA) at various sites on the peptide. Hydrogen abstraction reaction is the first step in the oxidative pathway initiated by reactive oxygen or nitrogen species, associated with oxidative stress. It is found that HA results in significant geometrical reorganization of the trialanine peptide. Depending on the HA site, terminal interactions in the radical fold conformers may become weaker or stronger compared to the parent molecule, and often change the character of the non-covalent bonding from amide stacking to hydrogen bonding.