Supermolecular Method Research Articles

A New Ab Initio Potential Energy Surface and Rovibrational Spectra for the CO-N2O Complex.

We constructed a new ab initio potential energy surface (PES) for CO-N2O which includes the intramolecular Q3 normal coordinate for the N2O ν3 antisymmetric stretching vibration. The intermolecular potential was evaluated employing the supermolecular method at the [CCSD(T)]-F12a level, with the aug-cc-pVTZ basis set plus bond functions. By integral over the intramolecular Q3 coordinate, we obtained the vibrationally averaged PESs for the CO-N2O system in the ground and ν3 excited states of N2O. Each PES features one nearly T-shaped global minimum and one skewed T-shaped local minimum. Based on these obtained PESs of CO-N2O, the radial discrete variable representation/angle finite base representation method and the Lanczos algorithm were applied for the calculations of bound states and rovibrational energy levels. The calculated ν3 vibrational band origin shift of the N2O monomer in CO-N2O is 2.7570 cm-1, matching well with the observed value of 2.9048 cm-1. The computed microwave and infrared transition frequencies, as well as the rotational parameters, are consistent with the experimental observations.

Accurate non-covalent interaction energies on noisy intermediate-scale quantum computers via second-order symmetry-adapted perturbation theory.

The calculation of non-covalent interaction energies on noisy intermediate-scale quantum (NISQ) computers appears to be challenging with straightforward application of existing quantum algorithms. For example, the use of the standard supermolecular method with the variational quantum eigensolver (VQE) would require extremely precise resolution of the total energies of the fragments to provide for accurate subtraction to the interaction energy. Here we present a symmetry-adapted perturbation theory (SAPT) method that may provide interaction energies with high quantum resource efficiency. Of particular note, we present a quantum extended random-phase approximation (ERPA) treatment of the SAPT second-order induction and dispersion terms, including exchange counterparts. Together with previous work on first-order terms (Chem. Sci., 2022, 13, 3094), this provides a recipe for complete SAPT(VQE) interaction energies up to second order, which is a well established truncation. The SAPT interaction energy terms are computed as first-level observables with no subtraction of monomer energies invoked, and the only quantum observations needed are the VQE one- and two-particle density matrices. We find empirically that SAPT(VQE) can provide accurate interaction energies even with coarsely optimized, low circuit depth wavefunctions from a quantum computer, simulated through ideal statevectors. The errors of the total interaction energy are orders of magnitude lower than the corresponding VQE total energy errors of the monomer wavefunctions. In addition, we present heme-nitrosyl model complexes as a system class for near term quantum computing simulations. They are strongly correlated, biologically relevant and difficult to simulate with classical quantum chemical methods. This is illustrated with density functional theory (DFT) as the predicted interaction energies exhibit a strong sensitivity with respect to the choice of functional. Thus, this work paves the way to obtain accurate interaction energies on a NISQ-era quantum computer with few quantum resources. It is the first step in alleviating one of the major challenges in quantum chemistry, where in-depth knowledge of both the method and system is required a priori to reliably generate accurate interaction energies.

The KOALA program: Wavefunction frozen‐density embedding

AbstractThe KOALA program is presented, and its capabilities are discussed. KOALA is an ab initio code that uses Gaussian‐type basis sets with a focus on a treatment of wavefunction embedding methods, for which all subsystems can be relaxed with their corresponding wavefunction density. Among the key features of the program is a Davidson solver that is capable of treating, for example, both linear response for coupled‐cluster methods and density functional theory, as well as solving the Z‐vector equations for orbital‐relaxed ground‐state and excited‐state molecular properties. This solver is combined with frozen‐density embedding, which circumvents the problem of the steep scaling of conventional supermolecular correlation methods, enabling the computation of anisotropic environment effects without using semiempirical methods. A brief theoretical overview is given, and case studies for which the program could be used are discussed, as well as the efficiency for systems containing a total of hundreds of atoms, which can be divided into smaller subsystems.

One-step and green strategy for exfoliation and stabilization of graphene by phosphate pillar[6]arene and its application for fluorescence sensing of paraquat

A one-step, safe, and green approach is reported for the synthesis of 2D graphene nanosheet in water phase exfoliated by the water-soluble phosphate pillar[6]arene (PP6). Compared with the conventional method that the graphite is firstly oxidized, exfoliated to graphene oxide and then reduced to graphene sheets, the present proposed method is directly exfoliated from graphite by one-step process without using any strong oxidizing agents, such as H2SO4 or KMnO4. More importantly, the graphene obtained by this environmentally friendly method possesses excellent crystalline structure. Besides, the prepared graphene could be stabilized through π-π stacking interaction between graphene and the hydrophobic segments of benzene rings in PP6, and PP6 functionalized graphene (PP6@graphene) simultaneously combines the fluorescence quenching property of graphene and molecular recognition capability of PP6. Therefore, we construct a competitive fluorescence assay based on the molecular recognition interaction between PP6@graphene and acridine orange (AO) for determination of paraquat (PQ), a nonselective herbicide with high toxicity to humans. The fluorescence of AO is completely quenched by fluorescence resonance energy transfer (FRET) interaction between AO and PP6@graphene, and the quenched fluorescence recovers upon the successive addition of PQ, because the inclusion capability of PP6 towards PQ is stronger than that of AO. Linear response ranges of 0.2–2 μM and 2–18 μM are obtained for determination of PQ and the detection limit is 0.06 μM (S/N = 3). The constructed sensing platform is also used to detect PQ in three water samples with satisfying results, which indicates that the competitive host-guest supermolecular recognition method has potential application in practical environmental risk assessment of PQ.

Electric properties of hydrated uracil: From micro- to macrohydration

The accurate description of solvent effects on electric and optical properties of a solvated molecule is a complex task involving appropriate consideration of short-range as well as long-range intermolecular interactions having direct (local field induced) and indirect (solvent structure induced) impacts on the properties. In this study, we investigate the effects of hydration on dipole moment and dipole polarizability of uracil (U), focusing on the evolution of the properties from micro- to macrohydration regime. The microhydrated structures were generated by Global Search Algorithm of Minima (GSAM). Our results show a general increase in both induced dipole moment and isotropic polarizability with the cluster size, with a sudden decrease of the polarizability when passing from U(H2O)5 to U(H2O)6. To explain the underlying effects, the variational-perturbational energy decomposition scheme (VP-EDS) was used. The interplay of hydrogen bonding between water molecules and the uracil molecule and hydrogen bonding between water molecules themselves is shown to be the driving force behind these trends. To represent the macrohydrated uracil, supermolecular (SM) and rigorous local field (RLF) methods were used, with representative structure generation performed by molecular dynamics (MD). The trends of induced electric properties with the cluster size are shown to be consistent between micro- and macrohydration regimes. While the induced dipole moment increases monotonically to a converged value of 1.305 ± 0.009 au, the induced isotropic polarizability, reaching maximum of 5.94 au for n = 8, slowly decreases again, and converges to the negative value (−1.21 ± 0.12 au), showing the decrease of the total polarizability of uracil in water. This study also clearly demonstrates that it is the electrostatic interaction which governs the significant property changes on going from micro- to macrohydration.

Facile Synthesis of Phytic Acid Impregnated Polyaniline for Enhanced U(VI) Adsorption

A novel phytic acid impregnated polyaniline (PA-PANI) was synthesized by a in situ polymerization and supermolecular self-assembly method and has been used as an adsorbent for efficient capture of ...

Geometry optimizations with the incremental molecular fragmentation method

Nuclear energy gradients for the incremental molecular fragmentation (IMF) method presented in our previous work [Meitei OR, Heßelmann A, Molecular energies from an incremental fragmentation method, J Chem Phys 144(8):084109, 2016] have been derived. Using the second-order Møller–Plesset perturbation theory method to describe the bonded and nonbonded energy and gradient contributions and the uncorrelated Hartree–Fock method to describe the correction increment, it is shown that the IMF gradient can be easily computed by a sum of the underlying individual derivatives of the energy contributions. The performance of the method has been compared against the supermolecular method by optimizing the structures of a range of polyglycine molecules with up to 36 glycine residues in the chain. It is shown that with a sensible set of parameters used in the fragmentation the supermolecular structures can be fairly well reproduced. In a few cases the optimization with the IMF method leads to structures that differ from the supermolecular ones. It was found, however, that these are more stable geometries also on the supermolecular potential energy surface.

Automatic Generation of Intermolecular Potential Energy Surfaces.

A method is developed for automatic generation of intermolecular two-body, rigid-monomer potential energy surfaces based on symmetry-adapted perturbation theory (SAPT). It is also possible to substitute SAPT interaction energies by values computed using sufficiently high-level supermolecular methods. The long-range component of the potential is obtained from a rigorous asymptotic expansion with ab initio computed coefficients which seamlessly connects to SAPT interaction energies at large separations. An accompanying software package has been developed and tested successfully on eight systems ranging in size from the Cl--H2O dimer to the cyclotrimethylene trinitramine dimer containing 42 atoms total. The potentials have a typical fit error of about 0.2 kcal/mol in the negative energy region. The accuracy may be further improved by including off-atomic sites or increasing their number. All aspects of potential development were designed to work reliably on a broad range of systems with no human intervention.

Structure and Energetics of Complexes of B12N12 with Hydrogen Halides-SAPT(DFT) and MP2 Study.

Molecular complexes of a fullerene analogue B12N12 with hydrogen halides (HCl, HBr, and HI) were studied with symmetry-adapted perturbation theory with density-functional theory applied for a description of monomers (SAPT(DFT)), Møller-Plesset theory to the second order (MP2), and its spin-component-scaled variant (SCS-MP2) in a limit of a complete basis set. For each halide five symmetry-distinct minimum structures of the complex have been found on the potential energy hypersurface, with interaction energies ranging from -6 to -18 kJ/mol. The natural bond orbital and the atom-in-molecules analysis of noncovalent bonds resulted in a division of these configurations into three categories: hydrogen-bonded, halogen-bonded, and those of a mixed type, involving simultaneously a hydrogen bonding and a π-hole bonding between halogen and boron atoms. A comparison of various approaches for the calculation of interaction energies shows that the SCS-MP2 supermolecular method gives results which are in a close agreement with SAPT(DFT), while the MP2 interaction energies are systematically more negative than the SAPT values. The ability of the B12N12 nanocage to bind hydrogen halides through several active sites on its surface puts under question the selectivity of the binding necessary in crystal engineering, especially for the hydrogen bromide and hydrogen iodide cases, which show small differences in stabilization energies for their minimum structures. The directionality of noncovalent bonds is explained on grounds of the anisotropy of some SAPT components, like electrostatics and induction, as well as by the σ-hole and π-hole models.

A new ab initio potential energy surface and infrared spectra for the Ne–CS2 complex

We report a new three-dimensional potential energy surface for Ne–CS2 including the Q3 normal mode for the υ3 antisymmetric stretching vibration of the CS2 molecule. The potential energies were calculated using the supermolecular method at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples [CCSD(T)] with a large basis set containing bond function. Two vibrationally averaged potentials with CS2 at both the ground (υ=0) and the first excited (υ=1)υ3 vibrational states were generated from the integration of the three-dimensional potential over the Q3 coordinate. Each potential was found to have a T-shaped global minimum and two equivalent linear local minima. The radial discrete variable representation (DVR)/angular finite basis representation (FBR) and the Lanczos algorithm were employed to obtain the rovibrational energy levels. The calculated band origin shifts were found to be 0.1812cm−1 and 0.1833cm−1 for 20Ne–CS2 and 22Ne–CS2, respectively, which are all in very good agreement with the experimental values of 0.1804cm−1 and 0.1827cm−1.

A new ab initio potential energy surface and infrared spectra for the Ar-CS₂ complex.

We report a new three-dimensional potential energy surface for Ar-CS2 involving the Q3 normal mode for the υ3 antisymmetric stretching vibration of the CS2 molecule. The potential energies were calculated using the supermolecular method at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples, using augmented correlation-consistent quadruple-zeta basis set plus midpoint bond functions. Two vibrationally averaged potentials with CS2 at both the ground (υ = 0) and the first excited (υ = 1)υ3 vibrational states were generated from the integration of the three-dimensional potential over the Q3 coordinate. Each potential was found to have a T-shaped global minimum and two equivalent linear local minima. The radial discrete variable representation /angular finite basis representation method and the Lanczos algorithm were applied to calculate the rovibrational energy levels. The calculated band origin shift of the complex (0.0622 cm(-1)) is very close to the observed one (0.0671 cm(-1)). The predicted infrared spectra and spectroscopic parameters based on the two averaged potentials are in excellent agreement with the available experimental data.

Synthesis, characterization and catalytic activity of nano-spherical MCM-41 modified with vanadium.

Vanadium modified MCM-41 nanospheres were synthesized by the impregnation and sol-gel super-molecular method respectively. Structure and morphology of the obtained materials were characterized using X-ray diffraction (XRD), inductively coupling plasma (ICP), Fourier transform infrared (FT-IR), scanning electron microscopy (SEM) and N2-adsorption-desorption techniques. The influence of particle sizes on their catalytic activities in styrene oxidation and benzene hydroxylation was investigated. Results revealed that all the samples had regular sphere shape and adjustable particle size within 40-160 nm, and exhibited high catalytic activities in the oxidation of styrene and hydroxylation of benzene. The smaller the particle size is, the higher the activity becomes. Meanwhile, the catalysts synthesized by the sol-gel method are more effective than that synthesized via impregnation method, indicating the vanadium species in the mesoporous framework are probably the catalytic active sites.

Density functional theory approach to gold-ligand interactions: Separating true effects from artifacts

Donor-acceptor interactions are notoriously difficult and unpredictable for conventional density functional theory (DFT) methodologies. This work presents a reliable computational treatment of gold-ligand interactions of the donor-acceptor type within DFT. These interactions require a proper account of the ionization potential of the electron donor and electron affinity of the electron acceptor. This is accomplished in the Generalized Kohn Sham framework that allows one to relate these properties to the frontier orbitals in DFT via the tuning of range-separated functionals. A donor and an acceptor typically require different tuning schemes. This poses a problem when the binding energies are calculated using the supermolecular method. A two-parameter tuning for the monomer properties ensures that a common functional, optimal for both the donor and the acceptor, is found. A reliable DFT approach for these interactions also takes into account the dispersion contribution. The approach is validated using the water dimer and the (HAuPH3)2 aurophilic complex. Binding energies are computed for Au4 interacting with the following ligands: SCN(-), benzenethiol, benzenethiolate anion, pyridine, and trimethylphosphine. The results agree for the right reasons with coupled-cluster reference values.

Highly Correlated Electronic Structure Calculations of the He–C3 van der Waals Complex and Collision-Induced Rotational Transitions of C3

An accurate 2D ab initio potential energy surface of the He-C3 collisional system is calculated using the supermolecular coupled-cluster method with up to perturbative quadruple excitations, CCSDT(Q). This interaction potential is then incorporated in full close-coupling calculations of rotational excitation/de-excitation cross sections in He + C3 collisions for rotational levels j = 0, 2, ..., 10 and collision energies up to 1000 cm(-1). Corresponding rate coefficients are reported for temperature between 1 and 100 K. Results are found to be in excellent agreement with available theoretical data that were restricted to the temperature range of 5-15 K. Implications of the computed rate coefficients to astrophysical models of C3 and carbon clusters in interstellar and circumstellar environments are discussed.

Excess enthalpies of binary mixtures of butylamines + propanols at 298.15 K

The molar excess enthalpies of eight systems of butylamines + propanols were determined at 298.15 K using a twin-microcalorimeter. All excess enthalpies were exothermic and large. An equilibrium constant K 1 expressed in terms of mole fractions and standard thermodynamic properties of formation (Δf H, Δf G, Δf S) of 1:1 complex were evaluated by ideal mixtures of monomeric molecules and their associated complexes. Concentration dependence of the FT-Raman spectrum showed systematic changes of bands. Spectroscopic considerations based on this and ab initio calculations on molecules were performed at the Mp2/6-311G(d,p) level of theory. Interaction energies between butylamine and propanol were calculated by the supermolecular and NBO methods. The results were discussed with previous results to clarify the steric and positional effect of the amino and hydroxyl group.

The Complete Control for the Nanosize of Spherical MCM-41

In this work, we present a systematic study on the complete control over the sphere diameters of MCM-41 nanospheres with different pore sizes. The mesoporous silica nanospheres with diameter range from 40 nm to 160 nm are synthesized by using cationic quaternary ammonium surfactants as template and TEOS as silicon source in sodium hydroxide aqueous solution via sol-gel supermolecular method. Nanospheres with fixed diameter can be obtained through the precise control over the molar ratio of NaOH/TEOS and other synthetic conditions. The range of sphere diameter for each sample prepared under adjustable reaction conditions is in a sharp distribution. Moreover, the formation mechanism for nanospheres with controlled morphological and structural features is proposed, and we suggest the optimal synthesis conditions of the MCM-41 nanospheres for the minimization of the Gibbs free energy deltaG. Besides, after depositing vanadium species on the MCM-41 support, the catalytic performance of V-MCM-41 for the selective oxidation of styrene by hydroperoxide increases with the diameter of the supports decreasing.

Interaction energies of large clusters from many-body expansion

In the canonical supermolecular approach, calculations of interaction energies for molecular clusters involve a calculation of the whole cluster, which becomes expensive as the cluster size increases. We propose a novel approach to this task by demonstrating that interaction energies of such clusters can be constructed from those of small subclusters with a much lower computational cost by applying progressively lower-level methods for subsequent terms in the many-body expansion. The efficiency of such "stratified approximation" many-body approach (SAMBA) is due to the rapid convergence of the many-body expansion for typical molecular clusters. The method has been applied to water clusters (H(2)O)(n), n = 6, 16, 24. For the hexamer, the best results that can be obtained with current computational resources in the canonical supermolecular method were reproduced to within about one tenth of the uncertainty of the canonical approach while using 24 times less computer time in the many-body expansion calculations. For (H(2)O)(24), SAMBA is particularly beneficial and we report interaction energies with accuracy that is currently impossible to obtain with the canonical supermolecular approach. Moreover, our results were computed using two orders of magnitude smaller computer resources than used in the previous best calculations for this system. We also show that the basis-set superposition errors should be removed in calculations for large clusters.

PREPARATION OF HIGH PERFORMANCE POLYMER MATERIALS THROUGH INTERMOLECULAR COMPLEXATION

Intermacromolecular complexation occurring among the macromolecules with complementary structure through the secondary binding forces,e.g.Coulomb forces,hydrogen bonding,van der Waals forces,charge transfer interactions etc.,is an effective supermolecular method for preparation and property enhancing of polymer materials.This paper summarizes our research work on intermolecular complexation in recent years,e.g.,realizing the thermal processing of PVA and developing a series of novel PVA products with high performance,preparing novel halogen free flame retardant,controlling the crystalline structure of POM and effectively improving its notched impact properties and friction and wear properties,etc.

Embedding vs Supermolecular Strategies in Evaluating the Hydrogen-Bonding-Induced Shifts of Excitation Energies

Shifts in the excitation energy of the organic chromophore, cis-7-hydroxyquinoline (cis-7HQ), corresponding to the π→π* transition in cis-7HQ and induced by the complexation with a variety of small hydrogen-bonded molecules, obtained with the frozen-density embedding theory (FDET), are compared with the results of the supermolecular equation-of-motion coupled-cluster (EOMCC) calculations with singles, doubles, and non-iterative triples, which provide the reference theoretical data, the supermolecular time-dependent density functional theory (TDDFT) calculations, and experiment. Unlike in the supermolecular EOMCC and TDDFT cases, where each complexation-induced spectral shift is evaluated by performing two separate calculations, one for the complex and another one for the isolated chromophore, the FDET shifts are evaluated as the differences of the excitation energies determined for the same many-electron system, representing the chromophore fragment with two different effective potentials. By considering eight complexes of cis-7HQ with up to three small hydrogen-bonded molecules, it is shown that the spectral shifts resulting from the FDET calculations employing non-relaxed environment densities and their EOMCC reference counterparts are in excellent agreement with one another, whereas the analogous shifts obtained with the supermolecular TDDFT method do not agree with the EOMCC reference data. The average absolute deviation between the complexation-induced shifts, which can be as large, in absolute value, as about 2000 cm-1, obtained using the non-relaxed FDET and supermolecular EOMCC approaches that represent two entirely different computational strategies, is only about 100 cm-1, i.e., on the same order as the accuracy of the EOMCC calculations. This should be contrasted with the supermolecular TDDFT calculations, which produce the excitation energy shifts that differ from those resulting from the reference EOMCC calculations by about 700 cm-1 on average. Among the discussed issues are the choice of the electronic density defining the environment with which the chromophore interacts, which is one of the key components of FDET considerations, the basis set dependence of the FDET, supermolecular TDDFT, and EOMCC results, the usefulness of the monomer vs supermolecular basis expansions in FDET considerations, and the role of approximations that are used to define the exchange-correlation potentials in FDET and supermolecular TDDFT calculations.

A graphene sheet as an efficient electron acceptor and conductor for photoinduced charge separation

Tetrasulfonated zinc phthalocyanine (Pc) was bound to graphene (G) sheets by the π–π stacking supermolecular method. The few-layer graphene sheets were obtained by chemically reducing graphite oxide and characterized by AFM, IR and UV–vis absorption methods. Photoinduced electron transfer (PET) within the nano assembly is revealed by laser flash photolysis, time resolved and steady state fluorescence, as well as UV–vis absorption techniques. A graphene sheet can be attached by up to 52,000 Pc molecules to form a super molecule G(Pc) 52,000, in which many Pc molecules can be simultaneously photoexcited to the S 1 state. One graphene sheet can simultaneously quench thousands of excited Pcs with a large rate constant of the order of 10 16 M −1 s −1 by PET. A graphene sheet not only accepts electrons from the excited Pcs on it but also delivers the captured electrons to its unexcited Pcs to form (Pc +) n G(Pc −) n , so that a large electron charge (i.e. n >> 1) is separated between unlinked Pc molecules with a small energy loss. These novel features of PET are explained by the following unique properties of graphene: (i) its excellent electron-transport and multi-electron-accepting ability, (ii) its multi-chromophore binding and concurrent multi-photon absorbing ability.