Weakly Bonded Systems

Sulfur Centered Hydrogen Bonding in Thioglycolic Acid and Its Clusters: A Computational Exploration

The conformational landscape of thioglycolic acid (TGA) was investigated by using the CCSD/cc-pVTZ level of theory. The GGC conformer was identified as the global minimum, followed by the GAC conformer. The calculated rotational constant for the GGC conformer exhibited good agreement with the previously reported experimental results. Subsequently, the study delved into the exploration of sulfur-centered hydrogen bonding in TGA's dimer and trimer clusters, employing the CCSD/cc-pVDZ level of theory. These clusters revealed the participation of both oxygen and sulfur atoms in noncovalent H-bonding, contributing to their stability. The presence of these noncovalent interactions in TGA clusters was elucidated through Atoms in Molecule (AIM), reduced density gradient (RDG), and natural bond order (NBO) analysis, while electrostatic potential (ESP) charge and vibrational mode analysis further supported these findings.

DFT Study of the Adsorption and SERS of Pyridine on M10N10 (M, N = Cu, Ag) Tetrahedral Clusters

This work presents a theoretical detailed analysis of the surface-enhanced Raman spectroscopy (SERS) of the pyridine-M10N10 (M, N = Ag, Cu) tetrahedral (Td) clusters considering two binding positions: vertex (V) and surface (S). In addition to the well-known monometallic Td structure, we added two different bimetallic Ag-Cu compositions, named Td1 and Td2 geometries. Density functional methodology with the use of BP86 and CAM-B3LYP exchange-correlation functionals (XCs) and LANL2DZ pseudopotential has been employed for analyzing the electronic structure and geometries, the chemical static (CHEM), and resonant Raman mechanisms (RR): charge transfer RR-CT and intracluster excitation RR-CR. The static CHEM mechanism shows an increase in the enhancement factors (EFs) of Py-V concerning Py-S positions, which can also be distinguished by the averaged adsorption energies and bond polarizabilities. The static SERS response for Cu-Py-V junction is from 5 to 10 times greater than Ag-Py-V EFs and up to 28 times greater than Py-S complexes. For the static Raman, we found that the analyses of ν8a and ν1 normal modes are related to the EF changes and allow us to distinguish V from S complexes. The TDDFT calculations show striking differences between BP86 and CAM-B3LYP XCs analyzed spectra, and CAM-B3LYP granted a clear distinction between V and S for the location of CT-type transitions. In addition, important differences were obtained from the analysis of the charge transfer excitations between both XCs. Resonant Raman calculations evidenced significant enhancements for RR-CT and RR-CR as compared to the static enhancements, and RR-CT can be distinguished from the RR-CR mechanism, while specific normal modes help to differentiate the vertex from the surface Py-junction. Bimetallic Ag-Cu nanostructures represent promising choices for SERS substrates, showing EFs higher than those of monometallic Ag.

Systematic Evaluation of Counterpoise Correction in Density Functional Theory

A widespread belief persists that the Boys-Bernardi function counterpoise (CP) procedure "overcorrects" supramolecular interaction energies for the effects of basis-set superposition error. To the extent that this is true for correlated wave function methods, it is usually an artifact of low-quality basis sets. The question has not been considered systematically in the context of density functional theory, however, where basis-set convergence is generally less problematic. We present a systematic assessment of the CP procedure for a representative set of functionals and basis sets, considering both benchmark data sets of small dimers and larger supramolecular complexes. The latter include layered composite polymers with ∼150 atoms and ligand-protein models with ∼300 atoms. Provided that CP correction is used, we find that intermolecular interaction energies of nearly complete-basis quality can be obtained using only double-ζ basis sets. This is less expensive as compared to triple-ζ basis sets without CP correction. CP-corrected interaction energies are less sensitive to the presence of diffuse basis functions as compared to uncorrected energies, which is important because diffuse functions are expensive and often numerically problematic for large systems. Our results upend the conventional wisdom that CP "overcorrects" for basis-set incompleteness. In small basis sets, CP correction is mandatory in order to demonstrate that the results do not rest on error cancellation.

An unrestricted approach for the accurate calculation of the interaction potentials of open-shell monomers: The case of O2-O2

The properties of molecular oxygen including its condensed phases continue to be of great relevance for the scientific community. The richness and complexity of its associated properties stem from the fact that it is a very stable diradical. Its open-shell nature leads to low-lying multiplets with total electronic spin S = 0, 1, 2 in the case of the dimer, (O₂)₂, and the accurate calculation of the intermolecular potentials represents a challenge to ab initio electronic structure methods. In this work, we present intermolecular potentials calculated at a very high level, thus competing with the most accurate restricted potentials obtained to date. This is accomplished by drawing on an analogy between the coupled and uncoupled representations of angular momentum and restricted vs unrestricted methodologies. The S = 2 state can be well represented by unrestricted calculations in which the spins of the unpaired electrons are aligned in parallel; however, for the state where they are aligned in antiparallel fashion, it would seem that the total spin is not well defined, i.e., the well-known spin contamination problem. We show that its energy corresponds to that of the S = 1 state and perform unrestricted coupled cluster calculations for these two states. Then, we obtain the S = 0 state through the Heisenberg Hamiltonian and show that this is very reliable in the well region of the potentials. We make extensive comparisons with the best restricted potentials [Bartolomei et al., Phys. Chem. Chem. Phys. 10(35), 5374-5380 (2008)] and with reliable experimental determinations, and a very good agreement is globally found.

Full Dimensional Potential Energy Function and Calculation of State-Specific Properties of the CO+N2 Inelastic Processes Within an Open Molecular Science Cloud Perspective

A full dimensional Potential Energy Surface (PES) of the CO + N₂ system has been generated by extending an approach already reported in the literature and applied to N₂-N₂ (Cappelletti et al., 2008), CO₂-CO₂ (Bartolomei et al., 2012), and CO₂-N₂ (Lombardi et al., 2016b) systems. The generation procedure leverages at the same time experimental measurements and high-level ab initio electronic structure calculations. The procedure adopts an analytic formulation of the PES accounting for the dependence of the electrostatic and non-electrostatic components of the intermolecular interaction on the deformation of the monomers. In particular, the CO and N₂ molecular multipole moments and electronic polarizabilities, the basic physical properties controlling the behavior at intermediate and long-range distances of the interaction components, were made to depend on relevant internal coordinates. The formulated PES exhibits substantial advantages when used for structural and dynamical calculations. This makes it also well suited for reuse in Open Molecular Science Cloud services.

Performance of local correlation methods for halogen bonding: The case of Br2-(H2O)n,n = 4,5 clusters and Br2@5(12)6(2) clathrate cage

The performance of local correlation methods is examined for the interactions present in clusters of bromine with water where the combined effect of hydrogen bonding (HB), halogen bonding (XB), and hydrogen-halogen (HX) interactions lead to many interesting properties. Local methods reproduce all the subtleties involved such as many-body effects and dispersion contributions provided that specific methodological steps are followed. Additionally, they predict optimized geometries that are nearly free of basis set superposition error that lead to improved estimates of spectroscopic properties. Taking advantage of the local correlation energy partitioning scheme, we compare the different interaction environments present in small clusters and those inside the 5(12)6(2) clathrate cage. This analysis allows a clear identification of the reasons supporting the use of local methods for large systems where non-covalent interactions play a key role.

Chemical Interactions and Spin Structure in (O2)4: Implications for the ε-O2 Phase

The chemical interactions and spin structure of (O2)4 in its ground singlet state are analyzed by means of Quantum Chemical Topology descriptors. The energetic contributions of the Interacting Quantum Atoms approach are used to obtain information about the class of interactions displayed along the dissociation path of (O2)4. The exchange-correlation contribution to the binding energy is non-negligible for the O2-O2 interactions at intermolecular distances close to those found for the pressure induced ε phase of solid (O2) and this strengthening of the intermolecular bonding is built up from a simultaneous weakening of the intramolecular bond. This result is of interest in connection with the observed softening of the IR vibron frequency in the lower pressure range of the ε phase. The spin structure in the real space along the dissociation process is interpreted with the help of the so-called electron number distribution functions. At large distances, the four triplet O2 molecules are arranged in a way consistent with an antiferromagnetic structure, whereas at short distances, a significant spin redistribution is driven by the exchange process and it involves a propensity toward a null magnetic moment per molecule. Such probability behavior can be related with the magnetic evolution of solid oxygen across the δ → ε phase transition. Additional calculations of (O2)4 excited states support the conclusion that the relative stabilization and magnetic features of the ground singlet state are due to the onset of the new intermolecular bonds, and not to an exclusive modification of the electronic character within the O2 molecules.

A theoretical investigation of the structure of 2-nitropyridine-N-oxide and the dependency of the NO2 torsional motion on the applied wavefunction and basis set

HF, B3LYP, and MP2 wave functions in combination with Pople 6-31, 6-311 augmented with polarization functions on all atoms and Dunning double- and triple-zeta basis sets have been employed to investigate the structures and torsional potential function of the nitro group in 2-nitropyridine-N-oxide (2-NPO) and a variety of its fluorinated derivatives. The augmentation of the basis sets with diffuse functions showed a marked effect on the profile and barriers of the NO2 torsional potential. Depending on the applied model chemistry, the heterocyclic ring in some 2-NPOs has proved to be non-planar. The non-planarity of the ring was characterized by Cremer-Pople puckering amplitude Q. The disruption of the ring planarity in some NPOs was accounted for the distinctive reactivity and impact sensitivity of these heterocycles. Consistently, the NBO and the AIM analyses furnished clear evidence for the accentuated weakness of the C-NO2 bond and provided evidence for the electronic interplay between the NO2 group, the fluorine substituent and the heterocyclic ring. Deletion of all off-diagonal Fock-matrix elements (NOSTAR) to separate hyperconjugative stabilizing interactions from steric interactions was used. The effect of nitration and fluorination on the aromaticity of the studied 2-NPOs was investigated by using the NICS descriptors NICS(1) and NICS(1)zz. These NICS indices have shown that the fluorination in para position to the nitro group exhibits the highest degree of aromaticity within the fluorinated 2-NPOs.

To address accuracy and precision using methods from analytical chemistry and computational physics

In this work the pesticides were determined by liquid chromatography-mass spectrometry (LC-MS). In present study the occurrence of imidacloprid in 343 samples of oranges, tangerines, date plum, and watermelons from Valencian Community (Spain) has been investigated. The nine additional pesticides were chosen as they have been recommended for orchard treatment together with imidacloprid. The Mulliken population analysis has been applied to present the charge distribution in imidacloprid. Partitioned energy terms and the virial ratios have been calculated for certain molecules entering in interaction. A new technique based on the comparison of the decomposed total energy terms at various configurations is demonstrated in this work. The interaction ability could be established correctly in the studied case. An attempt is also made in this work to address accuracy and precision. These quantities are well-known in experimental measurements. In case precise theoretical description is achieved for the contributing monomers and also for the interacting complex structure some properties of this latter system can be predicted to quite a good accuracy. Based on simple hypothetical considerations we estimate the impact of applying computations on reducing the amount of analytical work.

A simple natural orbital mechanism of “pure” van der Waals interaction in the lowest excited triplet state of the hydrogen molecule

A treatment of van der Waals (vdW) interaction by density-matrix functional theory requires a description of this interaction in terms of natural orbitals (NOs) and their occupation numbers. From an analysis of the configuration-interaction (CI) wave function of the 3Sigmau + state of H2 and the exact NO expansion of the two-electron triplet wave function, we demonstrate that the construction of such a functional is straightforward in this case. A quantitative description of the vdW interaction is already obtained with, in addition to the standard part arising from the Hartree-Fock determinant /1sigmag(r1)1sigmau(r2)/, only two additional terms in the two-electron density, one from the first "excited" determinant /2sigmag(r1)2sigmau(r2)/ and one from the state of 3Sigmau + symmetry belonging to the (1pig)1(1piu)1 configuration. The potential-energy curve of the 3Sigmau + state calculated around the vdW minimum with the exact density-matrix functional employing only these eight NOs and NO occupations is in excellent agreement with the full CI one and reproduces well the benchmark potential curve of Kolos and Wolniewicz [J. Chem. Phys. 43, 2429 (1965)]. The corresponding terms in the two-electron density rho2(r1,r2), containing specific products of NOs combined with prefactors that depend on the occupation numbers, can be shown to produce exchange-correlation holes that correspond precisely to the well-known intuitive picture of the dispersion interaction as an instantaneous dipole-induced dipole (higher multipole) effect. Indeed, (induced) higher multipoles account for almost 50% of the total vdW bond energy. These results serve as a basis for both a density-matrix functional theory of van der Waals bonding and for the construction of orbital-dependent functionals in density-functional theory that could be used for this type of bonding.

Basis set superposition error in MP2 and density-functional theory: A case of methane-nitric oxide association

A systematic study of basis set superposition error (BSSE) behavior in H(3)C-H[ellipsis (horizontal)][NO] complexes for both -H...N- and -H...O- orientations were carried out using MP2 and density-functional theory with Pople's [6-31G(d,p),6-311++G(nd,nd), where n=1,2,3, and 6-311++G(3df,3pd)] and Dunning's augmented correlation consistent basis sets [aug-cc-pVXZ (X=D and T)]. Corrected and uncorrected counterpoise potential-energy surfaces (PESs) were explored and differences obtained between them indicate that reliable optimizations of these molecular interactions must be carried out in a PES free of BSSE, even in the case of large basis sets and popularly used functionals such as B3LYP. Although all basis used could be always considered within a margin of approximation for representing molecular orbitals and show important values of BSSE, 6-311++G(2d,2p) basis set shows the best results in uncorrected PES with respect to the corrected ones. B3LYP functional produces erratic results: complexes appear repulsive and the intermolecular distances are always large, evidencing the lack of a correct dispersive forces treatment in the original parameterization. According to the MP2 results, the -H...N- interactions appear as slightly more stable than those of the -H...O- orientation.

Spin-orbit coupling in O2(υ)+O2 collisions: I. Electronic structure calculations on dimer states involving the XΣg−3, aΔg1, and bΣg+1 states of O2

The importance of vibrational-to-electronic (V-E) energy transfer mediated by spin-orbit coupling in the collisional removal of O2(X 3Sigmag-,upsilon>or=26) by O2 has been reported in a recent communication [F. Dayou, J. Campos-Martinez, M. I. Hernandez, and R. Hernandez-Lamoneda, J. Chem. Phys. 120, 10355 (2004)]. The present work provides details on the electronic properties of the dimer (O2)2 relevant to the self-relaxation of O2(X 3Sigmag-,upsilon>>0) where V-E energy transfer involving the O2(a 1Deltag) and O2(b 1Sigmag+) states is incorporated. Two-dimensional electronic structure calculations based on highly correlated ab initio methods have been carried out for the potential-energy and spin-orbit coupling surfaces associated with the ground singlet and two low-lying excited triplet states of the dimer dissociating into O2(X 3Sigmag-)+O2(X 3Sigmag-), O2(a 1Deltag)+O2(X 3Sigmag-), and O2(b 1Sigmag+)+O2(X 3Sigmag-). The resulting interaction potentials for the two excited triplet states display very similar features along the intermolecular separation, whereas differences arise with the ground singlet state for which the spin-exchange interaction produces a shorter equilibrium distance and higher binding energy. The vibrational dependence is qualitatively similar for the three studied interaction potentials. The spin-orbit coupling between the ground and second excited states is already nonzero in the O2+O2 dissociation limit and keeps its asymptotic value up to relatively short intermolecular separations, where the coupling increases for intramolecular distances close to the equilibrium of the isolated diatom. On the other hand, state mixing between the two excited triplet states leads to a noticeable collision-induced spin-orbit coupling between the ground and first excited states. The results are discussed in terms of specific features of the dimer electronic structure (including a simple four-electron model) and compared with existing theoretical and experimental data. This work gives theoretical insight into the origin of electronic energy-transfer mechanisms in O2+O2 collisions.

Potential energy surface discontinuities in local correlation methods

We have examined the occurrence of discontinuities in bond-breaking potential energy surfaces given by local correlation methods based on the Pulay-Saebø orbital domain approach. Our analysis focuses on three prototypical dissociating systems: the C-F bond in fluoromethane, the C-C bond in singlet, ketene, and the central C-C bond in propadienone. We find that such discontinuities do not occur in cases of homolytic bond cleavage due to the inability of the Pipek-Mezey orbital localization method to separate singlet-coupled charges on distant fragments. However, for heterolytic bond cleavage, such as that observed in singlet ketene and propadienone, discontinuities occur both at stretched geometries and near equilibrium. These discontinuities are usually small, but may be of the same order of magnitude as the localization error in some cases.

Determination of noncovalent interaction energies from electronic densities

Starting from the Hellmann-Feynman theorem, an expression is derived for the interaction energy in forming a noncovalently bound complex. It invokes only classical electrostatics, involving the charge distributions of the components as they are in the complex. We propose a method for obtaining these from the total charge distribution. Integration over the electronic densities is carried out by a numerical procedure slightly modified from that of Gavezzotti. We calculate the interaction energies for four molecular dimers at a variety of computational levels. The results are analyzed and compared to the best estimated values available in the literature.

Monomer basis-set truncation effects in calculations of interaction energies: A model study

Supermolecular interaction energies are analyzed in terms of the symmetry-adapted perturbation theory and operators defining the inaccuracy of the monomer wave functions. The basis set truncation effects are shown to be of first order in the monomer inaccuracy operators. On the contrary, the usual counterpoise correction schemes are of second order in these operators. Recognition of this difference is used to suggest an approach to corrections for basis-set truncation effects. Also earlier claims--that dimer-centered basis sets may lead to interaction energies free of basis-set superposition effects--are shown to be misleading. According to the present study the basis-set truncation contributions, evaluated by means of the symmetry-adapted perturbation theory with monomer-centered basis sets, provide physically and mathematically justified corrections to supermolecular results for interaction energies.

Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations

The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy.

Calculation of electrostatic and polarization energies from electron densities

We investigate procedures for calculating the electrostatic and polarization energies, Ees and Epol, associated with noncovalent interactions. The starting points are the electron densities of the isolated components and the complex; these could be obtained either computationally or experimentally. A slightly modified version of a scheme proposed by Gavezzotti is used to carry out numerical integrations over these electron densities. Our approach to estimating Epol is based upon partitioning the charge distributions of the components into overlapping and nonoverlapping regions. The effects of varying the integration parameters, computational techniques and basis sets are examined in detail for several noncovalently bound molecular dimers. Our results are in good agreement with the values of Ees and Epol produced by other methods, which require analytical integrations over interaction Hamiltonian matrix elements.

Intermolecular interactions in solution: Elucidating the influence of the solvent

A new approach for the analysis of intermolecular interactions in a solution is proposed. The changes in the interaction energy components due to the solvent effects are estimated on the basis of the interaction energy calculated in the presence of the electric field induced in a polarizable medium, or in the field of the effective fragment potentials. Obtained results indicate a significant increase in stabilization resulting from electrostatic interactions as a result of the cooperative interactions between interacting subsystems and solvent molecules.

Standardized Medium-Size Basis Sets for Calculations of Molecular Electric Properties: Group IIIA

The idea of what is called the basis set polarization method is reviewed and the available polarized basis sets are surveyed. Following the basis set polarization approach and certain empirical rules developed earlier, the first-order polarized basis sets for the Group IIIA elements are generated. These basis sets have been developed for both nonrelativistic and spin-averaged Douglas-Kroll relativistic calculations. Their performance is tested in calculations of atomic dipole polarizabilities and in high-level-correlated calculations of the dipole moments of GaF, InF, and TlF. The relativistic effects have been found to significantly affect the calculated molecular dipole moments of the studied fluorides. The results are in satisfactory agreement with reference data. The present study completes the library of the first-order polarized basis sets for all atoms of the main groups of the Periodic Table.