Static hyperpolarizability of the water dimer and the interaction hyperpolarizability of two water molecules

DFT and Molecular Docking Study of 1-(2´-Thiophen)-2-propen-1-one-3-(2,3,5-trichlorophenyl) (TTCP) Molecule as Antiviral to Covid-19 Main Protease

Thiophene-containing compounds have antiviral properties and may be among the drugs tested for the treatment of COVID-19 diseases. In order to better understand the molecular definition of the 1-(2´-Thiophen)-2-propen-1-one-3-(2,3,5-trichlorophenyl) molecule from thiophene-containing compounds, the physico-chemical (molecular structure analysis, spectroscopic properties, boundary orbital analysis) mechanisms underlying the protein-ligand interaction should be examined in detail. For this reason, geometric parameters, IR and UV-vis spectra, conformational analysis, electronic, NBO and NLO properties, molecular electrostatic potential map and Mulliken charge distributions of the TTCP molecule were investigated theoretically using DFT theory in the Gaussian program. Accordingly, molecular docking calculations with COVID-19 main protease (PDB 5R7Y) were performed to determine the pharmaceutical activities of the TTCP molecule against coronavirus diseases.

First hyperpolarizability of water at the air-vapor interface: a QM/MM study questions standard experimental approximations

Surface Second-Harmonic Generation (S-SHG) experiments provide a unique approach to probe interfaces. One important issue for S-SHG is how to interpret the S-SHG intensities at the molecular level. Established frameworks commonly assume that each molecule emits light according to an average molecular hyperpolarizability tensor β(-2ω,ω,ω). However, for water molecules, this first hyperpolarizability is known to be extremely sensitive to their environment. We have investigated the molecular first hyperpolarizability of water molecules within the liquid-vapor interface, using a quantum description with explicit, inhomogeneous electrostatic embedding. The resulting average molecular first hyperpolarizability tensor depends on the distance relative to the interface, and it practically respects the Kleinman symmetry everywhere in the liquid. Within this numerical approach, based on the dipolar approximation, the water layer contributing to the Surface Second Harmonic Generation (S-SHG) intensity is less than a nanometer. The results reported here question standard interpretations based on a single, averaged hyperpolarizability for all molecules at the interface. Not only the molecular first hyperpolarizability tensor significantly depends on the distance relative to the interface, but it is also correlated to the molecular orientation. Such hyperpolarizability fluctuations may impact the S-SHG intensity emitted by an aqueous interface.

Extremely large static and dynamic nonlinear optical response of small superalkali clusters NM3M' (M, M'=Li, Na, K)

Exploring novel nonlinear optical (NLO) materials with excess electron properties is essential for advancing the use of excess electron compounds in optics. The studied superalkali clusters NM₃M' (M, M' = Li, Na, K) are thermodynamically stable and their binding energies range from -27.10 to -53.84 kcal mol^-1. The observed significant values for VIPs suggest their electronic stabilities. Being excess electron candidate these clusters show significant β_o value (3.9 × 10⁷ au), which nicely correlates the hyperpolarizability reported by a two-level model (β_tl). Furthermore, these clusters exhibit a remarkable static second hyperpolarizability (γ_o) value of 1.1 × 10¹⁰ au for the NK₄ superalkali cluster. The hyper Rayleigh scattering (β_HRS) is also computed where the highest value of 2.9 × 10⁷ is recorded for NNa₃K superalkali. The obtained values of β_vec values (projection of hyperpolarizability on dipole moment vector) also signify the excellent nonlinearity of clusters. Besides, the calculated electro-optica pockel's effect β(-ω; ω,0) and second harmonic generation β(-2ω; ω, ω) values are much pronounced at larger dispersion frequency ω = 1064 nm. Moreover, the frequency-dependent second hyperpolarizability γ(ω) with dc-Kerr effect γ(-ω; ω,0,0) and electric field induced second harmonic generation γ(-2ω; ω,ω,0) show larger values at ω = 1064 nm. Thus the highest value of the dc-Kerr constant increases up to 1.0 × 10¹¹ au which also signifies the larger nonlinear refractive index of the studied cluster. We hope this work could open up new possibilities using superalkali clusters as NLO materials for optoelectronics, laser, second harmonic generation and as frequency doubler.

Second Harmonic Generation Responses of Ion Pairs Forming Dimeric Aggregates

A sequential approach combining molecular dynamics and density functional theory calculations has been worked out to unravel the second harmonic generation responses of anion-cation (AC) pairs when they form dimeric aggregates, where the cation is a stilbazolium derivative and the anions range from small inorganic iodide to medium-size organic p-toluenesulfonate. These complexes showed a strong self-aggregation behavior in molecular dynamics simulations within high-concentration conditions and formed stable dimeric aggregates, (AC)₂, which can adopt different structural shapes from stacked, Λ, to head-to-head configurations. These various structures are associated with different symmetries, which are shown to modulate the second- and third-order nonlinear optical (NLO) responses. By consolidating the NLO results of this work with those previously obtained for single AC pairs [ J. Chem. Inf. Model. 2020, 60, 4817-4826], we have been able to explain the experimentally observed variations of the electrical-field-induced second harmonic generation (EFISHG) responses of these complexes as a function of concentration [ ChemPhysChem 2010, 11, 495-507]. Moreover, results have highlighted that (i) the second-order contribution, μβ_//, dominates the global EFISHG response; (ii) the μβ_// responses of dimers are about half of those computed for the parent AC pairs, while the third-order contributions, γ_//, are reduced by only 10%; (iii) these distinct trends are ascribed to the formation of dimers adopting mainly Λ and head-to-head shapes, increasing the centrosymmetric character, in comparison to the monomers, a situation in which the second-order response cancels out as well as influences the dipole moment on μβ_//; (iv) the presence of a strong amino donor group in the cation enhances the μβ_// response by 1 order of magnitude and γ_// by about a factor of 2; and finally, (v) dimeric aggregation has similar effects on the hyper-Rayleigh scattering response, β_HRS, as on μβ_//, while it reduces the one-dimensional character of β_HRS. This work constitutes a step forward for the modeling of the NLO responses of AC aggregates in solution.

DFT and spatial confinement: a benchmark study on the structural and electrical properties of hydrogen bonded complexes

An extended set of 37 exchange correlation functionals, representing different DFT approximations, has been evaluated on a difficult playground represented by the dipole moment (μ_z), polarizability (α_zz), first hyperpolarizability (β_zzz), and the corresponding interaction-induced electrical properties (Δμ_z, Δα_zz, Δβ_zzz) of spatially confined hydrogen bonded (HB) dimers. A two-dimensional harmonic oscillator potential was used to exert the effect of spatial restriction. The performance of DFT methods in predicting hydrogen bond lengths in the studied molecular complexes upon confinement has also been examined. The data determined using a high-level CCSD(T) method serve as a reference. The conducted analyses allow us to conclude that methods rooted in DFT constitute a precise tool for the calculation of μ_z and α_zz as well as Δμ_z and Δα_zz, as most of the tested functionals provide results affected by rather small relative errors. On the other hand, an accurate description of the nonlinear optical response of the studied HB systems remains a great challenge for most of the analyzed DFT functionals, both in vacuum and in the presence of an analytical confining potential. Some of the tested DFT methods are found to be prone to catastrophic failure in the prediction of β_zzz as well as Δβ_zzz. The obtained results indicate that there is no great chasm in performance between functionals belonging to different DFT approximations or functionals including different amount of Hartree-Fock exchange when the values of dipole moment and first hyperpolarizability as well as the corresponding interaction-induced electrical properties are considered. However, a higher fraction of Hartree-Fock exchange improves the quality of predictions of α_zz and Δα_zz. Additionally, it has been shown that only three functionals from the examined set, namely B2PLYP, B3LYP and ωB97X-D, provide highly accurate structural parameters for the investigated systems. Of significant importance is the conclusion that the ωB97X-D functional, representing a modern and highly parametrized range-separated hybrid, demonstrates the most coherent behavior, showing rather small deviations from the reference data in the case of μ_z, α_zz, Δμ_z and Δα_zz as well as the structural parameters of the studied HB dimers. Moreover, our results indicate that the presence of spatial confinement has a rather small effect on the performance of DFT methods.

Gauging the performance of some density functionals including dispersion and nonlocal corrections for relative energies of water 20-mers

Currently, development of density functional theory approximations and their benchmarking for accurately modeling different types of molecular interactions become a very active field of research. In this report, performance of the dispersion (D3) and nonlocal (NL) corrected density functionals has been compared with generalized energy-based fragmentation approach at the complete basis set limit for predicting the relative energies of 10 low-energy isomers of water nanoclusters (H₂O)₂₀ as an illustrative example of hydrogen bonded systems. Considering a variety of exchange-correlation density functionals in combination with D3 and NL corrections we find that the D3 based approximations outperform the functionals incorporating NL correction. It is also shown that the LC-ωPBE-D3 and rPW86PBE-NL functionals have the best trend from the viewpoint of the order of stabilities in water nanoclusters under study.

Polarization response of clathrate hydrates capsulated with guest molecules

Clathrate hydrates are characterized by their water cages encapsulating various guest atoms or molecules. The polarization effect of these guest-cage complexes was studied with combined density functional theory and finite-field calculations. An addition rule was noted for these systems whose total polarizability is approximately equal to the polarizability sum of the guest and the cage. However, their distributional polarizability computed with Hirshfeld partitioning scheme indicates that the guest-cage interaction has considerable influence on their polarization response. The polarization of encapsulated guest is reduced while the polarization of water cage is enhanced. The counteraction of these two opposite effects leads to the almost unchanged total polarizability. Further analysis reveals that the reduced polarizability of encapsulated guest results from the shielding effect of water cage against the external field and the enhanced polarizability of water cage from the enhanced bonding of hydrogen bonds among water molecules. Although the charge transfer through the hydrogen bonds is rather small in the water cage, the polarization response of clathrate hydrates is sensitive to the changes of hydrogen bonding strength. The guest encapsulation strengthens the hydrogen bonding network and leads to enhanced polarizability.

Density functional theory (DFT) investigations on doped fullerene with heteroatom substitution

Structures and stabilities of dodecahedral fullerene C19X (X=Ni, Ti) and C20 have been investigated by quantum chemical calculations based on density functional theory. The geometrical structures, relative stabilities, dielectric constant of the doped cages were studied systematically and compared with those of the fullerene C20 cage. A series of dodecahedral functionalized derivatives have been studied at the B3LYP/6-31G level of density functional theory (DFT). The relative and formation energies of compounds, Mulliken charges, occupancy, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), the HOMO-LUMO band gap and chemical potential (μ) were calculated. The doping effect is discussed in terms of the change in the CC bond length and total dipole moment. The obtained result indicates that the CC bond length increases as a result of doping. The NBO analysis showed that there is a hyper conjugative interaction between the hetero atoms such as titanium and nickel lone-pair electron of doped fullerene with bonding and antibonding (σ(∗)) orbital of carbon atom of fullerene. The stability of the molecule, arising from charge delocalization, has been analyzed using Natural Bond Orbital (NBO) analysis. The nucleus - independent that more negative NICS values in doped fullerene than those of C20. The condensed Fukui Function and the newly introduced the atomic descriptors S (fk) to determine the local reactive sites of the molecular systems during electrophilic, nucleophilic and radical attacks have been calculated for the fullerene C20 compound.

Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline

Comprehensive investigation of geometrical and electronic structure in ground as well as the first excited state of 3,5-Difluoroaniline (C6H5NF2) was carried out. The experimentally observed spectral data (FT-TR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were measured by TD-DFT approach. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. Global and local reactivity descriptors were computed to predict reactivity and reactive sites on the molecule. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data obtained. Moreover, the thermodynamic properties were evaluated.

Structure and NLO properties of halogen (F, Cl) substituted formic acid dimers

In this work, using ab initio and density functional theory (DFT) methods halogen substituted formic acid (FA) dimer is studied. The dimer stability is due to the hydrogen bonds, either conventional (OH⋯O, OH⋯F, OH⋯Cl) or non-conventional (CH⋯O, CH⋯F, CH⋯Cl). Among all the dimers, trans-trans form is more stable than the trans-cis, and cis-cis form. Basis set extrapolated counterpoise corrected interaction energy results for the FA dimer are in excellent agreement with BSSE corrected MP2 interaction energy. Symmetry Adopted Perturbation Theory (SAPT) analysis reveals that the electrostatic effect plays a dominant role in stabilization among the dimers with maximum interaction energy. Chlorine substituted FA dimer has high hyperpolarizability, which makes them excellent candidate for nonlinear optical materials (NLO). The halogen substituted formic acid dimers have higher stability and polarizability value than the unsubstituted formic acid dimer. The hyperpolarizability values depend on the geometrical structures of halogenated formic acid dimers than the type of hydrogen bonds. The small excitation energy and HOMO-LUMO gap in the halogenated formic acid dimer has led to the strong nonlinear optical response. The depolarization ratio and Rayleigh scattering increases in formic acid dimer after the halogen atom substitution.

Effects of donor-acceptor groups on the structural and electronic properties of 4-(methoxymethyl)-6-methyl-5-nitro-2-oxo-1,2-dihydropyridine-3-carbonitrile

Quantum chemical calculations on the geometric parameters, harmonic vibrational wavenumbers and 1H and 13C nuclear magnetic resonance (NMR) chemical shifts values of 4-(methoxymethyl)-6-methyl-5-nitro-2-oxo-1,2-dihydropyridine-3-carbonitrile [C9H9N3O4] molecule in ground state were performed using the ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The results of optimized molecular structure were presented and compared with X-ray diffraction results. The theoretical vibrational frequencies and 1H and 13C NMR chemical shifts values were compared with experimental values of the investigated molecule. The observed and calculated values were found to be in good agreement. Since the title compound contains different electron-donor and -acceptor groups as well as lone pair electrons, and multiple bonds, the effects of these groups on the structural and electronic properties are found out. In addition, conformational, natural bond orbital (NBO), nonlinear optical (NLO) analysis, frontier molecular orbital energies, molecular surfaces, Mulliken charges and atomic polar tensor based charges were investigated using HF and DFT methods.

Quantum chemical calculations on the geometrical, conformational, spectroscopic and nonlinear optical parameters of 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine

The optimized geometry, (1)H and (13)C NMR chemical shifts, conformational and natural bond orbital (NBO) analyses, thermodynamic parameters, molecular surfaces, Mulliken, NBO and APT charges for 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine [C7H7Cl3N2] were investigated by the ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The calculated structural parameters (bond lengths, bond angles and dihedral angles) and (1)H and (13)C NMR chemical shifts values are compared with experimental values of the investigated compound. The observed and the calculated values are found to be in good agreement. The energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were calculated, and the obtained energies displayed that charge transfer occurs in 5-(2-Chloroethyl)-2,4-dichloro-6-methylpyrimidine compound. In addition, the linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated compound have been computed by using HF and DFT methods.

Molecular structure, Mulliken charge, frontier molecular orbital and first hyperpolarizability analysis on 2-nitroaniline and 4-methoxy-2-nitroaniline using density functional theory

In the present study, we made an attempt to calculate the energy gap, molecular dipole moment and first hyperpolarizability of 2-nitroaniline (2NA) and 4-methoxy-2-nitroaniline (4M2N) with a basis set 6-31G (d, p) function has been employed at density functional theory (DFT) methods. Geometry optimizations was carried out with DFT-B3LYP/6-31G (d, p), the results have revealed that intramolecular hydrogen bonding present in both the molecular system. We analyzed the energy gap, molecular dipole moment and hyperpolarizability changes due to substitution effect of the methoxy group in 2NA molecule. It is confirmed that strong electron acceptor and donor groups in a material yield higher NLO response.

Quantum mechanical force field for water with explicit electronic polarization

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Theoretical investigation of 5-(2-acetoxyethyl)-6-methylpyrimidin-2,4-dione: conformational study, NBO and NLO analysis, molecular structure and NMR spectra

Structural and conformational, natural bond orbital (NBO) and nonlinear optical (NLO) analysis was performed, and (1)H and (13)C NMR chemical shifts values of 5-(2-Acetoxyethyl)-6-methylpyrimidin-2,4-dione [C9H12N2O4] in the ground state were calculated by using Density Functional Theory (DFT-B3LYP/6-311++G(d,p)) and Hartree-Fock (HF/6-311++G(d,p)) methods. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. In addition, the molecular frontier orbital energies, thermodynamic parameters (in the range of 200-700 K), molecular surfaces, Mulliken charges and atomic polar tensor-based charges were investigated. Besides, the analysis of all possible conformational of the title compound, a detailed potential energy curve for τ1(C8O3C10O4), τ2 (C8O3C10C11) and τ3 (C5C7C8O3) dihedral angles were performed in steps of 10° from 0° to 360°, and depicted to find the most stable form. Finally, the calculated HOMO and LUMO energies show that charge transfer occurs within the title compound.

Synthesis, structural, spectroscopic and optical studies of charge transfer complex salts

New charge transfer molecular complex adducts of picric acid (C6H3N3O7) with triethylamine (C6H15N) and dimethylformamide (HCON(CH3)2) were synthesized successfully for the first time. Chemical composition and stoichiometry of the synthesized complex salts were verified by CHN elemental analysis. Solubility of the complex salts have been determined by gravimetric method and single crystals of two new salts were grown by low temperature solution growth technique. Crystal system, crystalline nature and cell parameters of the grown crystals were determined by single crystal X-ray diffraction (SXRD) and powder X-ray diffraction (PXRD) analyses. The formations of the charge-transfer complex, functional groups and the modes of vibrations have been confirmed by Fourier transform infrared (FTIR) spectroscopy. In order to know the linear and nonlinear optical suitability for device fabrication, UV-Vis (UV) spectral analysis and relative second harmonic generation (SHG) efficiency test were performed for the grown crystals.

DFT QUANTUM CHEMICAL STUDIES ON 1-[N-(2-PYRİDYL) AMİNOMETHYLİDENE]-2(1H)-NAPHTALENONE

Quantum chemical calculations of the structure, molecular electrostatic potential and thermodynamic functions have been performed using the density functional (DFT/B3LYP) method with the 6-311++G(d,p) basis set for the title compound 1-[N-(2-pyridyl)aminomethylidene}-2(1H)-Naphtalenone. The energetic behavior of the title compound in solvent media has been examined by applying the Onsager and the polarizable continuum model. To investigate second order nonlinear optical properties of the title compound, the electric dipole μ, the polarizability α and the first hyperpolarizability β were computed using the density functional B3LYP and CAM-B3LYP methods with the 6-311++G(d,p) basis set. According to our calculations, the title compound exhibits nonzero β value revealing second order NLO behavior. The changes of thermodynamic properties for the formation of the title compound with the temperature ranging from 200 K to 500 K have been obtained using the statistical thermodynamic method. The relationship between formation enthalpy and entropy changes has been investigated with the entropy–enthalpy compensation. Besides, natural bond orbital and frontier molecular orbital analysis of the title compound were investigated by theoretical calculations.