Second-order Interaction Energies Research Articles

Theoretical study on the structure, spectroscopic, and current–voltage behavior of 11-Cis and Trans retinal isomers in rhodopsin

In this study, the electronic transport properties of 11-Cis and Trans retinal, components of rhodopsin, were investigated as optical molecular switches using the nonequilibrium Green’s function (NEGF) formalism combined with first-principles density functional theory (DFT). These isomers, which can be reversibly converted into each other, were examined in detail. The structural and spectroscopic properties, including infrared (IR), Raman, nuclear magnetic resonance (NMR), and ultraviolet (UV) spectra, were analyzed using the hybrid B3LYP/6–311 + + G** level of theory. Complete vibrational assignments were performed for both forms utilizing the scaled quantum mechanical force field (SQMFF) methodology. To evaluate the conductivity of these molecules, we utilized current–voltage (I-V) characteristics, transmission spectra, molecular projected self-consistent Hamiltonian (MPSH), HOMO–LUMO gap, and second-order interaction energies (E2). The trendline extrapolation of the current–voltage plots confirmed our findings. We investigated the effect of different electrodes (Ag, Au, Pt) and various connection sites (hollow, top, bridge) on conductivity. The Ag electrode with the hollow site exhibited the highest efficiency. Our results indicate that the Cis form has higher conductivity than the Trans form.

Structural (X-ray), spectroscopic (FT-IR, FT-Raman) and computational (DFT) analysis of intermolecular interactions in 1H-indazole-3-carbaldehyde

The title compound, 1H-indazole-3-carbaldehyde, C8H6N2O (1) is important as it represents a rare example of indazole found in nature. The asymmetric unit of 1 consists of two independent molecules (1A and 1B) which are linked by N—H⋅⋅⋅O hydrogen bonds (N⋅⋅⋅O = 2.8178(15) Å and 2.8203(14) Å), forming one-dimensional chains. The crystal structure is stabilized by slipped face-to-face π⋅⋅⋅π interactions (Cg⋅⋅⋅Cg distances in the range 3.8492(8) – 4.1830(8) Å), C=O⋅⋅⋅π interactions (O⋅⋅⋅centroids distances in the range 3.3252(12) – 3.4795(11) Å) and weak non-classical C—H⋅⋅⋅N hydrogen bonds (C⋅⋅⋅N = 3.4377(18) Å). 3D Hirshfeld surface analysis, 2D fingerprint plots and molecular electrostatic potentials were applied for a detailed investigation of all the interactions participating in the crystal packing. The intermolecular interactions were also confirmed by Natural Bond Orbital (NBO) analysis at the B3LYP and B3LYP-D3 levels using the 6-31++G(d,p) basis set. The energies of the intermolecular interactions (the second-order interaction energies, E2) oscillate between 55.5 kJ⋅mol−1 and 22.3 kJ⋅mol−1 for strong N−H⋅⋅⋅O hydrogen bond. The E2 value for the C=O⋅⋅⋅π and π⋅⋅⋅π interactions are about 4.9 kJ⋅mol−1 and 3.6 kJ⋅mol−1, respectively. Moreover, the strength of the hydrogen bonds was evaluated using vibrational spectroscopy (FT-IR and FT-Raman) and DFT calculations at the B3LYP level within the 6-31++G(d,p) basis set. These studies additionally confirm the presence of various intermolecular interactions in the crystal of 1.

Electronic transport behavior of 1-(Phenyldiazenyl)naphthalen-2-ol and its derivatives as optical molecular switches: A first-principles approach

We studied the electronic transportation properties of 1-(Phenyldiazenyl)naphthalen-2-ol and its derivatives, as optical molecular switches, by using the nonequilibrium Green’s function (NEGF) formalism combined with the first-principles density functional theory (DFT). To describe this switching, we applied the geometrical and topological parameters, Time-dependent density functional theory (TD-DFT), and the second-order interaction energies, E(2), results. The mentioned switching for titled molecules occurred between their tautomers, hydrazo and azo forms, upon photoexcitation. According to our results the current rate of titled molecules is more than that the other reported molecules, about 40,000 nA. Therefore, titled molecules show appropriate potential for using in molecular switch tools. The transmittance spectra and I–V curves show the current of the azo tautomer is more than that in the hydrazo tautomer. This result agree with increasing of the intramolecular hydrogen bond strength, electron densities of aromatic and chelated rings, and the hyperconjugations in the azo forms. In addition, the −OCH3 and -NO2 groups, does not remarkably affected the current rate with Y (111) (Y =Au, Ag, and Pt) electrodes. The best performance obtained in Ag electrode, in while in the other reported molecular switchers Au electrode was appropriated.

Ultrafast Luminescence Decay in Rhenium(I) Complexes with Imidazo[4,5-f]-1,10-Phenanthroline Ligands: TDDFT Method

The interpretation of the ultrafast luminescence decay in [Re(Br(CO)3(N^N)] complexes as a new group of chromophoric imidazo[4,5-f]-1,10-phenanthroline ligands, including 1,2-dimethoxy benzene, tert-butyl benzene (L4) and 1,2,3-trimethoxy benzene, tert-butyl benzene (L6), was studied. Fac-[Re(Br(CO)3L4 and L6] with different aryl groups were calculated in singlet and triplet excited states. The calculations were performed in the gas phase and in the presence of chloroform as a solvent. The absorption and luminescence wavelengths, transition energy, and oscillator strength for singlet and triplet states were calculated for entitled complexes with L4 and L6 ligands. The UV-Vis spectrum and the singlet and triplet energy diagrams show a good agreement between our computational results and the experimental results, particularly in the case of a triplet state in chloroform. Spin-orbit coupling calculations show sufficient intensity and short wavelength in the UV-Vis absorption after SOC corrected absorption. The results of NBO calculations in the solvent show that rhenium acts as an acceptor by means of E(2), the second-order interaction energies between donor and acceptor orbitals, at the B3LYP/lanl2mb level of theory.

DFT investigation of the electronic structure and nonlinear optic properties (NLO) of 3-amino-4-(Boc-amino)pyridine

The molecular geometrical parameters, vibrational frequencies, electronic properties and nonlinear optical (NLO) behavior of 3-amino-4-(Boc-amino)pyridine have been evaluated using the B3LYP, CAM-B3LYP and B3PW91 levels of density functional theory (DFT). The dipole moment (μ) and first hyperpolarizability (β) values of the title complex show that the molecule can be a good candidate as NLO material. The energy of HOMO and LUMO levels and the HOMO–LUMO energy gap, hardness, softness and electronegativity have been analyzed using DFT/B3LYP method with the 6-31+G(d,p) basis set. To understand the effect of the different media (gas phase and in methanol solvent) in electronic transitions, the UV–Vis computations of the molecule have been performed using time-dependent DFT (TD-DFT)/6-31+G(d,p) by applying the integral equation formalism-polarized continuum model. The second-order interaction energies of 3-amino-4-(Boc-amino)pyridine have been calculated using natural bond orbital analysis.

Synthesis, spectroscopic investigation and biological activities of copper(II) complex of 2-(2,4-difluorophenyl)pyridine: A combined theoretical and experimental study

This paper reports the synthesis, crystal structure determination and spectroscopic characterization of a new copper (II) complex, [CuCl2(dfpy)2] [dfpy: 2-(2,4-difluorophenyl)pyridine]. The Cu(II) complex crystallizes in triclinic space group P1¯ and the Cu(II) ion lies on a crystallographic inversion center. The Cu(II) ion is four-coordinated in a square planar geometry in which Cu(II) atom bound to the dfpy ligands’ nitrogen atoms and chloride ions. Density Functional Theory (DFT) method with the B3LYP/6-31 + G (d, p) level has been used to obtain ground state geometry for the title complex. The experimental FT-IR spectrum of the Cu(II) complex has been analyzed and compared with theoretical data obtained by the B3LYP level of theory. The electronic transitions, HOMO-LUMO energies, chemical hardness, softness, and electronegativity have been explained using the time-dependent DFT (TD-DFT) method. The second-order interaction energies of the Cu(II) complex have been obtained from Natural Bond Orbital (NBO) analysis. The antimicrobial activities have been tested by using minimal inhibitory concentration method (MIC).

Spectroscopic, optical, DNA, antimicrobial and density functional theory studies of 5-Bromo-2-(trifluoromethyl)pyridine

The spectroscopic characterization of 5-Bromo-2-(trifluoromethyl)pyridine was performed by the applying of Fourier Transform-Infrared (FT-IR) and 1H and 13C Nuclear Magnetic Resonance (NMR) spectroscopies. The optimized geometric structure of 5-Bromo-2-(trifluoromethyl)pyridine was searched by density functional theory (DFT) on employing B3LYP, CAMB3LYP, and B3PW91 functional. The vibrational frequencies and chemical shift values were calculated by using B3LYP, CAMB3LYP, and B3PW91 levels with the 6–31++G(d, p) basis set. The non-linear optical (NLO) properties of 5-Bromo-2-(trifluoromethyl)pyridine were determined using the same methods The HOMO-LUMO energies were examined by applying time-dependent DFT (TD-DFT) method with integral equation formalism-polarized continuum model (IEF-PCM). The second-order interaction energies of the title molecule were derived from Natural Bond Orbital (NBO) analysis. The effect of the molecule on pBR322 plasmid DNA was monitored by agarose gel electrophoresis experiments. The antimicrobial activities were tested by using minimal inhibitory concentration method (MIC).

DFT studies of copper(II) complexes of cis-1,2-diaminocyclohexane (Dach) and crystal structure of [Cu(Dach)2(H2O)]Cl2

A copper(II) complex, [Cu(Dach)2(H2O)]Cl2 (1) (Dach = cis-1,2-Diaminocyclohexane) has been prepared and characterized by IR spectroscopy and X-ray crystallography. The crystal structure of complex 1 is ionic consisting of [Cu(Dach)2(H2O)]2+ cation and two chloride counter ions. The copper atom in the complex ion assumes a distorted square pyramidal geometry with water occupying the apical position. The adjacent molecules are joined by hydrogen bonding to form irregular chains. The structures of [Cu(Dach)2(H2O)]Cl2 (1) and three of its analogues, [Cu(Dach)2Cl]Cl·H2O (2), [Cu(Dach)2(H2O)Cl]Cl (3) and [Cu(Dach)2Cl2]·H2O (4) were predicted by DFT calculations. The DFT results reveal that in the gas phase, the structure 1 is less stable in comparison to the calculated structure, [Cu(Dach)2Cl2]·H2O (4). The additional calculations were performed for the complexes investigated in solution (water) using the polarizable continuum model. According to these calculations, the electronic energies (stabilities) of the complexes 1 and 4 in the solvent are comparable to each other. The atomic charges and second-order interaction energies between orbitals for complexes 1–4 were calculated with natural bond orbital (NBO) analysis.

Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II) Complexes: Combined Hirshfeld, AIM, and NBO Analyses.

Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM) analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II) complexes. Using AIM and natural bond orbital (NBO) analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r)) at the bond critical points (0.0031–0.0156 e/a03) fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇2ρ(r)) revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (|V(r)|/G(r)) and ρ(r) are highest for the O2⋯H15-N3 interaction in [Pt(COMe)2(2-pyCMe=NNH2)] (1); hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe)2(H2NN=CMe-CMe=NNH2)] (3), there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E(2), of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of dxy, dxz, and s atomic orbitals.

Spectroscopic and DFT studies of zinc(II) complexes of diamines and thiocyanate; crystal structure of (cis-1,2-diaminocyclohexane)bis(thiocyanato-κN)zinc(II)

Zinc(II) complexes of diamines, cis-1,2-diaminocyclohexane (Dach) and N,N,N,N-tetramethylethylenediamine (Tmen), [Zn(Dach)(NCS)2] (1) and [Zn(Tmen)(NCS)2] (2) have been prepared and characterized by elemental analysis, IR, 1H &13C NMR spectroscopy. The crystal structure of [Zn(Dach)(NCS)2] (1) was determined by X-ray crystallography. In 1, the Zn(II) atom is bound to one 1,2-diaminocyclohexane molecule and to two terminal thiocyanate ions via the nitrogen atoms adopting a slightly distorted tetrahedral geometry. In the crystal structure, molecules are linked through intermolecular NH⋯S hydrogen bonds, forming chains running along the a axis. The structures of 1 and 2 as well as of [Zn(En)(NCS)2] (3) (En = 1,2-diaminoethane) were predicted using theoretical (DFT) method. The interaction energies (ΔE) for NCS anions obtained by B3LYP-D3 method are about −140 kcal mol−1, while the calculated ΔE values for neutral organic ligands are about twice smaller. The atomic charges and second-order interaction energies between orbitals were calculated with natural bond orbital (NBO) analysis.

Experimental and computational study of the structure and spectroscopic properties of 1′,3′-Dihydrospiro[cyclohexane-1,2′-[2H]imidazo[4,5-b]pyridine

The optimized molecular geometry and vibrational frequencies of 1′,3′-Dihydrospiro[cyclohexane-1,2′-[2H]imidazo[4,5-b]pyridine] were calculated using Hartree Fock (HF) and Density Functional Theory (DFT) methods. The vibrational spectrum was experimentally recorded using Fourier Transform-Infrared (FT-IR). Gauge-independent atomic orbital (GIAO) 1H and 13C nuclear magnetic resonance (NMR) chemical shift values of the 1′,3′-Dihydrospiro[cyclohexane-1,2′-[2H]imidazo[4,5-b]pyridine] were calculated using DFT/B3LYP/6-311G + (d, p). The electronic properties such as HOMO-LUMO energies, absorption wavelengths, and excitation energy were investigated by time dependent DFT (TD-DFT) method with integral equation formalism-polarized continuum model (IEF-PCM). The mulliken charges on the atoms and second-order interaction energies were derived from NBO analysis. The electric dipole moment, the mean polarizability and the mean first hyperpolarizability values were also computed by using the DFT method. The effect of the molecule on pBR322 plasmid DNA was monitored by agarose gel electrophoresis experiments. The antimicrobial activities were tested by using minimal inhibitory concentration method (MIC).

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with −.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.

Density functional theory study of the regio‐ and stereoselectivity of 1,3-dipolar cycloaddition reactions between 2-ethylthio-4-phenyl-1-azetin and some substituted nitrile oxides

The mechanism (regio- and stereoselectivity) of 1,3-dipolar cycloaddition (1,3-DC) of 2-ethylthio-4-phenyl-1-azetin 1 with benzonitrile oxide 2a, 2-aminobenzonitrile oxide 2b and 2-azidobenzonitrile oxide 2c has been investigated by density functional theory-based reactivity indices and activation energy calculations at B3LYP/6-31G(d,p) level of theory in the gas and solvent phase. Thermodynamic and kinetic parameters of the possible ortho/meta regioisomeric and endo/exo stereoisomeric pathways have been determined. In order to rationalize complete endo selective fashion provided by these 1,3-DC cycloadditions, a natural steric analysis between NLMOs i,j for TS1ox and TS1on and also a second-order interaction energy, E 2, analysis between the donor–acceptor orbitals in these TSs were carried out. In all cases, the ortho pathways are more favorable compared to the meta alternatives and it is found that the endo pathway is preferred. Our results show that these cycloadditions follow an asynchronous one-step mechanism with a nonpolar character. Theoretical data are in good agreement with the experimental results.

Computational studies on structure and spectroscopic properties of 4-(Boc-amino) pyridine

The molecular modeling of 4-(Boc-amino) pyridine was carried out using B3LYP, CAMB3LYP and PBE1PBE levels of density functional theory (DFT). The vibrational frequencies of the title molecule in the ground state were computed by using B3LYP, CAMB3LYP and PBE1PBE methods with the 6-31G + (d, p) basis set. Gauge-independent atomic orbital (GIAO) 1H and 13C nuclear magnetic resonance (NMR) chemical shift values of the 4-(Boc-amino) pyridine were calculated by using the DFT/B3LYP with 6-31G + (d, p) basis set. The solvent effect on the NMR spectra of the molecule was also examined using the B3LYP method by applying the integral equation formalism-polarized continuum model (IEF-PCM). The electronic properties, such as HOMO-LUMO energies, absorption wavelengths and excitation energy, were investigated by time dependent DFT (TD-DFT) method with IEF-PCM. The mulliken charges on the atoms and second-order interaction energies were derived from NBO analysis. To investigate the nonlinear optical (NLO) properties of the title molecule, the electric dipole moment, the mean polarizability and the mean first hyperpolarizability were computed by using the DFT method with B3LYP, CAM-B3LYP and PBE1PBE levels.

Combined experimental–theoretical characterization of chelidamate nickel complex with 4-methylpyrimidine

A new chelidamate complex of nickel(II) ion, [Ni(chel)(H2O)2(mpd)]·2H2O [chel: chelidamate or 4-hydroxypyridine-2,6-dicarboxylate, mpd: 4-methylpyrimidine] was synthesized and characterized by single-crystal X-ray diffraction, UV–Vis and FT-IR spectroscopy. Intermolecular O–H⋯O and O–H⋯N hydrogen bonds and π–π stacking interactions appear to be effective in the stabilization of the crystal structure. Theoretical calculations have been carried out by using Hartree–Fock (HF)/6-31G (d) and Density Functional Theory (DFT)/6-31+G (d). Molecular geometry from X-ray experiment of Ni(II) complex in the ground state was compared using unrestricted hybrid density functional B3LYP. HOMO–LUMO energies, absorption wavelengths and excitation energy were computed by time dependent DFT (TD-DFT) method with polarizable continuum model. The observed FT-IR vibrational frequencies are analyzed and compared with theoretically predicted vibrational frequencies. The natural charges on the atoms and second-order interaction energies were derived from natural bond orbital analysis (NBO).

Theoretical investigation on electronic structures and stability of the dinuclear palladium and platinum complexes

The equilibrium geometries, metal–metal interaction, and metal–ligand interaction of dinuclear palladium(0) and platinum(0) complexes (M2(bq)2(nbe)2 and M2(bq)2(dafo), where M is Pt and Pd, dafo is 4,5-diazafluoren-9-one) were investigated using density functional theory. Natural bonding orbital (NBO) analysis indicates that there is no metal–metal σ-bond and the electrostatic interaction dominates the metal–metal interaction. The values of second-order interaction energies (E2) confirm the strong metal–ligand interactions and stabilization effect of the metal atoms. Thermochemistry suggests all of the four complexes to be stable species. The class of potential complexes is predicted stable enough for practical applications as highly efficient catalyst.

Theoretical estimates of the anapole magnetizabilities of C₄H₄X₂ cyclic molecules for X=O, S, Se, and Te.

Calculations have been carried out for C4H4X2 cyclic molecules, with X=O, S, Se, and Te, characterized by the presence of magnetic-field induced toroidal electron currents and associated orbital anapole moments. The orbital anapole induced by a static nonuniform magnetic field B, with uniform curl C=∇×B, is rationalized via a second-rank anapole magnetizability tensor a(αβ), defined as minus the second derivative of the second-order interaction energy with respect to the components C(α) and B(β). The average anapole magnetizability a̅ equals -χ̅, the pseudoscalar obtained by spatial averaging of the dipole-quadrupole magnetizability χ(α,βγ). It has different sign for D and L enantiomeric systems and can therefore be used for chiral discrimination. Therefore, in an isotropic chiral medium, a homogeneous magnetic field induces an electronic anapole A(α), having the same magnitude, but opposite sign, for two enantiomorphs.

The intramolecular cation–π interaction of some aryl amines and its drastic influence on the basicity of them: AIM and NBO analysis

In this study, drastic influence of the intramolecular cation–π interaction on the basicity of selected amines has been considered. The optimized minimum energy geometries of different studied amines and their protonated structures were determined by using DFT calculations at the B3LYP/6-311++G(d,p) level of theory. Geometry optimizations indicate that the most stable structures of protonated amines are stabilized by intramolecular cation–π interaction. The proton affinity (PA) of selected amines is controlled by the strength of intramolecular cation–π interaction of ammonium with aromatic ring. These cation–π interactions strongly influence the basicity of amines. Natural bond orbital (NBO) analysis was performed to calculate the second-order interaction energies (E(2)) between the donor and acceptor. Natural resonance theory (NRT) was used to calculate the natural bond order and predict bond polarity. Quantum theory of atoms in molecules (QTAIM) was also applied to determine the nature of cation–π interaction. QTAIM studies showed that the intramolecular cation–π interaction in these structures is electrostatic (closed-shell).

Theoretical study of substituent effects on Cs+/Sr2+–dibenzo-18-crown-6 complexes

The effect of electron-donating and -withdrawing substituents of Cs+/Sr2+–dibenzo-18-crown-6 complexes was studied by density functional theory (DFT) calculations. For the investigations the interaction energies were correlated to the second-order interaction energies, charge-transfer effects, and HOMO energies. Electron-donating substituents increase the crown ethers’ ability to complex metal ions, whereas electron-withdrawing substituents have the opposite effect. Natural bond orbital analysis indicates a small contribution of these substituents to the complex stability in the gas phase. In the condensed phase, the interaction energy of the complexes is significantly reduced because of solvation effects. The results demonstrate a discrepancy between gas and condensed phase in which Cs+ is bound to dibenzo-18-crown-6 better than Sr2+. We speculate that the species in water form 2:1 complexes consisting of two dibenzo-18-crown-6 molecules and one cation.

Structures and hydrogen bonds of biodegradable naphthenate ionic liquids

Biodegradable ionic liquids (bio-ILs) have attracted intensive attention due to toxicological and ecological reasons. It is critically important to understand the structural properties of bio-ILs at the molecular level. In this work, the interactions between four biodegradable naphthenate ionic liquids were investigated by density functional theory. The results indicate that multiple hydrogen bonds (H-bonds) are the major intermolecular structural feature between the cation and anion. These H-bonds were analyzed by natural bond orbital (NBO), quantum theory of atoms in molecules (AIM) and reduced density gradient (RDG) function. The influence of anionic structure on the interaction energy was studied. Based on the canonical orbital analysis, it is found that the σ-type orbital overlap and the partial charges transfer between the anion and cation, finally, result in the decrease of the energy and rationalize the location of the anion. Additionally, linear relationships between second-order interaction energies and the increment of electron density, as well as the interaction energies and the sum of the electron density at bond critical points for all studied [Ch][NA] ion pairs were found.