Localized Molecular Orbital Analysis Research Articles

Experimental and theoretical study of ornidazole

The Fourier transform infrared (FT-IR) and the Fourier transform Raman (FT-Raman) spectra of the title molecule in solid phase were recorded in the region 4000–400cm−1 and 4000–100cm−1 respectively. The geometrical parameters and energies were investigated with the help of Density Functional Theory (DFT) employing B3LYP method and 6-31G (d, p) basis set. The analysis was supported by electrostatic potential maps and calculation of HOMO–LUMO. UV, FT-IR and FT-Raman spectra of ornidazole were calculated and compared with experimental results. Thermodynamic properties like entropy, heat capacity, have been calculated for the molecule. The predicted first hyperpolarizability also shows that the molecule might have a reasonably good non-linear optical (NLO) behavior. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis.

Complexes of nitric oxide with water and imidazole

NO–Imi–H2O complexes can be used as models to investigate the interactions of histidine with nitric oxide and water in biological systems like myoglobin. We discuss here the water–imidazole, water–nitric oxide dimers and the trimolecular complexes of nitric oxide with water and imidazole from the donor–acceptor point of view using the natural bond orbitals and localized molecular orbital energy decomposition analysis schemes. The comparison between trimolecular and bimolecular complexes shows that in general, the stabilization energies are more sensitive to changes in the interactions of imidazole with water than to changes in the interactions with nitric oxide. The effect of imidazole ring protonation on the geometry and stabilization of the complexes is also investigated. We found that cooperative effects are more relevant in charged complexes and planar structures than in neutral species and nonplanar complexes. The driving forces governing the interactions between open and closed shell systems are also discussed with special emphasis on the role of lone pairs and unpaired electrons.

Tuning anion-π interaction via halogen substituent effects in cyanuric acids and its derivatives

Several anion-π complexes of isocyanuric acid, thioderivatives and their halogen substituted derivatives with chloride anion have been studied. The geometric and energetic features, charges transfer from chloride anion to the aromatic rings and “atoms-in-molecules” analysis are performed and discussed for these complexes. The results show that the strength of the anion-π interaction between cyanuric derivatives and chloride anion can be tuned by halogen-substituting. The localized molecular orbital energy decomposition analyses shows that, in the total interaction, exchange and electrostatic energies are the dominant stabilizing forces, and the polarization energies also make a favorable contribution. Finally, solvent effect significantly weakens the anion-π interaction between the isocyanuric derivatives and chloride anion, especially in polar solvents. © 2015 Wiley Periodicals, Inc.

Experimental and theoretical studies of (FT-IR, FT-Raman, UV–Visible and DFT) 4-(6-methoxynaphthalen-2-yl) butan-2-one

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000–50cm−1 and 4000–450cm−1 respectively for 4-(6-methoxynaphthalen-2-yl) butan-2-one (abbreviated as 4MNBO) molecule. Theoretical calculations were performed by density functional theory (DFT/B3LYP) method using 6–311G(d,p) and 6–311++G(d,p) basis sets. The difference between the observed and calculated wavenumber value of most of the fundamentals were very small. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The UV–Vis spectrum was recorded in the methanol solution. The energy, wavelength and oscillator’s strength were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Thermodynamic properties of 4MNBO at different temperature have been calculated. The molecular electrostatic potential surface (MESP) and Frontier molecular orbital’s (FMO’s) analysis were investigated using theoretical calculations.

A comparative study of the chalcogen bond, halogen bond and hydrogen bond S⋯O/Cl/H formed between SHX and HOCl.

Ab initio quantum chemistry methods were used to analyze the noncovalent interactions between HOCl and SHX (X = F, CN, NC, Cl, Br, NO2, CCH, CH3, H). Three energetic minimal configurations were characterized for each case, where the S center acts as a Lewis acid interacting with O to form a chalcogen bond, as well as a Lewis base interacting with Cl or H of HOCl to form halogen bond and hydrogen bond, respectively. An electronegative substituent such as F, CN, NC and NO2 tends to form a stronger chalcogen bond, while an electropositive substituent such as CCH, CH3 and H is inclined to form a more stable H-bonded complex. The chalcogen-bonded, halogen-bonded and H-bonded complexes are stabilized by charge transfers from Lp(O) to σ*(SX), from Lp(S) to σ*(ClO), and from Lp(S) to σ*(HO), respectively. As a result, the SHX unit becomes positively charged in halogen-bonded and hydrogen-bonded complexes but negatively charged in chalcogen-bonded complexes. Theory of atoms in molecules, natural bond orbital analysis, molecular electrostatic potential and localized molecular orbital energy decomposition analysis were applied to investigate these noncovalent bonds.

Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes--SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

Investigation of the resonance-assisted hydrogen bond in model β-diketones through localized molecular orbital analysis of the spin-spin coupling constants related to the O-H···O hydrogen bond.

The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons.

Experimental, quantum chemical and NBO/NLMO investigations of pantoprazole

The complete vibrational assignment and analysis of the fundamental modes of pantoprazole (PPZ) was carried out using the experimental FT-IR, FT-Raman and UV–Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT–B3LYP gradient calculations employing 6-31G (d, p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. HOMO–LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as electric dipole moment and first hyperpolarizability of PPZ have been computed using B3LYP quantum chemical calculation. Finally, the Mulliken population analysis on atomic charges of the title compound has been calculated.

Molecular conformational stability and Spectroscopic analysis of Parared with experimental techniques and quantum chemical calculations

The complete vibrational assignment and analysis of the fundamental modes of Parared was carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically from the optimized geometry of the compound from the DFT–B3LYP gradient calculations employing 6-31G(d,p) and 6-311++G(d,p) basis sets. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. HOMO–LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as electric dipole moment and first hyperpolarizability of Parared have been computed using B3LYP quantum chemical calculations. Finally, the Mulliken population analysis on atomic charges of the title compound has been calculated.

Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV–Vis spectroscopies combined with DFT calculations

The complete vibrational assignment and analysis of the fundamental vibrational modes of Trifluoperazine (TFZ) was carried out using the experimental FT-IR, FT-Raman and UV–Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-31G (d,p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. The HOMO–LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as first hyperpolarizability of TFZ have been computed using B3LYP quantum chemical calculation.

An investigation of chlorine ligands in transition-metal complexes via ³⁵Cl solid-state NMR and density functional theory calculations.

Chlorine ligands in a variety of diamagnetic transition-metal (TM) complexes in common structural motifs were studied using (35)Cl solid-state NMR (SSNMR), and insight into the origin of the observed (35)Cl NMR parameters was gained through first-principles density functional theory (DFT) calculations. The WURST-CPMG pulse sequence and the variable-offset cumulative spectrum (VOCS) methods were used to acquire static (35)Cl SSNMR powder patterns at both standard (9.4 T) and ultrahigh (21.1 T) magnetic field strengths, with the latter affording higher signal-to-noise ratios (S/N) and reduced experimental times (i.e., <1 h). Analytical simulations were performed to extract the (35)Cl electric field gradient (EFG) tensor and chemical shift (CS) tensor parameters. It was found that the chlorine ligands in various bonding environments (i.e., bridging, terminal-axial, and terminal-equatorial) have drastically different (35)Cl EFG tensor parameters, suggesting that (35)Cl SSNMR is ideal for characterizing chlorine ligands in TM complexes. A detailed localized molecular orbital (LMO) analysis was completed for NbCl5. It was found that the contributions of individual molecular orbitals must be considered to fully explain the observed EFG parameters, thereby negating simple arguments based on comparison of bond lengths and angles. Finally, we discuss the application of (35)Cl SSNMR for the structural characterization of WCl6 that has been grafted onto a silica support material. The resulting tungsten-chloride surface species is shown to be structurally distinct from the parent compound.

Normal coordinate analysis, molecular structure, vibrational, electronic spectra and NMR investigation of 4-Amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione by ab initio HF and DFT method

In the present work, the characterization of 4-Amino-3-phenyl-1H-1,2,4-triazole-5(4H)-thione (APTT) molecule was carried out by quantum chemical method and vibrational spectral techniques. The FT-IR (4000–400cm−1) and FT-Raman (4000–100cm−1) spectra of APTT were recorded in solid phase. The UV–Vis absorption spectrum of the APTT was recorded in the range of 200–400nm. The molecular geometry, harmonic vibrational frequencies and bonding features of APTT in the ground state have been calculated by HF and DFT methods using 6-311++G(d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO) and natural localized molecular orbital (NLMO) analysis. The electronic properties, such as excitation energies, absorption wavelength, HOMO and LUMO energies were performed by time depended DFT (TD-DFT) approach. The 1H and 13C nuclear magnetic resonance chemical shift of the molecule were calculated using the gauge-including atomic orbital (GIAO) method and compared with experimental results. Finally, the calculation results were analyzed to simulate infrared, FT-Raman and UV spectra of the title compound which shows better agreement with observed spectra.

A computational study of pnicogen−hydride interaction in complexes XH2P⋯HBeY

The pnicogen−hydride interaction in the complexes XH2P⋯HBeY (X=F, Cl and Br; Y=H, F, Cl, Br, and CH3) has been studied and characterized using ab initio quantum chemistry methods. P in XH2P and H in HBeY act as Lewis acid and base respectively. Calculation indicates that the interaction between XH2P and HBeY is strong, comparable with typical hydrogen bonds; the calculated binding energies with BSSE correction by MP4(SDQ)/aug-cc-PVTZ vary from the least 13.29kJ/mol of BrH2P⋅⋅⋅HBeF to the largest 45.63kJ/mol of FH2P⋅⋅⋅ HBeH. The binding energy increases with the acidity of P and the basicity of HBeY. An electron-withdrawing substituent X will enhance but an electron-withdrawing substituent Y will weaken the pnicogen−hydride interaction. Theory of atoms in molecules, natural bond orbitals and natural resonance theory, molecular electrostatic potential and localized molecular orbital energy decomposition analysis were applied to investigate the pnicogen–hydride bonds. A double-way charge transfers and intermolecular hyperconjugations from Lp(P) to σ∗(HBe) and from σ(HBe) to σ∗(XP) mainly contribute to the stability and bonding of the complexes.

Direct investigation of halogen bonds by solid-state multinuclear magnetic resonance spectroscopy and molecular orbital analysis.

Noncovalent interactions play a ubiquitous role in the structure, stability, and reactivity of a wide range of molecular and ionic cocrystals, pharmaceuticals, materials, and biomolecules. The halogen bond continues to be the focus of much attention, due in part to its strength and unique directionality. Here, we report a multifaceted experimental and computational study of halogen bonds in the solid state. A series of cocrystals of three different diiodobenzene molecules and various onium halide (Cl(-) or Br(-)) salts, designed to exhibit moderately strong halogen bonds (C-I···X(-)) in the absence of competing hydrogen bonds, has been prepared and characterized by single-crystal X-ray diffraction. Interestingly, a wide range of geometries about the halide anion are observed. (35/37)Cl and (79/81)Br solid-state NMR spectroscopy is applied to characterize the nuclear quadrupolar coupling constants (C(Q)) and asymmetry parameters (η(Q)) for the halogen-bonded anions at the center of bonding environments ranging from approximately linear to distorted square planar to octahedral. The relationship between the halogen bond environment and the quadrupolar parameters is elucidated through a natural localized molecular orbital (NLMO) analysis in the framework of density functional theory (DFT). These calculations reveal that the lone pair type orbitals on the halogen-bonded anion govern the magnitude and orientation of the quadrupolar tensor as the geometry about the anion is systematically altered. In -C-I···X(-)···I-C- environments, the value of η(Q) is well-correlated to the I···X(-)···I angle. (13)C NMR and DFT calculations show a correlation between chemical shifts and halogen bond strength (through the C-I distance) in o-diiodotetrafluorobenzene cocrystals. Overall, this work provides a chemically intuitive understanding of the connection between the geometry and electronic structure of halogen bonds and various NMR parameters with the aid of NLMO analysis.

Exploiting Weak Noncovalent Cation···π Interaction for Designing a Molecular Container for Storage of Methane Molecules with Lithiated Carbene Superbases

This study reports the multiprotonation sites exploiting noncovalent interactions to achieve hyperbasicity of an uncharged organic base. A new class of carbene based organic superbase has been designed to attain the proton affinity (PA) value of 301.9 kcal/mol at M06-2X/6-311+G**//B3LYP/6-31+G* level of theory. These designed scaffold molecules can possess three independent protonation sites, which is not available in the literature to date. The stabilization of the protonated forms of the superbases by noncovalent interactions such as C–H+···π interaction is responsible for augmenting the basicity of such carbene systems. The DFT calculated results show that such carbene systems can be suitable candidate for tris-protonation with pKa(MeCN) value of 43.3 and proton affinity value (MeCN) of 312.1 kcal/mol. Molecular electrostatic potential (MESP) analysis shows the existence of electron density at the reactive sites and the role of substituents to enhance the electron density in such designed systems. There is a good correlation with the absolute minima of the MESP (Vmin) located for such carbene systems with their calculated proton affinity values. The frontier molecular orbital energy of such carbenes also shows a good relationship with their proton affinity results. These carbene systems can be utilized further for selective binding of lithium ions over sodium ions. Such lithiated organic superbases can be used as a molecular container for the storage of hydrogen and methane molecules. The energy decomposition analysis (EDA) has been performed to explain the role of various factors which contribute to the total binding strength of the hydrogen or methane molecules with lithiated carbene superbases. The localized molecular orbital energy decomposition analysis reveals that the electrostatic and polarization effects are the major contributing factors in interactions with methane and hydrogen molecules. This is the first report where the organic superbase has been exploited as efficient methane storage materials.

Theoretical Study on the Ligand Exchange Reactions of Hypervalent Antimony and Tellurium Compounds

The ligand exchange reactions (LERs) of hypervalent compounds of antimony (R5Sb: R = Me, Ph) and tellurium (R4Te: R = Me, Ph) were analyzed via dispersion corrected density functional theory (DFT) and coupled cluster calculations. The dispersion force plays a key role in forming reactant/product complexes. For the phenyl ligand compounds, the pathway of the LER was predicted as being stepwise, while that for the methyl ligand compounds was predicted to be concerted. From the natural localized molecular orbital analysis for the reaction of Me4Te, it was found that the lone pair electrons of tellurium do not participate in LER. The LER of antimony compounds was elucidated to proceed along the mechanism similar to that of Me4Te. LER of a mixture of Me4Te and Me5Sb was shown to proceed more easily than that of each component.

On the Nature of Interactions of Radicals with Polar Molecules

Solvated radicals play an important role in many areas of chemistry, but to date, the nature of their interactions with polar solvent molecules lacks chemical interpretation. We present a computational quantum chemical analysis of the binding motives of binary complexes involving electron-poor and electron-rich radicals bound to water and hydrogen fluoride, considered here as model polar solvent molecules. By comparing the binding strengths of several open-shell and closed-shell complexes, in combination with natural localized molecular orbital analysis, we show that open-shell complexes can exhibit additional donor-acceptor interactions relative to analogous closed-shell systems. This may explain the unexpectedly large binding energies observed in some open-shell complexes. These exploratory results show that specific interactions in open-shell systems deserve more attention, and they imply that the quantum mechanical description of explicit solvent molecules needs to be considered carefully when designing simulation protocols for solvated radicals.

Experimental and theoretical study of p-nitroacetanilide

The spectroscopic properties of the p-nitroacetanilide (PNA) were examined by FT-IR, FT-Raman and UV–Vis techniques. FT-IR and FT-Raman spectra in solid state were observed in the region 4000–400cm−1 and 3500–100cm−1, respectively. The UV–Vis absorption spectrum of the compound that dissolved in ethanol was recorded in the range of 200–400nm. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional theory (DFT) employing B3LYP methods with the 6-31G(d,p) and 6-311+G(d,p) basis sets. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. HOMO–LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear optical (NLO) properties such as electric dipole moment and first hyperpolarizability have been computed using B3LYP quantum chemical calculation.

Molecular structure analysis and spectroscopic characterization of carbimazole with experimental (FT-IR, FT-Raman and UV–Vis) techniques and quantum chemical calculations

The complete vibrational assignment and analysis of the fundamental modes of carbimazole (CBZ) was carried out using the experimental FTIR, FT-Raman and UV–Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT–B3LYP gradient calculations employing 6-31G(d,p) and 6-311++G(d,p) basis sets. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. HOMO–LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as electric dipole moment and first hyperpolarizability of CBZ have been computed using B3LYP quantum chemical calculation. Finally, the Mulliken population analysis on atomic charges of the title compound has been calculated.

Theory of Divalent Main Group H2 Activation: Electronics and Quasiclassical Trajectories

Density functional theory (DFT), absolutely localized molecular orbital (ALMO) analysis, and quasiclassical trajectories (QCTs) were used to study the structure, barrier heights, thermodynamics, electronic properties, and dynamics of dihydrogen (H2) activation by singlet divalent main group compounds (ER2; E = C, Si, Ge). ALMO energy and charge decomposition calculations reveal that in the transition state CR2 acts as an ambiphile toward H2 because of equal forward-bonding and back-bonding orbital stabilization while SiR2 and GeR2 act as nucleophiles with dominant orbital energy stabilization arising from ER2 to H2 donation. Frontier molecular orbital (FMO) energy gaps do not provide a reasonable estimate of energy stabilization gained between the ER2 and H2 in the transition state or an accurate description of the nucleophilic versus electrophilic character because of electron repulsion and orbital overlap influences that are neglected. In CR2 transition states, forward-bonding and back-bonding are maximized in the nonleast motion geometry. In contrast, SiR2/GeR2 transition states have side-on geometries to avoid electron-electron repulsion. Electron repulsion, rather than orbital interactions, also determines the relative barrier heights of CR2 versus SiR2/GeR2 reactions. Examination of barrier heights and reaction energies shows a clear kinetic-thermodynamic relationship for ER2 activation of H2. A computational survey of R groups on ER2 divalent atom centers was performed to explore the possibility for H2 activation to occur with a low barrier and thermodynamically reversible. QCTs show that dihydrogen approach and reaction with CR2 may involve geometries significantly different than the static transition-state structure. In contrast, trajectories for dihydrogen addition to SiR2 involve geometries close to the side-on approach suggested by the static transition-state structure. QCTs also demonstrate that addition of H2 to CR2 and SiR2 is dynamically concerted with the average time gap of bond formation between E-H bonds of approximately 11 and 21 fs, respectively.