Scaled Quantum Mechanical Method Research Articles

Synthesis, structural analysis, and molecular docking of a novel 1,3,4-thiadiazole derivative: An experimental and molecular modeling studies

This study reports on the synthesis and characterization of a new thiadiazole derivative, (E)-N-(5-(2-nitrostyryl) -4-acetyl -4,5-dihydro -1,3,4-thiadiazol -2-yl) -N-phenylacetamide (ETDZ). The crystal structure was determined by single-crystal X-ray diffraction. ETDZ belongs to the monoclinic I2/a space group. The contribution of intermolecular interactions was assessed by Hirshfeld surface analysis and fingerprint plots. FT-IR, UV–Vis, and NMR (1H and 13C) techniques were used for spectroscopic characterization. The 1H and 13C NMR spectra were recorded in CDCl3 solvent. Density functional theory, employing the B3LYP functional and 6–311G(d,p) basis set in chloroform solvent, was used to calculate the structural and spectroscopic parameters of the molecule in the ground state. The vibrational wavenumbers were calculated and compared with the experimental FT-IR spectrum using the scaled quantum mechanics method. Isotropic chemical shifts were calculated using the Gauge invariant atomic orbital method. The calculated NMR chemical shifts and absorption wavelengths were compared with the experimental values, indicating good results from the DFT and TD-DFT methods. To get more information about charge transfer within the molecule, electronic properties such as HOMO and LUMO energies were studied using the DFT approach. The molecular electrostatic potential, frontier molecular orbital analysis, energy band gap, density of state, global chemical reactivity descriptors, and some thermodynamic functions were also calculated. Reduced density gradient and atom-in-molecule analysis were performed to investigate inter- and intra-non-covalent interactions. Molecular docking was carried out with the Eg5 kinesin protein, confirming the biological assets of the ETDZ ligand as a mitochondria disease and cancer agent.

Barrier Potential, Structure (Monomer and Dimer), Inter- and Intra-Molecular Interactions, Vibrational Analysis, Fukui Functions, MESP, NBO, UV and NMR Analysis of Pyridine-3-Carboxylic Acid Using Spectroscopic and DFT Approach

Pyridine-3-carboxylic (or nicotinic) (P3CA) acid has been recorded by using different spectroscopic tools like NMR (13C, 1H), UV–Vis, FT-IR and FT-Raman spectral analysis. The structural conformation examined by potential energy scan for the titled compound was obtained by using DFT computations through B3LYP method with 6–311++G(d,p) basis set. Using optimized monomer structure, the dimeric structures (head-to-tail and tail-to-tail) are obtained. The title compound exhibits inter-molecular as well as intra-molecular hydrogen bonding forming a supramolecular network. The geometrical parameters of both monomer and dimer are coinciding with the observed ones. Using vibrational frequencies, Infrared and Raman intensities were computed. The rms error between the experimental and scaled quantum mechanical frequencies is 9.77 cm−1 for P3CA. From the scaled quantum mechanical method, reliable vibrational assignments were made using PED. The site of chemical reactivity and selectivity of the title compound were estimated from frontier molecular orbitals and local reactivity descriptors. The reactive areas around the compound were evaluated by using MESP. The interactions of donor and acceptor are studied by NBO analysis. The 13C and 1H NMR chemical shifts of the title compound were determined using the gauge independent atomic orbital (GIAO) method in DMSO-d6 solution. By using UV–visible spectrum, the maximum absorption wavelength was obtained and compared with the TD-DFT method.

Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory.

Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460-470nm, ctenophore photoproteins absorb at 437nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein-substrate complex was optimized using a linear scaling quantum-mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60°of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified.

Theoretical investigations on the molecular structure, vibrational spectra, thermodynamics, HOMO–LUMO, NBO analyses and paramagnetic susceptibility properties of p-(p-hydroxyphenoxy)benzoic acid

The experimental FT-IR (4000–400cm−1) and FT-Raman (3500–100cm−1) spectra of p-(p-hydroxyphenoxy) benzoic acid have been recorded. Quantum chemical calculations of energies, geometries, and vibrational wavenumbers of p-(p-hydroxyphenoxy) benzoic acid (PPHPBA) are carried out using HF and DFT/B3LYP methods with 6-311G (d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show a good agreement with experimental data. The difference between the observed and scaled wave number values of most of the fundamentals is very small. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated with scaled quantum mechanical method. The calculated HOMO and LUMO energies allow the calculation of atomic and molecular properties and they also show that charge transfer occurs in the molecule. A detailed molecular picture of PPHPBA and its intermolecular interactions were obtained from NBO analysis. The temperature dependence of various thermodynamic parameters was also studied. The paramagnetic behavior of the molecule under consideration has been investigated and the variation of paramagnetic susceptibility with temperature has been studied.

Electrostatic polarization is critical for the strong binding in streptavidin‐biotin system

The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the traditional AMBER charge, and the other two, termed the polarized protein-specific charge, are based on a linear scaling quantum mechanical method and a continuous solvation model and have polarization effect partially or fully included. The result indicates that when nonpolarized AMBER force field is applied, the result is much underestimated. When electronic polarization is gradually included, the difference of binding affinity increases along with it. Using the linear-response approximation to eliminate the error in self-charging process, the corrected binding affinity agrees well with the experimental observation. This study is direct evidence indicating that polarization effect is critical for the strong binding in streptavidin-biotin system.

Vibrational spectroscopic study of 2, 6- and 2, 7-dimethylnaphthalenes by Density functional theory.

Fourier transform infrared and Fourier transform Raman spectra of 2, 6- and 2, 7-dimethylnaphthalenes in solid phase, have been investigated. The theoretical calculations of the vibrations of 2, 6- and 2, 7- dimethylnaphthalenes were performed by using density functional theory (DFT)-Beck3–Lee–Yang–Parr (B3LYP) levels with 6-31G* and 6- 311+G** basis sets. The complete assignments are performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanics method (SQM) by using MOLVIB program. The computational frequencies are in good agreement with the observed results. The comparisons between the observed and calculated frequencies are shown

Quantum chemical studies of FT-IR and Raman spectra of methyl 2,5-dichlorobenzoate

In this paper, experimental and theoretical studies on the molecular structure and vibrational spectra of methyl 2,5-dichlorobenzoate (MDCB) are presented. Fourier transform infrared and Raman spectra of the title molecule in the solid phase were recorded and analyzed. The geometrical parameters were calculated using DFT (B3LYP) with 6-311G(d,p) and 6-311++G(d,p) basis sets, and compared with the experimental data. The vibrational frequencies, infrared intensities and Raman scattering activities were also reported. The detailed assignments were given based on the total energy distribution of the vibrational modes, calculated with scaled quantum mechanics method. The observed and calculated frequencies are found to be in good agreement.

Structure of Graphene, and Mechanical and Bonding Characteristics of Single Wall Carbon Nanotube by Linear Scaling Quantum Mechanical Method

Using a linear scaling self-consistent-charge density functional tight binding (SCC-DFTB) and an ab initio Dmol method, the bonding characteristics and Young's modulus of (10, 0) and (10,10) single-walled carbon nanotubes are calculated. The structure of a graphene is also calculated. It is found that the C-C and C-H bond length, their distribution characteristics on the tube, and Young's modulus of the tube by linear scaling SCC-DFTB are identical to those by ab initio, while the computing cost by the linear scaling SCC-DFTB is reduced by more than 30 times as compared with that by the Dmol for the (10,0) and (10,10) tubes By computing the structure of a graphene it is also found that the linear scaling SCCDFTB is reliable and time-saving.

QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN–LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX

HIV-1 protease (PR) is a primary target for anti-HIV therapeutics. A well conserved water molecule, denoted as W301, is found in almost all the crystallographic structures of PR/inhibitor complexes and it plays an important role in PR/inhibitor binding. As the PR/inhibitor interaction depends on the ionization state of the cleavage site which contains an aspartyl dyad (Asp25/Asp25′), the determination of the protonation states of aspartyl dyad in PR may be essential for drug design. In this study, a linear scaling quantum mechanical method, molecular fragmentation with conjugate caps (MFCC), is used for interaction study of PR/ABT-538 and W301 at four different monoprotonation states of the Asp25/Asp25′. Combined method of MFCC and conductor-like polarizable continuum model (CPCM) is applied in binding affinity calculation for four minimum energy structures which are extracted from four different molecular dynamics trajectories corresponding to four different monoprotonation states of Asp25/Asp25′. Our result is in good agreement with previous result obtained by FEP/TI method, showing that the conserved W301 contributes significantly to the binding free energy of PR/ABT-538 complex and different protonation states of Asp25/Asp25′ have significant impact on the binding free energy contribution from W301.

Effect of ending surface on energy and Young's modulus of single-walled carbon nanotubes studied using linear scaling quantum mechanical method

Abstract By using a linear scaling self-consistent charge, density functional tight-binding (SCC-DFTB) method and an ab intio Dmol3 calculation, the energy and Young's modulus as a function of tube length for (10, 0) single-walled carbon nanotubes (SWCNTs) are investigated. It was found that with increasing the length of SWCNTs the Young's modulus increases rapidly, then, there is a slow increase, which ultimately approaches a constant value after the length is increased to ~20 nm, whereas a reversed variation tendency was found for the average energy of atoms in SWCNTs with a change of the tube length. We found that the characters of the length-dependent energy and Young's modulus stem from the changed Py-DOS of atoms in the ending region of the tube. Here one simple formula is proposed for quantitatively explaining the length-dependent energy and modulus.

Vibrational Analysis of α-d-Glucose Trapped in Ar Matrix

The FT-IR spectra of alpha-D-glucose have been investigated by means of matrix-isolation FT-IR spectroscopy in the 3700-200 cm-1 range and by B3LYP/6-311++G** density functional calculations. The joint analysis of the experimental and computed IR spectra supported the expected predominance of the most stable gg and gt conformers in the vapor phase and the minor contribution of the less stable tg conformer. Weak absorption bands at the edge of the OH stretching region are in agreement with small amounts of analogous conformers with clockwise arrangement of the hydrogen bonds (c-gg, c-gt, c-tg). The assignment of the IR spectra was carried out on the basis of the computed harmonic force field using the scaled quantum mechanical method of Pulay. Scale factors developed previously for the B3LYP/6-311++G** level proved to be well transferable except that for the OH torsion. The latter scale factor was adjusted on the basis of the present experimental data. On the basis of the calculated results, 99 bands have been assigned to the gg, gt, and tg conformers of alpha-D-glucose with average deviations of 5.0, 5.9, and 6.1 cm-1, respectively.

Vibrational spectra and conformational isomerism of calixarene building blocks. III. 2,6-Dimethylanisole and n-propyl-2,6-dimethylphenyl ether

The conformations and vibrational spectra of the 2,6-dimethylanisole and n-propyl-2,6-dimethylphenyl ether molecules have been analysed within the framework of density functional theory. The calculated force field (B3LYP/6-31G∗) has been transformed to internal coordinates, and the set of 10 different scaling factors has been applied. The scaled quantum mechanical method reproduces the experimental range of the IR and Raman spectra with high accuracy. According to the computations, the conformational behaviour of the alkyl aryl ethers studied is similar to the related dialkyl ether molecules, i.e. the CO–CC bond prefers the anti conformation, while the OC–CC bond prefers the gauche conformation. The major part of the vibrational spectra of the title compounds can be approximated by the sum of the vibrational modes of their constituent groups, these modes being transferable among the related molecules.

Tautomerism, hydrogen bonding and vibrational properties of 4-acetyl-3(5)-amino-5(3)-methylpyrazole

The structure and molecular vibrations of 4-acetyl-3(5)-amino-5(3)-methylpyrazole have been investigated by quantum chemical calculations and vibrational spectroscopy. The calculations predicted a predominance of the 5-amino-3-methyl form in the tautomeric equilibrium, however, the energy difference between the two tautomers is rather small, 2 kJ/mol at the B3-LYP/6-311++G** level of the theory. The most stable conformers of each tautomer are stabilized by intramolecular hydrogen bonding. This interaction plays an important role also in the tautomeric equilibrium contributing significantly to the stability of the 5-amino-3-methyl tautomer. Another characteristics of the hydrogen bonding is its strengthening effect on the conjugation of the NH 2 and CO groups with the pyrazole ring. The molecular vibrations of the title compound have been analysed by means of the scaled quantum mechanical method. Using joint theoretical and experimental information the FT-IR and FT-Raman spectra of solid 4-acetyl-3-amino-5-methylpyrazole have been assigned.

Vibrational and conformational analysis of a model compound of pernigraniline N,N′ diphenyl-1,4-benzoquinonediimine

Calculations based on scaled quantum mechanical method (B3LYP/6-31G*) were performed on a prototype unit of pernigraniline (PB), N, N′ diphenyl-1,4-benzoquinonediimine (B2Q1). Models with trans (E) and cis (Z), both in planar and non-planar configurations were used. The calculated infrared and Raman spectra were compared with experiments. The results, especially in the 200–600 cm−1 frequency range show that B2Q1 has a trans configuration with significant non planarity.

Investigation of the density-functional theory-derived scaled quantum mechanical method for cage-like systems: the vibrational analysis of adamantane

The Becke3—Lee—Yang—Parr(B3-LYP)/6-31G* derived scaled quantum mechanical (SQM) method has been investigated for cage-like systems using adamantane as the model molecule. The original scale factors were found to transfer well to adamantane except the general heavy atom scale factor for the CC stretching modes of the skeleton. For these vibrations a new individual scale factor was developed in the present study. A complete vibrational analysis of adamantane and adamantane-d 16 has been performed. The experimental vibrational spectra of the compounds were reinterpreted using the scaled B3-LYP/6-31G* harmonic force field. Some assignments of earlier less sophisticated investigations have been revised, and reliable predictions for the IR and Raman inactive fundamentals are proposed.

Investigation of the density-functional theory-derived scaled quantum mechanical method for cage-like systems: the vibrational analysis of adamantane

The Becke3—Lee—Yang—Parr(B3-LYP)/6-31G* derived scaled quantum mechanical (SQM) method has been investigated for cage-like systems using adamantane as the model molecule. The original scale factors were found to transfer well to adamantane except the general heavy atom scale factor for the CC stretching modes of the skeleton. For these vibrations a new individual scale factor was developed in the present study. A complete vibrational analysis of adamantane and adamantane-d 16 has been performed. The experimental vibrational spectra of the compounds were reinterpreted using the scaled B3-LYP/6-31G* harmonic force field. Some assignments of earlier less sophisticated investigations have been revised, and reliable predictions for the IR and Raman inactive fundamentals are proposed.

Molecular Structure and Molecular Vibrations of 1,3,5,7,-Tetramethyl-2,4,6,8,9,10- Hexathiaadamantane

The molecular structure and vibrations of 1,3,5,7,-tetramethyl-2,4,6,8,9,10-hexathiaadamantane have been determined by a joint computational, gas-phase electron diffraction, and spectroscopic investigation. The geometry and harmonic force field of the molecule was calculated at the Becke3-Lee-Yang-Parr/6-31G* level. Vibrational analysis was performed using FT-IR and FT-Raman spectra recorded in the 4000−150 cm-1 range and utilizing Pulay's DFT-based scaled quantum mechanical (SQM) method (DFT: density-functional theory). This SQM method was extended to molecules containing C−S structural motifs. The joint computational and electron diffraction analysis resulted in an equilibrium geometry of Td symmetry characterized by staggered orientation of the methyl groups with respect to their adjacent C−S bonds. The electron diffraction study yielded the following bond lengths (rg) and bond angles (with estimated total errors): C−S, 1.820 ± 0.004 Å; C−C, 1.536 ± 0.004 Å; C−H, 1.119 ± 0.005 Å; C−S−C, 102.2 ± 0.2°; H−C−H, 109.9 ± 0.7°. The barrier to methyl rotation was computed to be 17 kJ/mol in good agreement with that estimated from the average methyl torsion (with respect to the staggered form) of 10 ± 3° from the electron diffraction analysis.

Gas-phase infrared spectrum of indazole. Scaled quantum mechanical force field and complete spectrum assignment

The gas-phase IR spectrum of indazole has been recorded from 100 to 4000 cm–1, using a multipass cell heated to 120 °C, and completely assigned using theoretical predictions based on the scaled quantum mechanical (SQM) method. The single-crystal IR spectrum of this molecule, previously reported, has been compared with our data and partially reassigned. The harmonic force field of indazole, evaluated at the HF-SCF level using 6-31G** orbitals, is corrected by scaling the force field over a convenient set of internal coordinates. Scaling factors were determined by least-squares fitting of the theoretical to the experimental frequencies of two parent molecules, benzene and pyrazole and their perdeuteriated isotopomers. Our final prediction gives frequencies for indazole which, on average, differ from experiment by 24 cm–1. We confirm the validity of the SQM method as a practical tool for a complete analysis of vibrational spectra, even for molecules of this complexity.

A simple predictive model for planar vibrations of polycyclic benzenoid hydrocarbons

A very simple force field model is designed to be applied as a predictive means to all kinds of planar benzenoid hydrocarbons to the infinite size without any modifications and extra knowledge except for topological connections of hexagonal rings. The model involves only eight potential parameters including CC, CH, CCC, and CCH stretchings, CC–CCC and CC–CCH bendings, and two constants for conjugation effects which are essential for the description of strongly correlated collective motions of CC bonds. The CC–CC interaction constants in the standard set of parameters were found to be in good agreement with those for benzene experimentally determined by Ozkabak and Goodman and those obtained from scaled quantum mechanical (SQM) calculations by Pulay et al. The standard set of force constants in the present model were shown to be almost completely transferable for the known planar vibrations of typical benzenoids. It is of note that in comparison with the SQM method the present model gives a small difference of ∼16 cm−1 in average for the calculated planar frequencies of benzene and naphthalene. Further applications to large benzenoids including perylene, benzo(g,h,i)perylene, coronene, ovalene, and tribenzo-(a,g,m)coronene demonstrated that the present model predicts not only planar frequencies in an accuracy of ∼20 cm−1 but also vibronic band intensities in good agreement with experiment.

Comment Comparison of ab initio and scaled quantum mechanical methods for the calculation of vibrational structure: A reply to bose and polavarapu

Recent criticisms by Bose and Polavarapu of the scaled quantum mechanical (SQM) force field method for the calculation of vibrational structure are discussed. The SQM method can give quantitatively accurate frequencies, force constant matrix elements, and potential energy distributions of molecules, while the corresponding ab initio calculation using the same basis set can fail to give even qualitative agreement with experiment. The SQM method can be employed for molecules whose vibrational assignment is uncertain by transferrring SQM scale factors from related molecules. For molecules without symmetry whose vibrational assignment is certain, the SQM method is equivalent to an ab initio calculation in which all calculated frequencies are scaled using a single multiplicative factor.