FTIR and FT-Raman spectra, molecular geometry, vibrational assignments, first-order hyperpolarizability, ab initio and DFT calculations for 3,4-dimethoxybenzonitrile

Quantum chemical calculations of energies, geometrical structure and vibrational wave numbers of 3,4-dimethoxybenzonitrile (DMBN) were carried out by the ab initio Hartree-Fock (HF) and density functional theory (DFT) with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. Making use of the recorded data, the complete vibrational assignments are made and analysis of the observed fundamental bands of molecule is carried out. The geometries and normal modes of vibrations obtained from ab initio HF and B3LYP calculations are in good agreement with the experimentally observed data. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. The theoretical FTIR and FT-Raman spectra for the title molecule have been constructed.     

Investigation of conformational stability and vibrational spectra of halomethylsulfonyl isocyanates

The conformational behavior and structural stability of chloro- and fluoromethylsulfonyl isocyanates were investigated by quantum mechanical DFT and ab initio MP2 calculations. The 6-311++G^** basis set was employed to include polarization and diffuse functions in the calculations. The molecules were found to exist in a mixture of two stable gauche conformations. The potential scans were calculated from which the rotational barriers could be estimated. The vibrational frequencies and spectra were computed at B3LYP/6-311++G^** level. The potential energy distributions were then calculated to provide tentative vibrational assignment for the normal modes of the stable conformers of both molecules.     

Theoretical studies on the conformations and properties of phenylazonaphthalenes

The conformations of phenylazo‐2‐naphthalene (I) and phenylazo‐1‐naphthalene (II) have been studied using ab initio methods and density functional theory. The rotational potential energy surfaces about the C N bonds were calculated for both the trans and the cis forms at the PM3 and HF/STO‐3G levels. The PM3 method was found to be incapable for locating the energy minima correctly. The geometries of rotamers obtained from the HF/STO‐3G surface were fully optimized at the HF/6‐31G* and B3LYP/6‐31G* levels. Single‐point MP2/6‐31G* calculations have also been carried out at the HF/6‐31G* geometries. The vibrational spectra, standard thermodynamic functions, heats of formation, and equilibrium molar fractions have been obtained. According to the calculated results, I is comparatively more stable than II. The trans forms have much lower energies than the cis forms, implying that I and II mainly exist in the trans planar forms. The energy gap (ΔE) between the frontier molecular orbitals (MOs) of the cis forms are about 0.7 eV higher than those of the trans ones, indicating that change in geometry from trans to cis form will cause a hypsochromic effect. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 25–33, 2000     

Simplified ab initio calculations on small molecules with an extended balanced approximate MO formalism

Based on a test of different known simplified ab initio methods an approximate LCAO MO formalism is proposed which gives reasonable results in a minimal STO basis in comparison with ab initio calculations.     

Kernel energy method illustrated with peptides

We describe a kernel energy method (KEM) for applying quantum crystallography to large molecules, with an emphasis on the calculation of the molecular energy of peptides. The computational difficulty of representing the system increases only modestly with the number of atoms. The calculations are carried out on modern parallel supercomputers. By adopting the approximation that a full biological molecule can be represented by smaller “kernels” of atoms, the calculations are greatly simplified. Moreover, collections of kernels are, from a computational point of view, well suited for parallel computation. The result is a modest increase in computational time as the number of atoms increases, while retaining the ab initio character of the calculations. We describe a test of our method, and establish its accuracy using 15 different peptides of biological interest. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Facile Synthesis,Pure DFT Calculations,and PM3 Semiempirical MO Method Validation of Regiospecificity of Novel 1,4-Dihydropyrido[2,3-d]pyrimidine Derivatives

Reaction of 6-aminothiouracil (or uracil) with equimolar amounts of different ketones or diketones and the appropriate aromatic aldehydes afforded di- and tricyclic linear pyrido[2,3-d]pyrimidine derivatives 4, 6–12, 14, 16–18, 20, and 21, and pyrimido[4,5-b]quinoline derivatives 15 and 19 in good yields. The regiospecificity, which led to the formation of compound 4 not 5, was validated using ab initio at the HF/6–31 G⁺(d,p) level and pure density functional theory (DFT) calculations using BLYP energy functional and the basis set DNP via studying the thermodynamics of their possible conformers and regioisomers. In addition, the total energy of the transition state was calculated for compounds 12 and 13 to determine whether the reaction products were thermodynamically or kinetically controlled. Hence, the linear structures and the regiospecificities of the reactions for the structures reported in this article were established by elemental analysis, spectral data, ab initio calculations, pure DFT, and PM3 parameters.     

Density functional theory study on molecular structure and vibrational IR spectra of isocytosine

Density functional theory with the combined Becke3-LYP exchange-correlation energy functional [DFT(B3-LYP) method] using the 6-31G(d, p) basis set is applied to predict molecular parameters (geometries, rotational constants, dipole moments) and vibrational IR spectra (harmonic wavenumbers, absolute intensities) of six tautomers of the isocytosine molecule. The results are compared with the corresponding data calculated at the conventional ab initio Hartree-Fock (HF) level using the same basis set and with available experimental data. Calculations show that (a) three amino tautomers are slightly nonplanar species with, evidently, a distorted amino group, (b) the DFT (B3-LYP)/6-31G(d, p) method predicts better molecular parameters, than do the HF calculations, and (c) the DFT(B3-LYP)-calculated vibrational IR spectra of isocytosine agree well with the available recorded IR spectra, and they show marked improvement over the IR spectra predicted at the HF/6-31G(d, p) level. Tautomeric stabilities of isocytosine are discussed on the basis of computed electronic energies by the DFT(B3-LYP) and ab initio approaches [including the MP2 and MP4(SDQ) calculations of electronic energies] and predicted zero-point vibrational energies by DFT(B3-LYP) and HF methods. This relative energies at 0 K of the tautomeric forms of isocytosine predicted by both conventional ab initio and DFT(B3-LYP) methods correlate well with the experimental data, showing the predominance of the aminohydroxy tautomer of isocytosine for an isolated molecule. © 1997 John Wiley & Sons, Inc.     

Molecular (hyper)polarizabilities computed by pseudospectral methods

We have developed algorithms based on pseudospectral (PS) ab initio electronic structure methods for solving the first- and second-order Hartree-Fock/Kohn-Sham equations and evaluating molecular polarizabilities and first- and second-order hyperpolarizabilities in the spin-restricted and spin-unrestricted formalisms at the Hartree-Fock (HF) and density functional theory (DFT) levels. We carry out calculations on 50 small molecules to test the accuracy of the PS approach. Our results demonstrate that the molecular polarizability alpha computed by the PS method is essentially identical to the value obtained from conventional methods for both HF and DFT calculations, while the first-order hyperpolarizability beta and second-order hyperpolarizability gamma have mean unsigned percentage differences of 1.26% and 0.62% (HF) and 0.78% and 0.65% (DFT), respectively. We also present CPU timing comparisons between the PS and conventional methods at the 6-31 G(**) level for 14 molecules having 185 to 1185 basis functions. The timing results show that the PS method is 25 (PS-HF) and 13 (PS-DFT) times faster than the conventional method for a system with 500 basis functions. The PS methods are found scale as N(2.70) (PS-HF) and N(2.40) (PS-DFT), while the conventional methods scale as N(2.93) (PRISM-HF) and N(2.87) (PRISM-DFT), where N is the number of basis functions.     

A generalized higher order kernel energy approximation method

We present a general mathematical model that can be used to improve almost all fragment‐based methods for ab initio calculation of total molecular energy. Fragment‐based methods of computing total molecular energy mathematically decompose a molecule into smaller fragments, quantum‐mechanically compute the energies of single and multiple fragments, and then combine the computed fragment energies in some particular way to compute the total molecular energy. Because the kernel energy method (KEM) is a fragment‐based method that has been used with much success on many biological molecules, our model is presented in the context of the KEM in particular. In this generalized model, the total energy is not based on sums of all possible double‐, triple‐, and quadruple‐kernel interactions, but on the interactions of precisely those combinations of kernels that are connected in the mathematical graph that represents the fragmented molecule. This makes it possible to estimate total molecular energy with high accuracy and no superfluous computation and greatly extends the utility of the KEM and other fragment‐based methods. We demonstrate the practicality and effectiveness of our model by presenting how it has been used on the yeast initiator tRNA molecule, ytRN (1YFG in the Protein Data Bank), with kernel computations using the Hartree‐Fock equations with a limited basis of Gaussian STO‐3G type. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Two rotors potential scans and vibrational assignments for dihalomethylsulfonyl isocyanates

The conformational behavior and structural stability of dichloro and difluoromethyl-sulfonyl isocyanates were investigated by quantum mechanical DFT and ab initio calculations. The 6-311 + + G** basis set was employed to include polarization and diffuse functions in the calculation at B3LYP and MP2 levels. The molecules were found to exist in a mixture of trans-gauche and gauche-gauche conformations at ambient temperatures. From the calculations the isocyanate NCO moiety was predicted to nearly eclipse one of the sulfony S=O bonds in the two stable conformers of both molecules. The potential scans for the rotations of the two NCO and CX2H rotors were calculated from which the rotational barriers could be estimated. The vibrational frequencies, potential energy distributions, IR intensities as well as depolarization ratios were calculated.     

Nonempirical wave functions for very large molecules. I. The PRDDO/M method

We describe enhancements to the method of partial retention of diatomic differential overlap (PRDDO ). The new method, denoted PRDDO/M , employs a basis set of not quite orthogonal atomic orbitals (NQOAOS ) and utilizes sparse matrix techniques to greatly increase the computational efficiency for large molecules. Other modifications, including a complete reparametrization of the method against ab initio STO -3G calculations and implementation of integral screening/damping algorithms, are described. The method is an order of magnitude or more faster than are STO 3G single-point calculations using modern ab initio codes, with little loss in accuracy. © 1996 John Wiley & Sons, Inc.     

Embedded,graph-theoretically defined many-body approximations for wavefunction-in-DFT and DFT-in-DFT: Applications to gas- and condensed-phase ab initio molecular dynamics,and potential surfaces for quantum nuclear effects

We present a graph-theoretic approach to adaptively compute many-body approximations in an efficient manner to perform (a) accurate post-Hartree–Fock (HF) ab initio molecular dynamics (AIMD) at density functional theory (DFT) cost for medium- to large-sized molecular clusters, (b) hybrid DFT electronic structure calculations for condensed-phase simulations at the cost of pure density functionals, (c) reduced-cost on-the-fly basis extrapolation for gas-phase AIMD and condensed phase studies, and (d) accurate post-HF-level potential energy surfaces at DFT cost for quantum nuclear effects. The salient features of our approach are ONIOM-like in that (a) the full system (cluster or condensed phase) calculation is performed at a lower level of theory (pure DFT for condensed phase or hybrid DFT for molecular systems), and (b) this approximation is improved through a correction term that captures all many-body interactions up to any given order within a higher level of theory (hybrid DFT for condensed phase; CCSD or MP2 for cluster), combined through graph-theoretic methods. Specifically, a region of chemical interest is coarse-grained into a set of nodes and these nodes are then connected to form edges based on a given definition of local envelope (or threshold) of interactions. The nodes and edges together define a graph, which forms the basis for developing the many-body expansion. The methods are demonstrated through (a) ab initio dynamics studies on protonated water clusters and polypeptide fragments, (b) potential energy surface calculations on one-dimensional water chains such as those found in ion channels, and (c) conformational stabilization and lattice energy studies on homogeneous and heterogeneous surfaces of water with organic adsorbates using two-dimensional periodic boundary conditions.     

Structure and vibrational frequencies of 2-butanimine

The conformational behavior and structural stability of 2-butanimine were investigated by utilizing ab initio calculations with 6-311++G** basis set at HF, MP2, B3LYP and BLYP levels. The vibrational frequencies of 2-butanimine were computed. Complete vibrational assignments were made on the basis of normal coordinate calculations for stable conformer of the molecule. HF results without scaled quantum mechanical (SQM) force field procedure considered are in bad agreement with experimental values. Of the two DFT methods, BLYP reproduces the observed fundamental frequencies most satisfactorily with the mean absolute deviation of the non-CH stretching modes less than 21.3 cm(-1). The results indicate that BLYP calculation is a very promising approach for understanding the observed spectral features.     

Hydrogen bonding in acetylacetaldehyde: Theoretical insights from the theory of atoms in molecules

All the possible conformations of tautomeric structures (keto and enol) of acetylacetaldehyde (AAD) were fully optimized at HF, B3LYP, and MP2 levels with 6‐31G(d,p) and 6‐311++G(d,p) basis sets to determine the conformational equilibrium. Theoretical results show that two chelated enol forms have extra stability with respect to the other conformers, but identification of global minimum is very difficult. The high level ab initio calculations G2(MP2) and CBS‐QB3) also support the HF conclusion. It seems that the chelated enol forms have equal stability, and the energy gap between them is probably lies in the computational error range. Finally, the analysis of hydrogen bond in these molecules by quantum theory of atoms in molecules (AIM) and natural bond orbital (NBO) methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Vibrational spectroscopic, first-order hyperpolarizability and HOMO, LUMO studies of 1,2-dichloro-4-nitrobenzene based on Hartree-Fock and DFT calculations

The Fourier-transform infrared spectrum of 1,2-dichloro-4-nitrobenzene (DCNB) was recorded in the region 4000-400cm(-1). The Fourier-transform Raman spectrum of DCNB was also recorded in the region 3500-50cm(-1). Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of DCNB were carried out by ab initio HF and density functional theory (DFT/B3LYP) method with 6-31+G(d,p) basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The values of the total dipole moment (μ) and the first-order hyperpolarizability (β) of the investigated compound were computed using ab initio quantum mechanical calculations. The calculated results also show that the DCNB might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of DCNB is also reported based on total energy distribution (TED). The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title compound have also been constructed.     

Ab initio studies of arginine and deaminoarginine

L-Arginine and Deaminoarginine were studied via quantum chemical ab initio calculations using the STO -3G basis set for arginine and the STO -3G and 3–21G basis sets for deaminoarginine. It was found that the most stable conformations are the ones featuring the carboxyl group slightly twisted versus the rest of the molecule, which adopts an extended conformation. It was also found that the cyclic zwitterion is less stable than the neutral cyclic conformation and that there is a barrier to the proton transfer from the carboxyl's oxygen to one of guanidine moiety's nitrogens.     

Ab initio calculation of torsion and inversion barriers of the amino group in aminopyrimidines

Calculations of the barriers to internal rotation and inversion of the amino group in substituted pyrimidines have been performed. Torsion and inversion barriers were determined by several ab initio methods: HF, HF/MP2, MP4, CISD, QCISD, QCISD(T), CCSD, and CCSD(T). DFT method also employed. Dependencies of the calculated barrier heights on the basis set and the electron correlation level and on the substitution position of the nitrogen atom in the ring were studied. We have determined that for certain molecules relatively low level calculations may eventually provide adequate results, but in general, higher level calculations are necessary.     

A theoretical study on three conformational structures of 2,6‐distyrylpyridine

Ab initio methods at the levels HF/cc‐pVDZ, HF/6‐31G(d,p), MP2/cc‐pVDZ, and MP2/6‐31G(d,p), as well as methods based on density functional theory (DFT) employing the hybrid functional B3LYP with the basis sets cc‐pVDZ and 6‐31G(d,p), have been applied to study the conformers of 2,6‐distyrylpyridine. Bond distances, bond angles, and dihedral angles have been calculated at the B3LYP level. The calculated values were in good agreement with those measured by X‐ray diffraction analysis of 2,6‐distyrylpyridine. The values calculated using the Hartree‐Fock method and second‐order perturbation theory (MP2) were inconsistent. The optimized lowest‐energy geometries were calculated from the reported X‐ray structural data by the B3LYP/cc‐pVDZ method. Three conformations, A, B, and C, were proposed for 2,6‐distyrylpyridine. Calculations at the three levels of theory indicated that conformation A was the most stable structure, with conformations C and B being higher in energy by 1.10 and 2.57 kcal/mol, respectively, using the same method and basis function. The same trend in the relative energies of the three possible conformations was observed at the two levels of theory and with the different basis sets employed. The reported X‐ray data were utilized to optimize total molecular energy of conformation A at the different calculation levels. The bond lengths, bond angles, and dihedral angles were then obtained from the optimized geometries by ab initio methods and by applying DFT using the two basis functions cc‐pVDZ and 6‐31G(d,p). The values were analyzed and compared. The calculated total energies, the relative energies of the molecular orbitals, the gap between them, and the dipole moment for each conformational structure proposed for 2,6‐distyrylpyridine are also reported. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Comparative study of DFT methods applied to small titanium/oxygen compounds

The performance of a number of different local and nonlocal density functional theory (DFT) methods has been investigated for some small titanium—oxygen systems. Equilibrium geometries, ionization potentials, dipole moments, atomization energies, and harmonic vibrational frequencies have been calculated for the TiO, TiO₂, and Ti₂ molecules, and the results are compared with experimental data and ab initio calculations. It is shown that most DFT methods perform much better than the ab initio Hartree—Fock (HF), second-order perturbation theory (MP2), and configuration interaction including single and double excitations (CISD) treatments. For good agreement with experimental data, gradient corrections to the exchange part of the DFT functional are needed, as well as some type of correction for the errors in the calculated energy splittings between different atomic states of titanium. Hybrid methods including a mixture of HF exchange with DFT exchange correlation do not perform as well as “pure” DFT methods for the studied systems. © 1996 John Wiley & Sons, Inc.     

Reassessment of methyl rotation barriers and conformations by correlated quantum chemistry methods

Internal rotations of the methyl group in ortho‐substituted and 2,6‐disubstituted toluenes in their ground state have been investigated by means of various ab initio quantum chemistry methods. Computed barriers at the Hartree‐Fock (HF) level using medium sized basis sets agreed reasonably with experimental results in the case of the studied ortho‐substituted toluenes. However, this agreement worsens when using very large basis sets. Furthermore, the determination of the conformation and barriers of more weakly hindered methyl groups, that is, for 2,6‐dihalogenotoluenes or toluene itself, necessitates high level correlated computations, because of a possible failure of HF calculations in this case. Density functional theory (DFT) techniques required, in several cases, much more extended basis sets than the post‐HF Møller‐Plesset perturbation (MP2, MP4) ones, to insure the convergence of the computed barriers. Non‐negligible variations of the computed barriers when using different DFT functionals are observed for some systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2093–2100, 2003