Semiempirical Molecular Orbital Theory Research Articles

Topology Molecular Indices Relationship of Electronic Properties of N-Alkanes and Branched Alkanes

Eight electronic properties; HUMO, LUMO, HOMO-LUMO energy gap, dipole moment point-charge, dipole moment hybrid, molecular weight, heat of formation and zero-point energy of 60 normal and branched alkanes were examined using topology molecular indices. All the electronic properties were calculated using semi-empirical self-consistent molecular orbital theory. The relationship of electronic calculation properties with seven models of topology indices based on degree and/or distance were obtained in terms of their correlation, regression and principal component analysis. Most of the properties were well-modelled (r2 > 0.82) by topology molecular indices except the dipole moment point-charge and hybrid. The PCA resulted in 7 properties and 60 structures of alkanes that produced two principal components with eigenvalues of greater than 1. The first principal component explained 60.388%, while the second principal component explained 26.457%, bringing a cumulative value of 86.845% to the data variation.

Numerical Analysis for Light Absorption Spectra of the Base of DNA-Wrapped Single-Walled Carbon Nanotubes

This study numerically demonstrates the light absorption spectra of each base of DNA-wrapped single-walled carbon nanotubes (SWCNTs). Previous experimental and theoretical studies show that the optical properties of these composites are different from the bare SWCNTs. In this work, we investigated the bases of DNA that influence optical properties. To obtain stable molecular states for studying optical properties, molecular dynamics calculations were performed. Additionally, light absorption spectra in the ultraviolet-to-near-infrared region of one type of base-wrapped (e.g., adenine-, thymine-, cytosine-, or guanine-wrapped) SWCNTs were investigated by utilizing the semi-empirical molecular orbital theory using SCIGRESS commercial software. This method can significantly reduce the calculation time compared to the ab initio molecular orbital method, making the handling of composites of bases and SWCNTs possible. We found that the largest peaks appear at a wavelength of around 300 nm for all the composites. Furthermore, we found that the light absorption spectra above 570 nm are strongly influenced by adenine and cytosine. Thus, our computational results provide insight into the optical properties and the effects of base-SWCNTs that are difficult to investigate experimentally under the influence of solvents and various molecules.

Accurate Heats of Formation for Polycyclic Aromatic Hydrocarbons: A High-Level Ab Initio Perspective

Polycyclic aromatic hydrocarbons (PAHs) are key reference materials for the validation and parameterization of computationally cost-effective procedures such as density functional theory (DFT), semiempirical molecular orbital theory, and molecular mechanics. We obtain accurate heats of formation (ΔHf,298) for 20 PAHs with up to 18 carbon atoms by means of the explicitly correlated W1-F12 thermochemical procedure. The heats of formation are obtained via atomization reactions and quasi-isodesmic reactions involving CH4, C2H4, and C6H6 for which accurate experimental ΔHf,298 values are available from the active thermochemical tables (ATcT) network. We show that for large PAHs, the differences between W1-F12 heats of formation obtained from atomization and quasi-isodesmic reactions increase with the size of the system and range between 1.7 (C7H8) and 8.9 (chrysene, C18H12) kJ mol–1. This suggests that atomization reactions should be used with caution for obtaining heats of formation for medium-sized systems even when highly accurate thermochemical procedures (such as W1-F12 theory) are used. For eight PAH compounds (toluene, indene, acenaphthylene, biphenyl, diphenylmethane, anthracene, pyrene, and chrysene), our best theoretical values agree with the best experimental values to within ∼1 kJ mol–1; for six additional systems (indane, naphthalene, biphenylene, acenaphthene, phenanthrene, and m-terphenyl), the agreement between theory and experiment is good with deviations ranging between 2 and 4 kJ mol–1. However, for four systems (p-terphenyl, fluorene, pyracene, and pyracyclene), our best W1-F12 values suggest that the experimental ΔHf,298 values should be revised by significant amounts ranging from 6.5 and 24.4 kJ mol–1.

Erratum to "Toward a Quantum-Chemical Benchmark Set for Enzymatically Catalyzed Reactions: Important Steps and Insights".

We present steps toward the construction of a quantum-chemical benchmark set for enzymatically catalyzed reactions comprising different-quite sizable-model systems for five reactions. Our work is inspired by a study of semiempirical molecular-orbital theory methods against B3LYP-based structures and energies [ Kromann et al. PeerJ 2016 , 4 , e1994 ]. Taking the same model systems, we herein demonstrate first how adequate treatments of London dispersion and basis-set superposition error lead to structural differences compared to structures obtained at the popular B3LYP/6-31G(d,p) level. The changes observed by us have a significant influence on the final reaction barrier heights (BHs) and energies (REs), which are our main focus herein. We then proceed and carefully investigate different strategies to obtain either exact or estimated complete-basis-set BHs and REs with the help of the DLPNO-CCSD(T) approach, which offers an exciting path into exploring larger biochemically relevant structures at the coupled cluster level. On the basis of our analysis, we present three strategies for obtaining reliable values. While these recommendations constitute our main findings and are meant to be used as useful guidelines for others in the field, we demonstrate their applicability in a preliminary benchmark set comprising 16 BHs and 12 REs on which we assess 35 density functional theory (DFT) approximations. This preliminary benchmark study was used as an indicator for the validity of our approach toward generating such a benchmark set, based on the fact that we were able to reproduce major recommendations in the field of modern DFT, such as the reproduction of the famous Jacob's Ladder scheme, while also pointing out subtle differences to previous benchmark studies. We end our study by critically assessing the still popular choice to gauge the accuracy of low-level methods against B3LYP data, and we show the risks of such a strategy, adding to the ever-growing list of calls to move away from B3LYP as a standard black-box approach.

Toward a Quantum-Chemical Benchmark Set for Enzymatically Catalyzed Reactions: Important Steps and Insights.

We present steps toward the construction of a quantum-chemical benchmark set for enzymatically catalyzed reactions comprising different-quite sizable-model systems for five reactions. Our work is inspired by a study of semiempirical molecular-orbital theory methods against B3LYP-based structures and energies [ Kromann et al. PeerJ 2016 , 4 , e1994 ]. Taking the same model systems, we herein demonstrate first how adequate treatments of London dispersion and basis-set superposition error lead to structural differences compared to structures obtained at the popular B3LYP/6-31G(d,p) level. The changes observed by us have a significant influence on the final reaction barrier heights (BHs) and energies (REs), which are our main focus herein. We then proceed and carefully investigate different strategies to obtain either exact or estimated complete-basis-set BHs and REs with the help of the DLPNO-CCSD(T) approach, which offers an exciting path into exploring larger biochemically relevant structures at the coupled cluster level. On the basis of our analysis, we present three strategies for obtaining reliable values. While these recommendations constitute our main findings and are meant to be used as useful guidelines for others in the field, we demonstrate their applicability in a preliminary benchmark set comprising 16 BHs and 12 REs on which we assess 35 density functional theory (DFT) approximations. This preliminary benchmark study was used as an indicator for the validity of our approach toward generating such a benchmark set, based on the fact that we were able to reproduce major recommendations in the field of modern DFT, such as the reproduction of the famous Jacob's Ladder scheme, while also pointing out subtle differences to previous benchmark studies. We end our study by critically assessing the still popular choice to gauge the accuracy of low-level methods against B3LYP data, and we show the risks of such a strategy, adding to the ever-growing list of calls to move away from B3LYP as a standard black-box approach.

What is semiempirical molecular orbital theory approximating?

We elucidate the approaches used to incorporate electron correlation in existing semiempirical molecular orbital theory (SEMO) methods and compare them with the techniques used in other quantum chemical methods. After analyzing expressions for electron correlation in ab initio wavefunction theory, density functional theory, and density functional-based tight-binding (TB) methods, we suggest a framework for developing hybrid TB-SEMO methods. We provide a numerical proof-of-concept for such a method based on the OM2 method.

Computational study of some heterocyclic scaffolds derived from quinazoline and Mannich base Sydnone

Abstract The current study reports design and diversity-oriented synthesis of novel heterocycles incorporating thioureido linkage and mesoionic compounds could find new applications in biology. Employing reagent-based skeletal diversity approach; a facile synthesis of quinazoline and sydnone moiety has been accomplished. The synthesized compounds were characterized by IR and 1 H NMR-spectral data, and elemental analysis. The structural and electronic properties of newly synthesized compounds have been explored theoretically by performing semi-empirical molecular orbital theory at the level of PM6 of theory. Henceforth, computational chemistry can assist the experimental chemist or it can challenge the experimental chemist to find entirely new chemical objects. Keywords: Computational study, quinazoline, mannich base, thioureido linkage Cite this Article Modi J. Computational Study of Some Heterocyclic Scaffolds Derived from Quinazoline and Mannich Base Sydnone. Journal of Modern Chemistry & Chemical Technology . 2018; 9(3): 8–12p.

Synthesis, spectroscopic, thermal, fluorescence properties and molecular modeling of novel Pt(II) complex with schiff base containing NS donor atoms

New transition metal complex of Pt(II) of the Schiff base ligand with (E)-2-((1-(thiophen-2-yl)ethylidene)amino)phenol HL have been synthesized using the ultrasonic irradiation and characterized by physicochemical and spectroscopic methods. The IR spectrum of Pt(II) complex showed that the coordination in metal ions via the imine N and S atoms. Magnetic and UV–Vis spectra showed that the geometrical structure of Pt(II) complex is square planar. The molar conductance data revealed that Pt(II) complex is non-electrolyte. The thermodynamic parameters for thermal decomposition of Pt(II) complex was calculated from analysis of the TG-DTG curves using Hörowitz–Metzger method. The fluorescence of the ligand HL and its Pt(II) complex in different solvents and pH conditions have also been studied in detail. The quenching of the fluorescence intensity of the ligand can be noted obviously, in the presence of Pt(II) ion. Geometry optimization of the compounds was calculated by semiempirical molecular orbital theory PM3 method using Hyperchem 7.52 program.

Insights into doxycycline adsorption onto graphene nanosheet: a combined quantum mechanics, thermodynamics, and kinetic study.

Recently, pharmaceutically active compounds including antibiotics have been detected in drinking water at very low levels, mostly nanogram/liter concentrations, proposing that these materials were unaffected by water treatment processes. Adsorption processes were suggested to play a significant role in the removal of antibiotics. In this study, the adsorption behavior of doxycycline (DC) in aqueous solution was evaluated. The four factors influencing the adsorption of DC onto graphene nanosheet (GNS) were studied. The results showed that initial pH∼ 6 to 7 and contact time ∼ 200min are optimum. The monolayer adsorption capacity was reduced with the increasing temperature from 25 to 45°C. Nonlinear regressions were carried out to define the best fit model for every system. Among various models, the Hill isotherm model represented the equilibrium adsorption data of antibiotics while the kinetic data were well fitted by the Elovich kinetic model. The maximum adsorption capacity (q max) was 110mg.g-1, obtained from the Hill equation. Semiempirical molecular orbital theory was used to investigate the molecular interaction of the adsorption system. The experiments and semiempirical computation have systematically demonstrated that DC could be adsorbed onto GNS by π- π and electrostatic interactions. It was shown that there is a good compromise with the experimental results. Graphical abstract Insights into doxycycline adsorption onto graphene nanosheet: quantum mechanics, thermodynamics, and kinetic study.

Charge Transport in Organic Materials: Norm-Conserving Imaginary Time Propagation with Local Ionization Energy as the External Potential.

An additional charge carrier described as its wave function is propagated in imaginary time using stepwise matrix multiplication and a correction to ensure that the simulation is norm-conserving. The propagation Hamilton operator uses the local ionization energy of a rubrene single crystal, calculated with semiempirical molecular orbital theory, as an external potential for holes to model the interaction with the underlying molecular structure. Virtual electrodes are modeled by setting the potentials in the appropriate areas to constant values with the difference corresponding to the source-drain voltage. Although imaginary time cannot be interpreted directly as time, the simulated gate-dependent imaginary transfer rate is in acceptable qualitative agreement with the experimentally measured gate-dependent hole-transfer rate through a rubrene single crystal.

Assessment of semi-empirical molecular orbital calculations for describing magnetic interactions

We report a thorough comparison between the spin-unrestricted semi-empirical molecular orbital (SE-UMO) and density functional theory (UDFT) calculations for a variety of π-conjugated diradical molecules which exhibit through-bond magnetic exchange interactions. The spin-unrestricted neglect of diatomic differential overlap (NDDO)-based methods (UPM6 and UrPM6) and self-consistent charge density functional tight-biding (UDFTB) are examined. The UCAM-B3LYP method is used as a representative of UDFT. We have found that NDDO-based and UDFTB methods give different performances with respect to the results of UCAM-B3LYP. The degree of diradical character in the target systems decreases in the order of UPM6>UrPM6≈UCAM-B3LYP>UDFTB. The conventional UPM6 and UDFTB calculations tend to overestimate and underestimate the diradical character, respectively, whereas UrPM6 is able to provide much the same results as UCAM-B3LYP. This is convincing evidence that UrPM6 will be useful for in silico screening of materials science at much lower computational cost.

Determination of consistent semiempirical one-centre integrals based on coupled-cluster theory

ABSTRACTWe examine the one-centre integrals used in semiempirical molecular orbital theory, for the elements H–Ne. The currently used parameters do not provide good estimates for the relative energies of ionised states of atoms. Directly calculating the one-electron integrals Uss and Upp with coupled-cluster theory and fitting the two-electron repulsion integrals Gss and Gpp to accurate coupled-cluster ionisation curves improves this behaviour. Since all the remaining parameters can be derived from these, the number of fitted variables is reduced from seven to two. The two-parameter model provides qualitative agreement with coupled-cluster theory for all ionisation potentials (IPs) and the principal electron affinity (EA). To obtain quantitative agreement for the principal IP and EA, Uss and Upp are included as variables in a four-parameter model. We discuss the new parameters and implications for the development of new, consistent semiempirical Hamiltonians.

Dispersion-Corrected Mean-Field Electronic Structure Methods.

Mean-field electronic structure methods like Hartree-Fock, semilocal density functional approximations, or semiempirical molecular orbital (MO) theories do not account for long-range electron correlation (London dispersion interaction). Inclusion of these effects is mandatory for realistic calculations on large or condensed chemical systems and for various intramolecular phenomena (thermochemistry). This Review describes the recent developments (including some historical aspects) of dispersion corrections with an emphasis on methods that can be employed routinely with reasonable accuracy in large-scale applications. The most prominent correction schemes are classified into three groups: (i) nonlocal, density-based functionals, (ii) semiclassical C6-based, and (iii) one-electron effective potentials. The properties as well as pros and cons of these methods are critically discussed, and typical examples and benchmarks on molecular complexes and crystals are provided. Although there are some areas for further improvement (robustness, many-body and short-range effects), the situation regarding the overall accuracy is clear. Various approaches yield long-range dispersion energies with a typical relative error of 5%. For many chemical problems, this accuracy is higher compared to that of the underlying mean-field method (i.e., a typical semilocal (hybrid) functional like B3LYP).

Heats of formation of platonic hydrocarbon cages by means of high-level thermochemical procedures.

Hydrocarbon cages are key reference materials for the validation and parameterization of computationally cost-effective procedures such as density functional theory (DFT), semiempirical molecular orbital theory, and molecular mechanics. We obtain accurate total atomization energies (TAEs) and heats of formation (Δf H°298) for platonic and prismatic hydrocarbon cages by means of the Wn-F12 explicitly correlated thermochemical protocols. We consider the following kinetically stable (CH)n polycyclic hydrocarbon cages: (i) platonic hydrocarbons (tetrahedrane, cubane, and dodecahedrane), (ii) prismatic hydrocarbons (triprismane, cubane, and pentaprismane), and (iii) one truncated tetrahedrane (octahedrane). Our best theoretical heat of formation for cubane (144.8 kcal mol(-1)) suggests that the experimental value adopted by the NIST thermochemical database (142.7 ± 1.2 kcal mol(-1)) should be revised upwards by ∼2 kcal mol(-1). Our best heat of formation for dodecahedrane (20.2 kcal mol(-1)) suggests that the semiexperimental value (22.4 ± 1 kcal mol(-1)) should be revised downward by ∼2 kcal mol(-1). We use our benchmark Wn-F12 TAEs to evaluate the performance of a variety of computationally less demanding composite thermochemical procedures. These include the Gaussian-n (Gn) and the complete basis set (CBS) methods. The CBS-QB3 and CBS-APNO procedures show relatively poor performance with root-mean-squared deviations (RMSDs) of 4.2 and 2.5 kcal mol(-1), respectively. The best performers of the Gn procedures are G4 and G3(MP2)B3 (RMSD = 0.5 and 0.6 kcal mol(-1), respectively), while the worst performers are G3 and G4(MP2)-6X (RMSD = 2.1 and 2.9 kcal mol(-1), respectively). Isodesmic and even homodesmotic reactions involving these species are surprisingly challenging targets for DFT computations.

The Electronic Structure of Amorphous Carbon Nanodots.

We have studied hydrogen-passivated amorphous carbon nanostructures with semiempirical molecular orbital theory in order to provide an understanding of the factors that affect their electronic properties. Amorphous structures were first constructed using periodic calculations in a melt/quench protocol. Pure periodic amorphous carbon structures and their counterparts doped with nitrogen and/or oxygen feature large electronic band gaps. Surprisingly, descriptors such as the elemental composition and the number of sp(3)-atoms only influence the electronic structure weakly. Instead, the exact topology of the sp(2)-network in terms of effective conjugation defines the band gap. Amorphous carbon nanodots of different structures and sizes were cut out of the periodic structures. Our calculations predict the occurrence of localized electronic surface states, which give rise to interesting effects such as amphoteric reactivity and predicted optical band gaps in the near-UV/visible range. Optical and electronic gaps display a dependence on particle size similar to that of inorganic colloidal quantum dots.

Why many semiempirical molecular orbital theories fail for liquid water and how to fix them.

Water is an extremely important liquid for chemistry and the search for more accurate force fields for liquid water continues unabated. Neglect of diatomic differential overlap (NDDO) molecular orbital methods provide and intriguing generalization of classical force fields in this regard because they can account both for bond breaking and electronic polarization of molecules. However, we show that most standard NDDO methods fail for water because they give an incorrect description of hydrogen bonding, water's key structural feature. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that PM6 does not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. Finally, we identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry.

Synthesis of Optically Active Poly(m-phenyleneethynylene–aryleneethynylene)s Bearing Hydroxy Groups and Examination of the Higher Order Structures

Novel optically active poly(m-phenyleneethynylene–aryleneethynylene)s bearing hydroxy groups with various arylene units {poly[(S)-/(R)-1–3a]–poly[(R)-1–3e] and poly[(S)-2–3a]} were synthesized by the Sonogashira–Hagihara coupling polymerization of 3,5-diiodo-4-hydroxy-C6H4CONHCH(CH3)COXC12H25 [(S)-/(R)-1 (X = O), (S)-2 (X = NH)] with HC≡C–Ar–C≡CH [3a (Ar = 1,4-C6H4), 3b (Ar = 1,4-C6H4-1,4-C6H4−), 3c (Ar = 1,4-C6H4-1,4-C6H4-1,4-C6H4−), 3d (Ar = 2,5-dihexyl-1,4-C6H2), 3e (Ar = 2,5-didodecyl-1,4-C6H2)]. The yields and number-average molecular weights of the polymers were in the ranges 60–94% and 7,000–29,500 with no correlation between the yield and the Mn. Circular dichroism (CD), UV–vis, and fluorescence spectroscopic analyses indicated that poly[(S)-1–3a]–poly[(S)-1–3c] and poly[(S)-2–3a] formed predominantly one-handed helical structures in THF, while poly[(S)-1–3d] and poly[(S)-1–3e] showed no evidence for forming chirally ordered structures. All polymers emitted blue fluorescence. The solution state IR measurement revealed the presence of intramolecular hydrogen bonding between the amide groups at the side chains of poly[(S)-1–2a]. The helical structures and helix-forming abilities of the polymers were analyzed by the molecular mechanics (MM), semiempirical molecular orbital (MO) and density functional theory (DFT) methods. Tube-like structures, presumably formed by perpendicular aggregation of the helical polymers, were observed by atomic force microscopy (AFM).

Atomistic modelling of CVD synthesis of carbon nanotubes and graphene

We discuss the synthesis of carbon nanotubes (CNTs) and graphene by catalytic chemical vapour deposition (CCVD) and plasma-enhanced CVD (PECVD), summarising the state-of-the-art understanding of mechanisms controlling their growth rate, chiral angle, number of layers (walls), diameter, length and quality (defects), before presenting a new model for 2D nucleation of a graphene sheet from amorphous carbon on a nickel surface. Although many groups have modelled this process using a variety of techniques, we ask whether there are any complementary ideas emerging from the different proposed growth mechanisms, and whether different modelling techniques can give the same answers for a given mechanism. Subsequently, by comparing the results of tight-binding, semi-empirical molecular orbital theory and reactive bond order force field calculations, we demonstrate that graphene on crystalline Ni(111) is thermodynamically stable with respect to the corresponding amorphous metal and carbon structures. Finally, we show in principle how a complementary heterogeneous nucleation step may play a key role in the transformation from amorphous carbon to graphene on the metal surface. We conclude that achieving the conditions under which this complementary crystallisation process can occur may be a promising method to gain better control over the growth processes of both graphene from flat metal surfaces and CNTs from catalyst nanoparticles.

Theoretical study of phthalane oxidation and effect of substituents by using Hyperchem program

The effect of substituents on the relative stabilization energy (ERS) of phthalane-X carbocations has been studied with PM3 semi-empirical molecular orbital theory. The results show that the amino group gives ERS less than zero for very big amount and that will increase stability of carbocation by π-electron donation, whereas the nitro group gives height amount of ERS more than zero and that will lead to difficulties of an intermediate carbocation formation because of its strong σ- and π-accepting nature. ERS decreases with increase in the phenyl rings attached to cation. When electron withdraws substituents attached, it will destabilize the cation, because they act as π-electron donors. Key words: Relative stabilization energy (ERS), PM3 semi-empirical, isodesmic reactions.

The synthesis, characterization and antibacterial activities of dinuclear Ni(II), Cu(II) and Fe(III) Schiff base complexes

Schiff base; N,N′-bis-(2-hydroxy-1-naphthaldimine)-1,3-diaminopropanol (napdapOH) reacts with metal chlorides to form dinuclear complexes of the type [M2L2] · nCl2 where M = Ni, Cu, Fe and n = 0, 1. Schiff base complexes were characterized by using FT-IR, LC-MS, magnetic moments and conductance measurements. Coordination was found to be through the phenolic oxygen atoms and azomethine nitrogen atoms. The electronic properties of the compounds were investigated theoretically by performing semiempirical molecular orbital theory PM3 method in Hyperchem 7 (Release). The antibacterial activities of the compounds were investigated against Escherichia coli ATCC 11230, Bacillus subtilis RSKK 244, Bacillus megaterium RSKK 5117, Salmonella enteritidis ATCC 13076, Staphylococcus aureus ATCC 25923 by using microdilution method.