Total Energy Of Molecule Research Articles

QSAR Study of 4-Benzylpyridinone Derivatives: Non-Nucleoside Human Immunodeficiency Virus Type 1 Reverse Transcriptase Inhibitors

To study a series of derivatives of 4-Benzylpyridinone with inhibition activity on inverse transcriptase of HIV-1 using computational tools and bioinformatics. A Linear Regression Model (LRM) associated that anti-HIV-1 activity was obtained. This model was correlated with charge on nitrogen atom at the position 3 of 4-BP structure and the total energy of molecule. The LRM was statistically significant with p-value < 0.001, R2 = 0.9006, and a cross validation coefficient of R2cross = 0.8482. A discriminating analysis classified the molecules as active and inactive with high predictive power. In addition, six new molecules based on theoretical analysis were proposed as anti- HIV-1 activity candidate to be synthesized. An equation model that relates the anti-HIV-1 activities of molecules studied was obtained. This model depends basically of two molecular descriptors, the charge on the nitrogen atom in the position 3 and total energy. The charge on the nitrogen atom descriptor gives us an idea of more active site of the molecule while the energy is related with on overall stability of the molecule.

КВАНТОВО-ХИМИЧЕСКОЕ МОДЕЛИРОВАНИЕ ЭФФЕКТИВНОСТИ ИСПОЛЬЗОВАНИЯ ПОЛИАРИЛЕНОВ В ИНТЕРФЕЙСНЫХ СТРУКТУРАХ

This paper gives quantum-chemical analysis of polyarylene efficient use in interface structures. Quantumchemical calculations were performed for molecular systems representing simulated polyarylene polymer systems. The research involved 18 representatives of this class of compounds. Quantum-chemical calculations were conducted for all molecules using B3LYP/6-31+G(d) density functional theory method, and such energetic parameters were theoretically assessed as total energies of molecules and their negative and positive ions in molecular and optimized ionic geometries, energies of occupied and vacant molecular orbitals, magnitudes of vertical and adiabatic electron affinity and ionization potential as well as the dipole moment. The paper puts forward an algorithm for processing the results of quantum-chemical calculations based on the analysis of energy characteristics for monomeric units of polymers that makes it possible to reveal a certain relationship between chemical structure of an organic compound and electronic properties of the polymer-metal interface. The proposed algorithm allowed finding maximum deflection zones of energetic parameters and specific compounds, which are of interest for the formation of heterostructures.

Density functional approximations for orbital energies and total energies of molecules and solids.

The relation of Kohn-Sham (KS) orbital energies to ionization energies and electron affinities is different in molecules and solids. In molecules, the local density approximation (LDA) and generalized gradient approximations (GGA) approximate the exact ionization energy (I) and affinity (A) rather well with self-consistently calculated (total energy based) ILDFA and ALDFA, respectively. The highest occupied molecular orbital (HOMO) energy and lowest unoccupied molecular orbital (LUMO) energy, however, differ significantly (by typically 4-6 eV) from these quantities, ϵHLDFA(mol)>-I(mol)≈-ILDFA(mol), ϵLLDFA(mol)<-A(mol)≈-ALDFA(mol). In solids, these relations are very different, due to two effects. The (almost) infinite extent of a solid makes the difference of orbital energies and (L)DFA calculated ionization energy and affinity disappear: in the solid state limit, ϵH(L)DFA(solid)=-I(L)DFA(solid) and ϵL(L)DFA(solid)=-A(L)DFA(solid). Slater's relation ∂E/∂ni = ϵi for local density functional approximations (LDFAs) [and Hartree-Fock (HF) and hybrids] is useful to prove these relations. The equality of LDFA orbital energies and LDFA calculated -ILDFA and -ALDFA in solids does not mean that they are good approximations to the exact quantities. The LDFA total energies of the ions with a delocalized charge are too low, hence ILDFA(solid) < I and ALDFA(solid) > A, due to the local-approximation error, also denoted delocalization error, of LDFAs in extended systems. These errors combine to make the LDFA orbital energy band gap considerably smaller than the exact fundamental gap, ϵLLDFA(solid)-ϵHLDFA(solid)=ILDFA(solid)-ALDFA(solid)<I-A (the LDFA band gap problem). These results for density functional approximations are compared to exact KS and to HF and hybrids. For the exact KS HOMO energy, one has ϵHKS=-I. The exact KS LUMO energy does not approximate the experimental -A (neither in molecules nor in solids), but is considerably below, which is the main reason for the exact KS HOMO-LUMO energy gap being considerably below the fundamental gap I - A (the exact KS band gap problem).

Synthesis, characterization, antimicrobial activities, and QSAR studies of organotin(IV) complexes

ABSTRACTOrganotin complexes of type R2SnClL [where L = Schiff base obtained by the condensation of 2-(4-Bromo/Chloro-benzyloxy)-3-methoxy-benzaldehyde and nicotinic/isonicotinic hydrazides; R = Me, Et, Bu, and Ph] have been synthesized and characterized by elemental analysis, molar conductance, infrared and NMR (1H, 13C, and 119Sn) spectral analyses. The ligands and their organotin complexes have been evaluated for antimicrobial activity and the QSAR studies indicated that antimicrobial activity of target compounds is governed by total energy of molecule and topological descriptors.

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

Correlation energy within exact-exchange adiabatic connection fluctuation-dissipation theory: Systematic development and simple approximations

We have calculated the correlation energy of the homogeneous electron gas (HEG) and the dissociation energy curves of molecules with covalent bonds from a novel implementation of the adiabatic connection fluctuation dissipation (ACFD) expression including the exact exchange (EXX) kernel. The EXX kernel is defined from first order perturbation theory and used in the Dyson equation of time-dependent density functional theory. Within this approximation (RPAx), the correlation energies of the HEG are significantly improved with respect to the RPA up to densities of the order of $r_s \approx 10$. However, beyond this value, the RPAx response function exhibits an unphysical divergence and the approximation breaks down. Total energies of molecules at equilibrium are also highly accurate but we find a similar instability at stretched geometries. Staying within an exact first order approximation to the response function we use an alternative resummation of the higher order terms. This slight redefinition of RPAx fixes the instability in total energy calculations without compromising the overall accuracy of the approach.

Квантово-хімічне моделювання структури та спектральних характеристик молекулярних комплексів в системі «пентон-терлон»

The structure and spectral properties for molecular complexes, which formed by added monomer form of pentaplast as well as N- phenylbenzamide with some species of intermolecular interaction in system «penton-terlon» have been investigated at ab initio level of theory. It is shown, that the main contribution in total energy of molecules have included by dispersion forces, which realized between Chlorine atom of CH 2 Cl-group and Hydrogen atoms of benzene rings with amide fragment. The proposed theoretical models are validated in reflection of spectral and energetic characteristics of investigating system. Finally, the results of calculations are in good agreement with that data, which have been obtained for such type modeling previously.

Computational study of molecular properties with dual basis sets

We have studied the performance of dual basis (DB) sets for the evaluation of molecular properties via second order Møller-Plesset perturbation theory (MP2). In addition to savings derived from using a trimmed basis set for the underlying Hartree-Fock (HF) calculation, we pursued a systematic truncation of the virtual subspace for further reductions in computational overhead during the post-HF step. Calculated total energies and molecular properties within the DB framework without virtual space truncation are generally in excellent agreement with full basis calculations. When aug-cc-pV5Z is used as the parent basis, mean absolute error for DB-HF (DB-MP2) total energies of molecules within our test set is 9.7 × 10(-5) au (8.0 × 10(-5) au) while mean absolute relative errors for static electrical response properties like dipole moments, isotropic dipole polarizabilities and polarizability anisotropies are 0.15% (0.14%), 0.56% (0.72%), and 0.76% (0.83%) respectively. When DB is coupled with virtual space truncation at the MP2 level, the corresponding errors are larger but still within 2% of full basis values.

Theoretical study of isomerization and decomposition of propenal

We investigated the dynamics of isomerization and multi-channel dissociation of propenal (CH(2)CHCHO), methyl ketene (CH(3)CHCO), hydroxyl propadiene (CH(2)CH(2)CHOH), and hydroxyl cyclopropene (cyclic-C(3)H(3)-OH) in the ground potential-energy surface using quantum-chemical calculations. Optimized structures and vibrational frequencies of molecular species were computed with method B3LYP∕6-311G(d,p). Total energies of molecules at optimized structures were computed at the CCSD(T)∕6-311+G(3df,2p) level of theory. We established the potential-energy surface for decomposition to CH(2)CHCO + H, CH(2)CH + HCO, CH(2)CH(2)∕CH(3)CH + CO, CHCH∕CH(2)C + H(2)CO, CHCCHO∕CH(2)CCO + H(2), CHCH + CO + H(2), CH(3) + HCCO, CH(2)CCH + OH, and CH(2)CC∕cyclic-C(3)H(2) + H(2)O. Microcanonical rate coefficients of various reactions of trans-propenal with internal energies 148 and 182 kcal mol(-1) were calculated using Rice-Ramsperger-Kassel-Marcus and Variational transition state theories. Product branching ratios were derivable using numerical integration of kinetic master equations and the steady-state approximation. The concerted three-body dissociation of trans-propenal to fragments C(2)H(2) + CO + H(2) is the prevailing channel in present calculations. In contrast, C(3)H(3)O + H, C(2)H(3) + HCO and C(2)H(4) + CO were identified as major channels in the photolysis of trans-propenal. The discrepancy between calculations and experiments in product branching ratios indicates that the three major photodissociation channels occur mainly on an excited potential-energy surface whereas the other channels occur mainly on the ground potential-energy surface. This work provides profound insight in the mechanisms of isomerization and multichannel dissociation of the system C(3)H(4)O.

Plato: A localised orbital based density functional theory code

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation. Program summary Program title: Plato Catalogue identifier: AEFC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 219 974 No. of bytes in distributed program, including test data, etc.: 1 821 493 Distribution format: tar.gz Programming language: C/MPI and PERL Computer: Apple Macintosh, PC, Unix machines Operating system: Unix, Linux and Mac OS X Has the code been vectorised or parallelised?: Yes, up to 256 processors tested RAM: Up to 2 Gbytes per processor Classification: 7.3 External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTW Nature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces. Solution method: Localised orbital based density functional theory. Restrictions: Tight-binding and density functional theory only, no exact exchange. Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater–Koster tables for accuracy. Running time: Test cases will run in a few minutes, large calculations may run for several days.

A computational DFT analysis of OH chemisorption on catalytic Pt(111) nanoparticles

In this article, various energies and geometries of pure platinum nanoparticles and those of platinum nanoparticles with adsorbed OH were investigated. Fourteen different platinum clusters of 3–40 atoms were studied using spin-unrestricted density functional theory (DFT) with a double numerical plus polarization basis set. This range of sizes gave enough information for establishing the general trends that were the primary goal of the study. Three different shapes of platinum clusters were presented, and the effect of cluster size on binding energy, total energy, and HOMO–LUMO energy gap was investigated. Subsequently, same calculations were performed for those selected Pt clusters with OH adsorbate on the surface. The results show that the stability of both the pure clusters and the clusters with adsorbed OH molecule increases with an increase of cluster size. This fact indicates that direct influence of the size of Pt cluster on the reaction rate is possible, and the understanding of how cluster size would affect binding energy is important. As expected, the effect of cluster size on total energy of molecule was shown to be a linear function independent of cluster type. We also found that optimized (stable) Pt clusters were bigger in size than that of the initial clusters, or clusters with bulk geometry.

Substantivity and spatial structure of soluble polycyclic dyes for dyeing cellulose fibres

Several polycyclic dyes, derivatives of imidazole and imide derivatives of a perylenetetracarboxylic-3,4,9,10 anhydride have been synthesized. Dyes obtained by adding sulpho groups to original dye molecules were used to dye cellulose fibres in the same way as with direct dyes. The resultant dyeings have a good fastness to washing, abrasion and light. Probable sites of a substitution of sulpho groups in dyes were determined by calculating a total energy of molecules by means of a semiempirical molecular orbital AM1 method and also a reason of a substantivity of imidazole dyes was explained.

Fragment molecular orbital method: use of approximate electrostatic potential

Recently, we have proposed the fragment molecular orbital (FMO) method; an approximate MO method for calculating large molecules such as proteins. The method has been shown to reproduce ab initio total energies and geometries of molecules in good accuracy. The most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation. Numerical calculations on several polypeptides revealed that the approximations brought no significant loss of accuracy in the total energy of molecules and were of practical use.

CALCULATION OF THE TAUTOMERIC PROPERTIES OF 3-FORMYL-TETRINIC ACID BY THE AB INITIO AND DFT METHODS

We have carried out a nonempirical quantum‐chemical calculation with full optimization of the geometry of all theoretically possible tautomeric forms of 3‐formyl‐tetrinic acid (FTRA) according to the Moller–Plesset second‐order perturbation theory with the use of a 6–31G(d) double zeta basis set. The correlation corrections to the total energy of molecules for optimized geometric configurations were calculated in the 6‐31G(d,p) basis. All the possible tautomeric forms of FTRA and the harmonic vibrational frequencies were also calculated within the density functional theory (DFT) with the use of the Perdew–Burke–Ernzerhof (PBE) functional in a three‐exponent basis. It is shown that FTRA in vapors (in the perfect gas approximation) exists in the form of a mixture of three enol forms, among which two exo‐forms predominate. The frequencies and forms of normal vibrations for each cis‐enol tautomer in the region of vibrations of keto‐groups and double bonds differ widely, which permits identification of the tautomers present in the mixture. The possible mechanisms of enol‐enol transformations of 3‐acyltetrinic acids are discussed.

Relationship of energy characteristics and the Randic indices of imidazole and some azolides of sulfonic acids with chromatographic retention

Imidazole and some newly synthesized imidazolides and triazolides of sulfonic acids were investigated by reversed-phase chromatography. The Randic indices, the total energies of molecules, and the energies of the transition states to hydrolysis of imidazolides and triazolides in a neutral medium were calculated. Correlations between these parameters and the retention factors were elucidated.

Structural and electronic properties of a carbon monoxide monolayer

A new ab initio pseudofunction method based on solid state theoretical approaches has been developed which is designed to accurately calculate the electronic properties and total energy of molecules on surfaces and other interfacial systems. This method is used here to investigate critical bonding information of an isolated carbon monoxide layer in the C(2×2)-Ni(001) configuration characteristic of chemisorption on a Ni(001) surface. Results for a two-dimensional array of CO molecules give an equilibrium bond length of 1.138 Å versus 1.128 Å (experimental), derivative of dipole moment of 3.16 D/Å versus 3.14 D/Å (experimental), and a vibrational frequency of 2157 cm -1 versus 2170 cm -1 (experimental), where the experimental values correspond to free CO. Thus, the CO bond length and derivative of dipole moment and vibrational frequency are practically unaltered from that of free CO. We found, however, the dipole moment, 1.0 Debyes, and the 1π-4σ level separation, ∼2.4 eV, are substantially changed due to COCO coupling.

The use of Politzer's relationship in approximate MO LCAO calculations. I

E II approximations in the MO LCAO method, constructed on the basis of Politzer's relationship between the components of the potential energy, are suitable for the approximate calculation of the total energies of molecules. The electron density distributions obtained are unsatisfactory. An attempt to correct the unsatisfactory features of versions I and IA is made in Paper II.

Total energies of molecules with the local density functional approximation and gaussian basis sets

Total energies of small molecules were calculated with a local density functional (LDF) approximation within the LCAO MO SCF scheme. The local spin density functional (LSD) of Gunnarsson and Lundqvist was used. The basis sets used are of contracted gaussian type which allow comparison of LSD with Hartree-Fock (HF) results. The program for calculation of the LSD term was incorporated into the standard ab initio package. The LSD binding energies were in better agreement with experiment than those from HF.

Hellmann–Feynman and virial theorems and the total energy of molecules

Using the Hellmann–Feynman and virial theorems, a simple method has been developed to correct the potential energy curve of molecules obtained by an approximate calculation. The method is applied to the potential energy curves of N2, O2, F2, and CO calculated by the multiple scattering SCF-Xα theory, as an illustration.

On the use of overllapping spheres in the SCF Xα scattered-wave method

The use of overlapping spheres in the SCF Xα scattered-wave method is discussed. It leads to an improved description of both the ionization potentials and total energies of molecules where a substantial fraction of the charge due to the valence electrons is distributed over the interatomic region of constant potential. The effects of using improved exchange parameters for hydrogen-containing molecules are also considered. Results for ethylene, benzene, and carbon monoxide are reported.