LogP prediction performance with the SMD solvation model and the M06 density functional family for SAMPL6 blind prediction challenge molecules

This work presents a quantum mechanical model for predicting octanol-water partition coefficients of small protein-kinase inhibitor fragments as part of the SAMPL6 LogP Prediction Challenge. The model calculates solvation free energy differences using the M06-2X functional with SMD implicit solvation and the def2-SVP basis set. This model was identified as dqxk4 in the SAMPL6 Challenge and was the third highest performing model in the physical methods category with 0.49 log Root Mean Squared Error (RMSE) for predicting the 11 compounds in SAMPL6 blind prediction set. We also collaboratively investigated the use of empirical models to address model deficiencies for halogenated compounds at minimal additional computational cost. A mixed model consisting of the dqxk4 physical and hdpuj empirical models found improved performance at 0.34 log RMSE on the SAMPL6 dataset. This collaborative mixed model approach shows how empirical models can be leveraged to expediently improve performance in chemical spaces that are difficult for ab initio methods to simulate.     

Study of the formamide–methanol dimer with ab initio and density functional theory methods

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Assessment of the pairwise additive approximation and evaluation of many-body terms for water clusters

We have tested the ability of four commonly used density functionals (three of which are semilocal and one of which is nonlocal) to outperform accurate pairwise additive approximations in the prediction of binding energies for a series of water clusters ranging in size from dimer to pentamer. Comparison to results obtained with the Weizmann-1 (W1) level of wave function theory shows that while all density functionals are capable of outperforming the accurate pairwise data, the choice of basis set used is crucial to the performance of the method, and if a poor choice of basis set is made the errors obtained with density functional theory (DFT) can be larger than those obtained with the simple pairwise approximation. We have also compared the binding energies and many-body terms determined with DFT to those obtained with W1, and have found that all semilocal functionals have significant errors in the many-body components of the full interactions energy. Despite this limitation, however, we have found that, of the four functionals tested, PBE1W/MG3S is the most accurate for predicting the binding energies of the clusters.     

On the structure and spin states of Fe(III)-EDDHA complexes

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.     

A new database and benchmark of the bond energies of noble-gas-containing molecules

We have developed a new database of structures and bond energies of 59 noble-gas-containing molecules. The structures were calculated by CCSD(T)/aug-cc-pVTZ methods and the bond energies were obtained using the CCSD(T)/complete basis set method. Many wavefunction-based and density functional theory methods have been benchmarked against the 59 accurate bond energies. Our results show that the MPW1B95, B2GP-PLYP, and DSD-BLYP functionals with the aug-cc-pVTZ basis set excel in predicting the bond energies of noble-gas molecules with mean unsigned errors (MUEs) of 2.0 to 2.1 kcal/mol. When combinations of Dunning's basis sets are used, the MPW1B95, B2GP-PLYP, DSD-BLYP, and BMK functionals give significantly lower MUEs of 1.6 to 1.9 kcal/mol. Doubly hybrid methods using B2GP-PLYP and DSD-BLYP functionals and MP2 calculation also provide satisfactory accuracy with MUEs of 1.4 to 1.5 kcal/mol. If the Ng bond energies and the total atomization energies of a group of 109 main-group molecules are considered at the same time, the MPW1B95/aug-cc-pVTZ single-level method (MUE = 2.7 kcal/mol) and the B2GP-PLYP and DSD-PLYP functionals with combinations of basis sets or using the doubly hybrid method (MUEs = 1.9-2.2 kcal/mol) give the overall best result.     

Quantum DFT and DF–DFT study of vibrational spectra of sulfuric acid,sulfuric acid monohydrate,formic acid and its cyclic dimer

Rigorous theoretical treatment of vibrational frequencies is critically important for the interpretation of unassigned experimental vibrational spectra and accurate determination of thermodynamic properties of molecular clusters. IR spectra of trans monomers of sulfuric and acetic acids, sulfuric acid monohydrate and cyclic dimer of the formic acid have been studied using DFT and DF–DFT methods using BLYP, B3LYP and PW91 with 12 different Pople and Dunning basis sets. New data for above-mentioned structures have been reported, scaling factors have been calculated and a comprehensive analysis of the performance of BLYP, B3LYP and PW91 methods has been performed. Comparison of the obtained results with experiments shows that results of pure PW91 and BLYP are better than predictions of well-established hybrid B3LYP method. Our analysis shows on the existence of the considerable difference in scaling factors weighted to high and low frequencies. In the case of formic acid dimer, the deviation the predicted low frequencies from the experimental data is considerable that leads to quite large (∼6–7 kcal mol⁻¹) uncertainties in the absolute values of the cluster Gibbs free energy. In order to determine an efficient computational strategy that comprises accuracy and reasonable computational costs, the effect of density fitting (DF) and basis set superposition error (BSSE) on the vibration frequencies has been investigated. We found that application of the DF that substantially (2.5–3.5 times) increases the performance of pure PW91 and BLYP methods gives excellent results, which are very close to those of conventional DFT. This suggests that DF–DFT is a viable low-cost alternative to conventional DFT in predicting vibrational spectra. It has been found that while vibrational spectra obtained using the counterpoise correction (CP) for the BSSE do not deviate much from uncorrected ones, the difference in absorption intensities between corrected and uncorrected spectra obtained using small and medium-sized basis sets is considerable. This suggests that application of DF–DFT uncorrected for the BSSE with large basis sets is a more efficient strategy of predicting vibrational spectra than the application of conventional DFT with small basis sets.     

All electron fully relativistic Dirac–Fock calculation for darmstadtium carbide using prolapse free basis set

For the first time, ab inito all electron fully relativistic and correlated Dirac–Fock calculations with prolapse free basis set are reported for a Super Heavy Element. We investigated the relativistic effects on bonding and on some spectroscopic constants for the darmstadtium carbide and our results at DF/CCSD(T) with a prolapse free basis set suggest for R_e, ω_e and D_e the values of 174 pm, 1114 cm⁻¹ and 7.29 eV, respectively. These values are very similar to the values for PtC found on literature. It was also found that prolapse free basis set may be important to estimate the dissociation energy using Relativistic 4-components correlated methods.     

Path integral ground state study of finite-size systems: application to small (parahydrogen)N (N=2-20) clusters

We use the path integral ground state method to study the energetic and structural properties of small para-H2 clusters of sizes ranging from 2 to 20 molecules. A fourth order formula is used to approximate the short imaginary-time propagator and two interaction potentials are considered. Our results are compared to those of exact basis set calculations and other quantum Monte Carlo methods when available. We find that for all cluster sizes considered, our results show a lower ground state energy than literature values obtained by diffusion Monte Carlo and variational Monte Carlo. For the dimer and trimer, ground state energies are in good agreement with exact results obtained using the discrete variable representation. Structural properties are found to be insensitive to the choice of interaction potential. We explore the use of Pekeris coordinates to analyze the importance of linear arrangement in trimers and for trimers within clusters of larger size.     

A unified approach to kinetic processing of nonisothermal data

Basic problems of kinetic processing of nonisothermal data ascertained from thermal analysis measurements can be solved by isoconversional methods. Analysis of the dependence of the activation energy on conversion often permits the identification of the kinetic scheme for the process. This dependence may also be used to solve applied kinetic problems related to predicting the behavior of a substance outside the range of experimental temperatures. Methods for using this dependence for evaluating both the preexponential factor and the reaction model, as well as for detecting isokinetic relationships, have been discussed. Because all of these operations have a common origin in computing the dependence of the activation energy on conversion, isoconversional methods may be considered as a basis of a unified approach to kinetic processing of nonisothermal data. © 1996 John Wiley & Sons, Inc.     

Ab initio structural and vibrational investigation of sulfuric acid monohydrate

We employ ab initio methods to find stable geometries and to calculate potential energy surfaces and vibrational wavenumbers for sulfuric acid monohydrate. Geometry optimizations are carried out with the explicitly correlated coupled-cluster approach that includes single, double, and perturbative triple excitations (CCSD(T)-F12a) with a valence double-ζ basis set (VDZ-F12). Four different stable geometries are found, and the two lowest are within 0.41 kJ mol(-1) (or 34 cm(-1)) of each other. Vibrational harmonic wavenumbers are calculated at both the density-fitted local spin component scaled second-order M?ller-Plesset perturbation theory (DF-SCS-LMP2) with the aug-cc-pV(T+d)Z basis set and the CCSD-F12/VDZ-F12 level. Water O-H stretching vibrations and two highly anharmonic large-amplitude motions connecting the three lowest potential energy minima are considered by limiting the dimensionality of the corresponding potential energy surfaces to small two- or three-dimensional subspaces that contain only strongly coupled vibrational degrees of freedom. In these anharmonic domains, the vibrational problem is solved variationally using potential energy surfaces calculated at the CCSD(T)-F12a/VDZ-F12 level.     

Basis Sets Dependency in Constructing Spectroscopy-Accuracy Ab Initio Global Electric Dipole Moment Functions

Recently, more attention have been paid on the construction of dipole moment functions (DMF) using theoretical methods. However, the computational methods to construct DMFs are not validated as much as those for potential energy surfaces do. In this letter, using Ar...He as an example, we tested how spectroscopyaccuracy DMFs can be constructed using ab initio methods. We especially focused on the basis set dependency in this scenario, i.e., the convergence of DMF with the sizes of basis sets, basis set superposition error, and mid-bond functions. We also tested the explicitly correlated method, which converges with smaller basis sets than the conventional methods do. This work can serve as a pictorial sample of all these computational technologies behaving in the context of constructing DMFs.     

A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

Computational methods for predicting protein-ligand binding free energy continue to be popular as a potential cost-cutting method in the drug discovery process. However, accurate predictions are often difficult to make as estimates must be made for certain electronic and entropic terms in conventional force field based scoring functions. Mixed quantum mechanics/molecular mechanics (QM/MM) methods allow electronic effects for a small region of the protein to be calculated, treating the remaining atoms as a fixed charge background for the active site. Such a semi-empirical QM/MM scoring function has been implemented in AMBER using DivCon and tested on a set of 23 metalloprotein-ligand complexes, where QM/MM methods provide a particular advantage in the modeling of the metal ion. The binding affinity of this set of proteins can be calculated with an R(2) of 0.64 and a standard deviation of 1.88 kcal/mol without fitting and 0.71 and a standard deviation of 1.69 kcal/mol with fitted weighting of the individual scoring terms. In this study we explore using various methods to calculate terms in the binding free energy equation, including entropy estimates and minimization standards. From these studies we found that using the rotational bond estimate to ligand entropy results in a reasonable R(2) of 0.63 without fitting. We also found that using the ESCF energy of the proteins without minimization resulted in an R(2) of 0.57, when using the rotatable bond entropy estimate.     

O?O bond homolysis in hydrogen peroxide

O O bond homolysis in hydrogen peroxide (H₂O₂) has been studied using theoretical methods of four conceptually different types: hybrid DFT (B3LYP, M06‐2X), double‐hybrid DFT (B2‐PLYP), coupled‐cluster (CCSD(T)), and multiconfigurational (CASPT2). In addition, the effects of basis set size have also been analyzed. For all of these methods, the O O bond homolysis in hydrogen peroxide has been found to proceed through hydrogen bonded radical pair complexes. Reaction barriers for collapse of the radical pairs to hydrogen peroxide are minute, leading to an overall very flat potential energy surface. However, hydrogen bonding energies in the radical pair complex expressed as the energy difference to two separate hydroxyl radicals are sizeable and exceed 10 kJ/mol for all theoretical methods considered in this study. © 2017 Wiley Periodicals, Inc.     

Benchmark studies on the building blocks of DNA. 1. Superiority of coupled cluster methods in describing the excited states of nucleobases in the Franck-Condon region

Equation of motion excitation energy coupled-cluster (EOMEE-CC) methods including perturbative triple excitations have been used to set benchmark results for the excitation energy and oscillator strength of the building units of DNA, i.e., cytosine, guanine, adenine and thymine. In all cases the lowest twelve transitions have been considered including valence and Rydberg ones. Triple-ζ basis sets with diffuse functions have been used and the results are compared to CC2, CASPT2, TDDFT, and DFT/MRCI results from the literature. The results clearly show that it is only the EOMEE-CCSD(T) that is capable of providing accuracy of about 0.1 eV. EOMEE-CCSD systematically overshoots the energy of all types of transitions by 0.1-0.3 eV, whereas CC2 is surprisingly accurate for ππ* transitions but fails (often badly) for nπ* and Rydberg transitions. DFT and CASPT2 seem to give reliable results for the lowest transition, but the error increases fast with the excitation level. The differences in the excitation energies often change the energy ordering of the states, which should even influence the conclusions of excited state dynamics obtained with these approximate methods. The results call for further benchmark calculations on larger building blocks of DNA (nucleosides, basis pairs) at the CCSD(T) level.     

Geometry of density matrices. VI. Superoperators and unitary invariance

We examine and compare ways of dividing into subspaces the space whose elements are density matrices or other operators for the class of model problems defined by a finite one-particle basis set. One method of decomposition makes the significance of the subspaces apparent. We show that this decomposition is also complete, in the group-theoretic sense, for the group of unitary transformations of the set of one-electron basis functions. The irreducible subspaces are labeled by particle number and by an additional integer we call the reduction index. For spaces of particle-number-conserving operators, all subspaces with the same reduction index are isomorphic, and an analogous isomorphism exists for non-particle-number-conserving cases. The general linear group also plays a key role, and we introduce the term “canonical superoperators” to characterize those superoperators which commute with this group. When an appropriate basis set is chosen for the matrix spaces, the supermatrices corresponding to these superoperators have a particularly simple form: a block structure with the only nonzero blocks being multiples of unit matrices. The superoperators of interest can be constructed in terms of two operators, , and these two have been expressed simply in terms of creation and annihilation operators. When only real orthogonal transformations of the basis are considered, a further decomposition is possible. We have introduced superoperators associated with this decomposition.     

Static dipole polarizability and binding energy of sodium clusters Nan (n=1-10): A critical assessment of all-electron based post Hartree-Fock and density functional methods

A systematic all electron post Hartree-Fock as well as density functional theory (DFT) based calculations for the polarizability and binding energy of sodium metal clusters have been performed and an in-depth analysis of the discrepancy between the experimental and theoretical results is presented. A systematic investigation for the assessment of different DFT exchange-correlation functionals in predicting the polarizability values has also been reported. All the pure DFT functionals have been found to considerably underestimate the calculated polarizability values as compared to the MP2 results. DFT calculations using the full Hartree-Fock exchange along with one-parameter progressive correlation functional have, however, been shown to yield results in good agreement with the MP2 and experimental results. The possible sources of error present in the experimental measurements as well as in the different theoretical methods have also been analyzed. One of the most important conclusions of the present study is that the effect of electron correlation plays a significant role in determining the polarizability of the clusters and the MP2 method can be considered to be one of the most reliable methods for their prediction. It has also been noted that the polarizability value of the lower member clusters (Na2 and Na4) calculated by highly sophisticated methods such as, CCSD and CCSD(T) are found to be very close to the corresponding MP2 values. The polarizability and the binding energy of the clusters are found to be inversely related to each other and their correlation is rationalized by invoking the minimum polarizability principle. A good linear correlation between the polarizability and volume of the cluster has also been found to exist.     

Second row molecular orbital calculations: III. Semi-empirical calculations of geometries

The ability of four semi-empirical methods to predict geometries of molecules containing atoms in the second row of the periodic table is investigated for about 80 molecules. Non-empirical, minimal basis set calculations, with and without optimization of valence orbital exponents, are carried out for a number of diatomic molecules. While none of the methods are capable of predicting geometries with an accuracy comparable to the first row parametrization, the SPD' method of Santry and the related INDO method of Benson and Hudson appear to be the most consistent. The ab initio calculations do not suffer from the drawbacks exhibited by the latter two semi-empirical methods. From this it is concluded that the failure of such methods lies in the parametrization rather than in the use of a minimal basis set.     

Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately?

The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.     

Relevance of backbiting and beta-scission reactions in the free radical polymerization of Acrylonitrile

Summary: In this work, backbiting and beta-scission reactions are investigated through Quantum Chemistry methods by adopting the Becke 3 parameters and Lee Yang Parr functional (B3LYP) and 6-31G(d,p) basis set. Namely, the 1:3, 1:5 and 1:7 backbiting reactions are studied for acrylonitrile polymerization. It was found that the backbiting 1:5 is the most favorited because this kinetic event leads to the formation of a 6 membered transition state, while the backbiting 1:3 requires high activation energy due to the formation of a highly strained 4 membered ring. 7:3 backbiting reaction was also examined, since it is an alternative pathway that can explain the formation of defects generated by radicals in the third position. Simulations showed that this kinetic step is characterized by high rate constant because of its low activation energy. The right and left beta-scission reactions from the mid chain radicals formed by the considered backbiting reactions are also studied. Computational analysis demonstrated that all beta-scission reactions are endothermic and both the right and left beta-scission reactions have the same activation energy, which seems to be more influenced by the position of the mid chain radical.     

C4H10分子的价电子的结构研究

We report here the measurements of valence electron structure for the n-butane (C4H10) using high resolution (ΔE=0.9 eV FWHM, ΔP=0.1 a.u.) (e,2e) spectrometer. The impact energy was 1200eV plus binding energy (i.e. 1206 to 1232 eV) and symmetric non-coplanar kinematics was employed. The inner-and outer-valence energy spectrum is in agreement with published Photoelectron data. The experimental momentum profiles have been compared with calculations obtained using Hartree-Fock method with the minimum basis set and a high-level basis set, and also using density functional theory (DFT) density methods with a high level basis set. The agreement between theory and experiment for shape of orbital electron momentum distributions is generally good.