Generic implementation of semi-analytical CI gradients for NDDO-type methods

Generic semi-analytical energy gradients are derived and implemented for NDDO-type methods, by using numerical integral and Fock matrix derivatives in the context of an otherwise analytical approach for configuration interaction (CI) and other non-variational treatments. The correctness, numerical precision, and performance of this hybrid approach are established through comparisons with fully numerical and fully analytical calculations. The semi-analytical evaluation of the CI gradient is generally much faster than the fully numerical computation, but somewhat slower than a fully analytical calculation, which however shows the same scaling behavior. It is the method of choice whenever a fully analytical CI gradient is not available due to the lack of analytical integral derivatives. The implementation is generic in the sense that it can easily be extended to any new NDDO-type Hamiltonian. The present development of a semi-analytical CI gradient will facilitate studies of electronically excited states with recently proposed NDDO methods that include orthogonalization corrections. Dedicated to Professor Karl Jug on the occasion of his 65th birthday     

Tunable delocalization of unpaired electrons of nitroxide radicals for sickle-cell disease drug improvements

Hydroxyurea is a drug recently approved to treat sickle cell diseases. Hydroxyurea benefits the patients by increasing the level of fetal hemoglobin via a nitroxide radical pathway. Here, we report an unpaired-electron-delocalization approach to tune the stability of nitroxide radicals. In this approach, the substitution by an unsaturated alkyl group containing conjugated C=C double bonds for the hydrogen on the nitrogen atom attached to the hydroxyl of hydroxyurea can significantly increase its ability to generate nitroxide radical. Furthermore, the increase can be remarkably enhanced by increasing the number of conjugated C=C double bonds. For a hydroxyurea derivative that contains two conjugated C=C double bonds, the reaction rate to generate its radical is 118 times faster than that of hydroxyurea, and for a hydroxyurea derivative containing 20 conjugated C=C double bonds, the reaction rate to form its radical is 238 times faster than that of hydroxyurea. For this reason, hydroxyurea derivatives with conjugated C=C double bonds may constitute new potential drugs for the treatment of sickle-cell diseases.     

Efficient approach for the detection and identification of new androgenic metabolites by applying SRM GC‐CI‐MS/MS: a methandienone case study

Identification of anabolic androgenic steroids (AAS) is a vital issue in doping control and toxicology, and searching for metabolites with longer detection times remains an important task. Recently, a gas chromatography chemical ionization triple quadrupole mass spectrometry (GC‐CI‐MS/MS) method was introduced, and CI, in comparison with electron ionization (EI), proved to be capable of increasing the sensitivity significantly. In addition, correlations between AAS structure and fragmentation behavior could be revealed. This enables the search for previously unknown but expected metabolites by selection of their predicted transitions. The combination of both factors allows the setup of an efficient approach to search for new metabolites. The approach uses selected reaction monitoring which is inherently more sensitive than full scan or precursor ion scan. Additionally, structural information obtained from the structure specific CI fragmentation pattern facilitates metabolite identification. The procedure was demonstrated by a methandienone case study. Its metabolites have been studied extensively in the past, and this allowed an adequate evaluation of the efficiency of the approach. Thirty three metabolites were detected, including all relevant previously discovered metabolites. In our study, the previously reported long‐term metabolite (18‐nor‐17β‐hydroxymethyl,17α‐methyl‐androst‐1,4,13‐trien‐3‐one) could be detected up to 26 days by using GC‐CI‐MS/MS. The study proves the validity of the approach to search for metabolites of new synthetic AAS and new long‐term metabolites of less studied AAS and illustrates the increase in sensitivity by using CI. Copyright © 2016 John Wiley & Sons, Ltd.     

Single-ensemble nonequilibrium path-sampling estimates of free energy differences

We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional "toy" test system, the new (minimally optimized) method performs roughly one hundred times faster than either optimized "traditional" Jarzynski calculations or conventional thermodynamic integration. The simplicity of the underlying formalism suggests the approach will find broad applicability in molecular systems.     

An Efficient Algorithm for Calculating the Heat Capacity of a Large‐Scale Molecular System

We present an efficient algorithm for computing the heat capacity of a large‐scale molecular system. The new algorithm is based on a special Gaussian quadrature whose abscissas and weights are obtained by a simple Lanczos iteration. Our numerical results have indicated that this new computational scheme is quite accurate. We have also shown that this method is at least a hundred times faster than the earlier approach that is based on estimating the density of states and integrating with a simple quadrature formula.     

Unitary group approach to the many-electron problem. I. Matrix element evaluation and shift operators

This is the first paper in a series of three directed toward the evaluation of spin-dependent Hamiltonians directly in the spin-orbit basis. In this paper we present a new and complete derivation of the matrix elements of the U(n) generators in the electronic Gel'fand basis. The approach employed differs from previous treatments in that the matrix elements of nonelementary generators are obtained directly. A general matrix element formula is derived which explicitly demonstrates the segment level formalism obtained previously by Shavitt using different methods. A simple relationship between the matrix elements of raising and lowering generators is determined which indicates that in CI calculations, only the matrix elements of raising generators need be calculated. Some results on the matrix elements of products of two generators are also presented.     

An improvement of Davidson's iteration method: Applications to MRCI and MRCEPA calculations

Davidson's method is widely used for finding the lowest eigenvalues of large matrices. Recently, mathematicians have shown that Davidson's derivation could be improved. They have corrected the derivation yielding a new iteration method. In this article this new method is adapted for realistic MRCI and MRCEPA calculations. Results show that the new method converges significantly faster in H₂O and O₂ with moderately elongated bonds than Davidson's original method. The new method offers new insights into the rate of convergence of Davidson's original method. © 1996 by John Wiley & Sons, Inc.     

MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives

An algorithm for the rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas of internal atoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET-enkephalin using MSEED to compute the solvent-accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent-accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 potential only.     

Generalized-molecular-orbital theory: Simple multiconfiguration self-consistent-field method

Even after completing a multiconfiguration self-consistent-field (MCSCF ) calculation, one must often include additional configuration interaction (CI ) to obtain quantitative or semiquantitative results. There is some question of whether the prior MCSCF calculation is worthwhile, if additional CI is needed later. We have developed a new MCSCF computational method, which, because of our assumptions about the nature of the configurations, yields one Fock-like operator for all the “filled” orbitals (high occupation numbers) and a second Fock-like operator for all the “virtual” orbitals (low occupation numbers). Since there are only two matrices to build, our method is considerably faster than other MCSCF approaches. Because of these similarities to standard molecular-orbital (MO ) calculations, we have termed our approach generalized-molecular-orbital (GMO ) theory. However, the “virtual” orbitals, unlike those of standard MO theory, are optimized to correlate the “filled” ones and can he used in a subsequent CI calculation. Results are presented for the correlation energy of H₂O, the spectroscopic constants of N₂, the singlet–triplet energy separations in CH₂, and the nature of the chromium–chromium quadruple bond. Although these results are at a very low level of CI , the GMO approach appears to correct for the gross deficiencies of the single-determinant SCF procedure.     

Least-squares numerical Rayleigh-Ritz and minimum-variance methods for molecular calculations

A general method is presented to find in a least-squares sense a set of orthogonal eigenfunctions and their eigenvalues from local energy and numerical integration methods or by any other dissymmetric approach to solve the eigenvalue problem of a Hermitian operator. By this method a generalization of the minimum variance method to more than one eigenfunction is obtained, which is a variant of Scott's method. Also a new method is derived—called the minimum-overlap method—that is a least-squares numerical version of the standard Rayleigh-Ritz method. Test calculations on the atoms Be and Tm and the molecules H₂ and CO have been performed with both numerical Hartree-Fock and Hartree-Fock-Slater methods. The least-squares solutions are an improvement over other methods in the case of accurate basis sets. Numerical Hartree-Fock calculations of moderate accuracy are found to be considerably faster than the analytic method.     

New faster CHARMM molecular dynamics engine

We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. © 2013 Wiley Periodicals, Inc.     

Degradation of chlorinated polyethylene. I. Effect of antimony oxide on the rate of dehydrochlorination

The degradation of two chlorinated polyethylene compounds CPE 25 (45% chlorine) and CPE 16 (36% chlorine) was studied by following their rates of dehydrochlorination at two temperatures, 150°C and 180°C in pure nitrogen and pure oxygen atmospheres. Studies on the powdered polymers showed that the dehydrochlorination rate of CPE 25 is about fourteen times faster than that of CPE 16 in nitrogen atmospheres and only three to four times faster in oxygen. The molded polymers gave a lower rate of dehydrochlorination than when in the powdered form. This effect is attributed to diffusion factors. The antimony oxide brought about an induction period in the dehydrochlorination reaction during which only a small amount of HCl is evolved, followed by a very fast rate of dehydrochlorination both in oxygen and nitrogen atmospheres. The duration of the induction period increases with increase in the Sb₂O₃ concentration, but is followed by an accelerated HCl loss which is faster when Sb₂O₃ concentration is higher. This work provides supporting evidence that SbCl₃ was formed and lost during degradation. Mechanisms of dehydrochlorination are suggested for the reaction in the case of pure chlorinated polyethylene and for the polymer containing antimony oxide.     

Nitrogen-15 nuclear magnetic resonance spectroscopy. N?H proton exchange reactions of urea and substituted ureas

Proton-coupled nitrogen-15 NMR spectra of urea, N-methylurea, N,-N′-dimethylurea, N-methyl-N′-benzylurea and N-phenylurea have been obtained at natural abundance level in neutral, basic and acidic solutions at 25°C. Base-catalyzed N? H proton exchange of the ? NH₂ group of N-methylurea in water was found to be 1.5 times faster than that for the -NH- group, while the corresponding acid-catalyzed exchange is 7.5 times faster. Comparison of urea and N,-N′-dimethylurea in water shows urea to be 10 times faster in base but 2 times slower in acid. The ratio of the base-catalyzed N? H proton exchanges of the two -NH- groups of N-methyl-N′-benzylurea in dimethyl sulfoxide is close to unity, whereas the CH₃NH- group exchanges 4 times faster in acid. Similarly, the C₆H₅NH- group of N-methyl-N′-phenylurea exchanges 50 times faster than the CH₃NH- group in base and about 3 orders of magnitude slower in acid. The results are rationalized by consideration of steric and electronic effects.     

4,5'-dimethylangelicin: a new DNA-photobinding monofunctional agent.

Abstract— 4,5′-Dimethylangelicin is a new angular furocoumarin showing interesting photochemical and photosensitizing properties. In the dark it forms a complex with native DNA having higher values of the binding parameters than angelicin; by irradiation at 365 nm it is able to photobind with DNA several times faster than angelicin and in about the same degree as psoralen, without forming crosslinkages. It therefore behaves as a pure monofunctional reagent. The same high photobinding capacity with DNA is shown also in vivo in Ehrlich ascites tumor cells and bacterial E. coli cells. 4,5′-Dimethylangelicin is very active in inhibiting the DNA and RNA syntheses in Ehrlich ascites tumor cells alter irradiation at 365 nm, much more so than angelicin and in the same degree as psoralen. It is also more active than angelicin in decreasing the tumor transmitting capacity of the same cells and the colony-forming ability of E. coli cells, although to a lesser degree than psoralen. It is ineffective in producing erythema on guinea-pig skin. The involvement of repair processes of DNA in these photosensitized effects is discussed.     

CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration

A highly efficient conformer search algorithm based on a divide-and-conquer and recursive conformer build-up approach is presented in this paper. This approach is combined with consideration of local rotational symmetry so that conformer duplicates due to topological symmetry in the systematic search can be efficiently eliminated. This new algorithm, termed CAESAR (Conformer Algorithm based on Energy Screening and Recursive Buildup), has been implemented in Discovery Studio 1.7 as part of the Catalyst Component Collection. CAESAR has been validated by comparing the conformer models generated by the new method and Catalyst/FAST. CAESAR is consistently 5-20 times faster than Catalyst/FAST for all data sets investigated. The speedup is even more dramatic for molecules with high topological symmetry or for molecules that require a large number of conformers to be sampled. The quality of the conformer models generated by CAESAR has been validated by assessing the ability to reproduce the receptor-bound X-ray conformation of ligands extracted for the Protein Data Bank (PDB) and assessing the ability to adequately cover the pharmacophore space. It is shown that CAESAR is able to reproduce the receptor-bound conformation slightly better than the Catalyst/FAST method for a data set of 918 ligands retrieved from the PDB. In addition, it is shown that CEASAR covers the pharmacophore space as well or better than Catalyst/FAST.     

Mass spectrometry/gas chromatography-mass spectrometry approach for rapid screening/quantitative determination of perchloroethylene in air

A new mass spectrometry/gas chromatography-mass spectrometry (MS/GC-MS) approach has been developed for the screening and quantitative determination of perchloroethylene (PERC) in workplace and outdoor air samples, which could be extended to the screening and analysis of other analytes and samples. This approach may be rapidly modified in order to be used directly as an MS detector for screening purposes or alternatively as a common GC-MS, for confirmation. The screening alternative by MS is approximately 20 times faster than the quantitative-confirmatory determination by GC-MS. Detection limits of both alternatives are sufficiently low to screen and determine PERC in the above-mentioned matrixes. The advantage of this approach over others previously described is that, in the present case, the sample passes through the chromatographic column only when the confirmatory GC-MS is used. For the MS screening method, the chromatographic column is bypassed by using an appropriate selection valve. In this way, the column lifetime is extended and screening time is considerably shortened.     

Distance algorithm based procedure for non‐negative least squares

In chemistry and many other scientific disciplines, non‐negativity‐constrained estimation of models is of practical importance. The time required for estimating true least squares non‐negativity‐constrained models is typically many times longer than that for estimating unconstrained models. That is why it is necessary to find faster and faster non‐negative least squares (NNLS) algorithms. Very recently, the distance algorithm has been developed, and this algorithm can be adapted to solve NNLS regression task faster (in some cases) than the conventional algorithms. Based on some simulated investigation, DA_NNLS was the fastest for small‐sized and medium‐sized linear regression tasks. The visualization (geometry) of the NNLS task being solved by our new algorithm is discussed as well. Besides linear algebra, convex geometrical concepts and tools are suggested to investigate, to use, and to develop in chemometrics for exploiting the geometry of chemometry. Copyright © 2014 John Wiley & Sons, Ltd.     

Efficient transport of saccharides through a liquid membrane mediated by a cyclodextrin dimer

A new efficient system for transporting saccharides through a liquid membrane has been constructed. The transport rates of saccharides were accelerated greatly by the cyclodextrin dimer 2; by contrast, the corresponding cyclodextrin monomer 1 was not effective at mediating saccharide transport. The transport rate of D-ribose through a chloroform liquid membrane was 17 times faster when the cyclodextrin dimer 2 was used as the transporter than when the cyclodextrin monomer 1 was used. Similarly the transport rate of methyl D-galactopyranoside was 16 times faster by 2 than by 1.     

A multireference configuration interaction method based on the separated electron pair wave functions

A multireference configurational interaction method based on the separated electron pair (SEP) wave functions, SEP‐CI approach, has been developed as an approximation to the traditional CASSCF method. It differs from the CASSCF method in that active orbitals are obtained from the SEP wave function without further optimization in the subsequent CI calculations, and the active space is automatically constructed according to the occupation coefficients of SEP natural orbitals. These features make the present SEP‐CI method computationally much less demanding than the CASSCF method. The applicability of the SEP‐CI method is illustrated with sample calculations on the insertion reaction of BeH₂ and dissociation energies of LiH, BH, FH, H₂O, and N₂. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 39–47, 2006