NANOPACK: Parallel codes for semiempirical quantum chemical calculations of large systems in the sp‐ and spd‐basis

A parallel implementation of the conventionally used NDDO (MNDO, AM1, PM3, CLUSTER‐Z1) and modified NDDO‐WF (CLUSTER‐Z2) techniques for semiempirical quantum chemical calculations of large molecular systems in the sp‐ and spd‐basis, respectively, is described. The atom‐pair distribution of data over processors forms the basis of the parallelization. The technological aspects of designing scalable parallel calculations on supercomputers (using ScaLAPACK and MPI libraries) are discussed. The scaling of individual algorithms and the entire package was carried out for model systems with 894, 1920, and 2014 atomic orbitals. The package speed‐up provided by different multiprocessor systems involving a cluster of Intel PIII processors, Alpha‐21264‐processor‐built machine MBC‐1000M, and Cray‐T3E is analyzed. The effect of computer characteristics on the package performance is discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

A fast method of large-scale serial semiempirical calculations of docking complexes

A brief survey of the state of the art in methods of calculations of protein—ligand interaction energies in docking complexes is presented. A new computational technique is proposed that allows one to fundamentally improve the performance of large-scale serial calculations of docking complexes using the AM1/PM3 semiempirical methods. The technique explicitly allows for a specific feature of docking problems, viz., the need for calculating numerous ligand complexes with a specified protein whose noninteracting part remains “frozen” during computations. The interaction energies calculated using the new method differ only slightly from the results of complete AM1 calculations and the performance attained is high enough to solve practical drug design problems. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1759–1764, September, 2008.     

Faster gradients for semiempirical methods

A new algorithm for the numerical evaluation of gradients in semiempirical methods is described. The method is approximately twice as fast as the schemes currently employed and produces gradients of comparable accuracy. This method has been tested by comparing the results obtained by the new method with those of the previous numerical scheme, and also with those calculated analytically. The results of using the new gradients in geometry optimizations are also presented. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 629–635, 1999     

Interactive quantum chemistry: a divide-and-conquer ASED-MO method

We present interactive quantum chemistry simulation at the atom superposition and electron delocalization molecular orbital (ASED-MO) level of theory. Our method is based on the divide-and-conquer (D&C) approach, which we show is accurate and efficient for this non-self-consistent semiempirical theory. The method has a linear complexity in the number of atoms, scales well with the number of cores, and has a small prefactor. The time cost is completely controllable, as all steps are performed with direct algorithms, i.e., no iterative schemes are used. We discuss the errors induced by the D&C approach, first empirically on a few examples, and then via a theoretical study of two toy models that can be analytically solved for any number of atoms. Thanks to the precision and speed of the D&C approach, we are able to demonstrate interactive quantum chemistry simulations for systems up to a few hundred atoms on a current multicore desktop computer. When drawing and editing molecular systems, interactive simulations provide immediate, intuitive feedback on chemical structures. As the number of cores on personal computers increases, and larger and larger systems can be dealt with, we believe such interactive simulations-even at lower levels of theory-should thus prove most useful to effectively understand, design and prototype molecules, devices and materials.     

Parallel implementation of semiempirical quantum methods for the Intel platforms

The restructuring of quantum mechanical applications for use on message-passing, distributed memory multicomputers is found to be a challenge. A key computation in these large scale quantum chemistry packages is the determination of eigenvalues and eigenvectors of real sym metric matrices. These computations arise during geometry optimization and vibrational analysis, and typically consume at least half of the total computation time. This work illustrates the parallelization of both tasks within the semiempirical quantum chemistry code, MOPAC, on Intel parallel platforms. The application of this parallel code is demonstrated on novel organic systems.     

Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method

The application of combined quantum mechanical (QM) and molecular mechanical methods to large molecular systems requires an adequate treatment of the boundary between the two approaches. In this article, we extend the generalized hybrid orbital (GHO) method to the semiempirical parameterized model 3 (PM3) Hamiltonian combined with the CHARMM force field. The GHO method makes use of four hybrid orbitals, one of which is included in the QM region in self-consistent field optimization and three are treated as auxiliary orbitals that do not participate in the QM optimization, but they provide an effective electric field for interactions. An important feature of the GHO method is that the semiempirical parameters for the boundary atom are transferable, and these parameters have been developed for a carbon boundary atom consistent with the PM3 model. The combined GHO-PM3/CHARMM model has been tested on molecular geometry and proton affinity for a series of organic compounds.Acknowledgement We thank the National Institutes of Health for support of this research.Contribution to the Jacopo Tomasi Honorary Issue     

Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules

The aqueous solvation free energies of ionized molecules were computed using a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1, MNDO, and PM3 semiempirical molecular orbital methods for the solute molecule and the TIP3P molecular mechanics model for liquid water. The present work is an extension of our model for neutral solutes where we assumed that the total free energy is the sum of components derived from the electrostatic/polarization terms in the Hamiltonian plus an empirical “nonpolar” term. The electrostatic/polarization contributions to the solvation free energies were computed using molecular dynamics (MD) simulation and thermodynamic integration techniques, while the nonpolar contributions were taken from the literature. The contribution to the electrostatic/polarization component of the free energy due to nonbonded interactions outside the cutoff radii used in the MD simulations was approximated by a Born solvation term. The experimental free energies were reproduced satisfactorily using variational parameters from the vdW terms as in the original model, in addition to a parameter from the one-electron integral terms. The new one-electron parameter was required to account for the short-range effects of overlapping atomic charge densities. The radial distribution functions obtained from the MD simulations showed the expected H-bonded structures between the ionized solute molecule and solvent molecules. We also obtained satisfactory results by neglecting both the empirical nonpolar term and the electronic polarization of the solute, i.e., by implementing a nonpolarization model. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1028–1038, 1999     

The implementation of ab initio quantum chemistry calculations on transputers

Summary The RHF and geometry optimization sections of the ab initio quantum chemistry code, GAMESS, have been optimized for a network of parallel microprocessors, Inmos T800-20 transputers, using both indirect and direct SCF techniques. The results indicate great scope for implementation of such codes on small parallel computer systems, very high efficiencies having been achieved, particularly in the cases of direct SCF and geometry optimization with large basis sets.The work, although performed upon one particular parallel system, the Meiko Computing Surface, is applicable to a wide range of parallel systems with both shared and distributed memory.     

主成分分析方法在核酸碱基量子化学计算数据处理中的应用

由于碱基在核酸中的重要性 ,多年来一直有关于碱基的理论计算报道[1～ 7] 。本文将化学计量学中的主成分分析方法[8] 用来分析五种碱基 :腺嘌呤 (Ａ)、鸟嘌呤 (Ｇ)、胞嘧啶 (Ｃ)、尿嘧啶 (Ｕ)和胸腺嘧啶 (Ｔ)计算结果的几何参数 ,以期取得有用的结构信息。1　方法通过ＡＣＤ ＣｈｅｍＳｋｅｔｃｈ 3 .5 [9] 的三维优化 (分子力学方法ＣＨＡＲＭＭ力场 )获得碱基的起始几何结构 ,其原子编号见图 1。所有的计算均采用Ｇａｕｓｓｉａｎ 94程序[10 ] 在ＩＢＭ ＰＣ兼容机上完成。首先 ,对 5种碱基作了 6种半经验方法 (ＡＭ1、ＰＭ3、ＭＮＤＯ、…     

The excited-state chemistry of phycocyanobilin: a semiempirical study.

Based on previous time-resolved absorption studies, phycocyanobilin undergoes a photoreaction from an A- into a B- and C-form, with the latter two photoproducts showing absorption spectra red-shifted from A. To identify the molecular mechanism involved in the excited-state reactions, the structural origin of the red shift in the absorption spectra is investigated. Using semiempirical AM1 calculations that include configuration interaction by pair doubles excitation configuration interaction, the absorption spectra of different conformers as well as different protonation states were calculated. The results clearly indicate a pronounced red shift in the spectra of structures either protonated or deprotonated at the basic/acidic centres of the tetrapyrrole chromophore whereas, in contrast, conformational changes alone result in a blue shift. Furthermore, it is shown by quantum chemical calculations that the basicity of phycocyanobilin is much higher in the excited than in the ground state, with a decrease in the excited-state pK(B)* of approximately 9.5 units. The acidity is only slightly enhanced with a drop in pK(A)* of only approximately 1.6 units. From these findings, a reaction model for the excited-state processes in phycocyanobilin is proposed. According to this model, photoexcitation of phycocyanobilin triggers an excited-state proton transfer giving rise to the formation of a protonated species. In parallel, the local increase in the medium pH associated with protonation then forwards a deprotonation at an acidic NH-group so that in effect both protonated and deprotonated phycocyanobilin would arise from the initial photoreaction and account for the observed red shift in the spectra of the B- and C-forms.     

An optimized initialization algorithm to ensure accuracy in quantum Monte Carlo calculations

Quantum Monte Carlo (QMC) calculations require the generation of random electronic configurations with respect to a desired probability density, usually the square of the magnitude of the wavefunction. In most cases, the Metropolis algorithm is used to generate a sequence of configurations in a Markov chain. This method has an inherent equilibration phase, during which the configurations are not representative of the desired density and must be discarded. If statistics are gathered before the walkers have equilibrated, contamination by nonequilibrated configurations can greatly reduce the accuracy of the results. Because separate Markov chains must be equilibrated for the walkers on each processor, the use of a long equilibration phase has a profoundly detrimental effect on the efficiency of large parallel calculations. The stratified atomic walker initialization (STRAW) shortens the equilibration phase of QMC calculations by generating statistically independent electronic configurations in regions of high probability density. This ensures the accuracy of calculations by avoiding contamination by nonequilibrated configurations. Shortening the length of the equilibration phase also results in significant improvements in the efficiency of parallel calculations, which reduces the total computational run time. For example, using STRAW rather than a standard initialization method in 512 processor calculations reduces the amount of time needed to calculate the energy expectation value of a trial function for a molecule of the energetic material RDX to within 0.01 au by 33%.     

Mixed implicit/explicit solvation models in quantum mechanical calculations of binding enthalpy for protein–ligand complexes

An approach to quantum mechanical investigation of interactions in protein–ligand complexes has been developed that treats the solvation effect in a mixed scheme combining implicit and explicit solvent models. In this approach, the first solvation shell of the solvent around the solute is modeled with a limited number of hydrogen bonded explicit solvent molecules. The influence of the remaining bulk solvent is treated as a surrounding continuum in the conductor‐like screening model (COSMO). The enthalpy term of the binding free energy for the protein–ligand complexes was calculated using the semiempirical PM3 method implemented in the MOPAC package, applied to a trimmed model of the protein–ligand complex constructed with special rules. The dependence of the accuracy of binding enthalpy calculations on size of the trimmed model and number of optimized parameters was evaluated. Testing of the approach was performed for 12 complexes of different ligands with trypsin, thrombin, and ribonuclease with experimentally known binding enthalpies. The root‐mean‐square deviation (RMSD) of the calculated binding enthalpies from experimental data was found as ～1 kcal/mol over a large range. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Parallel internally contracted multireference configuration interaction

A parallel implementation of the internally contracted (IC) multireference configuration (MRCI) module of the MOLPRO quantum chemistry program is described. The global array (GA) toolkit has been used in order to map an existing disk-paging small-memory algorithm onto a massively parallel supercomputer, where disk storage is replaced by the combined memory of all processors. This model has enabled a rather complicated code to be ported to the parallel environment without the need for the wholesale redesign of algorithms and data structures. Examples show that the parallel ICMRCI program can deliver results in a fraction of the time needed for equivalent uncontracted MRCI computations. Further examples demonstrate that ICMRCI computations with up to 10⁷ variational parameters, and equivalent to uncontracted MRCI with 10⁹ configurations, are feasible. The largest calculation demonstrates a parallel efficiency of about 80% on 128 nodes of a Cray T3E-300. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1215–1228, 1998     

A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

A semiempirical quantum mechanical study of cationically catalyzed homopolymerization and copolymerization of vinyl ethers and epoxides

The purpose of this study was to use the semiempirical quantum mechanical computational method, AM1, to investigate vinyl ether cationic homopolymerization, epoxide homopolymerization, and copolymerization of selected vinyl ethers with a model epoxide (cyclohexene oxide). Homopolymerization studies of 19 vinyl ethers showed that activation enthalpies ranged between 0.0 and 15 kcal/mol, and that the enthalpies of reaction for homopolymerization were nearly all exothermic. Homopolymerization of three epoxides predicted low activation enthalpies, some of which were virtually activationless. All ring-opening epoxide polymerizations were exothermic. Copolymerization of three vinyl ethers with cyclohexene oxide gave activation enthalpies that varied between 2.7 and 4.0 kcal/mol, and the enthalpies of reaction for copolymerization were all exothermic.     

Interpretation of photoelectron spectra within the framework of the AM1 semiempirical method. 2. Pyridines

Analysis of the orbital structure of isomeric pyridines carried out using photoelectron spectroscopy and the AM1 (GF) method showed that this structure is independent of the nature of the substituent at C ²⁽⁶⁾ and C ³⁽⁵⁾ : <n<. All the possible sequences of the highest occupied MO of different symmetry (, ) are realized for 4-substituted pyridines.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 872–880, April, 1992.     

Parallel implementation of a divide and conquer semiempirical algorithm

We have implemented a parallel version of the semiempirical divide and conquer program DivCon previously developed in our laboratory. By utilizing a parallel machine we are able to leverage the linear scaling of the divide and conquer algorithm itself to perform semiempirical calculations on large bio-molecules. The utility of the implementation is demonstrated with a partial geometry optimization of hen egg white lysozyme in the gas phase. Received: 5 December 1997 / Accepted: 13 February 1998 / Published online: 17 June 1998