A Carbon Is a Carbon Is a Carbon: Orbital-Free Simulations of Hydrocarbon Chemistry without Resort to Atom Types.

Semiclassical electrons (aka Lewis dots) have been a mainstay of chemists' thinking about molecular structure, polarizability, and reactivity for over a century. This utility has motivated the development of a corresponding quantitative description. Here we devise pairwise potentials that describe the behavior of valence electron pairs in hydrocarbons, including those in single, double, bridge, and bent bonds of linear, branched, and cyclic compounds, including anionic and cationic states. Beyond predicting structures and energies, the new subatomistic force field, dubbed LEWIS-B, efficiently simulates carbocation addition to a double bond and cation migration to a neighboring carbon. A crucial feature of the semiclassical electrons is variable spread, a fourth degree of freedom in addition to three Cartesian coordinates. In spontaneously adapting to different environments, the spread provides a signature of electron stability, with more contracted clouds where the electron interactions are favorable and expanded clouds where electrons are less tightly held. In addition, the pair potentials provide insight into the subtle trade-offs that govern isomerizations and reactions.

Natural variation and CRISPR/Cas9-mediated mutation in GmPRR37 affect photoperiodic flowering and contribute to regional adaptation of soybean.

Flowering time is a critical determinant of the geographic distribution and regional adaptability of soybean (Glycine max) and is strongly regulated by photoperiod and temperature. In this study, quantitative trait locus (QTL) mapping and subsequent candidate gene analysis revealed that GmPRR37, encoding a pseudo-response regulator protein, is responsible for the major QTL qFT12-2, which was identified from a population of 308 recombinant inbred lines (RILs) derived from a cross between a very late-flowering soybean cultivar, 'Zigongdongdou (ZGDD)', and an extremely early-flowering cultivar, 'Heihe27 (HH27)', in multiple environments. Comparative analysis of parental sequencing data confirmed that HH27 contains a non-sense mutation that causes the loss of the CCT domain in the GmPRR37 protein. CRISPR/Cas9-induced Gmprr37-ZGDD mutants in soybean exhibited early flowering under natural long-day (NLD) conditions. Overexpression of GmPRR37 significantly delayed the flowering of transgenic soybean plants compared with wild-type under long photoperiod conditions. In addition, both the knockout and overexpression of GmPRR37 in soybean showed no significant phenotypic alterations in flowering time under short-day (SD) conditions. Furthermore, GmPRR37 down-regulated the expression of the flowering-promoting FT homologues GmFT2a and GmFT5a, and up-regulated flowering-inhibiting FT homologue GmFT1a expression under long-day (LD) conditions. We analysed haplotypes of GmPRR37 among 180 cultivars collected across China and found natural Gmprr37 mutants flower earlier and enable soybean to be cultivated at higher latitudes. This study demonstrates that GmPRR37 controls soybean photoperiodic flowering and provides opportunities to breed optimized cultivars with adaptation to specific regions and farming systems.

The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water.

The development of effective centroid potentials (ECPs) is explored with both the constrained-centroid and quasi-adiabatic force matching using liquid water as a test system. A trajectory integrated with the ECP is free of statistical noises that would be introduced when the centroid potential is approximated on the fly with a finite number of beads. With the reduced cost of ECP, challenging experimental properties can be studied in the spirit of centroid molecular dynamics. The experimental number density of H2O is 0.38% higher than that of D2O. With the ECP, the H2O number density is predicted to be 0.42% higher, when the dispersion term is not refit. After correction of finite size effects, the diffusion constant of H2O is found to be 21% higher than that of D2O, which is in good agreement with the 29.9% higher diffusivity for H2O observed experimentally. Although the ECP is also able to capture the redshifts of both the OH and OD stretching modes in liquid water, there are a number of properties that a classical simulation with the ECP will not be able to recover. For example, the heat capacities of H2O and D2O are predicted to be almost identical and higher than the experimental values. Such a failure is simply a result of not properly treating quantized vibrational energy levels when the trajectory is propagated with classical mechanics. Several limitations of the ECP based approach without bead population reconstruction are discussed.

Water graphene contact surface investigated by pairwise potentials from force-matching PAW-PBE with dispersion correction.

A pairwise additive atomistic potential was developed for modeling liquid water on graphene. The graphene-water interaction terms were fit to map the PAW-PBE-D3 potential energy surface using the adaptive force matching method. Through condensed phase force matching, the potential developed implicitly considers the many-body effects of water. With this potential, the graphene-water contact angle was determined to be 86° in good agreement with a recent experimental measurement of 85° ± 5° on fully suspended graphene. Furthermore, the PAW-PBE-D3 based model was used to study contact line hysteresis. It was found that the advancing and receding contact angles of water do agree on pristine graphene, however a long simulation time was required to reach the equilibrium contact angle. For water on suspended graphene, sharp peaks in the water density profile disappear when the flexibility of graphene was explicitly considered. The water droplet induces graphene to wrap around it leading to a slightly concave contact interface.

The effects of replacing the water model while decoupling water-water and water-solute interactions on computed properties of simple salts.

The effects of decoupling the water-water and water-solute interactions are studied with selected mono-valent ions as the solute. Using the ion-water cross terms developed for the BLYPSP-4F water model, we replaced the water potential with WAIL, TIP4P, and TIP3P without changing the ion-water parameters. When the adaptive force matching (AFM) derived BLYPSP-4F model is replaced by the other AFM derived WAIL model, the difference in ion properties, such as hydration free energies, radial distribution functions, relative diffusion constants, is negligible, demonstrating the feasibility for combining AFM parameters from different sources. Interestingly, when the AFM-derived ion-water cross-terms are used with a non-AFM based water model, only small changes in the ion properties are observed. The final combined models with TIP3P or TIP4P water reproduce the salt hydration free energies within 6% of experiments. The feasibility of combining AFM models with other non-AFM models is of significance since such combinations allow more complex systems to be studied without specific parameterization. In addition, the study suggests an interesting prospect of reusing the cross-terms when a part of a general force field is replaced with a different model. The prevailing practice, which is to re-derive all cross-terms with combining rules, may not have been optimal.

Liquid-liquid transition in supercooled water suggested by microsecond simulations.

The putative liquid-liquid phase transition in supercooled water has been used to explain many anomalous behaviors of water. However, no direct experimental verification of such a phase transition has been accomplished, and theoretical studies from different simulations contradict each other. We investigated the putative liquid-liquid phase transition using the Water potential from Adaptive Force Matching for Ice and Liquid (WAIL). The simulation reveals a first-order phase transition in the supercooled regime with the critical point at ~207 K and 50 MPa. Normal water is high-density liquid (HDL). Low-density liquid (LDL) emerges at lower temperatures. The LDL phase has a density only slightly larger than that of the ice-Ih and shows more long-range order than HDL. However, the transformation from LDL to HDL is spontaneous across the first-order phase transition line, suggesting the LDL configuration is not poorly formed nanocrystalline ice. It has been demonstrated in the past that the WAIL potential provides reliable predictions of water properties such as melting temperature and temperature of maximum density. Compared with other simple water potentials, WAIL is not biased by fitting to experimental properties, and simulation with this potential reflects the prediction of a high-quality first-principle potential energy surface.

Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching.

Simple non-polarizable potentials were developed for Na(+), K(+), Cl(-), and Br(-) using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration.

Bending the Curve: Molecular Manifestations of Electron Antisymmetry.

As very light fermions, electrons are governed by antisymmetric wave functions that lead to exchange integrals in the evaluation of the energy. Here we use the localized representation of orbitals to decompose the electronic energy in a fashion that isolates the enigmatic exchange contributions and characterizes their distinctive control over electron distributions. The key to this completely general analysis is considering the electrons in groups of three, drawing attention to the curvatures of pair potentials, rather than just their amplitudes and slopes. We show that a positive curvature at short distances is essential for the mutual distancing of electrons and a negative curvature at longer distances is essential to account for the influence of lone pairs on bond torsion. Neither curvature is available in the absence of the exchange contributions. Thus, although exchange energies are much shorter range than Coulomb energies, their influence on molecular geometry is profound and readily understood.

Extensive theoretical studies of a new energetic material: tetrazino-tetrazine-tetraoxide (TTTO).

[1,2,3,4]Tetrazino-[5,6-e]-[1,2,3,4]tetrazine-[1,3,5,7]tetraoxide (TTTO, C2N8O4) was suggested to be a possible candidate of high energy density materials (HEDM). The most stable conformation of TTTO is a planar structure with C2h symmetry. Using various high-level ab initio methods including Gaussian-n, Complete Basis Set, Full Coupled Cluster, and W1U models of chemistry together with density functional theory based models, the enthalpies of formation of TTTO at 0 K and standard state were calculated precisely. Moreover, the rovibrational and nuclear magnetic resonance properties were predicted as well. The solid state TTTO was studied using the crystal packing models with the Dreiding force-filed and the plane-wave periodic local-density approximation density functional theory. Three stable polymorphous cells of TTTO have been found with either P212121 or P21/C symmetry. The high heat of formation (>200 kcal/mol), the high density (>2.0 g/cm3), the planar nonpolar electronic structure, and the perfect oxygen balance lead TTTO be a very promising HEDM with exceptional performance. This work provides the first theoretical support for further experimental synthesis and testing.

Ab initio molecular dynamics study of the electronic structure of superoxide radical anion in solution.

Ab intitio molecular dynamics simulation of the electronic structure of the aqueous superoxide anion (O2(-)) has been carried out using the Car-Parrinello density functional theory at 298 and 310 K. The modeling system consists of one O2(-) solvated in 31 water molecules. On the basis of our 40 ps production run, the novel mechanism and the nature of the hydration of the superoxide anion in a relatively big aqueous environment have been revealed by using various radial distribution functions. The averaged coordinated water number was estimated to be 4.5. The calculated microscopic configurations of the first solvation shell are in good agreement with the experimental results. The vibrational frequency of the solvated O2(-) anion was red-shifted significantly in comparison with that of the free radical anion in the gas phase. The diffusion coefficient of O2(-) was estimated to be about 8 x 10(-5) cm2/s at 298 K. Comparisons with the previous force-field-based classical molecular dynamics simulations have been made, and the differences were discussed.

Surface Penetration without Enrichment: Simulations Show Ion Surface Propensities Consistent with Both Elevated Surface Tension and Surface Sensitive Spectroscopy.

Molecular dynamics was used to investigate ion surface propensities in NaCl, KBr, and CsI solutions with an MP2-based force field. Although NaCl is found to be strongly repelled from the liquid-vapor interface, softer ions, such as I-, penetrate closely to the interface. Despite the surface penetration, the concentration of CsI near the interface is still lower than that in the bulk, thus leading to no surface enrichment. The salt concentration is found to affect relative surface propensities of the ions. More significant surface penetration is observed at higher salt concentrations. Softer ions at higher concentrations form a complex multilayer arrangement that can not be characterized as a simple surface bilayer. The simulated ion distributions explain the spectroscopic evidence of surface perturbation by soft ions with a negative surface excess consistent with an increased surface tension of salt solutions.

Computational study of the reaction of CH2(X3B1) with CH3OH.

The reaction of triplet methylene with methanol is a key process in alcohol combustion but surprisingly this reaction has never been studied. The reaction mechanism is investigated by using various high-level ab initio methods, including the complete basis set extrapolation (CBS-QB3 and CBS-APNO), the latest Gaussian-n composite method (G4), and the Weizmann-1 method (W1U). A total of five product channels and six transition states are found. The dominant mechanism is direct hydrogen abstraction, and the major product channel is CH(3) + CH(3)O, involving a weak prereactive complex and a 7.4 kcal/mol barrier. The other hydrogen abstraction channel, CH(3) + CH(2)OH, is less important even though it is more exothermic and involves a similar barrier height. The rate coefficients are predicted in the temperature range 200-3000 K. The tunneling effect and the hindered internal rotational freedoms play a key role in the reaction. Moreover, the reaction shows significant kinetic isotope effect.

Accurate Prediction of the Hydration Free Energies of 20 Salts through Adaptive Force Matching and the Proper Comparison with Experimental References.

Simple pairwise potentials for five alkali ions and four halide ions were developed by only fitting to ab initio MP2 forces with the adaptive force matching (AFM) method. Without fitting to any experimental information, the AFM models predict the hydration free energies of all 10 fluoride and chloride salts formed by these ions within 1.5% of experimental references. The predicted hydration free energies for the 10 bromide and iodide salts are within 5-6% of experimental references with the larger error likely due to the neglect of explicit treatment of polarization and charge transfer. An inconsistency in the treatment of the gas phase entropy term between experimental and theoretical approaches is discussed. A new simplified hydration free energy for the ions is reported for use as a more appropriate experimental reference for further theoretical studies. The simulations show different dipole alignments for the hydration waters of cations and anions. While hydration waters of small cations tend to align their molecular dipole toward the ion, the dipole of one of the water OH bonds is aligned with the field of an anion.

Genetic variation of maturity groups and four E genes in the Chinese soybean mini core collection.

The mini core collection (MCC) has been established by streamlining core collection (CC) chosen from China National Genebank including 23,587 soybean (Glycine max) accessions by morphological traits and simple sequence repeat (SSR) markers. Few studies have been focused on the maturity that has been considered as one of the most critical traits for the determination of the adaptation-growing region of the soybean. In the current study, two hundred and ninty-nine accessions of MCC planted for two years at four locations namely in Heihe, Harbin, Jining and Wuhan cities in China were used to assess the variation of maturity in MCC and identify the integrated effect of 4 E loci on flowering and maturity time in soybean. Forty-two North American varieties served as references of maturity groups (MG). Each accession in MCC was classified by comparing with the MG references in the days from VE (emergence) and physiological maturity (R7). The results showed that MCC covered a large range of MGs from MG000 to MGIX/X. Original locations and sowing types were revealed as the major affecting factors for maturity groups of the MCC accessions. The ratio of the reproductive period to the vegetative period (R/V) varied among MCC accessions. Genotyping of 4 maturity genes (i.e. E1, E2, E3 and E4) in 228 accessions indicated that recessive alleles e1, e2, e3 and e4 promoted earlier flowering and shortened the maturity time with different effects, while the dominate alleles were always detected in accessions with longer maturity. The allelic combinations determined the diversification of soybean maturity groups and adaptation to different regions. Our results indicated that the maturity of Chinese soybean MCC showed genetic diversities in phenotype and genotype, which provided information for further MG classification, geographic adaptation analysis of Chinese soybean cultivars, as well as developing new soybean varieties with adaptation to specific regions.

The Effect of Core Correlation on the MP2 Hydration Free Energies of Li(+), Na(+), and K(.).

Simple nonpolarizable molecular mechanics potentials were developed for Li(+), Na(+), and K(+) with the adaptive force matching (AFM) method using the second order Møller-Plesset perturbation theory (MP2) with the frozen core approximation as reference. The effects of different choices of core orbitals and basis sets in the MP2 calculations were investigated for Na(+) and Li(+). For Na(+), correlating the 2s2p electrons in MP2 changes its hydration free energy by 18 kJ/mol, which is surprisingly large, constituting to about 5% of the intrinsic hydration free energy of the ion. Whereas correlating the 2s2p electrons with the aug-cc-pCVTZ basis set leads to the best agreement with experiments, with the aug-cc-pVTZ basis set, a better hydration free energy will be obtained if the 2s2p are kept as frozen core orbitals. Even with nonpolarizable energy expressions, the AFM derived ion potentials predict the experimental hydration free energies of the various salts within 2% of experimental values, suggesting the robustness of the fitting procedure. However, the 2% agreement can only be achieved if the core correlation is modeled appropriately in the MP2 reference calculations.

Continuous and Discontinuous Dynamic Crossover in Supercooled Water in Computer Simulations.

The dynamic crossover behavior of supercooled water as described by the first-principle based WAIL potential was investigated. Below the second liquid-liquid critical point, the viscosity shows a discontinuous jump consistent with a first-order phase transition between the high density liquid and the low density liquid. Above the critical point, a continuous transition occurs with only the first derivative of viscosity being discontinuous, and the dynamic crossover temperature is about 8 K below the thermodynamic switchover temperature. The 8 K shift can be explained by a delay in dynamic crossover, which does not occur until the more viscous liquid starts to dominate the population and jams the flow. On the basis of finite-size effects observed in our simulations, we believe that dynamic discontinuity may be observable above the critical point in confined water when the confinement is on a length scale shorter than the spatial correlation.

Fast and high-accuracy localization for three-dimensional single-particle tracking.

We report a non-iterative localization algorithm that utilizes the scaling of a three-dimensional (3D) image in the axial direction and focuses on evaluating the radial symmetry center of the scaled image to achieve the desired single-particle localization. Using this approach, we analyzed simulated 3D particle images by wide-field microscopy and confocal microscopy respectively, and the 3D trajectory of quantum dots (QDs)-labeled influenza virus in live cells. Both applications indicate that the method can achieve 3D single-particle localization with a sub-pixel precision and sub-millisecond computation time. The precision is almost the same as that of the iterative nonlinear least-squares 3D Gaussian fitting method, but with two orders of magnitude higher computation speed. This approach can reduce considerably the time and costs for processing the large volume data of 3D images for 3D single-particle tracking, which is especially suited for 3D high-precision single-particle tracking, 3D single-molecule imaging and even new microscopy techniques.

Ab initio study of the potential energy surface for the OH+CO-->H+CO2 reaction.

Potential energy surface for the reaction OH+CO-->H+CO2 has been calculated using the complete active space self-consistent-field and multireference configuration interaction methods with the correlation consistent triple-, quadruple-, and quintuple-zeta basis sets. A specific- reaction-parameters density functional theory has been suggested, in which the B3LYP functional is reoptimized to give the highly accurate potential energy surface with less computational efforts.

Computational study of the reaction of chlorinated vinyl radical with molecular oxygen (C2Cl3 + O2).

Eight exothermic product channels of the reaction of chlorinated vinyl radical (C2Cl3) with molecular oxygen (O2) have been investigated using ab initio quantum chemistry methods. The energetics of the reaction pathways were calculated at the second-order Moller-Plesset Gaussian-3 level of theory (G3MP2) using the B3LYP/6-311G(d) optimized geometries. It has been shown that the C2Cl3 + O2 reaction takes place via a barrierless addition to form the chlorinated vinylperoxy radical complex, which can decompose or isomerize to various products via the complicated mechanisms. Two major reaction routes were revealed, i.e., the three-member-ring reaction mechanism leading to ClCO + CCl2O, CO + CCl3O, CO2 + CCl3, Cl + (ClCO)2, etc., and the OO bond cleavage mechanism leading to O(3P) + C2Cl3O. The other mechanisms are shown to be unimportant. The results are validated by the calculations using the restricted coupled cluster theory [RCCSD(T)] with the complete basis set extrapolation. Variational transition state theory was employed to calculate the individual and total rate coefficients as a function of temperature and pressure (helium). The theoretical rate coefficients are in good agreement with the available experimental data. It was found that the total rate coefficients show strong negative temperature dependence in the range 200-2000 K. At room temperature (297 K), the total rate coefficients are shown to be nearly pressure independent over a wide range of helium pressures (1-10(9) Torr). The deactivation of the initial adduct, C2Cl3O2, is only significant at pressures higher than 1000 Torr. The three-member-ring reaction mechanism is always predominant over the OO bond cleavage.