Ab Initio Geometry Optimizations Research Articles

Machine Learning Diffusion Monte Carlo Forces

Diffusion Monte Carlo (DMC) is one of the most accurate techniques available for calculating the electronic properties of molecules and materials, yet it often remains a challenge to economically compute forces using this technique. As a result, ab initio molecular dynamics simulations and geometry optimizations that employ Diffusion Monte Carlo forces are often out of reach. One potential approach for accelerating the computation of "DMC forces" is to machine learn these forces from DMC energy calculations. In this work, we employ Behler-Parrinello Neural Networks to learn DMC forces from DMC energy calculations for geometry optimization and molecular dynamics simulations of small molecules. We illustrate the unique challenges that stem from learning forces without explicit force data and from noisy energy data by making rigorous comparisons of potential energy surface, dynamics, and optimization predictions among ab initio density functional theory (DFT) simulations and machine-learning models trained on DFT energies with forces, DFT energies without forces, and DMC energies without forces. We show for three small molecules─C2, H2O, and CH3Cl─that machine-learned DMC dynamics can reproduce average bond lengths and angles within a few percent of known experimental results at one hundredth of the typical cost. Our work describes a much-needed means of performing dynamics simulations on high-accuracy, DMC PESs and for generating DMC-quality molecular geometries given current algorithmic constraints.

Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions.

The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.

Assessing the potential of para-donor and para-acceptor substituted 5-benzylidenebarbituric acid derivatives as push–pull electronic systems: Experimental and quantum chemical study

Electronic interactions in donor-π-linker-acceptor systems with barbituric acid as an electron acceptor and possible electron donor were investigated to screen promising candidates with a push–pull character based on experimental and quantum chemical studies. The tautomeric properties of 5-benzylidenebarbituric acid derivatives were studied with NMR spectra, spectrophotometric determination of the pKa values, and quantum chemical calculations. Linear solvation energy relationships (LSER) and linear free energy relationships (LFER) were applied to the spectral data - UV frequencies and 13C NMR chemical shifts. The experimental studies of the nature of the ground and excited state of investigated compounds were successfully interpreted using a computational chemistry approach including ab initio MP2 geometry optimization and time-dependent DFT calculations of excited states. Quantification of the push–pull character of barbituric acid derivatives was performed by the 13CNMR chemical shift differences, Mayer π bond order analysis, hole-electron distribution analysis, and calculations of intramolecular charge transfer (ICT) indices. The results obtained show, that when coupled with a strong electron-donor, barbituric acid can act as the electron-acceptor in push–pull systems, and when coupled with a strong electron-acceptor, barbituric acid can act as the weak electron-donor.

Non-planarity in four-membered homo-cyclic compounds A4 (A = O, S, Se, Te, Po) and restoring their planarity: a study of the pseudo-Jahn–Teller effect

The bent D2d structures of the four-membered homo-cyclic compounds A4 (A = O, S, Se, Te, Po) were examined computationally to understand the pseudo-Jahn–Teller effect (PJTE). To do this, ab initio geometry optimizations and corresponding frequency calculations (at the MP2/cc-pVQZ-(PP) level of theory) show that all A4 compounds under-consideration are unstable in their planar (D4h) configuration. The ground state and six low-lying non-degenerate and degenerate electronic excited states were computed at the CASSCF (6,7)/cc-pVQZ-(PP) along the bending normal coordinate connecting the D4h and D2d geometries; these represent the adiabatic potential energy surfaces (APESs). Based on the APESs, the coupling between the ground state (1A1g) and the 1B2u excited state is demonstrated to be the reason for the planar structure bends from the high-symmetry D4h geometry into the lower-symmetry D2d stable equilibrium configuration. The solution to the PJTE (1A1g + 1B2u) ⊗ b2u problem is useful to answer the question of “how instability rises in A4 planar configuration?”. Although all A4 compounds in the series are non-planar with D4h symmetry, but geometrical optimizations and frequency calculations show that coordination of two noble gas cations (NG+ = He+, Ne+ and Ar+) above and below the σh plane of the A4 (A = O, S, Se) ring could restore ring planarity in (A4 NG)2+ complexes. The PJTE is also quenched in the A42+ (A = O, S, Se, Te, Po) cation and dication series, and planarity of the rings is also restored, i.e., the high-symmetry D4h structure becomes the equilibrium configuration.

A theoretical study of X‐H∙∙∙π and X∙∙∙π interactions in the complexes of furan, thiophene, pyrrole and hydrogen halides

AbstractBy using ab initio geometry optimization calculations we obtained thirteen stable complexes containing H∙∙∙π and X∙∙∙π interactions between Furan, Thiophene, Pyrrole and HX (X = F, Cl, Br) at the MP2/6‐311++G(3df,2pd) high level of theory. The interaction energies corrected for only ZPE and both ZPE and BSSE range from ‐7.92 to ‐28.47 kJ.mol‐1 and ‐3.28 to ‐22.33 kJ.mol‐1, respectively. The results show that for the same HX, the stability of complexes decreases in going from Pyrrole to Thiophene and finally to Furan moiety, and increases in the order of HF < HCl < HBr monomer with the same π‐system. The obtained results from AIM and MEP analyses indicate that the H∙∙∙π interaction is more stable than X∙∙∙π one in all the investigated complexes. It is found that the electrostatic, dispersion and induction energy terms significantly contribute to strength of the studied complexes, in which two formers are for H∙∙∙π hydrogen bonded complexes and two latters are for X∙∙∙π halogen bonded complexes.

Complexation of Chiral Zinc(II) Porphyrin Tweezer with Achiral Aliphatic Diamines Revisited: Molecular Dynamics, Electronic CD, and 1H NMR Analysis.

We have reported here the complexation and chiroptical behavior of the host-guest complexes using a new chiral Zn(II) bisporphyrin tweezer host and a series of achiral aliphatic diamine guests varying the chain length. (1R,2R)-Cyclohexanediamine covalently links two Zn(II) porphyrin moieties, which thereby produces a strong chiral field around the bisporphyrin tweezer framework. The chiral tweezer upon complexation with achiral guest exhibited large changes in the UV-vis spectra and CD exciton couplets due to a sudden change in the porphyrin disposition, which is controlled by the host-guest stoichiometry as well as the chain lengths of the diamine guest. Addition of smaller diamines (n: 2-5) to the host resulted in the formation of 1:1 sandwich and 1:2 open complexes, respectively, at the low and high guest concentration, which eventually display two-step inversions of the CD couplet. With longer diamines (n: 6-8), however, only 1:1 sandwich complexes are formed with retention of the CD sign. Similar observations were also reported by us recently using another chiral bisporphyrin tweezer having (1R,2R)-diphenylethylenediamine as the spacer. In an effort to obtain deeper insights into the sudden changes of interporphyrin disposition just by changing the length of the achiral diamines, we have extended a series of computational studies and correlated closely with the results obtained from the experiment. While the previously published study has relied on commonly applied Monte Carlo (MC) sampling of the potential energy surface in addition to being guided by porphyrin effective transition moment approximation, the present study uses a considerably more robust molecular modeling protocol, namely Molecular Dynamics (MD) simulations followed by full ab initio geometry optimization and TD-DFT CD prediction. The experimental data corroborate with the results obtained from the theoretical conformational analysis. The latter are also supported by experimental 1H NMR data empowered by the porphyrin ring-current effect. The NMR spectral patterns of pyrrolic protons of the free host and the 1:1 sandwich complexes appear very diagnostic and reflect the changes in the mutual porphyrin disposition on moving from the free host to the complexed ones with short and long diamines. Overall, the experimental NMR data underscore the sensitivity of pyrrolic protons chemical shifts to subtle alterations of the geometrical features, and as such, they come in agreement with the theoretically derived models.

Instability of two–dimensional structure of dichalcogenin and dipnictogenin octa–heterocyclic systems with 1,2–C6X2(X = O, S, Se, Te, N, P) unsaturated rings

The planar configuration and twisted structures of the dichalcogenin (DCG) and dipnictogenin (DPG) octa–heterocyclic systems with 1,2–C6X2 ring in their main skeleton were computed through ab initio geometry optimization and following frequency calculations. Whereas the C6X2 eight–membered unsaturated rings in the considered compounds are unstable in their planar configurations, the molecules distorted from their planar shape with C2v, high symmetry into the C2, lower symmetry, twisted equilibrium configuration. Based on adiabatic potential energy surface (APES) cross sections, coupling between the ground state (1A1) and 1A2 excited state and the PJTE (1A1 + 1A2 + ···) ⊗ a2 are the reasons for the C6X2 unsaturated rings’ two–dimensional structure instability. Moreover, substitution of two hydrogen atoms in bonding with nitrogen and phosphorus positions of DPGs with halogens significantly changed the effect in the 1,2–diazocine and 1,2–diphosphocine compounds. Furthermore, intramolecular hydrogen bonding in the systems with 1,2–C6X2 (X = O, N) rings affect two–dimensional instability of the molecular structure.

Direct Access by Mechanochemistry or Sonochemistry to Protonated Merocyanines: Components of a Four-State Molecular Switch.

Direct access to the protonated merocyanine forms of two substituted spiropyrans by mechanosynthesis or sonochemistry was explored. The compounds were formed by the condensation reaction of the methyleneindolium iodide salt with salicylaldehyde derivatives. X‐ray crystallography, 1H NMR spectroscopy, ab initio geometry optimization, and absorption spectroscopy were combined to provide a better understanding of the four‐state molecular switch system in which the newly synthesized protonated merocyanines were found to play a central role. The results of this study suggest that the stability of the protonated merocyanines requires acidic conditions, as treatment with base led to the corresponding unprotonated merocyanines, which in turn spontaneously converted into photochromic closed spiropyrans.

Rational Design of a Commensurate (3 + 3)-D Modulated Structure within the Fast-Ion Conducting Stabilized δ-Bi2O3 Series

We report the systematic design, preparation, and characterization of the first commensurate member of the oxide-ionic conducting, (3 + 3)-D modulated, Type II phases of doped δ-Bi2O3. The incommensurate Type II modulation vector e was previously described as continuously variable, but high-resolution synchrotron X-ray powder diffraction data show that close to the composition Bi23CrNb3O45, it “locks in” to e = 1/3. The space group of the resulting 3 × 3 × 3 fluorite-type supercell was found to be F43m by selected-area electron diffraction, and the structure was solved and Rietveld-refined against neutron powder diffraction data in conjunction with local structural information from X-ray absorption spectroscopy, high-resolution transmission electron microscopy, and ab initio geometry optimization calculations. The result unambiguously validates the crystal-chemical model of the Type II phases as being based on the local ordering of oxygen around transition metals M into tetrahedral clusters of MO6 octahe...

Rotational Spectrum and Structure of the 1,1-Difluoroethylene···Carbon Dioxide Complex.

Rotational spectra for five isotopologues of the 1:1 weak complex between 1,1-difluoroethylene (H2C═CF2) and carbon dioxide (CO2) have been measured using 480 MHz bandwidth chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy between 5.5 and 18.5 GHz. The observed structure of the complex is planar, with the CO2 aligned roughly parallel to the C═C bond, and experimental structural parameters derived from rotational constants are consistent with the most stable geometry predicted by basis set superposition error and zero point energy corrected ab initio geometry optimizations at the MP2/6-311++G(2d,2p) level. Comparisons with the recently characterized vinyl fluoride···carbon dioxide complex reveal slightly longer intermolecular distances in the present complex, but very similar binding energies.

Pseudo Jahn-Teller origin of puckering in cyclohexahomoatomic molecules E6 (E = S, Se, Te) and restoring S6 planar ring configuration

The pseudo Jahn-Teller effect (PJTE) is employed to explore the origin of the puckering structure of cyclohexasulfur (S6), cyclohexaselenium (Se6) and cyclohexatellurium (Te6) and their nondegenerate and degenerate vibronic excited states and their planar structure instabilities have investigated. The ab initio geometry optimization and frequency calculations show that all these cyclohexahomoatomic molecules chose D6h symmetry in the planar configuration, and according the S6 and Se6 experimental structure, the chair form of the molecules is stable structure. The vibronic coupling between the ground state 1A1g and excited state 1B2g is the cause of chair puckering in all these series compounds and the numerical solutions of the PJTE (1A1g+1B2g)⊗b2g problems describe their instability. The adiabatic potential energy surfaces (APES) cross sections of low-lying electronic states along the b2g puckering normal coordinates have calculated by the state-average complete active space self-consistent field (SA-CASSCF) method. The calculation results show that, the chair puckering instability in the S6 from unstable planar configuration with D6h symmetry to a stable D3d distorted geometry, is stronger than others, whereas it is weaker in Te6. Additionally, coordination two canions (X = H+, He2+) to the S6 chair structure restore the planarity of S6 puckered ring in the S6X2 systems, although the D6h symmetry in S6 planar ring configuration changes to the Cs symmetry in the systems.

Acid-base dissociation mechanisms and energetics at the silica–water interface: An activationless process

HypothesisSilanol groups at the silica–water interface determine not only the surface charge, but also have an important role in the binding of ions and biomolecules. As the pH is increased above pH 2, the silica surface develops a net negative charge primarily due to deprotonation of the silanol group. An improved understanding of the energetics and mechanisms of this fundamentally important process would further understanding of the relevant dynamics. SimulationsDensity Functional Theory ab initio molecular dynamics and geometry optimisations were used to investigate the mechanisms of surface neutralisation and charging in the presence of OH- and H3O+ respectively. This charging mechanism has received little attention in the literature. FindingsThe protonation or deprotonation of isolated silanols in the presence of H3O+ or OH-, respectively, was shown to be a highly rapid, exothermic reaction with no significant activation energy. This process occurred via a concerted motion of the protons through ‘water wires’. Geometry optimisations of large water clusters at the silica surface demonstrated proton transfer to the surface occurring via the rarely discussed ‘proton holes’ mechanism. This indicates that surface protonation is possible even when the hydronium ion is distant (at least 4 water molecules separation) from the surface.

Characterization of two isomers of the vinyl fluoride···carbon dioxide dimer by rotational spectroscopy.

Rotational spectra of two different structural forms of the 1:1 weak complex between vinyl fluoride (C2H3F) and carbon dioxide were measured using 480 MHz bandwidth chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy in the 5-17 GHz region. Both structures have the CO2 molecule situated in the plane of the vinyl fluoride, such that the CO2 is interacting either with a CHF side or with a HC═CF edge of the vinyl fluoride subunit. Both observed structures are close to those predicted by ab initio geometry optimizations (corrected for basis set superposition error) at the MP2/6-311++G(2d,2p) level. Dipole moment measurements and structural fits, including determinations of principal axis coordinates for all three carbon atoms, confirm the geometries of the assigned species.

Comprehensive analysis of energy minima of the 20 natural amino acids.

Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(═O)-N(H)-(H)Cα(R)-C(═O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of βL, γL, δL, and αL of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-Cα-C(═O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-Cα(HαCβ)-C'(═O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.

Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

Rotational Spectroscopic Studies of C–H···F Interactions in the Vinyl Fluoride···Difluoromethane Complex

Rotational spectra of the normal isotopic species and three (13)C isotopologues of the 1:1 complex between vinyl fluoride (CH2 ═ CHF) and difluoromethane (CH2F2) have been measured using 480 MHz bandwidth chirped-pulse Fourier-transform microwave spectroscopy in the 6.5-20 GHz region. A structure for this dimer has been determined by fitting the moments of inertia of all isotopologues and confirmed by calculation of Kraitchman single isotopic substitution coordinates. The structure is consistent with that determined by ab initio geometry optimization at the MP2/6-311++G(2d,2p) level and has the difluoromethane subunit located on the CHF side of the vinyl fluoride subunit with three C-H · · · F contacts and with the hydrogen atoms of the CH2F2 straddling the vinyl fluoride symmetry plane.

Comprehensive Comparative Study Using Ab Initio Computational Approaches on the Structures of Cisplatin, Oxaliplatin and BNP3029 (A Novel Substituted Cyano Ligand-based Platinum Analogue) and Activation Energy Barriers for the Attack of Nucleophiles on Cisplatin and BNP3029 and their Monoaquated Derivatives

Cisplatin is an important anti-cancer agent widely used in the clinic; however, it has several notable limitations. To develop novel platinum analogues, key characteristics were considered that may result in more effective platinum analogues. Herein results based on ab initio geometry optimizations (gas- and solution-phase) on cisplatin (1), oxaliplatin_1R_2R (2) and BNP3029 (3, a novel substituted cyano ligand-based platinum analogue, PtCl2[N≡C(CH2)3(C6H5)]2) using the recently published potentials and basis sets for platinum are presented. Optimized quantum mechanical derived geometries of the 3 platinum agents were in good agreement with available experimental geometries. The reactivity of BNP3029 was compared to cisplatin by computing the activation free energy barriers for the attack of various nucleophiles on both 1 and 3 and their monoaquated derivatives. Based on the activation energy barriers, it was determined that: (i) the reaction rate may be similar for the attack of water on cisplatin and BNP3029; (ii) the reaction rate for the attack of DNA bases was slower for monoaquated BNP3029 compared to monoaquated cisplatin; and (iii) the reaction rates for a thiol/thiolate attack on monoaquated cisplatin or monoaquated BN3029 were similar. BNP3029 demonstrated potent cytotoxic activity in a variety of human cancer cell lines in comparison to cisplatin and oxaliplatin and also had potent cytotoxic activity in several platinum resistant cell lines.

Solubility of triclocarban in pure alkanols at different temperatures

Triclocarban solubility in six pure alcohols was determined in the temperature interval from 278.15 to 318.15 K. The experimental solubility data were correlated by the Wilson, the nonrandom two liquid (NRTL) and the universal quasi-chemical (UNIQUAC) models. The data are well fitted with all three models for the six pure alcohols studied here. Also, ab initio geometry optimization of triclocarban was performed using the density functional theory (DFT) based on DMol3 method.

Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion

Infrared multiphoton dissociation (IRMPD) spectroscopy, using a free-electron laser, and ion mobility measurements, using both drift-cell and traveling-wave instruments, were used to investigate the structure of gas-phase peptide (AAHAL + 2H)(2+) ions produced by electrospray ionization. The experimental data from the IRMPD spectra and collisional cross section (Ω) measurements were consistent with the respective infrared spectra and Ω calculated for the lowest-energy peptide ion conformer obtained by extensive molecular dynamics searches and combined density functional theory and ab initio geometry optimizations and energy calculations. Traveling-wave ion mobility measurements were employed to obtain the Ω of charge-reduced peptide cation-radicals, (AAHAL + 2H)(+●), and the c(3), c(4), z(3), and z(4) fragments from electron-transfer dissociation (ETD) of (AAHAL + 2H)(2+). The experimental Ω for the ETD charge-reduced and fragment ions were consistent with the values calculated for fully optimized ion structures and indicated that the ions retained specific hydrogen bonding motifs from the precursor ion. In particular, the Ω for the doubly protonated ions and charge-reduced cation-radicals were nearly identical, indicating negligible unfolding and small secondary structure changes upon electron transfer. The experimental Ω for the (AAHAL + 2H)(+●) cation-radicals were compatible with both zwitterionic and histidine radical structures formed by electron attachment to different sites in the precursor ion, but did not allow their distinction. The best agreement with the experimental Ω was found for ion structures fully optimized with M06-2X/6-31+G(d,p) and using both projection approximation and trajectory methods to calculate the theoretical Ω values.

Investigation of 6-fluoroquinolones activity against Mycobacterium tuberculosis using theoretical molecular descriptors: a case study

Abstract A quantitative structure-activity relationship (QSAR) study on a set of 66 structurally-similar 6-fluoroquinolones was performed using a large pool of theoretical molecular descriptors. Ab initio geometry optimizations were carried out to reproduce the geometrical and electronic structure parameters. The resulting molecular structures were confirmed to be minima via harmonic frequency calculations. Obtained atomic charges, HOMO and LUMO energies, orbital electron densities, dipole moment, energy and many other properties served as quantum-chemical descriptors. A multiple linear regression (MLR) technique was applied to generate a linear model for predicting the biological activity, Minimal Inhibitory Concentration (MIC), treated as negative decade logarithm, (pMIC). The heuristic method was used to optimize the model parameters and select the most significant descriptors. The model was tested internally using the CV LOO procedure on the training set and validated against the external validation set. The result (Q 2 ext = 0.7393), which was obtained on an external, previously excluded validation data set, shows the predictive performances of this model (R 2tr = 0.7416, Q 2 tr = 0.6613) in establishing (Q)SAR of 6-fluoroquinolones. This validated model could be proficiently used to design new 6-fluoroquinolones with possible higher activity.