An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest

Phosphine versus Carbene Metal Interactions: Bond Energies

A variety of different ground-state structures of carbene and phosphine groups 1 and 2 cationic, group 11 cationic, and group 10 neutral complexes were studied using density functional theory (DFT) and correlated molecular orbital theory (CCSD(T)) methods. Geometries of complexes with phosphines were studied and compared to available experimental data. Among the three analyzed phosphine ligands, PH3, PMe3, and PPh3, PH3 was found to have noticeably smaller ligand binding energies (LBEs, ΔH298 K). PPh3 has the greatest LBEs with group 2 dications. The difference in LBEs for PMe3 and PPh3 in complexes with group 1 monocations and transition-metal (TM) complexes was significantly less pronounced. The stability and reactivity of phosphine complexes were analyzed and compared with those of previously studied N-heterocyclic carbenes (NHC). PH3 has smaller LBEs compared to NHC carbenes. The lower LBEs correlate with the hardness for M(11)+ complexes and correlate with both the hardness and ionic radii for the M(1)+ and M(2)2+ complexes. The presence of additional PH3 substituents on the metal center makes the LBE smaller compared to their unsubstituted or less substituted analogs. The presence of NH3 in a structure causes a smaller effect on binding, and, except for carbene-PtNH3, an increase in LBE was observed. Composite-correlated molecular orbital theory (G3MP2) was used to predict the LBE of various Lewis acidic ligands with PH3 and NHCs to contrast their binding behavior. Binding either phosphine or carbene to metal diamine complexes caused ligand exchange and transfer of NH3 to an outer coordination sphere.

A full-dimensional ab initio potential energy and dipole moment surfaces for (NH3)2

A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) for the ammonia dimer (NH₃)₂ are reported. The database of the PES consists of 27 736 ab initio energy points and all of these points were calculated at the UCCSD(T)-F12a/AVTZ level. The PES was fitted by using the fundamental invariant neural network (FI-NN) method that satisfies the permutational symmetry of identical atoms, and the root mean square fitting error for the PES is very small as low as 0.562 meV. The geometries for the (NH₃)₂ DMS are the same as those used for the PES and are calculated at the XYG3/AVTZ level. This PES can describe a variety of internal floppy motions, including all kinds of vibrational modes no matter intermolecular or intramolecular. The CCSD(T)-PES can dissociate correctly to two NH₃ monomers, with D_e = 1135.55 cm^-1 (13.58 kJ/mol) which agrees accurately with the 13.5 ± 0.3 kJ/mol predicted by previous work.

Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia

The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pK_a of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energies of the proton in a given solvent. We propose in this work a direct approach to compute the solvation energies of the proton in ammonia from large-sized neutral and protonated ammonia clusters. To undertake this investigation, we performed a geometry optimization of neutral and protonated ammonia 30-mer, 40-mer, and 50 mer to locate stable structures. These structures have been fully optimized at both APFD/6-31++g(d,p) and M06-2X/6-31++g(d,p) levels of theory. An infrared spectroscopic study of these structures has been provided to assess the reliability of our investigation. Using these structures, we have computed the absolute solvation free energy and the absolute solvation enthalpy of the proton in ammonia. It comes out that the absolute solvation free energy of the proton in ammonia is calculated to be -1192 kJ mol^-1 , whereas the absolute solvation enthalpy is evaluated to be -1214 kJ mol^-1 . © 2019 Wiley Periodicals, Inc.

Spectroscopic and Theoretical Study of Spin-Dependent Electron Transfer in an Iron(III) Superoxo Complex

It was shown previously (J. Am. Chem. Soc. 2014, 136, 10846) that bubbling of O2 into a solution of Fe(II)(BDPP) (H2BDPP = 2,6-bis[[(S)-2-(diphenylhydroxymethyl)-1-pyrrolidinyl]methyl]pyridine) in tetrahydrofuran at -80 °C generates a high-spin (SFe = (5)/2) iron(III) superoxo adduct, 1. Mössbauer studies revealed that 1 is an exchange-coupled system, [Formula: see text], where SR = (1)/2 is the spin of the superoxo radical, of which the spectra were not well enough resolved to determine whether the coupling was ferromagnetic (S = 3 ground state) or antiferromagnetic (S = 2). The glass-forming 2-methyltetrahydrofuran solvent yields highly resolved Mössbauer spectra from which the following data have been extracted: (i) the ground state of 1 has S = 3 (J < 0); (ii) |J| > 15 cm(-1); (iii) the zero-field-splitting parameters are D = -1.1 cm(-1) and E/D = 0.02; (iv) the major component of the electric-field-gradient tensor is tilted ≈7° relative to the easy axis of magnetization determined by the MS = ±3 and ±2 doublets. The excited-state MS = ±2 doublet yields a narrow parallel-mode electron paramagnetic resonance signal at g = 8.03, which was used to probe the magnetic hyperfine splitting of (17)O-enriched O2. A theoretical model that considers spin-dependent electron transfer for the cases where the doubly occupied π* orbital of the superoxo ligand is either "in" or "out" of the plane defined by the bent Fe-OO moiety correctly predicts that 1 has an S = 3 ground state, in contrast to the density functional theory calculations for 1, which give a ground state with both the wrong spin and orbital configuration. This failure has been traced to a basis set superposition error in the interactions between the superoxo moiety and the adjacent five-membered rings of the BDPP ligand and signals a fundamental problem in the quantum chemistry of O2 activation.

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

A procedure to determine the electrostatic parameters has been developed for a polarizable empirical force field based on the classical Drude oscillator model. Atomic charges and polarizabilities for a given molecule of interest were derived from restrained fitting to quantum-mechanical electrostatic potentials (ESP) calculated at the B3LYP/ cc-pVDZ or B3LYP/aug-cc-pVDZ levels on grid points located on concentric Connolly surfaces. The determination of the atomic polarizabilities requires a series of perturbed ESP maps, each one representing the electronic response of the molecule in the presence of a background charge placed on Connolly surfaces primarily along chemical bonds and lone pairs. Reference values for the partial atomic charges were taken from the CHARMM27 additive all-atom force field, and those for the polarizabilities were based on adjusted Miller's ahp atomic polarizability values. The fitted values of atomic polarizabilities were scaled to reflect the reduced polarization expected for the condensed media and/or to correct for the systematic underestimation of experimental molecular polarizabilities by B3LYP calculations. Following correction of the polarizabilities, the atomic charges were adjusted to reproduce gas-phase dipole moments. The developed scheme has been tested on a set of small molecules representing functional moieties of nucleic acids. The derived electrostatic parameters have been successfully applied in a preliminary polarizable molecular dynamics simulation of a DNA octamer in a box of water with sodium counterions. Thus, this study confirms the feasibility of the use of a polarizable force field based on a classical Drude model for simulations of biomolecules in the condensed phase.

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.

Structures and relative stabilities of ammonia clusters at different temperatures: DFT vs. ab initio

The global minimum energy structures of (NH₃)_n=2–10are pointed out for the first time at a given temperature.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

Computational study on the conformation and vibration frequencies of β-sheet of ε-polylysine in vacuum

Two oligomers, each containing 3 l-lysine residues, were used as model molecules for the simulation of the β-sheet conformation of ɛ-polylysine (ɛ-PLL) chains. Their C terminals were capped with ethylamine and N terminals were capped with α-l-aminobutanoic acid, respectively. The calculations were carried out with the hybrid two-level ONOIM (B3LYP/6-31G:PM3) computational chemistry method. The optimized conformation was obtained and IR frequencies were compared with experimental data. The result indicated that the two chains were winded around each other to form a distinct cyclohepta structure through bifurcated hydrogen bonds. The groups of amide and α-amidocyanogen coming from one chain and the carbonyl group from the other chain were involved in the cyclohepta structure. The bond angle of the bifurcated hydrogen bonds was 66.6°. The frequency analysis at ONIOM [B3LYP/6-31G (d):PM3] level showed the IR absorbances of the main groups, such as the amide and amidocyanogen groups, were in accordance with the experimental data.

AIScore chemically diverse empirical scoring function employing quantum chemical binding energies of hydrogen-bonded complexes

In this work we report on a novel scoring function that is based on the LUDI model and focuses on the prediction of binding affinities. AIScore extends the original FlexX scoring function using a chemically diverse set of hydrogen-bonded interactions derived from extensive quantum chemical ab initio calculations. Furthermore, we introduce an algorithmic extension for the treatment of multifurcated hydrogen bonds (XFurcate). Charged and resonance-assisted hydrogen bond energies and hydrophobic interactions as well as a scaling factor for implicit solvation were fitted to experimental data. To this end, we assembled a set of 101 protein-ligand complexes with known experimental binding affinities. Tightly bound water molecules in the active site were considered to be an integral part of the binding pocket. Compared to the original FlexX scoring function, AIScore significantly improves the prediction of the binding free energies of the complexes in their native crystal structures. In combination with XFurcate, AIScore yields a Pearson correlation coefficient of R P = 0.87 on the training set. In a validation run on the PDBbind test set we achieved an R P value of 0.46 for 799 attractively scored complexes, compared to a value of R P = 0.17 and 739 bound complexes obtained with the FlexX original scoring function. The redocking capability of AIScore, on the other hand, does not fully reach the good performance of the original FlexX scoring function. This finding suggests that AIScore should rather be used for postscoring in combination with the standard FlexX incremental ligand construction scheme.

Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.

Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions

We present a simple increment model for use in the rapid scoring of hydrogen bond strengths employing 15 chemically diverse donor and 28 acceptor terms. The increments cover a large variety of hydrogen bond donor and acceptor groups and are more specific than SYBYL atom types. The increments have been fitted to quantum chemical ab initio interaction energies of 81 small hydrogen-bonded complexes determined at the level of second-order Møller-Plesset perturbation theory (MP2). The complexes have been chosen such as to represent the most important types of donor-acceptor pairs found in biological systems. Sulphur is found to be a strong hydrogen bond acceptor while its donor capacities are weak. By taking CH acidic H donors into account, a linear correlation between MP2 energies and the increment model with a coefficient of correlation of r2=0.994 has been accomplished. The transferability of the fitted parameters has been assessed on a second set of complexes including larger molecules of biological relevance. Very good agreement has been achieved for noncyclic hydrogen bonds. Cooperative effects are not accounted for by the current increment model. For this reason, binding energies of strong cyclic hydrogen bonds, as e.g. present in DNA base pairs, are underestimated by about 30-40%.

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model

A polarizable empirical force field based on the classical Drude oscillator has been developed for the aliphatic alcohol series. The model is optimized with emphasis on condensed-phase properties and is validated against a variety of experimental data. Transferability of the developed parameters is emphasized by the use of a single electrostatic model for the hydroxyl group throughout the alcohol series. Aliphatic moiety parameters were transferred from the polarizable alkane parameter set, with only the Lennard-Jones parameters on the carbon in methanol optimized. The developed model yields good agreement with pure solvent properties with the exception of the heats of vaporization of 1-propanol and 1-butanol, which are underestimated by approximately 6%; special LJ parameters for the oxygen in these two molecules that correct for this limitation are presented. Accurate treatment of the free energies of aqueous solvation required the use of atom-type specific O(alcohol)-O(water) LJ interaction terms, with specific terms used for the primary and secondary alcohols. With respect to gas phase properties the polarizable model overestimates experimental dipole moments and quantum mechanical interaction energies with water by approximately 10 and 8 %, respectively, a significant improvement over 44 and 46 % overestimations of the corresponding properties in the CHARMM22 fixed-charge additive model. Comparison of structural properties of the polarizable and additive models for the pure solvents and in aqueous solution shows significant differences indicating atomic details of intermolecular interactions to be sensitive to the applied force field. The polarizable model predicts pure solvent and aqueous phase dipole moment distributions for ethanol centered at 2.4 and 2.7 D, respectively, a significant increase over the gas phase value of 1.8 D, whereas in a solvent of lower polarity, benzene, a value of 1.9 is obtained. The ability of the polarizable model to yield changes in dipole moment as well as the reproduction of a range of condensed phase properties indicates its utility in the study of the properties of alcohols in a variety of condensed phase environments as well as representing an important step in the development of a comprehensive force field for biological molecules.

Complex Formation of Trimethylaluminum and Trimethylgallium with Ammonia: Evidence for a Hydrogen-Bonded Adduct

We have investigated the formation of gas-phase adducts of trimethylaluminum and trimethylgallium with ammonia using room-temperature Fourier transform infrared experiments and density functional theory calculations. Our results indicate for the first time that, at higher partial pressures, a product distinct from the well-known (CH3)3M:NH3 adduct grows in for both M = Al and M = Ga. Comparison of the experimental and calculated IR spectra, along with calculations of the energetics, indicates that this second product is the result of hydrogen bonding of a second NH3 molecule to the (CH3)3M:NH3 adduct and can be written as (CH3)3M:NH3...NH3. The binding energy of this hydrogen-bonded adduct is calculated to be 26.8 kcal/mol for M = Al and 18.4 kcal/mol for M = Ga and is lower in energy (more stable) relative to the 1:1 (CH3)3M:NH3 adduct by 7.2 kcal/mol for M = Al and 6.6 kcal/mol for M = Ga. In contrast, an alternative complex involving the formation of two separate M-N donor-acceptor bonds, which is written as H3N:(CH3)3M:NH3, is calculated to be lower in energy relative to (CH3)3M:NH3 by only 0.1 kcal/mol for M = Al and 0.2 kcal/mol for M = Ga and is not observed experimentally. These results show that hydrogen bonding plays an important role in the interaction of ammonia with metal organic precursors involving Al, Ga, and In, under typical metal organic chemical vapor deposition AlGaInN growth conditions.

3-chloropropanoic acid (UMB66): a ligand for the gamma-hydroxybutyric acid receptor lacking a 4-hydroxyl group

Gamma-Hydroxybutyric acid (GHB) has gained in notoriety in recent years due to its association with sexual assaults. GHB is an endogenous ligand for GHB receptors, but its complete pharmacological mechanism of action in vivo remains unclear due to apparent GABAergic components. It has been proposed that the hydroxyl group in the 4-position acts as a hydrogen bond donor to the GHB receptor. Herein we show that 3-chloropropanoic acid possesses significant affinity for the GHB receptor, has no affinity for GABA receptors, and cannot undergo metabolism to GABAergic compounds. UMB66 is thus a selective agent for the study of GHB in vivo. These results, in combination with data from quantum mechanical calculations, suggest that the hydroxyl group of GHB actually acts as a hydrogen bond acceptor in contrast to the currently accepted model. This finding is anticipated to facilitate the rational design of novel agents with selectivity for GHB receptors that may be used to elucidate the mechanism of action of this common drug of abuse.

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water

The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.

Water dimer proton affinity from the kinetic method: dissociation energy of the water dimer

The proton affinity of water dimer was measured, using the kinetic method with nitrile reference bases, to be 808 +/- 6 kJ mol(-1). The difference between the measured value and the proton affinity of a single water molecule (690 +/- 4 kJ mol(-1)) reflects the difference in solvation energy for two neutral water molecules (the hydrogen bond energy of water dimer), and the energy for solvation of hydronium cation and water. Using the measured proton affinity of the dimer along with ancillary data yields an experimental value of the hydrogen bond energy of neutral water dimer, 18 +/- 9 kJ mol(-1), in good agreement with previous experimental and theoretical values. The proton affinity of the dimer measured by using alcohol references is ca 100 kJ mol(-1) too low, likely because the structure of the protonated cluster is not well-suited for kinetic method measurements. These results highlight the importance of choosing reference bases that form cluster ions consisting of a proton bound complex between the water dimer and the reference base.