Accurate thermochemistry from quantum chemical calculations?

The answer to the title question is definitely “yes” – at least for fairly small molecules. Computational procedures, namely the Weizmann (Wn) and Gaussian-3 (G3) family of methods, the complete basis set extrapolation scheme (CBS-x), the “high accuracy extrapolated ab initio thermochemistry” (HEAT) as well as the “correlation consistent composite approach” (ccCA), aimed at energies with chemical accuracy or even better (sub kJ?mol^?1) are described and several applications illustrating the level of accuracy that can be achieved are presented.     

Does the presence of water clusters induce the binding affinity of CK2 halogen ligands?: A quantum chemical perspective study

Protein–ligand interaction is the key factor in modeling of drugs and water molecules act as a bridge in linking protein and ligand, which was clearly depicted by Deepa (Cryst. Growth Des. 2017 , 17, 1299). This work is intended toward the significance of water cluster in the midst of ligand binding. Further the idea was accounted to have in‐depth analysis of the individual water molecules that interact with each part of the ligand, since in reality only very few crystal water molecules bind with the CK2 ligands. Further, bulk solvent effects have been modeled using Tomasi's polarized continuum model at M06‐2X/def2‐QZVP levels of theory has increased the stability of the complexes. The strength of individual water molecules and their binding nature with ligand will be depicted in detail by interaction energy and two body interaction energy calculations at M06‐2X/def2‐QZVP level of theory. The impact of noncovalent interactions (Hydrogen, σ‐hole and Π‐hole bonding) in bridging between water cluster cavity and ligand were deeply analysed using structural properties (bond distance and bond angle), 2DNCI plot, AIM and NBO analyses. The HOMO, LUMO energy values are discussed in detail for both monomer (ligand) and complexes (ligand with water clusters). It is expected that this study paves a novel path for the scientific community in modeling drugs with the clear understanding of the impact of water molecules on ligand.     

Can MM/GBSA calculations be sped up by system truncation?

We have studied whether calculations of the binding free energy of small ligands to a protein by the MM/GBSA approach (molecular mechanics combined with generalized Born and surface area solvation) can be sped up by including only a restricted number of atoms close to the ligand. If the protein is truncated before the molecular dynamics (MD) simulations, quite large changes are observed for the calculated binding energies, for example, 4 kJ/mol average difference for a radius of 19 Å for the binding of nine phenol derivatives to ferritin. The results are improved if no atoms are fixed in the simulations, with average and maximum errors of 2 and 3 kJ/mol at 19 Å and 3 and 6 kJ/mol at 7 Å. Similar results are obtained for two additional proteins, p38α MAP kinase and factor Xa. On the other hand, if energies are calculated on snapshots that are truncated after the MD simulation, all residues more than 8.5 Å from the ligand can be omitted without changing the energies by more than 1 kJ/mol on average (maximum error 1.4 kJ/mol). At the molecular mechanics level, the gain in computer time for such an approach is small. However, it shows what size of system should be used if the energies instead are calculated with a more demanding method, for example, quantum‐mechanics. © 2017 Wiley Periodicals, Inc.     

Can the four-coordinated, penta-valent oxygen in hydroxide water clusters be detected through experimental vibrational spectroscopy?

In this study, we construct the hydroxide water cluster, OH-(H2O)6, that (a) could support a stable hydroxide ion with a four-coordinated (pentavalent) hydroxide oxygen and (b) displays hydroxide ion migration. We study the energetic stability and dynamical evolution of the system at different internal temperatures and analyze the corresponding "dynamically averaged" vibrational density of states to discuss the conditions under which the pentavalent oxygen may be observed using vibrational action spectroscopy. We also provide an alternate hydroxide migration mechanism.     

Vibronic spectra of jet-cooled 2-aminopurine·H2O clusters studied by UV resonant two-photon ionization spectroscopy and quantum chemical calculations

For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine·H(2)O monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift δν of the S(1) ← S(0) transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (δν = -889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H(2)O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D(e) = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)ππ* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S(0) state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)ππ* state to the lower-lying (1)nπ* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)ππ* state of B is planar and decoupled from the (1)nπ* state. These observations agree with the calculations, which predict the (1)nπ* above the (1)ππ* state for isomer B but below the (1)ππ* for both 9H-2AP and isomer A.     

Elucidating the intermolecular hydrogen bonding interaction of proline with amides—quantum chemical calculations

Structural Chemistry - The hydrogen-bonded complexes formed between proline and amides have been investigated completely by the use of computational methods such as Atoms In Molecules (AIM),...     

Can the pi-facial selectivity of solvation be predicted by atomistic simulation?

This work is concerned with the rationalization and prediction of solvent and temperature effects in nucleophilic addition to alpha-chiral carbonyl compounds leading to facial diastereoselectivity. We study, using molecular dynamics simulations, the facial solvation of (R)-2-phenyl-propionaldehyde in n-pentane and n-octane at a number of temperatures and compare it with experimental selectivity data for the nBuLi addition leading to syn- and anti-(2R)-2-phenyl-3-heptanol, which give nonlinear Eyring plots with the presence of inversion temperatures. We have found from simulations that the facial solvation changes with temperature and alkane. Moreover, by introducing a suitable molecular chirality index we have been able to predict break temperatures (T(CI)) for the two solvents within less than 20 degrees of the inversion temperatures experimentally observed in the diastereoselective nBuLi addition. We believe this could lead to a viable approach for predicting inversion temperatures and other subtle solvent effects in a number of stereoselective reactions.     

Electronic structure of hydantoin studied by He I photoelectron spectroscopy and MNDO quantum—chemical calculations

The He I photoelectron spectra of hydantoin, 1-methyl-hydantoin, 3-methylhydantoin and 1,3-dimethylhydantoin are reported. Displacement of the bands upon the N-methylsubstitution indicates that HOMO and the third highest occupied MO are localized on the nitrogen atoms, the former on the amidic nitrogen and the latter on the imidic one. The second and the fourth highest occupied MO's are oxygen lone pairs. The MNDO method provides the same picture.     

Host–guest complexes of mixed glycol-phenanthroline cryptands: prediction of ion selectivity by quantum chemical calculations IV

Abstract Structures and complex-formation energies, calculated with DFT (B3LYP/LANL2DZp) for the cryptands [2.2.phen] and [2.phen.phen] with endohedrally complexed alkali and alkaline earth metal ions, were utilized to predict their ion selectivity. Both cryptands [2.2.phen] and [2.phen.phen] have a cavity size smaller than [2.2.2], [phen.phen.phen] and [bpy.bpy.bpy], and prefer to bind K⁺ and Sr²⁺, whereas [2.2.phen] that is larger than [2.phen.phen], has a preference for Ba²⁺, and [2.phen.phen] favours Na⁺ and Ca²⁺. The cryptand flexibility is mainly attributed to the presence of CH₂–N_SP3···N_SP3–CH₂ groups. Graphical abstract Host–Guest Complexes of mixed Glycol-Phenanthroline Cryptands—Prediction of Ion Selectivity by Quantum Chemical Calculations III Ralph Puchta* and Rudi van Eldik Keywords Cation selectivity Host–guest DFT DFT-studies allow a sensitive analysis of selectivity and cage size. Calculations predict a favourable binding of K⁺, Sr²⁺ and Ba²⁺ by [2.2.phen], and binding of K⁺, Na⁺, Ca²⁺ and Sr²⁺ by [2.phen.phen]. The cryptands fold around the ions by twisting their torsion angles in order to reach the best coordination mode for each cation. For “Prediction of ion selectivity by quantum chemical calculations III” see, R. Puchta, R. van Eldik. Aust. J. Chem. 60, 889–897 (2007).     

Can ortho-para transitions for water be observed?

The spectrum of water can be considered as the juxtaposition of the spectra of two molecules, with different total nuclear spin: ortho-H2O, and para-H2O. No transitions have ever been observed between the two different nuclear-spin isotopomers. The interconversion time is unknown and it is widely assumed that interconversion is forbidden without some other intervention. However, weak nuclear spin-rotation interaction occurs and can drive ortho to para transitions. Ab initio calculations show that the hyperfine nuclear spin-rotational coupling constants are about 30 kHz. These constants are used to explore the whole vibration-rotation spectrum with special emphasis on the coupling between nearby levels. Predictions are made for different spectral regions where the strongest transitions between ortho and para levels of water could be experimentally observed.     

How strong can the bend be on a DNA helix from cisplatin? DFT and MP2 quantum chemical calculations of cisplatin-bridged DNA purine bases

The B3LYP/6-31G(d) level of theory was used for the optimization of [Pt(NH(3))(4)](2+), [Pt(NH(3))(3)(H(2)O)](2+), cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), and related platinum complexes. In addition, water or ammonium ligands were replaced by DNA purine bases so that finally cis-diammineplatinum with two bases (Pt-bridged complexes) is obtained. Single point calculations using the MP2/6-31+G(d) method were performed on the obtained reference geometries and were utilized for estimating bond dissociation energies (BDEs) and stabilization energies, and for electron density analyses. After reoptimization, IR spectra were determined from HF second derivatives. It was found that replacement of both water and ammonium by the DNA base is an exothermic process (20-50 kcal/mol depending on the ligands present in the complex). Asymmetric structures with one interbase H-bond were obtained for cis-diammine[bond](N(7),N(7)'-diadenine)[bond]platinum and mixed cis-diammine[bond](N(7)-adenine)[bond](N(7)-guanine)[bond]platinum complexes. In the case of the diguanine Pt-bridge, a symmetrical complex with two ammonium...O(6) H-bonds was found. The higher stabilization energy of the di-guanine complex is linked to a larger component of the Coulombic interaction. However, the BDE of Pt[bond]N(7)(G) is smaller in this complex than the BDE of Pt[bond]N(7)(G) from the mixed Pt[bond]AG complex. Also, steric repulsion of the ligands is about 10 kcal/mol smaller for the asymmetrical Pt[bond]AA and Pt[bond]AG bridges. The influence of the trans effect on DBE can be clearly seen. Adenine exhibits the largest trans effect, followed by guanine, ammonium, and water. The strength of the H-bond can be determined from the IR spectra. The strongest H-bond is the interbase H-bridge between adenine and guanine in the mixed Pt[bond]AG complex; otherwise, the H-bonds of adenine complexes are weaker than in guanine complexes. BDE can be traced in the guanine-containing complexes. The nature of the covalent bonding is analyzed in terms of partial charges and MO. A general explanation of the lower affinity of transition metals to oxygen than nitrogen can be partially seen in the less favorable geometrical orientation of lone electron pairs of oxygen.     

Radiation-induced chemical reactions of carbon monoxide and hydrogen mixture—IV. On the water produced by the addition of small amounts of ammonia

The isotope content in water obtained from irradiated CO-H₂ mixture with added small amounts of NH₃ or their deuterated equivalents was compared. Compared with that in water obtained from CO-D₂ mixture with added NH₃, D content in water produced from the mixture with the substitution of ND₃ for NH₃ was increased remarkably. The NH₃ added to the mixture contributes to the water formation under irradiation.     

Can the light scattering depolarization ratio of small particles be greater than 1/3?

According to the theory of light scattering by small randomly oriented particles, the depolarized ratio of the scattered intensities, I(vh)/I(vv), cannot exceed 1/3. Here we show that this conclusion does not hold for nonspherical plasmon resonant metal particles. Our analysis is based on the Rayleigh approximation and the exact T-matrix method as applied to spheroids and circular cylinders with semispherical ends. For small particles, the condition I(vh)/I(vv) >1/3 can be satisfied within the upper left quadrant of the complex relative dielectric permeability Real(eps) < -2 (rods) and within the upper unit semicircle centered at Real(eps) = -1 (disks). For gold nanorods with the axis ratio exceeding 2, the maximal theoretical values I(vh)/I(vv) lie between 1/3 and 3/4 at wavelengths of 550-650 nm. The extinction and static light scattering spectra (450-850 nm, at 90 degrees degrees) as well as the depolarized ratio of He-Ne laser light scattering were measured with gold nanospheres (the average diameters of 21, 29, and 46 nm) and nanorods (the longitudinal plasmon resonance peak positions at 655, 692, and 900 nm). The measured depolarization ratios of nanospheres (0.07-0.16) and nanorods (0.3-0.48) are in good agreement with theoretical calculations based on estimations of the average particle size and shape.     

Can the provenance of the conflict minerals columbite and tantalite be ascertained by laser-induced breakdown spectroscopy?

Conflict minerals is a term applied to ores mined in conditions of armed conflict and human rights abuse. Niobium and tantalum are two rare metals whose primary natural occurrence is in the complex oxide minerals columbite and tantalite, the ore of which is commonly referred to as coltan. The illicit export of coltan ore from the Democratic Republic of the Congo is thought to be responsible for financing the ongoing civil conflicts in this region. Determining the chemical composition of an ore is one of the means of ascertaining its provenance. Laser-induced breakdown spectroscopy (LIBS) offers a means of rapidly distinguishing different geographic sources for a mineral because the LIBS plasma emission spectrum provides the complete chemical composition (i.e., “chemical fingerprint”) of any material in real time. To test this idea for columbite–tantalite, three sample sets were analyzed. Partial least squares discriminant analysis (PLSDA) allows correct sample-level geographic discrimination at a success rate exceeding 90%.     

More user-friendly phosphines? Molecular structure of methylphosphine and its adduct with borane, studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of methylphosphine (CH(3)PH(2)) and methylphosphine-borane (CH(3)PH(2).BH(3)) have been determined from gas-phase electron diffraction data and rotational constants, employing the SARACEN method. The experimental geometric parameters generally showed a good agreement with those obtained using ab initio calculations and previous microwave spectroscopy studies. In order to assess the accuracy of the calculated structures a range of ab initio methods were used, including the CCSD(T) method, with correlation-consistent basis sets. The structural environment around the phosphorus atom was found to change significantly upon complexation with borane, with the P-C bond length shortening and the bond angles widening.     

Can B3LYP be improved by optimization of the proportions of exchange and correlation functionals?

B3LYP is the most famous hybrid density functional theory model, which includes Hartree–Fock exchange, local exchange, gradient exchange correction, local correlation, and gradient correlation correction. Historically, the relative weight of each component in B3LYP, which is controlled by three empirical parameters (a₀, a_x, a_c), has not been optimized. In this work, we perform global optimization against accurate experimental reference, optimal empirical parameters, and the better version of B3LYP are obtained and denoted as OpB3LYP. The performance of OpB3LYP is widely tested over many species and chemical properties, the results show that the computational accuracy is significantly improved as compared to original B3LYP and the serious size dependence of B3LYP is remarkably overcome by the employment of OpB3LYP. The comparative assessment of OpB3LYP and other prevalent functionals indicates that OpB3LYP is a promising functional for large molecules. © 2015 Wiley Periodicals, Inc.     

On the value of c: can low affinity systems be studied by isothermal titration calorimetry?

Isothermal titration calorimetry (ITC) allows the determination of DeltaG degrees, DeltaH degrees, and DeltaS degrees from a single experiment and is thus widely used for studying binding thermodynamics in both biological and synthetic supramolecular systems. However, it is widely believed that it is not possible to derive accurate thermodynamic information from ITC experiments in which the Wiseman "c" parameter (which is the product of the receptor concentration and the binding constant, K(a)) is less than ca. 10, constraining its use to high affinity systems. Herein, experimental titrations and simulated data are used to demonstrate that this dogma is false, especially for low affinity systems, assuming that (1) a sufficient portion of the binding isotherm is used for analysis, (2) the binding stoichiometry is known, (3) the concentrations of both ligand and receptor are known with accuracy, and (4) there is an adequate level of signal-to-noise in the data. This study supports the validity of ITC for determining the value of K(a) and, hence, DeltaG degrees from experiments conducted under low c conditions but advocates greater caution in the interpretation of values for DeltaH degrees. Therefore, isothermal titration calorimetry is a valid and useful technique for studying biologically and synthetically important low affinity systems.     

Can we understand the different coordinations and structures of closed‐shell metal cation‐water clusters?

We present a model potential for studying M(q+)(H(2)O)(n=1,9) clusters where M stands for either Na(+), Cs(+), Ca(2+), Ba(2+), or La(3+). The potential energy surfaces (PES) are explored by the Monte Carlo growth method. The results for the most significant equilibrium structures of the PES as well as for energetics are favorably compared to the best ab initio calculations found in the literature and to experimental results. Most of these complexes have a different coordination number in cluster compared to experimental results in solution or solid phase. An interpretation of the coordination number in clusters is given. In order to well describe the transition between the first hydration sphere and the second one we show that an autocoherent treatment of the electric field is necessary to correctly deal with polarization effects. We also explore the influence of the cation properties (charge, size, and polarizability) on both structures and coordination number in clusters, as well as the meaning of the second hydration sphere. Such an approach shows that the leading term in the interaction energy for a molecule in the second hydration sphere is an electrostatic attraction to the cation and not a hydrogen bond with the water molecules in the first hydration sphere.     

Where does the planar-to-nonplanar turnover occur in small gold clusters?

Several levels of theory, including both Gaussian-based and plane wave density functional theory (DFT), second-order perturbation theory (MP2), and coupled cluster methods (CCSD(T)), are employed to study Au6 and Au8 clusters. All methods predict that the lowest energy isomer of Au6 is planar. For Au8, both DFT methods predict that the two lowest isomers are planar. In contrast, both MP2 and CCSD(T) predict the lowest Au8 isomers to be nonplanar.