Molecular structure of proline

The molecular structures of the two lowest-energy conformers of proline, Pro-I and Pro-II, have been characterized by ab initio electronic structure computations. An extensive MP2/6-31G* quartic force field for Pro-I, containing 62,835 unique elements in the internal coordinate space, was computed to account for anharmonic vibrational effects, including total zero-point contributions to isotopomeric rotational constants. New re and improved r0 least-squares structural refinements were performed to determine the heavy-atom framework of Pro-I, based on experimentally measured (A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J. C. Lopez, J. L. Alonso, Angew. Chem. 2002, 114, 4867; Angew. Chem. Int. Ed. 2002, 41, 4673) rotational constant sets of nine isotopomers and our ab initio data for structural constraints and zero-point vibrational (ZPV) shifts. Without the ab initio constraints, even the extensive set of empirical rotational constants cannot satisfactorily fix the molecular structure of the most stable conformer of proline, a 17-atom molecule with no symmetry. After imposing the ab initio constraints, excellent agreement between theory and experiment is found for the heavy-atom geometric framework, the root-mean-square (rms) residual of the empirical rotational constant fit being cut in half by adding ZPV corrections. The most significant disparity, about 0.07 A, between the empirical and the best ab initio structures, concerns the r(N...H) distance of the intramolecular hydrogen bond. Some of the experimental quartic centrifugal distortion constants assigned to Pro-II have been corrected based on data obtained from a theoretical force field.     

Molecular structures of the two most stable conformers of free glycine

The equilibrium molecular structures of the two lowest-energy conformers of glycine, Gly-Ip and Gly-IIn, have been characterized by high-level ab initio electronic structure computations, including all-electron cc-pVTZ CCSD(T) geometry optimizations and 6-31G* MP2 quartic force fields, the latter to account for anharmonic zero-point vibrational effects to isotopologic rotational constants. Based on experimentally measured vibrationally averaged effective rotational constant sets of several isotopologues and our ab initio data for structural constraints and zero-point vibrational shifts, least-squares structural refinements were performed to determine improved Born-Oppenheimer equilibrium (r(e)) structures of Gly-Ip and Gly-IIn. Without the ab initio constraints even the extensive set of empirical rotational constants available for 5 and 10 isotopologues of Gly-Ip and Gly-IIn, respectively, cannot satisfactorily fix their molecular structure. Excellent agreement between theory and experiment is found for the rotational constants of both conformers, the rms residual of the final fits being 7.8 and 51.6 kHz for Gly-Ip and Gly-IIn, respectively. High-level ab initio computations with focal point extrapolations determine the barrier to planarity separating Gly-IIp and Gly-IIn to be 20.5 +/- 5.0 cm(-1). The equilibrium torsion angle tau(NCCO) of Gly-IIn, characterizing the deviation of its heavy-atom framework from planarity, is (11 +/- 2) degrees. Nevertheless, in the ground vibrational state the effective structure of Gly-IIn has a plane of symmetry.     

Equilibrium structure and spectroscopic constants of maleic anhydride

The quadratic, cubic, and semi-diagonal quartic force fields of maleic anhydride have been calculated at the MP2 level of theory employing the cc-pVTZ basis set. The spectroscopic constants derived from the force field are in excellent agreement with the corresponding experimental values. The semi-experimental equilibrium structure has been derived from experimental ground state rotational constants and rovibrational corrections calculated from the cubic force field. This semi-experimental equilibrium structure is in excellent agreement with the ab initio structures computed at the CCSD(T) level of theory and it is closer to the ab initio structure than the purely experimental (or empirical) structures r ₀, r _m⁽¹⁾, and r _m⁽²⁾ obtained by microwave spectroscopy as well as the equilibrium structure derived from gas-phase electron diffraction data.     

Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc.     

Covalent Structures of Phosphorus: A Comprehensive Theoretical Study

Starting from earlier work by Baudler we introduce a chemical heuristic for the systematic deduction and classification of covalent partial structures of phosphorus in polycyclic phosphanes, phosphorus-rich polycyclic phosphides, and allotropes of phosphorus except the black forms. This approach is used to direct ab initio techniques (which also confirm the rules) in the quest for as yet unknown forms of molecular or macromolecular phosphorus. Based on calculated stabilities of systematically generated structural alternatives we rationalize the stabilities of Hittorf's phosphorus and of molecular P₄, confirm the possible existence of at least one other crystalline allotropic form of phosphorus, and provide insight into the probable structure of amorphous red phosphorus. In total, the combined approach of chemical heuristics and large scale ab initio calculations presented in this work supplies a coherent chemical understanding of covalent polyphosphorus structures.     

A first principles study on the structure of ice-VI: static distortion, molecular geometry, and proton ordering

We have studied the structure of ice-VI by examining all ice-rule-allowed structures in its primary unit cell of 10 water molecules with first principles methods. A significant amount of static distortions in the oxygen positions away from their crystallographic positions are found, which is in good agreements with significant higher-order terms in the atomic displacement parameters obtained from X-ray and neutron diffraction data. Structural anomalies (such as exceptionally short OH bonds and small H-O-H angles) noted in conventional crystal structure refinements were not seen in our ab initio calculations, and it is evident that these structural anomalies arose from oversimplified models in which static distortions are not properly accounted for. Our results also show that the molecular geometry of water in ice-VI is similar to but richer than those in ice-Ih and ice-VII. Larger distortions in bond lengths/angles and correlation between the molecular geometry and the neighboring environments were found. Different proton-ordering schemes proposed in the literature were examined, and our calculations provide evidence in favor of a ferroelectric phase of the proton-ordered counterpart of ice-VI at about 80 K.     

Ab initio study of electronic structures of Ptn clusters (n = 2–12)

Electronic structures of a series of Pt_n clusters (n = 2–12) have been calculated by ab initio method (SCF/MP2). The result shows that compared to that at the saturated coordination site, Pt at the unsaturated coordination site has lower Pt₆₅ electron occupancies, and the relationship between the electronic structure and the cluster size has been discussed. It is found that when the number of Pt in cluster reaches 7, electronic structures become more like the metallic ones. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62 : 427–436, 1997     

NMR crystallography of zeolites: refinement of an NMR-solved crystal structure using ab initio calculations of 29Si chemical shift tensors

An NMR structure refinement method for the NMR crystallography of zeolites is presented and demonstrated to give an NMR-determined crystal structure for the zeolite Sigma-2 that is in very good agreement with the single-crystal X-ray diffraction structure. The Si coordinates of the zeolite framework were solved from 29Si double-quantum NMR data obtained at a low magnetic field strength (7.0 T) and the Si and O coordinates were subsequently refined using the principal components of 29Si chemical shift tensors experimentally measured at an ultrahigh-field (21.1 T) and calculated using ab initio quantum chemical methods.     

Quantum Mechanical-Based Stability Evaluation of Crystal Structures for HIV-Targeted Drug Cabotegravir

The long-acting parenteral formulation of the HIV integrase inhibitor cabotegravir (GSK744) is currently being developed to prevent HIV infections, benefiting from infrequent dosing and high efficacy. The crystal structure can affect the bioavailability and efficacy of cabotegravir. However, the stability determination of crystal structures of GSK744 have remained a challenge. Here, we introduced an ab initio protocol to determine the stability of the crystal structures of pharmaceutical molecules, which were obtained from crystal structure prediction process starting from the molecular diagram. Using GSK744 as a case study, the ab initio predicted that Gibbs free energy provides reliable further refinement of the predicted crystal structures and presents its capability for becoming a crystal stability determination approach in the future. The proposed work can assist in the comprehensive screening of pharmaceutical design and can provide structural predictions and stability evaluation for pharmaceutical crystals.     

Chemical shift driven geometry optimization

A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out.     

A molecular dynamics study of small water clusters comparing two flexible models for water

We report results from a molecular dynamics study of small water clusters, (H₂O) _n=2,3,4,6,8, comparing the recent polarizable, dissociable (PD) model of Halley et al. with the central force Stillinger-Rahman (SR) model. Dynamics calculations in the microcanonical ensemble quantified short-time averaged temperatures and RMS bond length fluctuations, which, in combination with simulated thermal quenching, identified structures and structural and phase changes of the clusters. Both models generally pointed to similar global minimum energy configurations, but local minima configurations, relative energies, and RMS bond length fluctuations varied more significantly. The PD model, with its incorporation of many-body effects, more accurately reproduced the structural features of clusters predicted from ab initio calculations, although it over-estimated the binding energies. Solid-like, pre-melting, and liquid-like states were identified based upon RMS bond length fluctuations for the O-O, O-H and H-H pairs. The SR and PD models yielded very similar trends in melting temperature as a function of cluster size. This suggests that general trends in the melting phenomenon do not depend strongly upon details of the models. The melting temperatures for the dimer and tetramer closely resembled the bulk melting temperature, while those for other sizes were considerably lower.     

Pseudo‐Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP‐12 from First Principles

Long‐range pseudo‐contact NMR shifts (PCSs) provide important restraints for the structure refinement of proteins when a paramagnetic metal center is present, either naturally or introduced artificially. Here we show that ab initio quantum‐chemical methods and a modern version of the Kurland–McGarvey approach for paramagnetic NMR (pNMR) shifts in the presence of zero‐field splitting (ZFS) together provide accurate predictions of all PCSs in a metalloprotein (high‐spin cobalt‐substituted MMP‐12 as a test case). Computations of 314 ¹³C PCSs using g‐ and ZFS tensors based on multi‐reference methods provide a reliable bridge between EPR‐parameter‐ and susceptibility‐based pNMR formalisms. Due to the high sensitivity of PCSs to even small structural differences, local structures based either on X‐ray diffraction or on various DFT optimizations could be evaluated critically by comparing computed and experimental PCSs. Many DFT functionals provide insufficiently accurate structures. We also found the available 1RMZ PDB X‐ray structure to exhibit deficiencies related to binding of a hydroxamate inhibitor. This has led to a newly refined PDB structure for MMP‐12 (5LAB) that provides a more accurate coordination arrangement and PCSs.     

VBEFP: a valence bond approach that incorporates effective fragment potential method

An ab initio explicit solvation valence bond (VB) method, called VBEFP, is presented. The VBEFP method is one type of QM/MM approach in which the QM part of system is treated within the ab initio valence bond scheme and the solvent water molecules are accounted by the effective fragment potential (EFP) method, which is a polarized force field approach developed by Gordon et al. (J. Chem. Phys. 1996, 105, 1968). This hybrid method enables one to take the first-solvation shell and heterogeneous solvation effects into account explicitly with VB wave function. Therefore, the nature of chemical bonding and the mechanism of chemical reactions with explicit solvent environments can be explored at the ab inito VB level. In this paper, the hydrated metal-ligand complexes [M(2+)L](H(2)O)(n) (M(2+): Mg(2+), Zn(2+); L: NH(3), CH(2)O) are studied by the VBEFP method. Resonance energy and bond order are computed, and the influence of the solvent coordination and hydrogen bonding to the metal-ligand bonding are explored in the paper.     

精密从头算与ABEEM/MM模型对水团簇(H2O)11 9种低能结构的计算

用精密从头算方法研究了(H2O)11的9种低能异构体的性质, 包括优化的几何结构、结合能、偶极矩和氢键个数等, 并且得出了515-a是(H2O)11的全局最低能结构. 同时, 也用ABEEM/MM(atom bond electronegativity equalization method/molecular mechanics) 模型研究了这些性质, 与从头算的结果进行了比较, 得到了相符合的结果. 这显示了ABEEM/MM模型在描述中等大小的水分子团簇结构上是成功的.     

Resonance and aromaticity: an ab initio valence bond approach

Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randi?'s conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.     

Ab initio studies of structural features not easily amenable to experiment : Part 13. Structural consequences of methyl hyperconjugation in some CH3C(=X)Y systems

The molecular structures of several conformations of acetaldehyde, acetic acid and isobutene were completely refined by standard single determinant ab initio procedures on the 4–21G level. Calculated and experimental parameters are in close agreement in all the cases in which the experimental values can be considered as reliably established. In some examples, however, some essential structural features that should be found in CH₃C(=X)Y systems have not yet been resolved by any experimental technique. The structural consequences for methyl hyperconjugation in the various systems are discussed. The study demonstrates that high quality ab initio geometries can provide information which is complementary to experimental results. The calculations are particularly useful in discussing discrepancies between microwave and electron diffraction structures and in interpreting microwave substitution structure uncertainties which are often difficult to determine accurately.     

Semiempirical MO methods: the middle ground in molecular modeling

Semiempirical methods occupy an important middle ground between molecular mechanics and ab initio MO calculations in the repertoire of methods available for studying the structures, properties and reactions of molecules. They have a unique combination of speed and generality which makes it possible to study many chemical systems which are beyond the reach of classical force fields and too large for ab initio MO methods. Indeed, semiempirical calculations are often the first computational technique to be applied to a chemical problem. Three examples where semiempirical MO calculations have provided significant mechanistic insight are the cylcopropylcarbinyl cation, porphyrin structure and dynamics, and the role of C---H hydrogen bonds in polymer miscibility. In each case Semiempirical calculations have been at the fore, and their results have been generally confirmed by subsequent ab initio calculations and experiment.     

Modeling van der Waals interactions between proteins and inorganic surfaces from time-dependent density functional theory calculations

In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.