Scaled quantum mechanical force field for glycine in basic solution

We obtain scale factors for three glycinate-nH₂O ab initio force fields, using the 4–31G basis set, that can be used in building a scaled quantum mechanical force field for alanine and, subsequently, for peptides in aqueous solutions. Force constants from the fully optimized glycinate-nH₂O supermolecules were scaled by using experimentally determined vibrational frequencies of glycine in water at pH 13. Similar calculations were performed for methylamine and acetate. Scale factors for the stretching modes of acetate are within 2% of the related scale factors for glycinate. The scale factor for the NH₂ scissor mode in methylamine is also in agreement with that of glycinate. Changes in the scale factors as a function of the number of hydrating water molecules were also similar between glycinate and acetate. Amine groups showed relatively small changes. Scale factors for glycinate with no hydrating molecules were extrapolated from the supermolecule results, since the optimized structure of isolated glycinate obtained with the 4–31G basis set yielded one imaginary frequency. Good agreements between calculated and experimental frequencies for glycinate, acetate, and methyl amine were obtained for each set of scale factors. Scaling appears to compensate for the systematic effects of hydration on force constants, making it possible to obtain reliable frequency predictions for amino acids in water without resorting to expensive super-molecule calculations.     

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.     

Theoretical electronic structure of the molecule ScBr

The potential energy curves have been investigated for the 23 lowest electronic states in the ^2s+1Λ^± representation of the molecule ScBr via CASSCF and MRCI (single and double excitations with Davidson correction) calculations. Seventeen electronic states have been studied theoretically for the first time. The harmonic frequency ω_e, the internuclear distance r_e, and the electronic energy with respect to the ground state T_e have been calculated. By using the canonical functions approach, the eigenvalues E_v, the rotational constant B_v, and the abscissas of the turning points (R_min, R_max) have been calculated for electronic states up to the vibrational level v = 32. The comparison of these values to the theoretical and experimental results available in the literature shows a good agreement. © 2007 Wiley Periodicalsm Inc. Int J Quantum Chem, 2008     

Harmonic force field for glycine oligopeptides

The need for much more useful molecular dynamics simulations of nanosized system requires precise and unambiguous methods to determine force field parameters avoiding fitting procedures in favor of first principles ones. We use a procedure FUERZA to calculate force constant parameters for glycine oligopeptides using as an input the Hessian tensor from an ab initio calculation. For a molecular system having n atoms, The FUERZA procedure reduces the 3n × 3n problem to 3n 3 × 3 matrices representing atom‐atom interactions. The procedure reproduces quite well most of the frequencies and as expected, it overestimates somehow stretching frequencies of bonds with terminal atoms such as hydrogens but it yields precise results for all other frequencies. A harmonic force field is reported for glycine oligopeptides. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical calculation of the low laying electronic states of the molecular ion RbH+

Using an ab initio method, the potential energy has been calculated for the 29 lowest molecular states of symmetries ²Σ⁺, ²Π, ²Δ for the molecular ion RbH⁺. The calculation is based on nonempirical pseudopotentials and parameterized ?‐dependent polarization potentials. Gaussian basis sets have been used for both atoms. The spectroscopic constants for 18 electronic sates have been calculated by fitting the calculated energy values to a polynomial in terms of the internuclear distance R. Through the canonical functions approach the eigenvalue E_v, the abscissas of the corresponding turning points (R_min and R_max) and the rotational constants B_v have been calculated up to 24 vibrational levels for the considered bound states. The comparison of the present results with those available in literature shows a very good agreement. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Development of the force field parameters for phosphoimidazole and phosphohistidine

Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule--a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent.     

Theoretical structure of the low‐laying electronic states of the molecule YBr

An ab initio CASSCF and MRCI (single and double excitation plus Davidson correction) calculation have been performed for the molecule YBr. The potential energy curves of 20 electronic states in the representation ^2s+1Λ^(+/?) (neglecting the spin‐orbit effects) and 41 states in the representation Ω^(+/?) [including the spin‐orbit (SO) effects] have been calculated along with the corresponding spectroscopic constants. The SO effects are taken into account via a semi‐empirical SO pseudo‐potential for the yttrium atom, while they have been neglected for bromine. Very good agreement is displayed by comparing the present results with those obtained experimentally, up to now, of the three states X¹Σ⁺, (1)²Π, and (2)¹Σ⁺. New results have been obtained for 17 states ^2s+1Λ^(+/?), and their SO components yet not observed or calculated. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Conformers of dehydrogenated glycine isomers

We report a comprehensive ab initio investigation of the conformers of dehydrogenated glycine radicals using the STO-3G, 3-21G, and aug-cc-pVDZ (aVDZ) basis sets and the UHF and UMP2 (H₂N-CH-COOH and HN-CH₂-COOH) as well as MCSCF and MRCI (H₂N-CH₂-COO) methods via two different conformational search strategies generating initial structures for optimizations by (a) removing H atoms from glycine conformers and (b) scanning torsional angles describing internal rotation along the C C, C N, and C O (except for H₂N-CH₂-COO) bonds of the radicals. We find four H₂N-CH-COOH {In_CH, IIn_CH, IIIn_CH, IVn_CH} and seven HN-CH₂-COOH {Ip_NH, IIp_NH, IIIn_NH, IVp_NH Vn_NH, VIp_NH, VIIp_NH} conformers with classical(adiabatic) relative energies of {0.00(0.00), 1.57(1.55), 5.25(5.03), 9.85(9.72)} and {0.00(0.00), 0.78(1.06), 1.93(2.08), 3.34(3.16), 3.39(3.29), 5.00(4.86), 9.27(8.87)} kcal/mol, respectively, obtained with UCCSD(T)-F12b/aug-cc-pVTZ(+UCCSD(T)-F12b/aVDZ ZPE correction) and four H₂N-CH₂-COO {Ip_COO, IIn_COO, IIIp_COO, IVn_COO} conformers with MRCI-F12+Q/aVDZ(+MRCI/aVDZ ZPE correction) energies of {0.00(0.00), 1.65(1.64), 1.78(1.75), 2.21(2.21)} kcal/mol, where n and p denote C₁ and C_s symmetry. The MRCI-F12+Q[UCCSD(T)-F12b] In_CH → Ip_NH and In_CH → Ip_COO classical(adiabatic) isomerization energies are 18.51(17.32)[21.20(20.01)] and 31.88(31.66) kcal/mol, respectively.     

Conformers of gaseous protonated glycine

Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller–Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH₃⁺ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)₂⁺. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0–10 and 30–40 kcal mol⁻¹. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1862–1876, 1998     

Theoretical electronic studies of aluminum monobromide and aluminum monoiodide

By using CASSCF/MRCI methods, theoretical molecular calculations have been performed for 12 electronic states for AlBr molecule and 12 electronic states for AlI molecule in the representation ^2s+1Λ (neglecting spin‐orbit effects). Calculated potential energy curves are displayed. Spectroscopic constants including the harmonic vibrational wave number ω_e, the electronic energy T_e referred to the ground state and the equilibrium internuclear distance R_e are predicted for these singlet and triplet electronic states for both AlBr and AlI molecules. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

An ab initio force field for the cofactors of bacterial photosynthesis

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.     

Molecular structures of acetylene derivatives of tin

The geometry and force fields of the bis(trimethylstannyl)acetylene molecule (a conformer withD _3d symmetry corresponding to a minimum of the total energy of the molecule) were calculated by the RHF and MP2(fc) methods. The effective core potential in SBK form with the optimized 31G^* valence basis set was employed in the case of Sn atoms. The 6–31G^** and 6–311G^** basis sets were used for carbon and hydrogen atoms. Vibrational spectra of the light and perdeuterated isotopomers of bis(trimethylstannyl)acetylene were interpreted using the procedure of scaling the quantum-chemical force fields. For Part 5, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 616–626, April, 2000.     

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations

The interaction of Zn²⁺ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn²⁺ complex are first established via high‐level ab initio calculations. Two low‐energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas‐phase affinity of glycine for Zn²⁺. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn²⁺‐binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn²⁺–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all‐electron 6‐311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4‐31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn²⁺. Thus, the supermolecule is treated as a three‐body rather than a two‐body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 963–973, 2000     

Theoretical study of spectroscopic constants and molecular properties of rare‐gas diatomic cations

Ab initio and density functional methods are applied to study the spectroscopic constants and molecular properties of the diatomic cations He, Ne, Ar, HeNe⁺, and HeAr⁺. Among these cations, HeAr⁺ is found to be weakly bound and its spectroscopic constants are calculated using the Lennard‐Jones potential. The other molecules that are strongly bound obey Morse potential, and their spectroscopic constants are calculated accordingly. The calculated spectroscopic constants agree very well with the theoretical and experimental values wherever available. Most of the spectroscopic constants and molecular properties are reported for the first time. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Gas‐phase interactions of organotin compounds with glycine

Gas‐phase interactions of organotins with glycine have been studied by combining mass spectrometry experiments and quantum calculations. Positive‐ion electrospray spectra show that the interaction of di‐ and tri‐organotins with glycine results in the formation of [(R)₂Sn(Gly)‐H]⁺and [(R)₃Sn(Gly)]⁺ ions, respectively. Di‐organotin complexes appear much more reactive than those involving tri‐organotins. (MS/MS) spectra of the [(R)₃Sn(Gly)]⁺ ions are indeed simple and only show elimination of intact glycine, generating the [(R)₃Sn]⁺ carbocation. On the other hand, MS/MS spectra of [(R)₂Sn(Gly)‐H]⁺complexes are characterized by numerous fragmentation processes. Six of them, associated with elimination of H₂O, CO, H₂O + CO and formation of [(R)₂SnOH]⁺ (?57 u),[(R)₂SnNH₂]⁺( ?58 u) and [(R)₂SnH]⁺ (?73 u), are systematically observed. Use of labeled glycines notably concludes that the hydrogen atoms eliminated in water and H₂O + CO are labile hydrogens. A similar conclusion can be made for hydrogens of [(R₂)SnOH]⁺and [(R₂)SnNH₂]⁺ions. Interestingly, formation [(R)₂SnH]⁺ ions is characterized by a migration of one the α hydrogen of glycine onto the metallic center. Finally, several dissociation routes are observed and are characteristic of a given organic substituent. Calculations indicated that the interaction between organotins and glycine is mostly electrostatic. For [(R)₂Sn(Gly)‐H]⁺complexes, a preferable bidentate interaction of the type η²‐O,NH2 is observed, similar to that encountered for other metal ions. [(R)₃Sn]⁺ ions strongly stabilize the zwitterionic form of glycine, which is practically degenerate with respect to neutral glycine. In addition, the interconversion between both forms is almost barrierless. Suitable mechanisms are proposed in order to account for the most relevant fragmentation processes. Copyright © 2013 John Wiley & Sons, Ltd.     

Theoretical investigations on the geometric and electronic structures of phenylene-acetylene macrocycles.

The geometric and electronic structures of a series of conjugated macrocycles (phenylene-acetylene macrocycles, PAMs) have been studied theoretically with ab initio and semiempirical molecular orbital methods. The ab initio calculations at the HF/6-31G* level demonstrate that the model molecules may have a planar conformation. Bigger macrocycles, for example, 7PAM, 8PAM, and 9PAM, result in several energy minima. The boatlike conformation is the most energetically favored form. Based on the conformational analysis, a novel method for analyzing the ring-strain energy was proposed and used. In view of their potential applications as electronic materials, the electronic structures of a series of PAMs are also investigated. The LUMO-HOMO gaps of the planar PAMs show an odd-even difference behavior. In addition, the HOMOs of the planar species 3PAM, 5PAM, 7PAM, and 9PAM are doubly degenerated.     

Spectroscopic constants and molecular properties of rare‐gas diatomic molecule in Lennard‐Jones potential: Ab initio and density functional study

Ab initio and density functional theory (DFT) are applied to study the spectroscopic constants, molecular properties, and nature of force between two rare gas atoms of the weakly bound diatomic molecules He₂, Ne₂, Ar₂, HeNe, and HeAr in the Lennard‐Jones potential. A simple method is developed to calculate the spectroscopic constants of these molecules. The calculated spectroscopic constants and molecular properties agree very well with the experimental and theoretical results wherever available. Most of the spectroscopic constants and molecular properties are reported for the first time. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase

The recently introduced force field (FF) QMPFF3 is thoroughly validated in gas, liquid, and solid phases. For the first time, it is demonstrated that a physically well-grounded general purpose FF fitted exclusively to a comprehensive set of high level vacuum quantum mechanical data applied as it is to simulation of condensed phase provides high transferability for a wide range of chemical compounds. QMPFF3 demonstrates accuracy comparable with that of the FFs explicitly fitted to condensed phase data, but due to high transferability it is expected to be successful in simulating large molecular complexes.     

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ//MP2/6-31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc-pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone phi, psi dihedral crossterms or a phi, psi grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the phi, psi dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of phi and psi in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general.